Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold460
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: 276263
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
File 2 of 2
Found at i:160287 original size:144 final size:142
Alignment explanation
Indices: 159878--160302 Score: 440
Period size: 144 Copynumber: 2.9 Consensus size: 142
159868 ATTATACTTC
** *
159878 TTTTCTTACCTACCTCAAAGCCCACACAAGCTTGTGGCACCATGTTAATCTAGCCACAGTCCA-A
1 TTTTCTTACCTACCTCAAAG-GTACACAAGCTCGTGGCACCATGTTAATCTA-CCACAGTCCACA
* * ** *
159942 GAAAAGCTGGGCATCTATCAAGTCAAAGCCCACACAAGCTGGTAGCACTTATCTACCTTAATCCA
64 -AAAAGCTAGGCGTCTATCAAGTCAAAGCTAACACAAGCT-GTGGCACTTATCTACCTTAATCCA
* * ** *
160007 CAGATATTTGGACACC
127 CAAAGAGCTGGACACA
* ** * * *
160023 TTTCCTTAATTACCTCAAAGGTCATACAAGCTCGTGGCACCATGTTAATCTACTATAGTCCACAA
1 TTTTCTTACCTACCTCAAAGGT-ACACAAGCTCGTGGCACCATGTTAATCTACCACAGTCCACAA
* * * * *
160088 AAAGCTAGACGTCTATCAAGTCAAAGCTAATACAAGTTAGTGGCAATTATCTACCTTAGTCCACA
65 AAAGCTAGGCGTCTATCAAGTCAAAGCTAACACAAGCT-GTGGCACTTATCTACCTTAATCCACA
*
160153 AAGAGCTGGACTCA
129 AAGAGCTGGACACA
* ** *
160167 TTTTCTTACCTACCTCAAAGTGTACACAAGCTCATGGCACCACATTAATCTACCACAATCCACAA
1 TTTTCTTACCTACCTCAAAG-GTACACAAGCTCGTGGCACCATGTTAATCTACCACAGTCCACAA
* * * * * *
160232 AAAGCTAGGCGTCTATCGAA-TCAAAGCTTACACAAGCTGTTGGCACCTGTTTACCTCAATCCTC
65 AAAGCTAGGCGTCTATC-AAGTCAAAGCTAACACAAGCTG-TGGCACTTATCTACCTTAATCCAC
160296 AAAGAGC
128 AAAGAGC
160303 AGGATGCTTA
Statistics
Matches: 228, Mismatches: 47, Indels: 11
0.80 0.16 0.04
Matches are distributed among these distances:
143 1 0.00
144 178 0.78
145 49 0.21
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (142 bp):
TTTTCTTACCTACCTCAAAGGTACACAAGCTCGTGGCACCATGTTAATCTACCACAGTCCACAAA
AAGCTAGGCGTCTATCAAGTCAAAGCTAACACAAGCTGTGGCACTTATCTACCTTAATCCACAAA
GAGCTGGACACA
Found at i:163730 original size:98 final size:97
Alignment explanation
Indices: 163526--164354 Score: 491
Period size: 90 Copynumber: 8.5 Consensus size: 97
163516 ACTCCAACCT
* * * *
163526 CATTCTTCATAAAATATTAAATTTTCTTTTTGTCCTTAAATATTTTC-TGA---A---AAACTCT
1 CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTTAGGGAAACTCT
* ** *
163584 AACCCTACTACTCTGA-GATGATACT-TTAGACC
66 AACCCCACTACTC-GATGGCGATACTCTAAG-CC
*
163616 CGTTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTTTAGGGAAACTC
1 CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGAC-TTAGGGAAACTC
* ** * *
163681 CAACCTTACTACTTCGACGG-GATATTCTAAGCC
65 TAACCCCACTAC-TCGATGGCGATACTCTAAGCC
* * *
163714 CATTCTTCATGAAAAATCAAATTTTCTCTTTGTTCTTTAATATTTTC--G----A-GAAAACTCT
1 CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTTAGGGAAACTCT
*
163772 AACCCCACTACTCCATGGCGATACTCT-AGCC
66 AACCCCACTACTCGATGGCGATACTCTAAGCC
* *
163803 TAGTTCTTCATAAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATAATTCTTAACTTTA
1 CA-TTCTTCAT-AAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTC---A----TGAC-TTA
* * * * ** * *
163868 GGGAAACTTTAACCCCATTACTCCAAGGAAATACTCCAACCC
56 GGGAAACTCTAACCCCACTACTCGATGGCGATACTCTAAGCC
* * * * * *
163910 CAATCTTCATAAAAAATCAGATTTTTTTTTTGGTCTTAAATATTTTC-TG----A--GATACTCT
1 CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTTAGGGAAACTCT
* * *
163968 AATCCCACTACTCTGA-GGCAATACT-TTAGACC
66 AACCCCACTACTC-GATGGCGATACTCTAAG-CC
*
164000 CGTTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTTCAGGGAAACTC
1 CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTT-AGGGAAACTC
* * *
164065 TAACCCCGCAATTCCGATGG-GATACTCTAA-CC
65 TAACCCCACTACT-CGATGGCGATACTCTAAGCC
* * * *
164097 TCGTTCTTCATGAAAAATCAAATTTTCTCTTTATTCTTAAATATTTTCATAATTCTTGAATTTAG
1 -CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTC---A----TG-ACTTAG
* * * * * *
164162 GGAAACTCTAACCCTATTACTCCAAGGAGATACTCCAA-CC
57 GGAAACTCTAACCCCACTACTCGATGGCGATACTCTAAGCC
* * * ** * *
164202 CTATTCTTCATAAAAAAAATCAAATTTTCTTTTTTTTTCATATTTTCATAATTCTTGACTTCAGG
1 C-ATTCTTCAT--AAAAAATCAAATTTTC-TCTTTGTTCTTA-AAT-AT-TTTCATGACTT-AGG
* * * * *
164267 AAAACTCTAA-ACCATTACTCCGAAGG-GATACTCCAA-CC
58 GAAACTCTAACCCCACTACT-CGATGGCGATACTCTAAGCC
* * * *
164305 CTGTTCTTCATAAAAAATTAAATTTTCTTTTTGTTCCTAAATATTTTCAT
1 C-ATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCAT
164355 AATTCTTGAC
Statistics
Matches: 583, Mismatches: 94, Indels: 117
0.73 0.12 0.15
Matches are distributed among these distances:
89 11 0.02
90 141 0.24
91 42 0.07
92 1 0.00
95 1 0.00
96 2 0.00
97 7 0.01
98 138 0.24
99 12 0.02
100 10 0.02
101 16 0.03
103 32 0.05
104 24 0.04
105 73 0.13
106 39 0.07
107 19 0.03
108 9 0.02
109 1 0.00
110 2 0.00
111 3 0.01
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (97 bp):
CATTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCATGACTTAGGGAAACTCT
AACCCCACTACTCGATGGCGATACTCTAAGCC
Found at i:163811 original size:188 final size:188
Alignment explanation
Indices: 163516--164144 Score: 693
Period size: 188 Copynumber: 3.3 Consensus size: 188
163506 TCGAGGAAAG
* * * *
163516 ACTCCAACCTCATTCTTCAT-AAAATATTAAATTTTCTTTTTGTCCTTAAATATTTTCTGA-AAA
1 ACTCTAACC-CATTCTTCATGAAAA-ATCAAATTTTCTCTTTGTTCTTAAATATTTTCTGAGAAA
* *
163579 ACTCTAACCCTACTACT-C-TGAGATGATACTTTAGACCCGTTCTTCATAAAAAATCAAATTTTC
64 ACTCTAACCCCACTACTCCATG-G-CGATACTTTAGACCCGTTCTTCATAAAAAATCAAATTTTC
* ** *
163642 TCTTTGTTCTTAAATATTTTCATGACTTTAGGGAAACTCCAACCTTACTACTTCGACGGGAT
127 TCTTTGTTCTTAAATATTTTCATGACTTTAGGGAAACTCTAACCCCACTACTTCGAAGGGAT
* *
163704 ATTCTAAGCCCATTCTTCATGAAAAATCAAATTTTCTCTTTGTTCTTTAATATTTTC-GAGAAAA
1 ACTCTAA-CCCATTCTTCATGAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCTGAGAAAA
* *
163768 CTCTAACCCCACTACTCCATGGCGATACTCTAG-CCTAGTTCTTCATAAAAAAATCAAATTTTCT
65 CTCTAACCCCACTACTCCATGGCGATACTTTAGACC-CGTTCTTCAT-AAAAAATCAAATTTTCT
* * * *
163832 CTTTGTTCTTAAATATTTTCATAATTCTTAACTTTAGGGAAACTTTAACCCCATTAC-TCCAAGG
128 CTTTGTTCTTAAATATTTTC---A----TGACTTTAGGGAAACTCTAACCCCACTACTTCGAAGG
*
163896 AAAT
186 -GAT
* * * * * * * *
163900 ACTCCAACCCCAATCTTCATAAAAAATCAGATTTTTTTTTTGGTCTTAAATATTTTCTGAG-ATA
1 ACTCTAA-CCCATTCTTCATGAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCTGAGAAAA
* * *
163964 CTCTAATCCCACTACTCTGA-GGCAATACTTTAGACCCGTTCTTCATAAAAAATCAAATTTTCTC
65 CTCTAACCCCACTACTC-CATGGCGATACTTTAGACCCGTTCTTCATAAAAAATCAAATTTTCTC
* * * *
164028 TTTGTTCTTAAATATTTTCATGACTTCAGGGAAACTCTAACCCCGC-AATTCCGATGGGAT
129 TTTGTTCTTAAATATTTTCATGACTTTAGGGAAACTCTAACCCCACTACTT-CGAAGGGAT
* *
164088 ACTCTAACCTCGTTCTTCATGAAAAATCAAATTTTCTCTTTATTCTTAAATATTTTC
1 ACTCTAACC-CATTCTTCATGAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTC
164145 ATAATTCTTG
Statistics
Matches: 367, Mismatches: 53, Indels: 42
0.79 0.11 0.09
Matches are distributed among these distances:
187 7 0.02
188 149 0.41
189 49 0.13
190 2 0.01
192 2 0.01
195 42 0.11
196 110 0.30
197 6 0.02
ACGTcount: A:0.31, C:0.22, G:0.09, T:0.38
Consensus pattern (188 bp):
ACTCTAACCCATTCTTCATGAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTCTGAGAAAAC
TCTAACCCCACTACTCCATGGCGATACTTTAGACCCGTTCTTCATAAAAAATCAAATTTTCTCTT
TGTTCTTAAATATTTTCATGACTTTAGGGAAACTCTAACCCCACTACTTCGAAGGGAT
Found at i:164039 original size:90 final size:93
Alignment explanation
Indices: 163869--164146 Score: 244
Period size: 98 Copynumber: 3.0 Consensus size: 93
163859 TTAACTTTAG
* ** * * * ** *
163869 GGAAACTTTAACCCCATTACTCC-AAGGAAATACTCCAACCCCAATCTTCATAAAAAATCAGATT
1 GGAAACTCTAACCCCACAACTCCGATGG-AATACTCTAACCTCGTTCTTCATAAAAAATCAAATT
* * *
163933 TTTTTTTTGGTCTTAAATATTTTC-TG-A
65 TTCTCTTTGTTCTTAAATATTTTCATGCA
* * * * *
163960 -GATACTCTAATCCCACTACTCTGA-GGCAATACTTTAGACC-CGTTCTTCATAAAAAATCAAAT
1 GGAAACTCTAACCCCACAACTCCGATGG-AATACTCTA-ACCTCGTTCTTCATAAAAAATCAAAT
164022 TTTCTCTTTGTTCTTAAATATTTTCATGACTTCA
64 TTTCTCTTTGTTCTTAAATATTTTCATG----CA
* * * *
164056 GGGAAACTCTAACCCCGCAATTCCGATGGGATACTCTAACCTCGTTCTTCATGAAAAATCAAATT
1 -GGAAACTCTAACCCCACAACTCCGATGGAATACTCTAACCTCGTTCTTCATAAAAAATCAAATT
*
164121 TTCTCTTTATTCTTAAATATTTTCAT
65 TTCTCTTTGTTCTTAAATATTTTCAT
164147 AATTCTTGAA
Statistics
Matches: 151, Mismatches: 24, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
90 67 0.44
91 6 0.04
96 1 0.01
97 3 0.02
98 72 0.48
99 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (93 bp):
GGAAACTCTAACCCCACAACTCCGATGGAATACTCTAACCTCGTTCTTCATAAAAAATCAAATTT
TCTCTTTGTTCTTAAATATTTTCATGCA
Found at i:164330 original size:208 final size:208
Alignment explanation
Indices: 164077--164630 Score: 677
Period size: 210 Copynumber: 2.7 Consensus size: 208
164067 ACCCCGCAAT
* * * * * *
164077 TCCGATGGGATACTCTAA-CCTCGTTCTTCATGAAAAATCAAATTTTCTCTTTATTCTTAAATAT
1 TCCGAAGGGATACTCCAACCCT-GTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATAT
* * * * * *
164141 TTTCATAATTCTTGAATTTAGGGAAACTCTAACCCTATTACTCCAAGGAGATACTCCAACCCTAT
65 TTTCATAATTCTTGACTTTGGGGAAATTCCAACCCTACTACTCCAAGGAGATACTCCAA-CCTAG
* * *
164206 TC-TTCATAA-AAAAAATCAAATT-TTCTT-TTTTTTTCATATTTTCATAATTCTTGACTTCAGG
129 TCTTTCATAATAAAAAAT--AATTATTCTTAATATTTTCAAATTTTCATAA-TCTTGACTTCAGG
164267 AAAACTCTAAACCATTAC
191 AAAACTCTAAACCATTAC
*
164285 TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATTAAATTTTCTTTTTGTTCCTAAATATT
1 TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATT
* * * * ** *
164350 TTCATAATTCTTGACTTCGGGGAAATTCCAACCCTGCTACTTCGAGGAGATACTTTAACCTCGTC
66 TTCATAATTCTTGACTTTGGGGAAATTCCAACCCTACTACTCCAAGGAGATACTCCAACCTAGTC
*** * *
164415 TTTCATAATTCTTAAATATTTATTCTTAAATATTTTCAAATTTTCCTAATCTTGACTTCAGGAAA
131 TTTCATAA-TAAAAAATAATTATTCTT-AATATTTTCAAATTTTCATAATCTTGACTTCAGGAAA
164480 ACTCTAAACCATTAC
194 ACTCTAAACCATTAC
*
164495 TCCGAAGGGATACTCCAACCCTTTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATT
1 TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATT
** * * * ** *
164560 TTCATAATTCTTGACTTTGGGGAAATTCCAACCCCGCTGCTTCGAGGAGATACTTTAACCTCGTC
66 TTCATAATTCTTGACTTTGGGGAAATTCCAACCCTACTACTCCAAGGAGATACTCCAACCTAGTC
164625 TTTCAT
131 TTTCAT
164631 TAAAAACTTT
Statistics
Matches: 306, Mismatches: 33, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
207 5 0.02
208 111 0.36
209 8 0.03
210 166 0.54
211 16 0.05
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (208 bp):
TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATT
TTCATAATTCTTGACTTTGGGGAAATTCCAACCCTACTACTCCAAGGAGATACTCCAACCTAGTC
TTTCATAATAAAAAATAATTATTCTTAATATTTTCAAATTTTCATAATCTTGACTTCAGGAAAAC
