Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1301
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1559340
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.30
Warning! 165545 characters in sequence are not A, C, G, or T
File 4 of 4
Found at i:895194 original size:181 final size:180
Alignment explanation
Indices: 894610--895462 Score: 1463
Period size: 180 Copynumber: 4.7 Consensus size: 180
894600 AAAGGGTACC
* * * *
894610 GGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
** * * * * ** *
894675 TCAATTGTACATTTATCAAAGGTATGCATATTGTTAGAATTTTGATTTTTGATAATTTATCCAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
* * *
894740 AAATACCAGCTTTTGAACTTAGCCATTTTTTGGCATAATATTGCATATAG
131 AAATACCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
** *
894790 GGTACCCTCATTGTACGGATTTCTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
* *
894855 TCAATTGTACATATATCAGAGGTGTGCATAGTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
*
894920 AAATACCAGCTTTTAAACTTAGTCTTTTTTTGGCAAAATATTGCATATAG
131 AAATACCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
894970 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
895035 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATC-AAA
*
895100 AAAATTCCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
130 AAAATACCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
895151 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
*
895216 TCAATTGTACAGATATCAGAGGTGGGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
895281 AAATACCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
131 AAATACCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
895331 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
* *
895396 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATTATTTATGAAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
895461 AA
131 AA
895463 TAACAGTTTT
Statistics
Matches: 642, Mismatches: 30, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
180 465 0.72
181 177 0.28
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (180 bp):
GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
AAATACCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
Found at i:895273 original size:361 final size:361
Alignment explanation
Indices: 894610--895462 Score: 1465
Period size: 361 Copynumber: 2.4 Consensus size: 361
894600 AAAGGGTACC
* * * *
894610 GGTACCCTTATTGTACAGATAACTCCTCCTACAGTTTTCAAGATAGGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
** * * * * ** *
894675 TCAATTGTACATTTATCAAAGGTATGCATATTGTTAGAATTTTGATTTTTGATAATTTATC-CAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
* *
894739 AAAATACCAGCTTTTGAACTTAGCCATTTTTTGGCATAATATTGCATATAGGGTACCCTCATTGT
131 AAAATACCAGCTTTTAAACTTAGCCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
** * *
894804 ACGGATTTCTCCTCCTACAGTTCTCAAGATAGGAAGTTGTTCTTTTGCAGATCAATTGTACATAT
196 ACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGATCAATTGTACAGAT
*
894869 ATCAGAGGTGTGCATAGTGCTAGGATTTTGATTTCCGATAATTTATCAAAAAAATACCAGCTTTT
261 ATCAGAGGTGGGCATAGTGCTAGGATTTTGATTTCCGATAATTTATCAAAAAAATACCAGCTTTT
*
894934 AAACTTAGTCTTTTTTTGGCAAAATATTGCATATAG
326 AAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
894970 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
895035 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
* *
895100 AAAATTCCAGCTTTTAAACTTAGTCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
131 AAAATACCAGCTTTTAAACTTAGCCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
895165 ACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGATCAATTGTACAGAT
196 ACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGATCAATTGTACAGAT
*
895230 ATCAGAGGTGGGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAAAAATACCAGCTTTT
261 ATCAGAGGTGGGCATAGTGCTAGGATTTTGATTTCCGATAATTTATCAAAAAAATACCAGCTTTT
895295 AAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
326 AAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
895331 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
1 GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
* *
895396 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATTATTTATGAAAA
66 TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
895461 AA
131 AA
895463 TAACAGTTTT
Statistics
Matches: 466, Mismatches: 26, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
360 114 0.24
361 352 0.76
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (361 bp):
GGTACCCTCATTGTACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGA
TCAATTGTACAGATATCAGAGGTGTGCATATTGCTAGGATTTTGATTTCCGATAATTTATCAAAA
AAAATACCAGCTTTTAAACTTAGCCATTTTTTGGCAAAATATTGCATATAGGGTACCCTCATTGT
ACGGATAACTCCTCCTACAGTTCTCAAGATAAGAAGTTGTTCTTTTGCAGATCAATTGTACAGAT
ATCAGAGGTGGGCATAGTGCTAGGATTTTGATTTCCGATAATTTATCAAAAAAATACCAGCTTTT
AAACTTAGTCATTTTTTGGCAAAATATTGCATATAG
Found at i:900797 original size:11 final size:11
Alignment explanation
Indices: 900783--900815 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
900773 GATCCACTCT
900783 AGTAAACCC-G
1 AGTAAACCCAG
900793 AAGTAAACCCAG
1 -AGTAAACCCAG
900805 AGTAAACCCAG
1 AGTAAACCCAG
900816 GATTTAGTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (11 bp):
AGTAAACCCAG
Found at i:904341 original size:73 final size:72
Alignment explanation
Indices: 904221--904416 Score: 284
Period size: 73 Copynumber: 2.7 Consensus size: 72
904211 GAAACAGCCA
* *
904221 GACTGAAATTTACACGCCGCGTTTATCGATTGGTCGAAATCTACAGCGACTGAAACTGATGAGAA
1 GACTGAAA-TTACACGCCCCGTTTATCGATTGGTCGAAATCTACAGCGACTGAAACTGACGAGAA
*
904286 AGTGACAG
65 ACTGACAG
* *
904294 GACTGAAATCTACACGCCCCGTTTATCGATTGGTCGAAATCTGCAGCGGCTGAAACTGACGAGAA
1 GACTGAAAT-TACACGCCCCGTTTATCGATTGGTCGAAATCTACAGCGACTGAAACTGACGAGAA
904359 ACTGACAG
65 ACTGACAG
* * * *
904367 GACTGAAATTGACACGCCCTGTTTATCGATTGGTCCAAACCTATAGCGAC
1 GACTGAAATT-ACACGCCCCGTTTATCGATTGGTCGAAATCTACAGCGAC
904417 CTAGGAAAAA
Statistics
Matches: 110, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
72 2 0.02
73 108 0.98
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (72 bp):
GACTGAAATTACACGCCCCGTTTATCGATTGGTCGAAATCTACAGCGACTGAAACTGACGAGAAA
CTGACAG
Found at i:905875 original size:30 final size:30
Alignment explanation
Indices: 905841--905931 Score: 155
Period size: 30 Copynumber: 3.0 Consensus size: 30
905831 AATACGTTGC
905841 CGGTCCAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
* *
905871 CGGTCCAATAGATCGAATTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
*
905901 CGGTCTAATAGATCGCAGTCTATTGACCGG
1 CGGTCCAATAGATCGCAGTCTATTGACCGG
905931 C
1 C
905932 AGTTCAAAAT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.25
Consensus pattern (30 bp):
CGGTCCAATAGATCGCAGTCTATTGACCGG
Found at i:907878 original size:2 final size:2
Alignment explanation
Indices: 907873--907929 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
907863 CACACACACA
907873 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
907915 CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT C
907930 ACACACACAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:916170 original size:21 final size:22
Alignment explanation
Indices: 916121--916170 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
916111 TAACTCGGTT
916121 TTTTTGCGAATAAACACGAAAA
1 TTTTTGCGAATAAACACGAAAA
* * * *
916143 ATTTTGCGAATTAGCACG-TAA
1 TTTTTGCGAATAAACACGAAAA
916164 TTTTTGC
1 TTTTTGC
916171 TATATAACGC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (22 bp):
TTTTTGCGAATAAACACGAAAA
Found at i:918220 original size:201 final size:200
Alignment explanation
Indices: 917875--918275 Score: 793
Period size: 201 Copynumber: 2.0 Consensus size: 200
917865 TTGAGAAGCA
917875 CATACCTTTTGAGCCATTCTTAACATAAAATAAAACATAAAACCACGTCACATTTTTACAACTGT
1 CATACCTTTTGAGCCATTCTTAACATAAAATAAAACATAAAACCACGTCACATTTTTACAACTGT
917940 TTTTACACAATGCTAAACTCCGTATAAAATTGACATACTAATGGCTGTGATTTTCACTTTCGTTT
66 TTTTACACAATGCTAAACTCCGTATAAAATTGACATACTAATGGCTGTGATTTTCACTTTCGTTT
918005 TAACACTGATCACATGTTTTGCAGTGTAACTGTTTTTCCTGTCAACATGGGTGAAGAGAATGAAT
131 TAACACTGATCACATGTTTTGCAGTGTAACTGTTTTTCCTGTCAACATGGGTGAAGAGAATGAAT
918070 GTCTT
196 GTCTT
918075 NCATACCTTTTGAGCCATTCTTAACATAAAATAAAACATAAAACCACGTCACATTTTTACAACTG
1 -CATACCTTTTGAGCCATTCTTAACATAAAATAAAACATAAAACCACGTCACATTTTTACAACTG
918140 TTTTTACACAATGCTAAACTCCGTATAAAATTGACATACTAATGGCTGTGATTTTCACTTTCGTT
65 TTTTTACACAATGCTAAACTCCGTATAAAATTGACATACTAATGGCTGTGATTTTCACTTTCGTT
918205 TTAACACTGATCACATGTTTTGCAGTGTAACTGTTTTTCCTGTCAACATGGGTGAAGAGAATGAA
130 TTAACACTGATCACATGTTTTGCAGTGTAACTGTTTTTCCTGTCAACATGGGTGAAGAGAATGAA
918270 TGTCTT
195 TGTCTT
918276 TTCTCGGTTA
Statistics
Matches: 200, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
201 200 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (200 bp):
CATACCTTTTGAGCCATTCTTAACATAAAATAAAACATAAAACCACGTCACATTTTTACAACTGT
TTTTACACAATGCTAAACTCCGTATAAAATTGACATACTAATGGCTGTGATTTTCACTTTCGTTT
TAACACTGATCACATGTTTTGCAGTGTAACTGTTTTTCCTGTCAACATGGGTGAAGAGAATGAAT
GTCTT
Found at i:922782 original size:8 final size:8
Alignment explanation
Indices: 922775--922821 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
922765 TTTACAGACG
*
922775 GACGGACG
1 GACGGACA
922783 GACGGACA
1 GACGGACA
*
922791 GACAGACA
1 GACGGACA
*
922799 GACGGAAA
1 GACGGACA
*
922807 GACGGGC-
1 GACGGACA
922814 GACGGACA
1 GACGGACA
922822 AAAAGTGATC
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
7 6 0.19
8 25 0.81
ACGTcount: A:0.36, C:0.23, G:0.40, T:0.00
Consensus pattern (8 bp):
GACGGACA
Found at i:922788 original size:12 final size:12
Alignment explanation
Indices: 922768--922811 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
922758 TGAAAAGTTT
922768 ACAGACGGACGG
1 ACAGACGGACGG
* *
922780 ACGGACGGACAG
1 ACAGACGGACGG
*
922792 ACAGACAGACGG
1 ACAGACGGACGG
*
922804 AAAGACGG
1 ACAGACGG
922812 GCGACGGACA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.39, C:0.23, G:0.39, T:0.00
Consensus pattern (12 bp):
ACAGACGGACGG
Found at i:925994 original size:2 final size:2
Alignment explanation
Indices: 925987--926075 Score: 117
Period size: 2 Copynumber: 45.0 Consensus size: 2
925977 TGTGATTCAC
* * * * *
925987 CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT TT TT TT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
926029 -T CC CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
926070 CT CT CT
1 CT CT CT
926076 GAGAGCTGCA
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
1 1 0.01
2 81 0.99
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (2 bp):
CT
Found at i:932432 original size:164 final size:165
Alignment explanation
Indices: 932257--932699 Score: 592
Period size: 164 Copynumber: 2.7 Consensus size: 165
932247 AAAAAGTCGA
* *
932257 CTTTAACAGGAAGTTGACGTTCGATTGGAACAAAAATATATCCCACAATATGGCATGCCTAGATA
1 CTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAGA-A
* * * *
932322 AATAGTGTGTTTAAATTTCAAGCATCTACCATCAACAGTTGCTGAG-AATCTTTGACGAAAATTT
65 AATAGTGTGTTAAAATTTCAAGCATCTACCATAAACAGTTGCTGAGAAATCTTTAACAAAAATTT
*
932386 GTTCGAAAATTTAGGCTAAAAA-AAAATAAGTCGTC
130 GTTCGAAAATTTAGGCTAAAAATAAAAGAAGTCGTC
* *
932421 CTTTAACAGGAAGTTGATGTCCGATTGGTACAAAAATATATCCCACAATATGGCATACCT-GAAC
1 CTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAGAA-
* * *
932485 TAATAGTGTCTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAAATCTTTAACAAAAATT
65 -AATAGTGTGTTAAAATTTCAAGCATCTACCATAAACAGTTGCTGAGAAATCTTTAACAAAAATT
* *
932550 TGTTTGAAAATTTAGGCTAAAAATAAACGAAGTCGTC
129 TGTTCGAAAATTTAGGCTAAAAATAAAAGAAGTCGTC
* * * *
932587 ATTTAACAGGAAGTTGACGTCCGATTGGTA-AAAAATAATATCCTACAACATGGCATGCTTA-AC
1 CTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAAT-ATATCCCACAATATGGCATGCCTAGA-
* * * *
932650 AAATAGTGTGTTAAAATTTAAAGCATCT-GCATTGAATAGTTGCTGAGAAA
64 AAATAGTGTGTTAAAATTTCAAGCATCTACCA-TAAACAGTTGCTGAGAAA
932700 ATGCAACAGA
Statistics
Matches: 246, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
162 1 0.00
163 2 0.01
164 98 0.40
165 85 0.35
166 59 0.24
167 1 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.30
Consensus pattern (165 bp):
CTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATATGGCATGCCTAGAAA
ATAGTGTGTTAAAATTTCAAGCATCTACCATAAACAGTTGCTGAGAAATCTTTAACAAAAATTTG
TTCGAAAATTTAGGCTAAAAATAAAAGAAGTCGTC
Found at i:932657 original size:165 final size:161
Alignment explanation
Indices: 932242--932699 Score: 605
Period size: 165 Copynumber: 2.8 Consensus size: 161
932232 GTGAATATGC
* * *
932242 AAAATAAAAAGTCGACTTTAACAGGAAGTTGACGTTCGATTGGAACAAAAATATATCCCACAATA
1 AAAATAAAAAGTCGTCTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATA
* * * * *
932307 TGGCATGCCTAGATAAATAGTGTGTTTAAATTTCAAGCATCTACCATCAACAGTTGCTGAG-AAT
66 TGGCATGCTTA-ACAAATAGTGTGTTAAAATTTCAAGCATCTA-CATAAATAGTTGCTGAGAAAT
* *
932371 CTTTGACGAAAATTTGTTCGAAAATTTAGGCTA
129 CTTTAACAAAAATTTGTTCGAAAATTTAGGCTA
* *
932404 AAAAAAAATAAGTCGTCCTTTAACAGGAAGTTGATGTCCGATTGGTACAAAAATATATCCCACAA
1 AAAATAAA-AAGTCGT-CTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAA
* * * *
932469 TATGGCATACCTGAACTAATAGTGTCTTAAAATTTCAAGCATCTACGATAAATAGTTGCTGAGAA
64 TATGGCAT-GCTTAACAAATAGTGTGTTAAAATTTCAAGCATCTAC-ATAAATAGTTGCTGAGAA
*
932534 ATCTTTAACAAAAATTTGTTTGAAAATTTAGGCTA
127 ATCTTTAACAAAAATTTGTTCGAAAATTTAGGCTA
*
932569 AAAATAAACGAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTA-AAAAATAATATCCTAC
1 AAAATAAA--AAGTCGTC-TTTAACAGGAAGTTGACGTCCGATTGGTACAAAAAT-ATATCCCAC
* * * *
932633 AACATGGCATGCTTAACAAATAGTGTGTTAAAATTTAAAGCATCTGCATTGAATAGTTGCTGAGA
