Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold153
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3137677
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 499 characters in sequence are not A, C, G, or T
File 2 of 24
Found at i:190335 original size:165 final size:162
Alignment explanation
Indices: 190102--190500 Score: 434
Period size: 165 Copynumber: 2.4 Consensus size: 162
190092 AAATTATGGT
* *
190102 GTTTTCT-TCTTCGTAAATTTTTTTCGAGAAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATC
1 GTTTTCTATC-TCGTAAA-TTTTTT-GAGAAGATTTTTCTTGATTTTTAATTTTTTAAATTCATC
* * * *
190166 AAATATTAT-TTTTTAATTTATATTAAATCCA-TTTTCAAAAATTAATTCATTTTCATAAAATTT
63 AAATATT-TGTATTTAATTCATATTAAAT-CAGTATTAAAAAATTAATTCATTTTCAT-AAATTT
* * *
190229 TGA-ATTTTTCCTTGAAAT-TCTCTTATTTTCAAAAAATATA
125 T-ACATTTTT--TTGAAATCTC-CATATTTTCAAAAAACAGA
* *
190269 GTTTTTTA-CTCTGTAAATTTTTTGAGAGGATTTTTCTTGATTTTTAATTTTTTAAATTCATCAA
1 GTTTTCTATCTC-GTAAATTTTTTGAGAAGATTTTTCTTGATTTTTAATTTTTTAAATTCATCAA
* * *
190333 ATATTTGTATTTAATTCATATTAAATCAGTATTAAAAAATTAATTTATTTTCATGAGTTTTACAT
65 ATATTTGTATTTAATTCATATTAAATCAGTATTAAAAAATTAATTCATTTTCATAAATTTTACAT
* *
190398 TTTTTTTAAATCTCCATATTTTCAAAAAACCGA
130 TTTTTTGAAATCTCCATATTTTCAAAAAACAGA
* * * * * *
190431 GTTTTCTATCTCATAAATATTTTCGA-AACAATTTTTCTCGATTTTAAATTTTTTAAATTCATCT
1 GTTTTCTATCTCGTAAAT-TTTTTGAGAA-GATTTTTCTTGATTTTTAATTTTTTAAATTCATCA
190495 AATATT
64 AATATT
190501 GTTACAAAAC
Statistics
Matches: 199, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
162 34 0.17
163 49 0.25
164 14 0.07
165 82 0.41
166 8 0.04
167 12 0.06
ACGTcount: A:0.32, C:0.10, G:0.06, T:0.51
Consensus pattern (162 bp):
GTTTTCTATCTCGTAAATTTTTTGAGAAGATTTTTCTTGATTTTTAATTTTTTAAATTCATCAAA
TATTTGTATTTAATTCATATTAAATCAGTATTAAAAAATTAATTCATTTTCATAAATTTTACATT
TTTTTGAAATCTCCATATTTTCAAAAAACAGA
Found at i:193534 original size:154 final size:157
Alignment explanation
Indices: 193198--194327 Score: 637
Period size: 154 Copynumber: 7.3 Consensus size: 157
193188 TAAGTTCAAA
* * * ** *
193198 AAAATTAC-ATAAATGCCCCTAAGGG-ATACCTTCGACGTAGAAGTA-CTCGATACCCTTAAAGG
1 AAAATTACGA-AAATGCCCCTATGGGTATACCTTCGACGTAAAAGTATCCCGCCAACCTTAAAGG
* * * * * * *
193260 ACTTAAAAA-ATGTTATAAATGGGATGAGCCTGTCC-TAAATACCCACCTTC-GACATAAAAGTG
65 ACTTAAAAAGA-ATTATAACTGGGATGAACCTATCCTTAAATACCAACCTTCAG-CACAAAAGCG
* * * *
193322 GACTCGGTAACAACCTAAGACTTGATTCCAA
128 GACT-GGTGACAACCTAGGACTTGATTCTAG
* * *
193353 AAAATTACGAAAATACCCCAACGGGTATACCTTCGACGTAAAAGTATCCC-CCAACCTTAAAGGA
1 AAAATTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTATCCCGCCAACCTTAAAGGA
* * * * * *
193417 CTTAAAAAG-ACTAGAGA-TGAGATAAACCTATCC-TAAATACCCACCTTCAGTACAAAAGCGGA
66 CTTAAAAAGAATTATA-ACTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAAAGCGGA
*
193479 CTAGTGACAACCTAGGACTTGATTCTAG
130 CTGGTGACAACCTAGGACTTGATTCTAG
* * *
193507 AAAATTATGAAAATGCCCCTATGGGTATACCTT-GACGTAAAAGTATCCCGACAAACC-TAAAAG
1 AAAATTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTATCCCG-CCAACCTTAAAGG
* * * * * ** *
193570 ACATACAAAGAATTTTAACTGGGATGAACCTA-CCTTAAATATCAACTTTTGGCATAAAAGCGGA
65 ACTTAAAAAGAATTATAACTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAAAGCGGA
* ** * *
193634 CCCGGTGATGACCTAGGACTTAATTTTAG
130 -CTGGTGACAACCTAGGACTTGATTCTAG
* * *
193663 AGAATTACGAAAATGCCCCT-TGGGTATACCTT-GACGTAAAAGTATCCCGGCAACCCTAAAGGA
1 AAAATTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTATCCCGCCAACCTTAAAGGA
* * * * * *
193726 CTTCAAAAGAATTTTAACT-CGATGAACC-AACCTTAAATATCAACCTTCAGCATAAAAGCGGAC
66 CTTAAAAAGAATTATAACTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAAAGCGGAC
* *
193789 TCGATGATAACCTAGGACTTGATTCTAG
131 T-GGTGACAACCTAGGACTTGATTCTAG
* * * * *
193817 AAAATTACGAAAATGCCTCTA-GGGGATACTTTCGACGTAAAAGTA-CCTG--ATACTCCTAAAG
1 AAAATTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTATCCCGCCA-AC-CTTAAAG
* *** * * * * *
193878 GACTTAAAAA-AGATTTTAAAAAGGATGAACCTATCC-TAAATATCTACCTTCGGCATAAAAGTG
64 GACTTAAAAAGA-ATTATAACTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAAAGCG
** * * * *
193941 GACCCAGTAACAACCTAGGCCTT-AGTTATAA
128 GA-CTGGTGACAACCTAGGACTTGA-TTCTAG
* * * * * * ** *
193972 AAAATTACCAAAATGTCCCTA-GGGGATATCTTTGATGTAAAA--ATGCCCGATATTCC-TAAAG
1 AAAATTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTAT-CCCGCCA-ACCTTAAAG
* * * * * * * * * * **
194033 TACTTTAAAAGGATTTTAAAAATGATGGGGTGAATCTATCC-TATATACCCACCTTCGGCATGAA
64 GAC-TTAAAAAGA-ATT-ATAA--CTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAA
*** * * *
194097 AGCGGACCCAATGACAATCTAGGAC-TCAGTTCTAA
124 AGCGGA-CTGGTGACAACCTAGGACTTGA-TTCTAG
* ** * * ** * * *
194132 AAAATTATGAAAATATCCGTA-GAGG-ATACCTTCG-CTATAAAAGTA--CCGATACCCCTAAAC
1 AAAATTACGAAAATGCCCCTATG-GGTATACCTTCGAC-GTAAAAGTATCCCGCCAACCTTAAAG
* * ** * * * *
194192 GACTTAAAAAGGATTATAAATAAGATGAACCTATCC-TAAATACCCATCTTCGGCATAAAAGCGG
64 GACTTAAAAAGAATTATAACTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAAAGCGG
* *
194256 ACCCGGTGACAACCTAGGACTTGGCTT-T-G
129 A-CTGGTGACAACCTAGGACTT-GATTCTAG
* *
194285 AAAAGTTACGAAAATGCCCTTAAGGG-ATACCTTCGACGTAAAA
1 AAAA-TTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAA
194328 ATACTCGATA
Statistics
Matches: 782, Mismatches: 149, Indels: 89
0.77 0.15 0.09
Matches are distributed among these distances:
152 1 0.00
153 26 0.03
154 268 0.34
155 266 0.34
156 95 0.12
157 10 0.01
158 11 0.01
159 13 0.02
160 89 0.11
161 2 0.00
162 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (157 bp):
AAAATTACGAAAATGCCCCTATGGGTATACCTTCGACGTAAAAGTATCCCGCCAACCTTAAAGGA
CTTAAAAAGAATTATAACTGGGATGAACCTATCCTTAAATACCAACCTTCAGCACAAAAGCGGAC
TGGTGACAACCTAGGACTTGATTCTAG
Found at i:193785 original size:309 final size:310
Alignment explanation
Indices: 193198--194327 Score: 758
Period size: 309 Copynumber: 3.6 Consensus size: 310
193188 TAAGTTCAAA
* * * * * *
193198 AAAATTAC-ATAAATGCCCCTAAGGGATACCTTCGACGTAGAAGTACTCGA-TACCCTTAAAGGA
1 AAAATTACGA-AAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGACAAACC-TAAAAGA
* * ** * * * * * *
193261 CTTAAAAAATG-TTATAAATGGGATGAGCCTGTCCTAAATACCCACCTTCGACATAAAAGTGGAC
64 CATAAAAAA-GATTTTAAAAAGGATGAACCTATCCTAAATATCAACCTTCGGCATAAAAGCGGAC
* * ** * * ** * *
193325 TCGGTAACAACCTAAGACTTGATTCCAAAAAATTACGAAAATACCCCAACGGGTATACCTTCGAC
128 CCGGTGATGACCTAGGACTTAATTTTAGAGAATTACGAAAATACCCCAACGGGTATACCTTCGAC
* *
193390 GTAAAAGTATCCCCCAACCTTAAAGGACTTAAAAAGACTAGAGATGAGATAAACCTATCCTAAAT
193 GTAAAAGTATCCCCCAACCCTAAAGGACTTAAAAAGACTAGAGATGAGATAAACCTAACCTAAAT
* *
193455 ACCCACCTTCAGTACAAAAGCGGACTAG-TGACAACCTAGGACTTGATTCTAG
258 ACCAACCTTCAGCACAAAAGCGGACTAGATGACAACCTAGGACTTGATTCTAG
* *
193507 AAAATTATGAAAATGCCCCTATGGGTATACCTT-GACGTAAAAGTATCCCGACAAACCTAAAAGA
1 AAAATTACGAAAATGCCCCTA-GGGGATACCTTCGACGTAAAAGTA-CCCGACAAACCTAAAAGA
* *** * *
193571 CAT-ACAAAGAATTTTAACTGGGATGAACCTA-CCTTAAATATCAACTTTTGGCATAAAAGCGGA
64 CATAAAAAAG-ATTTTAAAAAGGATGAACCTATCC-TAAATATCAACCTTCGGCATAAAAGCGGA
* **
193634 CCCGGTGATGACCTAGGACTTAATTTTAGAGAATTACGAAAATGCCCC-TTGGGTATACCTT-GA
127 CCCGGTGATGACCTAGGACTTAATTTTAGAGAATTACGAAAATACCCCAACGGGTATACCTTCGA
* * * ** * *
193697 CGTAAAAGTATCCCGGCAACCCTAAAGGACTTCAAAAGAATTTTA-ACT-CGATGAACC-AACCT
192 CGTAAAAGTATCCC-CCAACCCTAAAGGACTTAAAAAG-ACTAGAGA-TGAGATAAACCTAACC-
* * * *
193759 TAAATATCAACCTTCAGCATAAAAGCGGACTCGATGATAACCTAGGACTTGATTCTAG
253 TAAATACCAACCTTCAGCACAAAAGCGGACTAGATGACAACCTAGGACTTGATTCTAG
* * * * ** * *
193817 AAAATTACGAAAATGCCTCTAGGGGATACTTTCGACGTAAAAGTACCTGATACTCCTAAAGGACT
1 AAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGACAAACCTAAAAGACA
* * *
193882 TAAAAAAGATTTTAAAAAGGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGACCCA
66 TAAAAAAGATTTTAAAAAGGATGAACCTATCCTAAATATCAACCTTCGGCATAAAAGCGGACCCG
* ** * * * * * * ** * * * * *
193947 GTAACAACCTAGGCCTTAGTTATAAAAAATTACCAAAATGTCCCTA-GGGGATATCTTTGATGTA
131 GTGATGACCTAGGACTTAATTTTAGAGAATTACGAAAATACCCCAACGGGTATACCTTCGACGTA
* * * * * * * * * * * *
194011 AAA--ATGCCCGATATTCCTAAAGTACTTTAAAAGGATTTTAAAAATGATGGGGTGAATCTATCC
196 AAAGTATCCCCCA-A-CCCTAAAGGAC-TTAAAAAGA--CT--AGA-GATGAGATAAACCTAACC
* * * ** * * * *
194074 TATATACCCACCTTCGGCATGAAAGCGGACCCA-ATGACAATCTAGGAC-TCAGTTCTAA
253 TAAATACCAACCTTCAGCACAAAAGCGGA-CTAGATGACAACCTAGGACTTGA-TTCTAG
* ** * * * * ** *
194132 AAAATTATGAAAATATCCGTAGAGGATACCTTCG-CTATAAAAGTA-CCGATACCCCTAAACGAC
1 AAAATTACGAAAATGCCCCTAGGGGATACCTTCGAC-GTAAAAGTACCCGACAAACCTAAAAGAC
* * * * * *
194195 TTAAAAAGGATTATAAATAA-GATGAACCTATCCTAAATACCCATCTTCGGCATAAAAGCGGACC
65 ATAAAAAAGATTTTAAA-AAGGATGAACCTATCCTAAATATCAACCTTCGGCATAAAAGCGGACC
** *** * * *
194259 CGGTGACAACCTAGGACTTGGCTTT-GAAAAGTTACGAAAATGCCCTTAA-GGG-ATACCTTCGA
129 CGGTGATGACCTAGGACTTAATTTTAGAGAA-TTACGAAAATACCC-CAACGGGTATACCTTCGA
194321 CGTAAAA
192 CGTAAAA
194328 ATACTCGATA
Statistics
Matches: 651, Mismatches: 136, Indels: 63
0.77 0.16 0.07
Matches are distributed among these distances:
307 1 0.00
308 25 0.04
309 225 0.35
310 177 0.27
311 5 0.01
313 5 0.01
314 119 0.18
315 90 0.14
316 4 0.01
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (310 bp):
AAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGACAAACCTAAAAGACA
TAAAAAAGATTTTAAAAAGGATGAACCTATCCTAAATATCAACCTTCGGCATAAAAGCGGACCCG
GTGATGACCTAGGACTTAATTTTAGAGAATTACGAAAATACCCCAACGGGTATACCTTCGACGTA
AAAGTATCCCCCAACCCTAAAGGACTTAAAAAGACTAGAGATGAGATAAACCTAACCTAAATACC
AACCTTCAGCACAAAAGCGGACTAGATGACAACCTAGGACTTGATTCTAG
Found at i:193956 original size:155 final size:153
Alignment explanation
Indices: 193198--194487 Score: 909
Period size: 155 Copynumber: 8.3 Consensus size: 153
193188 TAAGTTCAAA
* * *
193198 AAAATTAC-ATAAATGCCCCTAAGGGATACCTTCGACGTAGAAGTACTCGATACCCTTAAAGGAC
1 AAAATTACGA-AAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGATACCC-TAAAGGAC
** * * * * *
193262 TTAAAAA-ATGTTATAAATGGGATGAGCCTGTCCTAAATACCCACCTTCGACATAAAAGTGGACT
64 TTAAAAAGAT-TT-TAAAAAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
* * * * *
193326 CGGTAACAACCTAAGACTTGATTCCAA
127 CAGTGACAACCTAGGACTTGATTCTAG
* * * * *
193353 AAAATTACGAAAATACCCCAACGGGTATACCTTCGACGTAAAAGTATCCCCCA-ACCTTAAAGGA
1 AAAATTACGAAAATGCCCCTA-GGGGATACCTTCGACGTAAAAGTA--CCCGATACCCTAAAGGA
* * * * * * *
193417 CTTAAAAAGA--CTAGAGATGAGATAAACCTATCCTAAATACCCACCTTCAGTACAAAAGCGGA-
63 CTTAAAAAGATTTTA-AAAAG-GATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGAC
*
193479 CTAGTGACAACCTAGGACTTGATTCTAG
126 CCAGTGACAACCTAGGACTTGATTCTAG
* * * * *
193507 AAAATTATGAAAATGCCCCTATGGGTATACCTT-GACGTAAAAGTATCCCGACAAACCTAAAAGA
1 AAAATTACGAAAATGCCCCTA-GGGGATACCTTCGACGTAAAAGTA-CCCGA-TACCCTAAAGGA
* * *** * * * *
193571 CATACAAAGAATTTTAACTGGGATGAACCTA-CCTTAAATATCAACTTTTGGCATAAAAGCGGAC
63 CTTAAAAAG-ATTTTAAAAAGGATGAACCTATCC-TAAATACCCACCTTCGGCATAAAAGCGGAC
* ** * *
193635 CCGGTGATGACCTAGGACTTAATTTTAG
126 CCAGTGACAACCTAGGACTTGATTCTAG
* * *
193663 AGAATTACGAAAATGCCCCTTGGGTATACCTT-GACGTAAAAGTATCCCGGCA-ACCCTAAAGGA
1 AAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTA-CCC-G-ATACCCTAAAGGA
* *** * * * *
193726 CTTCAAAAGAATTTT-AACTCGATGAACC-AACCTTAAATATCAACCTTCAGCATAAAAGCGGAC
63 CTTAAAAAG-ATTTTAAAAAGGATGAACCTATCC-TAAATACCCACCTTCGGCATAAAAGCGGAC
* *
193789 TC-GATGATAACCTAGGACTTGATTCTAG
126 CCAG-TGACAACCTAGGACTTGATTCTAG
* * *
193817 AAAATTACGAAAATGCCTCTAGGGGATACTTTCGACGTAAAAGTACCTGATACTCCTAAAGGACT
1 AAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGATAC-CCTAAAGGACT
* * *
193882 TAAAAAAGATTTTAAAAAGGATGAACCTATCCTAAATATCTACCTTCGGCATAAAAGTGGACCCA
65 T-AAAAAGATTTTAAAAAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCCA
* * * *
193947 GTAACAACCTAGGCCTT-AGTTATAA
129 GTGACAACCTAGGACTTGA-TTCTAG
* * * * * * * * *
193972 AAAATTACCAAAATGTCCCTAGGGGATATCTTTGATGTAAAAATGCCCGATATTCCTAAAGTACT
1 AAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGATA-CCCTAAAGGAC-
* * * * *
194037 TTAAAAGGATTTTAAAAATGATGGGGTGAATCTATCCTATATACCCACCTTCGGCATGAAAGCGG
64 TTAAAAAGATTTT-AAAA--A--GGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGG
* * * *
194102 ACCCAATGACAATCTAGGAC-TCAGTTCTAA
