Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008654.1 Hibiscus syriacus cultivar Beakdansim tig00111648_pilon, whole genome shotgun sequence
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: 3533819
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 18
Found at i:387873 original size:14 final size:16
Alignment explanation
Indices: 387854--387931 Score: 56
Period size: 19 Copynumber: 4.7 Consensus size: 16
387844 CGAAATGGTT
387854 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
387868 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG-AA-GAAA
*
387887 ATCGCAATGCGAAATAAAA
1 ATCGCAA-GCG-AA-GAAA
387906 ATCGCAA-CG-AGAAA
1 ATCGCAAGCGAAGAAA
387920 ATCGCAATGCGA
1 ATCGCAA-GCGA
387932 TTTTCATTTC
Statistics
Matches: 54, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
14 17 0.31
15 1 0.02
16 4 0.07
17 2 0.04
18 1 0.02
19 29 0.54
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (16 bp):
ATCGCAAGCGAAGAAA
Found at i:387886 original size:19 final size:19
Alignment explanation
Indices: 387864--387931 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
387854 ATCGCAACGA
387864 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
387883 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
*
387902 AAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
387916 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
387932 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 2 0.05
17 2 0.05
19 29 0.66
ACGTcount: A:0.49, C:0.18, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:387975 original size:20 final size:20
Alignment explanation
Indices: 387950--388010 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
387940 TCGCATTGCG
*
387950 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
387970 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
387990 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
388010 A
1 A
388011 AATGAATGTC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:388255 original size:19 final size:19
Alignment explanation
Indices: 388231--388291 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
388221 CTTAAGTGAG
388231 ATCGCAATGCGAAAAGAAA
1 ATCGCAATGCGAAAAGAAA
*
388250 ATCGCAA--CG---AGATA
1 ATCGCAATGCGAAAAGAAA
*
388264 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAAAGAAA
388283 ATCGCAATG
1 ATCGCAATG
388292 ACAAAATCGC
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 11 0.32
16 2 0.06
17 2 0.06
19 19 0.56
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAAAGAAA
Found at i:388268 original size:33 final size:33
Alignment explanation
Indices: 388231--388303 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
388221 CTTAAGTGAG
* *
388231 ATCGCAATGCGAAAAGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAAAGAAAATCGCAACGACAAA
* *
388264 ATCGCAATGCGAAATGAAAATCGCAATGACAAA
1 ATCGCAATGCGAAAAGAAAATCGCAACGACAAA
388297 ATCGCAA
1 ATCGCAA
388304 CGATTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.19, G:0.19, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAAAGAAAATCGCAACGACAAA
Found at i:388358 original size:33 final size:33
Alignment explanation
Indices: 388303--388426 Score: 158
Period size: 33 Copynumber: 3.7 Consensus size: 33
388293 CAAAATCGCA
* * *
388303 ACGATTTTAATTTTCGCTTTGCGATTCCCTCGTT
1 ACGATTTTCA-TTTCGCATTGCGATTCTCTCGTT
388337 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
* ** *
388370 GCCTTTTTCATTTCGCATTGCGATTCTATCGTT
1 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
* *
388403 GCGATTTGCATTTCGCATTGCGAT
1 ACGATTTTCATTTCGCATTGCGAT
388427 GGTCAAATGA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
33 71 0.89
34 9 0.11
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (33 bp):
ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:389250 original size:24 final size:24
Alignment explanation
Indices: 389199--389252 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
389189 GTATTCGAAA
* * *
389199 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
389223 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
389247 TTTGAT
1 TTTGAT
389253 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:391787 original size:33 final size:33
Alignment explanation
Indices: 391741--391867 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
391731 GGAAATTACT
*
391741 ATCGCAATACGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
391774 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
391806 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
391840 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
391868 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:391832 original size:19 final size:19
Alignment explanation
Indices: 391741--391871 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
391731 GGAAATTACT
*
391741 ATCGCAATACGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
391760 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
391774 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
391793 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
391807 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
391826 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
391840 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