TCTAAACCATTAC
Found at i:164441 original size:14 final size:14
Alignment explanation
Indices: 164422--164449 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
164412 GTCTTTCATA
164422 ATTCTTAAATATTT
1 ATTCTTAAATATTT
164436 ATTCTTAAATATTT
1 ATTCTTAAATATTT
164450 TCAAATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTCTTAAATATTT
Found at i:164507 original size:105 final size:102
Alignment explanation
Indices: 164077--164576 Score: 415
Period size: 104 Copynumber: 4.8 Consensus size: 102
164067 ACCCCGCAAT
* * * * * * *
164077 TCCGATGGGATACTCTAA-CCTCGTTCTTCATGAAAAATCAAATTTTCTCTTTATTCTTAAATAT
1 TCCGAAGGGATACTCCAACCCT-GTTCTTCATAAAAAATTAAATTTTATTTTTATT-TTCAA-AT
* * * *
164141 TTTCATAATTCTTGAATTTAGGGAAACTCTAACCCTATTAC
63 TTTCATAATTCTTGACTTCAGGAAAACTCTAAACC-ATTAC
* * * *
164182 TCC-AAGGAGATACTCCAACCCTATTCTTCATAAAAAAAATCAAATTTTCTTTTT-TTTTCATAT
1 TCCGAAGG-GATACTCCAACCCTGTTCTTCAT--AAAAAATTAAATTTTATTTTTATTTTCAAAT
164245 TTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTAC
63 TTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTAC
* * * *
164285 TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATTAAATTTTCTTTTTGTTCCTAAATATT
1 TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATTAAATTTTATTTTTATT-TTCAA-ATT
* * * * *
164350 TTCATAATTCTTGACTTCGGGGAAATTC-CAACCCTGCTAC
64 TTCATAATTCTTGACTTCAGGAAAACTCTAAACCAT--TAC
* ** ***
164390 TTCG-AGGAGATACTTTAA-CCTCG-TCTTTCAT-AATTCTTAAATATTTATTCTTAAATATTTT
1 TCCGAAGG-GATACTCCAACCCT-GTTC-TTCATAAAAAATTAAAT-TTTATT-TT---TATTTT
*
164451 CAAATTTTCCTAA-TCTTGACTTCAGGAAAACTCTAAACCATTAC
58 CAAATTTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTAC
* * * * * *
164495 TCCGAAGGGATACTCCAACCCTTTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATT
1 TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATTAAATTTTATTTTTATT-TTCAA-ATT
164560 TTCATAATTCTTGACTT
64 TTCATAATTCTTGACTT
164577 TGGGGAAATT
Statistics
Matches: 319, Mismatches: 50, Indels: 53
0.76 0.12 0.13
Matches are distributed among these distances:
101 23 0.07
102 5 0.02
103 46 0.14
104 95 0.30
105 72 0.23
106 39 0.12
107 33 0.10
108 3 0.01
109 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (102 bp):
TCCGAAGGGATACTCCAACCCTGTTCTTCATAAAAAATTAAATTTTATTTTTATTTTCAAATTTT
CATAATTCTTGACTTCAGGAAAACTCTAAACCATTAC
Found at i:164524 original size:210 final size:211
Alignment explanation
Indices: 164236--164630 Score: 720
Period size: 210 Copynumber: 1.9 Consensus size: 211
164226 TTTTCTTTTT
*
164236 TTTTCATATTTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTACTCCGAAGGGATACTCC
1 TTTTCAAATTTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTACTCCGAAGGGATACTCC
*
164301 AACCCTGTTCTTCATAAAAAATTAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACT
66 AACCCTGTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACT
*
164366 TCGGGGAAATTCCAACCCTGCTACTTCGAGGAGATACTTTAACCTCGTCTTTCATAATTCTTAAA
131 TCGGGGAAATTCCAACCCCGCTACTTCGAGGAGATACTTTAACCTCGTCTTTCATAATTCTTAAA
164431 TATTTATTCTTAAATA
196 TATTTATTCTTAAATA
*
164447 TTTTCAAATTTTCCTAA-TCTTGACTTCAGGAAAACTCTAAACCATTACTCCGAAGGGATACTCC
1 TTTTCAAATTTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTACTCCGAAGGGATACTCC
*
164511 AACCCTTTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACT
66 AACCCTGTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACT
* *
164576 TTGGGGAAATTCCAACCCCGCTGCTTCGAGGAGATACTTTAACCTCGTCTTTCAT
131 TCGGGGAAATTCCAACCCCGCTACTTCGAGGAGATACTTTAACCTCGTCTTTCAT
164631 TAAAAACTTT
Statistics
Matches: 177, Mismatches: 7, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
210 162 0.92
211 15 0.08
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (211 bp):
TTTTCAAATTTTCATAATTCTTGACTTCAGGAAAACTCTAAACCATTACTCCGAAGGGATACTCC
AACCCTGTTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACT
TCGGGGAAATTCCAACCCCGCTACTTCGAGGAGATACTTTAACCTCGTCTTTCATAATTCTTAAA
TATTTATTCTTAAATA
Found at i:164612 original size:105 final size:103
Alignment explanation
Indices: 164002--164669 Score: 503
Period size: 105 Copynumber: 6.5 Consensus size: 103
163992 TTTAGACCCG
* *
164002 TTCTTCATAAAAAATCAAATTTTCTCTTTGTTCTTAAATATTTTC---A----TGACTTCAGGGA
1 TTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCAGGGA
* * * *
164060 AACTCTAACCCCGCAATTCCGATGGGATACTCTAACCTC
66 AACTCTAACCCCACTACTCCGA-GGGATACTCCAACCTC
* * * * * *
164099 GTTCTTCATGAAAAATCAAATTTTCTCTTTATTCTTAAATATTTTCATAATTCTTGAATTTAGGG
1 -TTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCAGGG
* * * *
164164 AAACTCTAACCCTATTACTCCAAGGAGATACTCCAACCCTA
65 AAACTCTAACCCCACTACTCCGAGG-GATACTCCAA-CCTC
**
164205 TTCTTCATAAAAAAAATCAAATTTTCTTTTT-TT--TTCATATTTTCATAATTCTTGACTTCAGG
1 TTCTTCAT--AAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCAGG
* * * *
164267 AAAACTCTAA-ACCATTACTCCGAAGGGATACTCCAACCCTG
64 GAAACTCTAACCCCACTACTCCG-AGGGATACTCCAA-CCTC
* *
164308 TTCTTCATAAAAAATTAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCGGGGA
1 TTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCAGGGA
* * ** * **
164373 AATTCCAACCCTGCTACTTCGAGGAGATACTTTAACCTC
66 AACTCTAACCCCACTACTCCGAGG-GATACTCCAACCTC
* *** * * * * * *
164412 GTCTTTCAT-AATTCTTAAATATTTATTCTTAAATATT-TTCAA-ATTTTCCTAA-TCTTGACTT
1 TTC-TTCATAAAAAATCAAAT-TTTCTT-TT---TGTTCCTAAATATTTTCATAATTCTTGACTT
* * * *
164473 CAGGAAAACTCTAA-ACCATTACTCCGAAGGGATACTCCAACCCTT
60 CAGGGAAACTCTAACCCCACTACTCCG-AGGGATACTCCAA-CCTC
**
164518 TTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTTGGGGA
1 TTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCAGGGA
* * * * * **
164583 AATTCCAACCCCGCTGCTTCGAGGAGATACTTTAACCTC
66 AACTCTAACCCCACTACTCCGAGG-GATACTCCAACCTC
* * * *
164622 GTCTTTCATTAAAAA-C---TTTTCTCTTTGTTTCTAAATATTTTCATAATT
1 TTC-TTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATT
164670 TTACCGTCGG
Statistics
Matches: 452, Mismatches: 86, Indels: 61
0.75 0.14 0.10
Matches are distributed among these distances:
98 43 0.10
101 54 0.12
102 5 0.01
103 40 0.09
104 117 0.26
105 118 0.26
106 41 0.09
107 28 0.06
108 3 0.01
109 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.40
Consensus pattern (103 bp):
TTCTTCATAAAAAATCAAATTTTCTTTTTGTTCCTAAATATTTTCATAATTCTTGACTTCAGGGA
AACTCTAACCCCACTACTCCGAGGGATACTCCAACCTC
Found at i:166359 original size:13 final size:13
Alignment explanation
Indices: 166341--166371 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
166331 ACATTTCTTC
166341 ATGTATCGATACA
1 ATGTATCGATACA
166354 ATGTATCGATACA
1 ATGTATCGATACA
*
166367 TTGTA
1 ATGTA
166372 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:166359 original size:33 final size:33
Alignment explanation
Indices: 166321--166385 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
166311 GTTACAAGCT
166321 ATGTATCGATACATT-T-CTTCATGTATCGATACA
1 ATGTATCGATACATTGTAC--CATGTATCGATACA
166354 ATGTATCGATACATTGTACCATGTATCGATAC
1 ATGTATCGATACATTGTACCATGTATCGATAC
166386 GATTCATAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (33 bp):
ATGTATCGATACATTGTACCATGTATCGATACA
Found at i:166379 original size:20 final size:18
Alignment explanation
Indices: 166353--166409 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 18
166343 GTATCGATAC
166353 AATGTATCGATACATTGT
1 AATGTATCGATACATTGT
*
166371 ACCATGTATCGATACGATTCAT
1 A--ATGTATCGATAC-ATT-GT
166393 AATGTATCGATACATTG
1 AATGTATCGATACATTG
166410 ATTTGAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 1 0.03
19 3 0.09
20 24 0.73
21 3 0.09
22 2 0.06
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (18 bp):
AATGTATCGATACATTGT
Found at i:166484 original size:13 final size:13
Alignment explanation
Indices: 166466--166496 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
166456 ACATTTCTTT
166466 ATGTATCGATACA
1 ATGTATCGATACA
166479 ATGTATCGATACA
1 ATGTATCGATACA
*
166492 TTGTA
1 ATGTA
166497 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:166491 original size:125 final size:125
Alignment explanation
Indices: 166269--166510 Score: 457
Period size: 125 Copynumber: 1.9 Consensus size: 125
166259 TCCCGTAGCC
166269 ATGTATCGATACAGTGATTTGAAATTATAGCTGTTTATAGCCGTTACAAGCTATGTATCGATACA
1 ATGTATCGATACAGTGATTTGAAATTATAGCTGTTTATAGCCGTTACAAGCTATGTATCGATACA
166334 TTTCTTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACGATTCATA
66 TTTCTTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACGATTCATA
* *
166394 ATGTATCGATACATTGATTTGAAATTATAGCTGTTTATAGCTGTTACAAGCTATGTATCGATACA
1 ATGTATCGATACAGTGATTTGAAATTATAGCTGTTTATAGCCGTTACAAGCTATGTATCGATACA
*
166459 TTTCTTTATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATAC
66 TTTCTTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATAC
166511 AAACAGTGAT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
125 114 1.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (125 bp):
ATGTATCGATACAGTGATTTGAAATTATAGCTGTTTATAGCCGTTACAAGCTATGTATCGATACA
TTTCTTCATGTATCGATACAATGTATCGATACATTGTACCATGTATCGATACGATTCATA
Found at i:166581 original size:13 final size:13
Alignment explanation
Indices: 166563--166589 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
166553 CAATTTGTCC
166563 ATGTATCGATACA
1 ATGTATCGATACA
166576 ATGTATCGATACA
1 ATGTATCGATACA
166589 A
1 A
166590 AGCAGCATGT
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:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:167704 original size:21 final size:20
Alignment explanation
Indices: 167679--167731 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
167669 TACAAGCCAA
**
167679 TGTATCGATACAATTTTTTTG
1 TGTATCGATACAA-TACTTTG
167700 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
167719 TGTATCGATACAA
1 TGTATCGATACAA
167732 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 16 0.55
20 2 0.07
21 11 0.38
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:168395 original size:18 final size:18
Alignment explanation
Indices: 168372--168407 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
168362 AATCAAAATA
168372 ATTTTAACAAATTCGTAC
1 ATTTTAACAAATTCGTAC
168390 ATTTTAACAAATTCGTAC
1 ATTTTAACAAATTCGTAC
168408 TTTCTCCCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.39
Consensus pattern (18 bp):
ATTTTAACAAATTCGTAC
Found at i:170306 original size:13 final size:13
Alignment explanation
