Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold13
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: 2744999
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 506982 characters in sequence are not A, C, G, or T
File 3 of 15
Found at i:489068 original size:20 final size:21
Alignment explanation
Indices: 489045--489098 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
489035 CATTTCAGGC
489045 ATGTATCAATACATTCACT-T
1 ATGTATCAATACATTCACTGT
* * *
489065 ATGTTTCGATACATTTACTGT
1 ATGTATCAATACATTCACTGT
*
489086 TTGTATCAATACA
1 ATGTATCAATACA
489099 ACAAAAATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (21 bp):
ATGTATCAATACATTCACTGT
Found at i:489965 original size:45 final size:45
Alignment explanation
Indices: 489901--489991 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
489891 AAAGTTAATT
*
489901 ATTAGCAGAAAGACAGAAGGGATCATATTCAAATAATAACTAAAA
1 ATTAGCAAAAAGACAGAAGGGATCATATTCAAATAATAACTAAAA
**
489946 ATTAGCAAAAAGATGGAAGGGATCATATTCAAATAATAACTAAAA
1 ATTAGCAAAAAGACAGAAGGGATCATATTCAAATAATAACTAAAA
489991 A
1 A
489992 CTAAAGATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.54, C:0.10, G:0.15, T:0.21
Consensus pattern (45 bp):
ATTAGCAAAAAGACAGAAGGGATCATATTCAAATAATAACTAAAA
Found at i:493390 original size:21 final size:20
Alignment explanation
Indices: 493343--493396 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
493333 CATTTCAGAC
* *
493343 ATGTATCAATACATTCACTT
1 ATGTATCGATACATTCACTA
493363 ATGTATCGATACATTCACTA
1 ATGTATCGATACATTCACTA
493383 ATTGTATCGATACA
1 A-TGTATCGATACA
493397 AATTATAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:501565 original size:20 final size:19
Alignment explanation
Indices: 501540--501592 Score: 79
Period size: 20 Copynumber: 2.7 Consensus size: 19
501530 AAAAAAACAG
*
501540 AATGTATCGATACATTTAA
1 AATGTATCGATACATTGAA
501559 CAATGTATCGATACATTGAA
1 -AATGTATCGATACATTGAA
501579 AATTGTATCGATAC
1 AA-TGTATCGATAC
501593 TTCTGGGTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 2 0.06
20 29 0.94
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.34
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:501605 original size:70 final size:70
Alignment explanation
Indices: 501491--501624 Score: 189
Period size: 70 Copynumber: 1.9 Consensus size: 70
501481 AATTAACTAG
** *
501491 ATGTATCTTTACATTAAAAAATGATCGATACATCTGGATAAAAAAACAGAATGTATCGATACATT
1 ATGTATCGATACATTAAAAAATGATCGATACATCTGGATAAAAAAACAAAATGTATCGATACATT
501556 TAACA
66 TAACA
* * * *
501561 ATGTATCGATACATTGAAAATTGTATCGATACTTCTGGGT-AAAAAACAAAATGTATCGATACAT
1 ATGTATCGATACATTAAAAAATG-ATCGATACATCTGGATAAAAAAACAAAATGTATCGATACAT
501625 GTACTGTTCA
Statistics
Matches: 56, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
70 42 0.75
71 14 0.25
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (70 bp):
ATGTATCGATACATTAAAAAATGATCGATACATCTGGATAAAAAAACAAAATGTATCGATACATT
TAACA
Found at i:507455 original size:21 final size:20
Alignment explanation
Indices: 507408--507461 Score: 81
Period size: 20 Copynumber: 2.6 Consensus size: 20
507398 CATTTGAGAC
*
507408 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTA
*
507428 ATGTATCAATACATTCACTA
1 ATGTATCGATACATTCACTA
507448 ATTGTATCGATACA
1 A-TGTATCGATACA
507462 AATCGTAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACATTCACTA
Found at i:508035 original size:155 final size:155
Alignment explanation
Indices: 507808--508547 Score: 649
Period size: 155 Copynumber: 4.8 Consensus size: 155
507798 ACTCAATTCT
* * ** * * *
507808 AAAAATTACAAAAATTCTTCTAAGGGATACCTTCAACGTAAAAGTACCCTAATACCCCTAAAAGA
1 AAAAATTATAAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTACTC-GATACCCCTAAAAGA
* * *
507873 CTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCC-CTCTTCGGCATAGAAGCGGACT
65 CTTAAAAAGATTATAAATGGGATGAACCTAACCTAAATATCCAC-CTTCGGCATAAAAGCAGACT
507937 TGGA-GACAACCTAGGACTTGGCTTTA
129 TGGACGACAACCTAGGACTTGGCTTTA
* * * * * *
507963 AAAAATTATGAAAATGTCTCTAAGGGATACCTTCGACGTAAAAGTACTCGATACTCTTAAATGAC
1 AAAAATTATAAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAAGAC
* * * * * * *
508028 TAAAAAAAATT-TAAA-GGGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCT-
66 TTAAAAAGATTATAAATGGGATGAACCTAACCTAAATATCCACCTTCGGCATAAAAGCAGACTTG
* ** * * *
508090 AACGATGACCTAAGA-TTCAGTTTTA
131 GACGACAACCTAGGACTT-GGCTTTA
* * * * *
508115 GAAAATTATAAAAATGCCCCCAAGGGATACCTTCGATGTGAAAA-TATCTCGATATCCTTAAAAG
1 AAAAATTATAAAAATGCCCCTAAGGGATACCTTCGACGT-AAAAGTA-CTCGATACCCCTAAAAG
* * **
508179 ACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCC-CCATTTGGCATTGAAGCAGAC
64 ACTTAAAAAGATTATAAATGGGATGAACCTAACCTAAATATCCACC-TTCGGCATAAAAGCAGAC
* * * * *
508243 TTGG-TGACAACTTAGAACTCGGCTCTA
128 TTGGACGACAACCTAGGACTTGGCTTTA
* * * * * ** *
508270 AAAAATTATGAAAACGCCCCT-AGAGGATACCTCCGACGTAAAAGTACCCAATACAGCTAAAAAA
1 AAAAATTATAAAAATGCCCCTAAG-GGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAAGA
* * * * *
508334 CTAAAAAAAGGATTTTAAAAGGGATGAACCTATCCTAAATATCCACCTTCGGTATAAAAGCAGAC
65 CT-TAAAAA-GATTATAAATGGGATGAACCTAACCTAAATATCCACCTTCGGCATAAAAGCAGAC
* * ** * *
508399 -TCGATGATGACCTAGGAC-TCGATTCTA
128 TTGGACGACAACCTAGGACTTGGCTT-TA
* * * * * * *
508426 AAAAATTACAAAAATACCCCTAGGGGATACCTTCAAAGTGAAAGTATCTCGATACCCCTAAAGGA
1 AAAAATTATAAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTA-CTCGATACCCCTAAAAGA
* **
508491 CTTAAAAAGATTATAAATGGGATGAACCTAACCTAAATGTCCACCTGGGGCATAAAA
65 CTTAAAAAGATTATAAATGGGATGAACCTAACCTAAATATCCACCTTCGGCATAAAA
508548 ACGGACCAGT
Statistics
Matches: 454, Mismatches: 112, Indels: 38
0.75 0.19 0.06
Matches are distributed among these distances:
151 3 0.01
152 87 0.19
153 33 0.07
154 45 0.10
155 172 0.38
156 97 0.21
157 17 0.04
ACGTcount: A:0.41, C:0.20, G:0.16, T:0.24
Consensus pattern (155 bp):
AAAAATTATAAAAATGCCCCTAAGGGATACCTTCGACGTAAAAGTACTCGATACCCCTAAAAGAC
TTAAAAAGATTATAAATGGGATGAACCTAACCTAAATATCCACCTTCGGCATAAAAGCAGACTTG
GACGACAACCTAGGACTTGGCTTTA
Found at i:508515 original size:311 final size:306
Alignment explanation
Indices: 507738--508528 Score: 937
Period size: 307 Copynumber: 2.6 Consensus size: 306
507728 GGTGTCTGCA
* ** * * * ** **
507738 GGATAAACCTAACCTAAATATCCACCTTTAACAAAAAAACAAACCCAGTGACAACCTAGGACTCA
1 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAGGACTC-
* ** * * * *
507803 ATTCT-AAAAATTACAAAAATTCTTCTAAGGGATACCTTCAACGTAAAAGTA-CCCTAATACCCC
65 ATTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTC-GATACCCC
507866 TAAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCTCTTCGGCATAGAAG
129 TAAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCTCTTCGGCATAGAAG
* * * * * * * *
507931 CGGACTTGGAGACAACCTAGGACTTGGCTTTAAAAAATTATGAAAATGTCTCTAAGGGATACCTT
194 CAGACTTGGAGACAACCTAGAACTCGGCTCTAAAAAATTATGAAAACGCCCCTAAGGGATACCTC
* * * **
507996 CGACGTAAAAGTACTCGATACTCTTAAATGACTAAAAAAAATTTAAAG
259 CGACGTAAAAGTACCCAATACGCTTAAAAAACTAAAAAAAATTTAAAG
* *
508044 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAAGATTCA
1 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAGGACTCA
* * * * * * * * * *
508109 GTTTTAGAAAATTATAAAAATGCCCCCAAGGGATACCTTCGATGTGAAAATATCTCGATATCCTT
66 -TTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTCGATACCCCT
* *
508174 AAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCC-CATTTGGCATTGAAG
130 AAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCTC-TTCGGCATAGAAG
* *
508238 CAGACTTGGTGACAACTTAGAACTCGGCTCTAAAAAATTATGAAAACGCCCCT-AGAGGATACCT
194 CAGACTTGGAGACAACCTAGAACTCGGCTCTAAAAAATTATGAAAACGCCCCTAAG-GGATACCT
508302 CCGACGTAAAAGTACCCAATACAGC-TAAAAAACTAAAAAAAGGATTTTAAAAG
258 CCGACGTAAAAGTACCCAATAC-GCTTAAAAAACTAAAAAAA--A-TTT-AAAG
* ** * * *
508355 GGATGAACCTATCCTAAATATCCACCTTCGGTATAAAAGCAGA-CTCGATGATGACCTAGGACTC
1 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCT-AACGATGACCTAGGACTC
*
508419 GATTCTAAAAAATTACAAAAATACCCCTAGGGGATACCTTCAAAGTGAAAGTATCTCGATACCCC
65 -ATTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTCGATACCCC
* *
508484 TAAAGGACTTAAAAAGATTATAAATGGGATGAACCTAACCTAAAT
129 TAAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAAT
508529 GTCCACCTGG
Statistics
Matches: 408, Mismatches: 65, Indels: 19
0.83 0.13 0.04
Matches are distributed among these distances:
305 1 0.00
306 58 0.14
307 187 0.46
308 3 0.01
309 1 0.00
310 5 0.01
311 152 0.37
312 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (306 bp):
GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAGGACTCA
TTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTCGATACCCCTA
AAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCTCTTCGGCATAGAAGCA
GACTTGGAGACAACCTAGAACTCGGCTCTAAAAAATTATGAAAACGCCCCTAAGGGATACCTCCG
ACGTAAAAGTACCCAATACGCTTAAAAAACTAAAAAAAATTTAAAG
Found at i:508633 original size:311 final size:304
Alignment explanation
Indices: 507738--508634 Score: 914
Period size: 307 Copynumber: 2.9 Consensus size: 304
507728 GGTGTCTGCA
* ** * * * ** **
507738 GGATAAACCTAACCTAAATATCCACCTTTAACAAAAAAACAAACCCAGTGACAACCTAGGACTCA
1 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAGGACTC-
* ** * * * *
507803 ATTCT-AAAAATTACAAAAATTCTTCTAAGGGATACCTTCAACGTAAAAGTA-CCCTAATACCCC
65 ATTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTC-GATACCCC
507866 TAAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCTCTTCGGCATAGAAG
129 TAAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCC-CTTCGGCATAGAAG
* * * * * *
507931 CGGACTTGGAGACAACCTAGGACTTGGCTT-TAAAAAATTATGAAAAT-GTCTCTAAGGGATACC
193 CGGACTTGGTGACAACTTAAGAC-TCGATTCTAAAAAATTATGAAAATCG-C-CTAAAGGATACC
* * * **
507994 TTCGACGTAAAAGTACTCGATACTCTTAAATGACTAAAAAAAATTTAAAG
255 TTCGACGTAAAAGTACCCAATACGCTTAAAAAACTAAAAAAAATTTAAAG
* *
508044 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAAGATTCA
1 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAGGACTCA
* * * * * * * * * *
508109 GTTTTAGAAAATTATAAAAATGCCCCCAAGGGATACCTTCGATGTGAAAATATCTCGATATCCTT
66 -TTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTCGATACCCCT
* *
508174 AAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCCATTTGGCATTGAAGC
130 AAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCC-TTCGGCATAGAAGC
* ** *
508239 AGACTTGGTGACAACTT-AGAACTCGGCTCTAAAAAATTATGAAAA-CGCCCCTAGAGGATACCT
194 GGACTTGGTGACAACTTAAG-ACTCGATTCTAAAAAATTATGAAAATCG--CCTAAAGGATACCT
*
508302 CCGACGTAAAAGTACCCAATACAGC-TAAAAAACTAAAAAAAGGATTTTAAAAG
256 TCGACGTAAAAGTACCCAATAC-GCTTAAAAAACTAAAAAAA--A-TTT-AAAG
* ** * * *
508355 GGATGAACCTATCCTAAATATCCACCTTCGGTATAAAAGCAGA-CTCGATGATGACCTAGGACTC
1 GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCT-AACGATGACCTAGGACTC
*
508419 GATTCTAAAAAATTACAAAAATACCCCTAGGGGATACCTTCAAAGTGAAAGTATCTCGATACCCC
65 -ATTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTCGATACCCC
* * * ** * *
508484 TAAAGGACTTAAAAAGATTATAAATGGGATGAACCTAACCTAAATGTCCACCTGGGGCATAAAAA
129 TAAAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCC-CCTTCGGCATAGAAG
** * * *
508549 CGGAC-CAGTGACAAGTTAAGACTCAATTCT-AAAAATTATGAAAATACGCCTAAAGATATACCT
193 CGGACTTGGTGACAACTTAAGACTCGATTCTAAAAAATTATGAAAAT-CGCCTAAAG-GATACCT
* *
508612 TCAACGTGAAAGTATCCCAATAC
256 TCGACGTAAAAGTA-CCCAATAC
508635 CCCTAAAGGA
Statistics
Matches: 486, Mismatches: 84, Indels: 37
0.80 0.14 0.06
Matches are distributed among these distances:
305 1 0.00
306 60 0.12
307 180 0.37
308 4 0.01
309 21 0.04
310 38 0.08
311 179 0.37
312 3 0.01
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (304 bp):
GGATAAACCTATCCTAAATATCCACCTTCGACATAAAAGCAAACCTAACGATGACCTAGGACTCA
TTCTAAAAAATTACAAAAATACCCCTAAGGGATACCTTCAAAGTGAAAGTATCTCGATACCCCTA
AAAGACTTAAAAAGATTATAGATGGGATGAACCTAACCTAAATATCCCCTTCGGCATAGAAGCGG
ACTTGGTGACAACTTAAGACTCGATTCTAAAAAATTATGAAAATCGCCTAAAGGATACCTTCGAC
GTAAAAGTACCCAATACGCTTAAAAAACTAAAAAAAATTTAAAG
Found at i:510168 original size:23 final size:22
Alignment explanation
Indices: 510137--510190 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
510127 GGTGGTGGTG
510137 TTTTATTT-CACCTTTTTATGCCA
1 TTTTATTTCCA-CTTTTTATG-CA
* *
510160 TTTTTTTTCCATTTTTTATGCA
1 TTTTATTTCCACTTTTTATGCA
510182 TTTTGATTT
1 TTTT-ATTT
510191 AATTTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 6 0.23
23 18 0.69
24 2 0.08
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTTATTTCCACTTTTTATGCA
Found at i:510902 original size:164 final size:164
Alignment explanation
Indices: 510679--511110 Score: 433
Period size: 164 Copynumber: 2.6 Consensus size: 164
510669 GAGAAAAGGG
* * * *
510679 AAATTTCAAGGAAAAAATCAAAAATGAATGACAATGAATGAATTTCTGAAAATTGATTTACTATT
1 AAATTTCAAGGAAAAAATCAAAAAT-AATGAAAATAAATGAATTTTTCAAAA-TGATTTACTATT
* * *
510744 AAATAACTAATAACATTTGATGAATTTTAAAAATTAAAAACCAAAAAAAATCTCCC-CGAAAAAA
64 AACTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAAAAAAATC-CCCTCGAAAAAA
*
510808 TTAAC-AGACTAGAAAAC-TCAGTTTTTC-AAAA-ACAA
128 TTAACGAG-CTAGAAAACTTC-GTATTTCAAAAATACAA
* * * * * *
510843 AAATTTCAAAGAAAAACTACAAAACTCATGAAAATAAATGAATTTTTCAAATATGATTTAATATG
1 AAATTTCAAGGAAAAAAT-CAAAAATAATGAAAATAAATGAATTTTTCAAA-ATGATTTACTATT
* * * * * * * *
510908 AGCTAAATGATGATATTTTATGAATTTTAAAAACTAAAAACTAAGAAAAATCCCCTCGAAAACAT
64 AACTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAAAAAAATCCCCTCGAAAAAAT
* * *
510973 TTACGAGGTAGAAAACTTCGTATTTCAAAAATAGAA
129 TAACGAGCTAGAAAACTTCGTATTTCAAAAATACAA
* * ** * **
511009 AAATTTTAAGGAAAAAATTCAAAAAGTTATGAAAATATGTGAATTTTTTCAAACTGATTTACTGG
1 AAATTTCAAGGAAAAAA-TCAAAAA-TAATGAAAATAAATGAA-TTTTTCAAAATGATTTACTAT
*
511074 TGACTAAATAATAATATTTGATGAATTTTCAAAAATT
63 TAACTAAATAATAATATTTGATGAATTTT-AAAAATT
511111 CAAACCCTGG
Statistics
Matches: 214, Mismatches: 43, Indels: 18
0.78 0.16 0.07