391859 ATCGCAACGCGAA
1 ATCGCAATGCGAA
391872 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:391848 original size:66 final size:66
Alignment explanation
Indices: 391742--391874 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
391732 GAAATTACTA
*
391742 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
391807 T
66 T
* *
391808 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
391873 T
66 T
391874 T
1 T
391875 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (66 bp):
TCGCAATACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:391899 original size:14 final size:14
Alignment explanation
Indices: 391882--391938 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
391872 TTTAATTTCG
391882 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
391896 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
391915 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
391929 CGTTGCGATT
1 CGTTGCGATT
391939 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:391918 original size:33 final size:33
Alignment explanation
Indices: 391867--391956 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
391857 AAATCGCAAC
* *
391867 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
391900 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
391933 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
391957 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:391920 original size:19 final size:19
Alignment explanation
Indices: 391896--391956 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
391886 GCGATTCTCT
391896 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
391915 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
391929 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
391948 CATTGCGAT
1 CGTTGCGAT
391957 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:392082 original size:14 final size:14
Alignment explanation
Indices: 392063--392099 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
392053 CATCAATTAA
392063 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
392077 ACAAATCACCTTTT
1 ACAAATCAACTTTT
392091 ACAAATCAA
1 ACAAATCAA
392100 TTAACCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:393506 original size:42 final size:40
Alignment explanation
Indices: 393421--393543 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 40
393411 GTGAATCGGG
* * * * *
393421 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTC-TCGAGGATGATAGGGGC
393463 CTCTTGAACGGTGGGATGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTCGAGG-ATGATAGGGGC
* * * *
393505 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAG-GGACTCTCGA-GGATGATAGG
393544 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.07
42 57 0.84
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.24
Consensus pattern (40 bp):
CTCTTGAACGGTGGGAGGGACTCTCGAGGATGATAGGGGC
Found at i:394005 original size:95 final size:94
Alignment explanation
Indices: 393824--394040 Score: 346
Period size: 95 Copynumber: 2.3 Consensus size: 94
393814 GAATAGTTTC
* *
393824 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAAAAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
* *
393889 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGATAAAGAACACACAGTTTAGCAG
*
393918 AATTGGCAGGAACCGAAAAAAATTTACTTTCAACCAAAAGACAAATA-AAAGACAAATACTAACT
1 AATTGGCAGCAACCG-AAAAAATTTACTTTCAACCAAAAGACAAA-ACAAAGACAAATACTAACT
393982 TCACAGTGATAAAGAACACACAGTTTAGCAG
64 TCACAGTGATAAAGAACACACAGTTTAGCAG
*
394013 AATTGGGCAGCAACCGAATAAATTTACT
1 AATT-GGCAGCAACCGAAAAAATTTACT
394041 AAGCAATCTA
Statistics
Matches: 113, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
94 13 0.12
95 89 0.79
96 11 0.10
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.20
Consensus pattern (94 bp):
AATTGGCAGCAACCGAAAAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGATAAAGAACACACAGTTTAGCAG
Found at i:395808 original size:33 final size:33
Alignment explanation
Indices: 395751--395838 Score: 158
Period size: 33 Copynumber: 2.6 Consensus size: 33
395741 ACGAGATAAT
395751 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
395785 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
395818 GAGAATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
395839 AAATCGTAAC
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 39 0.74
34 14 0.26
ACGTcount: A:0.39, C:0.23, G:0.27, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:395843 original size:19 final size:19
Alignment explanation
Indices: 395726--395871 Score: 105
Period size: 19 Copynumber: 8.1 Consensus size: 19
395716 TCTTTTGGTT
*
395726 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
395745 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
395765 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
395783 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
395799 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
395816 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
395832 GAAATGAAAATCGTAACGC
1 GAAATGAAAATCGCAACGC
*
395851 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
395870 GA
1 GA
395872 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 16, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 41 0.41