Indices: 170288--170351 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
170278 ATAATCCCCC
170288 TGTATCGATACAG
1 TGTATCGATACAG
*
170301 TGTATCGATACAT
1 TGTATCGATACAG
170314 TGTATCGATACAG
1 TGTATCGATACAG
*
170327 TGTATCGATACAT
1 TGTATCGATACAG
170340 TGTATCGATACA
1 TGTATCGATACA
170352 AAGAAAAATG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 48 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:170317 original size:26 final size:26
Alignment explanation
Indices: 170288--170351 Score: 128
Period size: 26 Copynumber: 2.5 Consensus size: 26
170278 ATAATCCCCC
170288 TGTATCGATACAGTGTATCGATACAT
1 TGTATCGATACAGTGTATCGATACAT
170314 TGTATCGATACAGTGTATCGATACAT
1 TGTATCGATACAGTGTATCGATACAT
170340 TGTATCGATACA
1 TGTATCGATACA
170352 AAGAAAAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (26 bp):
TGTATCGATACAGTGTATCGATACAT
Found at i:172437 original size:15 final size:15
Alignment explanation
Indices: 172417--172457 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
172407 GTTCATCGAT
172417 TTCATTTGGAGCTTC
1 TTCATTTGGAGCTTC
*
172432 TTCATTTTGAGCTTC
1 TTCATTTGGAGCTTC
*
172447 CTCAATTTGGA
1 TTC-ATTTGGA
172458 CATTTTTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 16 0.73
16 6 0.27
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (15 bp):
TTCATTTGGAGCTTC
Found at i:174287 original size:21 final size:21
Alignment explanation
Indices: 174258--174302 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
174248 AAGTTTTTAT
*
174258 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
174278 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
174300 TTT
1 TTT
174303 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:176554 original size:13 final size:13
Alignment explanation
Indices: 176536--176561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
176526 AATTTTTTTG
176536 TGTATCGATACAT
1 TGTATCGATACAT
176549 TGTATCGATACAT
1 TGTATCGATACAT
176562 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:177785 original size:13 final size:13
Alignment explanation
Indices: 177767--177808 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
177757 AAATAGTACC
177767 CAATGTATCGATA
1 CAATGTATCGATA
177780 CAATGTATCGATA
1 CAATGTATCGATA
* *
177793 CATTATATCGATA
1 CAATGTATCGATA
177806 CAA
1 CAA
177809 GGAATGTTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:181890 original size:19 final size:18
Alignment explanation
Indices: 181866--181933 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
181856 CAGTAGCTAA
181866 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
181885 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
181900 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
181917 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
181934 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 27 0.63
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:181906 original size:13 final size:13
Alignment explanation
Indices: 181888--181912 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
181878 ACAATACTTA
181888 TGTATCGATACAT
1 TGTATCGATACAT
181901 TGTATCGATACA
1 TGTATCGATACA
181913 ACACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:181910 original size:32 final size:32
Alignment explanation
Indices: 181869--181931 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
181859 TAGCTAATTA
*
181869 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
181901 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
181932 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:182866 original size:49 final size:49
Alignment explanation
Indices: 182794--183231 Score: 603
Period size: 49 Copynumber: 9.0 Consensus size: 49
182784 TTTTAAAAAT
* * * *
182794 GATGAAGGCGCCAATATGTTGAGTCAAGGCCAGCAATATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * * * *
182843 GATGAAGGTGACAATGTGCTGAGTCAAGGCCAGCTACATTGGACTAAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * * *
182892 GATAAAGGTGCCAATATGCTGATTCAAGGCTAGCTATGTTAGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * * * *
182941 GGTG-AGGTACCAATATGCTGATTTAAGGCCAGCTACATTGGACTTAAG
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
182989 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * * *
183038 GGTG-AGGTGCCATTGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
*
183086 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* * *
183135 GGTGAA-GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
* *
183183 TATGAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
183232 AGGGTTGCCA
Statistics
Matches: 338, Mismatches: 48, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
48 127 0.38
49 211 0.62
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
Found at i:182983 original size:97 final size:97
Alignment explanation
Indices: 182751--183231 Score: 667
Period size: 97 Copynumber: 4.9 Consensus size: 97
182741 GAGAAGAATG
* * * ** * *
182751 CCAATGTGCTGATTCAAGGTCAACGACATTGGGTTTTAAAAATGATGAAGGCGCCAATATGTTGA
1 CCAATGTGCTGATTCAAGGCCAGCTACATT-GGACTT--AAA-GATGAAGGTGCCAATATGCTGA
* * *
182816 GTCAAGGCCAGCAATATTGGACTTAAAGATGAAGGTGA
62 TTCAAGGCCAGCTATATTGGACTTAAAGGTG-AGGT-A
* * *
182854 -CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTAAAAGATAAAGGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCA
* * *
182918 AGGCTAGCTATGTTAGACTTAAAGGTGAGGTA
66 AGGCCAGCTATATTGGACTTAAAGGTGAGGTA
* * *
182950 CCAATATGCTGATTTAAGGCCAGCTACATTGGACTTAAGGATGAAGGTGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCA
*
183015 AGGCCAGCTATATTGGACTTAAAGGTGAGGTG
66 AGGCCAGCTATATTGGACTTAAAGGTGAGGTA
* *
183047 CCATTGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCA
1 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCA
* *
183112 AGGCCAGCTATATTGGACTTAAAGGTGAAGTG
66 AGGCCAGCTATATTGGACTTAAAGGTGAGGTA
* *
183144 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAATATGAAGGTGCCAATATGCTAATTCA
1 CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCA
183209 AGGCCAGCTATATTGGACTTAAA
66 AGGCCAGCTATATTGGACTTAAA
183232 AGGGTTGCCA
Statistics
Matches: 341, Mismatches: 36, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
96 1 0.00
97 265 0.78
98 44 0.13
99 3 0.01
101 3 0.01
102 25 0.07
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (97 bp):
CCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCA
AGGCCAGCTATATTGGACTTAAAGGTGAGGTA
Found at i:183276 original size:33 final size:33
Alignment explanation
Indices: 183234--183329 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
183224 GACTTAAAAG
* *
183234 GGTTGCCACCAACTTGTGTGGGCTTTAGAGAGT
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
*
183267 GGTTGCCACCGACTTATGTGGGCTTTAGAGAAT
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
*
183300 GGTTGCCATCGACTTGTGTGGGCTTTAGAG
1 GGTTGCCACCGACTTGTGTGGGCTTTAGAG
183330 GGGGTTATAC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.18, C:0.18, G:0.33, T:0.31
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTAGAGAAT
Found at i:183479 original size:34 final size:33
Alignment explanation
Indices: 183351--183904 Score: 339
Period size: 34 Copynumber: 17.2 Consensus size: 33
183341 AACTTGTGGG
*
183351 TTTAACAGGAGAAAGATGCCACGGAGTTGTGGAC
1 TTTAA-AGGAAAAAGATGCCACGGAGTTGTGGAC
* *
183385 TTAAAAGG-AAAAGGTGCCACGGAGTTGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
*
183417 TTTAAAAGGAAAAAGAATGCCACGGAGTTGTGGGC
1 TTT-AAAGGAAAAAG-ATGCCACGGAGTTGTGGAC
* *
183452 TTTAAAAGGAAAAAGATGCCACAGAGTTGCGGAC
1 TTT-AAAGGAAAAAGATGCCACGGAGTTGTGGAC
*
183486 -TT-----AAAAAGGTGCCACGGAGTTGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
* ** **
183513 -TTAGAAGG-AAAGGATGCCACTAAGTCATGGAC
1 TTTA-AAGGAAAAAGATGCCACGGAGTTGTGGAC
* * * *
183545 TTTGAA-GAAAATGATGCCACTGAGTCGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
* ** * *
183577 TTT-GA-G-AAAAGATTGCCATTGAGTCGTGGGC
1 TTTAAAGGAAAAAGA-TGCCACGGAGTTGTGGAC
* * * *
183608 TTT-GA-GACAAA-ATGCCACTGAGTCGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
* * *
183638 TTTTGAAGAAAAAAGATGCCACTGAGTTGTGGAC
1 -TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
* * *
183672 TTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGGC
1 TTT-AAAGGAAAAAGA-TGCCACGGAGTTGTGGAC
* *
183707 TTTAAAGGAAAAAGAGTGTCACGGAGTTGTGGGC
1 TTTAAAGGAAAAAGA-TGCCACGGAGTTGTGGAC
* * * *
183741 TTTGAA-GAAAATGATGCCACTGAGTCGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
* *
183773 -TT--A-GAAAAGAGATGCCACCGAGTCGTGGAC
1 TTTAAAGGAAAA-AGATGCCACGGAGTTGTGGAC
* * * * *
183803 -TTACAGGAAAAAGGGACGCCACTGAGTCGTAGAC
1 TTTAAAGGAAAAA--GATGCCACGGAGTTGTGGAC
* * * * *
183837 TTTGAAGGAAAGATATGCCACTGAGTCGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
* * * *
183870 TTT--GGGACAAA-ATGCCACTGAGTCGTGGAC
1 TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
183900 TTTAA
1 TTTAA
183905 GAAGGTATTT
Statistics
Matches: 431, Mismatches: 61, Indels: 58
0.78 0.11 0.11
Matches are distributed among these distances:
27 24 0.06
29 6 0.01
30 64 0.15
31 36 0.08
32 88 0.20
33 51 0.12
34 102 0.24
35 60 0.14
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (33 bp):
TTTAAAGGAAAAAGATGCCACGGAGTTGTGGAC
Found at i:183499 original size:27 final size:27
Alignment explanation
Indices: 183461--183515 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
183451 CTTTAAAAGG
183461 AAAAAGATGCCACAGAGTTGCGGACTT
1 AAAAAGATGCCACAGAGTTGCGGACTT
* * *
183488 AAAAAGGTGCCACGGAGTTGTGGACTT
1 AAAAAGATGCCACAGAGTTGCGGACTT
183515 A
1 A
183516 GAAGGAAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.29, T:0.20
Consensus pattern (27 bp):
AAAAAGATGCCACAGAGTTGCGGACTT
Found at i:183887 original size:228 final size:218
Alignment explanation
Indices: 183425--183904 Score: 531
Period size: 228 Copynumber: 2.1 Consensus size: 218
183415 ACTTTAAAAG
* * *
183425 GAAAAAGAATGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGATGCCACAGAGTTGCGGACTTAA
1 GAAAAA-AATGCCACTGAGTTGTGGACTTTAAAAAGAAAAAGATGCCACAGAGTTGCGGACTTAA
* *
183490 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAGGATGCCACTAAGTCATGGACTTTGAAGAAA
65 AAAGGTGCCACGGAGTTGTGGACTTAGAAGAAAAGGATGCCACTAAGTCATGGACTTAGAAGAAA
* ** * * * *
183555 ATGATGCCACTGAGTCGTGGACTTTGAGAAAAGATTGCCATTGAGTCGTGGGCTTTGAGACAAAA
130 ATGATGCCACCGAGTCGTGGACTTACAGAAAAGATCGCCACTGAGTCGTAGACTTTGAGACAAAA