Matches are distributed among these distances:
163 3 0.01
164 113 0.53
165 15 0.07
166 22 0.10
167 46 0.21
168 15 0.07
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (164 bp):
AAATTTCAAGGAAAAAATCAAAAATAATGAAAATAAATGAATTTTTCAAAATGATTTACTATTAA
CTAAATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAAAAAAATCCCCTCGAAAAAATTA
ACGAGCTAGAAAACTTCGTATTTCAAAAATACAA
Found at i:513945 original size:29 final size:29
Alignment explanation
Indices: 513903--513959 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
513893 AAGCCATCCG
* *
513903 AATAGCTTATGTTACAGAATTTTTTCTAA
1 AATAGCATATGTTACAGAATTTCTTCTAA
513932 AATAGCATATGTTACAGAATTTCTTCTA
1 AATAGCATATGTTACAGAATTTCTTCTA
513960 GGCTCATCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (29 bp):
AATAGCATATGTTACAGAATTTCTTCTAA
Found at i:515598 original size:21 final size:21
Alignment explanation
Indices: 515555--515598 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
515545 ATCATTTAAG
* *
515555 CTTAAAAGAATGTGATCTTAT
1 CTTAAAAGAATGTGATATAAT
**
515576 CTTAAAATCATGTGATATAAT
1 CTTAAAAGAATGTGATATAAT
515597 CT
1 CT
515599 CCAACTACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (21 bp):
CTTAAAAGAATGTGATATAAT
Found at i:521410 original size:21 final size:21
Alignment explanation
Indices: 521367--521410 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
521357 ATCATTTAAG
* *
521367 CTTAAAAGAATGTGATCTTAT
1 CTTAAAAGAATGTGATATAAT
**
521388 CTTAAAATCATGTGATATAAT
1 CTTAAAAGAATGTGATATAAT
521409 CT
1 CT
521411 CCAACTACTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (21 bp):
CTTAAAAGAATGTGATATAAT
Found at i:523962 original size:17 final size:17
Alignment explanation
Indices: 523938--523989 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
523928 TATTTTATTG
523938 TATTAAATTAATTTTAAT
1 TATTAAATTAATTTT-AT
523956 T-TTAAA-TAATTTTAT
1 TATTAAATTAATTTTAT
*
523971 TAATTAAATTAATATTAT
1 T-ATTAAATTAATTTTAT
523989 T
1 T
523990 TAATTTATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 10 0.33
18 10 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TATTAAATTAATTTTAT
Found at i:523990 original size:23 final size:23
Alignment explanation
Indices: 523964--524008 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
523954 ATTTTAAATA
*
523964 ATTTTATTAATTAA-ATTAATATT
1 ATTTAATTAA-TAATATTAATATT
*
523987 ATTTAATTTATAATATTAATAT
1 ATTTAATTAATAATATTAATAT
524009 AATCACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATTTAATTAATAATATTAATATT
Found at i:527426 original size:19 final size:19
Alignment explanation
Indices: 527402--527444 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
527392 GTTTGCAACC
527402 AAATTGTTTTGGTCATTTT
1 AAATTGTTTTGGTCATTTT
527421 AAATTGTTTTGGTCATTTT
1 AAATTGTTTTGGTCATTTT
527440 AAATT
1 AAATT
527445 TGGTCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.56
Consensus pattern (19 bp):
AAATTGTTTTGGTCATTTT
Found at i:528844 original size:2 final size:2
Alignment explanation
Indices: 528837--528862 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
528827 GTATACATGC
528837 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
528863 GTTGCGGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:530204 original size:35 final size:35
Alignment explanation
Indices: 530134--530207 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
530124 TTACATATTT
*
530134 AATAATTTAATATTTTTATTAAATTATAAAATATA
1 AATAATTTAATATTTGTATTAAATTATAAAATATA
* *
530169 AATAATTTAATATATTGT-TTAATATT-TACATTATA
1 AATAATTTAATAT-TTGTATTAA-ATTATAAAATATA
530204 AATA
1 AATA
530208 TATAGTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 28 0.82
36 6 0.18
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (35 bp):
AATAATTTAATATTTGTATTAAATTATAAAATATA
Found at i:531067 original size:13 final size:12
Alignment explanation
Indices: 531016--531059 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
531006 TTGTGAAATT
*
531016 ATTTTTTGCTAA
1 ATTTTTTACTAA
531028 ATTTTTTACTAA
1 ATTTTTTACTAA
* *
531040 ATTTATTATTAA
1 ATTTTTTACTAA
531052 ATTTTTTA
1 ATTTTTTA
531060 GTTAAATTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (12 bp):
ATTTTTTACTAA
Found at i:531297 original size:46 final size:45
Alignment explanation
Indices: 531224--531310 Score: 138
Period size: 46 Copynumber: 1.9 Consensus size: 45
531214 TTAAATCTTG
* *
531224 AAAAACAATCTAAAAAATGAATGTAAAATATCCAAAAACATCACT
1 AAAAACAACCTAAAAAATCAATGTAAAATATCCAAAAACATCACT
*
531269 AAAAACAACCCTAAAAAATCAATTTAAAATATCCAAAAACAT
1 AAAAACAA-CCTAAAAAATCAATGTAAAATATCCAAAAACAT
531311 TTGTAATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
45 8 0.21
46 30 0.79
ACGTcount: A:0.61, C:0.17, G:0.02, T:0.20
Consensus pattern (45 bp):
AAAAACAACCTAAAAAATCAATGTAAAATATCCAAAAACATCACT
Found at i:535265 original size:16 final size:16
Alignment explanation
Indices: 535224--535271 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
535214 TTCCTGTTCG
535224 TAAAATAATAATATTT
1 TAAAATAATAATATTT
535240 T--AATAA-AATATTT
1 TAAAATAATAATATTT
535253 TAAAATAATAATATTT
1 TAAAATAATAATATTT
535269 TAA
1 TAA
535272 TAATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.28
14 5 0.17
15 5 0.17
16 11 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAAAATAATAATATTT
Found at i:535275 original size:14 final size:14
Alignment explanation
Indices: 535227--535275 Score: 73
Period size: 14 Copynumber: 3.4 Consensus size: 14
535217 CTGTTCGTAA
535227 AATAATAATATTTT
1 AATAATAATATTTT
535241 AATAA-AATATTTT
1 AATAATAATATTTT
535254 AAAATAATAATATTTT
1 --AATAATAATATTTT
535270 AATAAT
1 AATAAT
535276 TTATTTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
13 8 0.25
14 11 0.34
15 5 0.16
16 8 0.25
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATAATAATATTTT
Found at i:535280 original size:13 final size:13
Alignment explanation
Indices: 535227--535281 Score: 56
Period size: 13 Copynumber: 3.9 Consensus size: 13
535217 CTGTTCGTAA
535227 AATAATAATATTTT
1 AATAAT-ATATTTT
*
535241 AATAAAATATTTT
1 AATAATATATTTT
535254 AAAATAATAATATTTT
1 --AATAAT-ATATTTT
*
535270 AATAATTTATTT
1 AATAATATATTT
535282 AAATTTAAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
13 12 0.34
14 11 0.31
15 5 0.14
16 7 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AATAATATATTTT
Found at i:536078 original size:47 final size:45
Alignment explanation
Indices: 536025--536112 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 45
536015 TTAAAAATAT
536025 ATATTTT-TATTTAAATTTAATTATAAAATATATAATATTAATATAAA
1 ATATTTTATATTTAAA-TTAATTAT-AAATA-ATAATATTAATATAAA
**
536072 ATATTTTATATTTTTATTAATTATAAATAATAATATTAATA
1 ATATTTTATATTTAAATTAATTATAAATAATAATATTAATA
536113 ATATGAATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
45 12 0.32
46 5 0.13
47 15 0.39
48 6 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (45 bp):
ATATTTTATATTTAAATTAATTATAAATAATAATATTAATATAAA
Found at i:536220 original size:14 final size:14
Alignment explanation
Indices: 536196--536229 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
536186 TTTTATCATT
*
536196 AAATTTATTTAAAA
1 AAATATATTTAAAA
*
536210 TAATATATTTAAAA
1 AAATATATTTAAAA
536224 AAATAT
1 AAATAT
536230 CTCTAACCGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATATATTTAAAA
Found at i:536728 original size:21 final size:20
Alignment explanation
Indices: 536683--536732 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
536673 AATTTATTTT
* *
536683 TTAAATTTTTATTTAATTAA
1 TTAATTTTTTACTTAATTAA
*
536703 TTAATTTTTTACTTAATTTA
1 TTAATTTTTTACTTAATTAA
536723 TATAATTTTT
1 T-TAATTTTT
536733 AATTTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAATTTTTTACTTAATTAA
Found at i:537417 original size:14 final size:14
Alignment explanation
Indices: 537398--537437 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
537388 TTATATTAAA
537398 TAAATATTTAAAAC
1 TAAATATTTAAAAC
* * *
537412 TAAATATTCATAAT
1 TAAATATTTAAAAC
537426 TAAATATTTAAA
1 TAAATATTTAAA
537438 TTTATATTTC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (14 bp):
TAAATATTTAAAAC
Found at i:538024 original size:22 final size:21
Alignment explanation
Indices: 537965--538014 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
537955 AAACCACGTT
537965 AATAAAAATAAGATTTTGACA
1 AATAAAAATAAGATTTTGACA
537986 AATAAAAATAAGATTTTGACA
1 AATAAAAATAAGATTTTGACA
*
538007 TATAAAAA
1 AATAAAAA
538015 AATTTATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.60, C:0.04, G:0.08, T:0.28
Consensus pattern (21 bp):
AATAAAAATAAGATTTTGACA
Found at i:538106 original size:2 final size:2
Alignment explanation
Indices: 538099--538125 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
538089 GAAAAATTAA
538099 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
538126 CGGGAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:538589 original size:3 final size:3
Alignment explanation
Indices: 538581--538609 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
538571 TGATCTGCCT
538581 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
538610 GAAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:543216 original size:3 final size:3
Alignment explanation
Indices: 543208--543258 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
543198 AATGCTTTAG
543208 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
543256 ATT
1 ATT
543259 TTTTGGTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:543596 original size:27 final size:27
Alignment explanation
Indices: 543542--543596 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
543532 AAAAGGGCTT
**
543542 ACGAAAAGGAAAGTAAAATGATGGAAA
1 ACGAAAAGGAAAGTAAAATGATAAAAA
*
543569 ACGAAGAGGAAAGTAAAATGATAAAAA
1 ACGAAAAGGAAAGTAAAATGATAAAAA
543596 A
1 A
543597 AAAGGGTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.04, G:0.24, T:0.11
Consensus pattern (27 bp):
ACGAAAAGGAAAGTAAAATGATAAAAA
Found at i:543794 original size:21 final size:20
Alignment explanation
Indices: 543769--543820 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
543759 TATTTTTATT
543769 TAAATA-TAATTATAAAATATA
1 TAAATATTAA-TATAAAATA-A
543790 TAAATATTAATATAAAATAA
1 TAAATATTAATATAAAATAA
543810 T-AAT-TTAATAT
1 TAAATATTAATAT
543821 TATAATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.23
19 3 0.10
20 2 0.07
21 15 0.50
22 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATATTAATATAAAATAA
Found at i:544088 original size:16 final size:15
Alignment explanation
Indices: 544067--544117 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 15
544057 CATATTATAA
544067 TTATATTTAATATATT
1 TTATATTTAATA-ATT
544083 TTATATTTACATAAATT
1 TTATATTTA-AT-AATT
544100 TTGATATATTAATAATT
1 TT-ATAT-TTAATAATT
544117 T
1 T
544118 ATTTAATAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
16 9 0.29
17 12 0.39
18 7 0.23
19 3 0.10
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTATATTTAATAATT
Found at i:544114 original size:18 final size:17
Alignment explanation
Indices: 544067--544114 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
544057 CATATTATAA
*
544067 TTATAT-TTAATATATT
1 TTATATATTAATAAATT
544083 TTATAT-TTACATAAATT
1 TTATATATTA-ATAAATT
544100 TTGATATATTAATAA
1 TT-ATATATTAATAA
544115 TTTATTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 9 0.32
17 8 0.29
18 8 0.29
19 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTATATATTAATAAATT
Found at i:545942 original size:25 final size:25
Alignment explanation
Indices: 545909--545961 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
545899 TTTAATTTTA
545909 AATAAATA-TTAAATATAATAAATAT
1 AATAAATATTTAAATATAAT-AATAT
* * *
545934 AATATATATTTTAATTTAATAATAT
1 AATAAATATTTAAATATAATAATAT
545959 AAT
1 AAT
545962 TTTTTATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
26 9 0.38
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAAATATTTAAATATAATAATAT
Found at i:549589 original size:26 final size:26
Alignment explanation
Indices: 549553--549606 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
549543 ACTTAGGTTT
549553 GAGCTCACACTAGCTTAAATTACTTA
1 GAGCTCACACTAGCTTAAATTACTTA
549579 GAGCTCACACTAGCTTAAATTACTTA
1 GAGCTCACACTAGCTTAAATTACTTA
549605 GA
1 GA
549607 TTATGTATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (26 bp):
GAGCTCACACTAGCTTAAATTACTTA
Found at i:551506 original size:26 final size:27
Alignment explanation
Indices: 551477--551527 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
551467 TTCAAAAAGA
*
551477 AATAGGGTTAGAATAT-TCCCTCGAGG
1 AATACGGTTAGAATATCTCCCTCGAGG
* *
551503 AATACGGTTGGAATATCTCTCTCGA
1 AATACGGTTAGAATATCTCCCTCGA
551528 TGAAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 14 0.67
27 7 0.33
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (27 bp):
AATACGGTTAGAATATCTCCCTCGAGG
Found at i:557648 original size:52 final size:52
Alignment explanation
Indices: 557500--557628 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
557490 CGAAATATGA
*
557500 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
557552 AAATTTGCTTGCATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
557604 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
557629 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:557655 original size:13 final size:13
Alignment explanation
Indices: 557637--557661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
557627 CAAAGATCAG
557637 TGTATCGATACAA
1 TGTATCGATACAA
557650 TGTATCGATACA
1 TGTATCGATACA
557662 TTTGAGTAAT
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:557743 original size:32 final size:33
Alignment explanation
Indices: 557702--557765 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