124 ACCCAGTGACAACCTAGGACTTGA-TTCTAG
* ** * * * *
194132 AAAATTATGAAAATATCCGTAGAGGATACCTTCG-CTATAAAAGTA-CCGATACCCCTAAACGAC
1 AAAATTACGAAAATGCCCCTAGGGGATACCTTCGAC-GTAAAAGTACCCGATA-CCCTAAAGGAC
* *
194195 TTAAAAAGGATTATAAATAA-GATGAACCTATCCTAAATACCCATCTTCGGCATAAAAGCGGACC
64 TTAAAAA-GATTTTAAA-AAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACC
* *
194259 CGGTGACAACCTAGGACTTGGCTT-T-G
127 CAGTGACAACCTAGGACTT-GATTCTAG
* * * * * **
194285 AAAAGTTACGAAAATGCCCTTAAGGGATACCTTCGACGTAAAAATACTCGATAACCTGAGTGGA-
1 AAAA-TTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGATACCCT-AAAGGAC
* ** ** * * *
194349 TACTAAAAAGATTATGGATTGGATGAACTTATCCTAAATGA-CCACCTTCGACATAAAAGCGAAC
64 T--TAAAAAGATTTTAAAAAGGATGAACCTATCCTAAAT-ACCCACCTTCGGCATAAAAGCGGAC
* * * *
194413 GCAGTGACAACCTAGGA-GTCAGTTCGAG
126 CCAGTGACAACCTAGGACTTGA-TTCTAG
* * ** *
194441 AAAAATTACTG-AAATACCCTTAGAAGATACCTTTGACGTAAAAGTAC
1 -AAAATTAC-GAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTAC
194488 TAGATAGTTC
Statistics
Matches: 902, Mismatches: 181, Indels: 103
0.76 0.15 0.09
Matches are distributed among these distances:
152 5 0.01
153 23 0.03
154 269 0.30
155 335 0.37
156 132 0.15
157 13 0.01
158 13 0.01
159 21 0.02
160 91 0.10
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (153 bp):
AAAATTACGAAAATGCCCCTAGGGGATACCTTCGACGTAAAAGTACCCGATACCCTAAAGGACTT
AAAAAGATTTTAAAAAGGATGAACCTATCCTAAATACCCACCTTCGGCATAAAAGCGGACCCAGT
GACAACCTAGGACTTGATTCTAG
Found at i:196673 original size:167 final size:168
Alignment explanation
Indices: 196323--196755 Score: 415
Period size: 167 Copynumber: 2.6 Consensus size: 168
196313 GAGAGTTTTT
** * ** *
196323 TAACAATAT-TAGATGAATTTTAAAAATTTTAAACCAAGAGAAATCCTTTC-AAAAATATTTATG
1 TAACAATATATA-ATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCGAAAAA-ATTTACG
* * * * * * * * *
196386 AGGTAGAAAA-CTCGGT-TTTTCAAAA-ATAG-AGAGA-TTTAAAG-AAAATATTCAAAACTCAT
64 AAGAAGAAAATCTC-GTAATTTGAAAACA-AGAAGA-ATTTTAAGGAAAAAAATTAAAAATTTAT
* * * *
196445 AAAAATAAATTAAGTTTTCAAAACTGGTTTAATATGAATTAAA
126 GAAAATAAATTAAGTTTTAAAAACTGATTTAATATAAATTAAA
* ** *
196488 TTACAATATATAATGAATTTTAAAAATTAAAAATGAAGAAAAATGCC-CTC-AAAATAATTTACG
1 TAACAATATATAATGAATTTTAAAAATTAAAAACCAAGAAAAAT-CCTCCCGAAAA-AATTTACG
* * *
196551 GAGTAGAAAATTCTC-T-TTTTCGAAAACAAGAA-AATTTTAAGGAAAAAAATTAAAAATTTATG
64 AAGAAGAAAA-TCTCGTAATTT-GAAAACAAGAAGAATTTTAAGGAAAAAAATTAAAAATTTATG
* *
196613 AAAATGAATTAATTTTTAAAAACTGATTTAATATAAATTAAA
127 AAAATAAATTAAGTTTTAAAAACTGATTTAATATAAATTAAA
* * *
196655 TAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCGAAAAAATTTACGAA
1 TAACAATATATAATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCGAAAAAATTTACGAA
196720 GAAGAAAATCTCGTAATTTGAAAACAAGAAGAATTT
66 GAAGAAAATCTCGTAATTTGAAAACAAGAAGAATTT
196756 CGAAAGAAAA
Statistics
Matches: 221, Mismatches: 32, Indels: 27
0.79 0.11 0.10
Matches are distributed among these distances:
165 61 0.28
166 24 0.11
167 124 0.56
168 12 0.05
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (168 bp):
TAACAATATATAATGAATTTTAAAAATTAAAAACCAAGAAAAATCCTCCCGAAAAAATTTACGAA
GAAGAAAATCTCGTAATTTGAAAACAAGAAGAATTTTAAGGAAAAAAATTAAAAATTTATGAAAA
TAAATTAAGTTTTAAAAACTGATTTAATATAAATTAAA
Found at i:198960 original size:34 final size:33
Alignment explanation
Indices: 198920--199174 Score: 170
Period size: 34 Copynumber: 7.6 Consensus size: 33
198910 ATACAAATTT
*
198920 AGTTTTTCATTTAAAATTGAAGTGTCAATGAAAG
1 AGTTTTTCATTTAAAGTTGAAGT-TCAATGAAAG
* ** *
198954 AGTTTTTCATTTAAAGTTAAAAGCTT-GGTGGAAG
1 AGTTTTTCATTTAAAGTT-GAAG-TTCAATGAAAG
*** *
198988 AGTTTTTCATTTTAAAGTTGAAGCTTTGGTGAAGG
1 AGTTTTTCA-TTTAAAGTTGAAG-TTCAATGAAAG
*
199023 AGTTTTTCATTTAAAGTTGAAAATT---TGACAGATG
1 AGTTTTTCATTTAAAGTTG-AAGTTCAATGA-A-A-G
* *
199057 AGTTTTTCATTTTAAAGTTAAAAG-TC--TGAGA-
1 AGTTTTTCA-TTTAAAGTT-GAAGTTCAATGAAAG
*
199088 AGTTTTTCATTTTAAAGTTGAAGCCTCAATGAAAG
1 AGTTTTTCA-TTTAAAGTTGAAG-TTCAATGAAAG
* * *
199123 AATTTTTCATTTAATGTTGAAGTTTCGATG-AA-
1 AGTTTTTCATTTAAAGTTGAAG-TTCAATGAAAG
199155 AGTTTTTCATTTAAAGTTGA
1 AGTTTTTCATTTAAAGTTGA
199175 TGCTTTGGTG
Statistics
Matches: 183, Mismatches: 22, Indels: 34
0.77 0.09 0.14
Matches are distributed among these distances:
30 3 0.02
31 22 0.12
32 21 0.11
33 3 0.02
34 81 0.44
35 52 0.28
36 1 0.01
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (33 bp):
AGTTTTTCATTTAAAGTTGAAGTTCAATGAAAG
Found at i:199010 original size:69 final size:67
Alignment explanation
Indices: 198920--199172 Score: 205
Period size: 69 Copynumber: 3.8 Consensus size: 67
198910 ATACAAATTT
* * *
198920 AGTTTTTCATTTAAAATTGAAGTGTCAATGAAAGAGTTTTTCATTTAAAGTTAAAAGCTTGGTGG
1 AGTTTTTCATTTAAAGTTGAAGTGTCGATGAAA-AGTTTTTCATTTAAAGTTAAAAGCTTGATGG
198985 AAG
65 AAG
* * * *
198988 AGTTTTTCATTTTAAAGTTGAAGCT-TTGGTGAAGGAGTTTTTCATTTAAAGTTGAAAA-TTTGA
1 AGTTTTTCA-TTTAAAGTTGAAG-TGTCGATGAA-AAGTTTTTCATTTAAAGTT-AAAAGCTTGA
** *
199051 CAGATG
62 TGGAAG
** * * **
199057 AGTTTTTCATTTTAAAGTT-AAAAGTC--TGAGAAGTTTTTCATTTTAAAGTT-GAAGCCTCAAT
1 AGTTTTTCA-TTTAAAGTTGAAGTGTCGATGAAAAGTTTTTCA-TTTAAAGTTAAAAG-CTTGAT
*
199118 GAAAG
63 GGAAG
* * *
199123 AATTTTTCATTTAATGTTGAAGTTTCGATG-AAAGTTTTTCATTTAAAGTT
1 AGTTTTTCATTTAAAGTTGAAGTGTCGATGAAAAGTTTTTCATTTAAAGTT
199173 GATGCTTTGG
Statistics
Matches: 145, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
64 2 0.01
65 17 0.12
66 37 0.26
67 10 0.07
68 14 0.10
69 60 0.41
70 5 0.03
ACGTcount: A:0.33, C:0.07, G:0.19, T:0.42
Consensus pattern (67 bp):
AGTTTTTCATTTAAAGTTGAAGTGTCGATGAAAAGTTTTTCATTTAAAGTTAAAAGCTTGATGGA
AG
Found at i:200244 original size:14 final size:15
Alignment explanation
Indices: 200222--200258 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
200212 TTTAATATTT
200222 AAAAA-AAATTTT-A
1 AAAAATAAATTTTAA
200235 AAAAATAAATTTTAA
1 AAAAATAAATTTTAA
200250 AAAAATAAA
1 AAAAATAAA
200259 GTCTATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 7 0.32
15 10 0.45
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAAATAAATTTTAA
Found at i:200251 original size:13 final size:12
Alignment explanation
Indices: 200219--200254 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
200209 TTATTTAATA
200219 TTTAAAAAAAAT
1 TTTAAAAAAAAT
200231 TTTAAAAAATAAAT
1 TTT-AAAAA-AAAT
200245 TTTAAAAAAA
1 TTTAAAAAAA
200255 TAAAGTCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 5 0.23
13 10 0.45
14 7 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TTTAAAAAAAAT
Found at i:200451 original size:30 final size:30
Alignment explanation
Indices: 200417--200495 Score: 70
Period size: 30 Copynumber: 2.6 Consensus size: 30
200407 AAAAAGTAAG
*
200417 TTATTTATATTTTTTAAATTTAATAAAAAA
1 TTATTTATATTTTTTAAATTAAATAAAAAA
* ** *
200447 TTA-TTAAATTATTAAAAATTAAATTAAAAA
1 TTATTTATATT-TTTTAAATTAAATAAAAAA
* *
200477 TAAATATATATTTTTTAAA
1 T-TATTTATATTTTTTAAA
200496 AAATTATAAT
Statistics
Matches: 36, Mismatches: 10, Indels: 5
0.71 0.20 0.10
Matches are distributed among these distances:
29 6 0.17
30 19 0.53
31 6 0.17
32 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (30 bp):
TTATTTATATTTTTTAAATTAAATAAAAAA
Found at i:200709 original size:20 final size:19
Alignment explanation
Indices: 200680--200727 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
200670 GCTTTGCTAT
200680 TTTAAAATATTATAATTATA
1 TTTAAAATATTAT-ATTATA
* *
200700 TTTAAGATATTATATTATT
1 TTTAAAATATTATATTATA
200719 TTTATAAAT
1 TTTA-AAAT
200728 TTAATTTGTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (19 bp):
TTTAAAATATTATATTATA
Found at i:202413 original size:2 final size:2
Alignment explanation
Indices: 202406--202439 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
202396 GTCTTATCAT
202406 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
202440 ACACACACAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:202444 original size:2 final size:2
Alignment explanation
Indices: 202439--202465 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
202429 CTCTCTCTCT
202439 CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA C
202466 TAGAGGCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:207168 original size:2 final size:2
Alignment explanation
Indices: 207161--207203 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
207151 ACGAAGAAAC
207161 GA GA GA GA GA GA GA GA GA GA GA GA GA 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
207203 G
1 G
207204 GCTCACCTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:207398 original size:26 final size:27
Alignment explanation
Indices: 207367--207417 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
207357 TAATATTAAT
207367 AATTTAT-TA-TTATATAAATTTTAAAA
1 AATTTATATATTTATAT-AATTTTAAAA
*
207393 AATTTATATATTTATATTATTTTAA
1 AATTTATATATTTATATAATTTTAA
207418 TTATTTTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 7 0.32
27 9 0.41
28 6 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
AATTTATATATTTATATAATTTTAAAA
Found at i:207773 original size:21 final size:19
Alignment explanation
Indices: 207737--207786 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
207727 TGATTTGATG
* * *
207737 ATAAAAATAAAAAAAATAA
1 ATAAAAAGACAAAAAAGAA
207756 ATAGACAAAGACAAAAAAGAA
1 ATA-A-AAAGACAAAAAAGAA
207777 ATAAAAAGAC
1 ATAAAAAGAC
207787 TCTTAAGCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.35
20 2 0.08
21 15 0.58
ACGTcount: A:0.76, C:0.06, G:0.08, T:0.10
Consensus pattern (19 bp):
ATAAAAAGACAAAAAAGAA
Found at i:208321 original size:20 final size:20
Alignment explanation
Indices: 208298--208475 Score: 84
Period size: 19 Copynumber: 9.2 Consensus size: 20
208288 ATTATTAATT
208298 TTATAATTTATATATTTATA
1 TTATAATTTATATATTTATA
208318 TTAT-ATTTATATA-TT-T-
1 TTATAATTTATATATTTATA
208334 TTA-AATATTATA-A-TTATA
1 TTATAAT-TTATATATTTATA
*
208352 TTTAAAATATTATATATTTATA
1 -TTATAAT-TTATATATTTATA
*
208374 -TA-AATTTTAATATATTAATAA
1 TTATAA-TTT-ATATATTTAT-A
* *
208395 TTTATATTTTATAAATTT-TA
1 -TTATAATTTATATATTTATA
*
208415 ATA-AATTTAT-T-TTTATA
1 TTATAATTTATATATTTATA
* *
208432 TTAT-ACTTATAT-TATTATT
1 TTATAATTTATATAT-TTATA
208451 TTAT-ATTT-TATATTATATAA
1 TTATAATTTATATATT-TAT-A
208471 TTATA
1 TTATA
208476 TCTTATTTAA
Statistics
Matches: 124, Mismatches: 12, Indels: 43
0.69 0.07 0.24
Matches are distributed among these distances:
16 11 0.09
17 16 0.13
18 14 0.11
19 33 0.27
20 30 0.24
21 3 0.02
22 11 0.09
23 5 0.04
24 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (20 bp):
TTATAATTTATATATTTATA
Found at i:208476 original size:20 final size:20
Alignment explanation
Indices: 208422--208481 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
208412 TTAATAAATT
*
208422 TATTTTTATATTATA-CTTA
1 TATTATTATATTATATCTTA
* *
208441 TATTATTATTTTATATTTTA
1 TATTATTATATTATATCTTA
208461 TATTA-TATAATTATATCTTA
1 TATTATTAT-ATTATATCTTA
208481 T
1 T
208482 TTAAAATTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
19 16 0.47
20 18 0.53
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (20 bp):
TATTATTATATTATATCTTA
Found at i:209570 original size:22 final size:20
Alignment explanation
Indices: 209542--209582 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
209532 TAAAAAAATT
209542 ATTTTTTAAATATTTTATATTA
1 ATTTTTTAAA-A-TTTATATTA
*
209564 ATTTTTTTAAATTTATATT
1 ATTTTTTAAAATTTATATT
209583 CGAAATAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTAAAATTTATATTA
Found at i:211399 original size:12 final size:11
Alignment explanation
Indices: 211382--211421 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
211372 GAAAAACGGG
211382 AAAAAAAAAGA
1 AAAAAAAAAGA
*
211393 AAGAAAAAAGA
1 AAAAAAAAAGA
*
211404 AAAAAAGTAAGA
1 AAAAAA-AAAGA
211416 AAAAAA
1 AAAAAA
211422 GGAAAAGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:211408 original size:23 final size:22
Alignment explanation
Indices: 211362--211409 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
211352 CTTTGAACCC
* *
211362 AAAAAAAAAAGAAAAACGGGAAA
1 AAAAAAAAAAGAAAAA-AGAAAA
*
211385 AAAAAAGAAAGAAAAAAGAAAA
1 AAAAAAAAAAGAAAAAAGAAAA