20 27 0.27
21 2 0.02
ACGTcount: A:0.42, C:0.20, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:395889 original size:19 final size:19
Alignment explanation
Indices: 395867--395911 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
395857 AAAATCGCAA
*
395867 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
* *
395886 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
395905 TGCGATT
1 TGCGATT
395912 CTCTCGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.51
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:396488 original size:20 final size:20
Alignment explanation
Indices: 396463--396516 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
396453 GGCGCTATGT
396463 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
396483 AAATCGCGTTGCGAAAGTCA
1 AAATCGCGTTGCGAAAGTCA
** *
396503 GTATCTCGTTGCGA
1 AAATCGCGTTGCGA
396517 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (20 bp):
AAATCGCGTTGCGAAAGTCA
Found at i:396577 original size:41 final size:41
Alignment explanation
Indices: 396485--396579 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
396475 GAAAGTCAAA
* * * * ** *
396485 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
*
396526 ATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
396568 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
396580 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:402326 original size:3 final size:3
Alignment explanation
Indices: 402318--402394 Score: 73
Period size: 3 Copynumber: 25.3 Consensus size: 3
402308 ATGTTATTTA
* * * * * *
402318 TAT TAT TAT TAT TAT TAT AAT AAT TAT TAT TAT AAT TAT AAT AAT AAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
402366 AAT TAT TAT TAT TAT TAA TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
402395 TAATATTACA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (3 bp):
TAT
Found at i:402872 original size:22 final size:22
Alignment explanation
Indices: 402847--402891 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
402837 ACAATGCAGC
402847 AAAGAAACAG-AAAAGAAAAAAG
1 AAAGAAA-AGAAAAAGAAAAAAG
*
402869 AAAGAAAAGAAAAAGAAAGAAG
1 AAAGAAAAGAAAAAGAAAAAAG
402891 A
1 A
402892 GAAGCTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAGAAAAGAAAAAGAAAAAAG
Found at i:402883 original size:15 final size:15
Alignment explanation
Indices: 402855--402894 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
402845 GCAAAGAAAC
402855 AGAAAAGAAAAAAGAA
1 AGAAAAG-AAAAAGAA
402871 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAGAA
*
402886 AGAAGAGAA
1 AGAAAAGAA
402895 GCTTACCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAGAA
Found at i:415210 original size:18 final size:17
Alignment explanation
Indices: 415187--415225 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
415177 AAAAAATAAT
*
415187 AAAAAACAAGAGAAAAGA
1 AAAAAACAAAAG-AAAGA
*
415205 AAAAAAGAAAAGAAAGA
1 AAAAAACAAAAGAAAGA
415222 AAAA
1 AAAA
415226 GAAAAAGAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAAAACAAAAGAAAGA
Found at i:415212 original size:15 final size:14
Alignment explanation
Indices: 415197--415230 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
415187 AAAAAACAAG
415197 AGAAAAG-AAAAAA
1 AGAAAAGAAAAAAA
415210 AGAAAAGAAAGAAAA
1 AGAAAAGAAA-AAAA
415225 AGAAAA
1 AGAAAA
415231 AGAGGGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 2 0.11
15 10 0.53
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AGAAAAGAAAAAAA
Found at i:415215 original size:13 final size:13
Alignment explanation
Indices: 415175--415230 Score: 51
Period size: 15 Copynumber: 4.0 Consensus size: 13
415165 TATGCTTAAT
*
415175 GAAAAAAATAATAA
1 GAAAAAAAGAA-AA
415189 -AAAACAAGAGAAAA
1 GAAAA-AA-AGAAAA
415203 GAAAAAAAGAAAA
1 GAAAAAAAGAAAA
415216 GAAAGAAAAAGAAAA
1 G-AA-AAAAAGAAAA
415231 AGAGGGGTCA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 11 0.31
14 8 0.22
15 17 0.47
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (13 bp):
GAAAAAAAGAAAA
Found at i:416508 original size:83 final size:83
Alignment explanation
Indices: 416369--417010 Score: 1004
Period size: 83 Copynumber: 7.7 Consensus size: 83
416359 ACATTAGCTG
416369 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
416434 AAACCAATCAATGAATTT
66 AAACTAATCATTGAATTT
416452 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
416517 AAACTAAACATT--ATCTG
66 AAACTAATCATTGAAT-TT
416534 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
416599 AAACTAATCATTGAATTT
66 AAACTAATCATTGAATTT
* * *
416617 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
416682 AAACTAATCATTGAATTT
66 AAACTAATCATTGAATTT
*
416700 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
416765 AAACCAATCATTGAATTT
66 AAACTAATCATTGAATTT
* * * *
416783 GGAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
1 -GAA-AGATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT
416847 GGTAAAACTAATCATTGAATTT
62 GGTAAAACTAATCATTGAATTT
*
416869 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
416934 AAACCAATCATTGAATTT
66 AAACTAATCATTGAATTT
* * * *
416952 GAAAGAAAT-AAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATCT
1 GAAAG--ATGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCT
417011 AATTTGGTTT