557692 AGTAGCTTAA
557702 ATTGTATCGATACAA-AACTTATGTATCGATAT
1 ATTGTATCGATACAACAACTTATGTATCGATAT
*
557734 ATTGTATCGATACAACACCTTATGTATCGATA
1 ATTGTATCGATACAACAACTTATGTATCGATA
557766 CAAATCGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAACAACTTATGTATCGATAT
Found at i:558450 original size:49 final size:49
Alignment explanation
Indices: 558277--558895 Score: 657
Period size: 49 Copynumber: 12.6 Consensus size: 49
558267 AGATGATGAT
*
558277 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A---A
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* * * *
558320 GGTGCTAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAAGATGACAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---GA
* *
558372 GGCGCCAATATGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* * *
558421 GGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGACTTAAATG-TGGTAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA-GATGG---A
* * *
558473 GGTGCCAATATGCTAATT-AAGGCCATCGATATTGGACTTAAAGATGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
*
558521 GGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* * * *
558570 GGTGCCAATGTGCTAATTCAAGGCTAGAGACATTGGACTTAAATG-TGGTAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAA-GATGG---A
* * * * *
558622 GGTGCCAATATGCTGATT-AAAGCCAGCGATATTAGACTTAATGATGAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* *
558670 GGTGCCAATGTGCTGTTTCAAGGCCAGCGACATTGGACTTAAAGATGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* * * *
558719 GGTTCCAATATGCTGATTTAAGGCTAGTGACATTGGACTTAAAGATGGA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* * * *
558768 GGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGACTTCAATG-TGGTAAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT-AAAGATGG---A
* ** * *
558820 GGTGCCAATATGCAGATTCAAGGCCAATGATATTGGACTTAAAGATGAA
1 GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
* **
558869 GGTGTCAATATGCCAATTCAAGGCCAG
1 GGTGCCAATATGCTGATTCAAGGCCAG
558896 TGATATTAGG
Statistics
Matches: 483, Mismatches: 67, Indels: 46
0.81 0.11 0.08
Matches are distributed among these distances:
43 36 0.07
45 1 0.00
46 1 0.00
48 34 0.07
49 243 0.50
50 7 0.01
51 47 0.10
52 114 0.24
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (49 bp):
GGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGA
Found at i:558560 original size:149 final size:150
Alignment explanation
Indices: 558316--558892 Score: 727
Period size: 149 Copynumber: 3.8 Consensus size: 150
558306 ATATTGGACT
* * * * *
558316 TAAAGGTGCTAATGTGCTGATTCAAGGTCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAAT
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATG---AAGGTGCCAAT
* *
558381 ATGCTGATTTAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAAGGCT
63 ATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATATGCTAATTCAAGGCT
*
558446 AGCGACATTGGACTTAAATGTGG
128 AGAGACATTGGACTTAAATGTGG
* * * *
558469 TAAAGGTGCCAATATGCTAATT-AAGGCCATCGATATTGGACTTAAAGATGGAGGTGCCAATGTG
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATG
*
558533 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAAGGCTAGA
66 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATATGCTAATTCAAGGCTAGA
558598 GACATTGGACTTAAATGTGG
131 GACATTGGACTTAAATGTGG
* * * * * *
558618 TAAAGGTGCCAATATGCTGATT-AAAGCCAGCGATATTAGACTTAATGATGAAGGTGCCAATGTG
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATG
* * * * *
558682 CTGTTTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTTCCAATATGCTGATTTAAGGCTAGT
66 CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATATGCTAATTCAAGGCTAGA
558747 GACATTGGACTTAAA-GATGG
131 GACATTGGACTTAAATG-TGG
* * *
558767 ---AGGTGCCAATGTGCTAATTCAAGGCTAGCGACATTGGACTTCAATG-TGGTAAAGGTGCCAA
1 TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTT-AAAGAT-G--AAGGTGCCAA
* ** * * * *
558828 TATGCAGATTCAAGGCCAATGATATTGGACTTAAAGATGAAGGTGTCAATATGCCAATTCAAGGC
62 TATGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATATGCTAATTCAAGGC
558893 CAGTGATATT
Statistics
Matches: 377, Mismatches: 41, Indels: 15
0.87 0.09 0.03
Matches are distributed among these distances:
146 17 0.05
147 18 0.05
148 6 0.02
149 229 0.61
150 63 0.17
152 25 0.07
153 19 0.05
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.26
Consensus pattern (150 bp):
TAAAGGTGCCAATATGCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGAAGGTGCCAATATG
CTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATATGCTAATTCAAGGCTAGA
GACATTGGACTTAAATGTGG
Found at i:558735 original size:198 final size:199
Alignment explanation
Indices: 558269--558902 Score: 790
Period size: 198 Copynumber: 3.2 Consensus size: 199
558259 GATGAGAAAG
* * *
558269 ATGATGATGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-A---AGGTGCTAA
1 ATGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGATGGAGGTGCCAA
* * * * * *
558328 TGTGCTGATTCAAGGTCAGCGACATTGGACTTAAAGATGACAAAGGCGCCAATATGCTGATTTAA
66 TGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATG---GAGGTGCCAATGTGCTAATTCAA
* * * * *
558393 GGCCAGCGACATTGGACTTAAA-GATGG---AGGTGCCAATGTGCTAATTCAAGGCTAGCGACAT
128 GGCTAGCGACATTGGACTTAAATG-TGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
558454 TGGACTTAA
192 TGGACTT-A
*
558463 ATG-TGGTAAAGGTGCCAATATGCTAATT-AAGGCCATCGATATTGGACTTAAAGATGGAGGTGC
1 ATGAT-G--AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGATGGAGGTGC
558526 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAA
63 CAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAA
* *
558591 GGCTAGAGACATTGGACTTAAATGTGGTAAAGGTGCCAATATGCTGATT-AAAGCCAGCGATATT
128 GGCTAGCGACATTGGACTTAAATGTGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT
*
558655 AGACTTA
193 GGACTTA
* ** * *
558662 ATGATGAAGGTGCCAATGTGCTGTTTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTTCCAA
1 ATGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGATGGAGGTGCCAA
* * * *
558727 TATGCTGATTTAAGGCTAGTGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAAGGC
66 TGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAAGGC
* * **
558792 TAGCGACATTGGACTTCAATGTGGTAAAGGTGCCAATATGCAGATTCAAGGCCAATGATATTGGA
131 TAGCGACATTGGACTTAAATGTGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
558857 CTTA
196 CTTA
* * * *
558861 AAGATGAAGGTGTCAATATGCCAATTCAAGGCCAGTGATATT
1 ATGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATT
558903 AGGCTTGAAG
Statistics
Matches: 381, Mismatches: 43, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
193 1 0.00
194 4 0.01
195 20 0.05
196 18 0.05
197 18 0.05
198 181 0.48
199 58 0.15
200 18 0.05
201 63 0.17
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (199 bp):
ATGATGAAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAGATGGAGGTGCCAA
TGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAGATGGAGGTGCCAATGTGCTAATTCAAGGC
TAGCGACATTGGACTTAAATGTGGTAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
CTTA
Found at i:559009 original size:32 final size:33
Alignment explanation
Indices: 558968--559614 Score: 803
Period size: 32 Copynumber: 20.2 Consensus size: 33
558958 CATTGAGCTT
*
558968 AGAAGGGTTGCTACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* ** * *
559001 AGTA-GGTTGCCACTAACTTATGTGGGCTTTAA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
559033 AAAAGGGTTGCCATCGACTTGTGTGAGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
559065 AAAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
559097 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559129 AGAAGGGTTGCCATCGACTTGTGTGAGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559161 AAAAGGGTTGCCATCGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559193 AGAAAGGTTACCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
559225 AGAAGGGTTGCCACGGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559257 AAAAGGGTTGCCACCAACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * * *
559289 AGAAGGGTTTCGACTGACTTATGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559321 AAAAGGGTTGCCACCGACTTGTGTAGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559353 AGAAGGGTTGCTACCGACTTGTGTTGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
559385 AAAAAGGTTGCCACTGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
559417 AGAAGGGTTACCACCGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* * *
559449 AAAAGGGTTGTCACCAACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
559481 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559513 AGAAGGGTTACCACCGACTTGTGTAGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
559545 AAAAGGGTTGCCATCGACTTGTGTGGGCTTTA-
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
559577 AGAAGGGTTGCCACC-AGCTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGA-CTTGTGTGGGCTTTAG
559609 AGAAGG
1 AGAAGG
559615 TTTCTCCACT
Statistics
Matches: 530, Mismatches: 70, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
31 1 0.00
32 505 0.95
33 24 0.05
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:559848 original size:13 final size:13
Alignment explanation
Indices: 559830--559854 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
559820 CAACGGTGTT
559830 TTATAACTTTTTG
1 TTATAACTTTTTG
559843 TTATAACTTTTT
1 TTATAACTTTTT
559855 AGGATTTTCC
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:0.24, C:0.08, G:0.04, T:0.64
Consensus pattern (13 bp):
TTATAACTTTTTG
Found at i:560109 original size:19 final size:19
Alignment explanation
Indices: 560085--560149 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
560075 TTTCAACGAT
560085 TTGTATCGATACAAAAATG
1 TTGTATCGATACAAAAATG
560104 TTGTATCGATAC---AA--
1 TTGTATCGATACAAAAATG
* *
560118 -TGTATCGATACATAAGTG
1 TTGTATCGATACAAAAATG
560136 TTGTATCGATACAA
1 TTGTATCGATACAA
560150 TGTATCGATA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
16 3 0.08
19 24 0.63
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (19 bp):
TTGTATCGATACAAAAATG
Found at i:560123 original size:13 final size:13
Alignment explanation
Indices: 560105--560187 Score: 67
Period size: 13 Copynumber: 5.5 Consensus size: 13
560095 ACAAAAATGT
560105 TGTATCGATACAA
1 TGTATCGATACAA
560118 TGTATCGATACATAA
1 TGTATCGATAC--AA
560133 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
560150 TGTATCGATACATAA
1 TGTATCGATAC--AA
560165 GTTTGTATCGATACAA
1 ---TGTATCGATACAA
560181 TGTATCG
1 TGTATCG
560188 CTACGAAGCT
Statistics
Matches: 59, Mismatches: 0, Indels: 22
0.73 0.00 0.27
Matches are distributed among these distances:
13 29 0.49
15 4 0.07
16 2 0.03
17 2 0.03
18 11 0.19
19 11 0.19
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:560124 original size:32 final size:32
Alignment explanation
Indices: 560086--560187 Score: 179
Period size: 32 Copynumber: 3.2 Consensus size: 32
560076 TTCAACGATT
* *
560086 TGTATCGATACAAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
560118 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
560150 TGTATCGATACATAAGT-TTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
560181 TGTATCG
1 TGTATCG
560188 CTACGAAGCT
Statistics
Matches: 68, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
31 21 0.31
32 47 0.69
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:560249 original size:13 final size:13
Alignment explanation
Indices: 560231--560255 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
560221 ATTACCCAAA
560231 TGTATCGATACAT
1 TGTATCGATACAT
560244 TGTATCGATACA
1 TGTATCGATACA
560256 CTGATCTTTG
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:560320 original size:52 final size:52
Alignment explanation
Indices: 560264--560392 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
560254 CACTGATCTT
*
560264 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATGCACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
* *
560316 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
560368 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
560393 TCATATTTCG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:563500 original size:32 final size:32
Alignment explanation
Indices: 563464--563569 Score: 123
Period size: 32 Copynumber: 3.4 Consensus size: 32
563454 AGTTTGAGTA
*
563464 GGCTTTGAGAAGGGTTGCCACCGACTTGTGTG
1 GGCTTTGAGAAGGGTTGCCACCAACTTGTGTG
* *
563496 GGCTTTAAGAAGGGTTGCCATCAACTTGTGTG
1 GGCTTTGAGAAGGGTTGCCACCAACTTGTGTG
* *
563528 GGCTTT--GAAGAGG-TGCCACTAAC-T-AGTG
1 GGCTTTGAGAAG-GGTTGCCACCAACTTGTGTG
563556 GGCTTTGAGAAGGG
1 GGCTTTGAGAAGGG
563570 ATTCGTGTTG
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
28 9 0.14
29 3 0.05
30 16 0.25
31 2 0.03
32 35 0.54
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.27
Consensus pattern (32 bp):
GGCTTTGAGAAGGGTTGCCACCAACTTGTGTG
Found at i:564861 original size:7 final size:7
Alignment explanation
Indices: 564851--564901 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
564841 TCCTTCCCCC
*
564851 TTTTCTT
1 TTTTGTT
564858 TTTT-TT
1 TTTTGTT
564864 TTTTGTAT
1 TTTTGT-T
564872 TTTT-TT
1 TTTTGTT
*
564878 GTTTGTT
1 TTTTGTT
564885 TTTTG-T
1 TTTTGTT
564891 TTTTGTT
1 TTTTGTT
564898 TTTT
1 TTTT
564902 TTGTGTGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 16 0.42
7 17 0.45
8 5 0.13
ACGTcount: A:0.02, C:0.02, G:0.10, T:0.86
Consensus pattern (7 bp):
TTTTGTT
Found at i:564876 original size:14 final size:13
Alignment explanation
Indices: 564851--564903 Score: 70
Period size: 13 Copynumber: 4.0 Consensus size: 13
564841 TCCTTCCCCC
*
564851 TTTTCTTTTTTTT
1 TTTTGTTTTTTTT
564864 TTTTGTATTTTTTT
1 TTTTGT-TTTTTTT
* *
564878 GTTTGTTTTTTGT
1 TTTTGTTTTTTTT
564891 TTTTGTTTTTTTT
1 TTTTGTTTTTTTT