62 AATATGGCATGCTTAACAAATAGTGTGTTAAAATTTCAAGCATCTACA-TAAATAGTTGCTGAGA
932698 AA
126 AA
932700 ATGCAACAGA
Statistics
Matches: 258, Mismatches: 29, Indels: 15
0.85 0.10 0.05
Matches are distributed among these distances:
162 7 0.03
163 7 0.03
164 95 0.37
165 97 0.38
166 52 0.20
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (161 bp):
AAAATAAAAAGTCGTCTTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACAATA
TGGCATGCTTAACAAATAGTGTGTTAAAATTTCAAGCATCTACATAAATAGTTGCTGAGAAATCT
TTAACAAAAATTTGTTCGAAAATTTAGGCTA
Found at i:934252 original size:18 final size:18
Alignment explanation
Indices: 934231--934271 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
934221 CTCTTGATTT
934231 AGCTATATAGCTTGAATA
1 AGCTATATAGCTTGAATA
* *
934249 AGCTATATAGCTTTATTA
1 AGCTATATAGCTTGAATA
934267 AGCTA
1 AGCTA
934272 CTCAAAGTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AGCTATATAGCTTGAATA
Found at i:936059 original size:13 final size:13
Alignment explanation
Indices: 936041--936065 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
936031 GTTCGGATAT
936041 TTGGATTTTGTTC
1 TTGGATTTTGTTC
936054 TTGGATTTTGTT
1 TTGGATTTTGTT
936066 GGATTCATCT
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:0.08, C:0.04, G:0.24, T:0.64
Consensus pattern (13 bp):
TTGGATTTTGTTC
Found at i:945408 original size:6 final size:6
Alignment explanation
Indices: 945397--945428 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
945387 TGCTATACCC
945397 TCGGCG TCGGCG TCGGCG TCGGCG TCGGCG TC
1 TCGGCG TCGGCG TCGGCG TCGGCG TCGGCG TC
945429 CGGACCTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.47, T:0.19
Consensus pattern (6 bp):
TCGGCG
Found at i:945758 original size:177 final size:176
Alignment explanation
Indices: 945545--946312 Score: 976
Period size: 177 Copynumber: 4.3 Consensus size: 176
945535 AAAGACTAGG
** * * *
945545 ATGCTGAATCTGAGTCC-TAAATTTCAGATGCTGGAGGTGGTTAAGGTTGTTGGACCAGGTTAAA
1 ATGCTGAATCTGAG-CCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAA
*
945609 GTTTTTGTTGCAGGTGCCCTTTGATAGCA-ATATCTAAGTTACTGCAGGTCCGT-ACTTCACCAA
65 GTTTTTGTTGCAGGTGCCCTTTGAT-G-ATATATCTAAGTTACTGCTGGTCC-TAACTTCACCAA
*
945672 ACTTGCATGGATGGTGTGTCTTATGATACTGATGCACCAGACAGGCTTGA
127 ACTTGCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA
* * *
945722 GTGCTGAATCTGAGCTATAGGTTTCAGATGCTGGAGGGGGTTAAGGTTTTTGGAGCAGGTTAAAG
1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAG
945787 TTTTTGTTGCAGGTGCCCTTTGATAGCA-ATATCTAAGTTACTGCTGGTCCCT-ACTTCACCAAA
66 TTTTTGTTGCAGGTGCCCTTTGAT-G-ATATATCTAAGTTACTGCTGGT-CCTAACTTCACCAAA
* * *
945850 CTTGCATGGATGGTGTGTCTTATGATAATGATGCACCAGGCAGGCTTTG-
128 CTTGCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGC-TTGA
* * * * * *
945899 GTGCTGAATCTGAGCTATAGGTTACAGATGCTGAAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAG
1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAG
* ** * *
945964 TTTTTGTTGCAGGTGCCCTCTGATGATGATATCTTGGTTACTACTGGTCCTAACTTCACCAGACT
66 TTTTTGTTGCAGGTGCCCTTTGATGAT-ATATCTAAGTTACTGCTGGTCCTAACTTCACCAAACT
946029 T-CTATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA
130 TGC-ATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA
* * *
946076 ATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTTAGAGCTGGTTAAAG
1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAG
* *** * * * * * *
946141 TTTTAGAAACAGGTGCCCTATGATGATTATATTTTAGTTATTGCTTGTCCTAACTTCACCAGACT
66 TTTTTGTTGCAGGTGCCCTTTGATGA-TATATCTAAGTTACTGCTGGTCCTAACTTCACCAAACT
* * *
946206 TCCATGGATGGTGCGTCTTATGATACTGATGCACCTGACAGGCCTGA
130 TGCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA
* * * *
946253 ATGCTGAGTCTGAGCCATAGGTTTCAGATGCTGGA-TATGGTTAAGTTTTTTGGAACAGGT
1 ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGA-GGTTAAGGTTTTTGGAGCAGGT
946313 CACATGTTTA
Statistics
Matches: 533, Mismatches: 47, Indels: 22
0.89 0.08 0.04
Matches are distributed among these distances:
175 1 0.00
176 10 0.02
177 515 0.97
178 7 0.01
ACGTcount: A:0.23, C:0.17, G:0.27, T:0.33
Consensus pattern (176 bp):
ATGCTGAATCTGAGCCATAGGTTTCAGATGCTGGAGGAGGTTAAGGTTTTTGGAGCAGGTTAAAG
TTTTTGTTGCAGGTGCCCTTTGATGATATATCTAAGTTACTGCTGGTCCTAACTTCACCAAACTT
GCATGGATGGTGCGTCTTATGATACTGATGCACCAGACAGGCTTGA
Found at i:946644 original size:152 final size:154
Alignment explanation
Indices: 946361--946644 Score: 380
Period size: 152 Copynumber: 1.8 Consensus size: 154
946351 GCTAAAAAAT
* *
946361 ATATCTTAGTTATTACAGGTCCTAACTTCACCAAACTTGAATGGATGGTGTGTCTTATGATACAG
1 ATATCTTAGTTATTACAGGTCCTAACTTCACCAAACTTGAATGGATGATGCGTCTTATGATACAG
* * *
946426 ATGCACCTGACAGGCATGGATGTTGAATCTGAGCCATAGGTTGCGGATGCTGTAGCAGGTTAAGT
66 ATG--CC-GACAGGCATGCATGCTGAATCTGAGCCATAGGTTGCGGATGCTGGAGCAGGTTAAGT
946491 TTCAATTGCTAGTGCCCTCTGATGATG
128 TTCAATTGCTAGTGCCCTCTGATGATG
* *
946518 ATATCTTAGTTATTACTGGT-CTGAACTTCACCAAACTTGCATGGA-GATGCGTCTTATGTATAC
1 ATATCTTAGTTATTACAGGTCCT-AACTTCACCAAACTTGAATGGATGATGCGTCTTATG-ATAC
* * * *
946581 TGATG-C-ACAGGCTTGCATGCTGAATCTGAGCCATAGGTTTCGGATGCTGGATG-AGGTTTAGT
64 AGATGCCGACAGGCATGCATGCTGAATCTGAGCCATAGGTTGCGGATGCTGGA-GCAGGTTAAGT
946643 TT
128 TT
946645 TTTTGGAACA
Statistics
Matches: 113, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
152 50 0.44
153 1 0.01
154 1 0.01
156 13 0.12
157 48 0.42
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (154 bp):
ATATCTTAGTTATTACAGGTCCTAACTTCACCAAACTTGAATGGATGATGCGTCTTATGATACAG
ATGCCGACAGGCATGCATGCTGAATCTGAGCCATAGGTTGCGGATGCTGGAGCAGGTTAAGTTTC
AATTGCTAGTGCCCTCTGATGATG
Found at i:947027 original size:15 final size:15
Alignment explanation
Indices: 947007--947042 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
946997 ATACAATATT
*
947007 ATATTGTATCATACG
1 ATATTGTATAATACG
*
947022 ATATTGTATAATATG
1 ATATTGTATAATACG
947037 ATATTG
1 ATATTG
947043 GTTTCTGTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.14, T:0.44
Consensus pattern (15 bp):
ATATTGTATAATACG
Found at i:947166 original size:50 final size:50
Alignment explanation
Indices: 947008--947167 Score: 162
Period size: 50 Copynumber: 3.2 Consensus size: 50
946998 TACAATATTA
* * * * *
947008 TATTGTATCATACGATATTGTATAATATGATATTGGTTTCTGTAATTTAC
1 TATTGTATCATACAATATTGTATAATATGATATTGGTTTATATAATATAT
* * ** * * * * *
947058 AATTATATCACGCAAAACTGTATTATATGATATT-G-TAATATTATATAT
1 TATTGTATCATACAATATTGTATAATATGATATTGGTTTATATAATATAT
* *
947106 TATCGTATCATACAATATTGTATAATATGATATTGGTTTATATGATATAT
1 TATTGTATCATACAATATTGTATAATATGATATTGGTTTATATAATATAT
947156 TATTGTATCATA
1 TATTGTATCATA
947168 TGATACAATA
Statistics
Matches: 83, Mismatches: 25, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
48 33 0.40
49 2 0.02
50 48 0.58
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.46
Consensus pattern (50 bp):
TATTGTATCATACAATATTGTATAATATGATATTGGTTTATATAATATAT
Found at i:947204 original size:15 final size:15
Alignment explanation
Indices: 947076--947207 Score: 52
Period size: 15 Copynumber: 8.1 Consensus size: 15
947066 CACGCAAAAC
*
947076 TGTATTATATGATAT
1 TGTATTATATAATAT
*
947091 TGTAATATTATATATTAT
1 TG---TATTATATAATAT
* * *
947109 CGTATCATACAATAT
1 TGTATTATATAATAT
* *
947124 TGTATAATATGATAT
1 TGTATTATATAATAT
*
947139 TGGTTTATATGATATATTAT
1 T-G--TAT-T-ATATAATAT
947159 TGTATCATATGATACA-AT
1 TGTAT--TAT-ATA-ATAT
*
947177 ATGTA-TGTATAATAT
1 -TGTATTATATAATAT
947192 TGTATTATATAATAT
1 TGTATTATATAATAT
947207 T
1 T
947208 TCACTTTATC
Statistics
Matches: 87, Mismatches: 16, Indels: 28
0.66 0.12 0.21
Matches are distributed among these distances:
14 5 0.06
15 39 0.45
16 3 0.03
17 5 0.06
18 22 0.25
19 5 0.06
20 8 0.09
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (15 bp):
TGTATTATATAATAT
Found at i:947272 original size:15 final size:15
Alignment explanation
Indices: 947253--947294 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
947243 ATACAATGTT
*
947253 ATATCAAATTATACA
1 ATATCATATTATACA
* *
947268 GTATCATATGATACA
1 ATATCATATTATACA
947283 ATATCATATTAT
1 ATATCATATTAT
947295 GTATCAAATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATCATATTATACA
Found at i:947347 original size:27 final size:27
Alignment explanation
Indices: 947302--947357 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
947292 TATGTATCAA
947302 ATATCATACAATATCATACAATACAAT
1 ATATCATACAATATCATACAATACAAT
** * *
947329 ATATCATACTGTATTATACAATATAAT
1 ATATCATACAATATCATACAATACAAT
947356 AT
1 AT
947358 CATATGTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.14, G:0.02, T:0.36
Consensus pattern (27 bp):
ATATCATACAATATCATACAATACAAT
Found at i:956863 original size:15 final size:15
Alignment explanation
Indices: 956843--956872 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
956833 AGTGGAGCCT
956843 CAGATATCCGGACGC
1 CAGATATCCGGACGC
956858 CAGATATCCGGACGC
1 CAGATATCCGGACGC
956873 TTCACTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.27, T:0.13
Consensus pattern (15 bp):
CAGATATCCGGACGC
Found at i:963546 original size:156 final size:155
Alignment explanation
Indices: 963260--964105 Score: 698
Period size: 156 Copynumber: 5.4 Consensus size: 155
963250 CACAAGTTTA
* * * * *
963260 AGCTATTCTGGTCAAATAGTTTTTAAAAAGAAAATTTTTAAAGATTTTCTCTATATATTCCTATG
1 AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTTTAAAGATTTTCTCTATATA----TA--
* * * *
963325 TAAAATTTCATCCCCCATTGTGGCCTCACCGTACCCCGGGACTATGATTTAAACAAACTTGAATC
60 -AAAA-TTCATCCCCCATTGTGGCCCCACCCTACCCCGGGACCATGATTTGAACAAACTTGAATC
963390 TATA-TGATTTTGGGATGCTTCCACTCAAATTTG
123 TATACT-ATTTTGGGATGCTTCCACTCAAATTTG
* * ** *
963423 GGCTTTCCTGGCCTAATAG-TTTTCATCAGAAGATTTTTAAAGATTTTCTCTATATATAAAAATT
1 AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTTTAAAGATTTTCTCTATATATAAAAATT
* * *
963487 TATCCCCCATTGTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACT
66 CATCCCCCATTGTGGCCCCACCCTA-CCCC-GGGACCATGATTTGAACAAACTTGAATCTATACT
* ** * * *
963552 ATCTACGGATGCTTACACACCAA----
129 ATTTTGGGATGCTTCCACTCAAATTTG
* * * ** * * * *
963575 A-CTTTTCTGGCCAAATAGTTTTTAAAAAGAAAATTTTCTCTATA-TAT-TCT-TGTGTAAAAAT
1 AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTT-TAAAGATTTTCTCTATATATAAAAAT
* ** ** * * * *
963636 TCATCCCCCATTGTGGCCTCACTGTACCCCATGACTATGATTTAAAAAAACTTGAATCTATACGA
65 TCATCCCCCATTGTGGCCCCACCCTACCCCGGGACCATGATTTGAACAAACTTGAATCTATACTA
* * *
963701 TCTGGGGATGCTTCTACTCAAATTTCG
130 TTTTGGGATGCTTCCACTCAAATTT-G
*** *
963728 -GCTTTTCTGGCCTAATAG-TTTTCATCTGAAGATTTTTAAAGATTTTCTCTATATATAAAAATT
1 AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTTTAAAGATTTTCTCTATATATAAAAATT
*
963791 CATACCCCAATTG-GGCCCCACCCTACTCCCCGGCG-CCATGATTTGAACAAACTTGAATCTATA
66 CAT-CCCCCATTGTGGCCCCACCCTA--CCCCGG-GACCATGATTTGAACAAACTTGAATCTATA
* * *
963854 CTA-TCTGAGGATGCCTCCAGTCAAATTTG
127 CTATTTTG-GGATGCTTCCACTCAAATTTG
* * *
963883 AGCTTTTCTGGCCTAATAGTTTTTGAGAAAAAAATTTTTAAAGATATTCTCTATATATTCCTATG
1 AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTTTAAAGAT-TT-TCTCTATA----TA--
* * * *
963948 TAAAAATCCATTCCCCCATTGCGGCCCCGCCATACCCCGGGGACCATGATTTGAACAAACTTGAA
58 TAAAAATTCA-TCCCCCATTGTGGCCCCACCCTACCCC-GGGACCATGATTTGAACAAACTTGAA
* * * * *
964013 TCTTTACTA-TCTGAGGATGCTTCCATTTATATTTG
121 TCTATACTATTTTG-GGATGCTTCCACTCAAATTTG
* * * * *
964048 AGATTTTCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATATTCTCTATATAT
1 AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTTTAAAGATTTTCTCTATATAT
964106 TCCTATGTAA
Statistics
Matches: 547, Mismatches: 103, Indels: 72
0.76 0.14 0.10
Matches are distributed among these distances:
148 44 0.08
149 4 0.01
150 30 0.05
151 21 0.04
152 31 0.06
153 22 0.04
154 45 0.08
155 18 0.03
156 112 0.20
157 22 0.04
158 4 0.01
159 9 0.02
162 33 0.06
163 23 0.04
164 6 0.01
165 112 0.20
166 11 0.02
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (155 bp):
AGCTTTTCTGGCCTAATAGTTTTTCAGAAGAAAATTTTTAAAGATTTTCTCTATATATAAAAATT
CATCCCCCATTGTGGCCCCACCCTACCCCGGGACCATGATTTGAACAAACTTGAATCTATACTAT
TTTGGGATGCTTCCACTCAAATTTG
Found at i:963832 original size:304 final size:304
Alignment explanation
Indices: 963303--964105 Score: 932
Period size: 304 Copynumber: 2.6 Consensus size: 304
963293 ATTTTTAAAG
* *
963303 ATTTTCTCTATATATTCCTATGTAAAATTTCATCCCCCATTGTGGCCTCACCGTACCCCGGGACT
1 ATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTGGCCTCACCGTACCCCAGGACT
* * * * *
963368 ATGATTTAAACAAACTTGAATCTATATGATTTTGGGATGCTTCCACTCAAATTTGGGCTTTCCTG
66 ATGATTTAAAAAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCAAATTTCGGCTTTCCTG
* *
963433 GCCTAATAGTTTTCATCAGAAGATTTTTAAAGATTTTCTCTATATATAAAAATTTATCCCCCATT
131 GCCTAATAGTTTTCATCAGAAGATTTTTAAAGATTTTCTCTATATATAAAAATTCATCCCCAATT
*
963498 GTGGCCCCGCCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCT-ACGGAT
196 GTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGA-GGAT
963562 GCTTACACACCAAACTTTTCTGGCCAAATAGTTTTTAAAAAGAAA
260 GCTTACACACCAAACTTTTCTGGCCAAATAGTTTTTAAAAAGAAA
* * * *
963607 ATTTTCTCTATATATTCTTGTGTAAAAATTCATCCCCCATTGTGGCCTCACTGTACCCCATGACT
1 ATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTGGCCTCACCGTACCCCAGGACT
* *
963672 ATGATTTAAAAAAACTTGAATCTATACGATCTGGGGATGCTTCTACTCAAATTTCGGCTTTTCTG
66 ATGATTTAAAAAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCAAATTTCGGCTTTCCTG
*
963737 GCCTAATAGTTTTCATCTGAAGATTTTTAAAGATTTTCTCTATATATAAAAATTCATACCCCAAT
131 GCCTAATAGTTTTCATCAGAAGATTTTTAAAGATTTTCTCTATATATAAAAATTCAT-CCCCAAT
*
963802 TG-GGCCCCACCCTACTCCCC-GGCG-CCATGATTTGAACAAACTTGAATCTATACTATCTGAGG
195 TGTGGCCCCACCCTAC-CCCCAGG-GACCATGATTTGAACAAACTTGAATCTACACTATCTGAGG