183620 TGCCACTGAGTCGTGGACTTTTGAA
195 TGCCACTGAGTCGTGGACTTTTG-A
* *
183645 GAAAAAAGATGCCACTGAGTTGTGGACTTTAAAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
1 GAAAAAA-ATGCCACTGAGTTGTGGACTTTAAAAAGAAAAAGA-TGCCACAGAGTTGCGGAC-TT
* * * * * *
183710 AAAGGAAAAAGAGTGTCACGGAGTTGTGGGCTTTGAAGAAAATGATGCCACTGAGTCGTGGACTT
63 -----AAAAAG-GTGCCACGGAGTTGTGGACTTAGAAGAAAAGGATGCCACTAAGTCATGGACTT
*
183775 AGAA-AAGA-GATGCCACCGAGTCGTGGACTTACAGGAAAAAGGGA-CGCCACTGAGTCGTAGAC
122 AGAAGAAAATGATGCCACCGAGTCGTGGACTTACA-G-AAAA--GATCGCCACTGAGTCGTAGAC
183837 TTTGAAGGA-AAGATATGCCACTGAGTCGTGGAC-TTTG-
183 TTTG-A-GACAA-A-ATGCCACTGAGTCGTGGACTTTTGA
* * *
183874 GGACAAAATGCCACTGAGTCGTGGACTTTAA
1 GAAAAAAATGCCACTGAGTTGTGGACTTTAA
183905 GAAGGTATTT
Statistics
Matches: 219, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
219 1 0.00
220 38 0.17
221 16 0.07
222 2 0.01
226 22 0.10
227 10 0.05
228 76 0.35
229 23 0.11
230 5 0.02
231 7 0.03
232 19 0.09
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (218 bp):
GAAAAAAATGCCACTGAGTTGTGGACTTTAAAAAGAAAAAGATGCCACAGAGTTGCGGACTTAAA
AAGGTGCCACGGAGTTGTGGACTTAGAAGAAAAGGATGCCACTAAGTCATGGACTTAGAAGAAAA
TGATGCCACCGAGTCGTGGACTTACAGAAAAGATCGCCACTGAGTCGTAGACTTTGAGACAAAAT
GCCACTGAGTCGTGGACTTTTGA
Found at i:185183 original size:14 final size:14
Alignment explanation
Indices: 185166--185219 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
185156 CCTTTGCACT
*
185166 TTTTTTGTGTGTTG
1 TTTTTTGTGTTTTG
*
185180 -TTTTTGTTGTTTTT
1 TTTTTTG-TGTTTTG
185194 TTTTTTGTGTTTTG
1 TTTTTTGTGTTTTG
*
185208 TTTTTTATGTTT
1 TTTTTTGTGTTT
185220 ACTTTTGACT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
13 6 0.18
14 22 0.65
15 6 0.18
ACGTcount: A:0.02, C:0.00, G:0.19, T:0.80
Consensus pattern (14 bp):
TTTTTTGTGTTTTG
Found at i:185225 original size:28 final size:28
Alignment explanation
Indices: 185166--185225 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
185156 CCTTTGCACT
**
185166 TTTTTTGTGTGTTGTTTTTGTTGTTTTT
1 TTTTTTGTGTGTTGTTTTTGTTGTTTAC
*
185194 TTTTTTGTGTTTTGTTTTT-TATGTTTAC
1 TTTTTTGTGTGTTGTTTTTGT-TGTTTAC
185222 TTTT
1 TTTT
185226 GACTTTTTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.03, C:0.02, G:0.17, T:0.78
Consensus pattern (28 bp):
TTTTTTGTGTGTTGTTTTTGTTGTTTAC
Found at i:190772 original size:20 final size:20
Alignment explanation
Indices: 190727--190778 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
190717 GTAGCCAAAC
* **
190727 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
190747 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
190766 TTGTATCGATACA
1 TTGTATCGATACA
190779 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:194845 original size:15 final size:15
Alignment explanation
Indices: 194825--194855 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
194815 TAAAAATGTC
*
194825 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
194840 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
194855 C
1 C
194856 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:196939 original size:13 final size:13
Alignment explanation
Indices: 196921--196958 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
196911 CATTTTTCTT
196921 TGTATCGATACAA
1 TGTATCGATACAA
*
196934 TGTATCGATACAC
1 TGTATCGATACAA
196947 TGTATCGATACA
1 TGTATCGATACA
196959 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:197113 original size:20 final size:20
Alignment explanation
Indices: 197070--197115 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
197060 AAATCTTTTG
197070 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
197091 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
197111 CAAAA
1 CAAAA
197116 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:199544 original size:13 final size:13
Alignment explanation
Indices: 199526--199551 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
199516 TACACCAAGT
199526 ATGTATCGATACA
1 ATGTATCGATACA
199539 ATGTATCGATACA
1 ATGTATCGATACA
199552 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:199548 original size:32 final size:33
Alignment explanation
Indices: 199507--199571 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
199497 GTAGCCAAAC
* **
199507 ATGTATCGATACACCAAGTA-TGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
199539 ATGTATCGATACACAAAAAATTGTATCGATACA
1 ATGTATCGATACACAAAAAATTGTATCGATACA
199572 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACACAAAAAATTGTATCGATACA
Found at i:201880 original size:3 final size:3
Alignment explanation
Indices: 201867--201899 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
201857 CTTCATCCGA
*
201867 ATC ACC ATC ATC ATC ATC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
201900 TTCTTCCTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:203520 original size:33 final size:33
Alignment explanation
Indices: 203482--203548 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
203472 GTTACAAGCT
*
203482 ATGTATCGATACATTTCT-TCATGTATCGATACA
1 ATGTATCGATA-ATTTCTACCATGTATCGATACA
* *
203515 ATGTATCGATATTTTGTACCATGTATCGATACA
1 ATGTATCGATAATTTCTACCATGTATCGATACA
203548 A
1 A
203549 ATAGTGATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (33 bp):
ATGTATCGATAATTTCTACCATGTATCGATACA
Found at i:205268 original size:40 final size:40
Alignment explanation
Indices: 205155--205259 Score: 183
Period size: 40 Copynumber: 2.6 Consensus size: 40
205145 GCTTAAGTTT
*
205155 AATGATACTTGTCTGCTCCTTTTTAATCAATGTTACCTTC
1 AATGATACTTGTCTGCTCCTTTTTAATCAATGTTAACTTC
*
205195 AATGATACTTGTCCGCTCCTTTTTAATCAATGTTAACTTC
1 AATGATACTTGTCTGCTCCTTTTTAATCAATGTTAACTTC
205235 AATGATACTTGTCTGCTTCCTTTTT
1 AATGATACTTGTCTGC-TCCTTTTT
205260 CGCAATGTTG
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 53 0.87
41 8 0.13
ACGTcount: A:0.22, C:0.22, G:0.10, T:0.46
Consensus pattern (40 bp):
AATGATACTTGTCTGCTCCTTTTTAATCAATGTTAACTTC
Found at i:205418 original size:15 final size:15
Alignment explanation
Indices: 205390--205483 Score: 59
Period size: 15 Copynumber: 6.0 Consensus size: 15
205380 AGTCAATTTA
205390 AAATCAAATTTAAATT
1 AAAT-AAATTTAAATT
* *
205406 AAATAAATATAAA-A
1 AAATAAATTTAAATT
205420 AAATTAAAAGTTTAAATT
1 AAA-T-AAA-TTTAAATT
*
205438 AAAAAAATTTAAATT
1 AAATAAATTTAAATT
* *
205453 CAAA-AAATATATATT
1 -AAATAAATTTAAATT
205468 CAAA-AAATTTTAAATT
1 -AAATAAA-TTTAAATT
205484 CGAAATAATC
Statistics
Matches: 63, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
14 3 0.05
15 33 0.52
16 19 0.30
17 5 0.08
18 3 0.05
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (15 bp):
AAATAAATTTAAATT
Found at i:205457 original size:16 final size:16
Alignment explanation
Indices: 205425--205507 Score: 71
Period size: 15 Copynumber: 5.2 Consensus size: 16
205415 TAAAAAAATT
*
205425 AAAAGTTTAAATT-AA
1 AAAAATTTAAATTCAA
205440 AAAAATTTAAATTC-A
1 AAAAATTTAAATTCAA
* *
205455 AAAAATATATATTCAA
1 AAAAATTTAAATTCAA
* *
205471 AAAATTTTAAATTCGA
1 AAAAATTTAAATTCAA
* * *
205487 AATAATCTAAACTTGAA
1 AAAAATTTAAA-TTCAA
205504 AAAA
1 AAAA
205508 CTTAAAGCTG
Statistics
Matches: 52, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
15 25 0.48
16 21 0.40
17 6 0.12
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (16 bp):
AAAAATTTAAATTCAA
Found at i:206951 original size:19 final size:19
Alignment explanation
Indices: 206923--206959 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
206913 CTATTTACAT
*
206923 TATTTATGAAATTCAAATC
1 TATTTATGAAATCCAAATC
*
206942 TATTTTTGAAATCCAAAT
1 TATTTATGAAATCCAAAT
206960 TTCCAAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (19 bp):
TATTTATGAAATCCAAATC
Found at i:207498 original size:16 final size:16
Alignment explanation
Indices: 207477--207538 Score: 56
Period size: 15 Copynumber: 3.8 Consensus size: 16
207467 AATACAATTA
207477 TTATATAATTTTATAT
1 TTATATAATTTTATAT
207493 TTATATAAATTTTTATTAT
1 TTATAT-AA-TTTTA-TAT
* *
207512 TTTTAAAATTTTA-AT
1 TTATATAATTTTATAT
207527 TT-TAGTAATTTT
1 TTATA-TAATTTT
207539 GTCATTACAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 2 0.05
15 10 0.26
16 6 0.15
17 7 0.18
18 7 0.18
19 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATATAATTTTATAT
Found at i:207506 original size:18 final size:19
Alignment explanation
Indices: 207473--207523 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 19
207463 TATAAATACA
207473 ATTA-TTATAT-AA-TTTT
1 ATTATTTATATAAATTTTT
207489 A-TATTTATATAAATTTTT
1 ATTATTTATATAAATTTTT
*
207507 ATTATTTTTA-AAATTTT
1 ATTATTTATATAAATTTT
207524 AATTTTAGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.07
16 7 0.23
17 2 0.07
18 12 0.40
19 7 0.23
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTATTTATATAAATTTTT
Found at i:207732 original size:16 final size:16
Alignment explanation
Indices: 207713--207762 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
207703 AAATAACTCG
207713 AATCTAAAAAAATTTA
1 AATCTAAAAAAATTTA
* *
207729 AATCTAAAAATATCTA
1 AATCTAAAAAAATTTA
* *
207745 AATTTAAAATAA-TTA
1 AATCTAAAAAAATTTA
207760 AAT
1 AAT
207763 TTAATTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 5 0.18
16 23 0.82
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
AATCTAAAAAAATTTA
Found at i:207770 original size:20 final size:21
Alignment explanation
Indices: 207745--207787 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
207735 AAAATATCTA
207745 AATTTAAAATAAT-TAAATTT
1 AATTTAAAATAATATAAATTT
207765 AATTTAAAATAATATAAATTT
1 AATTTAAAATAATATAAATTT
207786 AA
1 AA
207788 AAATAATCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATTTAAAATAATATAAATTT
Found at i:213277 original size:1 final size:1
Alignment explanation
Indices: 213271--213298 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
213261 TACTCTCCAA
213271 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGG
213299 CTGAATCTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:213626 original size:2 final size:2
Alignment explanation
Indices: 213619--213652 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
213609 CTCCTCATTA
213619 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
213653 TTCTTATGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:216873 original size:19 final size:20
Alignment explanation