211407 AAA
1 AAA
211410 GTAAGAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 7 0.32
23 15 0.68
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAAAGAAAA
Found at i:211421 original size:20 final size:20
Alignment explanation
Indices: 211362--211427 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 20
211352 CTTTGAACCC
*
211362 AAAAAAA-AAAGAAAAACGGG
1 AAAAAAAGAAAGAAAAA-AGG
211382 AAAAAAAAAGAAAGAAAAAA-G
1 --AAAAAAAGAAAGAAAAAAGG
*
211403 AAAAAAAGTAAGAAAAAAAGG
1 AAAAAAAGAAAG-AAAAAAGG
211424 AAAA
1 AAAA
211428 GAGGTGGCAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
19 11 0.28
20 6 0.15
21 6 0.15
22 7 0.18
23 9 0.23
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAAGAAAAAAGG
Found at i:211422 original size:12 final size:10
Alignment explanation
Indices: 211363--211421 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
211353 TTTGAACCCA
211363 AAAAAAAAAG
1 AAAAAAAAAG
***
211373 -AAAAACGGG
1 AAAAAAAAAG
211382 AAAAAAAAAG
1 AAAAAAAAAG
211392 AAAGAAAAAAG
1 AAA-AAAAAAG
211403 AAAAAAAGTAAG
1 AAAAAAA--AAG
211415 AAAAAAA
1 AAAAAAA
211422 GGAAAAGAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 6 0.15
10 13 0.33
11 10 0.26
12 10 0.26
ACGTcount: A:0.81, C:0.02, G:0.15, T:0.02
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:211427 original size:19 final size:19
Alignment explanation
Indices: 211384--211420 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
211374 AAAACGGGAA
211384 AAAAAAAGAAAGAAAAAAG
1 AAAAAAAGAAAGAAAAAAG
*
211403 AAAAAAAGTAAGAAAAAA
1 AAAAAAAGAAAGAAAAAA
211421 AGGAAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.03
Consensus pattern (19 bp):
AAAAAAAGAAAGAAAAAAG
Found at i:215134 original size:20 final size:20
Alignment explanation
Indices: 215089--215162 Score: 94
Period size: 21 Copynumber: 3.6 Consensus size: 20
215079 GGCATGGTTT
**
215089 TGTATCGATACATTTAAGACA
1 TGTATCGATACATTTACTA-A
*
215110 TGTATCGATACATTTACTTA
1 TGTATCGATACATTTACTAA
*
215130 TGTATCGATACATTCACTAA
1 TGTATCGATACATTTACTAA
215150 TTGTATCGATACA
1 -TGTATCGATACA
215163 AATTGTAGAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 19 0.40
21 28 0.60
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATTTACTAA
Found at i:217934 original size:13 final size:13
Alignment explanation
Indices: 217916--217940 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
217906 CTTATGCTTA
217916 GTATCGATACATT
1 GTATCGATACATT
217929 GTATCGATACAT
1 GTATCGATACAT
217941 GATCATTATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:217937 original size:33 final size:32
Alignment explanation
Indices: 217895--217959 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 32
217885 CATATCCAGA
* *
217895 TGTATCGATACCTTATGC-TTAGTATCGATACAT
1 TGTATCGATACATGAT-CATTA-TATCGATACAT
217928 TGTATCGATACATGATCATTATATCGATACAT
1 TGTATCGATACATGATCATTATATCGATACAT
217960 GCACAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATGATCATTATATCGATACAT
Found at i:222816 original size:79 final size:79
Alignment explanation
Indices: 222725--223000 Score: 333
Period size: 79 Copynumber: 3.6 Consensus size: 79
222715 GAGATAGTAA
* * *
222725 CGGGGTTGGAGTATCCCCTTGAAAATAACGGGCTTGGAGTATCCCCGATTGTGAAAAATCAATGA
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAAT-A
222790 -TTTAGAAATAAAAC
65 TTTTAGAAATAAAAC
* * * * *
222804 CGGGGTTGGAGTATCCCCTCGGAGATAACGGGGTTGGAGTATCCTCGATTATGAGAAATTAATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
*
222869 TTTAGAAATAAAGC
66 TTTAGAAATAAAAC
222883 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC------G----AT-AATAT
1 CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
* *
222937 TTTAGGAATAAAGC
66 TTTAGAAATAAAAC
* *
222951 CGGGGGTTGGAGCATCCCCTCAAAAATAACGGGGTTGGAGTATCCCCGAT
1 C-GGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
223001 GATTAACGGG
Statistics
Matches: 177, Mismatches: 15, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
68 19 0.11
69 45 0.25
73 1 0.01
78 1 0.01
79 111 0.63
ACGTcount: A:0.30, C:0.17, G:0.28, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATCAATAT
TTTAGAAATAAAAC
Found at i:222978 original size:69 final size:68
Alignment explanation
Indices: 222863--223000 Score: 240
Period size: 69 Copynumber: 2.0 Consensus size: 68
222853 TATGAGAAAT
* *
222863 TAATATTTTAGAAATAAAGCCGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCC
1 TAATATTTTAGAAATAAAGCCGGGGTTGGAGCATCCCCTCAAAAATAACGGGGTTGGAGTATCCC
222928 CGA
66 CGA
*
222931 TAATATTTTAGGAATAAAGCCGGGGGTTGGAGCATCCCCTCAAAAATAACGGGGTTGGAGTATCC
1 TAATATTTTAGAAATAAAGCC-GGGGTTGGAGCATCCCCTCAAAAATAACGGGGTTGGAGTATCC
222996 CCGA
65 CCGA
223000 T
1 T
223001 GATTAACGGG
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
68 20 0.30
69 46 0.70
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (68 bp):
TAATATTTTAGAAATAAAGCCGGGGTTGGAGCATCCCCTCAAAAATAACGGGGTTGGAGTATCCC
CGA
Found at i:222995 original size:28 final size:27
Alignment explanation
Indices: 222953--223024 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
222943 AATAAAGCCG
*
222953 GGGGTTGGAGCATCCCCTCAAAAATAAC
1 GGGGTTGGAGTATCCCC-CAAAAATAAC
* ** *
222981 GGGGTTGGAGTATCCCCGATGATTAAC
1 GGGGTTGGAGTATCCCCCAAAAATAAC
*
223008 GGGGTTGGGGTATCCCC
1 GGGGTTGGAGTATCCCC
223025 GATGAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
27 22 0.58
28 16 0.42
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCCAAAAATAAC
Found at i:223015 original size:27 final size:27
Alignment explanation
Indices: 222977--223029 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
222967 CCCTCAAAAA
222977 TAACGGGGTTGGAGTATCCCCGATGAT
1 TAACGGGGTTGGAGTATCCCCGATGAT
*
223004 TAACGGGGTTGGGGTATCCCCGATGA
1 TAACGGGGTTGGAGTATCCCCGATGA
223030 AAAATTGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.36, T:0.25
Consensus pattern (27 bp):
TAACGGGGTTGGAGTATCCCCGATGAT
Found at i:223101 original size:51 final size:52
Alignment explanation
Indices: 223030--223128 Score: 143
Period size: 52 Copynumber: 1.9 Consensus size: 52
223020 TCCCCGATGA
223030 AAAATTGATGTTTTAGAAAT-AAAATCGGAGTT-GGAGTATCCCCGATTATAG
1 AAAATTGATGTTTTAGAAATAAAAATCGGAGTTGGGA-TATCCCCGATTATAG
223081 AAAATT-AGTGTTTT-GAAAATAAAAATCGGAGTTGGGATATCCCCGATT
1 AAAATTGA-TGTTTTAG-AAATAAAAATCGGAGTTGGGATATCCCCGATT
223129 GCGGAGAATT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
50 2 0.05
51 16 0.36
52 23 0.52
53 3 0.07
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (52 bp):
AAAATTGATGTTTTAGAAATAAAAATCGGAGTTGGGATATCCCCGATTATAG
Found at i:234890 original size:80 final size:79
Alignment explanation
Indices: 234801--235117 Score: 390
Period size: 79 Copynumber: 4.0 Consensus size: 79
234791 ATATTTCCCG
* * *
234801 ATGAGAAATTTAATATTTTGGAGATAGTAA-C-GGGGTTGGAGTATCCCCTTGAAAATAACGGGC
1 ATGAGAAA-TTAATATTTTGGAAATA--AAGCTGGGGTTGGAGTATCCCCTCGAAAATAACGGGG
234864 TTGGAGTATCCCCGATT
63 TTGGAGTATCCCCGATT
* * * * * * * *
234881 GTGAAAAATTGATGA-TTTGGAAATAAAACTGAGGTTGGAGTATCCCTTCGGAGATAACGGGGTT
1 ATGAGAAATTAAT-ATTTTGGAAATAAAGCTGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTT
*
234945 GGAGTATCCCGGATT
65 GGAGTATCCCCGATT
* *
234960 ATGAGAAATTAATATTTTAGAAATAAAGCTGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTA
1 ATGAGAAATTAATATTTTGGAAATAAAGCTGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
235025 GAGTATCCCCGATT
66 GAGTATCCCCGATT
** * *
235039 ATGAGAAATCGATATTTTAGG-AATAAAGCCGGGGGTTGGAGCATCCCCTCGAAAATAACGGGGT
1 ATGAGAAATTAATATTTT-GGAAATAAAG-CTGGGGTTGGAGTATCCCCTCGAAAATAACGGGGT
235103 TGGAGTATCCCCGAT
64 TGGAGTATCCCCGAT
235118 GATAAACGGG
Statistics
Matches: 203, Mismatches: 28, Indels: 12
0.84 0.12 0.05
Matches are distributed among these distances:
77 2 0.01
78 2 0.01
79 144 0.71
80 55 0.27
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (79 bp):
ATGAGAAATTAATATTTTGGAAATAAAGCTGGGGTTGGAGTATCCCCTCGAAAATAACGGGGTTG
GAGTATCCCCGATT
Found at i:235112 original size:28 final size:28
Alignment explanation
Indices: 235070--235141 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 28
235060 AATAAAGCCG
*
235070 GGGGTTGGAGCATCCCCTCGAAAAT-AAC
1 GGGGTTGGAGTATCCCC-CGAAAATAAAC
**
235098 GGGGTTGGAGTAT-CCCCGATGATAAAC
1 GGGGTTGGAGTATCCCCCGAAAATAAAC
*
235125 GGGGTTGGGGTATCCCC
1 GGGGTTGGAGTATCCCC
235142 GATGAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.13
27 18 0.47
28 15 0.39
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.21
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCCGAAAATAAAC
Found at i:235137 original size:27 final size:27
Alignment explanation
Indices: 235095--235146 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
235085 CCTCGAAAAT
235095 AACGGGGTTGGAGTATCCCCGATGATA
1 AACGGGGTTGGAGTATCCCCGATGATA
*
235122 AACGGGGTTGGGGTATCCCCGATGA
1 AACGGGGTTGGAGTATCCCCGATGA
235147 AAAATTGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.21
Consensus pattern (27 bp):
AACGGGGTTGGAGTATCCCCGATGATA
Found at i:235219 original size:52 final size:53
Alignment explanation
Indices: 235145--235248 Score: 153
Period size: 53 Copynumber: 2.0 Consensus size: 53
235135 TATCCCCGAT
235145 GAAAAATTGATGTTTTAGAAAT-AAAATCGGAGTT-GGAGTATCCCCGATTATA
1 GAAAAATTGATGTTTTAGAAATAAAAATCGGAGTTGGGA-TATCCCCGATTATA
235197 GAAAAATT-AGTGTTTT-GAAAATAAAAATCGGAGTTGGGATATCCCCGATTAT
1 GAAAAATTGA-TGTTTTAG-AAATAAAAATCGGAGTTGGGATATCCCCGATTAT
235249 GGAGAATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
51 2 0.04
52 18 0.38
53 25 0.52
54 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (53 bp):
GAAAAATTGATGTTTTAGAAATAAAAATCGGAGTTGGGATATCCCCGATTATA
Found at i:237634 original size:13 final size:13
Alignment explanation
Indices: 237616--237641 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
237606 ACAAAGATCC
237616 ATGTATCGATACA
1 ATGTATCGATACA
237629 ATGTATCGATACA
1 ATGTATCGATACA
237642 TGGAATAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:237701 original size:13 final size:13
Alignment explanation
Indices: 237679--237736 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
237669 GGCAGTAGCT
*
237679 TTGTAGCGATACA
1 TTGTATCGATACA
237692 TTGTATCGATATAACA
1 TTGTATCG--AT-ACA
237708 CTTATGTATCGATACA
1 --T-TGTATCGATACA
237724 TTGTATCGATACA
1 TTGTATCGATACA
237737 ATACTTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 19 0.50
14 1 0.03
15 2 0.05
16 6 0.16
17 2 0.05
18 1 0.03
19 7 0.18
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:237726 original size:32 final size:32
Alignment explanation
Indices: 237680--237755 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
237670 GCAGTAGCTT
* *
237680 TGTAGCGATACATTGTATCGATATAACACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
*
237712 TGTATCGATACATTGTATCGATACAATACTTA
1 TGTATCGATACATTGTATCGATACAACACTTA
237744 TGTATCGATACA
1 TGTATCGATACA
237756 AATCGCTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACACTTA
Found at i:237754 original size:19 final size:18
Alignment explanation
Indices: 237693--237757 Score: 68
Period size: 19 Copynumber: 3.8 Consensus size: 18
237683 AGCGATACAT
*
237693 TGTATCGATATAACACTTA
1 TGTATCGATACAA-ACTTA
237712 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
237725 TGTATCGATACAATACTTA
1 TGTATCGATACAA-ACTTA
237744 TGTATCGATACAAA
1 TGTATCGATACAAA
237758 TCGCTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 13
0.74 0.02 0.25
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 2 0.05
19 23 0.59
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:239505 original size:896 final size:896
Alignment explanation
Indices: 237774--239515 Score: 3484
Period size: 896 Copynumber: 1.9 Consensus size: 896
237764 AAATTTAAAA
237774 TTTTTGACCGTTGGGACCTTGTATCGATACATTATTCAAATGTATCGATACATTTGGATAAATTT
1 TTTTTGACCGTTGGGACCTTGTATCGATACATTATTCAAATGTATCGATACATTTGGATAAATTT
237839 TTTTTTTCAAACACTCTATCTCAACTAAGGACAATGGGAAATGGATTCGTCCCCACATACGTCCA
66 TTTTTTTCAAACACTCTATCTCAACTAAGGACAATGGGAAATGGATTCGTCCCCACATACGTCCA
237904 ATCCTCCACCTACTAGCTAGGCTTCAACTTGTCGAAAATTAGCTCGGACAAAATGAGGTGTCTAC