564904 GTGTGTGTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
13 22 0.65
14 12 0.35
ACGTcount: A:0.02, C:0.02, G:0.09, T:0.87
Consensus pattern (13 bp):
TTTTGTTTTTTTT
Found at i:564918 original size:27 final size:27
Alignment explanation
Indices: 564863--564921 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
564853 TTCTTTTTTT
* * *
564863 TTTTTGTATTTTTTTGTTTGTTTTTTG
1 TTTTTGTATTTTTTTGTGTGTTGTGTG
564890 TTTTTGT-TTTTTTTGTGTGTGTGTGTG
1 TTTTTGTATTTTTTTGTGTGT-TGTGTG
564917 TTTTT
1 TTTTT
564922 TTTACGAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 12 0.43
27 16 0.57
ACGTcount: A:0.02, C:0.00, G:0.20, T:0.78
Consensus pattern (27 bp):
TTTTTGTATTTTTTTGTGTGTTGTGTG
Found at i:576444 original size:52 final size:52
Alignment explanation
Indices: 576359--576484 Score: 225
Period size: 52 Copynumber: 2.4 Consensus size: 52
576349 ATATGAAGAG
* *
576359 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
576411 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
576463 TTGCCTGCATGTATCGATACAT
1 TTGCCTGCATGTATCGATACAT
576485 AGATCAGTGT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:576496 original size:52 final size:51
Alignment explanation
Indices: 576359--576503 Score: 220
Period size: 52 Copynumber: 2.8 Consensus size: 51
576349 ATATGAAGAG
*
576359 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
576411 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
576463 TTGCCTGCATGTATCGATACA-TAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
576504 ATGTACCGAT
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
50 1 0.01
51 2 0.02
52 83 0.97
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:576594 original size:33 final size:33
Alignment explanation
Indices: 576557--576623 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
576547 AGTAGCTTAA
576557 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
576590 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
576623 A
1 A
576624 AACCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:576597 original size:13 final size:13
Alignment explanation
Indices: 576579--576603 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576569 CAAAAAAATA
576579 TGTATCGATACAT
1 TGTATCGATACAT
576592 TGTATCGATACA
1 TGTATCGATACA
576604 ACACTTTATG
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:576872 original size:13 final size:13
Alignment explanation
Indices: 576854--576878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576844 GGAAAATCCT
576854 AAAAAGTTATAAC
1 AAAAAGTTATAAC
576867 AAAAAGTTATAA
1 AAAAAGTTATAA
576879 AACACCGTTG
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:0.64, C:0.04, G:0.08, T:0.24
Consensus pattern (13 bp):
AAAAAGTTATAAC
Found at i:577671 original size:227 final size:224
Alignment explanation
Indices: 577274--577760 Score: 577
Period size: 227 Copynumber: 2.2 Consensus size: 224
577264 CCACTGTGCA
* * *
577274 GATTCAAGGCCTGCAACACTGGACTTAAAGATTAAAAAGGATGAAGAGTGATAAAAGGACCAATA
1 GATTCAAGGCCAGCAACATTGGACTTAAAGA-TAAAAAGGATGAAAAGTGATAAAAGGACCAATA
* * *
577339 CGTTGATTCACGACCAACGATACTGGGTTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCA
65 CGTTGATTCACGACCAACGATACTGGGCTTAAAAATGAGAAAAAGGATGTCAATGTGCTAATTCA
* * * * *
577404 CGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACAT
130 AGGCCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATATGCTAATTCAAGGCCAACAACAT
**
577469 GGGGTTTTAAAGATGATGAAGGTGCCAATATGCT
195 -GGGACTTAAAG--G-TGAAGGTGCCAATATGCT
* * * * * *
577503 GATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATGA-GAAAAGTGATAAAGATG-CCAATA
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATAAAAAGGATGAAAAGTGATAAA-AGGACCAATA
* * *
577566 TGTTGATTCACGGCCAACGATATTGGGCTTAAAAATGAGAAAAAGGATGTCAATGTGCTAATTCA
65 CGTTGATTCACGACCAACGATACTGGGCTTAAAAATGAGAAAAAGGATGTCAATGTGCTAATTCA
* * * *** *
577631 AGGCCCGCTACATT-GAACTTAAAGATG-GAAAAGGTGCCAATATGCTAATTCAAGGCCAGTTAT
130 AGGCCAGCGACATTAG-ACTTAAAGATGAGAAAA-ATGCCAATATGCTAATTCAAGGCCAACAAC
* *
577694 ATTGGACTTAAAGGTGAAGGTGCCAATGTGCT
193 ATGGGACTTAAAGGTGAAGGTGCCAATATGCT
* *
577726 GAGTCAAGGCCAGCTACATTGGACTTAAAGATAAA
1 GATTCAAGGCCAGCAACATTGGACTTAAAGATAAA
577761 GGTGCCAATA
Statistics
Matches: 219, Mismatches: 36, Indels: 12
0.82 0.13 0.04
Matches are distributed among these distances:
223 47 0.21
224 1 0.00
226 14 0.06
227 122 0.56
228 8 0.04
229 27 0.12
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (224 bp):
GATTCAAGGCCAGCAACATTGGACTTAAAGATAAAAAGGATGAAAAGTGATAAAAGGACCAATAC
GTTGATTCACGACCAACGATACTGGGCTTAAAAATGAGAAAAAGGATGTCAATGTGCTAATTCAA
GGCCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATATGCTAATTCAAGGCCAACAACATG
GGACTTAAAGGTGAAGGTGCCAATATGCT
Found at i:577733 original size:49 final size:49
Alignment explanation
Indices: 577616--578033 Score: 493
Period size: 49 Copynumber: 8.7 Consensus size: 49
577606 AAAAGGATGT
* * *
577616 CAATGTGCTAATTCAAGGCCCGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * * *
577668 CAATATGCTAATTCAAGGCCAGTTATATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
577717 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
577766 CAATATGCTGATTCAAGGCCAGCTATATTGGAC-T---GA--ATGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
577809 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
577857 CAATGTGCTGATTCCAGGCTAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
577906 CAATATGCTGATTCAGGGCCAGCGATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
577949 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
577998 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
578034 GAAGGGTTGC
Statistics
Matches: 314, Mismatches: 39, Indels: 29
0.82 0.10 0.08
Matches are distributed among these distances:
43 74 0.24
44 1 0.00
45 3 0.01
47 2 0.01
48 44 0.14
49 154 0.49
51 1 0.00
52 35 0.11
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:577843 original size:92 final size:94
Alignment explanation
Indices: 577628--578033 Score: 416
Period size: 92 Copynumber: 4.3 Consensus size: 94
577618 ATGTGCTAAT
* * * * *
577628 TCAAGGCCCGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTAATTCAAGGCCAGTTA
1 TCAAGGCCAGCTACATTGGACTTAAAG-T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTA
* * *
577693 TATTGGACTTAAAGGTGAAGGTGCCAATGTGCTGAG
62 CATTGGACTT--A-GAGAAGGTGCCAATATGCTGAG
* *
577729 TCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATAT
1 TCAAGGCCAGCTACATTGGACTTAAAG-TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
* *
577794 TGGAC-T-GA-ATGGTGCCAATGTGCTGAG
65 TGGACTTAGAGAAGGTGCCAATATGCTGAG
* * *
577821 TCAAGGCCAGCTACATTGGACTTAAAGGT-GAGGTGCCAATGTGCTGATTCCAGGCTAGCTACAT
1 TCAAGGCCAGCTACATTGGACTTAAA-GTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
*
577885 TGGACTTAAAGATGAAGGTGCCAATATGCTGAT
65 TGGACTT--AGA-GAAGGTGCCAATATGCTGAG
* * *
577918 TCAGGGCCAGCGATATTGGAC-T----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
1 TCAAGGCCAGCTACATTGGACTTAAAGTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
*
577978 GGACTTAAAGAAGAAGGTGCCAATATGCTGAT
66 GGACTT--AG-AGAAGGTGCCAATATGCTGAG
* *
578010 TCAAGGCCAGCTATATTGGGCTTA
1 TCAAGGCCAGCTACATTGGACTTA
578034 GAAGGGTTGC
Statistics
Matches: 271, Mismatches: 23, Indels: 29
0.84 0.07 0.09
Matches are distributed among these distances:
91 36 0.13
92 127 0.47
93 4 0.01
95 2 0.01
96 1 0.00
97 35 0.13
98 39 0.14
101 27 0.10
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (94 bp):
TCAAGGCCAGCTACATTGGACTTAAAGTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT
GGACTTAGAGAAGGTGCCAATATGCTGAG
Found at i:577916 original size:140 final size:141
Alignment explanation
Indices: 577660--578033 Score: 579
Period size: 140 Copynumber: 2.7 Consensus size: 141
577650 TAAAGATGGA
* * * *
577660 AAAGGTGCCAATATGCTAATTCAAGGCCAGTTATATTGGACTTAAAGGTGAAGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAATGTGC
* *
577725 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
66 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCG
577790 ATATTGGACTG
131 ATATTGGACTG
* *
577801 AATGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAATGTGC
* * * *
577865 TGATTCCAGGCTAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAGGGCCAGCG
66 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCG
*
577930 ATATTGGACTT
131 ATATTGGACTG
** *
577941 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAATGTGC
* *
578006 TGATTCAAGGCCAGCTATATTGGGCTTA
66 TGATTCAAGGCCAGCTACATTGGACTTA
578034 GAAGGGTTGC
Statistics
Matches: 210, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
140 129 0.61
141 81 0.39
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (141 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGAAGGTGCCAATGTGC
TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCG
ATATTGGACTG
Found at i:578265 original size:32 final size:31
Alignment explanation
Indices: 578026--578257 Score: 342
Period size: 32 Copynumber: 7.3 Consensus size: 31
578016 CCAGCTATAT
*
578026 TGGGC-TTAGAAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
578056 TGGGCTTTAGAGAGTGGTTGCCACCAACTTGTG
1 TGGGCTTTAGA-AG-GGTTGCCACCGACTTGTG
578089 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCGACTTGTG
578121 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTG
*
578154 TGGGCTTT-GAAGAAGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTG
578186 TGGGCTTTAGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACCGACTTGTG
578218 TGGGCTTTAGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACCGACTTGTG
578250 TGGGCTTT
1 TGGGCTTT
578258 GGGAAGGGAG
Statistics
Matches: 192, Mismatches: 3, Indels: 12
0.93 0.01 0.06
Matches are distributed among these distances:
30 5 0.03
31 7 0.04
32 118 0.61
33 58 0.30
34 4 0.02
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.29
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:578265 original size:64 final size:63
Alignment explanation
Indices: 578026--578257 Score: 344
Period size: 65 Copynumber: 3.6 Consensus size: 63
578016 CCAGCTATAT
* *
578026 TGGGC-TTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAGAGTGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGA-AGAGGTTGCCACCGACTTGTG
*
578089 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGA-AGGGTTGCCACCAACTTGTGTGGGCTTTAGAAG-AGGTTGCCACCGACTTGTG
578154 TGGGCTTT-GAAGAAGGTTGCCACCAACTTGTGTGGGCTTTAGGAAG-GGTTGCCACCGACTTGT
1 TGGGCTTTAGAAG--GGTTGCCACCAACTTGTGTGGGCTTTA-GAAGAGGTTGCCACCGACTTGT
578217 G
63 G
*
578218 TGGGCTTTAGGAAGGGTTGCCACCGACTTGTGTGGGCTTT
1 TGGGCTTTA-GAAGGGTTGCCACCAACTTGTGTGGGCTTT
578258 GGGAAGGGAG
Statistics
Matches: 156, Mismatches: 5, Indels: 15
0.89 0.03 0.09
Matches are distributed among these distances:
63 7 0.04
64 60 0.38
65 81 0.52
66 8 0.05
ACGTcount: A:0.18, C:0.19, G:0.35, T:0.29
Consensus pattern (63 bp):
TGGGCTTTAGAAGGGTTGCCACCAACTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTGTG
Found at i:578306 original size:34 final size:33
Alignment explanation
Indices: 578268--578815 Score: 420
Period size: 34 Copynumber: 16.8 Consensus size: 33
578258 GGGAAGGGAG
*
578268 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAA-GGAA
** *
578302 AAAGAGTGCCATAGAGTTGTGGGCTTTAAAAAGAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
578337 AAAGGTGCCACAGAGTTTTGGGCTTTGAAAAGGGAA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
*
578373 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAACGAA
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* *
578408 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGA
1 AAAGATGCCACGGAGTTGTGGGC-TT-AAAAGGAA
* * * *
578443 AAAGGTGCCACGAAGTTGTGGTCTTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
578477 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
578510 AAAGAGTGCCACGGAGTTGTGGGCTTTGAAACG--
1 AAAGA-TGCCACGGAGTTGTGGGC-TTAAAAGGAA
* * *
578543 -AAGGTGCCACGGAGTCGTGGACTTAGAAA-GAA
1 AAAGATGCCACGGAGTTGTGGGCTTA-AAAGGAA
*
578575 AAAGAGTGCCACAGAGTTGTGGGCTTAAAAGG--
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
578607 ---G-TGCCACGGAGTTGTGGACTTAGAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTA-AAAGGAA
* * *
578637 AAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
578670 AAAGAGTGCCACGGAATTGTGGGCTTTAGA-G-A
1 AAAGA-TGCCACGGAGTTGTGGGCTTAAAAGGAA
** * * *
578702 AAAGATGCCATTGAGTCGTGGACTT---TGGAA
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
578732 AGAGATGCCACTGAGTTGTGGGCTTAAAAGG--
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
*
578763 ---G-TGCCACGGAGTTGTGGACTTAAAAGG-A
1 AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
578791 AAAGGTGCCACGGAGTCGTGGGCTT
1 AAAGATGCCACGGAGTTGTGGGCTT
578816 TGCAGAAAAG
Statistics
Matches: 421, Mismatches: 61, Indels: 66
0.77 0.11 0.12
Matches are distributed among these distances:
27 43 0.10
28 5 0.01
29 2 0.00
30 25 0.06
31 35 0.08
32 27 0.06
33 33 0.08
34 147 0.35
35 68 0.16
36 17 0.04
37 19 0.05
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (33 bp):
AAAGATGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:578353 original size:69 final size:68
Alignment explanation
Indices: 578268--578691 Score: 498
Period size: 71 Copynumber: 6.3 Consensus size: 68
578258 GGGAAGGGAG
* **
578268 AAAGATGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCATAGAGTTGTGGGCTTTAAAA
1 AAAGGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
578333 AGAA
65 AGAA
* * *
578337 AAAGGTGCCACAGAGTTTTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGAC-TT-AAAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
578402 AACGAA
63 AAAGAA
* * * *