Statistics
Matches: 518, Mismatches: 29, Indels: 21
0.91 0.05 0.04
Matches are distributed among these distances:
81 2 0.00
82 77 0.15
83 305 0.59
84 17 0.03
85 14 0.03
86 103 0.20
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (83 bp):
GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACTAATCATTGAATTT
Found at i:416884 original size:169 final size:167
Alignment explanation
Indices: 416369--417010 Score: 1033
Period size: 169 Copynumber: 3.8 Consensus size: 167
416359 ACATTAGCTG
*
416369 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * * * *
416434 AAACCAATCAATGAATTT-GAA-AGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAG
66 AAACCAATCATTGAATTTGGAAGAAAT-AAGGAGCCCATAGCATCTTCTGGAAGTGTTCTTTGAG
* *
416497 TTATCTGATCTGGTTTGGTAAAACTAAACATT--ATCTG
130 TTATCTGATCTGGTTTGGTAAAACTAATCATTGAAT-TT
*
416534 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* ** * * * *
416599 AAACTAATCATTGAATTTGGAAG-AGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGT
66 AAACCAATCATTGAATTTGGAAGAAATAAGGAGCCCATAGCATCTTCTGGAAGTGTTCTTTGAGT
416663 TATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
131 TATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
416700 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
416765 AAACCAATCATTGAATTTGGAAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGA
66 AAACCAATCATTGAATTTGGAAGAAATAAGGAG-CCC-ATAGCATCTTCTGGAAGTGTTCTTTGA
416830 GTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
129 GTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
416869 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
*
416934 AAACCAATCATTGAATTTGAAAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGA
66 AAACCAATCATTGAATTTGGAAGAAATAAGGAG-CCC-ATAGCATCTTCTGGAAGTGTTCTTTGA
*
416999 ATTATCTGATCT
129 GTTATCTGATCT
417011 AATTTGGTTT
Statistics
Matches: 452, Mismatches: 18, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
165 148 0.33
166 90 0.20
167 7 0.02
168 2 0.00
169 205 0.45
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (167 bp):
GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTTGGAAGAAATAAGGAGCCCATAGCATCTTCTGGAAGTGTTCTTTGAGT
TATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
Found at i:416913 original size:252 final size:248
Alignment explanation
Indices: 416369--417010 Score: 1034
Period size: 248 Copynumber: 2.6 Consensus size: 248
416359 ACATTAGCTG
*
416369 GAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
416434 AAACCAATCAATGAATTTGAAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 AAACCAATCATTGAATTTGAAAGAAGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* * * * *
416499 ATCTGATCTGGTTTGGTAAAACTAAACATTATCTGGAAAGATGAATGTGCTCATAGCATCTTCTG
131 ATCTGATCTGGTTTGGTAAAACCAAACATTATCTGGAAAAATGAAGGAGCCCATAGCATCTTCTG
416564 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
196 GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
* *
416617 GGAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTCCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* *
416682 AAACTAATCATTGAATTTGAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
66 AAACCAATCATTGAATTTGAAAGAAGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
* *
416747 ATCTGATCTGGTTTGGTAAAACCAATCATTGAATTTGGAAGAAAT-AAGGAGACCCAATAGCATC
131 ATCTGATCTGGTTTGGTAAAACCAAACATT--ATCTGGAA-AAATGAAGGAG-CCC-ATAGCATC
416811 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
191 TTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
416869 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
1 GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
* * * *
416934 AAACCAATCATTGAATTTGAAAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGA
66 AAACCAATCATTGAATTTGAAAG-AAGAATGTG-CTC-ATAGCATCTTCTGGAAGTGTTCTTTGA
*
416999 ATTATCTGATCT
128 GTTATCTGATCT
417011 AATTTGGTTT
Statistics
Matches: 364, Mismatches: 22, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
248 152 0.42
250 11 0.03
251 5 0.01
252 151 0.41
253 5 0.01
254 2 0.01
255 38 0.10
ACGTcount: A:0.29, C:0.13, G:0.22, T:0.36
Consensus pattern (248 bp):
GAAAGAGGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTA
AAACCAATCATTGAATTTGAAAGAAGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTT
ATCTGATCTGGTTTGGTAAAACCAAACATTATCTGGAAAAATGAAGGAGCCCATAGCATCTTCTG
GAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAAACTAATCATTGAATTT
Found at i:418027 original size:113 final size:113
Alignment explanation
Indices: 417741--419089 Score: 2063
Period size: 113 Copynumber: 12.0 Consensus size: 113
417731 GCAAAGATTT
* *
417741 AAATCCATCACTTGATGGATCAGCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
417806 AATGG-TGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTTTCTC
66 AA-GGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTTTGCTC
* * * *
417855 AAATCTATCACTTAATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
417920 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * *
417968 AAATCTATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
418033 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * ***
418081 AAATCTATCACTTGATGGATTATCTTTTCTATTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCA-GAGGAAGTTCATAATGAGAAGAACTCATCTGAA