131 ATCCTCCACCTACTAGCTAGGCTTCAACTTGTCGAAAATTAGCTCGGACAAAATGAGGTGTCTAC
237969 ACCTAACATAAGTTATTTTCATCCATTCGGATGTAAATGTTTTGTATTAATAATGGGAAAAAAAC
196 ACCTAACATAAGTTATTTTCATCCATTCGGATGTAAATGTTTTGTATTAATAATGGGAAAAAAAC
238034 CTTAGTAAATTCGACGCTAAAAGTGATGAAAGAATTTCTCTTGGTTATTCAACAAACCCTAAAGC
261 CTTAGTAAATTCGACGCTAAAAGTGATGAAAGAATTTCTCTTGGTTATTCAACAAACCCTAAAGC
238099 TTATCGAGTGTTTAATAAAAGAACTTTGGTTGTTGAAGAATCAATCCATGTTGTTTTTGATGAAT
326 TTATCGAGTGTTTAATAAAAGAACTTTGGTTGTTGAAGAATCAATCCATGTTGTTTTTGATGAAT
238164 TTAACTCTTCCGTGAGGAAGGTATCTCTTTTTGACAATGATGCAGAAATTTATGAAGAAAATCTA
391 TTAACTCTTCCGTGAGGAAGGTATCTCTTTTTGACAATGATGCAGAAATTTATGAAGAAAATCTA
238229 GAACAAGCATCACACTAGGAGCAAGAAGAAAATGTTCAAATCGAAGAAGCTCCAAAAGAAGTTGA
456 GAACAAGCATCACACTAGGAGCAAGAAGAAAATGTTCAAATCGAAGAAGCTCCAAAAGAAGTTGA
238294 TGAATAAGAGCCAACTCAAACTGAAAGAAAACATTCGAGGGAGATGACTTATGTGCAAAAAGGTG
521 TGAATAAGAGCCAACTCAAACTGAAAGAAAACATTCGAGGGAGATGACTTATGTGCAAAAAGGTG
238359 AGATTATCATAATCCAAATCATGGGATAAGAACTAGATCTTCCCTTAGAAATACTTGTGATTATG
586 AGATTATCATAATCCAAATCATGGGATAAGAACTAGATCTTCCCTTAGAAATACTTGTGATTATG
238424 TTGCATTTCTCTCTCAAATAGAACCTAAGAGCATAGACGAGGTTACACAAGATGAAAATTAGATT
651 TTGCATTTCTCTCTCAAATAGAACCTAAGAGCATAGACGAGGTTACACAAGATGAAAATTAGATT
238489 ATGGCTATGCAAGAAAAATTGAAACAATTTGAGAGAAGTAAGGTTTGGTCTTTAGTAAAAAGATC
716 ATGGCTATGCAAGAAAAATTGAAACAATTTGAGAGAAGTAAGGTTTGGTCTTTAGTAAAAAGATC
238554 GGGTGATCATCCAATTATAGGAAATAAATGGGTGTTTAGAAATAAATTGGATGAAGATGGAACCG
781 GGGTGATCATCCAATTATAGGAAATAAATGGGTGTTTAGAAATAAATTGGATGAAGATGGAACCG
238619 TTGGGAAATGGATTTTGACCGTTGGGAAATAAATCGGGTGAAAAGGTTTGG
846 TTGGGAAATGGATTTTGACCGTTGGGAAATAAATCGGGTGAAAAGGTTTGG
238670 TTTTTGACCGTTGGGACCTTGTATCGATACATTATTCAAATGTATCGATACATTTGGATAAATTT
1 TTTTTGACCGTTGGGACCTTGTATCGATACATTATTCAAATGTATCGATACATTTGGATAAATTT
238735 TTTTTTTCAAACACTCTATCTCAACTAAGGACAATGGGAAATGGATTCGTCCCCACATACGTCCA
66 TTTTTTTCAAACACTCTATCTCAACTAAGGACAATGGGAAATGGATTCGTCCCCACATACGTCCA
238800 ATCCTCCACCTACTAGCTAGGCTTCAACTTGTCGAAAATTAGCTCGGACAAAATGAGGTGTCTAC
131 ATCCTCCACCTACTAGCTAGGCTTCAACTTGTCGAAAATTAGCTCGGACAAAATGAGGTGTCTAC
238865 ACCTAACATAAGTTATTTTCATCCATTCGGATGTAAATGTTTTGTATTAATAATGGGAAAAAAAC
196 ACCTAACATAAGTTATTTTCATCCATTCGGATGTAAATGTTTTGTATTAATAATGGGAAAAAAAC
238930 CTTAGTAAATTCGACGCTAAAAGTGATGAAAGAATTTCTCTTGGTTATTCAACAAACCCTAAAGC
261 CTTAGTAAATTCGACGCTAAAAGTGATGAAAGAATTTCTCTTGGTTATTCAACAAACCCTAAAGC
238995 TTATCGAGTGTTTAATAAAAGAACTTTGGTTGTTGAAGAATCAATCCATGTTGTTTTTGATGAAT
326 TTATCGAGTGTTTAATAAAAGAACTTTGGTTGTTGAAGAATCAATCCATGTTGTTTTTGATGAAT
239060 TTAACTCTTCCGTGAGGAAGGTATCTCTTTTTGACAATGATGCAGAAATTTATGAAGAAAATCTA
391 TTAACTCTTCCGTGAGGAAGGTATCTCTTTTTGACAATGATGCAGAAATTTATGAAGAAAATCTA
239125 GAACAAGCATCACACTAGGAGCAAGAAGAAAATGTTCAAATCGAAGAAGCTCCAAAAGAAGTTGA
456 GAACAAGCATCACACTAGGAGCAAGAAGAAAATGTTCAAATCGAAGAAGCTCCAAAAGAAGTTGA
239190 TGAATAAGAGCCAACTCAAACTGAAAGAAAACATTCGAGGGAGATGACTTATGTGCAAAAAGGTG
521 TGAATAAGAGCCAACTCAAACTGAAAGAAAACATTCGAGGGAGATGACTTATGTGCAAAAAGGTG
239255 AGATTATCATAATCCAAATCATGGGATAAGAACTAGATCTTCCCTTAGAAATACTTGTGATTATG
586 AGATTATCATAATCCAAATCATGGGATAAGAACTAGATCTTCCCTTAGAAATACTTGTGATTATG
239320 TTGCATTTCTCTCTCAAATAGAACCTAAGAGCATAGACGAGGTTACACAAGATGAAAATTAGATT
651 TTGCATTTCTCTCTCAAATAGAACCTAAGAGCATAGACGAGGTTACACAAGATGAAAATTAGATT
239385 ATGGCTATGCAAGAAAAATTGAAACAATTTGAGAGAAGTAAGGTTTGGTCTTTAGTAAAAAGATC
716 ATGGCTATGCAAGAAAAATTGAAACAATTTGAGAGAAGTAAGGTTTGGTCTTTAGTAAAAAGATC
239450 GGGTGATCATCCAATTATAGGAAATAAATGGGTGTTTAGAAATAAATTGGATGAAGATGGAACCG
781 GGGTGATCATCCAATTATAGGAAATAAATGGGTGTTTAGAAATAAATTGGATGAAGATGGAACCG
239515 T
846 T
239516 AGTTAGAAAT
Statistics
Matches: 846, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
896 846 1.00
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (896 bp):
TTTTTGACCGTTGGGACCTTGTATCGATACATTATTCAAATGTATCGATACATTTGGATAAATTT
TTTTTTTCAAACACTCTATCTCAACTAAGGACAATGGGAAATGGATTCGTCCCCACATACGTCCA
ATCCTCCACCTACTAGCTAGGCTTCAACTTGTCGAAAATTAGCTCGGACAAAATGAGGTGTCTAC
ACCTAACATAAGTTATTTTCATCCATTCGGATGTAAATGTTTTGTATTAATAATGGGAAAAAAAC
CTTAGTAAATTCGACGCTAAAAGTGATGAAAGAATTTCTCTTGGTTATTCAACAAACCCTAAAGC
TTATCGAGTGTTTAATAAAAGAACTTTGGTTGTTGAAGAATCAATCCATGTTGTTTTTGATGAAT
TTAACTCTTCCGTGAGGAAGGTATCTCTTTTTGACAATGATGCAGAAATTTATGAAGAAAATCTA
GAACAAGCATCACACTAGGAGCAAGAAGAAAATGTTCAAATCGAAGAAGCTCCAAAAGAAGTTGA
TGAATAAGAGCCAACTCAAACTGAAAGAAAACATTCGAGGGAGATGACTTATGTGCAAAAAGGTG
AGATTATCATAATCCAAATCATGGGATAAGAACTAGATCTTCCCTTAGAAATACTTGTGATTATG
TTGCATTTCTCTCTCAAATAGAACCTAAGAGCATAGACGAGGTTACACAAGATGAAAATTAGATT
ATGGCTATGCAAGAAAAATTGAAACAATTTGAGAGAAGTAAGGTTTGGTCTTTAGTAAAAAGATC
GGGTGATCATCCAATTATAGGAAATAAATGGGTGTTTAGAAATAAATTGGATGAAGATGGAACCG
TTGGGAAATGGATTTTGACCGTTGGGAAATAAATCGGGTGAAAAGGTTTGG
Found at i:242991 original size:13 final size:13
Alignment explanation
Indices: 242975--243001 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
242965 AATGGTTTTC
242975 TTGCTATTATGGA
1 TTGCTATTATGGA
242988 TTGCTATTATGGA
1 TTGCTATTATGGA
243001 T
1 T
243002 GATTTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.22, T:0.48
Consensus pattern (13 bp):
TTGCTATTATGGA
Found at i:243179 original size:38 final size:38
Alignment explanation
Indices: 243133--243211 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
243123 ATATAAAGAA
*
243133 TTTTTATAACAATAAGGGGGAGAAAATCTTGAAAATTT
1 TTTTTATAACAATAACGGGGAGAAAATCTTGAAAATTT
243171 TTTTTATAACAATAACGGGGAGAAAATCTTGAAAATTT
1 TTTTTATAACAATAACGGGGAGAAAATCTTGAAAATTT
243209 TTT
1 TTT
243212 AAAATGAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (38 bp):
TTTTTATAACAATAACGGGGAGAAAATCTTGAAAATTT
Found at i:243821 original size:20 final size:20
Alignment explanation
Indices: 243798--243859 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
243788 TGCTTTGTAT
243798 TGATACATTGTATCGATACA
1 TGATACATTGTATCGATACA
*
243818 TGAT-CATTATATCGATACA
1 TGATACATTGTATCGATACA
*
243837 TG-CACAATTGTATCGATACA
1 TGATAC-ATTGTATCGATACA
243857 TGA
1 TGA
243860 AACTGGCAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
19 17 0.47
20 19 0.53
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (20 bp):
TGATACATTGTATCGATACA
Found at i:245711 original size:22 final size:22
Alignment explanation
Indices: 245686--245734 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
245676 CTAAAAGAAG
245686 CAAACAAGCTACATTGCTTGTT
1 CAAACAAGCTACATTGCTTGTT
* *
245708 CAAACCAGTTACATTGCTTGTT
1 CAAACAAGCTACATTGCTTGTT
*
245730 TAAAC
1 CAAAC
245735 TAGCGAAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (22 bp):
CAAACAAGCTACATTGCTTGTT
Found at i:251579 original size:20 final size:20
Alignment explanation
Indices: 251551--251627 Score: 118
Period size: 20 Copynumber: 3.9 Consensus size: 20
251541 GTAAAAAGAC
* *
251551 AAAATGTATCGATGCATTCA
1 AAAATGTATCGATACATTGA
* *
251571 TACATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
251591 AAAATGTATCGATACATTGA
1 AAAATGTATCGATACATTGA
251611 AAAATGTATCGATACAT
1 AAAATGTATCGATACAT
251628 CTGGGTAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.31
Consensus pattern (20 bp):
AAAATGTATCGATACATTGA
Found at i:251649 original size:71 final size:71
Alignment explanation
Indices: 251574--251709 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 71
251564 GCATTCATAC
* * * *
251574 ATGTATCGATACATTGAAAAATGTATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTCAAAAATATATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAA
251639 GACAGA
66 GACAGA
* *
251645 ATGTATCGATACATTCATACATATATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAA
1 ATGTATCGATACATTCAAAAATATATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAA
251710 TGTGACTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
71 59 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (71 bp):
ATGTATCGATACATTCAAAAATATATCGATACATTAAAAAATGTATCGATACATCTAGGTAAAAA
GACAGA
Found at i:251660 original size:91 final size:91
Alignment explanation
Indices: 251503--251698 Score: 304
Period size: 91 Copynumber: 2.2 Consensus size: 91
251493 TTTTAACTAG
** *
251503 ATGTATCGATACATTATTCAATGTATCGATACATCTAAGTAAAAAGACAAAATGTATCGATGCAT
1 ATGTATCGATACATTATAAAATGTATCGATACATCTAAGTAAAAAGACAAAATGTATCGATACAT
* *
251568 TCATACATGTATCGATACATTGAAAA
66 TCATACATATATCGATACATTAAAAA
** *
251594 ATGTATCGATACATTGA-AAAATGTATCGATACATCTGGGTAAAAAGACAGAATGTATCGATACA
1 ATGTATCGATACATT-ATAAAATGTATCGATACATCTAAGTAAAAAGACAAAATGTATCGATACA
251658 TTCATACATATATCGATACATTAAAAA
65 TTCATACATATATCGATACATTAAAAA
251685 ATGTATCGATACAT
1 ATGTATCGATACAT
251699 CTAGGTAAAA
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
91 95 0.99
92 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (91 bp):
ATGTATCGATACATTATAAAATGTATCGATACATCTAAGTAAAAAGACAAAATGTATCGATACAT
TCATACATATATCGATACATTAAAAA
Found at i:251673 original size:20 final size:20
Alignment explanation
Indices: 251648--251698 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
251638 AGACAGAATG
* * *
251648 TATCGATACATTCATACATA
1 TATCGATACATTAAAAAATA
*
251668 TATCGATACATTAAAAAATG
1 TATCGATACATTAAAAAATA
251688 TATCGATACAT
1 TATCGATACAT
251699 CTAGGTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (20 bp):
TATCGATACATTAAAAAATA
Found at i:252398 original size:42 final size:42
Alignment explanation
Indices: 252339--252454 Score: 207
Period size: 42 Copynumber: 2.8 Consensus size: 42
252329 TATTCTTATG
252339 ATTAGCTTTGTAATTTATTATTAT-AGTTAAATAAAAAATATA
1 ATTAGCTTTGTAATTTATTATTATGA-TTAAATAAAAAATATA
*
252381 ATTAGCATTGTAATTTATTATTATGATTAAATAAAAAATATA
1 ATTAGCTTTGTAATTTATTATTATGATTAAATAAAAAATATA
252423 ATTAGCTTTGTAATTTATTATTATGATTAAAT
1 ATTAGCTTTGTAATTTATTATTATGATTAAAT
252455 TTATTTTTAT
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
42 70 0.99
43 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.47
Consensus pattern (42 bp):
ATTAGCTTTGTAATTTATTATTATGATTAAATAAAAAATATA
Found at i:254989 original size:89 final size:89
Alignment explanation
Indices: 254862--255350 Score: 547
Period size: 89 Copynumber: 5.5 Consensus size: 89
254852 ATAAAATTAA
* * * * *
254862 TCTTGGAACTCGAAAGATATGACAGATGCATGTAGGTATCAGATTTTTTCTGACACGACAGAAAA
1 TCTTGAAACCCGAAAGATATGACAGATGCATATGGGTATCAGATTCTTTCTGACACGACAGAAAA
254927 TATTTGACTAATGCCTAATAAATT
66 TATTTGACTAATGCCTAATAAATT
* * ** * * * *
254951 TTTTGGAACATGAAAGATGTGACAGATGCATATGGGTATTATATTCCTTCTGACAC-ACTAGAAA
1 TCTTGAAACCCGAAAGATATGACAGATGCATATGGGTATCAGATTCTTTCTGACACGAC-AGAAA
*
255015 ATATTTGACTAATACCTAATAAATT
65 ATATTTGACTAATGCCTAATAAATT
* * * * * * * * * *
255040 TTTTGGAATCCGAAAGATGTGACAGATGTATATGGGTATCAGATTCCTTATGACACAATAAAAAA
1 TCTTGAAACCCGAAAGATATGACAGATGCATATGGGTATCAGATTCTTTCTGACACGACAGAAAA
255105 TATTTGACTAATGCCTAATAAATT
66 TATTTGACTAATGCCTAATAAATT
* * * * *
255129 TCTTGAAACCCGAAAGGTATAACAGATGAATGTGGGTATCAGATTCCTTT-TGACACGATAGAAA
1 TCTTGAAACCCGAAAGATATGACAGATGCATATGGGTATCAGATT-CTTTCTGACACGACAGAAA
* *
255193 ATATTTGACTAATGCGTACTAAATT
65 ATATTTGACTAATGCCTAATAAATT
* * * * *
255218 TCTTGAAACCCGAAA-AGTGTGACAAATGCATGTGGGTATCAGATTCTTTCTAACACGA-TGAAA
1 TCTTGAAACCCGAAAGA-TATGACAGATGCATATGGGTATCAGATTCTTTCTGACACGACAG-AA
255281 AATATTTGACTAATGCCTAATAAATT
64 AATATTTGACTAATGCCTAATAAATT
* * * *
255307 TCTTAAAACCCAAAAGATATGACAAATGCATA-GGGTATTAGATT
1 TCTTGAAACCCGAAAGATATGACAGATGCATATGGGTATCAGATT
255351 TAATAAATTT
Statistics
Matches: 345, Mismatches: 48, Indels: 15
0.85 0.12 0.04
Matches are distributed among these distances:
88 18 0.05
89 322 0.93
90 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.31
Consensus pattern (89 bp):
TCTTGAAACCCGAAAGATATGACAGATGCATATGGGTATCAGATTCTTTCTGACACGACAGAAAA
TATTTGACTAATGCCTAATAAATT
Found at i:255515 original size:89 final size:88
Alignment explanation
Indices: 255350--255614 Score: 304
Period size: 89 Copynumber: 3.0 Consensus size: 88
255340 GGTATTAGAT
* * *
255350 TTAATAAATTTTTTAAAACCCGAAAGATGTGACAGATGCATAT-GAGTATCAGATT-CTTTCTGA
1 TTAATAAATTTTTGAAAA-TCGAAAGATGTGACAGATGCATGTGGA-TATCAGATTCCTTT-TGA
* * *
255413 TACGACAGAAAATATTTGACTAATGC