* * ** * * *
963864 ATGCCTCCAGTCAAATTTGAGCTTTTCTGGCCTAATAGTTTTTGAGAAAAAAATTTTTAAA
258 ATGCTTACACACCAA----A-CTTTTCTGGCCAAATAGTTTTT-----AAAAA----GAAA
* * * * * * *
963925 GATATTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTGCGGCCCCGCCATACCCCGGGG
1 -ATTTTCTCTATATATTCCTATGTAAAAATTCA-TCCCCCATTGTGGCCTCACCGTACCCC-AGG
* * * * * * * * * *
963990 ACCATGATTTGAACAAACTTGAATCTTTACTATCTGAGGATGCTTCCATTTATATTT-GAGATTT
63 ACTATGATTTAAAAAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCAAATTTCG-GCTTT
* * * ** *
964054 TCTGGCCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATATTCTCTATATAT
127 CCTGGCCTAATAG-TTTTCATCAGAAGATTTTTAAAGATTTTCTCTATATAT
964106 TCCTATGTAA
Statistics
Matches: 423, Mismatches: 53, Indels: 28
0.84 0.11 0.06
Matches are distributed among these distances:
304 231 0.55
305 14 0.03
308 1 0.00
309 21 0.05
314 5 0.01
318 3 0.01
319 28 0.07
320 23 0.05
321 64 0.15
322 33 0.08
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (304 bp):
ATTTTCTCTATATATTCCTATGTAAAAATTCATCCCCCATTGTGGCCTCACCGTACCCCAGGACT
ATGATTTAAAAAAACTTGAATCTATACGATCTGGGGATGCTTCCACTCAAATTTCGGCTTTCCTG
GCCTAATAGTTTTCATCAGAAGATTTTTAAAGATTTTCTCTATATATAAAAATTCATCCCCAATT
GTGGCCCCACCCTACCCCCAGGGACCATGATTTGAACAAACTTGAATCTACACTATCTGAGGATG
CTTACACACCAAACTTTTCTGGCCAAATAGTTTTTAAAAAGAAA
Found at i:964023 original size:165 final size:164
Alignment explanation
Indices: 963610--964133 Score: 597
Period size: 165 Copynumber: 3.2 Consensus size: 164
963600 AAAGAAAATT
* * * * ** ** *
963610 TTCTCTATATATTCTTGTGTAAAAATTCA-TCCCCCATTGTGGCCTCACTGTACCCC-ATGACTA
1 TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTG-GGCCCCACCATACCCCGGCGACCA
* * * * *
963673 TGATTTAAAAAAACTTGAATCTATACGATCTGGGGATGCTTCTACTCAAATTTCG-GCTTTTCTG
65 TGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCACTCAAATTT-GAGCTTTTCTG
* ***
963737 GCCTAATAG-TTTTCATCTGAAGATTTTTAAAGAT-
129 GCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATA
* * * * *
963771 TT-TCTCTATA----TA--TAAAAATTCATACCCCAATTGGGCCCCACCCTACTCCCCGGCG-CC
1 TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTGGGCCCCACCATA--CCCCGGCGACC
* *
963828 ATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCCTCCAGTCAAATTTGAGCTTTTCTG
64 ATGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTG
* *
963893 GCCTAATAGTTTTTGAGAAAAAAATTTTTAAAGATA
129 GCCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATA
* *
963929 TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTGCGGCCCCGCCATACCCCGGGGACCA
1 TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTG-GGCCCCACCATACCCCGGCGACCA
* * * * *
963994 TGATTTGAACAAACTTGAATCTTTACTATCTGAGGATGCTTCCATTTATATTTGAGATTTTCTGG
65 TGATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGG
*
964059 CCAAATAGTTTTTGAGAAGAAGATTTTTAAAGATA
130 CCTAATAGTTTTTGAGAAGAAGATTTTTAAAGATA
964094 TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTG
1 TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTG
964134 NNNNNNNNNN
Statistics
Matches: 308, Mismatches: 39, Indels: 28
0.82 0.10 0.07
Matches are distributed among these distances:
154 19 0.06
155 9 0.03
156 71 0.23
157 20 0.06
158 2 0.01
159 7 0.02
160 7 0.02
161 2 0.01
163 2 0.01
164 7 0.02
165 152 0.49
166 10 0.03
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (164 bp):
TTCTCTATATATTCCTATGTAAAAATCCATTCCCCCATTGGGCCCCACCATACCCCGGCGACCAT
GATTTGAACAAACTTGAATCTATACTATCTGAGGATGCTTCCACTCAAATTTGAGCTTTTCTGGC
CTAATAGTTTTTGAGAAGAAGATTTTTAAAGATA
Found at i:1006131 original size:486 final size:485
Alignment explanation
Indices: 1005220--1006190 Score: 1933
Period size: 486 Copynumber: 2.0 Consensus size: 485
1005210 TAACTGAGTA
1005220 TACATGCTTTCACCCAAAAATGCTTGTGTAACAACGTCAGGAGTAAGCCCTTATAAATGATAGAA
1 TACATGCTTTCACCCAAAAATGCTTGTGTAACAACGTCAGGAGTAAGCCCTTATAAATGATAGAA
1005285 TATCATCACTCACGAGCACGGATAACGGCACATGTGACTGCAAATACACAAACGCTCTGTATGCA
66 TATCATCACTCACGAGCACGGATAACGGCACATGTGACTGCAAATACACAAACGCTCTGTATGCA
1005350 CCCATATCTCGCTATTTTCTTTTGTTCTTCTGGGTCGACTTTAGGGGGCAATCGCAACATTTTCA
131 CCCATATCTCGCTATTTTCTTTTGTTCTTCTGGGTCGACTTTAGGGGGCAATCGCAACATTTTCA
1005415 AGTTCGTTTCAATCTCTAGCACATGCAATGATTTTCAATGTCATTCAATAGCATTGTTTACCGTT
196 AGTTCGTTTCAATCTCTAGCACATGCAATGATTTTCAATGTCATTCAATAGCATTGTTTACCGTT
1005480 ATAAAGATGAGAAAGAGAAAAACGCATATAAGACTATGAATATGGGTTTCATTTTTTTGGTCCAT
261 ATAAAGATGAGAAAGAGAAAAACGCATATAAGACTATGAATATGGGTTTCATTTTTTTGGTCCAT
1005545 TGTCTTTTTCACCACGTGGTGTTTTGGCCCTGCAGTATATACCTGTGTAATTAAGGCTGTCCATC
326 TGTCTTTTTCACCACGTGGTGTTTTGGCCCTGCAGTATATACCTGTGTAATTAAGGCTGTCCATC
1005610 CATAACTATCATATTTCATATCTATTAGATTGCAAGTTTAATCACCAAAATTTTAATGTGATTTT
391 CATAACTATCATATTTCATATCTATTAGATTGCAAGTTTAATCACCAAAATTTTAATGTGATTTT
1005675 AAAGGGTTTATTAAATAATAATTTAATTCT
456 AAAGGGTTTATTAAATAATAATTTAATTCT
1005705 NTACATGCTTTCACCCAAAAATGCTTGTGTAACAACGTCAGGAGTAAGCCCTTATAAATGATAGA
1 -TACATGCTTTCACCCAAAAATGCTTGTGTAACAACGTCAGGAGTAAGCCCTTATAAATGATAGA
1005770 ATATCATCACTCACGAGCACGGATAACGGCACATGTGACTGCAAATACACAAACGCTCTGTATGC
65 ATATCATCACTCACGAGCACGGATAACGGCACATGTGACTGCAAATACACAAACGCTCTGTATGC
1005835 ACCCATATCTCGCTATTTTCTTTTGTTCTTCTGGGTCGACTTTAGGGGGCAATCGCAACATTTTC
130 ACCCATATCTCGCTATTTTCTTTTGTTCTTCTGGGTCGACTTTAGGGGGCAATCGCAACATTTTC
1005900 AAGTTCGTTTCAATCTCTAGCACATGCAATGATTTTCAATGTCATTCAATAGCATTGTTTACCGT
195 AAGTTCGTTTCAATCTCTAGCACATGCAATGATTTTCAATGTCATTCAATAGCATTGTTTACCGT
1005965 TATAAAGATGAGAAAGAGAAAAACGCATATAAGACTATGAATATGGGTTTCATTTTTTTGGTCCA
260 TATAAAGATGAGAAAGAGAAAAACGCATATAAGACTATGAATATGGGTTTCATTTTTTTGGTCCA
1006030 TTGTCTTTTTCACCACGTGGTGTTTTGGCCCTGCAGTATATACCTGTGTAATTAAGGCTGTCCAT
325 TTGTCTTTTTCACCACGTGGTGTTTTGGCCCTGCAGTATATACCTGTGTAATTAAGGCTGTCCAT
1006095 CCATAACTATCATATTTCATATCTATTAGATTGCAAGTTTAATCACCAAAATTTTAATGTGATTT
390 CCATAACTATCATATTTCATATCTATTAGATTGCAAGTTTAATCACCAAAATTTTAATGTGATTT
1006160 TAAAGGGTTTATTAAATAATAATTTAATTCT
455 TAAAGGGTTTATTAAATAATAATTTAATTCT
1006191 GGTTGTAACG
Statistics
Matches: 485, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
486 485 1.00
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (485 bp):
TACATGCTTTCACCCAAAAATGCTTGTGTAACAACGTCAGGAGTAAGCCCTTATAAATGATAGAA
TATCATCACTCACGAGCACGGATAACGGCACATGTGACTGCAAATACACAAACGCTCTGTATGCA
CCCATATCTCGCTATTTTCTTTTGTTCTTCTGGGTCGACTTTAGGGGGCAATCGCAACATTTTCA
AGTTCGTTTCAATCTCTAGCACATGCAATGATTTTCAATGTCATTCAATAGCATTGTTTACCGTT
ATAAAGATGAGAAAGAGAAAAACGCATATAAGACTATGAATATGGGTTTCATTTTTTTGGTCCAT
TGTCTTTTTCACCACGTGGTGTTTTGGCCCTGCAGTATATACCTGTGTAATTAAGGCTGTCCATC
CATAACTATCATATTTCATATCTATTAGATTGCAAGTTTAATCACCAAAATTTTAATGTGATTTT
AAAGGGTTTATTAAATAATAATTTAATTCT
Found at i:1014479 original size:2 final size:2
Alignment explanation
Indices: 1014472--1014534 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
1014462 CTTTGACCAT
*
1014472 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC -C T- TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1014512 TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC T
1014535 GTAATTGGTA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
1 2 0.04
2 55 0.96
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1017495 original size:21 final size:20
Alignment explanation
Indices: 1017471--1017519 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1017461 GAGCACTGAT
*
1017471 TTTCCAATTTTAAAGTTGAAA
1 TTTCCAACTTT-AAGTTGAAA
* **
1017492 TTTCTAACTTTAAGTTGATT
1 TTTCCAACTTTAAGTTGAAA
1017512 TTTCCAAC
1 TTTCCAAC
1017520 ATAAATCTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.31, C:0.14, G:0.08, T:0.47
Consensus pattern (20 bp):
TTTCCAACTTTAAGTTGAAA
Found at i:1021820 original size:15 final size:15
Alignment explanation
Indices: 1021800--1021829 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1021790 GTATGAAGCA
1021800 TTGTTATCAATGAGT
1 TTGTTATCAATGAGT
1021815 TTGTTATCAATGAGT
1 TTGTTATCAATGAGT
1021830 CAGATTCTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.20, T:0.47
Consensus pattern (15 bp):
TTGTTATCAATGAGT
Found at i:1024996 original size:19 final size:19
Alignment explanation
Indices: 1024974--1025016 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
1024964 TTTATATGGT
1024974 TGTAATTATCACATC-TAGA
1 TGTAATTATCACATCAT-GA
*
1024993 TGTAATTATTACATCATGA
1 TGTAATTATCACATCATGA
1025012 TGTAA
1 TGTAA
1025017 AAACATTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 21 0.95
20 1 0.05
ACGTcount: A:0.37, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
TGTAATTATCACATCATGA
Found at i:1046723 original size:14 final size:14
Alignment explanation
Indices: 1046704--1046731 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1046694 AATGTACTTG
1046704 CCCTATATTGTTAA
1 CCCTATATTGTTAA
1046718 CCCTATATTGTTAA
1 CCCTATATTGTTAA
1046732 TCTAAAACTC
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:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (14 bp):
CCCTATATTGTTAA
Found at i:1049136 original size:2 final size:2
Alignment explanation
Indices: 1049129--1049153 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1049119 ATCATTACAT
1049129 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
1049154 AACAAGAAAA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1055553 original size:13 final size:14
Alignment explanation
Indices: 1055523--1055550 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1055513 GCACAATTTC
1055523 ATAAATTTGTAAAA
1 ATAAATTTGTAAAA
1055537 ATAAATTTGTAAAA
1 ATAAATTTGTAAAA
1055551 TAATGGTCCA
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:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (14 bp):
ATAAATTTGTAAAA
Found at i:1059600 original size:12 final size:12
Alignment explanation
Indices: 1059583--1059607 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1059573 GTTAAACTGT
1059583 AAAAAAAAATTA
1 AAAAAAAAATTA
1059595 AAAAAAAAATTA
1 AAAAAAAAATTA
1059607 A
1 A
1059608 TGATTTCTGT
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:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAAAAAATTA
Found at i:1063591 original size:33 final size:33
Alignment explanation
Indices: 1063554--1063619 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
1063544 TCCGTAAAAC
1063554 CAAGCCATGTATAGATTCACCTTTTTCAATTTT
1 CAAGCCATGTATAGATTCACCTTTTTCAATTTT
*
1063587 CAAGCCATGTATAGATTTACCTTTTTCAATTTT
1 CAAGCCATGTATAGATTCACCTTTTTCAATTTT
1063620 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (33 bp):
CAAGCCATGTATAGATTCACCTTTTTCAATTTT
Found at i:1063804 original size:25 final size:26
Alignment explanation
Indices: 1063746--1063805 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
1063736 AAAAGATGAA
* *
1063746 ACAAGAAAATAAATTGAAATATTCTG
1 ACAAGAAAATAAAATCAAATATTCTG
*
1063772 TCAA-AAAATGAAAATCAAAT-TTCT-
1 ACAAGAAAAT-AAAATCAAATATTCTG
1063796 ACAAGAAAAT
1 ACAAGAAAAT
1063806 TCCATTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 3 0.11
25 14 0.50
26 11 0.39
ACGTcount: A:0.57, C:0.10, G:0.08, T:0.25
Consensus pattern (26 bp):
ACAAGAAAATAAAATCAAATATTCTG
Found at i:1064516 original size:61 final size:61
Alignment explanation
Indices: 1064291--1064886 Score: 711
Period size: 61 Copynumber: 9.7 Consensus size: 61
1064281 GTTACAACTT
* * *
1064291 ACACAGACTTGATATCTACCCATTAATTGTGTAAGGTACAATAGAAACAACATTTACTATACAAC
1 ACACAAACTTGATATCTACCC--T--TTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* * * * * * *
1064356 ACACATACTTTAAATCTACTCATTAATTGTGTAGGGTACAACAGAGACAACTTTCACTATAC-A-
1 ACACAAACTTGATATCTAC-C-CT--TTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* *
1064419 ACACAAACTTGATTTCTACCCCTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* * * * * *
1064480 ACATAAACTTGATTTCTACCCTTTGTGTAAGATACAAAAGAGACAATATTCACTATACTAC
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* * * *
1064541 ATC-CAGACTTGATATTTACCCATTGTGTAAGGTACAATAGAGACAACATTTACTATACAAC
1 A-CACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* * *
1064602 ACACAAACTTAATTTCTACCCCTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* **
1064663 ACACAGACTTGATATCTACCCTTTGCATAAGGTACAAT--AGACAACATTCACTATACAAC
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* * * *
1064722 ACACAGACTTGATATCTACCCTTTGCGTAAGGTACAAT--AGACAACATTTATTATACAAC
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
* ** *
1064781 ACACAGACTTGATATCTACCAATTGTGTAAGGTACAACAGAGACAACATTCACTATACAAC
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
** *
1064842 ACACAAACTTGATATCTACCAATTGTGTAAGGTACGATAGAGACA
1 ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACA
1064887 TTATTTACTA
Statistics
Matches: 465, Mismatches: 58, Indels: 20
0.86 0.11 0.04
Matches are distributed among these distances:
59 144 0.31
60 2 0.00
61 250 0.54
62 2 0.00
63 15 0.03
64 1 0.00
65 50 0.11
66 1 0.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (61 bp):
ACACAAACTTGATATCTACCCTTTGTGTAAGGTACAATAGAGACAACATTCACTATACAAC
Found at i:1068166 original size:2 final size:2
Alignment explanation
Indices: 1068159--1068188 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1068149 TAATGTGCAC
1068159 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
1068189 GATGGGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1088832 original size:17 final size:17
Alignment explanation
Indices: 1088810--1088842 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1088800 AACTCTCAGT
1088810 TTAGCCGATAACTGGTC
1 TTAGCCGATAACTGGTC
1088827 TTAGCCGATAACTGGT
1 TTAGCCGATAACTGGT
1088843 ACAGTACCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (17 bp):