418145 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
**
418194 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAA
*
418258 GAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
**
418307 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAA
418371 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
**
418420 AAATCCATCACTTGATGGATTATCTTTTCCAGTTCG-AGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCCATCACTTGATGGATTATCTTTTCCAG-AGGAAGTTCATAATGAGAAGAACTCATCTGAA
418484 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
418533 AAATCCATCACTTGATGGATTAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
418598 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * * *
418646 AAATCCATTACTTGATGGATTAGCTTTTCCAGAAGAAGTTCATAATGAGAAGAACTCATTTAAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
418711 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
418759 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
418824 AAGGAAGAAGAAGTTCTTAATGAGAAGAATTTGTTTAGCTTTTTTCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
418872 AAATCCATCACTTGATGGATCAACTTTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
418937 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAGCTTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
418985 AAATCCATCACTTGATGGGTCAGT-TTTTCCAGA-GAAGTTCATAATGAGAAGAACTCATC---A
1 AAATCCATCACTTGATGGATTA-TCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAA
* ** *
419045 GGA-GAAGAAGAAGTTCATAATGAGAAGAGCTTATTCAACCTTTTG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
419090 AATGACTCTA
Statistics
Matches: 1178, Mismatches: 52, Indels: 16
0.95 0.04 0.01
Matches are distributed among these distances:
108 37 0.03
109 3 0.00
112 26 0.02
113 1016 0.86
114 96 0.08
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (113 bp):
AAATCCATCACTTGATGGATTATCTTTTCCAGAGGAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:418624 original size:20 final size:20
Alignment explanation
Indices: 418563--418626 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
418553 TAGCTTTTCC
418563 AGAAGAAGTTCATAATGAGA
1 AGAAGAAGTTCATAATGAGA
** *
418583 AGAACTCA-TT--TAAAGAAGGA
1 AGAA-GAAGTTCATAATG-A-GA
418603 AGAAGAAGTTCATAATGAGA
1 AGAAGAAGTTCATAATGAGA
418623 AGAA
1 AGAA
418627 TTTGTTCAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 20 0.62
21 2 0.06
22 4 0.12
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (20 bp):
AGAAGAAGTTCATAATGAGA
Found at i:418737 original size:20 final size:20
Alignment explanation
Indices: 418676--418739 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
418666 TAGCTTTTCC
418676 AGAAGAAGTTCATAATGAGA
1 AGAAGAAGTTCATAATGAGA
** *
418696 AGAACTCA-TT--TAAAGAAGGA
1 AGAA-GAAGTTCATAATG-A-GA
418716 AGAAGAAGTTCATAATGAGA
1 AGAAGAAGTTCATAATGAGA
418736 AGAA
1 AGAA
418740 TTTGTTCAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 20 0.62
21 2 0.06
22 4 0.12
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (20 bp):
AGAAGAAGTTCATAATGAGA
Found at i:419072 original size:17 final size:17
Alignment explanation
Indices: 419017--419072 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
419007 GTTTTTCCAG
419017 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
*
419034 AGAA-CTCATCAGGA-GAAGA
1 AGAAGTTCAT-A--ATG-AGA
419053 AGAAGTTCATAATGAGA
1 AGAAGTTCATAATGAGA
419070 AGA
1 AGA
419073 GCTTATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 12
0.69 0.04 0.27
Matches are distributed among these distances:
16 4 0.13
17 12 0.39
18 2 0.06
19 9 0.29
20 4 0.13
ACGTcount: A:0.48, C:0.09, G:0.25, T:0.18
Consensus pattern (17 bp):
AGAAGTTCATAATGAGA
Found at i:419316 original size:3 final size:3
Alignment explanation
Indices: 419310--419392 Score: 78
Period size: 3 Copynumber: 27.3 Consensus size: 3
419300 TTCATTTTAA
* *
419310 TAT TAT T-T ATAT TAT TAT TAT TAT TAT TAT AAT TAT TAT TAT AAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
419355 AAT AAT AAT AAT AAT TAT TAT TAT TAT TAT ATAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT T
419393 TAATATTACA
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
2 1 0.01
3 68 0.93
4 4 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:419881 original size:22 final size:22
Alignment explanation
Indices: 419856--419900 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
419846 ACAACGCAGC
419856 AAAGAAACAG-AAAAGAAAAAAG
1 AAAGAAA-AGAAAAAGAAAAAAG
*
419878 AAAGAAAAGAAAAAGAAAGAAG
1 AAAGAAAAGAAAAAGAAAAAAG
419900 A
1 A
419901 GAAGCTTACC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (22 bp):
AAAGAAAAGAAAAAGAAAAAAG
Found at i:419892 original size:15 final size:15
Alignment explanation
Indices: 419864--419903 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
419854 GCAAAGAAAC
419864 AGAAAAGAAAAAAGAA
1 AGAAAAG-AAAAAGAA
419880 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAAGAA
*
419895 AGAAGAGAA
1 AGAAAAGAA
419904 GCTTACCGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AGAAAAGAAAAAGAA
Found at i:420819 original size:20 final size:22
Alignment explanation
Indices: 420768--420819 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
420758 ATAGTCATAA
*
420768 ATATATATAATAAATAATTTAT
1 ATATATTTAATAAATAATTTAT
*
420790 ATATATTTTAATAAATTATTT-T
1 ATATA-TTTAATAAATAATTTAT