578408 AAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAG-GTGCCACGAAGTTGTGGTCTTTAAA
1 AAAGGTGCCACGGAGTTGTGGAC-TT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
578472 AAGAA
64 AAGAA
* * *
578477 AAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAC
1 AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
578542 G--
66 GAA
* *
578543 -AAGGTGCCACGGAGTCGTGGACTTAGAAA-GAAAAAGAGTGCCACAGAGTTGTGGGC-TT-AAA
1 AAAGGTGCCACGGAGTTGTGGACTTA-AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
578604 AG--
65 AGAA
* *
578606 ---GGTGCCACGGAGTTGTGGACTTAGAAAAGAAAAAG-GTGCCACGGAGTCGTGGGC-TTAAAA
1 AAAGGTGCCACGGAGTTGTGGACTTA-AAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAA
578666 AGAA
65 AGAA
*
578670 AAAGAGTGCCACGGAATTGTGG
1 AAAG-GTGCCACGGAGTTGTGG
578692 GCTTTAGAGA
Statistics
Matches: 315, Mismatches: 28, Indels: 25
0.86 0.08 0.07
Matches are distributed among these distances:
61 45 0.14
62 12 0.04
63 4 0.01
64 2 0.01
65 50 0.16
66 2 0.01
67 11 0.03
68 42 0.13
69 68 0.22
70 9 0.03
71 70 0.22
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (68 bp):
AAAGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
GAA
Found at i:578604 original size:27 final size:27
Alignment explanation
Indices: 578574--578815 Score: 115
Period size: 27 Copynumber: 8.0 Consensus size: 27
578564 CTTAGAAAGA
*
578574 AAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
* *
578601 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
*
578628 AGAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTT
1 --AAAAG----A-GTGCCACGGAGTTGTGGGCTT
*
578662 AAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTT
1 -------AAAAGAGTGCCACGGAGTTGTGGGC-TT
* ** * *
578697 AGAGAAAAGATGCCATTGAGTCGTGGACTTT
1 A-A-AAGAG-TGCCACGGAGTTGTGGGC-TT
* *
578728 GGAAAGAGATGCCACTGAGTTGTGGGCTT
1 -AAAAGAG-TGCCACGGAGTTGTGGGCTT
* *
578757 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
*
578784 AAAAGGAAAAGGTGCCACGGAGTCGTGGGCTT
1 AAAA-G---A-GTGCCACGGAGTTGTGGGCTT
578816 TGCAGAAAAG
Statistics
Matches: 165, Mismatches: 28, Indels: 39
0.71 0.12 0.17
Matches are distributed among these distances:
27 46 0.28
28 7 0.04
29 8 0.05
30 24 0.15
31 17 0.10
32 19 0.12
34 36 0.22
35 3 0.02
39 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:578650 original size:160 final size:157
Alignment explanation
Indices: 578273--578907 Score: 620
Period size: 160 Copynumber: 3.9 Consensus size: 157
578263 GGGAGAAAGA
* ** *
578273 TGCCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCATAGAGTTGTGGGCTTTAAAAAGAAA
1 TGCCACGGAGTTGTGGACTTAAAA-AGAAAAAG-GTGCCACGGAGTCGTGGGC-TTAAAAAGAAA
* * * * * *
578338 AAG-GTGCCACAGAGTTTTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
63 AAGAGTGCCACGGAGTTGTGGGCTTTG-AAA-CG---AAGA-TGCCACGGAGTCGTGGAC-TTAG
* *
578402 AACGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAGG
121 AA-GAAAAAGATGCCACTGAGTTGTGGGC-TT-AAAA--G----GG
* * * * * *
578448 TGCCACGAAGTTGTGGTCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAA
1 TGCCACGGAGTTGTGGAC-TTAAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAA
*
578513 GAGTGCCACGGAGTTGTGGGCTTTGAAACGAAGGTGCCACGGAGTCGTGGACTTAGAAAGAAAAA
65 GAGTGCCACGGAGTTGTGGGCTTTGAAACGAAGATGCCACGGAGTCGTGGACTTAG-AAGAAAAA
*
578578 GAGTGCCACAGAGTTGTGGGCTTAAAAGGG
129 GA-TGCCACTGAGTTGTGGGCTTAAAAGGG
578608 TGCCACGGAGTTGTGGACTTAGAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAA
1 TGCCACGGAGTTGTGGACTTA-AAAAGAAAAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAA
* ** * *
578673 GAGTGCCACGGAATTGTGGGCTTTAGAGAA--AAGATGCCATTGAGTCGTGGACTTTG--GAAAG
65 GAGTGCCACGGAGTTGTGGGCTTT-GA-AACGAAGATGCCACGGAGTCGTGGACTTAGAAGAAAA
578734 AGATGCCACTGAGTTGTGGGCTTAAAAGGG
128 AGATGCCACTGAGTTGTGGGCTTAAAAGGG
* *** *
578764 TGCCACGGAGTTGTGGACTT-AAAAGGAAAAGGTGCCACGGAGTCGTGGGCTT-TGCAGAAAAGG
1 TGCCACGGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAAG
** * * * * * * *
578827 A-TGCCACTAAGTCGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGACTTTGAAGAAAAGG
66 AGTGCCACGGAGTTGTGGGCTTTGAAAC-GAAGATGCCACGGAGTCGTGGACTTAGAAGAAAAAG
*
578891 ATGCCACTGAGTCGTGG
130 ATGCCACTGAGTTGTGG
578908 ACTTTGAGAA
Statistics
Matches: 403, Mismatches: 45, Indels: 44
0.82 0.09 0.09
Matches are distributed among these distances:
150 1 0.00
151 2 0.00
152 16 0.04
153 33 0.08
154 31 0.08
155 21 0.05
156 46 0.11
157 7 0.02
159 3 0.01
160 102 0.25
161 2 0.00
162 2 0.00
164 1 0.00
166 4 0.01
167 12 0.03
168 35 0.09
169 3 0.01
172 1 0.00
173 15 0.04
174 37 0.09
175 23 0.06
176 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (157 bp):
TGCCACGGAGTTGTGGACTTAAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAAG
AGTGCCACGGAGTTGTGGGCTTTGAAACGAAGATGCCACGGAGTCGTGGACTTAGAAGAAAAAGA
TGCCACTGAGTTGTGGGCTTAAAAGGG
Found at i:578668 original size:95 final size:95
Alignment explanation
Indices: 578300--578695 Score: 386
Period size: 95 Copynumber: 4.0 Consensus size: 95
578290 CTTAAAAGGG
* ** * * ** *
578300 AAAAAGAGTGCCATAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACAGAGTTTTGGGCTTTGA
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAG-AAAAGGTGCCACGGAGTCGTGGAC-TT-A
*
578365 AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
63 AAA-AGAAAAAGAGTGCCACGGAGTTGTGGGC-TT
* * * *
578400 AAAACGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAGGTGCCACGAAGTTGTGGT
1 ---A--AAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAAAGGTGCCACGGAGTCGTGGA
*
578465 CTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGACTT
59 C-TTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* *
578502 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAACG--AAGGTGCCACGGAGTCGTGGAC
1 ------AAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAGGTGCCACGGAGTCGTGGAC
* *
578565 TTAGAAAGAAAAAGAGTGCCACAGAGTTGTGGGCTT
60 TTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
* * *
578601 -AAAAGGGTGCCACGGAGTTGTGGACTTAGAAAAGAAAAAGGTGCCACGGAGTCGTGGGCTTAAA
1 AAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAG-AAAAGGTGCCACGGAGTCGTGGACTTAAA
*
578665 AAGAAAAAGAGTGCCACGGAATTGTGGGCTT
65 AAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
578696 TAGAGAAAAG
Statistics
Matches: 252, Mismatches: 30, Indels: 30
0.81 0.10 0.10
Matches are distributed among these distances:
92 30 0.12
95 54 0.21
98 13 0.05
99 38 0.15
101 1 0.00
102 2 0.01
103 49 0.19
104 7 0.03
105 34 0.13
106 23 0.09
107 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.20
Consensus pattern (95 bp):
AAAAAGGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAGGTGCCACGGAGTCGTGGACTTAAAA
AGAAAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:578840 original size:121 final size:124
Alignment explanation
Indices: 578635--578911 Score: 348
Period size: 121 Copynumber: 2.2 Consensus size: 124
578625 CTTAGAAAAG
* *
578635 AAAAAGGTGCCACGGAGTCGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAATTGTGGGCTTTAGA
1 AAAAAGGTGCCACGGAGTCGTGGACTTAAAAAGAAAAAGAGTGCCACGGAATCGTGGGCTTTAGA
* * * *
578700 GAAAAGATGCCATTGAGTCGTGGACTTTG-GA-AAGAGATGCCACTGAGTTGTGGGCTT
66 GAAAAGATGCCACTAAGTCGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGGCTT
* * * *
578757 AAAAGGGTGCCACGGAGTTGTGGACTT-AAAAGGAAAAG-GTGCCACGGAGTCGTGGGCTTT-GC
1 AAAAAGGTGCCACGGAGTCGTGGACTTAAAAAGAAAAAGAGTGCCACGGAATCGTGGGCTTTAG-
*
578819 AGAAAAGGATGCCACTAAGTCGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGACTTT
65 AGAAAA-GATGCCACTAAGTCGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGGC-TT
*
578881 GAAGAAAAGGATGCCACTGAGTCGTGGACTT
1 --A-AAAAGG-TGCCACGGAGTCGTGGACTT
578912 TGAGAAGAGA
Statistics
Matches: 132, Mismatches: 14, Indels: 12
0.84 0.09 0.08
Matches are distributed among these distances:
119 1 0.01
120 26 0.20
121 32 0.24
122 26 0.20
123 21 0.16
124 2 0.02
126 1 0.01
127 5 0.04
128 18 0.14
ACGTcount: A:0.31, C:0.16, G:0.32, T:0.21
Consensus pattern (124 bp):
AAAAAGGTGCCACGGAGTCGTGGACTTAAAAAGAAAAAGAGTGCCACGGAATCGTGGGCTTTAGA
GAAAAGATGCCACTAAGTCGTGGACTTTGAGACAAAAGATGCCACTGAGTCGTGGGCTT
Found at i:578896 original size:96 final size:95
Alignment explanation
Indices: 578372--578943 Score: 270
Period size: 95 Copynumber: 5.9 Consensus size: 95
578362 TGAAAAGGGA
* * * * *
578372 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAACGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 AAAAGA-TGCCACGGAGTCGTGGAC-TTAAAA-GGAAAAGGTGCCACGGAGTCGTGGACTTTG--
* * * * *
578437 AAGGGAAAAG-GTGCCACGAAGTTGTGGTCTTTAAAAAGA-
61 -A--GAAAAGATTGCCACTAAGTCGTGGACTTT---GAGAC
* * * * *
578476 AAAAGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGA-A
1 AAAAGATGCCACGGAGTCGTGGACTTAAAAGG-AAAAG-GTGCCACGGAGTCGTGGACTTTGAGA
* ** *
578540 ACGAAG-GTGCCACGGAGTCGTGGACTTAGAAAGA-
64 A--AAGATTGCCACTAAGTCGTGGACTTTG--AGAC
* * * * *
578574 AAAAGAGTGCCACAGAGTTGTGGGCTTAAAA-G----GGTGCCACGGAGTTGTGGACTTAGAAAA
1 AAAAGA-TGCCACGGAGTCGTGGACTTAAAAGGAAAAGGTGCCACGGAGTCGTGGACTTTG---A
* ** * **
578634 GAAAA-AGGTGCCACGGAGTCGTGGGCTTAAAAAGA-
62 GAAAAGA-TTGCCACTAAGTCGTGGACTT--TGAGAC
* * * * * * **
578669 AAAAGAGTGCCACGGAATTGTGGGCTTTAGA-GAAAAGATGCCATTGAGTCGTGGACTTTG-GAA
1 AAAAGA-TGCCACGGAGTCGTGGACTTAAAAGGAAAAGGTGCCACGGAGTCGTGGACTTTGAGAA
* * *
578732 AGAGA-TGCCACTGAGTTGTGGGC-TT---A-
65 A-AGATTGCCACTAAGTCGTGGACTTTGAGAC
* * * *
578758 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAGGTGCCACGGAGTCGTGGGCTTTGCAGAA
1 AAAAGATGCCACGGAGTCGTGGACTTAAAAGGAAAAGGTGCCACGGAGTCGTGGACTTTG-AGAA
578823 AAGGA-TGCCACTAAGTCGTGGACTTTGAGAC
65 AA-GATTGCCACTAAGTCGTGGACTTTGAGAC
* ** *
578854 AAAAGATGCCACTGAGTCGTGGACTTTGAA-GAAAAGGATGCCACTGAGTCGTGGACTTTGAGAA
1 AAAAGATGCCACGGAGTCGTGGACTTAAAAGGAAAAGG-TGCCACGGAGTCGTGGACTTTGAGAA
* *
578918 GAGATTGCCACTGAGTCGTGGACTTT
65 AAGATTGCCACTAAGTCGTGGACTTT
578944 AAGAAGGTAT
Statistics
Matches: 384, Mismatches: 52, Indels: 73
0.75 0.10 0.14
Matches are distributed among these distances:
88 20 0.05
89 30 0.08
90 1 0.00
91 21 0.05
92 23 0.06
93 1 0.00
94 5 0.01
95 105 0.27
96 47 0.12
97 4 0.01
98 9 0.02
99 61 0.16
100 1 0.00
101 1 0.00
102 10 0.03
103 40 0.10
104 5 0.01
ACGTcount: A:0.31, C:0.15, G:0.33, T:0.21
Consensus pattern (95 bp):
AAAAGATGCCACGGAGTCGTGGACTTAAAAGGAAAAGGTGCCACGGAGTCGTGGACTTTGAGAAA
AGATTGCCACTAAGTCGTGGACTTTGAGAC
Found at i:578930 original size:31 final size:30
Alignment explanation
Indices: 578669--578948 Score: 253
Period size: 32 Copynumber: 9.1 Consensus size: 30
578659 CTTAAAAAGA
* * * *
578669 AAAAGAGTGCCACGGAATTGTGGGCTTTAGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTT-GAG
*
578701 AAAAGATGCCATTGAGTCGTGGACTTTG-G
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* *
578730 AAAGAGATGCCACTGAGTTGTGGGC-TT-A-
1 AAA-AGATGCCACTGAGTCGTGGACTTTGAG
* * * * **
578758 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCACTGAGTCGTGGACTT-TGA-G
* * *
578790 AAAAGGTGCCACGGAGTCGTGGGCTTTGCAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
*
578821 AAAAGGATGCCACTAAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
578852 ACAAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 --AAAAGATGCCACTGAGTCGTGGACTTTG-AG
578885 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* *
578916 AAGAGATTGCCACTGAGTCGTGGACTTTAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
578947 AA
1 AA
578949 GGTATTTGAA
Statistics
Matches: 209, Mismatches: 25, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
27 17 0.08
28 4 0.02
29 6 0.03
30 22 0.11
31 57 0.27
32 97 0.46
33 6 0.03
ACGTcount: A:0.30, C:0.15, G:0.32, T:0.23
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:578949 original size:31 final size:30
Alignment explanation
Indices: 578636--578948 Score: 238
Period size: 32 Copynumber: 10.1 Consensus size: 30
578626 TTAGAAAAGA
* * * *
578636 AAAAGGTGCCACGGAGTCGTGGGCTTAAAAAG
1 AAAAGATGCCACTGAGTCGTGGACTT--TAAG
* * * *
578668 AAAAAGAGTGCCACGGAATTGTGGGCTTTAGAG
1 -AAAAGA-TGCCACTGAGTCGTGGACTTTA-AG
* *
578701 AAAAGATGCCATTGAGTCGTGGACTTT-GG
1 AAAAGATGCCACTGAGTCGTGGACTTTAAG
* *
578730 AAAGAGATGCCACTGAGTTGTGGGC-TT-A-
1 AAA-AGATGCCACTGAGTCGTGGACTTTAAG
* * * * *
578758 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGG
1 AAAAGATGCCACTGAGTCGTGGACTT-TAA-G
* * * *
578790 AAAAGGTGCCACGGAGTCGTGGGCTTTGCAG
1 AAAAGATGCCACTGAGTCGTGGACTTT-AAG
* *
578821 AAAAGGATGCCACTAAGTCGTGGACTTTGAGAC
1 AAAA-GATGCCACTGAGTCGTGGACTTT-A-AG
578854 AAAAGATGCCACTGAGTCGTGGACTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTT-AAG
*
578885 AAAAGGATGCCACTGAGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTAAG
*
578916 AAGAGATTGCCACTGAGTCGTGGACTTTAAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTAAG
578947 AA
1 AA
578949 GGTATTTGAA
Statistics
Matches: 232, Mismatches: 35, Indels: 28
0.79 0.12 0.09
Matches are distributed among these distances:
27 17 0.07
28 4 0.02
29 6 0.03
30 21 0.09
31 56 0.24
32 98 0.42
33 12 0.05
34 18 0.08
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.22
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTAAG
Found at i:579920 original size:18 final size:17
Alignment explanation
Indices: 579885--579933 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
579875 TGAAAAGGGG
579885 TTTTTCCTTTCTTCT-TTT
1 TTTTTCCTTT-TT-TGTTT
579903 TTTTTCCTTTTTTGTTT
1 TTTTTCCTTTTTTGTTT
* *
579920 TGTTTCTTTTTTTG
1 TTTTTCCTTTTTTG
579934 GAAAAGAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 1 0.04
17 17 0.61
18 10 0.36
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTTTCCTTTTTTGTTT
Found at i:586533 original size:12 final size:12
Alignment explanation
Indices: 586518--586544 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
586508 GCAAAGATCA
586518 GGGAGAAGATAG
1 GGGAGAAGATAG
586530 GGGAGAAGATAG
1 GGGAGAAGATAG
586542 GGG