TTAGCCGATAACTGGTC
Found at i:1090760 original size:19 final size:19
Alignment explanation
Indices: 1090736--1090826 Score: 94
Period size: 19 Copynumber: 4.6 Consensus size: 19
1090726 CTATAATACG
1090736 TAATATACGATTATATGTC
1 TAATATACGATTATATGTC
* * * *
1090755 TAATATACAATT-TTTTTG
1 TAATATACGATTATATGTC
*
1090773 TATACATACGATATATATGATAC
1 TA-ATATACGAT-TATATG-T-C
1090796 TAATATACGATTATATGTC
1 TAATATACGATTATATGTC
1090815 TAATATACGATT
1 TAATATACGATT
1090827 TTTTCATGAA
Statistics
Matches: 57, Mismatches: 10, Indels: 10
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.09
19 31 0.54
20 2 0.04
21 8 0.14
22 9 0.16
23 2 0.04
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (19 bp):
TAATATACGATTATATGTC
Found at i:1090823 original size:41 final size:37
Alignment explanation
Indices: 1090736--1090826 Score: 92
Period size: 41 Copynumber: 2.3 Consensus size: 37
1090726 CTATAATACG
* * *
1090736 TAATATACGATTATATGTCTAATATACAATTTTTTTG
1 TAATATACGATTATATGTCTAATATACAATTTATGTC
* *
1090773 TATACATACGATATATATGATACTAATATACGATTATATGTC
1 TA-ATATACGAT-TATATG-T-CTAATATACAATT-TATGTC
1090815 TAATATACGATT
1 TAATATACGATT
1090827 TTTTCATGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
37 2 0.05
38 8 0.19
39 6 0.14
40 2 0.05
41 20 0.47
42 5 0.12
ACGTcount: A:0.38, C:0.10, G:0.09, T:0.43
Consensus pattern (37 bp):
TAATATACGATTATATGTCTAATATACAATTTATGTC
Found at i:1094316 original size:2 final size:2
Alignment explanation
Indices: 1094306--1094381 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
1094296 ACTCTGCATG
*
1094306 TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1094348 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1094382 CCCACCCACT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.01, C:0.50, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1097985 original size:21 final size:21
Alignment explanation
Indices: 1097941--1097986 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1097931 GAAGTAGAGA
* *
1097941 AAGATGAGGAGGAAGAAGATG
1 AAGAAGAGGAGGAAGAAGAAG
* *
1097962 AAGAAGAGGAGGATGACGAAG
1 AAGAAGAGGAGGAAGAAGAAG
1097983 AAGA
1 AAGA
1097987 TTCAAGTCAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.41, T:0.07
Consensus pattern (21 bp):
AAGAAGAGGAGGAAGAAGAAG
Found at i:1103122 original size:15 final size:15
Alignment explanation
Indices: 1103084--1103134 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1103074 TGGTCAGTAC
1103084 ATCATCAT-AT-TTT
1 ATCATCATCATCTTT
*
1103097 CATCGTCATCATCTTT
1 -ATCATCATCATCTTT
*
1103113 ATCATCATCATCATT
1 ATCATCATCATCTTT
1103128 ATCATCA
1 ATCATCA
1103135 CCTATCAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 7 0.22
15 22 0.69
16 3 0.09
ACGTcount: A:0.29, C:0.25, G:0.02, T:0.43
Consensus pattern (15 bp):
ATCATCATCATCTTT
Found at i:1106095 original size:12 final size:12
Alignment explanation
Indices: 1106078--1106105 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
1106068 CAGTGTCAGA
1106078 AGCAGACAGTGC
1 AGCAGACAGTGC
1106090 AGCAGACAGTGC
1 AGCAGACAGTGC
1106102 AGCA
1 AGCA
1106106 CAGAGTACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.25, G:0.32, T:0.07
Consensus pattern (12 bp):
AGCAGACAGTGC
Found at i:1113025 original size:57 final size:58
Alignment explanation
Indices: 1112930--1113042 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 58
1112920 ATCTTATGGA
* * *
1112930 ACAAATATGTGTCCATACTTTGAGCAATGATATGTATATGATATTTATGGTACAAAGT
1 ACAAATATGTGTCCATACTTTGACCAATGATATATATATGATATTTATGGAACAAAGT
*
1112988 ACAAATAT-T-TCCATTCTTTGAACCAATGATATATATATGATATTTATGGAACAAA
1 ACAAATATGTGTCCATACTTTG-ACCAATGATATATATATGATATTTATGGAACAAA
1113043 TATTTCCTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
56 10 0.20
57 32 0.64
58 8 0.16
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (58 bp):
ACAAATATGTGTCCATACTTTGACCAATGATATATATATGATATTTATGGAACAAAGT
Found at i:1113044 original size:50 final size:45
Alignment explanation
Indices: 1113011--1113113 Score: 152
Period size: 45 Copynumber: 2.2 Consensus size: 45
1113001 TTCTTTGAAC
1113011 CAATGATATATATATGATATTTATGGAACAAATATTTCCTTGGAA
1 CAATGATATATATATGATATTTATGGAACAAATATTTCCTTGGAA
* *
1113056 CAATGATATGTATATGGTATTTATGGAACAAATATGTTCGTACTTGGAA
1 CAATGATATATATATGATATTTATGGAACAAATAT-TTC---CTTGGAA
1113105 CAATGATAT
1 CAATGATAT
1113114 GTACCGGTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
45 33 0.63
46 3 0.06
49 16 0.31
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.37
Consensus pattern (45 bp):
CAATGATATATATATGATATTTATGGAACAAATATTTCCTTGGAA
Found at i:1113149 original size:55 final size:55
Alignment explanation
Indices: 1113021--1113169 Score: 201
Period size: 55 Copynumber: 2.9 Consensus size: 55
1113011 CAATGATATA
*
1113021 TATATGATATTTATGGAACAAATAT-TTC---CTTGGAACAATGATA--T----G
1 TATATGGTATTTATGGAACAAATATGTTCGTACTTGGAACAATGATATGTACCGG
1113066 TATATGGTATTTATGGAACAAATATGTTCGTACTTGGAACAATGATATGTACCGG
1 TATATGGTATTTATGGAACAAATATGTTCGTACTTGGAACAATGATATGTACCGG
* *
1113121 TATATGGTATTTATGGAACATATATGTTCGTACTTGGAACAATTATATG
1 TATATGGTATTTATGGAACAAATATGTTCGTACTTGGAACAATGATATG
1113170 GGGTTGTCTT
Statistics
Matches: 91, Mismatches: 3, Indels: 10
0.88 0.03 0.10
Matches are distributed among these distances:
45 24 0.26
46 3 0.03
49 15 0.16
51 1 0.01
55 48 0.53
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (55 bp):
TATATGGTATTTATGGAACAAATATGTTCGTACTTGGAACAATGATATGTACCGG
Found at i:1113391 original size:15 final size:15
Alignment explanation
Indices: 1113371--1113421 Score: 75
Period size: 15 Copynumber: 3.4 Consensus size: 15
1113361 TCAGACAAAT
1113371 TGACAATAACCGAAG
1 TGACAATAACCGAAG
*
1113386 TGACAATTACCGAAG
1 TGACAATAACCGAAG
* *
1113401 TGACAATAACAGAGG
1 TGACAATAACCGAAG
1113416 TGACAA
1 TGACAA
1113422 GCTTGTGGGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (15 bp):
TGACAATAACCGAAG
Found at i:1114618 original size:34 final size:34
Alignment explanation
Indices: 1114575--1114647 Score: 146
Period size: 34 Copynumber: 2.1 Consensus size: 34
1114565 CCCAGATACC
1114575 CCTTTATTACCATACTGAATCAGTGTCTTGATGT
1 CCTTTATTACCATACTGAATCAGTGTCTTGATGT
1114609 CCTTTATTACCATACTGAATCAGTGTCTTGATGT
1 CCTTTATTACCATACTGAATCAGTGTCTTGATGT
1114643 CCTTT
1 CCTTT
1114648 TAATCATAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (34 bp):
CCTTTATTACCATACTGAATCAGTGTCTTGATGT
Found at i:1118155 original size:58 final size:57
Alignment explanation
Indices: 1118065--1118181 Score: 171
Period size: 58 Copynumber: 2.0 Consensus size: 57
1118055 GTATAGTAAT
1118065 CTGGTCAAAACTTTAGTATATCCTTGCGACAATTTTTCTACAACCTAATATTACTGAA
1 CTGGTCAAAACTTTAGTATATCCTTGCGACAA-TTTTCTACAACCTAATATTACTGAA
* ** * * *
1118123 CTGGTCAAAACTTTGGTATATTTTTGCGACAATTTTCTGCAATCTTATATTACTGAA
1 CTGGTCAAAACTTTAGTATATCCTTGCGACAATTTTCTACAACCTAATATTACTGAA
1118180 CT
1 CT
1118182 ACTGTTCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 24 0.45
58 29 0.55
ACGTcount: A:0.30, C:0.19, G:0.12, T:0.39
Consensus pattern (57 bp):
CTGGTCAAAACTTTAGTATATCCTTGCGACAATTTTCTACAACCTAATATTACTGAA
Found at i:1129704 original size:18 final size:18
Alignment explanation
Indices: 1129681--1129734 Score: 99
Period size: 18 Copynumber: 3.0 Consensus size: 18
1129671 CCACATTGAG
1129681 GTACCTTAAGTGTGCCAT
1 GTACCTTAAGTGTGCCAT
1129699 GTACCTTAAGTGTGCCAT
1 GTACCTTAAGTGTGCCAT
*
1129717 GTACCTTAACTGTGCCAT
1 GTACCTTAAGTGTGCCAT
1129735 TGGTGGGTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.33
Consensus pattern (18 bp):
GTACCTTAAGTGTGCCAT
Found at i:1170060 original size:19 final size:20
Alignment explanation
Indices: 1170024--1170061 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
1170014 TCAATTGCAT
* *
1170024 CATGTCATTTGATTTTAATA
1 CATGTCATTTCATATTAATA
1170044 CATGT-ATTTCATATTAAT
1 CATGTCATTTCATATTAAT
1170062 TTGTGCAGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.50
Consensus pattern (20 bp):
CATGTCATTTCATATTAATA
Found at i:1174557 original size:41 final size:37
Alignment explanation
Indices: 1174461--1174561 Score: 105
Period size: 37 Copynumber: 2.6 Consensus size: 37
1174451 CCTTTTACCG
*
1174461 GTATTCTTAGATATTGCTGCAGTAGAAACTTTAATAT
1 GTATTCTTAGATATTGCTGCAGTAGAAACTTAAATAT
* * * *
1174498 G-ATCCCTTAAATATTGCTGCATTAGAAACTTAACATCTT
1 GTAT-TCTTAGATATTGCTGCAGTAGAAACTTAA-AT-AT
1174537 GTTTATTCTTAGATATTGCTGCAGT
1 G--TATTCTTAGATATTGCTGCAGT
1174562 TTAAACCTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
36 2 0.04
37 26 0.52
38 2 0.04
39 2 0.04
41 16 0.32
42 2 0.04
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (37 bp):
GTATTCTTAGATATTGCTGCAGTAGAAACTTAAATAT
Found at i:1179336 original size:63 final size:63
Alignment explanation
Indices: 1179237--1179509 Score: 501
Period size: 63 Copynumber: 4.3 Consensus size: 63
1179227 ATCTCACTTT
*
1179237 CCCACTGACTCAAGCTCAGCTGCAGAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
1 CCCACTGAATCAAGCTCAGCTGCAGAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
*
1179300 CCCACTGAATCAAGCTCAGCTGCAGATCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
1 CCCACTGAATCAAGCTCAGCTGCAGAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
* *
1179363 CTCACTGAATCAAGCTCAGCTGCAAAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
1 CCCACTGAATCAAGCTCAGCTGCAGAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
*
1179426 CCCACTGAATCAAGCTCAGCTGCAGATCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
1 CCCACTGAATCAAGCTCAGCTGCAGAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
1179489 CCCACTGAATCAAGCTCAGCT
1 CCCACTGAATCAAGCTCAGCT
1179510 AGGTATTGAC
Statistics
Matches: 202, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 202 1.00
ACGTcount: A:0.34, C:0.31, G:0.15, T:0.20
Consensus pattern (63 bp):
CCCACTGAATCAAGCTCAGCTGCAGAGCCTGATCAAATCCTTCAAAACCAAACAGGTATTGAC
Found at i:1179517 original size:31 final size:31
Alignment explanation
Indices: 1179479--1179538 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
1179469 AAAACCAAAC
1179479 AGGTATTGACCCCACTGAATCAAGCTCAGCT
1 AGGTATTGACCCCACTGAATCAAGCTCAGCT
1179510 AGGTATTGACCCCACTGAATCAAGCTCAG
1 AGGTATTGACCCCACTGAATCAAGCTCAG
1179539 TGAAAGATCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (31 bp):
AGGTATTGACCCCACTGAATCAAGCTCAGCT
Found at i:1181637 original size:15 final size:16
Alignment explanation
Indices: 1181605--1181647 Score: 70
Period size: 15 Copynumber: 2.8 Consensus size: 16
1181595 AATGCACATT
1181605 TTCACATGTGATAAAA
1 TTCACATGTGATAAAA
1181621 TTCACATGTGA-AAAA
1 TTCACATGTGATAAAA
*
1181636 TTCAAATGTGAT
1 TTCACATGTGAT
1181648 GATTTTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.33
Consensus pattern (16 bp):
TTCACATGTGATAAAA
Found at i:1181668 original size:16 final size:16
Alignment explanation
Indices: 1181647--1181681 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1181637 TCAAATGTGA
*
1181647 TGATTTTTTTCAAATG
1 TGATTTTTCTCAAATG
*
1181663 TGATTTTTCTCACATG
1 TGATTTTTCTCAAATG
1181679 TGA
1 TGA
1181682 AAAAAGCAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.23, C:0.11, G:0.14, T:0.51
Consensus pattern (16 bp):
TGATTTTTCTCAAATG
Found at i:1190035 original size:15 final size:15
Alignment explanation
Indices: 1190015--1190043 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1190005 TCTTCATTTT
1190015 AACAAATATGTTTAA
1 AACAAATATGTTTAA
1190030 AACAAATATGTTTA
1 AACAAATATGTTTA
1190044 TTTTTCTGAA
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:0.52, C:0.07, G:0.07, T:0.34
Consensus pattern (15 bp):
AACAAATATGTTTAA
Found at i:1200190 original size:18 final size:17
Alignment explanation
Indices: 1200167--1200200 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
1200157 ACTTACCAGT
1200167 TTTATTTTTTATTTTTTA
1 TTTATTTTTT-TTTTTTA
1200185 TTTATTTTTTTTTTTT
1 TTTATTTTTTTTTTTT
1200201 GGGGGGGTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTATTTTTTTTTTTTA
Found at i:1206826 original size:35 final size:34
Alignment explanation
Indices: 1206745--1206839 Score: 100
Period size: 35 Copynumber: 2.7 Consensus size: 34
1206735 GGTAAGTTAA
* * *
1206745 CATACCTTAAAACATACCAAGATAAATGAACCACAG
1 CATACC-TAAAA-ATACCAAGGTAAATCAACCAAAG
**
1206781 CATATATAAAATATACCAAGGTAAATCAACCAAAG
1 CATACCTAAAA-ATACCAAGGTAAATCAACCAAAG
*
1206816 CATACCTAAAAACTGCCAAGGTAA
1 CATACCTAAAAA-TACCAAGGTAA
1206840 GTTAATGATA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
34 1 0.02
35 44 0.90
36 4 0.08
ACGTcount: A:0.51, C:0.22, G:0.09, T:0.18
Consensus pattern (34 bp):
CATACCTAAAAATACCAAGGTAAATCAACCAAAG
Found at i:1209647 original size:32 final size:32
Alignment explanation
Indices: 1209607--1209703 Score: 185
Period size: 32 Copynumber: 3.0 Consensus size: 32
1209597 AAAGGTACGG
1209607 CAATCAAGCCCACTATTACTTGCCAATGACTT
1 CAATCAAGCCCACTATTACTTGCCAATGACTT
1209639 CAATCAAGCCCACTATTACTTGCCAATGACTT
1 CAATCAAGCCCACTATTACTTGCCAATGACTT
*
1209671 CAATCAAGCCCACTATTACTTGCCAATGGCTT
1 CAATCAAGCCCACTATTACTTGCCAATGACTT
1209703 C
1 C
1209704 CATTCTTCTT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 64 1.00
ACGTcount: A:0.30, C:0.32, G:0.10, T:0.28
Consensus pattern (32 bp):
CAATCAAGCCCACTATTACTTGCCAATGACTT
Found at i:1213677 original size:61 final size:61
Alignment explanation
Indices: 1213582--1213699 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
1213572 GACCCGTTAT
* * *
1213582 TGTATGATTCTCATGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGATTAG
1 TGTATGAATCCCAAGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGATTAG
1213643 TGTATGAATCCCAAGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGA
1 TGTATGAATCCCAAGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGA
1213700 AGAGAGTGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (61 bp):
TGTATGAATCCCAAGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGATTAG
Found at i:1213916 original size:70 final size:70
Alignment explanation
Indices: 1213638--1213916 Score: 298
Period size: 70 Copynumber: 3.8 Consensus size: 70
1213628 AGTGTGGAGG
*
1213638 ATTAGTGTATGAATCCCAA-GTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGAAG
1 ATTAGTGTATGAAT-CCAATGTCACTATCTCTCTTTGATTTGACCAGTGAGAAGTGT---GGAAG
1213702 AGAGTGTTT
62 AGAGTGTTT
* * *
1213711 ATTAGTGTATGAATTCC-ATTTCGA-TATCTCTCTTTGATTTGAACAGTACCAGGTAAGTAGTGT
1 ATTAGTGTATGAA-TCCAATGTC-ACTATCTCTCTTTGATTTGACCAGT--GA-G-AAGT-GTG-
* *
1213774 AGAGGAGAGGGTTT
58 -GAAGAGAGTGTTT
* *
1213788 ATTAGTGTATGAATCCAATGTCACTATCTCTCTTTGATTT-AGCCAATGA-ATAGAGTGGAAGAG
1 ATTAGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGA-CCAGTGAGA-AGTGTGGAAGAG
1213851 AGTGTTT
64 AGTGTTT
* *
1213858 ATGAGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGA
1 ATTAGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCAGTGAGAAGTGTGGA
1213917 GGATTAGTGT
Statistics
Matches: 173, Mismatches: 17, Indels: 35
0.77 0.08 0.16
Matches are distributed among these distances:
70 62 0.36
71 2 0.01
72 5 0.03
73 40 0.23
74 2 0.01
75 3 0.02
76 6 0.03
77 51 0.29
78 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.35
Consensus pattern (70 bp):
ATTAGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCAGTGAGAAGTGTGGAAGAGAG
TGTTT
Found at i:1213956 original size:61 final size:61
Alignment explanation
Indices: 1213861--1213980 Score: 213
Period size: 61 Copynumber: 2.0 Consensus size: 61
1213851 AGTGTTTATG
*
1213861 AGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCTGTGAGAAGTGTGGAGGATT
1 AGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCAGTGAGAAGTGTGGAGGATT
* *
1213922 AGTGTATGAATCCAGTGTCACTATCTCTCTTTGATTTGACCAGTGAGTAGTGTGGAGGA
1 AGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCAGTGAGAAGTGTGGAGGA
1213981 AGAGAGCAGT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 56 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (61 bp):
AGTGTATGAATCCAATGTCACTATCTCTCTTTGATTTGACCAGTGAGAAGTGTGGAGGATT
Found at i:1214669 original size:160 final size:159
Alignment explanation
Indices: 1214397--1214783 Score: 560
Period size: 160 Copynumber: 2.4 Consensus size: 159
1214387 GGTCCACCAA
*
1214397 CAGTTTCCGCTCATTTTCTTCGCAGAGGATGAACATATTGAAATGGAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCA-TTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * * *
1214462 TCATGATAATATCTAGATCAAGTTCGATATTGGGTATGATTGAGCTATTTTCGAGAGAGTTATGG
65 TCATGATAATATCTAGATCAAGTTCGATATTGGGTAAGATCGAGCTA-TTTCAACAGAGTTATGG
*
1214527 CCCTTGGACGTAGAAAAA-TCGAGTTATTTG
129 CCCTTGGACATAGAAAAATTCGAGTTATTTG
1214557 CAGTTTCCGCTCATCTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1 CAGTTTCCGCTCAT-TTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
* * *
1214622 TCATGATATTATCTAGGTCAAGTTCGATATTGGGTAAGATCGAGCTATTTCAACAGAGTTGTGGC
65 TCATGATAATATCTAGATCAAGTTCGATATTGGGTAAGATCGAGCTATTTCAACAGAGTTATGGC
** *
1214687 GTTTTGACATAGAAAAATTCGAGTTATTTG
130 CCTTGGACATAGAAAAATTCGAGTTATTTG
* * * * * * *
1214717 CAGTTTCCACTCATTTCCTTTGAAGAGGGTGCACATATTGATATGAAATTTAGTATACAGGTTTA
1 CAGTTTCCGCTCATTT-CTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTA
1214782 TC
65 TC
1214784 TAAATAATAC
Statistics
Matches: 205, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
159 31 0.15
160 174 0.85
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (159 bp):
CAGTTTCCGCTCATTTCTTCGCAGAGGATGAACATATTGAAATGAAATTTGGTATACAGGTTTAT
CATGATAATATCTAGATCAAGTTCGATATTGGGTAAGATCGAGCTATTTCAACAGAGTTATGGCC
CTTGGACATAGAAAAATTCGAGTTATTTG
Found at i:1216222 original size:20 final size:21
Alignment explanation
Indices: 1216197--1216244 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
1216187 AGGAGTGAGG
* * *
1216197 TTTTATGA-CCCATTTATGTC
1 TTTTATGAGCCAATTTATATA
1216217 TTTTAT-AGCCAATTTATATA
1 TTTTATGAGCCAATTTATATA
1216237 TTTTATGA
1 TTTTATGA
1216245 ATATTCTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.27, C:0.12, G:0.08, T:0.52
Consensus pattern (21 bp):
TTTTATGAGCCAATTTATATA
Found at i:1221096 original size:21 final size:21
Alignment explanation
Indices: 1221070--1221109 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1221060 ACATACANCT
1221070 TTGACCTCTGTGTCAGTGACC
1 TTGACCTCTGTGTCAGTGACC
*
1221091 TTGACCTCTTTGTCAGTGA
1 TTGACCTCTGTGTCAGTGA
1221110 AATCAAGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.25, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGACCTCTGTGTCAGTGACC
Found at i:1224004 original size:21 final size:21
Alignment explanation
Indices: 1223902--1224007 Score: 108
Period size: 21 Copynumber: 5.1 Consensus size: 21
1223892 TGTTTATCAA
*
1223902 TGACCTTGACCTCTGTGTCAA
1 TGACCTTGACCTCTGTGTCAG
* * *
1223923 TAACTTTGACCTCTATGTCAG
1 TGACCTTGACCTCTGTGTCAG
** * *
1223944 TGACCTCAACCAC--TGTCAA
1 TGACCTTGACCTCTGTGTCAG
*
1223963 TGACTTTGACCTCTGTGTCAG
1 TGACCTTGACCTCTGTGTCAG
*
1223984 TGACCTTGACCTCTTTGTCAG
1 TGACCTTGACCTCTGTGTCAG
1224005 TGA
1 TGA
1224008 AATCAAGCTC
Statistics
Matches: 66, Mismatches: 17, Indels: 4
0.76 0.20 0.05
Matches are distributed among these distances:
19 14 0.21
21 52 0.79
ACGTcount: A:0.21, C:0.27, G:0.18, T:0.34
Consensus pattern (21 bp):
TGACCTTGACCTCTGTGTCAG
Found at i:1226967 original size:16 final size:16
Alignment explanation
Indices: 1226923--1226957 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1226913 AGTTAACTAG
1226923 ATGATGCACA-AAAAAT
1 ATGATGCA-AGAAAAAT
1226939 ATGATGCAAGAAAAAT
1 ATGATGCAAGAAAAAT
1226955 ATG
1 ATG
1226958 GATCTAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 1 0.06
16 17 0.94
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (16 bp):
ATGATGCAAGAAAAAT
Found at i:1227129 original size:11 final size:11
Alignment explanation
Indices: 1227113--1227138 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1227103 ATCGATACGA
1227113 ATTGGTATGAT
1 ATTGGTATGAT
1227124 ATTGGTATGAT
1 ATTGGTATGAT
1227135 ATTG
1 ATTG
1227139 CATCATACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.27, T:0.46
Consensus pattern (11 bp):
ATTGGTATGAT
Found at i:1227710 original size:18 final size:18
Alignment explanation
Indices: 1227683--1227723 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1227673 CTCCAGATTT
*
1227683 AGCTATATAGCTTGAATA
1 AGCTAAATAGCTTGAATA
* *
1227701 AGCTAAATAGCTTTATTA
1 AGCTAAATAGCTTGAATA
1227719 AGCTA
1 AGCTA
1227724 TTCAGAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (18 bp):
AGCTAAATAGCTTGAATA
Found at i:1232115 original size:171 final size:170
Alignment explanation
Indices: 1231805--1232146 Score: 648
Period size: 172 Copynumber: 2.0 Consensus size: 170
1231795 ACATGTATAC
1231805 TTGCATATAGAAAATCTGTCAAAATACTTCTCCAGAATTTCAATGCTACAGTTTTTTTCTTTTCT
1 TTGCATATAGAAAATCTGTCAAAATACTTCTCCAGAATTTCAATGCTACAGTTTTTTTCTTTTCT
*
1231870 AAGATCTTTAAAAAAGCATACGGTCAAGTTTGTACAACCCATAATCCAGGAATAGAGAAAATCTT
66 AAGATCTTTAAAAAAGCATAAGGTCAAGTTTGTACAACCCATAATCCAGGAATAGAGAAAATCTT
*
1231935 TGAAAAAAAATATCTATCCTTGCCCATTTTTTATCCCCTT
131 TGAAAAAAAATATCTATCCTTGCCCATTTTATATCCCCTT
1231975 NTTGCATATAGAAAATCTGTCAAAATACTTCTCCAGAATTTCAATGCTACAGTTTTTTTTCTTTT
1 -TTGCATATAGAAAATCTGTCAAAATACTTCTCCAGAATTTCAATGCTACAG-TTTTTTTCTTTT
1232040 CTAAGATCTTTAAAAAAGCATAAGGTCAAGTTTGTACAACCCATAATCCAGGAATAGAGAAAATC
64 CTAAGATCTTTAAAAAAGCATAAGGTCAAGTTTGTACAACCCATAATCCAGGAATAGAGAAAATC
1232105 TTTGAAAAAAAATATCTATCCTTGCCCATTTTATATCCCCTT
129 TTTGAAAAAAAATATCTATCCTTGCCCATTTTATATCCCCTT
1232147 GCACAACTTA
Statistics
Matches: 168, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
171 51 0.30
172 117 0.70
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (170 bp):
TTGCATATAGAAAATCTGTCAAAATACTTCTCCAGAATTTCAATGCTACAGTTTTTTTCTTTTCT
AAGATCTTTAAAAAAGCATAAGGTCAAGTTTGTACAACCCATAATCCAGGAATAGAGAAAATCTT
TGAAAAAAAATATCTATCCTTGCCCATTTTATATCCCCTT
Found at i:1236183 original size:50 final size:50
Alignment explanation
Indices: 1236108--1236241 Score: 205
Period size: 50 Copynumber: 2.7 Consensus size: 50
1236098 ATTTACCATC
*
1236108 TTAACGCACTTTGAAAAAAAATTTCAAAGTGGGTTAACCTGGTCCAAAAT
1 TTAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTAACCTGGTCCAAAAT
* * ** *
1236158 TTAACGCACTTTGAAAAAAATTTTCAAAGTGCGTTGATTTGGTCCCAAAT
1 TTAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTAACCTGGTCCAAAAT
*
1236208 TTGACGCACTTTGAAAAAAAATTTCAAAGTGCGT
1 TTAACGCACTTTGAAAAAAAATTTCAAAGTGCGT
1236242 AATTTTTTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 76 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (50 bp):
TTAACGCACTTTGAAAAAAAATTTCAAAGTGCGTTAACCTGGTCCAAAAT
Found at i:1239483 original size:34 final size:34
Alignment explanation
Indices: 1239440--1239795 Score: 329
Period size: 34 Copynumber: 10.3 Consensus size: 34
1239430 ACATTACTAG
* * *
1239440 AGAGTCACATGAAATGTTCTAAAATGACATTTCT
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
** * * *
1239474 AGAGTCACATGAAATGTTCCGGTAAGACATATCAG
1 AGAGTCACATGAAATGTTCCAATATGACATTTC-C
* * * *
1239509 AGAGTCATATGAAATGTTCCAGTATGATATTTTC
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
* ** *
1239543 TGAACCACATGAAATGTTCCAATATGAAATTTCC
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
* *
1239577 AGAGTCACATAAAATGTTCCAATATGAAATTTCC
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
***
1239611 AGAGTCACATGAAATGTTCTTGTATGGA-ATTTCC
1 AGAGTCACATGAAATGTTCCAATAT-GACATTTCC
** * **
1239645 AGAACCACATGAAATGTTGCAGCATGACATTTCC
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
* * **
1239679 AGAGTCAAATGAAATGTTGCAGCATGACATTTCC
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
* *
1239713 ATG-GTCACATGACATGTTCCAATATGACATTTCTAG
1 A-GAGTCACATGAAATGTTCCAATATGACATTTC--C
* *
1239749 AGAGTCGCATGACATGTTCCAATATGACATTTCC
1 AGAGTCACATGAAATGTTCCAATATGACATTTCC
1239783 AGAGAGTCACATG
1 --AGAGTCACATG
1239796 CATGAAATGT
Statistics
Matches: 266, Mismatches: 47, Indels: 16
0.81 0.14 0.05
Matches are distributed among these distances:
33 2 0.01
34 193 0.73
35 31 0.12
36 40 0.15
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (34 bp):
AGAGTCACATGAAATGTTCCAATATGACATTTCC
Found at i:1239571 original size:15 final size:14
Alignment explanation
Indices: 1239551--1239611 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
1239541 TCTGAACCAC
1239551 ATGAAATGTTCCAAT
1 ATGAAAT-TTCCAAT
1239566 ATGAAATTTCCAGAGT
1 ATGAAATTTCCA-A-T
*
1239582 CACATAAAATGTTCCAAT
1 ---ATGAAAT-TTCCAAT
1239600 ATGAAATTTCCA
1 ATGAAATTTCCA
1239612 GAGTCACATG
Statistics
Matches: 38, Mismatches: 2, Indels: 13
0.72 0.04 0.25
Matches are distributed among these distances:
14 10 0.26
15 14 0.37
16 1 0.03
18 1 0.03
19 7 0.18
20 5 0.13
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.31
Consensus pattern (14 bp):
ATGAAATTTCCAAT
Found at i:1239624 original size:19 final size:19
Alignment explanation
Indices: 1239566--1239625 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
1239556 ATGTTCCAAT
1239566 ATGAAATTTCCAGAGTCAC
1 ATGAAATTTCCAGAGTCAC
*
1239585 ATAAAATGTTCCA-A-T---
1 ATGAAAT-TTCCAGAGTCAC
1239600 ATGAAATTTCCAGAGTCAC
1 ATGAAATTTCCAGAGTCAC
1239619 ATGAAAT
1 ATGAAAT
1239626 GTTCTTGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 5 0.15
15 7 0.21
16 1 0.03
18 1 0.03
19 14 0.42
20 5 0.15
ACGTcount: A:0.42, C:0.17, G:0.13, T:0.28
Consensus pattern (19 bp):
ATGAAATTTCCAGAGTCAC
Found at i:1239660 original size:102 final size:102
Alignment explanation
Indices: 1239445--1239795 Score: 364
Period size: 102 Copynumber: 3.4 Consensus size: 102
1239435 ACTAGAGAGT
* * * * * * *
1239445 CACATGAAATGTTCTAAAATGACATTTCTAGAGTCACATGAAATGTTCCGGTAAGACATATCAGA
1 CACATGAAATGTTCCAATATGACATTTCCAGAGTCACATGAAATGTTCCAGTATGACATTTC-CA
* * * *
1239510 GAGTCATATGAAATGTTCCAGTATGATATTTTCTGAAC
65 GAGTCACATGAAATGTTCCAGTATGACATTTCCAGAAC
* * * *
1239548 CACATGAAATGTTCCAATATGAAATTTCCAGAGTCACATAAAATGTTCCAATATGAAATTTCCAG
1 CACATGAAATGTTCCAATATGACATTTCCAGAGTCACATGAAATGTTCCAGTATGACATTTCCAG
**
1239613 AGTCACATGAAATGTTCTTGTATGGA-ATTTCCAGAAC
66 AGTCACATGAAATGTTCCAGTAT-GACATTTCCAGAAC
* ** * * *
1239650 CACATGAAATGTTGCAGCATGACATTTCCAGAGTCAAATGAAATGTTGCAGCATGACATTTCCAT
1 CACATGAAATGTTCCAATATGACATTTCCAGAGTCACATGAAATGTTCCAGTATGACATTTCCA-
* * * *
1239715 G-GTCACATGACATGTTCCAATATGACATTTCTAGAGAGT
65 GAGTCACATGAAATGTTCCAGTATGACATTTCCAGA-A-C
* *
1239754 CGCATGACATGTTCCAATATGACATTTCCAGAGAGTCACATG
1 CACATGAAATGTTCCAATATGACATTTCC--AGAGTCACATG
1239796 CATGAAATGT
Statistics
Matches: 203, Mismatches: 38, Indels: 11
0.81 0.15 0.04
Matches are distributed among these distances:
101 2 0.01
102 111 0.55
103 56 0.28
104 24 0.12
106 10 0.05
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (102 bp):
CACATGAAATGTTCCAATATGACATTTCCAGAGTCACATGAAATGTTCCAGTATGACATTTCCAG
AGTCACATGAAATGTTCCAGTATGACATTTCCAGAAC
Found at i:1244285 original size:187 final size:186
Alignment explanation
Indices: 1243965--1244334 Score: 722
Period size: 187 Copynumber: 2.0 Consensus size: 186
1243955 ATGTACGGAT
1243965 CACAAGCCCGACACTTTATCCACTCGGCTATGATGTAAGTTATATGTTCCTGTCGATAAAATCCT
1 CACAAGCCCGACACTTTATCCACTCGGCTATGATGTAAGTTATATGTTCCTGTCGATAAAATCCT
1244030 TTTAATAAATCAAAATGTTGTTTCGATCAGACGTCAGCCATTTTATGACGATGTGTTATTCCACC