Indices: 216849--216895 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
216839 TTCTTTGCAA
*
216849 GTATCGATACAGTG-GTTAT
1 GTATCGATACAGTGCATTAT
*
216868 GTATCGATACTGTGCATTAT
1 GTATCGATACAGTGCATTAT
216888 GTATCGAT
1 GTATCGAT
216896 GCATCTGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (20 bp):
GTATCGATACAGTGCATTAT
Found at i:218193 original size:12 final size:12
Alignment explanation
Indices: 218176--218200 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
218166 TAAATCTTGG
218176 ACAATATCAGCA
1 ACAATATCAGCA
218188 ACAATATCAGCA
1 ACAATATCAGCA
218200 A
1 A
218201 AGATGAAGTA
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:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
ACAATATCAGCA
Found at i:223952 original size:3 final size:3
Alignment explanation
Indices: 223944--223974 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
223934 TCTGAGTCAC
*
223944 CAT CAT CAT CAT CAT CAT CAT CAT CTT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
223975 GTCCTTGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.29, C:0.35, G:0.00, T:0.35
Consensus pattern (3 bp):
CAT
Found at i:225092 original size:10 final size:10
Alignment explanation
Indices: 225070--225106 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
225060 GGTGGAGGAG
225070 TCGACATATTT
1 TCGACA-ATTT
225081 TCGACAATTT
1 TCGACAATTT
225091 TCGACAATTT
1 TCGACAATTT
225101 TCGACA
1 TCGACA
225107 TATGGTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 20 0.77
11 6 0.23
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (10 bp):
TCGACAATTT
Found at i:225411 original size:52 final size:52
Alignment explanation
Indices: 225347--225493 Score: 224
Period size: 52 Copynumber: 2.8 Consensus size: 52
225337 TGCCAAGAAA
*
225347 ATGTATCGATACACTGATCTTTGTATCAATACATGCAGGCAAATTTACCCAG
1 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTACCCAG
* *
225399 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAACTTTGCCCAG
1 ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTACCCAG
***
225451 ATGTATCGATACACT-ATGAAATGTATCGATACATGCAGGCAAA
1 ATGTATCGATACACTGAT-CTTTGTATCGATACATGCAGGCAAA
225494 ATTTCATATT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (52 bp):
ATGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTACCCAG
Found at i:229193 original size:34 final size:32
Alignment explanation
Indices: 229150--229212 Score: 92
Period size: 34 Copynumber: 1.9 Consensus size: 32
229140 TACAAGCCAA
229150 TGTATCGATACAAT-TTGGTCATGTATCGATAAAT
1 TGTATCGATAC-ATCTT-GT-ATGTATCGATAAAT
229184 TGTATCGATACATCTTGTATGTATCGATA
1 TGTATCGATACATCTTGTATGTATCGATA
229213 CAAATAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 11 0.39
33 4 0.14
34 13 0.46
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (32 bp):
TGTATCGATACATCTTGTATGTATCGATAAAT
Found at i:229302 original size:19 final size:20
Alignment explanation
Indices: 229278--229327 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
229268 TTCTTTGCAA
*
229278 GTATCGATACAGTG-GTTAT
1 GTATCGATACAGTGCATTAT
*
229297 GTATCGATACTGTGCATTAT
1 GTATCGATACAGTGCATTAT
*
229317 GTATCAATACA
1 GTATCGATACA
229328 TCTGAAGGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (20 bp):
GTATCGATACAGTGCATTAT
Found at i:233087 original size:33 final size:35
Alignment explanation
Indices: 233034--233101 Score: 104
Period size: 33 Copynumber: 2.0 Consensus size: 35
233024 CTCCTTGCTT
* *
233034 TGTTTTTTTTTTTCTCCTTTTGTTTGATTCGATTC
1 TGTTTTTTTCTTTCTCCTTTTGCTTGATTCGATTC
233069 TGTTTTTTTCTTT-T-CTTTTGCTTGATTCGATTC
1 TGTTTTTTTCTTTCTCCTTTTGCTTGATTCGATTC
233102 CCCTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
33 18 0.58
34 1 0.03
35 12 0.39
ACGTcount: A:0.06, C:0.15, G:0.12, T:0.68
Consensus pattern (35 bp):
TGTTTTTTTCTTTCTCCTTTTGCTTGATTCGATTC
Found at i:233109 original size:33 final size:33
Alignment explanation
Indices: 233050--233115 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
233040 TTTTTTTCTC
* ***
233050 CTTTTGTTTGATTCGATTCTGTTTTTTTCTTTT
1 CTTTTGCTTGATTCGATTCCCCTTTTTTCTTTT
*
233083 CTTTTGCTTGATTCGATTCCCCTTTTTTTTTTT
1 CTTTTGCTTGATTCGATTCCCCTTTTTTCTTTT
233116 GTCACTTCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.06, C:0.17, G:0.11, T:0.67
Consensus pattern (33 bp):
CTTTTGCTTGATTCGATTCCCCTTTTTTCTTTT
Found at i:233730 original size:10 final size:10
Alignment explanation
Indices: 233715--233747 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
233705 GCATGAAAGC
233715 AATGCAATGA
1 AATGCAATGA
*
233725 AATGCAATGC
1 AATGCAATGA
233735 AATGC-ATGA
1 AATGCAATGA
233744 AATG
1 AATG
233748 TTTTTGAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 7 0.33
10 14 0.67
ACGTcount: A:0.45, C:0.12, G:0.21, T:0.21
Consensus pattern (10 bp):
AATGCAATGA
Found at i:233733 original size:15 final size:14
Alignment explanation
Indices: 233702--233738 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
233692 CAGCAGTTTT
233702 AATGC-ATGAAAGC
1 AATGCAATGAAAGC
233715 AATGCAATGAAATGC
1 AATGCAATGAAA-GC
233730 AATGCAATG
1 AATGCAATG
233739 CATGAAATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.19
Consensus pattern (14 bp):
AATGCAATGAAAGC
Found at i:233820 original size:14 final size:14
Alignment explanation
Indices: 233801--233895 Score: 69
Period size: 14 Copynumber: 7.1 Consensus size: 14
233791 GAAAGAAAAC
*
233801 ATGCATGAAATGTA
1 ATGCATGAAATGAA
**
233815 ATGCATGAAACAAA
1 ATGCATGAAATGAA
233829 ATGCATGAAATGAA
1 ATGCATGAAATGAA
*
233843 CAT-CACGTGAAATG-C
1 -ATGCA--TGAAATGAA
*
233858 ATGCATGAAATGTA
1 ATGCATGAAATGAA
233872 ATG--T--AA-GAA
1 ATGCATGAAATGAA
233881 ATGCATGAAATGAA
1 ATGCATGAAATGAA
233895 A
1 A
233896 ATTATGTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
9 5 0.08
10 2 0.03
11 1 0.02
12 1 0.02
13 9 0.14
14 34 0.54
15 4 0.06
16 7 0.11
ACGTcount: A:0.47, C:0.11, G:0.20, T:0.22
Consensus pattern (14 bp):
ATGCATGAAATGAA
Found at i:233868 original size:29 final size:26
Alignment explanation
Indices: 233829--233921 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 26
233819 ATGAAACAAA
233829 ATGCATGAAATGAACATCACGTGAAATGC
1 ATGCATGAAATGAA-AT-A-GTGAAATGC
* *
233858 ATGCATGAAATGTAAT-GT--AA-GAA
1 ATGCATGAAATGAAATAGTGAAATG-C
233881 ATGCATGAAATGAAAATTATGTGAAATGC
1 ATGCATGAAATG-AAA-TA-GTGAAATGC
233910 ATGCATGAAATG
1 ATGCATGAAATG
233922 TAATCCATAA
Statistics
Matches: 52, Mismatches: 4, Indels: 16
0.72 0.06 0.22
Matches are distributed among these distances:
22 1 0.02
23 14 0.27
24 2 0.04
25 3 0.06
27 2 0.04
28 2 0.04
29 27 0.52
30 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.25
Consensus pattern (26 bp):
ATGCATGAAATGAAATAGTGAAATGC
Found at i:233905 original size:52 final size:55
Alignment explanation
Indices: 233800--233925 Score: 177
Period size: 52 Copynumber: 2.3 Consensus size: 55
233790 TGAAAGAAAA
*
233800 CATGCATGAAATGTAATGCATGAAACAAAATGCATGAAATGAACATCACGTGAAATG
1 CATGCATGAAATGTAATG-AT-AAACAAAATGCATGAAATGAAAATCACGTGAAATG
* * *
233857 CATGCATGAAATGTAATG-T-AA-GAAATGCATGAAATGAAAATTATGTGAAATG
1 CATGCATGAAATGTAATGATAAACAAAATGCATGAAATGAAAATCACGTGAAATG
233909 CATGCATGAAATGTAAT
1 CATGCATGAAATGTAAT
233926 CCATAAAATG
Statistics
Matches: 65, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
52 44 0.68
53 2 0.03
55 1 0.02
57 18 0.28
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (55 bp):
CATGCATGAAATGTAATGATAAACAAAATGCATGAAATGAAAATCACGTGAAATG
Found at i:233912 original size:25 final size:25
Alignment explanation
Indices: 233827--233912 Score: 86
Period size: 25 Copynumber: 3.4 Consensus size: 25
233817 GCATGAAACA
* * *
233827 AAATGCATGAAATGAACATCACGTG
1 AAATGCATGAAATGAAAATTATGTG
*
233852 AAATGCATG-CATG-AAATGTAATGTAAG
1 AAATGCATGAAATGAAAAT-T-ATGT--G
233879 AAATGCATGAAATGAAAATTATGTG
1 AAATGCATGAAATGAAAATTATGTG
233904 AAATGCATG
1 AAATGCATG
233913 CATGAAATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
23 3 0.06
24 3 0.06
25 22 0.44
27 14 0.28
28 4 0.08
29 4 0.08
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.24
Consensus pattern (25 bp):
AAATGCATGAAATGAAAATTATGTG
Found at i:233935 original size:52 final size:51
Alignment explanation
Indices: 233826--233985 Score: 165
Period size: 52 Copynumber: 3.3 Consensus size: 51
233816 TGCATGAAAC
* **
233826 AAAATGCATGAAATGAACATCACGTGAAATGCATGCATGAAATGTAATGTA
1 AAAATGCATGAAATGAAAATCACGTGAAATGCATGCATGAAATGTAATCCA
* *
233877 AGAAATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGTAATCC-
1 A-AAATGCATGAAATGAAAATCACGTGAAATGCATGCATGAAATGTAATCCA
* * * *
233928 ---AT--A--AAATGAAAATTACGTAAAAGGCATGCATGAAATGTAATGCA
1 AAAATGCATGAAATGAAAATCACGTGAAATGCATGCATGAAATGTAATCCA
233972 CAAAATGCATGAAA
1 -AAAATGCATGAAA
233986 GTATGCATGA
Statistics
Matches: 90, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
43 36 0.40
45 1 0.01
47 2 0.02
48 2 0.02
50 1 0.01
51 1 0.01
52 47 0.52
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (51 bp):
AAAATGCATGAAATGAAAATCACGTGAAATGCATGCATGAAATGTAATCCA
Found at i:233937 original size:43 final size:43
Alignment explanation
Indices: 233888--233978 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
233878 GAAATGCATG
* * * *
233888 AAATGAAAATTATGTGAAATGCATGCATGAAATGTAATCCATA
1 AAATGAAAATTACGTAAAAGGCATGCATGAAATGTAATCCACA
*
233931 AAATGAAAATTACGTAAAAGGCATGCATGAAATGTAATGCACA
1 AAATGAAAATTACGTAAAAGGCATGCATGAAATGTAATCCACA
233974 AAATG
1 AAATG
233979 CATGAAAGTA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.48, C:0.10, G:0.18, T:0.24
Consensus pattern (43 bp):
AAATGAAAATTACGTAAAAGGCATGCATGAAATGTAATCCACA
Found at i:233993 original size:12 final size:12
Alignment explanation
Indices: 233976--234000 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
233966 AATGCACAAA
233976 ATGCATGAAAGT
1 ATGCATGAAAGT
233988 ATGCATGAAAGT
1 ATGCATGAAAGT
234000 A
1 A
234001 AAAGCAAGCA
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:0.08, G:0.24, T:0.24
Consensus pattern (12 bp):
ATGCATGAAAGT
Found at i:234262 original size:14 final size:14
Alignment explanation
Indices: 234243--234284 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
234233 TAATTAATTA
234243 ATTATTACTA-TATT
1 ATTATTA-TATTATT
234257 ATTATTATATTATT
1 ATTATTATATTATT
* *
234271 AATATTTTATTATT
1 ATTATTATATTATT