420812 A-ATATTTA
1 ATATATTTA
420820 TTTTTCAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 4 0.15
21 3 0.11
22 7 0.26
23 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATATTTAATAAATAATTTAT
Found at i:425555 original size:23 final size:21
Alignment explanation
Indices: 425524--425565 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
425514 AAAATTTATA
425524 TAATATTATAAATTAATAAATTT
1 TAATATTATAAA--AATAAATTT
*
425547 TAATCTTATAAAAATAAAT
1 TAATATTATAAAAATAAAT
425566 CTTCGCGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
23 11 0.61
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATTATAAAAATAAATTT
Found at i:425652 original size:19 final size:20
Alignment explanation
Indices: 425611--425654 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
425601 ATGACTCTTT
**
425611 TAAAAATAAATTTTAATCTTA
1 TAAAAATAAA-TTTAATAATA
425632 TAAAAATAAA-TTAATAATA
1 TAAAAATAAATTTAATAATA
425651 TAAA
1 TAAA
425655 TGTAACGCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 11 0.52
21 10 0.48
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TAAAAATAAATTTAATAATA
Found at i:432533 original size:22 final size:22
Alignment explanation
Indices: 432505--432551 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
432495 GTCTTTAAAA
432505 CCCCCATCAATCATTTTCAAAG
1 CCCCCATCAATCATTTTCAAAG
432527 CCCCCATCAATCATTTTCAAAG
1 CCCCCATCAATCATTTTCAAAG
432549 CCC
1 CCC
432552 TTACTGCTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.30, C:0.40, G:0.04, T:0.26
Consensus pattern (22 bp):
CCCCCATCAATCATTTTCAAAG
Found at i:437941 original size:6 final size:6
Alignment explanation
Indices: 437930--437955 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
437920 GCTTTTAAAA
437930 AAAACT AAAACT AAAACT AAAACT AA
1 AAAACT AAAACT AAAACT AAAACT AA
437956 TGGGCCCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAACT
Found at i:438008 original size:2 final size:2
Alignment explanation
Indices: 438001--438041 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
437991 TATGTAAAAC
438001 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
438042 CACATTTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:438221 original size:2 final size:2
Alignment explanation
Indices: 438148--438202 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
438138 ATAAAAACAT
* *
438148 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
438190 T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
438203 GTAAAACAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:438360 original size:18 final size:18
Alignment explanation
Indices: 438326--438360 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
438316 TCGAAAATAA
*
438326 TAAAAAAAAATAGAAAAT
1 TAAAAAAAAATAAAAAAT
*
438344 TAAAAAAAATTAAAAAA
1 TAAAAAAAAATAAAAAA
438361 AATTGTAATG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
TAAAAAAAAATAAAAAAT
Found at i:438363 original size:10 final size:10
Alignment explanation
Indices: 438339--438364 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
438329 AAAAAAATAG
438339 AAAATTAAAA
1 AAAATTAAAA
438349 AAAATTAAAA
1 AAAATTAAAA
438359 AAAATT
1 AAAATT
438365 GTAATGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:445586 original size:3 final size:3
Alignment explanation
Indices: 445571--445641 Score: 115
Period size: 3 Copynumber: 23.7 Consensus size: 3
445561 TTTTTACCCA
* *
445571 TAT TAT AAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
445619 CAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TA
445642 AAAATATATT
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:447060 original size:13 final size:13
Alignment explanation
Indices: 447044--447083 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
447034 ATATAATAAA
447044 TAAATATTTATTT
1 TAAATATTTATTT
*
447057 TAAATAAATTATTT
1 TAAAT-ATTTATTT
447071 T-AATATTTATTT
1 TAAATATTTATTT
447083 T
1 T
447084 TCAGTATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:447798 original size:18 final size:18
Alignment explanation
Indices: 447753--447799 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
447743 TGTCAAATTA
447753 TTTA-TTTATTTATTATT
1 TTTATTTTATTTATTATT
**
447770 TTTATAATATTTA-TATGT
1 TTTATTTTATTTATTAT-T
447788 TTTATTTTATTT
1 TTTATTTTATTT
447800 GCAAGTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.29
18 17 0.71
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTTATTTTATTTATTATT
Found at i:458842 original size:54 final size:54
Alignment explanation
Indices: 458756--458921 Score: 269
Period size: 54 Copynumber: 3.1 Consensus size: 54
458746 CAATGATTGA
458756 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* *
458810 GAACATCTGAGCAGAAACTACAGGAAAAGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * * **
458864 GAACATCTGAGCAGAAGCCACATGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
458918 GAAC
1 GAAC
458922 CTGCTATTCT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 103 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:459336 original size:23 final size:22
Alignment explanation
Indices: 459282--459358 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
459272 TCTACATTCA
*
459282 TCAAAGATGATAGATTCTCTCT
1 TCAAAGATGATAGATTCTCTTT
*
459304 TCAAAGATGATAGATTCCCTTTT