66 TTTAATAAATCAAAATGTTGTTTCGATCAGACGTCAGCCATTTTATGACGATGTGTTATTCCACC
1244095 TTAACAAAATTATTCAATGGAAGCATGTATCAATTAGGTTATCTTATAAGAAANGCA
131 TTAACAAAATTATTCAATGGAAGCATGTATCAATTAGGTTATCTTATAAGAAA-GCA
*
1244152 CACAGGCCCGACACTTTATCCACTCGGCTATGATGTAAGTTATATGTTCCTGTCGATAAAATCCT
1 CACAAGCCCGACACTTTATCCACTCGGCTATGATGTAAGTTATATGTTCCTGTCGATAAAATCCT
1244217 TTTAATAAATCAAAATGTTGTTTCGATCAGACGTCAGCCATTTTATGACGATGTGTTATTCCACC
66 TTTAATAAATCAAAATGTTGTTTCGATCAGACGTCAGCCATTTTATGACGATGTGTTATTCCACC
1244282 TTAACAAAATTATTCAATGGAAGCATGTATCAATTAGGTTATCTTATAAGAAA
131 TTAACAAAATTATTCAATGGAAGCATGTATCAATTAGGTTATCTTATAAGAAA
1244335 TGAATTTTAA
Statistics
Matches: 182, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
187 182 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (186 bp):
CACAAGCCCGACACTTTATCCACTCGGCTATGATGTAAGTTATATGTTCCTGTCGATAAAATCCT
TTTAATAAATCAAAATGTTGTTTCGATCAGACGTCAGCCATTTTATGACGATGTGTTATTCCACC
TTAACAAAATTATTCAATGGAAGCATGTATCAATTAGGTTATCTTATAAGAAAGCA
Found at i:1246149 original size:39 final size:39
Alignment explanation
Indices: 1246042--1247460 Score: 2015
Period size: 39 Copynumber: 36.0 Consensus size: 39
1246032 AAATAATCAC
*
1246042 TTTTATTTTCGACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* * * * *
1246081 TTTTATTTTTGGCC-CTTCGCCCTCGTTCTCTGAGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1246119 TTTTATTTTCGACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1246158 TTTTATTTTCGACCATTTCGCCCTCGTTTTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
** * *
1246197 AGTTATTTTCAACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1246236 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* * *
1246275 TTTTATTTTCGATCATATCGCCCTCGTTTTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1246314 TTTTATTTTCAACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1246353 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1246392 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCATGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1246431 TCTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1246470 TTTTATTTTCAACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1246509 TTTTATTTTCGACCATTTCGACTTTGTCGCCCTCGTTTTCCATGGGCA
1 TTTTATTTTCGA-C----C-A--TT-TCGCCCTCGTTCTCCGTGGGCA
*
1246557 TTTTATTTTCGACCATCTC-CTCCTTC-TTCAT-CGTGGGCA
1 TTTTATTTTCGACCATTTCGC-CC-TCGTTC-TCCGTGGGCA
*
1246596 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCATGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1246635 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1246674 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1246713 TTTTATTTTCGACCATTTCGCCCTCGTTTTCCGTGGGGA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* * * *
1246752 ATTTATTTTCAACCATTTCGCCCTCCTTCTCCATGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1246791 TTTTATTTTCGACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1246830 TTTTATTTTCGACCATTTCGCCCTCGTTTTCCGTGGGTA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* ** *
1246869 ATTTATTTTTTACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1246908 TTTTAGTTTCGACCATTTCGCCCTCCTTCAT-CGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTC-TCCGTGGGCA
* * *
1246947 TTTTATTTTCGACCATATCGCCCTCGTTTTCCATGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1246986 TTTTATTTTCAACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1247025 TTTTATATTCGACCATTTCGCCCTCGTTCTCCATGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1247064 TCTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1247103 TTTTA-TTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1247141 TTTTATTTTCGACCATTTCGACCTTTTTGCCCTCGTTCTTCATGGGCA
1 TTTTATTTTCGACCATTT----C-----GCCCTCGTTCTCCGTGGGCA
* *
1247189 TTTTATTTTCGACCATCTCCCCCTTC-TTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCC-TCGTTCTCCGTGGGCA
*
1247228 TTTTATTTTCGACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* * * *
1247267 TTTCATTTTCAACCATTTCGCCTTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1247306 TTTTATTTTCGACCATTTCGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
*
1247345 TTTTATTTTCGACCATTTCGCCCTCGTTCTTCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
* *
1247384 TTTTATTTTCGACCATTTTGCCCTCCTTCTCCGTGGGCA
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
** *
1247423 TTTTATTTTTAACCATTTCGCCCTCCTTCTCCGTGGGC
1 TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGC
1247461 GCATTTAAAA
Statistics
Matches: 1239, Mismatches: 111, Indels: 60
0.88 0.08 0.04
Matches are distributed among these distances:
38 77 0.06
39 1077 0.87
40 9 0.01
42 1 0.00
43 2 0.00
44 2 0.00
45 1 0.00
47 3 0.00
48 67 0.05
ACGTcount: A:0.12, C:0.31, G:0.16, T:0.42
Consensus pattern (39 bp):
TTTTATTTTCGACCATTTCGCCCTCGTTCTCCGTGGGCA
Found at i:1249633 original size:2 final size:2
Alignment explanation
Indices: 1249626--1249683 Score: 98
Period size: 2 Copynumber: 29.0 Consensus size: 2
1249616 TGACTGGTTT
* *
1249626 GA GA GA GA GA GA GT GA GA GA GA GA GT GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1249668 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
1249684 ATATTCAGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
GA
Found at i:1250481 original size:39 final size:39
Alignment explanation
Indices: 1250427--1250696 Score: 438
Period size: 39 Copynumber: 7.0 Consensus size: 39
1250417 CTCAAAAATC
** *
1250427 TTAATATTTATTGATTATATTGTTATTGACGTTAATGAT
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
*
1250466 TTAATATTTATTGATTATATTGTTATTGACGTTGATGTT
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
*
1250505 TTAATATTTATTGATTATATTGTTATTGACCTTGCTG-T
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
*
1250543 TT--TATTTATTGATTATATTGTTATTGACCTTGCTGTT
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
*
1250580 TTAATATTTATTGATTATATTGTTATTGATGTTGCTGTT
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
1250619 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
* *
1250658 TTCATATTTATTGATTATATTGTTATTGATGTTGCTGTT
1 TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
1250697 ATTGTTATTG
Statistics
Matches: 219, Mismatches: 9, Indels: 6
0.94 0.04 0.03
Matches are distributed among these distances:
36 33 0.15
37 3 0.01
38 3 0.01
39 180 0.82
ACGTcount: A:0.24, C:0.05, G:0.14, T:0.57
Consensus pattern (39 bp):
TTAATATTTATTGATTATATTGTTATTGACGTTGCTGTT
Found at i:1250584 original size:114 final size:116
Alignment explanation
Indices: 1250430--1250696 Score: 439
Period size: 114 Copynumber: 2.3 Consensus size: 116
1250420 AAAAATCTTA
** *
1250430 ATATTTATTGATTATATTGTTATTGACGTTAATGATTTAATATTTATTGATTATATTGTTATTGA
1 ATATTTATTGATTATATTGTTATTGACGTTGCTGTTTTAATATTTATTGATTATATTGTTATTGA
1250495 CGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTG-TTT
66 CGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTTTT
*
1250545 -TATTTATTGATTATATTGTTATTGACCTTGCTGTTTTAATATTTATTGATTATATTGTTATTGA
1 ATATTTATTGATTATATTGTTATTGACGTTGCTGTTTTAATATTTATTGATTATATTGTTATTGA
* * *
1250609 TGTTGCTGTTTTAATATTTATTGATTATATTGTTATTGACGTTGCTGTTTT
66 CGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTTTT
*
1250660 CATATTTATTGATTATATTGTTATTGATGTTGCTGTT
1 -ATATTTATTGATTATATTGTTATTGACGTTGCTGTT
1250697 ATTGTTATTG
Statistics
Matches: 140, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
114 104 0.74
115 3 0.02
117 33 0.24
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.57
Consensus pattern (116 bp):
ATATTTATTGATTATATTGTTATTGACGTTGCTGTTTTAATATTTATTGATTATATTGTTATTGA
CGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTTTT
Found at i:1250705 original size:153 final size:153
Alignment explanation
Indices: 1250427--1250706 Score: 463
Period size: 153 Copynumber: 1.8 Consensus size: 153
1250417 CTCAAAAATC
1250427 TTAATATTTATTGATTATATTGTTATTGACGTTAATGATTTAATATTTATTGATTATATTGTTAT
1 TTAATATTTATTGATTATATTGTTATTGACGTTAATGATTTAATATTTATTGATTATATTGTTAT
*
1250492 TGACGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTTTTATTTATTGATT
66 TGACGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTTTTAGTTATTGATT
1250557 ATATTGTTATTGACCTTGCTGTT
131 ATATTGTTATTGACCTTGCTGTT
* ** *
1250580 TTAATATTTATTGATTATATTGTTATTGATGTTGCTGTTTTAATATTTATTGATTATATTGTTAT
1 TTAATATTTATTGATTATATTGTTATTGACGTTAATGATTTAATATTTATTGATTATATTGTTAT
* * **
1250645 TGACGTTGCTGTTTTCATATTTATTGATTATATTGTTATTGATGTTGCTGTTATT-GTTATTG
66 TGACGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTT-TTAGTTATTG
1250707 TTGTAGATGT
Statistics
Matches: 117, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
153 115 0.98
154 2 0.02
ACGTcount: A:0.24, C:0.05, G:0.15, T:0.57
Consensus pattern (153 bp):
TTAATATTTATTGATTATATTGTTATTGACGTTAATGATTTAATATTTATTGATTATATTGTTAT
TGACGTTGATGTTTTAATATTTATTGATTATATTGTTATTGACCTTGCTGTTTTAGTTATTGATT
ATATTGTTATTGACCTTGCTGTT
Found at i:1250707 original size:27 final size:27
Alignment explanation
Indices: 1250675--1250726 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
1250665 TTATTGATTA
* *
1250675 TATTGTTATTGATGTTGCTGTTATTGT
1 TATTGTTATAGATGTCGCTGTTATTGT
* *
1250702 TATTGTTGTAGATGTCGGTGTTATT
1 TATTGTTATAGATGTCGCTGTTATT
1250727 TTAATCTATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.15, C:0.04, G:0.25, T:0.56
Consensus pattern (27 bp):
TATTGTTATAGATGTCGCTGTTATTGT
Found at i:1252456 original size:41 final size:41
Alignment explanation
Indices: 1252399--1252482 Score: 159
Period size: 41 Copynumber: 2.0 Consensus size: 41
1252389 GCTCGTCACG
*
1252399 AAGTTTTTCAACCTTTTATATATACCACCTCTATACAATAA
1 AAGTTTTTCAACCTTTTATACATACCACCTCTATACAATAA
1252440 AAGTTTTTCAACCTTTTATACATACCACCTCTATACAATAA
1 AAGTTTTTCAACCTTTTATACATACCACCTCTATACAATAA
1252481 AA
1 AA
1252483 TACTTTATTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (41 bp):
AAGTTTTTCAACCTTTTATACATACCACCTCTATACAATAA
Found at i:1258498 original size:2 final size:2
Alignment explanation
Indices: 1258491--1258562 Score: 99
Period size: 2 Copynumber: 36.0 Consensus size: 2
1258481 TGATATTTGC
* * * * *
1258491 AG AG AG AG AG AG AG CG AG AC AG AC AG AC AG AC 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
1258533 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
1258563 CGTTGCTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.49, C:0.07, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1258824 original size:5 final size:5
Alignment explanation
Indices: 1258816--1259221 Score: 231
Period size: 5 Copynumber: 79.4 Consensus size: 5
1258806 GAATTTTGAG
* * * * * *
1258816 ATACC ATACC ATACC ATACC ATACC ATACC ATACT ATACT ATACT ATACT
1 ATACT ATACT ATACT ATACT ATACT ATACT ATACT ATACT ATACT ATACT
1258866 ATACT ATACT ATACT ATACT ATACT ATA-T CATACT ATACT ATACT ATACT
1 ATACT ATACT ATACT ATACT ATACT ATACT -ATACT ATACT ATACT ATACT
* * * * * * *
1258916 ATACT ATACT AGA-T CATACT A-AGCT TTACT TTACT A-CCT ACACT TTTCT
1 ATACT ATACT ATACT -ATACT ATA-CT ATACT ATACT ATACT ATACT ATACT
** * * * * * * *
1258965 AGCCT ATTCT A-ATCT TTACT GTATT ATACAAT AAACCT -TACC ACACT
1 ATACT ATACT ATA-CT ATACT ATACT ATAC--T ATA-CT ATACT ATACT
* * * *
1259012 ACAC- A-ACT ATAACGT ATA-T A-AC- ATAAT AAACTAT ATACT AAACTAT
1 ATACT ATACT AT-AC-T ATACT ATACT ATACT ATAC--T ATACT ATAC--T
* * * * *
1259058 ATACT AGTACC ATACTAT ATACT ATAAT ATATT ATACT GTACT GTACT
1 ATACT A-TACT ATAC--T ATACT ATACT ATACT ATACT ATACT ATACT
* * * *
1259106 ATATT ACACT ATACT GGTACT ATACT ATACT GGTACT ATACT ATACT ATTACT
1 ATACT ATACT ATACT -ATACT ATACT ATACT -ATACT ATACT ATACT A-TACT
*
1259159 ATACT ATACC AGTACT ATACT ATACT ATACT ATACT ATACT ATACT ATACT
1 ATACT ATACT A-TACT ATACT ATACT ATACT ATACT ATACT ATACT ATACT
1259210 ATACT ATACT AT
1 ATACT ATACT AT
1259222 GGTCCAAACG
Statistics
Matches: 321, Mismatches: 49, Indels: 62
0.74 0.11 0.14
Matches are distributed among these distances:
3 4 0.01
4 12 0.04
5 257 0.80
6 29 0.09
7 18 0.06
8 1 0.00
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.36
Consensus pattern (5 bp):
ATACT
Found at i:1259055 original size:12 final size:12
Alignment explanation
Indices: 1259038--1259063 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1259028 TATAACATAA
1259038 TAAACTATATAC
1 TAAACTATATAC
1259050 TAAACTATATAC
1 TAAACTATATAC
1259062 TA
1 TA
1259064 GTACCATACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
TAAACTATATAC
Found at i:1259393 original size:16 final size:17
Alignment explanation
Indices: 1259372--1259403 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1259362 TGGCAAATTT
1259372 TTTGAG-AAATCTCAGA
1 TTTGAGAAAATCTCAGA
1259388 TTTGAGAAAATCTCAG
1 TTTGAGAAAATCTCAG
1259404 CGTTGGTGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (17 bp):
TTTGAGAAAATCTCAGA
Found at i:1259596 original size:40 final size:40
Alignment explanation
Indices: 1259541--1259616 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
1259531 TGAAAAAATA
1259541 GCTTCATATGAAAAAGAACCGCTTATAGATGTACATACAT
1 GCTTCATATGAAAAAGAACCGCTTATAGATGTACATACAT
*
1259581 GCTTCATATGAAAAAGAACCGCTTATAGATTTACAT
1 GCTTCATATGAAAAAGAACCGCTTATAGATGTACAT
1259617 GCATTGATTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.29
Consensus pattern (40 bp):
GCTTCATATGAAAAAGAACCGCTTATAGATGTACATACAT
Found at i:1268695 original size:30 final size:30
Alignment explanation
Indices: 1268661--1268785 Score: 196
Period size: 30 Copynumber: 4.2 Consensus size: 30
1268651 TTTCACTTGT
* * * *
1268661 GGTGCTTTCTGTCCCACATGAGTACTTGCA
1 GGTGCTTTTTGTACTACATGAGTACTAGCA