1 GGG
586545 GGCTGGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.56, T:0.07
Consensus pattern (12 bp):
GGGAGAAGATAG
Found at i:586839 original size:52 final size:52
Alignment explanation
Indices: 586759--586878 Score: 195
Period size: 52 Copynumber: 2.3 Consensus size: 52
586749 AAAAGTTTCT
* *
586759 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAATTTGCG
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGCC
* * *
586811 TGCATATATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGCC
586863 TGCATGTATCGATACA
1 TGCATGTATCGATACA
586879 AAGATCAGTG
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGCC
Found at i:586891 original size:52 final size:51
Alignment explanation
Indices: 586759--586898 Score: 183
Period size: 52 Copynumber: 2.7 Consensus size: 51
586749 AAAAGTTTCT
*
586759 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAATTTGCG
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGCC
* * * *
586811 TGCATATATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAATTTGCC
*
586863 TGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TGCATGTATCGATACATTA-AT-AGTGTATCGATACA
586899 ATGTACCGAT
Statistics
Matches: 77, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 2 0.03
52 75 0.97
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (51 bp):
TGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAATTTGCC
Found at i:586989 original size:33 final size:33
Alignment explanation
Indices: 586952--587018 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
586942 AGTAGCTTAA
586952 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
586985 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
587018 A
1 A
587019 AACCATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:586992 original size:13 final size:13
Alignment explanation
Indices: 586974--586998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
586964 CAAAAAAATA
586974 TGTATCGATACAT
1 TGTATCGATACAT
586987 TGTATCGATACA
1 TGTATCGATACA
586999 ACACTTTATG
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:591085 original size:19 final size:19
Alignment explanation
Indices: 591061--591122 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
591051 TTTTGAATTT
591061 CAAATAATTTGTATCGATA
1 CAAATAATTTGTATCGATA
**
591080 CAAATAGTAAATGTATCGATA
1 CAAATA--ATTTGTATCGATA
591101 C--ATAAGTGTTGTATCGATA
1 CAAATAA-T-TTGTATCGATA
591120 CAA
1 CAA
591123 TGTATCGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
17 1 0.03
19 20 0.61
21 12 0.36
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (19 bp):
CAAATAATTTGTATCGATA
Found at i:591128 original size:13 final size:13
Alignment explanation
Indices: 591110--591134 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
591100 ACATAAGTGT
591110 TGTATCGATACAA
1 TGTATCGATACAA
591123 TGTATCGATACA
1 TGTATCGATACA
591135 TAAGTTTTGT
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:591130 original size:32 final size:32
Alignment explanation
Indices: 591089--591160 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
591079 ACAAATAGTA
591089 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
*
591121 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
591153 AATGTATC
1 AATGTATC
591161 ACTATGAAGC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:591147 original size:19 final size:19
Alignment explanation
Indices: 591068--591153 Score: 76
Period size: 19 Copynumber: 4.7 Consensus size: 19
591058 TTTCAAATAA
*
591068 TTTGTATCGATACAAATAGT
1 TTTGTATCGATACATA-AGT
**
591088 AAATGTATCGATACATAAGT
1 -TTTGTATCGATACATAAGT
*
591108 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
591123 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
591140 TTTGTATCGATACA
1 TTTGTATCGATACA
591154 ATGTATCACT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 23 0.43
20 3 0.06
21 13 0.24
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:591204 original size:21 final size:21
Alignment explanation
Indices: 591178--591219 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
591168 AGCTACTGCC
591178 AAGGAAATGTATCAATACATT
1 AAGGAAATGTATCAATACATT
* *
591199 AAGGAAGTGTATCGATACATT
1 AAGGAAATGTATCAATACATT
591220 GTATCGATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCAATACATT
Found at i:591224 original size:13 final size:13
Alignment explanation
Indices: 591206--591231 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
591196 ATTAAGGAAG
591206 TGTATCGATACAT
1 TGTATCGATACAT
591219 TGTATCGATACAT
1 TGTATCGATACAT
591232 CGATTTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:593679 original size:51 final size:51
Alignment explanation
Indices: 593599--593767 Score: 205
Period size: 51 Copynumber: 3.3 Consensus size: 51
593589 ATCTTTCATC
* * * *
593599 TCGGGGATACTCCAA-TCCCGGTTTCATTTCCAAAACATCAATTTTTCTTAA
1 TCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTTTCATAA
* * * *
593650 TCGGGGATACTCCAACTCCGATTTTATTTCTAAAATACCTATTTTCCATAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAA
* * * *
593701 TCGGGGATACTCCAACTCCGATTTTATTTTCAAAACACCGACTTTTCACAA
1 TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAA
*
593752 TCGGGCATACTCCAAC
1 TCGGGGATACTCCAAC
593768 CCATTATTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
51 100 0.99
52 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
TCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTTCATAA
Found at i:593939 original size:79 final size:79
Alignment explanation
Indices: 593703--594004 Score: 409
Period size: 79 Copynumber: 3.9 Consensus size: 79
593693 TTCCATAATC
* * * *
593703 GGGGATACTCCAACTCC-GATTTTATTT-TCAAAACACCGACTTTTCACAATCGGGCATACTCCA
1 GGGGATACTCCAAC-CCTGATTTTATTTCT-AAAACACCAATTTTTCATAATCGGGGATACTCCA
*
593766 A-CCCATTATTTTCGA
64 ACCCCGTTATTTTCGA
* * *
593781 GGGGACACTCCAACCCCGATTTTATTTCGAAAACACCAA-TTTT--TAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
593843 CCCGTTATTTTCAA
66 CCCGTTATTTTCGA
* * *
593857 GGGGATACTCTAACCCTGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
*
593922 CCCGTTATTTTTGA
66 CCCGTTATTTTCGA
* *
593936 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATTCTCCATAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
594001 CCCG
66 CCCG
594005 GTTTTATTTC
Statistics
Matches: 198, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
75 16 0.08
76 45 0.23
77 10 0.05
78 32 0.16
79 95 0.48
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (79 bp):
GGGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATTTTTCATAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:594012 original size:51 final size:51
Alignment explanation
Indices: 593936--594155 Score: 323
Period size: 51 Copynumber: 4.3 Consensus size: 51
593926 TTATTTTTGA
* *
593936 GGGGATACTCCAACCCTGATTTTATTTCTAAAACACCAATTCTCCATAATC
1 GGGGATACTCCAACCCTGATCTTATTTCTAAAACACCAATTCTCCACAATC
* * *
593987 GGGGATACTCCAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACCCTGATCTTATTTCTAAAACACCAATTCTCCACAATC
* * *
594038 GGGGATATTCTAACTCTGATCTTATTTCTAAAACACCAATTCTCCACAATC
1 GGGGATACTCCAACCCTGATCTTATTTCTAAAACACCAATTCTCCACAATC
* * * * *
594089 GGGGATATTCCAACTCTGATCTTATTTCTAAAACACTAATTTTTCACAATC
1 GGGGATACTCCAACCCTGATCTTATTTCTAAAACACCAATTCTCCACAATC
594140 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
594156 AGTTATTTCA
Statistics
Matches: 154, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 154 1.00
ACGTcount: A:0.30, C:0.27, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCTGATCTTATTTCTAAAACACCAATTCTCCACAATC
Found at i:594173 original size:28 final size:29
Alignment explanation
Indices: 594137--594207 Score: 119
Period size: 28 Copynumber: 2.5 Consensus size: 29
594127 ATTTTTCACA
594137 ATCGGGGATACTCCAACCCAGTTATTT-C
1 ATCGGGGATACTCCAACCCAGTTATTTCC
594165 ATCGGGGATACTCCAACCCAGTTATTTCC
1 ATCGGGGATACTCCAACCCAGTTATTTCC
*
594194 A-AGGGGATACTCCA
1 ATCGGGGATACTCCA
594208 TCCCCGGCTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 39 0.95
29 2 0.05
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCAGTTATTTCC
Found at i:594272 original size:51 final size:51
Alignment explanation
Indices: 594197--594315 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
594187 TATTTCCAAG
* * *
594197 GGGATACTCCATCCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCA
1 GGGATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATCA
* * **
594248 GGGATAC-CTCAACCCCAGCCTTATTTCTAAAATATTGATTTCTCATAATTG
1 GGGATACTC-CAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATCA
594299 GGGATACTCCAACCCCA
1 GGGATACTCCAACCCCA
594316 TTATTTTCAC
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
50 1 0.02
51 57 0.97
52 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.31
Consensus pattern (51 bp):
GGGATACTCCAACCCCAGCCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:606844 original size:24 final size:22
Alignment explanation
Indices: 606817--606872 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 22
606807 CTTCTCTTCT
*
606817 AAAAAAAACAACAAAAACAAAAGC
1 AAAAAAAAAAACAAAAA-AAAA-C
606841 AAAAAAAAAAACAAAAAAAAAC
1 AAAAAAAAAAACAAAAAAAAAC
*
606863 AAAGAAAAAA
1 AAAAAAAAAA
606873 GAGAGAAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 10 0.33
23 4 0.13
24 16 0.53
ACGTcount: A:0.86, C:0.11, G:0.04, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAACAAAAAAAAAC
Found at i:606847 original size:27 final size:26
Alignment explanation
Indices: 606817--606872 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 26
606807 CTTCTCTTCT
*
606817 AAAAAAAAC-AACAAAAACAAAAGCAAA
1 AAAAAAAACAAAAAAAAAC-AAAG-AAA
606844 AAAAAAAACAAAAAAAAACAAAGAAA
1 AAAAAAAACAAAAAAAAACAAAGAAA
606870 AAA
1 AAA
606873 GAGAGAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 6 0.22
27 13 0.48
28 8 0.30
ACGTcount: A:0.86, C:0.11, G:0.04, T:0.00
Consensus pattern (26 bp):
AAAAAAAACAAAAAAAAACAAAGAAA
Found at i:606848 original size:10 final size:10
Alignment explanation
Indices: 606818--606872 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 10
606808 TTCTCTTCTA
606818 AAAAAAACAAC
1 AAAAAAA-AAC
606829 AAAAACAAAAGC
1 AAAAA-AAAA-C
606841 AAAAAAAAAAAC
1 --AAAAAAAAAC
606853 AAAAAAAAAC
1 AAAAAAAAAC
606863 AAAGAAAAAA
1 AAA-AAAAAA
606873 GAGAGAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
10 13 0.33
11 13 0.33
12 4 0.10
13 4 0.10
14 5 0.13
ACGTcount: A:0.85, C:0.11, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:608019 original size:55 final size:54
Alignment explanation
Indices: 607843--608505 Score: 626
Period size: 55 Copynumber: 11.4 Consensus size: 54
607833 CTCCTTTCAC
*
607843 TTTTCAGTCCTCAAAGAGTAGGATGCCTTTTCATTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGATG-C----C-TTTCAAAGCCCACACAAGTTGGTGGCA
* * *
607903 CCTTTCAATCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGG--A----TGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
607964 CCTTTCAGTCCTCAAAGAGCAGGATGCCTTTAAAAGCCCACACAAGTTAGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
608019 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
** * *
608074 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAACCCACACAGGTTGGTGGCA
1 TTTTC-AGTCCTCAAAGAGCAGGATGCC-TTTC-----AAAGCCCACACAAGTTGGTGGCA
* ** *
608135 TTTTCCAGTCCTCAAAAAGCAGGACACCTCTT-AAAGCCCACACAAGTTAGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGCCT-TTCAAAGCCCACACAAGTTGGTGGCA
* *
608190 TTTTCCAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
608245 CCTTTCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
608300 TTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTGGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGC-----C-TTTCAAAGCCCACACAAGTTGGTGGCA
* * *
608361 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAACCCGCACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATG-C----CTTTCAAAGCCCACACAAGTTGGTGGCA
608421 TTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGATGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCA
* *
608482 CTTCCTAGTCCTCAAAGAGCAGGA
1 TTTTC-AGTCCTCAAAGAGCAGGA
608506 CGCTCTCTCC
Statistics
Matches: 527, Mismatches: 43, Indels: 64
0.83 0.07 0.10
Matches are distributed among these distances:
54 9 0.02
55 237 0.45
56 8 0.02
57 1 0.00
59 2 0.00
60 52 0.10
61 212 0.40
62 3 0.01
63 1 0.00
66 1 0.00
67 1 0.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (54 bp):
TTTTCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:608146 original size:171 final size:170
Alignment explanation
Indices: 607876--608781 Score: 880
Period size: 171 Copynumber: 5.3 Consensus size: 170
607866 TGCCTTTTCA
* *
607876 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAAAGAGCAGGACACCTTTTCCTTTC
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT
*
607941 AAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGATGCCTTTAAAAGCCCAC
66 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTT-AAAGCCCAC
*
608005 ACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGCC
129 ACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
* *
608047 TTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTC-AGTCCTCAAAGAGCAGGACACCTTTTCCTTT
* * * **
608111 TAAAACCCACACAGGTTGGTGGCATTTTCCAGTCCTCAAAAAGCAGGACACCTCTTAAAGCCCAC
65 TAAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCT-TTAAAGCCCAC
* *
608176 ACAAGTTAGTGGCA-TTTTCCAGTCCTTAAAGAGCAGGACGCC
129 ACAAGTTAGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACGCC
* *
608218 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAAGACGCC-TTT-C----
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT
*
608277 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAG
66 AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGC-----C-TTT-AAAG
** *
608342 CCCACACAAGTGGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTC
124 CCCACACAAGTTAGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACG-C----C
* * * ** *
608394 TTTCAAAACCCGCACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGACACCTTTTCCTTT
* * * *
608458 TAAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGACG-C--T----CTCTC
65 TAAAGCCCACACAAGTTGGTGGCATTTTCC-AGTCCTCAAAGAGCAGGATGCCTTTAAAGCCCAC
* ** *
608515 -C---TT--T--CGCCTTTTTGTCCTCAAAGAGCAGGATGCC
129 ACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
* ** * * * *
608549 TTTTAAAGCCCACACAAGCCGATGGCA-CTTTCAGTCCTCAAAGAACATGACACCTTCTCCTTTT
1 TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT
*
608613 AAAGCCCACACAAGTTGGTGGCACTTTT-GAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAA
66 AAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGC---C--TTT--AAA
* * *
608677 GCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTTTCC
123 GCCCACACAAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGG--A-C--GCC
* * *
608730 TTTTCAAAGCCCACACGAGTTGGTGGCACATTTTAGTCCTCAAAGAGCAGGA
1 -TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGA
608782 TGCACTTTAT
Statistics
Matches: 604, Mismatches: 74, Indels: 102
0.77 0.09 0.13
Matches are distributed among these distances:
154 71 0.12
155 25 0.04
156 2 0.00
158 1 0.00
159 1 0.00
160 19 0.03
161 3 0.00
162 2 0.00
164 1 0.00
165 44 0.07
167 1 0.00
168 6 0.01
169 1 0.00
170 16 0.03
171 236 0.39
172 9 0.01
173 1 0.00
174 1 0.00
175 3 0.00
176 69 0.11
177 2 0.00
178 2 0.00
181 6 0.01
182 63 0.10
183 19 0.03
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (170 bp):
TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAAAGAGCAGGACACCTTTTCCTTTT
AAAGCCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTTAAAGCCCACAC
AAGTTAGTGGCACCTTTCAGTCCTCAAAGAGCAGGACGCC
Found at i:608515 original size:61 final size:59
Alignment explanation
Indices: 607843--608519 Score: 695
Period size: 61 Copynumber: 11.6 Consensus size: 59
607833 CTCCTTTCAC
* * *
607843 TTTT-CAGTCCTCAAAGAGTAGGATGCCTTTTCATTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCC--TTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
607903 CCTTT-CAATCCTCAAAGAGCAGGACACCTTTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCCAGTCCTCAAAGAGCAGGACGCC--TTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
607964 CCTTT-CAGTCCTCAAAGAGCAGGA----TGCCTTTAAAAGCCCACACAAGTTAGTGGCA
1 -TTTTCCAGTCCTCAAAGAGCAGGACGCCTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
608019 CCTTT-CAGTCCTCAAAGAGCAAGACG----CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCCAGTCCTCAAAGAGCAGGACGCCTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
608074 TTTTCTAGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAACCCACACAGGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCC--TTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
608135 TTTTCCAGTCCTCAAAAAGCAGGACACC-T-C-TT-AAAGCCCACACAAGTTAGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
608190 TTTTCCAGTCCTTAAAGAGCAGGACG----CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
608245 CCTTT-CAGTCCTCAAAGAGCAAGACG----CCTTTCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCCAGTCCTCAAAGAGCAGGACGCCTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
608300 TTTTCCAGTCCTCAAAGAGTAGGATGCTTTTTCTTTTCAAAGCCCACACAAGTGGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGC--CTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
608361 TTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTTCAAAACCCGCACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCC-TTCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
608421 TTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 TTTTCCAGTCCTCAAAGAGCAGGACGCC-T-TCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
608482 -CTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTC
1 TTTTCC-AGTCCTCAAAGAGCAGGACGC-CT-TCCTTTC
608520 GCCTTTTTGT
Statistics
Matches: 536, Mismatches: 56, Indels: 48
0.84 0.09 0.08
Matches are distributed among these distances:
53 1 0.00
54 8 0.01
55 227 0.42
56 5 0.01
58 1 0.00
60 59 0.11
61 234 0.44
62 1 0.00
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (59 bp):
TTTTCCAGTCCTCAAAGAGCAGGACGCCTTCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:608620 original size:60 final size:61
Alignment explanation
Indices: 608547--608781 Score: 298
Period size: 61 Copynumber: 3.9 Consensus size: 61
608537 GAGCAGGATG
** * * *
608547 CCTTTT-AAAGCCCACACAAGCCGATGGCAC-TTTCAGTCCTCAAAGAACATGACACCTTCT
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAGCAGGACACCTT-T
* * **
608607 CCTTTT-AAAGCCCACACAAGTTGGTGGCACTTTTGAGTCCTCAAAGAGCAGGA-TGCTTT
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAGCAGGACACCTTT
* * *
608666 CTTTTTGCAAAGCCCACACAAGTTGGTGGCACCTTCCAGTCCTCAAAGAGCAGGACACCTTT
1 CCTTTT-CAAAGCCCACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAGCAGGACACCTTT
* *
608728 CCTTTTCAAAGCCCACACGAGTTGGTGGCACATTTTAGTCCTCAAAGAGCAGGA
1 CCTTTTCAAAGCCCACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAGCAGGA
608782 TGCACTTTAT
Statistics
Matches: 152, Mismatches: 19, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
59 6 0.04
60 30 0.20
61 107 0.70
62 9 0.06
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (61 bp):
CCTTTTCAAAGCCCACACAAGTTGGTGGCACATTTCAGTCCTCAAAGAGCAGGACACCTTT
Found at i:608709 original size:215 final size:216
Alignment explanation
Indices: 608332--608721 Score: 576
Period size: 215 Copynumber: 1.8 Consensus size: 216
608322 GATGCTTTTT
** * * * * *
608332 CTTTTCAAAGCCCACACAAGTGGGTGGCATTTTCCAGTCCTCAAAGAGCAGGACGCCTTTTCTTT
1 CTTTTCAAAGCCCACACAAGCCGATGGCACTTTCCAGTCCTCAAAGAACAGGACACCTTTCCTTT
*
608397 CAAAACCCGCACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAA
66 CAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAA
608462 GCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCTTTT
131 GCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCTTTT
608527 TGTCCTCAAAGAGCAGGATGC
196 TGTCCTCAAAGAGCAGGATGC
*
608548 CTTTT-AAAGCCCACACAAGCCGATGGCACTTT-CAGTCCTCAAAGAACATGACACCTTCTCCTT
1 CTTTTCAAAGCCCACACAAGCCGATGGCACTTTCCAGTCCTCAAAGAACAGGACACCTT-TCCTT
* * * *
608611 TTAAAGCCCACACAAGTTGGTGGCACTTTT-GAGTCCTCAAAGAGCAGGATG-CTT-TCTTTTTG
65 TCAAAACCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTT-
608673 CAAAGCCCACACAAGTTGGTGGCACCTTCC-AGTCCTCAAAGAGCAGGAC
128 -AAAGCCCACACAAGTTGGTGGCA-CTTCCTAGTCCTCAAAGAGCAGGAC
608722 ACCTTTCCTT
Statistics
Matches: 156, Mismatches: 13, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
213 6 0.04
214 25 0.16
215 111 0.71
216 14 0.09
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (216 bp):
CTTTTCAAAGCCCACACAAGCCGATGGCACTTTCCAGTCCTCAAAGAACAGGACACCTTTCCTTT
CAAAACCCACACAAGTTGGTGGCATTTTCCAGTCCTCAAAGAGCAGGATGCCTTCTCCTTTTAAA
GCCCACACAAGTTGGTGGCACTTCCTAGTCCTCAAAGAGCAGGACGCTCTCTCCTTTCGCCTTTT
TGTCCTCAAAGAGCAGGATGC
Found at i:608740 original size:122 final size:115
Alignment explanation
Indices: 608523--608789 Score: 358
Period size: 122 Copynumber: 2.3 Consensus size: 115
608513 TCCTTTCGCC
* *
608523 TTTTTGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCCGATGGCACTTTCAGTCCTC
1 TTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCCGATGGCACTTCCAGTCCTC
*
608588 AAAGAACATGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCAC-
66 AAAGAACAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACA
** *
608637 TTTTGAGTCCTCAAAGAGCAGGATGCTTTCTTTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
1 TTTT-AGTCCTCAAAGAGCAGGATGC---C-TTTT--AAAGCCCACACAAGCCGATGGCA-CTTC
* *
608702 CAGTCCTCAAAGAGCAGGACACCTT-TCCTTTTCAAAGCCCACACGAGTTGGTGGCACA
58 CAGTCCTCAAAGAACAGGACACCTTCTCCTTTT-AAAGCCCACACAAGTTGGTGGCACA
608760 TTTTAGTCCTCAAAGAGCAGGATGCACTTT
1 TTTTAGTCCTCAAAGAGCAGGATGC-CTTT
608790 ATTTTCCTCT
Statistics
Matches: 134, Mismatches: 9, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
114 4 0.03
115 20 0.15
118 1 0.01
119 7 0.05
120 1 0.01
121 27 0.20
122 70 0.52
123 4 0.03
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (115 bp):
TTTTAGTCCTCAAAGAGCAGGATGCCTTTTAAAGCCCACACAAGCCGATGGCACTTCCAGTCCTC
AAAGAACAGGACACCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACA
Found at i:609357 original size:19 final size:20
Alignment explanation
Indices: 609333--609413 Score: 66
Period size: 19 Copynumber: 4.2 Consensus size: 20
609323 TTTTGAATTT
609333 CAAATAA-TTTGTATCGATA
1 CAAATAAGTTTGTATCGATA
*
609352 CAAAT-AGTAAATGTATCGATA
1 CAAATAAGT--TTGTATCGATA
*
609373 C--ATAAGTGTTGTATCAATA
1 CAAATAAGT-TTGTATCGATA
609392 C--ATAAGTTTTGTATCGATA
1 CAAATAAG-TTTGTATCGATA
609411 CAA
1 CAA
609414 TGTATCGTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
18 1 0.02
19 34 0.68
20 4 0.08
21 11 0.22
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (20 bp):
CAAATAAGTTTGTATCGATA
Found at i:609463 original size:21 final size:21
Alignment explanation
Indices: 609437--609478 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
609427 AGCTACTGCC
609437 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
*
609458 AAGGAAGTGTATCGATACATT
1 AAGGAAATGTATCGATACATT
609479 GTATCGATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:609502 original size:20 final size:21
Alignment explanation
Indices: 609467--609507 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
609457 TAAGGAAGTG
609467 TATCGATACATTGTATCGATA
1 TATCGATACATTGTATCGATA
*
609488 TATCGAT-CTTTGTATCGATA
1 TATCGATACATTGTATCGATA
609508 CATCTAGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (21 bp):
TATCGATACATTGTATCGATA
Found at i:612033 original size:68 final size:72
Alignment explanation
Indices: 611916--612191 Score: 211
Period size: 79 Copynumber: 3.7 Consensus size: 72
611906 CCAACTTTGA
* * * * * *
611916 TTTTATTTCTAAAATACCTATTTTCCATAATCGGGGATACTTCATCCCCGTTATTTCCAAGGGGA
1 TTTTATTTCTGAAACACCAATTTTTC--AATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGA
611981 CA-CC-A-G
64 CACCCAACG
* *
611987 TTTTATTTC-GAAAACACCAATTTTTC-ATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGAC
1 TTTTATTTCTG-AAACACCAATTTTTCAATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGAC
612050 ACTCCAACCTCGG
65 AC-CCAA---C-G
* ***
612063 TTTTATTTCTGAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAGGGGA
1 TTTTATTTCTGAAACACCAATTTTTC--AATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGA
*
612128 TACTCCAACCCCAG
64 CAC-CCAA---C-G
* ** *
612142 TTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTTCAACCCCG
1 TTTTATTTCTGAAACACCAATT-T-TTCAATCGGGGATACTCCAACCCCG
612192 ATTTTATTTT
Statistics
Matches: 172, Mismatches: 18, Indels: 22
0.81 0.08 0.10
Matches are distributed among these distances:
68 34 0.20
70 2 0.01
71 22 0.13
76 24 0.14
77 1 0.01
79 87 0.51
80 1 0.01
81 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (72 bp):
TTTTATTTCTGAAACACCAATTTTTCAATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGACA
CCCAACG
Found at i:612117 original size:79 final size:78
Alignment explanation
Indices: 611983--612191 Score: 289
Period size: 79 Copynumber: 2.7 Consensus size: 78
611973 CAAGGGGACA
611983 CCAGTTTTATTTC-GAAAACACCAATTTTTC--ATCGGGGATACTCCAACCCCGTTATTTTCGAG
1 CCAGTTTTATTTCTG-AAACACCAATTTTTCAAATCGGGGATACTCCAACCCCGTTATTTTCGAG
612045 GGGACACTCCAACC
65 GGGACACTCCAACC
* * * *
612059 TCGGTTTTATTTCTGAAACATCAATTTTTCATAATCGGGGATACTCCAACCCCGTTATTTTTGAG
1 CCAGTTTTATTTCTGAAACACCAATTTTTCA-AATCGGGGATACTCCAACCCCGTTATTTTCGAG
*
612124 GGGATACTCCAACC
65 GGGACACTCCAACC
* * * *
612138 CCAGTTTTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTTCAACCCCG
1 CCAGTTTTATTTCTGAAACACCAATTTTTCA-AATCGGGGATACTCCAACCCCG
612192 ATTTTATTTT
Statistics
Matches: 116, Mismatches: 13, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
76 25 0.22
77 1 0.01
79 90 0.78
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (78 bp):
CCAGTTTTATTTCTGAAACACCAATTTTTCAAATCGGGGATACTCCAACCCCGTTATTTTCGAGG
GGACACTCCAACC
Found at i:612199 original size:51 final size:51
Alignment explanation
Indices: 612123--612353 Score: 259
Period size: 51 Copynumber: 4.5 Consensus size: 51
612113 TTATTTTTGA
*
612123 GGGGATACTCCAACCCC-AGTTTTATTTCTAAAACACCAATTCTCCACAATC
1 GGGGATACTTCAACCCCGA-TTTTATTTCTAAAACACCAATTCTCCACAATC
*
612174 GGGGATACTTCAACCCCGATTTTATTTTTAAAACACCAATTCTCCACAATC
1 GGGGATACTTCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
* * * * *
612225 GGGGATATTTCAACTCTGATCTTATTTCTAAAACACCAATTCTCCACAATT
1 GGGGATACTTCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
* * * * * * * *
612276 GGGGATA-TTCCAACTCTGATCTTATTTTTAAAACACTAATTTTTCACAATT
1 GGGGATACTT-CAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
* *
612327 GGGGATGCTCCAACCCCGTTATTTTAT
1 GGGGATACTTCAACCCCG--ATTTTAT
612354 CGGGGATACT
Statistics
Matches: 158, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
50 2 0.01
51 148 0.94
52 2 0.01
53 6 0.04
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
GGGGATACTTCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
Found at i:612301 original size:102 final size:102
Alignment explanation
Indices: 612144--612332 Score: 290
Period size: 102 Copynumber: 1.9 Consensus size: 102
612134 AACCCCAGTT
*
612144 TTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTTCAACCCCGATTTTATTTTTAAAACA
1 TTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTTCAACCCCGATCTTATTTTTAAAACA
612209 CCAATTCTCCACAATCGGGGATATTTCAACTCTGATC
66 CCAATTCTCCACAATCGGGGATATTTCAACTCTGATC
* * *