1 TCAAAGATGATAGATTCTC-TTT
* *
459327 TTAAAGATGACAGATTCTCTTT
1 TCAAAGATGATAGATTCTCTTT
459349 TCAAAGATGA
1 TCAAAGATGA
459359 AAGCTTTATC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
22 30 0.62
23 18 0.38
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (22 bp):
TCAAAGATGATAGATTCTCTTT
Found at i:459996 original size:24 final size:23
Alignment explanation
Indices: 459953--459997 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
459943 GTAATTAATG
*
459953 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
459976 AGAAGAAATTCATAATG-AGAAG
1 AGAAG-AATTCAT-ATGAAGAAG
459998 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.26
24 12 0.63
25 2 0.11
ACGTcount: A:0.51, C:0.07, G:0.24, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:459996 original size:113 final size:113
Alignment explanation
Indices: 459834--460691 Score: 945
Period size: 113 Copynumber: 7.6 Consensus size: 113
459824 AAGGAAGAAG
*
459834 AAGTTCATAATGAGAAGAACTCATCT---G-A--AAGAATAAATTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * *
459893 CAACTTTTTGTTCAAAACCATCACTTGATGGATCAAAC-TTTCCAGAGA
66 CAACCTTTTGTTCAAATCCATCATTTGATGGATC-AACTTTTCCAGAGA
* *
459941 AAG-TAATTAATGAGAAGAATTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
1 AAGTTCA-TAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* * *
460005 TCAACCTTTTGCTCAAATCCATTATTTGATGGATCAGCTTTTCCAGAGA
65 TCAACCTTTTGTTCAAATCCATCATTTGATGGATCAACTTTTCCAGAGA
*
460054 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * * * *
460119 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-GTA
66 CAACCTTTTGTTCAAATCCATCATTTGATGGATCAACTTTTCCAGAG-A
* ** *
460167 GAGTTCATAATGAGAAGAACTCATCAT-CTGAA-GAAGAATAAATTCATAATGAGAAGAATTTGT
1 AAGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* * *
460230 TCAACCTTTTGCTCAAATCCATTATTTGATGGATCAGCTTTTCCAGAGA
65 TCAACCTTTTGTTCAAATCCATCATTTGATGGATCAACTTTTCCAGAGA
*
460279 AAGTTCATAATGAGAAGAA--C-TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
* * * * *
460341 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAG-GTA
66 CAACCTTTTGTTCAAATCCATCATTTGATGGATCAACTTTTCCAGAG-A
* * ** *
460389 GAGTTCATAATGAGAAGAACTCGTCAT-CTGAA-GAAGAAGAAATTCATAATGAGAAGAATTTTT
1 AAGTTCATAATGAGAAGAACTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGT
* * *
460452 TCAACCTTTTGCTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAG-
65 TCAACCTTTTGTTCAAATCCATCATTTGATGGATCAACTTTTCCAGAGA
* **
460500 AAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAG---TTCACAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
** * * * *
460561 CAACCTTTTACAT-AATTTTATCACAGAAGCAAATAGATTAGCATCAAC-TTTCCAGAGA
66 CAACCTTTT-GTTCAA----ATC-C---ATC-ATTTGA-T-GGATCAACTTTTCCAGAGA
* * **
460619 AAGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
460684 CAACCTTT
66 CAACCTTT
460692 GTTTGATTCT
Statistics
Matches: 637, Mismatches: 76, Indels: 60
0.82 0.10 0.08
Matches are distributed among these distances:
106 2 0.00
107 21 0.03
108 30 0.05
109 7 0.01
110 89 0.14
111 34 0.05
112 160 0.25
113 201 0.32
114 4 0.01
116 2 0.00
117 4 0.01
118 10 0.02
119 37 0.06
120 7 0.01
123 29 0.05
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (113 bp):
AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTT
CAACCTTTTGTTCAAATCCATCATTTGATGGATCAACTTTTCCAGAGA
Found at i:460259 original size:225 final size:223
Alignment explanation
Indices: 459834--460569 Score: 1104
Period size: 222 Copynumber: 3.3 Consensus size: 223
459824 AAGGAAGAAG
*
459834 AAGTTCATAATGAGAAGAACTCATCTGA-AAGAA-TA-AA-TTCATAATGAGAAGAATTTGTTCA
1 AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
* * ** * * * * *
459895 ACTTTTTGTTCAAAACCATCACTTGATGGATCAA-ACTTTCCAGAG-AAAG-TAATTAATGAGAA
66 ACCTTTTGTTTAAATTCATCATTTGATGGATTAACA-TTGCCAG-GTAGAGTTCA-TAATGAGAA
* **
459957 GAATTCATC-TGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAA
128 GAACTCATCAT-CTGAA-GAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAA
460021 ATCCATTATTTGATGGATCAGCTTTTCCAGAGA
191 ATCCATTATTTGATGGATCAGCTTTTCCAGAGA
460054 AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTG-AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTT
460119 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAG
64 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAG
*
460184 AACTCATCATCTGAAGAAGAATAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
129 AACTCATCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
460249 CATTATTTGATGGATCAGCTTTTCCAGAGA
194 CATTATTTGATGGATCAGCTTTTCCAGAGA
460279 AAGTTCATAATGAGAAGAA--C-TCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTT
1 AAGTTCATAATGAGAAGAACTCATCTG-AGAA-GAAGAAGAAGTTCATAATGAGAAGAATTTGTT
460341 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAG
64 CAACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAG
* *
460406 AACTCGTCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTTTTCAACCTTTTGCTCAAATC
129 AACTCATCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
* *
460471 CATCACTTGATGGATCAGCTTTTCCAGAG-
194 CATTATTTGATGGATCAGCTTTTCCAGAGA
* **
460500 AAGTTCATAATGAGAAGAACTCATCT--GAAGAAGAAGAAGTTCACAATGAGAAGAGCTTGTTCA
1 AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
460563 ACCTTTT
66 ACCTTTT
460570 ACATAATTTT
Statistics