234285 TTTTTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 2 0.08
14 23 0.92
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTATTATATTATT
Found at i:234289 original size:11 final size:11
Alignment explanation
Indices: 234244--234306 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
234234 AATTAATTAA
* *
234244 TTATTACTATA
1 TTATTATTATT
*
234255 TTATTATTATA
1 TTATTATTATT
*
234266 TTATTAATATT
1 TTATTATTATT
*
234277 TTATTATTTTT
1 TTATTATTATT
* * *
234288 TTGTTTTTTTT
1 TTATTATTATT
234299 TTATTATT
1 TTATTATT
234307 CATATTAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 43 1.00
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTATTATT
Found at i:238284 original size:159 final size:159
Alignment explanation
Indices: 237995--238313 Score: 638
Period size: 159 Copynumber: 2.0 Consensus size: 159
237985 GGAAGTGAGC
237995 TATTTGCCTTCGTGAGTAACCCTCCGCATAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
1 TATTTGCCTTCGTGAGTAACCCTCCGCATAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
238060 TGCTCTCGTGAGTAACCCTCTGCATTTGCATAGGGAAATACATCTACCAGATCGAACTCGATTCA
66 TGCTCTCGTGAGTAACCCTCTGCATTTGCATAGGGAAATACATCTACCAGATCGAACTCGATTCA
238125 TCAAACCCGCGATGGGCCTAGAATCGAGG
131 TCAAACCCGCGATGGGCCTAGAATCGAGG
238154 TATTTGCCTTCGTGAGTAACCCTCCGCATAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
1 TATTTGCCTTCGTGAGTAACCCTCCGCATAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
238219 TGCTCTCGTGAGTAACCCTCTGCATTTGCATAGGGAAATACATCTACCAGATCGAACTCGATTCA
66 TGCTCTCGTGAGTAACCCTCTGCATTTGCATAGGGAAATACATCTACCAGATCGAACTCGATTCA
238284 TCAAACCCGCGATGGGCCTAGAATCGAGG
131 TCAAACCCGCGATGGGCCTAGAATCGAGG
238313 T
1 T
238314 GCCTCGACTG
Statistics
Matches: 160, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
159 160 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (159 bp):
TATTTGCCTTCGTGAGTAACCCTCCGCATAGGCATAGCAATAACTTCCAGGATGTAAATTACCTA
TGCTCTCGTGAGTAACCCTCTGCATTTGCATAGGGAAATACATCTACCAGATCGAACTCGATTCA
TCAAACCCGCGATGGGCCTAGAATCGAGG
Found at i:242315 original size:43 final size:45
Alignment explanation
Indices: 242251--242438 Score: 227
Period size: 48 Copynumber: 4.1 Consensus size: 45
242241 TTAAAGATGG
*
242251 AAAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGACTT-
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
242295 AAAA-GTGCCAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAA
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A
* *
242340 ATATGAAGGTGCCAATATGCTGATTTAAGGCCAGCGATATTGGACTTA
1 A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
242388 AAGGCAAGGTGCCAATATGCTGATTCAAGGCCAGTTATATTGGGCTTA
1 AA---AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
242436 AAA
1 AAA
242439 GGAGACGCCA
Statistics
Matches: 122, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
43 35 0.29
44 4 0.03
45 2 0.02
46 1 0.01
47 1 0.01
48 45 0.37
49 34 0.28
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (45 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
Found at i:242382 original size:92 final size:97
Alignment explanation
Indices: 242208--242437 Score: 299
Period size: 92 Copynumber: 2.4 Consensus size: 97
242198 AAAAGGATGT
** *
242208 CAATGTGCTGATTCAAGGCCAGCTACATTAAACTTAAAGATGGAAAAGGTGCCAATATGTTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAATATGCTGATT
*
242273 CAAGGCCAGCTATATTGGACTT-AA-AA-GTGC
65 CAAGGCCAGCGATATTGGACTTAAAGAAGGTGC
* * *
242303 CAATGTGCTGATTCAAGGTCAGCTACATTGGACTTAAATAT-G-AAGGTGCCAATATGCTGATTT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
242366 AAGGCCAGCGATATTGGACTTAAAGGCAAGGTGC
66 AAGGCCAGCGATATTGGACTTAAA-G-AAGGTGC
* * * *
242400 CAATATGCTGATTCAAGGCCAGTTATATTGGGCTTAAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
242438 AGGAGACGCC
Statistics
Matches: 118, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
92 39 0.33
93 2 0.02
94 1 0.01
95 37 0.31
96 2 0.02
97 37 0.31
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (97 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAAGAAGGTGC
Found at i:242514 original size:28 final size:28
Alignment explanation
Indices: 242457--242580 Score: 135
Period size: 28 Copynumber: 4.3 Consensus size: 28
242447 CACCAACTTG
*
242457 TGTGGGCTTTTGAAAGGTTTG-CA-TCAACT
1 TGTGGGCTTTTG-AAGG-TTGCCACT-GACT
* *
242486 TGTGTGCTTTTGAAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
242514 TGTGGGCTTTTAAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* *
242542 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTG--AAGGTTGCCACTGACT
242572 TGTGGGCTT
1 TGTGGGCTT
242581 AAAAAGAAAA
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
27 3 0.04
28 44 0.54
29 12 0.15
30 23 0.28
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.37
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:242543 original size:56 final size:58
Alignment explanation
Indices: 242457--242580 Score: 148
Period size: 58 Copynumber: 2.2 Consensus size: 58
242447 CACCAACTTG
* * * *
242457 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGTGCTTTTG-AAGGTTGCTACTGACT
1 TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAAGGGTGCCACTAACT
*
242514 TGTGGGCTTTT-AAAGG-TTGCCA-CTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAGGTTTG-CATC-AACTTGTGGGCTTTTG-AAAGGGTGCCACTAACT
242572 TGTGGGCTT
1 TGTGGGCTT
242581 AAAAAGAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
55 4 0.07
56 21 0.36
57 11 0.19
58 22 0.38
ACGTcount: A:0.18, C:0.15, G:0.30, T:0.37
Consensus pattern (58 bp):
TGTGGGCTTTTGAAAGGTTTGCATCAACTTGTGGGCTTTTGAAAGGGTGCCACTAACT
Found at i:242565 original size:30 final size:30
Alignment explanation
Indices: 242483--242801 Score: 199
Period size: 29 Copynumber: 10.6 Consensus size: 30
242473 GTTTGCATCA
* * *
242483 ACTTGTGTGCTTTTG--AAGGTTGCTACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
242511 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
*
242539 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
** * *
242569 ACTTGTGGGCTTAAAAAGAAAAAGAGTGCTA-TAG
1 ACTTGTGGGCTT---TTG-AAAAGGGTGCCACT-G
* * ** * *
242603 AGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGG
1 ACTTGTGGGCTT----TTG-AAAAGGGTGCCACTG
* * * * *
242638 AGTTGTGGACTTTGGAAAA-GATGCCACCG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
**
242667 ACTTGTGGGCTTCGGAAAAGGGTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
* *
242697 ATTTGTGGG-TTTTG--AAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
***
242724 ACTTGTGGGCTTTTGAAAAAAAAATGCCACTG
1 ACTTGTGGGCTTTTG--AAAAGGGTGCCACTG
* *
242756 ACTTGTGGGC-TTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
242785 ACTTGTGGGCTTTTGAA
1 ACTTGTGGGCTTTTGAA
242802 GGGTGAGGAA
Statistics
Matches: 239, Mismatches: 35, Indels: 32
0.78 0.11 0.10
Matches are distributed among these distances:
27 20 0.08
28 44 0.18
29 50 0.21
30 50 0.21
31 5 0.02
32 20 0.08
33 2 0.01
34 20 0.08
35 28 0.12
ACGTcount: A:0.26, C:0.15, G:0.29, T:0.29
Consensus pattern (30 bp):
ACTTGTGGGCTTTTGAAAAGGGTGCCACTG
Found at i:242641 original size:35 final size:34
Alignment explanation
Indices: 242554--242644 Score: 103
Period size: 35 Copynumber: 2.6 Consensus size: 34
242544 TGGGCTTTTG
* * *
242554 AAAAGGGTGCCACTA-ACTTGTGGGCTTAAAAAGA
1 AAAAGAGTGCCAC-AGAGTTGTGAGCTTAAAAAGA
* *
242588 AAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGA
1 AAAAGAGTGCCACAGAGTTGTGAGCTTA-AAAAGA
*
242623 AAAAGAGTGCCACGGAGTTGTG
1 AAAAGAGTGCCACAGAGTTGTG
242645 GACTTTGGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
33 1 0.02
34 21 0.45
35 25 0.53
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.21
Consensus pattern (34 bp):
AAAAGAGTGCCACAGAGTTGTGAGCTTAAAAAGA
Found at i:242703 original size:59 final size:59
Alignment explanation
Indices: 242622--242796 Score: 183
Period size: 59 Copynumber: 2.9 Consensus size: 59
242612 CTTACAAAAG
* * *
242622 AAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCG-
1 AAAAAGAGTGCCACTGACTTGTGG-CTTTGGAAAAGATGCCACTGACTTGTGGGCTTCGA
* * * * * * * *
242681 GAAAAGGGTGCCACTGATTTGTGGGTTTTG-AAGGTTGCCACTGACTTGTGGGCTTTTGA
1 AAAAAGAGTGCCACTGACTTGTGGCTTTGGAAAAGATGCCACTGACTTGTGGGC-TTCGA
* * *
242740 AAAAAAAATGCCACTGACTTGTGGGCTTTGAAAAAGATGCCACTGACTTGTGGGCTT
1 AAAAAGAGTGCCACTGACTTGT-GGCTTTGGAAAAGATGCCACTGACTTGTGGGCTT
242797 TTGAAGGGTG
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
57 20 0.22
58 7 0.08
59 37 0.40
60 7 0.08
61 21 0.23
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.27
Consensus pattern (59 bp):
AAAAAGAGTGCCACTGACTTGTGGCTTTGGAAAAGATGCCACTGACTTGTGGGCTTCGA
Found at i:244247 original size:1 final size:1
Alignment explanation
Indices: 244241--244317 Score: 73
Period size: 1 Copynumber: 77.0 Consensus size: 1
244231 ATCCGGACCC
* * * * * * * * *
244241 TTTTTTTTGTTTTGTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTGTTTTTGTTTTTTTTGTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
244306 TTTTTTTTTTTT
1 TTTTTTTTTTTT
244318 GTGGAGGACG
Statistics
Matches: 58, Mismatches: 18, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (1 bp):
T
Found at i:244255 original size:5 final size:5
Alignment explanation
Indices: 244241--244319 Score: 94
Period size: 5 Copynumber: 16.2 Consensus size: 5
244231 ATCCGGACCC
* *
244241 TTTT- TTTTG TTTTG TTTTG TTTTT TTTTG TTTTTG TTTTT TTTTG TTTTTG
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG -TTTTG TTTTG TTTTG -TTTTG
244292 TTTT- TTTTG TTTTG TTTT- TTTT- TTTTG T
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG T
244320 GGAGGACGCC
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
4 16 0.24
5 40 0.61
6 10 0.15
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (5 bp):
TTTTG
Found at i:244263 original size:16 final size:15
Alignment explanation
Indices: 244241--244317 Score: 99
Period size: 16 Copynumber: 5.3 Consensus size: 15
244231 ATCCGGACCC
*
244241 TTTTT-TTTGTTTTG
1 TTTTTGTTTTTTTTG
244255 -TTTTGTTTTTTTTTG
1 TTTTTG-TTTTTTTTG
244270 TTTTTGTTTTTTTTTG
1 TTTTTG-TTTTTTTTG
244286 TTTTTGTTTTTTTTG
1 TTTTTGTTTTTTTTG
244301 -TTTTGTTTTTTTT-
1 TTTTTGTTTTTTTTG
244314 TTTT
1 TTTT
244318 GTGGAGGACG
Statistics
Matches: 58, Mismatches: 1, Indels: 8
0.87 0.01 0.12
Matches are distributed among these distances:
13 4 0.07
14 16 0.28
15 17 0.29
16 21 0.36