63 CACAACAGAAAATATTTAACTAATGC
*
255439 TTAATAAATTTCTTGAAAATCGAAAGATGTGACAGATGTATGTGGATATCAGATTCCTTTTGACA
1 TTAATAAATTT-TTGAAAATCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTTTTGACA
255504 CAACA-AGAAATATTTAACTAATGC
65 CAACAGA-AAATATTTAACTAATGC
* * * * * *
255528 CTAATAAATTTTTTGAAACTCGAAAGATGTGAGAAATGCATGAGG-TATCAAATTCCTTTTGACA
1 TTAATAAA-TTTTTGAAAATCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTTTTGACA
* * *
255592 TAATAGAAAATATTTCACTAATG
65 CAACAGAAAATATTTAACTAATG
255615 AAACGACATA
Statistics
Matches: 153, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
88 37 0.24
89 101 0.66
90 15 0.10
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.33
Consensus pattern (88 bp):
TTAATAAATTTTTGAAAATCGAAAGATGTGACAGATGCATGTGGATATCAGATTCCTTTTGACAC
AACAGAAAATATTTAACTAATGC
Found at i:255526 original size:231 final size:231
Alignment explanation
Indices: 255120--255568 Score: 591
Period size: 231 Copynumber: 1.9 Consensus size: 231
255110 GACTAATGCC
* * * *
255120 TAATAAATTTCTTGAAACCCGAAAGGTATAACAGATGAATGTGGGTATCAGATTCCTTTTGACAC
1 TAATAAATTTCTTAAAACCCGAAAGATATAACAGATGAATATGAGTATCAGATTCCTTTTGACAC
* * *
255185 GATAGAAAATATTTGACTAATGCGTACTAAATTTCTTGAAACCCGAAAAGTGTGACAAATGCATG
66 GACAGAAAATATTTGACTAATGCGTAATAAATTTCTTGAAAACCGAAAAGTGTGACAAATGCATG
* ** *
255250 TGGGTATCAGATTCTTTCTAACACGATGAAAAATATTTGACTAATGCCTAATAAATTTCTTAAAA
131 TGGATATCAGATTCTTTCTAACACGAACAAAAATATTTAACTAATGCCTAATAAATTTCTTAAAA
255315 CCCAAAAGATATGACAAATGCATAGGGTATTAGATT
196 CCCAAAAGATATGACAAATGCATAGGGTATTAGATT
* * * * *
255351 TAATAAATTTTTTAAAACCCGAAAGATGTGACAGATGCATATGAGTATCAGATT-CTTTCTGATA
1 TAATAAATTTCTTAAAACCCGAAAGATATAACAGATGAATATGAGTATCAGATTCCTTT-TGACA
* * * *
255415 CGACAGAAAATATTTGACTAATGCTTAATAAATTTCTTGAAAATCG-AAAGATGTGACAGATGTA
65 CGACAGAAAATATTTGACTAATGCGTAATAAATTTCTTGAAAACCGAAAAG-TGTGACAAATGCA
* *
255479 TGTGGATATCAGATTCCTTT-TGACAC-AACAAGAAATATTTAACTAATGCCTAATAAATTTTTT
129 TGTGGATATCAGATT-CTTTCTAACACGAACAA-AAATATTTAACTAATGCCTAATAAATTTCTT
* * * * *
255542 GAAACTCGAAAGATGTGAGAAATGCAT
192 AAAACCCAAAAGATATGACAAATGCAT
255569 GAGGTATCAA
Statistics
Matches: 187, Mismatches: 27, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
230 11 0.06
231 172 0.92
232 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (231 bp):
TAATAAATTTCTTAAAACCCGAAAGATATAACAGATGAATATGAGTATCAGATTCCTTTTGACAC
GACAGAAAATATTTGACTAATGCGTAATAAATTTCTTGAAAACCGAAAAGTGTGACAAATGCATG
TGGATATCAGATTCTTTCTAACACGAACAAAAATATTTAACTAATGCCTAATAAATTTCTTAAAA
CCCAAAAGATATGACAAATGCATAGGGTATTAGATT
Found at i:259975 original size:13 final size:13
Alignment explanation
Indices: 259957--259981 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259947 ACACATAGTA
259957 TGTATCGATACAT
1 TGTATCGATACAT
259970 TGTATCGATACA
1 TGTATCGATACA
259982 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:259998 original size:33 final size:32
Alignment explanation
Indices: 259937--260004 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
259927 GTAGCTAAAC
**
259937 TTGTATCAATACACATAGTATGTATCGATACA
1 TTGTATCAATACACATAAAATGTATCGATACA
*
259969 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCAATACA-CATAAAATGTATCGATACA
260002 TTG
1 TTG
260005 GCTTGTAACG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (32 bp):
TTGTATCAATACACATAAAATGTATCGATACA
Found at i:261560 original size:22 final size:20
Alignment explanation
Indices: 261519--261579 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
261509 CCGTGTGAAT
* *
261519 ATATATAATATTTTAGATTA
1 ATATATAAAATTTTAAATTA
261539 ATATGATAAAATTATTAAATT-
1 ATAT-ATAAAATT-TTAAATTA
* *
261560 ATTTTTAAAATTTTAAATTA
1 ATATATAAAATTTTAAATTA
261580 TTAAATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 7 0.21
20 11 0.32
21 10 0.29
22 6 0.18
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
ATATATAAAATTTTAAATTA
Found at i:261609 original size:27 final size:27
Alignment explanation
Indices: 261547--261600 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
261537 TAATATGATA
261547 AAATTATTAAATTATTTTTAAAATTTT
1 AAATTATTAAATTATTTTTAAAATTTT
261574 AAATTATTAAATTATTTTT-AAATTTT
1 AAATTATTAAATTATTTTTAAAATTTT
261600 A
1 A
261601 TGTATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 8 0.30
27 19 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AAATTATTAAATTATTTTTAAAATTTT
Found at i:261902 original size:29 final size:29
Alignment explanation
Indices: 261870--261950 Score: 91
Period size: 29 Copynumber: 2.9 Consensus size: 29
261860 TTTTAAAAAA
261870 TATTTAAATAATGTTTTATATTTTTATTG
1 TATTTAAATAATGTTTTATATTTTTATTG
*
261899 TATTTAAATAAAT-TTTTAT-TTTTTGTTTG
1 TATTTAAAT-AATGTTTTATATTTTT-ATTG
*
261928 TATTTAATTAA-G--TTATATTTTTA
1 TATTTAAATAATGTTTTATATTTTTA
261951 AGTGAAAGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
26 4 0.09
27 5 0.11
28 7 0.16
29 26 0.58
30 3 0.07
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (29 bp):
TATTTAAATAATGTTTTATATTTTTATTG
Found at i:261946 original size:28 final size:27
Alignment explanation
Indices: 261870--261949 Score: 79
Period size: 28 Copynumber: 2.8 Consensus size: 27
261860 TTTTAAAAAA
*
261870 TATTTAAATAATGTTTTATATTTTTATTG
1 TATTTAATTAA-GTTTTAT-TTTTTATTG
* * *
261899 TATTTAAATAAATTTTTATTTTTTGTTTG
1 TATTT-AATTAAGTTTTATTTTTT-ATTG
*
261928 TATTTAATTAAGTTATATTTTT
1 TATTTAATTAAGTTTTATTTTT
261950 AAGTGAAAGA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 19 0.45
29 19 0.45
30 4 0.10
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (27 bp):
TATTTAATTAAGTTTTATTTTTTATTG
Found at i:263471 original size:16 final size:16
Alignment explanation
Indices: 263437--263474 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
263427 TTTTTATATT
*
263437 TTATTTATGTTTTATA
1 TTATTTATATTTTATA
263453 TTATATTATATTTTA-A
1 TTAT-TTATATTTTATA
263469 TTATTT
1 TTATTT
263475 TTTATTACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 9 0.45
17 9 0.45
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
TTATTTATATTTTATA
Found at i:263480 original size:16 final size:17
Alignment explanation
Indices: 263428--263472 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
263418 CGAATCATAT
* *
263428 TTTTATATTTTATTTATG
1 TTTTATATTATA-TTATA
263446 TTTTATATTATATTATA
1 TTTTATATTATATTATA
263463 TTTTA-ATTAT
1 TTTTATATTAT
263473 TTTTTATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 5 0.20
17 9 0.36
18 11 0.44
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTATATTATATTATA
Found at i:266648 original size:17 final size:17
Alignment explanation
Indices: 266612--266645 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
266602 TAAAATAAAA
*
266612 TAAAATAAATTTTCATT
1 TAAAATAAATCTTCATT
266629 TAAAATAAATCTT-ATT
1 TAAAATAAATCTTCATT
266645 T
1 T
266646 TAACATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATAAATCTTCATT
Found at i:267175 original size:2 final size:2
Alignment explanation
Indices: 267168--267192 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
267158 CAAAAATTTA
267168 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
267193 AATTCGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:272262 original size:2 final size:2
Alignment explanation
Indices: 272255--272313 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
272245 CTTGGAGAAG
272255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
272297 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
272314 GAGAAATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:274109 original size:14 final size:14
Alignment explanation
Indices: 274085--274119 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
274075 CAAAGGAAGG
274085 AAAATTATAAATATT
1 AAAA-TATAAATATT
*
274100 AAAATATAAATTTT
1 AAAATATAAATATT
274114 AAAATA
1 AAAATA
274120 ATTAGATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAATATAAATATT
Found at i:274251 original size:16 final size:15
Alignment explanation
Indices: 274185--274251 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 15
274175 AATTTATTAT
274185 AATTATAAATATAATAA
1 AATTATAAA-A-AATAA
* *
274202 ATATTATAATAAATATT
1 A-ATTATAAAAAATA-A
*
274219 AATAATAAAAAATTAA
1 AATTATAAAAAA-TAA
274235 AATTATAAAATAATAA
1 AATTATAAAA-AATAA
274251 A
1 A
274252 TATAATATCA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
16 26 0.65
17 7 0.17
18 7 0.17
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTATAAAAAATAA
Found at i:275963 original size:27 final size:27
Alignment explanation
Indices: 275925--275995 Score: 101
Period size: 27 Copynumber: 2.7 Consensus size: 27
275915 ATTTTTTTAT
*
275925 AATTAATTATTTTAATTTAAATAATAAA
1 AATTATTTATTTTAATTTAAAT-ATAAA
*
275953 AA-TATTTATTTAAATTTAAATATAAA
1 AATTATTTATTTTAATTTAAATATAAA
275979 AATTATTT-TTTTAATTT
1 AATTATTTATTTTAATTT
275996 TTAACATTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
26 15 0.38
27 22 0.56
28 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTATTTATTTTAATTTAAATATAAA
Found at i:275994 original size:26 final size:27
Alignment explanation
Indices: 275925--275995 Score: 92
Period size: 26 Copynumber: 2.6 Consensus size: 27
275915 ATTTTTTTAT
*
275925 AATTAATTATTTTAATTTAAATAATAAA
1 AATT-ATTTTTTTAATTTAAATAATAAA
*
275953 AA-TATTTATTTAAATTTAAAT-ATAAA
1 AATTATTT-TTTTAATTTAAATAATAAA
275979 AATTATTTTTTTAATTT
1 AATTATTTTTTTAATTT
275996 TTAACATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
26 18 0.47
27 18 0.47
28 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATTATTTTTTTAATTTAAATAATAAA
Found at i:279590 original size:32 final size:33
Alignment explanation
Indices: 279529--279590 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
279519 CACTCAAATA
*
279529 TATCGATACATGTTGCTTAGTATTGATATATTG
1 TATCGATACATGTTGCTTAGTATTAATATATTG
*
279562 TATCGATACATGTT-CTTTGTATTAATATA
1 TATCGATACATGTTGCTTAGTATTAATATA
279591 CCATGAAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 13 0.48
33 14 0.52
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.47
Consensus pattern (33 bp):
TATCGATACATGTTGCTTAGTATTAATATATTG
Found at i:282334 original size:72 final size:72
Alignment explanation
Indices: 282217--282392 Score: 311
Period size: 72 Copynumber: 2.5 Consensus size: 72
282207 TCCTGTAGCT
* *
282217 ATGTATCGATACAATGCATAATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTT
1 ATGTATCGATACAATTCATCATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTT
282282 AGAAGTA
66 AGAAGTA
282289 ATGTATCGATACAATTCATCATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTT
1 ATGTATCGATACAATTCATCATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTT
282354 AGAAGTA
66 AGAAGTA
282361 ATGTATCGATAC-ATT-ATCCATGTATCGATACA
1 ATGTATCGATACAATTCAT-CATGTATCGATACA
282393 AACAGTAGTA
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
70 2 0.02
71 17 0.17
72 82 0.81
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (72 bp):
ATGTATCGATACAATTCATCATGTATCGATACATTGATTTGAAATTATAGCCGTTTATAGCCGTT
AGAAGTA
Found at i:283566 original size:79 final size:79
Alignment explanation
Indices: 283448--283599 Score: 232
Period size: 79 Copynumber: 1.9 Consensus size: 79
283438 AGTACCCCTG
* ***
283448 ATTATGGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTTGGAAATAACAGGG
1 ATTATAGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGG
283513 TTGGAGTATCCTTA
66 TTGGAGTATCCTTA
* * * *
283527 ATTATAGAAAATTGGTGTTTTGAAAATAAAATTGGGGTTGGAGTATCCCCTCAAAAATAACGGGG
1 ATTATAGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGG
283592 TTGGAGTA
66 TTGGAGTA
283600 ACCCCGCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
79 65 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.30
Consensus pattern (79 bp):
ATTATAGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGTATCCCCTCAAAAATAACAGGG
TTGGAGTATCCTTA
Found at i:283594 original size:28 final size:28
Alignment explanation
Indices: 283560--283631 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
283550 AAATAAAATT
*
283560 GGGGTTGGAGTATCCCCTCAAAAATAAC