* *
1268691 GGTGCTTTTTGTACTAGATGAGCACTAGCA
1 GGTGCTTTTTGTACTACATGAGTACTAGCA
1268721 GGTGCTTTTTGTACTACATGAGTACTAGCA
1 GGTGCTTTTTGTACTACATGAGTACTAGCA
1268751 GGTGCTTTTTGTACTACATGAGTACTAGCA
1 GGTGCTTTTTGTACTACATGAGTACTAGCA
1268781 GGTGC
1 GGTGC
1268786 CTGAATAACT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 87 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (30 bp):
GGTGCTTTTTGTACTACATGAGTACTAGCA
Found at i:1279550 original size:200 final size:200
Alignment explanation
Indices: 1279207--1279607 Score: 802
Period size: 200 Copynumber: 2.0 Consensus size: 200
1279197 GCTCTGAGAG
1279207 ATAAAAAAAAAAGCACCACAAATATTTGTATTTCAAAAACAACATGATATGCATTGCCACACCCT
1 ATAAAAAAAAAAGCACCACAAATATTTGTATTTCAAAAACAACATGATATGCATTGCCACACCCT
1279272 ACCACAAGACAGTAAAAATAGGATTCCCTGCAATATAGAGACAGTCACAGCTATCACTTTAATCC
66 ACCACAAGACAGTAAAAATAGGATTCCCTGCAATATAGAGACAGTCACAGCTATCACTTTAATCC
1279337 TAAAAAACTAAATCAATCACAAACAGTACACACATTCTTTAGATTTAAACTGAATTAAGGTACTA
131 TAAAAAACTAAATCAATCACAAACAGTACACACATTCTTTAGATTTAAACTGAATTAAGGTACTA
1279402 AAACC
196 AAACC
1279407 ATAAAAAAAAAAGCACCACAAATATTTGTATTTCAAAAACAACATGATATGCATTGCCACACCCT
1 ATAAAAAAAAAAGCACCACAAATATTTGTATTTCAAAAACAACATGATATGCATTGCCACACCCT
1279472 ACCACAAGACAGTAAAAATAGGATTCCCTGCAATATAGAGACAGTCACAGCTATCACTTTAATCC
66 ACCACAAGACAGTAAAAATAGGATTCCCTGCAATATAGAGACAGTCACAGCTATCACTTTAATCC
1279537 TAAAAAACTAAATCAATCACAAACAGTACACACATTCTTTAGATTTAAACTGAATTAAGGTACTA
131 TAAAAAACTAAATCAATCACAAACAGTACACACATTCTTTAGATTTAAACTGAATTAAGGTACTA
1279602 AAACC
196 AAACC
1279607 A
1 A
1279608 CCATAGCCAT
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
200 201 1.00
ACGTcount: A:0.46, C:0.21, G:0.09, T:0.23
Consensus pattern (200 bp):
ATAAAAAAAAAAGCACCACAAATATTTGTATTTCAAAAACAACATGATATGCATTGCCACACCCT
ACCACAAGACAGTAAAAATAGGATTCCCTGCAATATAGAGACAGTCACAGCTATCACTTTAATCC
TAAAAAACTAAATCAATCACAAACAGTACACACATTCTTTAGATTTAAACTGAATTAAGGTACTA
AAACC
Found at i:1281494 original size:2 final size:2
Alignment explanation
Indices: 1281487--1281533 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1281477 GGATGATTGA
1281487 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
1281529 AG AG A
1 AG AG A
1281534 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1287934 original size:2 final size:2
Alignment explanation
Indices: 1287927--1287971 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1287917 NNNNNNNNNN
1287927 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
1287969 AG A
1 AG A
1287972 TGTACACATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1292582 original size:35 final size:35
Alignment explanation
Indices: 1292536--1292607 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
1292526 GTATTCCATA
1292536 AACAATGAATTCCTAATCAGCATGACAAAGTAAAG
1 AACAATGAATTCCTAATCAGCATGACAAAGTAAAG
*
1292571 AACAATGAATTCCTAATTAGCATGACAAAGTAAAG
1 AACAATGAATTCCTAATCAGCATGACAAAGTAAAG
1292606 AA
1 AA
1292608 ATCAAAGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.50, C:0.15, G:0.14, T:0.21
Consensus pattern (35 bp):
AACAATGAATTCCTAATCAGCATGACAAAGTAAAG
Found at i:1296860 original size:26 final size:26
Alignment explanation
Indices: 1296824--1296877 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
1296814 AATTGTGGTT
1296824 TACTCTTGTAAAGCAAATCAGTGAAA
1 TACTCTTGTAAAGCAAATCAGTGAAA
*
1296850 TACTCTTGTAAATCAAATCAGTGAAA
1 TACTCTTGTAAAGCAAATCAGTGAAA
1296876 TA
1 TA
1296878 TTGGCATCGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.30
Consensus pattern (26 bp):
TACTCTTGTAAAGCAAATCAGTGAAA
Found at i:1300429 original size:10 final size:10
Alignment explanation
Indices: 1300414--1300483 Score: 113
Period size: 10 Copynumber: 6.8 Consensus size: 10
1300404 ATTTTTGTCA
1300414 TTGGGGTTCC
1 TTGGGGTTCC
1300424 TTGGGGTATCC
1 TTGGGGT-TCC
*
1300435 TTGAGGTTCC
1 TTGGGGTTCC
1300445 TTGGGGTTCC
1 TTGGGGTTCC
1300455 TTGGGGTTTCC
1 TTGGGG-TTCC
1300466 TTGGGGTTCC
1 TTGGGGTTCC
1300476 TTGGGGTT
1 TTGGGGTT
1300484 AAAAGACGCA
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
10 37 0.66
11 19 0.34
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (10 bp):
TTGGGGTTCC
Found at i:1300444 original size:21 final size:20
Alignment explanation
Indices: 1300414--1300483 Score: 113
Period size: 21 Copynumber: 3.4 Consensus size: 20
1300404 ATTTTTGTCA
1300414 TTGGGGTTCCTTGGGGTATCC
1 TTGGGGTTCCTTGGGGT-TCC
*
1300435 TTGAGGTTCCTTGGGGTTCC
1 TTGGGGTTCCTTGGGGTTCC
1300455 TTGGGGTTTCCTTGGGGTTCC
1 TTGGGG-TTCCTTGGGGTTCC
1300476 TTGGGGTT
1 TTGGGGTT
1300484 AAAAGACGCA
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
20 10 0.22
21 36 0.78
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (20 bp):
TTGGGGTTCCTTGGGGTTCC
Found at i:1300452 original size:31 final size:31
Alignment explanation
Indices: 1300414--1300483 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
1300404 ATTTTTGTCA
1300414 TTGGGGTTCCTTGGGGTATCCTTGAGGTTCC
1 TTGGGGTTCCTTGGGGTATCCTTGAGGTTCC
* *
1300445 TTGGGGTTCCTTGGGGTTTCCTTGGGGTTCC
1 TTGGGGTTCCTTGGGGTATCCTTGAGGTTCC
1300476 TTGGGGTT
1 TTGGGGTT
1300484 AAAAGACGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.03, C:0.17, G:0.39, T:0.41
Consensus pattern (31 bp):
TTGGGGTTCCTTGGGGTATCCTTGAGGTTCC
Found at i:1313758 original size:88 final size:88
Alignment explanation
Indices: 1313609--1313784 Score: 334
Period size: 88 Copynumber: 2.0 Consensus size: 88
1313599 CTCACTATAA
*
1313609 CCTCTGAAGTCCACATTTCATTTCATATCATTAGATACAGTTTCTTACAGCAAGTGTATAATCAG
1 CCTCTGAAGTCCACATTTCATTTCATATCATTAGATACAGTTTCTTACAGCAAGTATATAATCAG
1313674 CTGAAATAATTCTGCATGGTCCT
66 CTGAAATAATTCTGCATGGTCCT
*
1313697 CCTCTGAAGTCCACATTTCATTTCATATCATTAGATACAGTTTCTTACAGCATGTATATAATCAG
1 CCTCTGAAGTCCACATTTCATTTCATATCATTAGATACAGTTTCTTACAGCAAGTATATAATCAG
1313762 CTGAAATAATTCTGCATGGTCCT
66 CTGAAATAATTCTGCATGGTCCT
1313785 TCATTTGGGA
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.36
Consensus pattern (88 bp):
CCTCTGAAGTCCACATTTCATTTCATATCATTAGATACAGTTTCTTACAGCAAGTATATAATCAG
CTGAAATAATTCTGCATGGTCCT
Found at i:1317538 original size:12 final size:12
Alignment explanation
Indices: 1317521--1317545 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1317511 AGGCTGTTTT
1317521 TCCATTCCTTCA
1 TCCATTCCTTCA
1317533 TCCATTCCTTCA
1 TCCATTCCTTCA
1317545 T
1 T
1317546 TCTTACAGGT
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:0.16, C:0.40, G:0.00, T:0.44
Consensus pattern (12 bp):
TCCATTCCTTCA
Found at i:1319359 original size:26 final size:26
Alignment explanation
Indices: 1319277--1319978 Score: 746
Period size: 26 Copynumber: 27.3 Consensus size: 26
1319267 ATATTACAAA
*
1319277 ATTACAAGTTTACGGTCTTAC-AACC
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319302 AATACAAGTTTACA--CTCACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* * * *
1319326 AATCCAAGTTTGCAATCTT-CTAAACC
1 ATTACAAGTTTACAGTCTTAC-AAACC
* *
1319352 ATTACAAGTTTAAAGTCTTCCAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* **
1319378 ATTACAGGTTTTTAGTCTTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
*
1319404 ATTACAGGTTTACAGTCTTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319430 ATCACAGGTTTACAGTCTTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
*
1319456 ATTACAGGTTTACAGTCTTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
1319482 ATTAC-AGATTTAC--TCTTACAAACC
1 ATTACAAG-TTTACAGTCTTACAAACC
* * * * *
1319506 A-AATGAA-TTAACAATTTTACAAACC
1 ATTA-CAAGTTTACAGTCTTACAAACC
* *
1319531 AATACAAGTTT-CA-TCTTACAAACT
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319555 AATACAAGTTTACAGTCTTATAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
1319581 ATTACAAGTTTACAGTCTTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
*
1319607 ATTACAAGTTTACAGTCTTACAAACT
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319633 AATACAAGTTTACAGTCTTACAAACT
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319659 AATACAAGTTTACAGTCCTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319685 TTTACAAGTTTACAGTCTTACAAACT
1 ATTACAAGTTTACAGTCTTACAAACC
* * **
1319711 AATACAAGGTTACAGTCCCACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319737 TTTACAAGTTTACAGTCTTATAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* **
1319763 ATTGCAAGTTTACAGTCCCACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
**
1319789 AACACAAGTTTACAGTCTTACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* * *
1319815 AATGCAAGTTTACAGTCTCACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319841 -TATACAAGTTTATAGTCTTACAAACT
1 AT-TACAAGTTTACAGTCTTACAAACC
* * *
1319867 AATACAATTTTACAGTCTCACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* * *
1319893 TTTACAAGTTTACAGTCTTATAAACT
1 ATTACAAGTTTACAGTCTTACAAACC
* * *
1319919 AATACAATTTTACAGTCTCACAAACC
1 ATTACAAGTTTACAGTCTTACAAACC
* *
1319945 TTTACATGTTTACAGTCTTACAAA-C
1 ATTACAAGTTTACAGTCTTACAAACC
1319970 ATTACAAGT
1 ATTACAAGT
1319979 ATCTTACAAA
Statistics
Matches: 566, Mismatches: 95, Indels: 32
0.82 0.14 0.05
Matches are distributed among these distances:
23 9 0.02
24 48 0.08
25 40 0.07
26 468 0.83
27 1 0.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.30
Consensus pattern (26 bp):
ATTACAAGTTTACAGTCTTACAAACC
Found at i:1319619 original size:8 final size:9
Alignment explanation
Indices: 1319582--1319707 Score: 51
Period size: 8 Copynumber: 14.7 Consensus size: 9
1319572 TTATAAACCA
1319582 TTACAAGT-
1 TTACAAGTC
1319590 TTAC-AGTC
1 TTACAAGTC
**
1319598 TTACAAACC
1 TTACAAGTC
1319607 ATTACAAGT-
1 -TTACAAGTC
1319616 TTAC-AGTC
1 TTACAAGTC
*
1319624 TTACAA-AC
1 TTACAAGTC
1319632 TAATACAAGT-
1 T--TACAAGTC
1319642 TTAC-AGTC
1 TTACAAGTC
*
1319650 TTACAA-AC
1 TTACAAGTC
1319658 TAATACAAGT-
1 T--TACAAGTC
1319668 TTAC-AGTC
1 TTACAAGTC
* **
1319676 CTACAAACC
1 TTACAAGTC
1319685 TTTACAAGT-
1 -TTACAAGTC
1319694 TTAC-AGTC
1 TTACAAGTC
1319702 TTACAA
1 TTACAA
1319708 ACTAATACAA
Statistics
Matches: 86, Mismatches: 14, Indels: 35
0.64 0.10 0.26
Matches are distributed among these distances:
7 15 0.17
8 41 0.48
9 7 0.08
10 23 0.27
ACGTcount: A:0.39, C:0.21, G:0.08, T:0.32
Consensus pattern (9 bp):
TTACAAGTC
Found at i:1320215 original size:17 final size:16
Alignment explanation
Indices: 1320190--1320224 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1320180 CTGACGTGAG
1320190 ACCAGTTCTCGCCGAGT
1 ACCAGTTCTCGCC-AGT
*
1320207 ACCATTTCTCGCCAGT
1 ACCAGTTCTCGCCAGT
1320223 AC
1 AC
1320225 ATTGTGACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.20, C:0.37, G:0.17, T:0.26
Consensus pattern (16 bp):
ACCAGTTCTCGCCAGT
Found at i:1332591 original size:18 final size:18
Alignment explanation
Indices: 1332568--1332607 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
1332558 TTCTGTAACA
*
1332568 TGTTCTGAGTTTGTTGCG
1 TGTTCTGAGTTTGTTGCC
1332586 TGTTCTGAGTTTGTTGCC
1 TGTTCTGAGTTTGTTGCC
1332604 TGTT
1 TGTT
1332608 GTGAATTGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.12, G:0.30, T:0.53
Consensus pattern (18 bp):
TGTTCTGAGTTTGTTGCC
Found at i:1361683 original size:168 final size:165
Alignment explanation
Indices: 1361462--1362369 Score: 1042
Period size: 168 Copynumber: 5.4 Consensus size: 165
1361452 AAGGAGATTG
* * ** ** * * *
1361462 TGGATATCATAAACCATGTATTCAGTTTTTTGCCCACATGTGTGGGGGTAGAGAAGAAGATTTTT
1 TGGACATCAT-AACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTT
* * * *
1361527 AAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCACCCTTGAGCCTGAACACCTAACA
65 -AAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACC
* *
1361592 AAGGGGTCATGGATTTCACAATTTTAGTAGAGGCCATCA
129 CAGGGGTCATGAATTTCACAATTTT-GTAGAGGCC-TCA
* ** ** * *
1361631 TGGACATCATAACCATGTATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTA
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTTA
* *
1361696 AGATTTAAAACAGTTTTACTATATGGCCATATTGCATGGCCCCACCCTAGAGCCTGAACACCTAA
66 AGATTTAAAACAGTTTTACTATATGGCCATA-T---TGGCCCCACCCTAGAGCCTGAACCCCTGA
**
1361761 CAAAGGGGTCATGAATTTCACAATTTTGATAGAGGGCCTCA
127 CCCAGGGGTCATGAATTTCACAATTTTG-TAGA-GGCCTCA
* *
1361802 TGGACATCATAACCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTTT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGA-TTTTT
* * *
1361867 AAGATTTAAAACAGTTTTACTATATGGTCACATTGGCCCCACCCTAGAGCCTTAACCCCTGACCC
65 AAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCC
1361932 AGGGGTCATGAATTTCACAATTTTGATAGAGGGCCTCA
130 AGGGGTCATGAATTTCACAATTTTG-TAGA-GGCCTCA
* * * *
1361970 TGGACATTATAATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTT-T
* * * * * *
1362035 AAGATTTAATACATTTTTACTATTTAGCCATATTGGCCCCACCTTAGATCCTGAACCCCTGACCC
65 AAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCC
* * *
1362100 AGGGGTCATAAATTTCACAATTTAGGTAGAGGGCTTCA
130 AGGGGTCATGAATTTCACAATTT-TGTAGA-GGCCTCA
* * * * *
1362138 TGGACATCATAATCATGCATTTAGTTTTTAACAAATATATATGGTAGTAAAGAAGAAGATTTTCT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTT-T
* * * *
1362203 AAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCACCCTCGAGCCAGAACCCCTGACCC
65 AAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCC
* * * *
1362268 TGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTCA
130 AGGGGTCATGAATTTCACAATTTT-GTAGA-GGCCTCA
** * ** ** ***
1362306 TGGACATCATAACCATGCAACCGGTTTTTTCCTCACATGCGTGGGAGTAGAGAAGAAGATTTTT
1 TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTT
1362370 GAAAATTTGG
Statistics
Matches: 667, Mismatches: 62, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
167 37 0.06
168 468 0.70