612246 TTATTTCTAAAACACCAATTCTCCACAATTGGGGATA-TTCCAACTCTGATCTTATTTTTAAAAC
1 TTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTT-CAACCCCGATCTTATTTTTAAAAC
* * * *
612310 ACTAATTTTTCACAATTGGGGAT
65 ACCAATTCTCCACAATCGGGGAT
612333 GCTCCAACCC
Statistics
Matches: 78, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
101 2 0.03
102 76 0.97
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (102 bp):
TTATTTCTAAAACACCAATTCTCCACAATCGGGGATACTTCAACCCCGATCTTATTTTTAAAACA
CCAATTCTCCACAATCGGGGATATTTCAACTCTGATC
Found at i:612367 original size:28 final size:28
Alignment explanation
Indices: 612327--612400 Score: 96
Period size: 28 Copynumber: 2.6 Consensus size: 28
612317 TTTCACAATT
* * *
612327 GGGGATGCTCCAACCCCGTTATTT-TATC
1 GGGGATACTCCAACCCCGTTATTTCCA-A
*
612355 GGGGATACTCCAACCCAGTTATTTCCAA
1 GGGGATACTCCAACCCCGTTATTTCCAA
612383 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
612401 GCTTTATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (28 bp):
GGGGATACTCCAACCCCGTTATTTCCAA
Found at i:612448 original size:51 final size:50
Alignment explanation
Indices: 612384--612501 Score: 155
Period size: 51 Copynumber: 2.3 Consensus size: 50
612374 TATTTCCAAG
* *
612384 GGGATACTCCAACCCCGGCTTTATTTCCAAAATATTGATTTCTCACAATCA
1 GGGATACT-CAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
* * **
612435 GGGATACCTCAACCCCGACCTTATTTCTAAAATATTGATTTCTCATAATTG
1 GGGATA-CTCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
612486 GGGATACTCTAACCCC
1 GGGATACTC-AACCCC
612502 ATTATTTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
50 3 0.05
51 54 0.92
52 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (50 bp):
GGGATACTCAACCCCGACCTTATTTCCAAAATATTGATTTCTCACAATCA
Found at i:623291 original size:172 final size:172
Alignment explanation
Indices: 622869--623320 Score: 567
Period size: 172 Copynumber: 2.6 Consensus size: 172
622859 TTTATTTCTC
* * * * *
622869 AAAAAAATT-ATTTCGTACCTTAATGG-AGAACCAAAAAGATACGAAAAGTTTTAAAAAATTTTA
1 AAAAAATTTCATTTCGTACCTTAATGGAAGATCC-AAAAGATATGAAAA-TTTTTAAATATTTTA
* *
622932 TACCTCCACGGATACCCATGGGAATATTAGAAATTCTAAAAAATTCAGGTGATAATTTTTATTGG
64 TACCTCCACGGATACCCATGGGAATATTAGAAATTATGAAAAATTCAGGTGATAATTTTTATTGG
*
622997 ATGAAAAAGAATTATTTATTATTTTATTTTATTATTTATTATTTT
129 ATGAAAAAGAATTATTTATTA-TTTATTTTATTATTTATTAATTT
* * * * *
623042 AAAAAATTTCATTTCGTACCCTATTGGAAGCTCGAAAAGATATGAAAAGTTTTAAATATTTTTAT
1 AAAAAATTTCATTTCGTACCTTAATGGAAGATCCAAAAGATATGAAAATTTTTAAATA-TTTTAT
* * * *
623107 ACC-CTTACGGATACTCATGGGAATATTAAAAATTTTGAAAAATTCAGGTGATAATTTTTTATTG
65 ACCTC-CACGGATACCCATGGGAATATTAGAAATTATGAAAAATTCAGGTGATAA-TTTTTATTG
*
623171 GATGAAAAAGAATTATTTATTA-TTA-TTTATTATTTTTTAAATTT
128 GATGAAAAAGAATTATTTATTATTTATTTTATTATTTATT-AATTT
* * *
623215 -GAAAATTTCATTTTGTACCTTAATGGAAG-TCCAAAAGGATATGAAATTTTTTAAATATTTCTA
1 AAAAAATTTCATTTCGTACCTTAATGGAAGATCCAAAA-GATATGAAAATTTTTAAATATTT-TA
*
623278 TACCTCGACGGATACCCATGGGAATATTAGAAATATATGAAAA
64 TACCTCCACGGATACCCATGGGAATATTAGAAAT-TATGAAAA
623321 TGATTAGTAT
Statistics
Matches: 241, Mismatches: 28, Indels: 20
0.83 0.10 0.07
Matches are distributed among these distances:
171 9 0.04
172 86 0.36
173 31 0.13
174 81 0.34
175 34 0.14
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.38
Consensus pattern (172 bp):
AAAAAATTTCATTTCGTACCTTAATGGAAGATCCAAAAGATATGAAAATTTTTAAATATTTTATA
CCTCCACGGATACCCATGGGAATATTAGAAATTATGAAAAATTCAGGTGATAATTTTTATTGGAT
GAAAAAGAATTATTTATTATTTATTTTATTATTTATTAATTT
Found at i:624868 original size:18 final size:19
Alignment explanation
Indices: 624847--624882 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
624837 AAAAATTCAA
624847 AATTTATGAAAA-TGAATG
1 AATTTATGAAAACTGAATG
*
624865 AATTTTTGAAAACTGAAT
1 AATTTATGAAAACTGAAT
624883 TAATGTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (19 bp):
AATTTATGAAAACTGAATG
Found at i:624879 original size:166 final size:165
Alignment explanation
Indices: 624649--625299 Score: 819
Period size: 165 Copynumber: 3.9 Consensus size: 165
624639 TGGTTTTTTT
* * *
624649 AAAAAAAGGGAGATTTTAAGGAAAAAATTTC-AAATTCATGGAAATGAATGAATTTTTGAAAACT
1 AAAAAAAGAGA-ATTTCAAGGAAAAAA-TTCAAAATTCATGAAAATGAATGAATTTTTGAAAACT
* *
624713 GAATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAATCAAAAACCAAGAAAAATCTC
64 GAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATC-C
*
624778 CCCAAAAAAATTACGGAATAGAAAACTTCATATTTCGA
128 CCCAAAAAAATTACGGAATAGAAAACTTCGTATTTCGA
* *
624816 AAAAAAAGAGAATTTCAAGTAAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAACTGA
1 AAAAAAAGAGAATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTGA
* * *
624881 ATTAATGTGAAATAAATAATAATATTTTATGATTTTTAAAAAT-AAATAAACAAGAAAAATCCCC
66 ATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAA-AAACAAGAAAAATCCCC
** * *
624945 CCTAAAAATATAC-AAAGTAGAAAACTTTGTATTTCG-
130 CAAAAAAAT-TACGGAA-TAGAAAACTTCGTATTTCGA
* * * *
624981 AAAAAAGGAGAATTTCAAGGAAAAAATTCAAAATTTATGAAAATGAATGAATTTTTGAAAAATAA
1 AAAAAAAGAGAATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTGA
*
625046 ATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAAACAAAAAACAAGAAAAATCCCCC
66 ATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCCCCC
* * * * * *
625111 AAAATATTTACAGAGTAAAAAACTCCGTATTTC-A
131 AAAAAAATTACGGAATAGAAAACTTCGTATTTCGA
* * * * * * *
625145 AAGAGAAGATAATTTCATGGAAAAAA-ACGAAAAGCTCATGAAAATGAAAGAATTTTTGAAAACT
1 AAAAAAAGAGAATTTCAAGGAAAAAATTC-AAAA-TTCATGAAAATGAATGAATTTTTGAAAACT
* * * *
625209 GATTTAATATGAAATAAATAATAACATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCT
64 GAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCC-
* *
625274 CCCATAAAAATTTACGGAGTAGAAAA
128 CCCA-AAAAAATTACGGAATAGAAAA
625300 TAAGGAAATT
Statistics
Matches: 423, Mismatches: 50, Indels: 22
0.85 0.10 0.04
Matches are distributed among these distances:
163 1 0.00
164 43 0.10
165 225 0.53
166 126 0.30
167 28 0.07
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.27
Consensus pattern (165 bp):
AAAAAAAGAGAATTTCAAGGAAAAAATTCAAAATTCATGAAAATGAATGAATTTTTGAAAACTGA
ATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAATCAAAAAACAAGAAAAATCCCCC
AAAAAAATTACGGAATAGAAAACTTCGTATTTCGA
Found at i:625284 original size:331 final size:331
Alignment explanation
Indices: 624650--625299 Score: 898
Period size: 331 Copynumber: 2.0 Consensus size: 331
624640 GGTTTTTTTA
* * * *
624650 AAAAAAGGGAGATTTTAAGGAAAAAATTTCAAATTCATGGAAATGAATGAATTTTTGAAAACTGA
1 AAAAAAGGGAGATTTCAAGGAAAAAATTTCAAATTCATGAAAATGAATGAATTTTTGAAAAATAA
* *
624715 ATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAATCAAAAACCAAGAAAAATCTCCC
66 ATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAAACAAAAAACAAGAAAAATCTCCC
* * * * *
624780 CAAAAAAATTACGGAATAGAAAACTTCATATTTCGAAAAAAAAGAGAATTTCAAGTAAAAAATTC
131 CAAAAAAATTACAGAATAAAAAACTCCATATTTCGAAAAAAAAGAGAATTTCAAGGAAAAAATAC
* * * * * *
624845 AAAATTTATGAAAATGAATGAATTTTTGAAAACTGAATTAATGTGAAATAAATAATAATATTTTA
196 AAAACTCATGAAAATGAAAGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAACATTTGA
* *
624910 TGATTTTTAAAAATAAATAAACAAGAAAAATCCCCCCTAAAAATATACAAAGTAGAAAACTTTGT
261 TGAATTTTAAAAATAAATAAACAAGAAAAATCCCCCATAAAAATATACAAAGTAGAAAACTTTGT
624975 ATTTCG
326 ATTTCG
*
624981 AAAAAA-GGAGAATTTCAAGGAAAAAA-TTCAAAATTTATGAAAATGAATGAATTTTTGAAAAAT
1 AAAAAAGGGAG-ATTTCAAGGAAAAAATTTC-AAATTCATGAAAATGAATGAATTTTTGAAAAAT
*
625044 AAATTAATATGAAATAAATAATAATATTTGATGAATTTTAAAAAACAAAAAACAAGAAAAATC-C
64 AAATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAAACAAAAAACAAGAAAAATCTC
* * * * * * * *
625108 CCCAAAATATTTACAGAGTAAAAAACTCCGTATTTC-AAAGAGAAGATAATTTCATGGAAAAAA-
129 CCCAAAAAAATTACAGAATAAAAAACTCCATATTTCGAAAAAAAAGAGAATTTCAAGGAAAAAAT
*
625171 ACGAAAAGCTCATGAAAATGAAAGAATTTTTGAAAACTGATTTAATATGAAATAAATAATAACAT
194 AC-AAAA-CTCATGAAAATGAAAGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAACAT
* * **
625236 TTGATGAATTTTAAAAATTAAA-AACCAAGAAAAATCCTCCCATAAAAATTTACGGAGTAGAAAA
257 TTGATGAATTTTAAAAA-TAAATAAACAAGAAAAATCC-CCCATAAAAATATACAAAGTAGAAAA
625300 TAAGGAAATT
Statistics
Matches: 279, Mismatches: 34, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
328 1 0.00
329 26 0.09
330 117 0.42
331 135 0.48
ACGTcount: A:0.53, C:0.09, G:0.11, T:0.28
Consensus pattern (331 bp):
AAAAAAGGGAGATTTCAAGGAAAAAATTTCAAATTCATGAAAATGAATGAATTTTTGAAAAATAA
ATTAATATGAAATAAATAATAATATTTAATGAATTTTAAAAAACAAAAAACAAGAAAAATCTCCC
CAAAAAAATTACAGAATAAAAAACTCCATATTTCGAAAAAAAAGAGAATTTCAAGGAAAAAATAC
AAAACTCATGAAAATGAAAGAATTTTTGAAAACTGAATTAATATGAAATAAATAATAACATTTGA
TGAATTTTAAAAATAAATAAACAAGAAAAATCCCCCATAAAAATATACAAAGTAGAAAACTTTGT
ATTTCG
Found at i:625341 original size:152 final size:151
Alignment explanation
Indices: 625174--625451 Score: 375
Period size: 152 Copynumber: 1.8 Consensus size: 151
625164 GAAAAAAACG
* *
625174 AAAAGCTCATGAAAATGAA-AGAATTTTTGAAAACTGATTTAATATGAAAT-AAATAATAACATT
1 AAAAACTCATGAAAAT-AAGA-AATTTTTGAAAACTGATTTAATA-GAAATCAAATAATAACATA
* * *
625237 TGATGAATTTTAAAAA-TTAAAAACCAAGAAAAATCCTCCCATA-AAAATTTACGGAGTAGAAAA
63 TGATAAATTTTAAAAAGTTAAAAACCAAG-AAAATCCTCCCA-AGAAAATTTACGAAGAAGAAAA
625300 TAAGGAAATTTCGAGAAAAAAAATTC
126 TAAGGAAATTTCGAGAAAAAAAATTC
* * *
625326 AAAAACTCATGAAAATAAGTAAATTTTTGAAATCTGATTTAATAGGAATCAAATAATAATATATG
1 AAAAACTCATGAAAATAAG-AAATTTTTGAAAACTGATTTAATAGAAATCAAATAATAACATATG
* * *
625391 ATAAATTTTAAAAAGTTTAAACCCATGAAAATCCTCCCAAGAAAATTTACGAAGAAGAAAA
65 ATAAATTTTAAAAAGTTAAAAACCAAGAAAATCCTCCCAAGAAAATTTACGAAGAAGAAAA
625452 CCACTAATTT
Statistics
Matches: 110, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
151 7 0.06
152 93 0.85
153 10 0.09
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (151 bp):
AAAAACTCATGAAAATAAGAAATTTTTGAAAACTGATTTAATAGAAATCAAATAATAACATATGA
TAAATTTTAAAAAGTTAAAAACCAAGAAAATCCTCCCAAGAAAATTTACGAAGAAGAAAATAAGG
AAATTTCGAGAAAAAAAATTC
Found at i:628158 original size:20 final size:21
Alignment explanation
Indices: 628135--628188 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
628125 CATTTCAAGC
628135 ATATATCGATACATTCACT-T
1 ATATATCGATACATTCACTGT
* *
628155 ATATATCAATACATTTACTGT
1 ATATATCGATACATTCACTGT
* *
628176 TTGTATCGATACA
1 ATATATCGATACA
628189 AATTATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (21 bp):
ATATATCGATACATTCACTGT
Found at i:628647 original size:326 final size:328
Alignment explanation
Indices: 628075--628698 Score: 991
Period size: 327 Copynumber: 1.9 Consensus size: 328
628065 ACATTTACTT
* * * * *
628075 ATGTATCGATACATTTCCTTTCCAGAATGCATGGTGGTTTTATATCTATACATTTCAAGCATATA
1 ATGTATCGATACATTTACTCTCCAAAATGCAGGGTGGTTTTATATCGATACATTTCAAGCATATA
* * * *
628140 TCGATACATTCACTTATATATCAATACATTTACTGTTTGTATCGATACAAATTATAAAAATCTAA
66 TCAATACATTCACTTATATATCAATACATTTACTGTTTATATCAATACAAATTACAAAAATCTAA
*
628205 AATTTTTGACCGTTGGGACCTTGTATCGATACATTCAAGAAATGTATCGATACATTTAGACAAAA
131 AATTTTTGACCGTTGGGACCTTGTATCGATACATTCAAGAAATGTATCGATACATTTAGAAAAAA
* * *
628270 ATGTGACTTTTTCATTCTTTTTGTCTCCTAGACATCTTATTTCAATAAGGGATGATGGGAAATGG
196 ATGTGACTTTTTCATTCTTTTTGCCTCCTAGACATCATATTTCAATAAGGGATAATGGGAAATGG
*
628335 TTTTGTGCTTGAC-AAAAGTCCCGGTTACCTAAAAATACAATGGATAATGTATCGATACAAACAG
261 TTTCGTGCTTGACAAAAAGTCCCGGTTACCTAAAAATACAATGGATAATGTATCGATACAAACAG
628399 TAA
326 TAA
* * * *
628402 ATGTATCGATACTTTTACTCTCCAAAATGCAGGGTGGTTTTGTATCGATACATTTCAGGCATGTA
1 ATGTATCGATACATTTACTCTCCAAAATGCAGGGTGGTTTTATATCGATACATTTCAAGCATATA
* * * * * *
628467 TCAATATATTCATTTATGTATCAATACATTTACTGTTTATATCAATACAAATTGCAAAAATTTTA
66 TCAATACATTCACTTATATATCAATACATTTACTGTTTATATCAATACAAATTACAAAAATCTAA
*
628532 AATTTTTGACCGTTGGGACC-TGTGTCGATACATTCAAGAAATGTATCGATACATTTAGAAAAAA
131 AATTTTTGACCGTTGGGACCTTGTATCGATACATTCAAGAAATGTATCGATACATTTAGAAAAAA
*
628596 ATGTGACTTTTTCATTCTTTTTGCCTTCTAGACATCATATTTCAATAAGGGATAATGGGAAATGG
196 ATGTGACTTTTTCATTCTTTTTGCCTCCTAGACATCATATTTCAATAAGGGATAATGGGAAATGG
*
628661 TTTCGTGCTTGACAAAAAGTCTCGGTTACCTAAAAATA
261 TTTCGTGCTTGACAAAAAGTCCCGGTTACCTAAAAATA
628699 ATTTTTCGTT
Statistics
Matches: 269, Mismatches: 27, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
326 115 0.43
327 154 0.57
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (328 bp):
ATGTATCGATACATTTACTCTCCAAAATGCAGGGTGGTTTTATATCGATACATTTCAAGCATATA
TCAATACATTCACTTATATATCAATACATTTACTGTTTATATCAATACAAATTACAAAAATCTAA
AATTTTTGACCGTTGGGACCTTGTATCGATACATTCAAGAAATGTATCGATACATTTAGAAAAAA
ATGTGACTTTTTCATTCTTTTTGCCTCCTAGACATCATATTTCAATAAGGGATAATGGGAAATGG
TTTCGTGCTTGACAAAAAGTCCCGGTTACCTAAAAATACAATGGATAATGTATCGATACAAACAG
TAA
Found at i:629304 original size:25 final size:25
Alignment explanation
Indices: 629276--629327 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
629266 ACCTTGAGAA
629276 AGGTATCTCTTAACAATGATGATGT
1 AGGTATCTCTTAACAATGATGATGT
629301 AGGTATCTCTTAACAATGATGATGT
1 AGGTATCTCTTAACAATGATGATGT
629326 AG
1 AG
629328 AGATTTACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.35
Consensus pattern (25 bp):
AGGTATCTCTTAACAATGATGATGT
Found at i:634860 original size:52 final size:52
Alignment explanation
Indices: 634733--634862 Score: 120
Period size: 52 Copynumber: 2.5 Consensus size: 52
634723 ATAAAGGTGC
* * * * * *
634733 CAATATGCTAATTCAAGACCAGTGATATTAGGCTTAAAGATGTAAAGAATGT
1 CAATGTGCTGATTCAAGACCAGCGACATTAGACTTAAAGATGTAAAGAATCT
* * ** *
634785 CAATGTGTTGATTCACGTTCAGCGACATTAGACTTGAAGATG-AGAAGAATACT
1 CAATGTGCTGATTCAAGACCAGCGACATTAGACTTAAAGATGTA-AAGAAT-CT
*
634838 -AATGTGCTGATTCAAGGCCAGCGAC
1 CAATGTGCTGATTCAAGACCAGCGAC
634863 GTTGGTCTTA
Statistics
Matches: 61, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
51 1 0.02
52 59 0.97
53 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.27
Consensus pattern (52 bp):
CAATGTGCTGATTCAAGACCAGCGACATTAGACTTAAAGATGTAAAGAATCT
Done.