1 GGGGTTGGAGTATCCCCGCAAAAATAAC
* * *
283588 GGGGTTGGAGTAACCCCGCGAAAATAAT
1 GGGGTTGGAGTATCCCCGCAAAAATAAC
*
283616 GGGGTTGAAGTATCCC
1 GGGGTTGGAGTATCCC
283632 GGATTGTGAA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.31, T:0.21
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGCAAAAATAAC
Found at i:283675 original size:78 final size:78
Alignment explanation
Indices: 283587--283788 Score: 316
Period size: 79 Copynumber: 2.6 Consensus size: 78
283577 TCAAAAATAA
* * * * *
283587 CGGGGTTGGAGTAACCCCGCGAAAATAATGGGGTTGAAGTATCCCGGATTGTGA-AAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCC-GATTGTGAGAAATCAATAT
283651 TTTAGAAATAAAGC
65 TTTAGAAATAAAGC
283665 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCC-CGATTGTGAGAAATCAATAT
* *
283730 TTTAGGAATAAAGT
65 TTTAGAAATAAAGC
283744 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCC
1 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCC
283789 CGATGATTAA
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
78 48 0.42
79 67 0.58
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.25
Consensus pattern (78 bp):
CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCGATTGTGAGAAATCAATATT
TTAGAAATAAAGC
Found at i:283807 original size:27 final size:28
Alignment explanation
Indices: 283744--283816 Score: 103
Period size: 27 Copynumber: 2.6 Consensus size: 28
283734 GGAATAAAGT
**
283744 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
* *
283772 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
283799 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
283817 AATTATGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:283846 original size:185 final size:185
Alignment explanation
Indices: 283428--283865 Score: 481
Period size: 185 Copynumber: 2.4 Consensus size: 185
283418 GGAGATGACG
* * * *
283428 ACGGGGCTGGAGTA-CCCCTGATTATGGAAAATCGGTGTTCTGAAAATAAAATCGGGGTTGGAGT
1 ACGGGGTTGGAGTATCCCC-GATTAT-GAAAATCGGTATTTTGGAAATAAAATCGGGGTTGGAGT
* * *** *
283492 ATCCCCTTGGAAATAACAGGGTTGGAGTATCCTTAATTATAGAAAATTGGTGTTTTGAAAATAAA
64 ATCCCCTCGGAAATAACAGGGTTGGAGTATCCTCAATTATAGAAAATCAATATTTTGAAAATAAA
*
283557 ATTGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTAACCCCGCGAAAATA
129 ATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTAACCCCGCGAAAATA
* * * * ** * **
283614 ATGGGGTTGAAGTATCCCGGATTGTGAAAATCAATATTTTAGAAATAAAGCCGGGGTTGGAGTAT
1 ACGGGGTTGGAGTATCCCCGATTATGAAAATCGGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
* * * *
283679 CCCCTCGGAAATAACGGGGTTGGAGTATCCTCGATTGT-GAGAAATCAATATTTT-AGGAATAAA
66 CCCCTCGGAAATAACAGGGTTGGAGTATCCTCAATTATAGA-AAATCAATATTTTGA-AAATAAA
* ** * * *
283742 GTCGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGT-ATCCC-CGATGATTA
129 ATCGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTAACCCCGCGA-AAATA
* * * *
283798 ACGGGGTTGGAGTATCCCCAATTATGAAAAATTGGTATTTTGGAAATAAAATCAGAGTTGGAGTA
1 ACGGGGTTGGAGTATCCCCGATTATG-AAAATCGGTATTTTGGAAATAAAATCGGGGTTGGAGTA
283863 TCC
65 TCC
283866 TCGATTATAG
Statistics
Matches: 204, Mismatches: 43, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
183 3 0.01
184 31 0.15
185 151 0.74
186 16 0.08
187 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (185 bp):
ACGGGGTTGGAGTATCCCCGATTATGAAAATCGGTATTTTGGAAATAAAATCGGGGTTGGAGTAT
CCCCTCGGAAATAACAGGGTTGGAGTATCCTCAATTATAGAAAATCAATATTTTGAAAATAAAAT
CGGGGTTGGAGTATCCCCTCAAAAATAACGGGGTTGGAGTAACCCCGCGAAAATA
Found at i:283858 original size:106 final size:107
Alignment explanation
Indices: 283665--283865 Score: 253
Period size: 106 Copynumber: 1.9 Consensus size: 107
283655 GAAATAAAGC
** * * * *
283665 CGGGGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCTCGATTGTGAGAAATCAATAT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
* * *
283730 TTTAGGAATAAAGTCGGGGTTGGAGTATCCCCTCGGAAATAA
66 TTTAGGAATAAAATCAGAGTTGGAGTATCCCCTCGGAAATAA
* * ***
283772 CGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGTATCCCCAATTATGAAAAATTGGTAT
1 CGGGGTTGGAGTATCCCCGAGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
283836 TTT-GGAAATAAAATCAGAGTTGGAGTATCC
66 TTTAGG-AATAAAATCAGAGTTGGAGTATCC
283866 TCGATTATAG
Statistics
Matches: 79, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
105 2 0.03
106 58 0.73
107 19 0.24
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (107 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAACGGGGTTGGAGTATCCCCAATTATGAAAAATCAATAT
TTTAGGAATAAAATCAGAGTTGGAGTATCCCCTCGGAAATAA
Found at i:283929 original size:50 final size:50
Alignment explanation
Indices: 283803--283984 Score: 222
Period size: 50 Copynumber: 3.6 Consensus size: 50
283793 GATTAACGGG
* * *
283803 GTTGGAGTATCCCCAATTATGAAAAATTGGTATTTTGGAAATAAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTT-GAAAAAAAATCAGA
* * * *
283854 GTTGGAGTATCCTCGATTAT-AGAAAATTGGTGTTTTGAAAAAAAACCGGG
1 GTTGGAGTATCCCCGATTATGA-AAAATTGGTGTTTTGAAAAAAAATCAGA
* * *
283904 GTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTCGAAAATAAAAATCAGA
1 GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTG-AAA-AAAAATCAGA
*
283956 GTTGGAGTATCTCCGATTATGAAAAATTG
1 GTTGGAGTATCCCCGATTATGAAAAATTG
283985 AGAAACTTAA
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
50 43 0.39
51 34 0.31
52 33 0.30
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (50 bp):
GTTGGAGTATCCCCGATTATGAAAAATTGGTGTTTTGAAAAAAAATCAGA
Found at i:283931 original size:101 final size:101
Alignment explanation
Indices: 283799--283980 Score: 278
Period size: 101 Copynumber: 1.8 Consensus size: 101
283789 CGATGATTAA
* *
283799 CGGGGTTGGAGTATCCCCAATTATGAAAAATTGGTATTTTGGAAAT-AAAATCAGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATTGGTATTTCGAAAATAAAAATCAGAGTTGGAGTA
283863 TC-CTCGATTATAGAAAATTGGTGTTTTGAAAAAAAAC
66 TCTC-CGATTAT-GAAAATTGGTGTTTTGAAAAAAAAC
* * * *
283900 CGGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTCGAAAATAAAAATCAGAGTTGGAGTA
1 CGGGGTTGGAGTATCCCCAATTATGAAAAATTGGTATTTCGAAAATAAAAATCAGAGTTGGAGTA
283965 TCTCCGATTATGAAAA
66 TCTCCGATTATGAAAA
283981 ATTGAGAAAC
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
101 45 0.62
102 27 0.37
103 1 0.01
ACGTcount: A:0.35, C:0.11, G:0.25, T:0.30
Consensus pattern (101 bp):
CGGGGTTGGAGTATCCCCAATTATGAAAAATTGGTATTTCGAAAATAAAAATCAGAGTTGGAGTA
TCTCCGATTATGAAAATTGGTGTTTTGAAAAAAAAC
Found at i:287042 original size:40 final size:40
Alignment explanation
Indices: 286998--287097 Score: 105
Period size: 42 Copynumber: 2.5 Consensus size: 40
286988 ATCCCACTTT
*
286998 TTGAGGACAAAG-GAAAAGAGAATGAAATAG-GTCTTGCTCC
1 TTGAGGACAAAGAGAAAAGA-AAAGAAA-AGTGTCTTGCTCC
* *
287038 TTGAGGACAAAGAGAGAGAAGAAAAGGAAAGTGTCTTGCTTC
1 TTGAGGACAAAGAGA-A-AAGAAAAGAAAAGTGTCTTGCTCC
* *
287080 TTGAGGATAAAGTGAAAA
1 TTGAGGACAAAGAGAAAA
287098 AGAGTACGTC
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
40 14 0.27
41 5 0.10
42 28 0.55
43 4 0.08
ACGTcount: A:0.42, C:0.09, G:0.29, T:0.20
Consensus pattern (40 bp):
TTGAGGACAAAGAGAAAAGAAAAGAAAAGTGTCTTGCTCC
Found at i:287161 original size:42 final size:41
Alignment explanation
Indices: 287114--287206 Score: 98
Period size: 42 Copynumber: 2.2 Consensus size: 41
287104 CGTCCCATTT
* *
287114 TTTGAGGACAAACGAAAAAGGGAAACGAAA-TACGTCCTGCTC
1 TTTGAGGACAAA-GAAAAA-GGAAAAGAAAGTACATCCTGCTC
* * * *
287156 TTTGAGGATGAAAGAAAGAGGAAAATAAAGTGCATCCTGCTC
1 TTTGAGGA-CAAAGAAAAAGGAAAAGAAAGTACATCCTGCTC
287198 TTTGAGGAC
1 TTTGAGGAC
287207 TAAAAAGTGC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
41 8 0.19
42 31 0.74
43 3 0.07
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (41 bp):
TTTGAGGACAAAGAAAAAGGAAAAGAAAGTACATCCTGCTC
Found at i:287281 original size:55 final size:55
Alignment explanation
Indices: 287190--287942 Score: 800
Period size: 55 Copynumber: 13.3 Consensus size: 55
287180 ATAAAGTGCA
* * *
287190 TCCTGCTCTTTGAGGAC-TAAAAAGTGCCACCAACTCGTGTGGGCTTCGAAAGGCG
1 TCCTGCTCTTTGAGGACTTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * * *
287245 TCCTGCTTTTTAAGGA-TTGAAAGGTGTCACCAACTCGTGTGGGCTTTGAAAAGAAAAGGCG
1 TCCTGCTCTTTGAGGACTTGAAA-ATGCCACCAACTTGTGTGGGCTTT-----G-AAAGGCG
* *
287306 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GCG
* * * * *
287367 TTCTGCTCTTTGAGGACTGGAAAATGCCACTAACTTGTGTGGGCTTTGAAAAGCA
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
287422 TCATGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTAGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
287477 TCCTACTCTTTGAGGAC-TGAAAAATGCCACCAACTTATGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * *
287532 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGAGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
287587 TCCTGCTTTTTGAGGACTGGAAAATGCAACCAACTTGTGTGGGCTTTGAAAGGCA
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* * * *
287642 TCCTACTCTTTGAGGACTAGAACATGCCACCAACTTGTGTGGGCTTTAAAAGGCG
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
*
287697 TCCTGCTCTTTGAGGAC-TGAAAAATGCCACCAACTTGTGTGAGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACTTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
* *
287752 TCCTGCTCTTTGAGGAC-TGAAAGGTGCCACCAACTTGTGTGGGCTTTGAAAAAAGAAAGCA
1 TCCTGCTCTTTGAGGACTTGAAA-ATGCCACCAACTTGTGTGGGCTTTG---AAAG---GCG
* * *
287813 TCCTGCTCTTTGAGGGCAT-AAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGCG
* * * * *
287873 TCATGCTCTTTGAGGAC-TGAAAGTGCCACCAGCTTGTGTGGGCTTTAAAAGGCA
1 TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
287927 TCCTGCTCTTTGAGGA
1 TCCTGCTCTTTGAGGA
287943 TAAAAAGGTG
Statistics
Matches: 605, Mismatches: 61, Indels: 65
0.83 0.08 0.09
Matches are distributed among these distances:
54 25 0.04
55 375 0.62
56 7 0.01
58 4 0.01
59 1 0.00
60 71 0.12
61 111 0.18
62 7 0.01
63 3 0.00
65 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (55 bp):
TCCTGCTCTTTGAGGACTTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGCG
Found at i:287527 original size:27 final size:27
Alignment explanation
Indices: 287442--287527 Score: 64
Period size: 27 Copynumber: 3.1 Consensus size: 27
287432 TGAGGACTAG
* *
287442 AAAATGCCACCAACTTGTGTAGGCTTT
1 AAAATGCCACCAACTTATGTGGGCTTT
* ** * * * * **
287469 AAAAGGCGTCCTACTCTTTGAGGACTGA
1 AAAATGCCACCAACT-TATGTGGGCTTT
287497 AAAATGCCACCAACTTATGTGGGCTTT
1 AAAATGCCACCAACTTATGTGGGCTTT
287524 AAAA
1 AAAA
287528 GGCGTCCTGC
Statistics
Matches: 39, Mismatches: 19, Indels: 2
0.65 0.32 0.03
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.27
Consensus pattern (27 bp):
AAAATGCCACCAACTTATGTGGGCTTT
Found at i:288114 original size:154 final size:154
Alignment explanation
Indices: 287833--288191 Score: 565
Period size: 154 Copynumber: 2.3 Consensus size: 154
287823 TGAGGGCATA
* * *
287833 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCATGCTCTTTGAGGACTGAAAGTG
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATGCTCTTTAAAGACTGAAAGTG
* * *
287898 CCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTGAGGATAAAAAGGTGAACGGAGAGA
66 CCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTAAGGAAAAAAAGGTGAAAGGAGAGA
**
287963 GCGTCCTGCTTTTTGAGGACTAGG
131 GCGTCCTGCCCTTTGAGGACTAGG
* * * *
287987 AAGTGCCACCAACTTGTGTAGGCTTTAAAAGGAAAAGGTGTCCTGCTCTTTAAAGACTGAAGGTG
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATGCTCTTTAAAGACTGAAAGTG
*
288052 CCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTAAGGAAAAAAATGTGAAAGGAGAGA
66 CCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTAAGGAAAAAAAGGTGAAAGGAGAGA
288117 GCGTCCTGCCCTTTGAGGACTAGG
131 GCGTCCTGCCCTTTGAGGACTAGG
** * *
288141 AAGTGCCACCAACTTAAGTGGGCTTTAAAAGGAAAAGGCATCTTGCTCTTT
1 AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATGCTCTTT
288192 GAGGACTAAA
Statistics
Matches: 186, Mismatches: 19, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
154 186 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (154 bp):
AAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAAAAGGCGTCATGCTCTTTAAAGACTGAAAGTG
CCACCAGCTTGTGTGGGCTTTAAAAGGCATCCTGCTCTTTAAGGAAAAAAAGGTGAAAGGAGAGA