169 10 0.01
170 1 0.00
171 112 0.17
172 39 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (165 bp):
TGGACATCATAACCATGCATTCAGTTTTTAACAAACATATATGGGAGTAGAGAAGAAGATTTTTA
AGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCACCCTAGAGCCTGAACCCCTGACCCA
GGGGTCATGAATTTCACAATTTTGTAGAGGCCTCA
Found at i:1361858 original size:339 final size:332
Alignment explanation
Indices: 1361504--1362369 Score: 1147
Period size: 336 Copynumber: 2.6 Consensus size: 332
1361494 CCCACATGTG
*
1361504 TGGGGGTAGAGAAGAAGATTTTTAAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTTT-AAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCA
* * * ** *
1361569 CCCTTGAGCCTGAACACCTAACAAAGGGGTCATGGATTTCACAATTTTAGTAGAGGCCATCATGG
65 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTT-GTAGAGGCC-TCATGG
* *
1361634 ACATCATAACCATGTATTCAGTTTTTTGCTCACATGTGTGGGAGTAGAGAAGAAGATTTTTAAGA
128 ACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTTTAAGA
*
1361699 TTTAAAACAGTTTTACTATATGGCCATATTGCATGGCCCCACCCTAGAGCCTGAACACCTAACAA
193 TTTAAAACAGTTTTACTATATAGCCATA-T---TGGCCCCACCCTAGAGCCTGAACACCTAACAA
* *
1361764 AGGGGTCATGAATTTCACAATTTTGATAGAGGGCCTCATGGACATCATAACCATGCATTTAGTTT
254 AGGGGTCATAAATTTCACAATTTAGATAGAGGGCCTCATGGACATCATAACCATGCATTTAGTTT
1361829 TTAACAAATATATA
319 TTAACAAATATATA
* *
1361843 TGGGAGTAGAGAAGAAGATTTTTTAAGATTTAAAACAGTTTTACTATATGGTCACATTGGCCCCA
1 TGGGAGTAGAGAAGAAGA-TTTTTAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCA
*
1361908 CCCTAGAGCCTTAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGATAGAGGGCCTCATGG
65 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTG-TAGA-GGCCTCATGG
* * * * ** * * *
1361973 ACATTATAATCATGCATTTAGTTTTTAACAAATATATATGGGAGTAGAGAAGAAGATTTTCTAAG
128 ACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTT-TAAG
* * * * * * * **
1362038 ATTTAATACATTTTTACTATTTAGCCATATTGGCCCCACCTTAGATCCTGAACCCCTGACCCAGG
192 ATTTAAAACAGTTTTACTATATAGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAACAAAGG
* * *
1362103 GGTCATAAATTTCACAATTTAGGTAGAGGGCTTCATGGACATCATAATCATGCATTTAGTTTTTA
257 GGTCATAAATTTCACAATTTAGATAGAGGGCCTCATGGACATCATAACCATGCATTTAGTTTTTA
1362168 ACAAATATATA
322 ACAAATATATA
* * * *
1362179 TGGTAGTAAAGAAGAAGATTTTCTAAGATTTAATACATTTTTACTATATGGCCATATTGGCCCCA
1 TGGGAGTAGAGAAGAAGATTTT-TAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCA
* * * * * *
1362244 CCCTCGAGCCAGAACCCCTGACCCTGGGGCCATAAATTTCACAATTTTGGTAGAGGGCTTCATGG
65 CCCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTT-GTAGA-GGCCTCATGG
** * * *
1362309 ACATCATAACCATGCAACCGGTTTTTTCCTCACATGCGTGGGAGTAGAGAAGAAGATTTTT
128 ACATCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTTT
1362370 GAAAATTTGG
Statistics
Matches: 458, Mismatches: 63, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
335 5 0.01
336 256 0.56
337 1 0.00
338 1 0.00
339 157 0.34
340 38 0.08
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (332 bp):
TGGGAGTAGAGAAGAAGATTTTTAAGATTTAAAACAGTTTTACTATATGGCCATATTGGCCCCAC
CCTAGAGCCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGTAGAGGCCTCATGGACA
TCATAACCATGCATTCAGTTTTTTACTCACATGTGTGGGAGTAGAGAAGAAGATTTTTAAGATTT
AAAACAGTTTTACTATATAGCCATATTGGCCCCACCCTAGAGCCTGAACACCTAACAAAGGGGTC
ATAAATTTCACAATTTAGATAGAGGGCCTCATGGACATCATAACCATGCATTTAGTTTTTAACAA
ATATATA
Found at i:1362549 original size:7 final size:7
Alignment explanation
Indices: 1362539--1362570 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1362529 AAAATTGTTA
1362539 ACGCACG
1 ACGCACG
1362546 ACGCACG
1 ACGCACG
1362553 ACGCACAG
1 ACGCAC-G
1362561 ACGCACG
1 ACGCACG
1362568 ACG
1 ACG
1362571 ACGGACGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.31, C:0.41, G:0.28, T:0.00
Consensus pattern (7 bp):
ACGCACG
Found at i:1362565 original size:15 final size:14
Alignment explanation
Indices: 1362539--1362570 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
1362529 AAAATTGTTA
1362539 ACGCACGACGCACG
1 ACGCACGACGCACG
1362553 ACGCACAGACGCACG
1 ACGCAC-GACGCACG
1362568 ACG
1 ACG
1362571 ACGGACGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.31, C:0.41, G:0.28, T:0.00
Consensus pattern (14 bp):
ACGCACGACGCACG
Found at i:1364741 original size:22 final size:20
Alignment explanation
Indices: 1364713--1364756 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1364703 TTCACAAGTC
*
1364713 ATGCAGAGAGATATAAAAGAAA
1 ATGCAGA-AAATATAAAA-AAA
1364735 ATGCAGAAAATATAAAAAAA
1 ATGCAGAAAATATAAAAAAA
1364755 AT
1 AT
1364757 CATGAATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.64, C:0.05, G:0.16, T:0.16
Consensus pattern (20 bp):
ATGCAGAAAATATAAAAAAA
Found at i:1370709 original size:2 final size:2
Alignment explanation
Indices: 1370702--1370730 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1370692 AAAATTTAGC
1370702 AG 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 AG A
1370731 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1378050 original size:166 final size:166
Alignment explanation
Indices: 1377772--1378698 Score: 1303
Period size: 166 Copynumber: 5.6 Consensus size: 166
1377762 AAAGAATCAT
* ** *
1377772 CTGGCTGATTAGTTTCT--G-AGAAGATTTTCAAAGATTTACCCTATATATTCCTTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
* * * *
1377834 TTGACCCCCCCCATTGTGGCCCCACCCTA-CCCCTGGGGATCATTATTTTCACAACTTTGAATCT
66 TCGA--TCCCCCATTGTGGCCCCACCCTACCCCCAGGGG-TCATGATTTTCACAACTTTGAATCT
*
1377898 ACACTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTC
128 ACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
*** * * * * *
1377937 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGAAAAACTCTGTTTATTCCTATGTAAAACA
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
* * *
1378002 TCGA-CCTCCCATTGTGGCCCAAACCTACCCCCAGGGGTCATGATTTTCACAAATTTGAATCTAC
66 TCGATCC-CCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTAC
*
1378066 ACTACCTGAGTATGCTTCCACACAAGTTTCAGCTTTC
130 ACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * *
1378103 CTGGCTAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATAATCATATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
*
1378168 TCGATCCCCCATTGTGGCCCCAACCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACA
66 TCGATCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACA
*
1378233 CTACCTGAGGATGCTTCCACACAAGTTCCAGCTTTGC
131 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTT-C
1378270 C-GGC-GAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAAC
1 CTGGCTG-ATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAAC
* * *
1378333 TTCGATCCCCCATTGTGGCCCCACCCTACCCCCGGGGGTCATGATTTTCACAACTTTAAAATTTA
65 TTCGATCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTT-GAATCTA
* *
1378398 CACTACCTGAGGATGCATCCACACAAGTGTCAGCTTTC
129 CACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * *
1378436 CTGTCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACG
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
* * * * *
1378501 TCGATCCCCTATTGTGGCCCCACCCTACCCTCGGGGGTCATGATTTTCACAAATTTGAATCTTCA
66 TCGATCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACA
* * *
1378566 CTACCTAAGGATGCATCCACACAAGTGTCAGCTTTC
131 CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
* * * * *
1378602 CTGGCCGATTAGTTTCTGAGAAGAAGATTTTTAAAGAATTACTTTTTATATTCATATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
1378667 TCGA-CCCTCCATTGTGGCCCCACCCTACCCCC
66 TCGATCCC-CCATTGTGGCCCCACCCTACCCCC
1378699 NNNNNNNNNN
Statistics
Matches: 687, Mismatches: 63, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
165 22 0.03
166 464 0.68
167 163 0.24
168 38 0.06
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (166 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
TCGATCCCCCATTGTGGCCCCACCCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACA
CTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTC
Found at i:1378570 original size:333 final size:328
Alignment explanation
Indices: 1377772--1378698 Score: 1304
Period size: 333 Copynumber: 2.8 Consensus size: 328
1377762 AAAGAATCAT
* ** *
1377772 CTGGCTGATTAGTTTCT--G-AGAAGATTTTCAAAGATTTACCCTATATATTCCTTTGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
* * * *
1377834 TTGACCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATTATTTTCACAACTTTGAATCTA
66 TCGA--TCCCCCATTGTGGCCCCACCCTACCCC-GGGGGTCATGATTTTCACAACTTTGAATCTA
*
1377899 CACTACCTGAGGATGCTTTCACACAAGTTTCAGCTTTCCTGGCTGATTAGTTTCTGAGAAGAAGA
128 CACTACCTGAGGATGCTTCCACACAAG-TTCAGCTTTCCTGGC-GATTAGTTTCTGAGAAGAAGA
** * * * * * *
1377964 TTTTTAAAGAAAAACTCTGTTTATTCCTATGTAAAACATCGACCTCCCATTGTGGCCCAAACCTA
191 TTTTTAAAGAATTACTCTATATATTCCTATGTTAAACTTCGACC-CCCATTGTGGCCCCACCCTA
* * * *
1378029 CCCCCAGGGGTCATGATTTTCACAAATTTGAATCTACACTACCTGAGTATGCTTCCACACAAGTT
255 CCCCCAGGGGTCATGATTTTCACAAATTTAAATCTACACTACCTGAGGATGCATCCACACAAGTG
1378094 TCAGCTTTC
320 TCAGCTTTC
* * *
1378103 CTGGCTAATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATAATCATATGTTAAACT
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
* *
1378168 TCGATCCCCCATTGTGGCCCCAACCTACCCCCAGGGGTCATGATTTTCACAACTTTGAATCTACA
66 TCGATCCCCCATTGTGGCCCCACCCTA-CCCCGGGGGTCATGATTTTCACAACTTTGAATCTACA
1378233 CTACCTGAGGATGCTTCCACACAAGTTCCAGCTTTGCC-GGCGAATTAGTTTCTGAGAAGAAGAT
130 CTACCTGAGGATGCTTCCACACAAGTT-CAGCTTT-CCTGGCG-ATTAGTTTCTGAGAAGAAGAT
* *
1378297 TTTTAAAGATTTACTGTATATATTCCTATGTTAAACTTCGATCCCCCATTGTGGCCCCACCCTAC
192 TTTTAAAGAATTACTCTATATATTCCTATGTTAAACTTCGA-CCCCCATTGTGGCCCCACCCTAC
* * *
1378362 CCCCGGGGGTCATGATTTTCACAACTTTAAAATTTACACTACCTGAGGATGCATCCACACAAGTG
256 CCCCAGGGGTCATGATTTTCACAAATTT-AAATCTACACTACCTGAGGATGCATCCACACAAGTG
1378427 TCAGCTTTC
320 TCAGCTTTC
* * *
1378436 CTGTCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTAAAACG
1 CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
* * *
1378501 TCGATCCCCTATTGTGGCCCCACCCTACCCTCGGGGGTCATGATTTTCACAAATTTGAATCTTCA
66 TCGATCCCCCATTGTGGCCCCACCCTACCC-CGGGGGTCATGATTTTCACAACTTTGAATCTACA
* *
1378566 CTACCTAAGGATGCATCCACACAAGTGTCAGCTTTCCTGGCCGATTAGTTTCTGAGAAGAAGATT
130 CTACCTGAGGATGCTTCCACACAAGT-TCAGCTTTCCTGG-CGATTAGTTTCTGAGAAGAAGATT
* * *
1378631 TTTAAAGAATTACTTTTTATATTCATATGTTAAACTTCGACCCTCCATTGTGGCCCCACCCTACC
193 TTTAAAGAATTACTCTATATATTCCTATGTTAAACTTCGACCC-CCATTGTGGCCCCACCCTACC
1378696 CCC
257 CCC
1378699 NNNNNNNNNN
Statistics
Matches: 534, Mismatches: 48, Indels: 26
0.88 0.08 0.04
Matches are distributed among these distances:
331 19 0.04
332 192 0.36
333 279 0.52
334 44 0.08
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.33
Consensus pattern (328 bp):
CTGGCTGATTAGTTTCTGAGAAGAAGATTTTTAAAGATTTACTGTATATATTCCTATGTTAAACT
TCGATCCCCCATTGTGGCCCCACCCTACCCCGGGGGTCATGATTTTCACAACTTTGAATCTACAC
TACCTGAGGATGCTTCCACACAAGTTCAGCTTTCCTGGCGATTAGTTTCTGAGAAGAAGATTTTT
AAAGAATTACTCTATATATTCCTATGTTAAACTTCGACCCCCATTGTGGCCCCACCCTACCCCCA
GGGGTCATGATTTTCACAAATTTAAATCTACACTACCTGAGGATGCATCCACACAAGTGTCAGCT
TTC
Found at i:1385895 original size:18 final size:18
Alignment explanation
Indices: 1385869--1385910 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1385859 AAACCACTTC
*
1385869 ATGTTGGTAAATAAAGCT
1 ATGTAGGTAAATAAAGCT
*
1385887 ATGTAGGTAAATCAAGCT
1 ATGTAGGTAAATAAAGCT
*
1385905 ACGTAG
1 ATGTAG
1385911 CTTAATCTAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.24, T:0.29
Consensus pattern (18 bp):
ATGTAGGTAAATAAAGCT
Found at i:1399365 original size:30 final size:30
Alignment explanation
Indices: 1399331--1399391 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
1399321 ATTTTGAACT
*
1399331 GCCGGTCAATAGACTGGGATTTATTAGACC
1 GCCGGTCAATAGACTGGGATCTATTAGACC
* *
1399361 GCCGGTCAATAGACTGTGATCTATTGGACC
1 GCCGGTCAATAGACTGGGATCTATTAGACC
1399391 G
1 G
1399392 GCAACATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (30 bp):
GCCGGTCAATAGACTGGGATCTATTAGACC
Found at i:1399972 original size:159 final size:158
Alignment explanation
Indices: 1399683--1400000 Score: 627
Period size: 159 Copynumber: 2.0 Consensus size: 158
1399673 AAAATCTTAG
1399683 TATAGTGCATAATGGCATGAAAACCATCTGCAATATGCAAATTGTAAACCCCGAAAACTAAAAAA
1 TATAGTGCATAATGGCATGAAAACCATCTGCAATATGCAAATTGTAAACCCCGAAAACTAAAAAA
1399748 GGAATTAGGTAATAAAACAATTATTTAATGCTTGAACAGTCAATAGAACAGAATTTTTTTCCCTT
66 GGAATTAGGTAATAAAACAATTATTTAATGCTTGAACAGTCAATAGAACAGAATTTTTTTCCCTT
1399813 GGTGCAGGGAACAGCTCAGTATGATCTA
131 GGTGCAGGGAACAGCTCAGTATGATCTA
1399841 NTATAGTGCATAATGGCATGAAAACCATCTGCAATATGCAAATTGTAAACCCCGAAAACTAAAAA
1 -TATAGTGCATAATGGCATGAAAACCATCTGCAATATGCAAATTGTAAACCCCGAAAACTAAAAA
1399906 AGGAATTAGGTAATAAAACAATTATTTAATGCTTGAACAGTCAATAGAACAGAATTTTTTTCCCT
65 AGGAATTAGGTAATAAAACAATTATTTAATGCTTGAACAGTCAATAGAACAGAATTTTTTTCCCT
1399971 TGGTGCAGGGAACAGCTCAGTATGATCTA
130 TGGTGCAGGGAACAGCTCAGTATGATCTA
1400000 T
1 T
1400001 TGCCCGAGGC
Statistics
Matches: 159, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
158 1 0.01
159 158 0.99
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.27
Consensus pattern (158 bp):
TATAGTGCATAATGGCATGAAAACCATCTGCAATATGCAAATTGTAAACCCCGAAAACTAAAAAA
GGAATTAGGTAATAAAACAATTATTTAATGCTTGAACAGTCAATAGAACAGAATTTTTTTCCCTT
GGTGCAGGGAACAGCTCAGTATGATCTA
Found at i:1402065 original size:2 final size:2
Alignment explanation
Indices: 1402053--1402093 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1402043 GCATTGCTGC
* * *
1402053 TG TG CG TG TG TG TG TG TG TG TG TG TA TG TA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1402094 CCATTTTAGC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.05, C:0.02, G:0.44, T:0.49
Consensus pattern (2 bp):
TG
Done.