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (15 bp):
TTTTTGTTTTTTTTG
Found at i:244315 original size:31 final size:30
Alignment explanation
Indices: 244241--244317 Score: 102
Period size: 31 Copynumber: 2.5 Consensus size: 30
244231 ATCCGGACCC
* *
244241 TTTTTTTTGTTTTGTTTTGTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTGTTTTTTTTTGT
244271 TTTTGTTTTTTTTTGTTTTTG-TTTTTTTTGT
1 TTTT-TTTTTTTTT-TTTTTGTTTTTTTTTGT
*
244302 TTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTT
244318 GTGGAGGACG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.07
30 13 0.31
31 21 0.50
32 5 0.12
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (30 bp):
TTTTTTTTTTTTTTTTTTGTTTTTTTTTGT
Found at i:260732 original size:85 final size:85
Alignment explanation
Indices: 260589--260890 Score: 408
Period size: 85 Copynumber: 3.6 Consensus size: 85
260579 AAGGTCACAG
* * * *
260589 GCAGATTTTAGATGAGGCAGTCTTCAGGGTCAAAGCTGATAGGCAGAATGAAAGGTAAGAAAGTC
1 GCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGAATGAAAGGTAAGAAAGTC
260654 TCTAAGGTCAAAGCCGACAA
66 TCTAAGGTCAAAGCCGACAA
* * * * * *
260674 GCAGACTTTAGATGAGGTAGTCTCCAGGGCCAAAGTCGACAGGTAGACTGAAGGGTAAGAAAGTC
1 GCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGAATGAAAGGTAAGAAAGTC
* *
260739 TCCAAGGTCAAAGCCGACAG
66 TCTAAGGTCAAAGCCGACAA
* * * *
260759 GCAAATTTTAGATGAGGCAGTCTTCAGGGTCAAAGCCGATAGGCAGAATGAAAGGTAAGAAAGTC
1 GCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGAATGAAAGGTAAGAAAGTC
260824 TCTAAGGTCAAAGCCGAC-A
66 TCTAAGGTCAAAGCCGACAA
* * * *
260843 GACAGACTTTAGATGAGGTAGTCTCTAAGGTCAAAGCCGACAGACAGA
1 G-CAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGA
260891 CTTTAGATGA
Statistics
Matches: 184, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
84 1 0.01
85 183 0.99
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (85 bp):
GCAGACTTTAGATGAGGCAGTCTCCAGGGTCAAAGCCGACAGGCAGAATGAAAGGTAAGAAAGTC
TCTAAGGTCAAAGCCGACAA
Found at i:260830 original size:170 final size:163
Alignment explanation
Indices: 260485--260892 Score: 620
Period size: 170 Copynumber: 2.5 Consensus size: 163
260475 AAAAGGTTGA
* * * * *
260485 AAAGTCTCCAGGGTCAAAGCTGACAAGCAGACTTTAGATGAGGCAGTCTCCCGGGTCAAAGTCGA
1 AAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAGGGTCAAAGTCGA
*
260550 CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCACAGGCAGATTTTAGATGAGGCAGTCTTCA
66 CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCACAGGCAAATTTTAGATGAGGCAGTCTTCA
*
260615 GGGTCAAAGCTGATAGGCAGAATGAAAGGTAAG
131 GGGTCAAAGCCGATAGGCAGAATGAAAGGTAAG
*
260648 AAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAGGGCCAAAGTCGA
1 AAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAGGGTCAAAGTCGA
*
260713 CAGGTAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAAATTTTAGATGAGGCA
66 CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGT------C-ACAGGCAAATTTTAGATGAGGCA
260778 GTCTTCAGGGTCAAAGCCGATAGGCAGAATGAAAGGTAAG
124 GTCTTCAGGGTCAAAGCCGATAGGCAGAATGAAAGGTAAG
* * *
260818 AAAGTCTCTAAGGTCAAAGCCGAC-AGACAGACTTTAGATGAGGTAGTCTCTAAGGTCAAAGCCG
1 AAAGTCTCTAAGGTCAAAGCCGACAAG-CAGACTTTAGATGAGGTAGTCTCCAGGGTCAAAGTCG
*
260882 ACAGACAGACT
65 ACAGGCAGACT
260893 TTAGATGAGG
Statistics
Matches: 222, Mismatches: 15, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
163 92 0.41
169 3 0.01
170 127 0.57
ACGTcount: A:0.35, C:0.19, G:0.28, T:0.18
Consensus pattern (163 bp):
AAAGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAGGGTCAAAGTCGA
CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCACAGGCAAATTTTAGATGAGGCAGTCTTCA
GGGTCAAAGCCGATAGGCAGAATGAAAGGTAAG
Found at i:260878 original size:212 final size:212
Alignment explanation
Indices: 260650--261104 Score: 591
Period size: 212 Copynumber: 2.1 Consensus size: 212
260640 AAGGTAAGAA
*
260650 AGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAGGGCCAAAG-TCGA-
1 AGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAAGGCCAAAGCT-GAT
* * * *
260713 CAGGTAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGACAGGCAAATTTTA-GATGAGGC
65 AAGG-AGACTGAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTGATG-TGAGGC
* * *
260777 AGTCT-TCAGGGTCAAAGCCGATAGGCAGAATGAAAG-GTAAGAAAGTCTCTAAGGTCAAAGCCG
128 AGTCTCT-AGGGTCAAAGCCGACAGGCAGAAT-AAAGAGTAAGAAAGTCTCCAAGGTCAAAGCCA
*
260840 ACAGACAGACTTT-AGATGAGGT
191 ACAGACAGACTTTAAG-TGAGAT
* *
260862 AGTCTCTAAGGTCAAAGCCGAC-AGACAGACTTTAGATGAGGTAGTCTCTAAGGTCAAAGCTGAT
1 AGTCTCTAAGGTCAAAGCCGACAAG-CAGACTTTAGATGAGGTAGTCTCCAAGGCCAAAGCTGAT
* * **
260926 AAGGAGACTGAAGGGTAAAAAAGTCTCCAAGGTCAATGCTGACAGGCTGACTTGATGTGAGGCAG
65 AAGGAGACTGAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTGATGTGAGGCAG
* * * *
260991 TCTCTAGGGTCAAAGCTGACAGGCAGACTAAAGAGTGAGAAAGTCTCCAAGGTCAAAGCTAACAG
130 TCTCTAGGGTCAAAGCCGACAGGCAGAATAAAGAGTAAGAAAGTCTCCAAGGTCAAAGCCAACAG
*
261056 GCAGACTTTAAGTGAGAT
195 ACAGACTTTAAGTGAGAT
* * *
261074 AGTTTCTAGGGTCAAAGTCGACAAGCAGACT
1 AGTCTCTAAGGTCAAAGCCGACAAGCAGACT
261105 AAGGGTAGGA
Statistics
Matches: 212, Mismatches: 23, Indels: 16
0.84 0.09 0.06
Matches are distributed among these distances:
211 6 0.03
212 196 0.92
213 10 0.05
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.20
Consensus pattern (212 bp):
AGTCTCTAAGGTCAAAGCCGACAAGCAGACTTTAGATGAGGTAGTCTCCAAGGCCAAAGCTGATA
AGGAGACTGAAGGGTAAAAAAGTCTCCAAGGTCAAAGCCGACAGGCAAACTTGATGTGAGGCAGT
CTCTAGGGTCAAAGCCGACAGGCAGAATAAAGAGTAAGAAAGTCTCCAAGGTCAAAGCCAACAGA
CAGACTTTAAGTGAGAT
Found at i:261273 original size:85 final size:85
Alignment explanation
Indices: 260607--261315 Score: 394
Period size: 85 Copynumber: 8.4 Consensus size: 85
260597 TAGATGAGGC
* * * * *
260607 AGTCTTCAGGGTCAAAGCTGATAGGCAGA-ATGAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTG-AAGGTAAGAAAGTCTCTAAGGTCAAAGCCGA
* * *
260671 CAAGCAGACTTTA-GATGAGG-T
65 CAGGCAGAC-TTAGGGT-AGGAA
* * * * *
260692 AGTCTCCAGGGCCAAAGTCGACAGGTAGAC-TGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAA-GGTAAGAAAGTCTCTAAGGTCAAAGCCGA
* * * *
260756 CAGGCAAATTTTA-GATGAGG-C
65 CAGGCAGA-CTTAGGGT-AGGAA
* * * *
260777 AGTCTTCAGGGTCAAAGCCGATAGGCAGA-ATGAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTG-AAGGTAAGAAAGTCTCTAAGGTCAAAGCCGA
* * *
260841 CAGACAGACTTTA-GATGAGG-T
65 CAGGCAGAC-TTAGGGT-AGGAA
* * * * * ** *
260862 AGTCTCTAAGGTCAAAGCCGACAGACAGACTT-TAGATGAGGTAGTCTCTAAGGTCAAAGCTGAT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGA-
* * **
260926 AAGG-AGACTGAAGGGTAAAAA
65 CAGGCAGACT-TAGGGTAGGAA
* * * * * ** * *
260947 AGTCTCCAAGGTCAATGCTGACAGGCTGACTTG-ATGTGAGGCAGTCTCTAGGGTCAAAGCTGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGAC
* *
261011 AGGCAGACTAAAGAGT-GAGAA
66 AGGCAGACT-TAGGGTAG-GAA
** * * * * * *
261032 AGTCTCCAAGGTCAAAGCTAACAGGCAGACTTTAA-GTGAGATAGTTTCTAGGGTCAAAGTCGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGAC
* *
261096 AAGCAGACTAAGGGTAGGAA
66 AGGCAGACTTAGGGTAGGAA
* **** * * * * * * * * **
261116 AATCTTTGGGGTCAAAGCCAATAGGTAAACTT-TAGATGAAG-CAGTCTCTAGGGTCAAAGTTGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAAGGT-AAGAAAGTCTCTAAGGTCAAAGCCGA
*
261179 CAGGCAGACTGAGGGTAGGAA
65 CAGGCAGACTTAGGGTAGGAA
** *
261200 AGTCTCCAAGGTCAAAGTTGACAGGCAGA-TTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCGA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAA-GGTAAGAAAGTCTCTAAGGTCAAAGCCGA
* * *
261264 CAGGTAGACTTTA-GATAAGG-T
65 CAGGCAGAC-TTAGGGT-AGGAA
* * *
261285 AGTCTCTAAGGTCAAAGCCAACAGGTAGACT
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACT
261316 AAAGGTAGGC
Statistics
Matches: 491, Mismatches: 109, Indels: 47
0.76 0.17 0.07
Matches are distributed among these distances:
83 4 0.01
84 128 0.26
85 349 0.71
86 10 0.02
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (85 bp):
AGTCTCCAAGGTCAAAGCCGACAGGCAGACTTGAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGAC
AGGCAGACTTAGGGTAGGAA
Found at i:261289 original size:127 final size:128
Alignment explanation
Indices: 260485--261320 Score: 537
Period size: 127 Copynumber: 6.6 Consensus size: 128
260475 AAAAGGTTGA
* * * * ***
260485 AAAGTCTCCAGGGTCAAAGCTGACAAGCAGACTTTAGATGAGGCAGTCTCCCGGGTCAAAG-TCG
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCT-G
** * *
260549 ACAGGCAGACTGAAGGGTAAGAAAGTCTCCAA-G-----GTC-ACAGGCAGATTTTA-GATGAG
65 ACAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGATTGAAGGGTAAG
** * * * * ** * * ** *
260605 GCAGTCT-TCAGGGTCAAAGCTGATAGGCAGAATGAAAGGTAAGAAAGTCTCTAAGGTCAAAGCC
1 AAAGTCTCT-AAGGTCAAAGCCGACAGGCAGACT-TTAGATGAGGCAGTCTCTAAGGTCAAAGCT
* ** * * ** * * * *
260669 GACAAGCAGACTTTA-GATGAGGTAGTCTCCAGGGCCAAAGTCGACAGGTAGACTGAAGGGTAAG
64 GACAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGATTGAAGGGTAAG
* * * * *
260733 AAAGTCTCCAAGGTCAAAGCCGACAGGCAAATTTTAGATGAGGCAGTCT-TCAGGGTCAAAGCCG
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCT-AAGGTCAAAGCTG
* * * * * * * * *
260797 ATAGGCAGAATGAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCGACAGACAGACTT-TA-GATGAG
65 ACAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGA-TTGAAGGGTAAG
** * *
260860 GTAGTCTCTAAGGTCAAAGCCGACAGACAGACTTTAGATGAGGTAGTCTCTAAGGTCAAAGCTGA
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCTGA
* * * * * *
260925 TAAGG-AGACTGAAGGGTAAAAAAGTCTCCAAGGTCAATG-CTGACAGGCTGACTTG-A-TGTGA
66 -CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTC-GACAGGCAGA-TTGAAGGGTAA
260986 G
128 G
** * * ** ** * *
260987 GCAGTCTCTAGGGTCAAAGCTGACAGGCAGACTAAAGAGTGAGAAAGTCTCCAAGGTCAAAGCTA
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGA-TGAGGCAGTCTCTAAGGTCAAAGCTG
* * * * * * * * *
261052 ACAGGCAGACTTTAA--GTGAGATAGTTTCTAGGGTCAAAGTCGACAAGCAGACT-AAGGGTAGG
65 ACAGGCAGAC-TGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGATTGAAGGGTAAG
* * ** * * * * * * *
261114 AAAATCTTTGGGGTCAAAGCCAATAGGTAAACTTTAGATGAAGCAGTCTCTAGGGTCAAAGTTGA
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCTGA
* *
261179 CAGGCAGACTG-AGGGTAGGAAAGTCTCCAAGGTCAAAGTTGACAGGCAGATTGAAGGGTAAG
66 CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGATTGAAGGGTAAG
* * * * **
261241 AAAGTCTCCAAGGTCAAAGCCGACAGGTAGACTTTAGATAAGGTAGTCTCTAAGGTCAAAGCCAA
1 AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCTGA
* *
261306 CAGGTAGACTAAAGG
66 CAGGCAGACTGAAGG
261321 TAGGCCAGTT
Statistics