GCGTCCTGCCCTTTGAGGACTAGG
Found at i:289167 original size:1 final size:1
Alignment explanation
Indices: 289161--289252 Score: 67
Period size: 1 Copynumber: 92.0 Consensus size: 1
289151 AAGCAGATTC
* * * * * * * * *
289161 TTTTTTTTATCTTTTTTCTTTGTTTTTTTTATTTTTTTGTTTTTTTGTTTTTTTGTTTTTTTTAT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * *
289226 TTTGCTTTTTTTTTTGTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
289253 AGAAAAGAAG
Statistics
Matches: 66, Mismatches: 25, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (1 bp):
T
Found at i:289186 original size:22 final size:21
Alignment explanation
Indices: 289161--289253 Score: 77
Period size: 21 Copynumber: 4.4 Consensus size: 21
289151 AAGCAGATTC
289161 TTTTTTTTATCTTTTTTCTTTG
1 TTTTTTTTAT-TTTTTTCTTTG
*
289183 TTTTTTTTATTTTTTTGTTT-
1 TTTTTTTTATTTTTTTCTTTG
* *
289203 TTTTGTTTT-TTTGTTTTTTTTA
1 TTTT-TTTTATTT-TTTTCTTTG
* *
289225 TTTTGCTTT-TTTTTTT-GTTG
1 TTTT-TTTTATTTTTTTCTTTG
289245 TTTTTTTTA
1 TTTTTTTTA
289254 GAAAAGAAGG
Statistics
Matches: 61, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
19 3 0.05
20 13 0.21
21 24 0.39
22 21 0.34
ACGTcount: A:0.04, C:0.03, G:0.08, T:0.85
Consensus pattern (21 bp):
TTTTTTTTATTTTTTTCTTTG
Found at i:289198 original size:33 final size:33
Alignment explanation
Indices: 289175--289243 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
289165 TTTTATCTTT
289175 TTTCTTTGTTTTTTTTATTTTTTTGTTTTTTTG
1 TTTCTTTGTTTTTTTTATTTTTTTGTTTTTTTG
*
289208 TTTTTTTGTTTTTTTTATTTTGCTTT-TTTTTTTG
1 TTTCTTTGTTTTTTTTATTTT--TTTGTTTTTTTG
289242 TT
1 TT
289244 GTTTTTTTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
33 20 0.61
34 10 0.30
35 3 0.09
ACGTcount: A:0.03, C:0.03, G:0.09, T:0.86
Consensus pattern (33 bp):
TTTCTTTGTTTTTTTTATTTTTTTGTTTTTTTG
Found at i:289205 original size:16 final size:15
Alignment explanation
Indices: 289172--289252 Score: 92
Period size: 15 Copynumber: 5.3 Consensus size: 15
289162 TTTTTTTATC
*
289172 TTTTTTCTTTGTTTTT
1 TTTTTTTTTTG-TTTT
289188 TTTATTTTTTTGTTTT
1 TTT-TTTTTTTGTTTT
289204 TTTGTTTTTTTG-TTT
1 TTT-TTTTTTTGTTTT
* *
289219 TTTTTATTTTGCTTT
1 TTTTTTTTTTGTTTT
*
289234 TTTTTTTGTTGTTTT
1 TTTTTTTTTTGTTTT
289249 TTTT
1 TTTT
289253 AGAAAAGAAG
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
14 7 0.12
15 25 0.44
16 18 0.32
17 7 0.12
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.86
Consensus pattern (15 bp):
TTTTTTTTTTGTTTT
Found at i:289213 original size:37 final size:37
Alignment explanation
Indices: 289161--289251 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 37
289151 AAGCAGATTC
* *
289161 TTTTTTTTATCTTTTTTCTTTGTTTT-TTTTATTTTTT
1 TTTTTTTTGT-TTTTTTCTTTGTTTTATTTTACTTTTT
* * *
289198 TGTTTTTTTGTTTTTTTGTTTTTTTTATTTTGCTTTTT
1 T-TTTTTTTGTTTTTTTCTTTGTTTTATTTTACTTTTT
*
289236 TTTTTGTTGTTTTTTT
1 TTTTTTTTGTTTTTTT
289252 TAGAAAAGAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
37 28 0.61
38 18 0.39
ACGTcount: A:0.03, C:0.03, G:0.08, T:0.86
Consensus pattern (37 bp):
TTTTTTTTGTTTTTTTCTTTGTTTTATTTTACTTTTT
Found at i:289251 original size:29 final size:29
Alignment explanation
Indices: 289171--289253 Score: 105
Period size: 29 Copynumber: 2.8 Consensus size: 29
289161 TTTTTTTTAT
* *
289171 CTTTTTTCTTTGTT-TTTTTTATTTTTTTG
1 CTTTTTTTTTTGTTGTTTTTT-TTATTTTG
* *
289200 TTTTTTTGTTTTTTTGTTTTTTTTATTTTG
1 CTTTTTT-TTTTGTTGTTTTTTTTATTTTG
289230 CTTTTTTTTTTGTTGTTTTTTTTA
1 CTTTTTTTTTTGTTGTTTTTTTTA
289254 GAAAAGAAGG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.48
30 18 0.39
31 6 0.13
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.84
Consensus pattern (29 bp):
CTTTTTTTTTTGTTGTTTTTTTTATTTTG
Found at i:301786 original size:79 final size:79
Alignment explanation
Indices: 301648--301900 Score: 244
Period size: 79 Copynumber: 3.2 Consensus size: 79
301638 AGATTACGAT
* * * *
301648 AGGGTTAGAGTACCCCTGATTATGGAAAATCGGTGTTCTGAAAATAAAATCAGAGTTGGAGTATC
1 AGGGTTGGAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCAGAGTTGGAGTATC
*
301713 CCCTTTG-AAATAAC
66 CCC-TCGAAAATAAC
* * *
301727 AGGGTTGGAGTATCCCTAATTATAGAAAATTGGTGTTTTGAAAATAAAATC-GGGATTGGAGTAT
1 AGGGTTGGAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCAGAG-TTGGAGTAT
301791 CCCCTCGAAAATAAC
65 CCCCTCGAAAATAAC
* ** * ** * * * ** *
301806 GGGGTTGGAGTATCCCCGATTGT-GAGAAATCAATATT-TTAGGAATAAAGCCAGGGTTGGAGTA
1 AGGGTTGGAGTATCCCTAATTATAGA-AAATCGGTGTTCTGA-AAATAAAATCAGAGTTGGAGTA
*
301869 TCCCCTCGGAAATAAC
64 TCCCCTCGAAAATAAC
*
301885 GGGGTTGGAGTATCCC
1 AGGGTTGGAGTATCCC
301901 CGATGATTAA
Statistics
Matches: 148, Mismatches: 21, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
78 8 0.05
79 137 0.93
80 3 0.02
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (79 bp):
AGGGTTGGAGTATCCCTAATTATAGAAAATCGGTGTTCTGAAAATAAAATCAGAGTTGGAGTATC
CCCTCGAAAATAAC
Found at i:301919 original size:27 final size:28
Alignment explanation
Indices: 301858--301927 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
301848 AATAAAGCCA
**
301858 GGGTTGGAGTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
* *
301886 GGGTTGGAGTATCCCCGATG-ATTAACG
1 GGGTTGGAGTATCCCCGAGGAAATAACG
301913 GGGTTGGAGTATCCC
1 GGGTTGGAGTATCCC
301928 AAATTATGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.21, C:0.20, G:0.34, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGAGGAAATAACG
Found at i:302061 original size:102 final size:101
Alignment explanation
Indices: 301911--302095 Score: 289
Period size: 102 Copynumber: 1.8 Consensus size: 101
301901 CGATGATTAA
* * *
301911 CGGGGTTGGAGTATCCCAAATTATGAAAATTGGTGTTTTGAAAATAAAATTGGAGCTGGAGTATC
1 CGGGGTTGGAGTATCCCAAATTATGAAAATTGGTGTTTCGAAAATAAAATCGGAGCTAGAGTATC
*
301976 CCCGATTATAGAAAATTGGTGTTTTGAAAAAAACAC
66 CCCGATTATAAAAAATTGGTGTTTTGAAAAAAACAC
** * *
302012 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCGGAGTTAGAGTAT
1 CGGGGTTGGAGTATCCCAAATTATG-AAAATTGGTGTTTCGAAAATAAAATCGGAGCTAGAGTAT
302077 CCCCGATTATAAAAAATTG
65 CCCCGATTATAAAAAATTG
302096 AGAAACTTAA
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
101 22 0.29
102 53 0.71
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (101 bp):
CGGGGTTGGAGTATCCCAAATTATGAAAATTGGTGTTTCGAAAATAAAATCGGAGCTAGAGTATC
CCCGATTATAAAAAATTGGTGTTTTGAAAAAAACAC
Found at i:302092 original size:51 final size:51
Alignment explanation
Indices: 301915--302095 Score: 231
Period size: 51 Copynumber: 3.6 Consensus size: 51
301905 GATTAACGGG
** * *
301915 GTTGGAGTATCCCAAATTAT-GAAAATTGGTGTTTTGAAAATAAAATTGGA
1 GTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAATCGGA
* * * *
301965 GCTGGAGTATCCCCGATTATAGAAAATTGGTGTTTTGAAAA-AAACACCGGG
1 GTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAA-ATCGGA
* * *
302016 GTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTCGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAATCGGA
*
302067 GTTAGAGTATCCCCGATTATAAAAAATTG
1 GTTGGAGTATCCCCGATTATAAAAAATTG
302096 AGAAACTTAA
Statistics
Matches: 112, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
50 20 0.18
51 89 0.79
52 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATAAAAAATTGGTGTTTTGAAAATAAAATCGGA
Found at i:304554 original size:19 final size:21
Alignment explanation
Indices: 304530--304579 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
304520 AGCGATACAC
304530 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGTA
*
304549 TGTATCGATACATTTACTGTT
1 TGTATCGATACATTTACTGTA
304570 TGTATCGATA
1 TGTATCGATA
304580 TGTTTGGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 12 0.43
20 5 0.18
21 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (21 bp):
TGTATCGATACATTTACTGTA
Found at i:307180 original size:21 final size:21
Alignment explanation
Indices: 307154--307193 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
307144 GATTTTGATG
* *
307154 AAAAATGAAGTATTTTGTAGT
1 AAAAATGAAGAAATTTGTAGT
307175 AAAAATGAAGAAATTTGTA
1 AAAAATGAAGAAATTTGTA
307194 AAAGATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (21 bp):
AAAAATGAAGAAATTTGTAGT
Found at i:307387 original size:20 final size:21
Alignment explanation
Indices: 307357--307395 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
307347 ATCTAAATTT
307357 TTCAGATGTATCGATACATCC
1 TTCAGATGTATCGATACATCC
307378 TTCA-ATGTATCGATACAT
1 TTCAGATGTATCGATACAT
307396 TCTGAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCAGATGTATCGATACATCC
Found at i:312773 original size:13 final size:13
Alignment explanation
Indices: 312733--312780 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 13
312723 TCGTTAGAAG
312733 CAATGTATCGATA
1 CAATGTATCGATA
312746 CAA--T-TC-AT-
1 CAATGTATCGATA
312754 C-ATGTATCGATA
1 CAATGTATCGATA
312766 CAATGTATCGATA
1 CAATGTATCGATA
312779 CA
1 CA
312781 TTGTCCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
7 1 0.03
8 1 0.03
9 3 0.10
10 4 0.14
11 3 0.10
12 1 0.03
13 16 0.55
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:312795 original size:32 final size:32
Alignment explanation
Indices: 312733--312800 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
312723 TCGTTAGAAG
312733 CAATGTATCGATACAATTCATCATGTATCGATA
1 CAATGTATCGATACAATTCA-CATGTATCGATA
*
312766 CAATGTATCGATACATTGTC-CATGTATCGATA
1 CAATGTATCGATACAAT-TCACATGTATCGATA
312798 CAA
1 CAA
312801 ACAATGGTAG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 15 0.45
33 16 0.48
34 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.32
Consensus pattern (32 bp):
CAATGTATCGATACAATTCACATGTATCGATA
Found at i:312858 original size:20 final size:20
Alignment explanation
Indices: 312833--312883 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
312823 TAGTTTCATA
**
312833 TATCGATACAATTGTCCATG
1 TATCGATACAATTGAACATG
*
312853 TATCGATAC-AGTGAACATG
1 TATCGATACAATTGAACATG
312872 TATCGATACAAT
1 TATCGATACAAT
312884 GTATCGATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 16 0.62
20 10 0.38
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (20 bp):
TATCGATACAATTGAACATG
Found at i:312887 original size:13 final size:13
Alignment explanation
Indices: 312869--312895 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
312859 TACAGTGAAC
312869 ATGTATCGATACA
1 ATGTATCGATACA
312882 ATGTATCGATACA
1 ATGTATCGATACA
312895 A
1 A
312896 AGCATGATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:319322 original size:17 final size:17
Alignment explanation
Indices: 319293--319340 Score: 80
Period size: 17 Copynumber: 2.9 Consensus size: 17
319283 TAAATTTGGC
*
319293 TAAAATTGA-AATAAGG
1 TAAAATTCACAATAAGG
319309 TAAAATTCACAATAAGG
1 TAAAATTCACAATAAGG
319326 TAAAATTCACAATAA
1 TAAAATTCACAATAA
319341 AGGGGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.56, C:0.08, G:0.10, T:0.25
Consensus pattern (17 bp):
TAAAATTCACAATAAGG
Found at i:320168 original size:20 final size:19
Alignment explanation
Indices: 320139--320178 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
320129 GCCCAATGGC
320139 TATGATTGTATCGATACAT
1 TATGATTGTATCGATACAT
320158 TATGAATTGTATCGATACAT
1 TATG-ATTGTATCGATACAT
320178 T
1 T
320179 GAGCCCAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (19 bp):
TATGATTGTATCGATACAT
Found at i:336904 original size:28 final size:28
Alignment explanation
Indices: 336864--337385 Score: 677
Period size: 28 Copynumber: 18.1 Consensus size: 28
336854 CGTTTATCTC
336864 TTCAAAGCCCACAAGTCAGTGGCACCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
* *
336892 TTCAAAGCCCACAAGTCAGTAGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* *
336921 TTCAAAGCCCACAAATTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* * *
336950 TTCAAAGTCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
336978 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
337007 TTCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
337035 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
337063 TTCAAAGCCCATGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACCTT
*
337093 TTCAAAGCCCACAAATCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
337122 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
337150 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
337179 TTCAAAGCCCACAAGTTAATGGCATCC-T
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTT
* * *
337207 TTCAAAGCCCATAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
*
337235 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
*
337264 TTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTT
337292 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTT
* *
337321 TTCAAAGCCCACACGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACA--AGTCAGTGG-CAC-CTT
*
337353 TTCAAAGCCCACACAAGTTAGTGGCACCATT
1 TTCAAAG-CC-CACAAGTCAGTGGCACC-TT
337384 TT
1 TT
337386 TTTTAAAAAA
Statistics
Matches: 441, Mismatches: 36, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
27 2 0.00
28 203 0.46
29 166 0.38
30 30 0.07
31 14 0.03
32 20 0.05
33 2 0.00
34 4 0.01
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTT
Found at i:336981 original size:57 final size:56
Alignment explanation
Indices: 336864--337380 Score: 692
Period size: 57 Copynumber: 9.0 Consensus size: 56
336854 CGTTTATCTC
* * *
336864 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTAGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCA-CCCT
* * * *
336921 TTCAAAGCCCACAAATTAGTGGCACTCTTTTCAAAGTCCATAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCT
*
336978 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAATCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCT
*
337035 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCATGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCA--CAAGTCAGTGGCACCCT
*
337093 TTCAAAGCCCACAAATCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * *
337150 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTTAATGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCAC-CTTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
337207 TTCAAAGCCCATAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
337264 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* * *
337321 TTCAAAGCCCACACGAGTCGGTGGTAACTCTTTTCAAAGCCCACACAAGTTAGTGGCACC
1 TTCAAAGCCCACA--AGTCAGTGG-CAC-CTTTTCAAAG-CC-CACAAGTCAGTGGCACC
337381 ATTTTTTTTA
Statistics
Matches: 416, Mismatches: 33, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
56 38 0.09
57 264 0.63
58 64 0.15
59 21 0.05
60 2 0.00
61 9 0.02
62 3 0.01
63 15 0.04
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:337956 original size:20 final size:20
Alignment explanation
Indices: 337933--338010 Score: 113
Period size: 20 Copynumber: 3.9 Consensus size: 20
337923 AAAGCACCCA
337933 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTCTTC
* *
337953 AATGTATCGATACATGT-ATG
1 AATGTATCGATACAT-TCTTC
*
337973 AATGTATCGATACATTCTTT
1 AATGTATCGATACATTCTTC
337993 AATGTATCGATACATTCT
1 AATGTATCGATACATTCT
338011 GTGTTTTTAC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
19 1 0.02
20 50 0.96
21 1 0.02
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTCTTC
Found at i:343220 original size:13 final size:13
Alignment explanation
Indices: 343202--343226 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
343192 TTTAACGATT
343202 TGTATCGATACAA
1 TGTATCGATACAA
343215 TGTATCGATACA
1 TGTATCGATACA
343227 TAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:343302 original size:21 final size:19
Alignment explanation
Indices: 343276--343331 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 19
343266 TGCCAAGAAA
*
343276 ATGTATCGATACATTACTCAT
1 ATGTATCGATACATGA-TC-T
*
343297 ATGTATTGATACACTGATCT
1 ATGTATCGATACA-TGATCT
*
343317 TTGTATCGATACATG
1 ATGTATCGATACATG
343332 CAGGCAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
19 2 0.07
20 12 0.40
21 14 0.47
22 2 0.07
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATGATCT
Found at i:343441 original size:52 final size:53
Alignment explanation
Indices: 343318--343447 Score: 208
Period size: 53 Copynumber: 2.5 Consensus size: 53
343308 CACTGATCTT
* * *
343318 TGTATCGATACATGCAGGCAAATTTGCCTAGATATATCGATACCCCTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCAATACCACTATGAAA
* *
343371 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCAATA-CACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCAATACCACTATGAAA
343423 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
343448 TCATATTTCG
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
52 33 0.46
53 38 0.54
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (53 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATATATCAATACCACTATGAAA
Found at i:344800 original size:13 final size:13
Alignment explanation
Indices: 344782--344808 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
344772 ACAATATTCT
344782 TTGTATCGATACA
1 TTGTATCGATACA
344795 TTGTATCGATACA
1 TTGTATCGATACA
344808 T
1 T
344809 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:344970 original size:20 final size:20
Alignment explanation
Indices: 344932--344971 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
344922 TTACAAATTT
344932 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
344953 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
344972 CATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:347209 original size:20 final size:20
Alignment explanation
Indices: 347184--347253 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
347174 CCCTTGAATG
347184 TATCGATACACACCCAAATA
1 TATCGATACACACCCAAATA
* ** ** *
347204 TATCGATACATTATGC-TTTG
1 TATCGATACA-CACCCAAATA
*
347224 TATCGATACACGCCCAAATA
1 TATCGATACACACCCAAATA
347244 TATCGATACA
1 TATCGATACA
347254 TTATGGTTTG
Statistics
Matches: 35, Mismatches: 13, Indels: 4
0.67 0.25 0.08
Matches are distributed among these distances:
19 1 0.03
20 32 0.91
21 2 0.06
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (20 bp):
TATCGATACACACCCAAATA
Found at i:347240 original size:40 final size:40
Alignment explanation
Indices: 347182--347273 Score: 166
Period size: 40 Copynumber: 2.3 Consensus size: 40
347172 AACCCTTGAA
347182 TGTATCGATACACACCCAAATATATCGATACATTATGCTT
1 TGTATCGATACACACCCAAATATATCGATACATTATGCTT
* *
347222 TGTATCGATACACGCCCAAATATATCGATACATTATGGTT
1 TGTATCGATACACACCCAAATATATCGATACATTATGCTT
347262 TGTATCGATACA
1 TGTATCGATACA
347274 TGTTCATTGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.34, C:0.21, G:0.13, T:0.33
Consensus pattern (40 bp):
TGTATCGATACACACCCAAATATATCGATACATTATGCTT
Found at i:347285 original size:19 final size:20
Alignment explanation
Indices: 347261--347314 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
347251 ACATTATGGT
**
347261 TTGTATCGATACATGTTC-A
1 TTGTATCGATACATGGACAA
347280 TTGTATCGATACATGGACAA
1 TTGTATCGATACATGGACAA
347300 TTGTATCGATACATG
1 TTGTATCGATACATG
347315 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.50
20 16 0.50
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGGACAA
Found at i:347732 original size:20 final size:20
Alignment explanation
Indices: 347707--347775 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
347697 CTGCCAAGGA
347707 AATGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
347727 AATGTATCGATAC---A-T-
1 AATGTATCGATACATTATTC
347742 --TGTATCGATACATTATTC
1 AATGTATCGATACATTATTC
347760 AATGTATCGATACATT
1 AATGTATCGATACATT
347776 GTATCGATAC
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.26
16 2 0.05
17 2 0.05
20 27 0.64
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTATTC
Found at i:347747 original size:13 final size:13
Alignment explanation
Indices: 347729--347800 Score: 93
Period size: 13 Copynumber: 6.0 Consensus size: 13
347719 CATTATTCAA
347729 TGTATCGATACAT
1 TGTATCGATACAT
347742 TGTATCGATACA-
1 TGTATCGATACAT
*
347754 T-TAT---T-CAA
1 TGTATCGATACAT
347762 TGTATCGATACAT
1 TGTATCGATACAT
347775 TGTATCGATACAT
1 TGTATCGATACAT
347788 TGTATCGATACAT
1 TGTATCGATACAT
347801 CGATCTTTGT
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
7 2 0.04
8 2 0.04
9 3 0.06
11 3 0.06
12 2 0.04
13 40 0.77
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:347751 original size:33 final size:33
Alignment explanation
Indices: 347709--347820 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
347699 GCCAAGGAAA
347709 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
347742 TGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTATTCAATGTATCGATACAT
* * ** *
347775 TGTATCGATACATTGTATCGATACATCGAT-CTT
1 TGTATCGATACATTAT-TCAATGTATCGATACAT
347808 TGTATCGATACAT
1 TGTATCGATACAT
347821 CTGGGAAGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
33 63 0.86
34 10 0.14
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.39
Consensus pattern (33 bp):
TGTATCGATACATTATTCAATGTATCGATACAT
Found at i:347812 original size:46 final size:46
Alignment explanation
Indices: 347729--347820 Score: 141
Period size: 46 Copynumber: 2.0 Consensus size: 46
347719 CATTATTCAA
*
347729 TGTATCGATACATTGTATCGATACATTATTCAATGTATCGATACAT
1 TGTATCGATACATTGTATCGATACATGATTCAATGTATCGATACAT
**
347775 TGTATCGATACATTGTATCGATACATCGA-TCTTTGTATCGATACAT
1 TGTATCGATACATTGTATCGATACAT-GATTCAATGTATCGATACAT
347821 CTGGGAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
46 41 0.98
47 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.39
Consensus pattern (46 bp):
TGTATCGATACATTGTATCGATACATGATTCAATGTATCGATACAT
Found at i:347866 original size:20 final size:20
Alignment explanation
Indices: 347841--347892 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
347831 TACCCAGATG
347841 TATCGATACATTGCTCATTC
1 TATCGATACATTGCTCATTC
*
347861 TATCGATACATTGCTCATTG
1 TATCGATACATTGCTCATTC
347881 TATCGATACATT
1 TATCGATACATT
347893 CAGGCATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.12, T:0.40
Consensus pattern (20 bp):
TATCGATACATTGCTCATTC
Found at i:350325 original size:51 final size:51
Alignment explanation
Indices: 350264--350395 Score: 198
Period size: 51 Copynumber: 2.6 Consensus size: 51
350254 GTTATTTTCG
* *
350264 AGGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTCCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAAT
* *
350315 AGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAAT
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAAT
*
350366 AAGGGATACTCCAACCCCG---TTATTTCCAAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAA
350396 GGGATACTTC
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
48 11 0.15
51 64 0.85
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.30
Consensus pattern (51 bp):
AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCACAAT
Found at i:350400 original size:79 final size:79
Alignment explanation
Indices: 350315--350623 Score: 350
Period size: 79 Copynumber: 3.9 Consensus size: 79
350305 TTTCCACAAT
* * * *
350315 AGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCACAATAAGGGATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCAGGGATACTCCAA
* * *
350380 CCCCGTTATTTCCA
66 CCCTGTTATTTTCG
* * ** * * * *
350394 AAGGGATACTTCAACCCCGACCTTATTTCTAAATCATCGATTTTTCATAATCGGGGATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCAGGGATACTCCAA
350459 CCCTGTTATTTTCG
66 CCCTGTTATTTTCG
* * * * *
350473 AGGGGATACTCCAACACCGATTTCATTTTCAAAATACTGATTTTT-ATAATCAGGGATACTCCAA
1 AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCAGGGATACTCCAA
350537 CCCTGTTATTTTCG
66 CCCTGTTATTTTCG
*** * * * * *
350551 AGGGGATACTCCAACCCCGATTTTTATTTCTGGAATATCGATTTTCCATAATCGGGGATACTCTA
1 AGGGGATACTCCAACCCCGA-TTTTATTTCCAAAACACCGATTTTTCATAATCAGGGATACTCCA
350616 ACCCTGTT
65 ACCCTGTT
350624 GTTATCTCCA
Statistics
Matches: 189, Mismatches: 39, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
78 51 0.27
79 114 0.60
80 24 0.13
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (79 bp):
AGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCGATTTTTCATAATCAGGGATACTCCAA
CCCTGTTATTTTCG
Done.