Matches: 532, Mismatches: 155, Indels: 50
0.72 0.21 0.07
Matches are distributed among these distances:
120 38 0.07
121 32 0.06
124 1 0.00
125 1 0.00
126 65 0.12
127 300 0.56
128 91 0.17
129 4 0.01
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (128 bp):
AAAGTCTCTAAGGTCAAAGCCGACAGGCAGACTTTAGATGAGGCAGTCTCTAAGGTCAAAGCTGA
CAGGCAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGTCGACAGGCAGATTGAAGGGTAAG
Found at i:261302 original size:42 final size:42
Alignment explanation
Indices: 260585--261315 Score: 377
Period size: 42 Copynumber: 17.3 Consensus size: 42
260575 CTCCAAGGTC
* * * *
260585 ACAGGCAGATTTTAGATGAGGCAGTCT-TCAGGGTCAAAGCTG
1 ACAGGCAGACTTTAGATGAGGAAGTCTCT-AAGGTCAAAGCCG
* * ** * * *
260627 ATAGGCAGAATGAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCG
1 ACAGGCAGACT-TTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
* * * * * *
260670 ACAAGCAGACTTTAGATGAGGTAGTCTCCAGGGCCAAAGTCG
1 ACAGGCAGACTTTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
* ** * * * *
260712 ACAGGTAGACTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCG
1 ACAGGCAGACTTTA-GATGAGGAAGTCTCTAAGGTCAAAGCCG
* * * *
260755 ACAGGCAAATTTTAGATGAGGCAGTCT-TCAGGGTCAAAGCCG
1 ACAGGCAGACTTTAGATGAGGAAGTCTCT-AAGGTCAAAGCCG
* * ** * * *
260797 ATAGGCAGAATGAAAGGTAAGAAAGTCTCTAAGGTCAAAGCCG
1 ACAGGCAGACT-TTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
* *
260840 ACAGACAGACTTTAGATGAGGTAGTCTCTAAGGTCAAAGCCG
1 ACAGGCAGACTTTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
* * *
260882 ACAGACAGACTTTAGATGAGGTAGTCTCTAAGGTCAAAGCTG
1 ACAGGCAGACTTTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
* ** * * ** * * *
260924 ATAAGG-AGACTGAAGGGTAAAAAAGTCTCCAAGGTCAATGCTG
1 A-CAGGCAGACTTTA-GATGAGGAAGTCTCTAAGGTCAAAGCCG
* * * * *
260967 ACAGGCTGACTTGATG-TGAGGCAGTCTCTAGGGTCAAAGCTG
1 ACAGGCAGACTTTA-GATGAGGAAGTCTCTAAGGTCAAAGCCG
** * * **
261009 ACAGGCAGACTAAAGAGTGAGAAAGTCTCCAAGGTCAAAGCTA
1 ACAGGCAGACTTTAGA-TGAGGAAGTCTCTAAGGTCAAAGCCG
* * *
261052 ACAGGCAGACTTTA-AGTGA-GATAGTTTCTAGGGTCAAAGTCG
1 ACAGGCAGACTTTAGA-TGAGGA-AGTCTCTAAGGTCAAAGCCG
* * * * * ** *
261094 ACAAGCAGAC-TAAG-GGTAGGAAAATCTTTGGGGTCAAAGCCA
1 ACAGGCAGACTTTAGATG-AGG-AAGTCTCTAAGGTCAAAGCCG
* * * * * * **
261136 ATAGGTAAACTTTAGATGAAGCAGTCTCTAGGGTCAAAGTTG
1 ACAGGCAGACTTTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
* * * **
261178 ACAGGCAGAC-TGAG-GGTAGGAAAGTCTCCAAGGTCAAAGTTG
1 ACAGGCAGACTTTAGATG-AGG-AAGTCTCTAAGGTCAAAGCCG
* * * * *
261220 ACAGGCAGA-TTGAAGGGTAAGAAAGTCTCCAAGGTCAAAGCCG
1 ACAGGCAGACTT-TA-GATGAGGAAGTCTCTAAGGTCAAAGCCG
* * * *
261263 ACAGGTAGACTTTAGATAAGGTAGTCTCTAAGGTCAAAGCCA
1 ACAGGCAGACTTTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
*
261305 ACAGGTAGACT
1 ACAGGCAGACT
261316 AAAGGTAGGC
Statistics
Matches: 514, Mismatches: 150, Indels: 50
0.72 0.21 0.07
Matches are distributed among these distances:
40 2 0.00
41 10 0.02
42 307 0.60
43 187 0.36
44 8 0.02
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (42 bp):
ACAGGCAGACTTTAGATGAGGAAGTCTCTAAGGTCAAAGCCG
Found at i:262718 original size:36 final size:38
Alignment explanation
Indices: 262667--262738 Score: 103
Period size: 36 Copynumber: 1.9 Consensus size: 38
262657 TTTTATTCAA
** *
262667 TTTTTTTCTTCTTTTTTTTATATTTTATATTTTTTCCC
1 TTTTTTTCTTCTTTTTTTTATACATAATATTTTTTCCC
262705 TTTTTTTC-T-TTTTTTTTATACATAATATTTTTTC
1 TTTTTTTCTTCTTTTTTTTATACATAATATTTTTTC
262739 ACACTATCTA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 22 0.71
37 1 0.03
38 8 0.26
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (38 bp):
TTTTTTTCTTCTTTTTTTTATACATAATATTTTTTCCC
Found at i:274488 original size:20 final size:20
Alignment explanation
Indices: 274450--274488 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
274440 TGAAGAAAAG
* *
274450 AATCAAAGGAAAATTAAGTA
1 AATCAAAGCAAAATGAAGTA
*
274470 AATCAAAGCAAAGTGAAGT
1 AATCAAAGCAAAATGAAGT
274489 CTAAAAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.56, C:0.08, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCAAAGCAAAATGAAGTA
Found at i:274617 original size:22 final size:21
Alignment explanation
Indices: 274575--274632 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 21
274565 GTTTTTGTTT
274575 TTTTCCTTTGCTG-TTTCGCTG
1 TTTT-CTTTGCTGCTTTCGCTG
274596 CTTTTCTTTGCTGCTATT-GCTG
1 -TTTTCTTTGCTGCT-TTCGCTG
*
274618 ATTTCGTTTGCTGCT
1 TTTTC-TTTGCTGCT
274633 GATATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 12 0.38
22 18 0.56
23 2 0.06
ACGTcount: A:0.03, C:0.22, G:0.19, T:0.55
Consensus pattern (21 bp):
TTTTCTTTGCTGCTTTCGCTG
Found at i:275103 original size:15 final size:16
Alignment explanation
Indices: 275083--275115 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
275073 TCCTCTCCTC
275083 TTTTTTCTCC-TTTGT
1 TTTTTTCTCCTTTTGT
275098 TTTTTTCTCCTTTTGT
1 TTTTTTCTCCTTTTGT
275114 TT
1 TT
275116 GATTTGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.00, C:0.18, G:0.06, T:0.76
Consensus pattern (16 bp):
TTTTTTCTCCTTTTGT
Found at i:275788 original size:15 final size:13
Alignment explanation
Indices: 275757--275790 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
275747 CAGTAGCTTT
275757 AATGCATGAAAGC
1 AATGCATGAAAGC
275770 AATGCTATGAAATGC
1 AATGC-ATGAAA-GC
275785 AATGCA
1 AATGCA
275791 ATGCATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 5 0.26
14 7 0.37
15 7 0.37
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (13 bp):
AATGCATGAAAGC
Found at i:275879 original size:14 final size:14
Alignment explanation
Indices: 275836--276003 Score: 77
Period size: 14 Copynumber: 12.0 Consensus size: 14
275826 GAACATTAGG
*
275836 TGAAATGCATG-CA
1 TGAAATGCATGAAA
* *
275849 TGAAATGTAATG-TA
1 TGAAATG-CATGAAA
275863 TGAAATGCATGAAA
1 TGAAATGCATGAAA
*
275877 TGAAAAT-TATGTGAAA
1 TG-AAATGCA--TGAAA
*
275893 TG-CATGCATGAAA
1 TGAAATGCATGAAA
*
275906 TGTAATGCATGAAA
1 TGAAATGCATGAAA
*
275920 TGAAAAT-TATGTGAAA
1 TG-AAATGCA--TGAAA
*
275936 TG-CATGCATGAAA
1 TGAAATGCATGAAA
275949 T-ATAATGCATGAAA
1 TGA-AATGCATGAAA
*
275963 TGAAAATTACATGAAA
1 TG-AAA-TGCATGAAA
*
275979 TG-CATGCATGAAA
1 TGAAATGCATGAAA
*
275992 --ATATGCATGAAA
1 TGAAATGCATGAAA
276004 GTAAAAGCAT
Statistics
Matches: 121, Mismatches: 17, Indels: 35
0.70 0.10 0.20
Matches are distributed among these distances:
12 10 0.08
13 31 0.26
14 44 0.36
15 11 0.09
16 25 0.21
ACGTcount: A:0.46, C:0.08, G:0.20, T:0.27
Consensus pattern (14 bp):
TGAAATGCATGAAA
Found at i:275879 original size:52 final size:52
Alignment explanation
Indices: 275815--275964 Score: 192
Period size: 52 Copynumber: 3.1 Consensus size: 52
275805 TTTGAAAAGC
* *
275815 ATGCATGAAATGAACATTAGGTGAAATGCATGCATGAAATGTAATGTATGAA
1 ATGCATGAAATGAAAATTAGGTGAAATGCATGCATGAAATGTAATGCATGAA
*
275867 ATGCATGAAATGAAAATTATGTGAAATGCATGCATG--A---AATG--T--A
1 ATGCATGAAATGAAAATTAGGTGAAATGCATGCATGAAATGTAATGCATGAA
* *
275910 ATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATATAATGCATGAA
1 ATGCATGAAATGAAAATTAGGTGAAATGCATGCATGAAATGTAATGCATGAA
275962 ATG
1 ATG
275965 AAAATTACAT
Statistics
Matches: 87, Mismatches: 2, Indels: 18
0.81 0.02 0.17
Matches are distributed among these distances:
43 37 0.43
45 2 0.02
47 4 0.05
48 4 0.05
50 2 0.02
52 38 0.44
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (52 bp):
ATGCATGAAATGAAAATTAGGTGAAATGCATGCATGAAATGTAATGCATGAA
Found at i:275914 original size:18 final size:18
Alignment explanation
Indices: 275891--275959 Score: 57
Period size: 18 Copynumber: 3.4 Consensus size: 18
275881 AATTATGTGA
275891 AATGCATGCATGAAATGT
1 AATGCATGCATGAAATGT
*
275909 AATGCATGAAATGAAAATTATGT
1 AATGCATG-CATG--AA--ATGT
*
275932 GAAATGCATGCATGAAATAT
1 --AATGCATGCATGAAATGT
275952 AATGCATG
1 AATGCATG
275960 AAATGAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
18 16 0.39
19 3 0.07
20 3 0.07
21 2 0.05
22 2 0.05
23 4 0.10
24 3 0.07
25 8 0.20
ACGTcount: A:0.43, C:0.09, G:0.20, T:0.28
Consensus pattern (18 bp):
AATGCATGCATGAAATGT
Found at i:275919 original size:43 final size:43
Alignment explanation
Indices: 275866--276003 Score: 235
Period size: 43 Copynumber: 3.3 Consensus size: 43
275856 TAATGTATGA
*
275866 AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATGT
1 AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATAT
275909 AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATAT
1 AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATAT
**
275952 AATGCATGAAATGAAAATTACATGAAATGCATGCATGAAA-AT
1 AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATAT
275994 -ATGCATGAAA
1 AATGCATGAAA
276004 GTAAAAGCAT
Statistics
Matches: 92, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
41 10 0.11
42 2 0.02
43 80 0.87
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (43 bp):
AATGCATGAAATGAAAATTATGTGAAATGCATGCATGAAATAT
Found at i:275983 original size:25 final size:25
Alignment explanation
Indices: 275952--276003 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
275942 CATGAAATAT
275952 AATGCATGAAATGAAAAT-TACATGA
1 AATGCATG-AATGAAAATATACATGA
* *
275977 AATGCATGCATGAAAATATGCATGA
1 AATGCATGAATGAAAATATACATGA
276002 AA
1 AA
276004 GTAAAAGCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.50, C:0.10, G:0.17, T:0.23
Consensus pattern (25 bp):
AATGCATGAATGAAAATATACATGA
Found at i:275989 original size:29 final size:28
Alignment explanation
Indices: 275807--275991 Score: 93
Period size: 29 Copynumber: 6.6 Consensus size: 28
275797 GAAATGTTTT
* **
275807 TGAAAAGCATGCATGAAATGAACATTAGG
1 TGAAATGCATGCATGAAATGAA-ATTACA
*
275836 TGAAATGCATGCATGAAATGTAATGT--A
1 TGAAATGCATGCATGAAATGAAAT-TACA
**
275863 TG-AA---ATGCATGAAATGAAAATTATG
1 TGAAATGCATGCATGAAATG-AAATTACA
* *
275888 TGAAATGCATGCATGAAATGTAA-TGCA
1 TGAAATGCATGCATGAAATGAAATTACA
* * * *
275915 TGAAATGAAAAT-TATGTGAAATG-CA-TGCA
1 TGAAATG--CATGCA--TGAAATGAAATTACA
**
275944 TGAAATATAATGCATGAAATGAAAATTACA
1 TGAAAT-GCATGCATGAAATG-AAATTACA
275974 TGAAATGCATGCATGAAA
1 TGAAATGCATGCATGAAA
275992 ATATGCATGA
Statistics
Matches: 121, Mismatches: 18, Indels: 34
0.70 0.10 0.20
Matches are distributed among these distances:
23 13 0.11
24 3 0.02
25 2 0.02
26 4 0.03
27 17 0.14
28 8 0.07
29 58 0.48
30 16 0.13
ACGTcount: A:0.45, C:0.08, G:0.21, T:0.26
Consensus pattern (28 bp):
TGAAATGCATGCATGAAATGAAATTACA
Done.