Matches: 481, Mismatches: 22, Indels: 26
0.91 0.04 0.05
Matches are distributed among these distances:
220 65 0.14
221 23 0.05
222 198 0.41
223 5 0.01
224 4 0.01
225 101 0.21
226 81 0.17
227 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (223 bp):
AAGTTCATAATGAGAAGAACTCATCTGAGAAGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCA
ACCTTTTGTTTAAATTCATCATTTGATGGATTAACATTGCCAGGTAGAGTTCATAATGAGAAGAA
CTCATCATCTGAAGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCA
TTATTTGATGGATCAGCTTTTCCAGAGA
Found at i:460684 original size:123 final size:123
Alignment explanation
Indices: 460491--460779 Score: 387
Period size: 123 Copynumber: 2.4 Consensus size: 123
460481 TGGATCAGCT
460491 TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT---GAA-GAAGAAGAAGTTCACAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGA
* *
460551 AGAGCTTGTTCAACCTTT-TACATAATTTTATCACAGAA-GCAAATAGATTAGCATCAAC-
66 AGAGCTTGTTCAACCTTTGT--ATAATTCTATCACAGAATG-AAATAGATCAGCATCAACA
* *
460609 TTTCCAGAGAAAGTTCATAATGAGAAGAAATCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGA
* * * * *
460674 AGAGCTTGTTCAACCTTTGTTTGATTCTATCACAGAATGAGATAGATCAGTATCAGCA
66 AGAGCTTGTTCAACCTTTGTATAATTCTATCACAGAATGAAATAGATCAGCATCAACA
* * *
460732 TTTCCATAAAAAGTTCATAATAAGAAGAACTCATCTGAAGAAGGAAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
460780 GAATTTGTTC
Statistics
Matches: 150, Mismatches: 13, Indels: 11
0.86 0.07 0.06
Matches are distributed among these distances:
118 9 0.06
119 25 0.17
122 31 0.21
123 84 0.56
124 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (123 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGA
AGAGCTTGTTCAACCTTTGTATAATTCTATCACAGAATGAAATAGATCAGCATCAACA
Found at i:461975 original size:14 final size:15
Alignment explanation
Indices: 461956--461985 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
461946 GGGCTTTGTA
461956 ATTTAATAT-TATTT
1 ATTTAATATATATTT
461970 ATTTAATATATATTT
1 ATTTAATATATATTT
461985 A
1 A
461986 ATAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTAATATATATTT
Found at i:461992 original size:3 final size:3
Alignment explanation
Indices: 461984--462066 Score: 130
Period size: 3 Copynumber: 27.7 Consensus size: 3
461974 AATATATATT
*
461984 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
462032 TAA TAA TGA TAA TAA TAA TAA TAA TTA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
462067 TGGGTAAAAA
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 74 1.00
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:462679 original size:116 final size:116
Alignment explanation
Indices: 462383--463021 Score: 890
Period size: 116 Copynumber: 5.6 Consensus size: 116
462373 GATAGAATTA
462383 TTGAACAAGTTC-T-T-ATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
* * * *
462445 GAACTCTACTTGGCAATGTTGATCCATCCAATGATGAATTC-AA-AAAGA-
66 GAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAG
462493 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
*
462558 GAACTCTACCTGGCAACGTTGATCCATCAAATGATGAATTCAAACAAAAAG
66 GAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAG
* **
462609 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTAAGAAAACGAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
* *
462674 GAACTCTAACTGGCAACGTTGATCCATCAAATGATGAATTCAAACAAAAAG
66 GAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAG
* *
462725 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACAAGTTCTTCTTATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
* ** * * * *
462790 GAAC-CTTCTCTGGCAAAAATAATCCATCAAGTGATGAATTCAGACAAAAGG
66 GAACTCTAC-CTGGCAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAG
* *
462841 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTATTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
* ** * * * * * *
462903 GAACTTTTTCTGGAAAAGCTAATCCATCAATTTGATGAATTCAAATAAAAGG
66 GAACTCTACCTGGCAAAGTTGATCCATCAA-ATGATGAATTCAAACAAAAAG
*
462955 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
1 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
463017 GAACT
66 GAACT
463022 TTCTCTGGAA
Statistics
Matches: 485, Mismatches: 35, Indels: 14
0.91 0.07 0.03
Matches are distributed among these distances:
110 12 0.02
111 1 0.00
112 1 0.00
113 121 0.25
114 88 0.18
115 6 0.01
116 256 0.53
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (116 bp):
TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTAT
GAACTCTACCTGGCAAAGTTGATCCATCAAATGATGAATTCAAACAAAAAG
Found at i:463824 original size:83 final size:83
Alignment explanation
Indices: 463685--464098 Score: 677
Period size: 83 Copynumber: 5.0 Consensus size: 83
463675 TCTCCTATGA
463685 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
463750 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
463768 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
*
463833 TTCCAGAAAATGCTATTG
66 TTCCAGAAGATGCTATTG
463851 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
* * *
463916 TTCTAAAAAATGCTATTG
66 TTCCAGAAGATGCTATTG
* * * *
463934 GCAAATTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
*
463998 CTTCCAGAAGATGCTATTA
65 CTTCCAGAAGATGCTATTG
* * **
464017 GCAAATTCATCTTCTAAATTCAATAATTTATTCTGTCCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
464082 CTTCCAGAAGATGCTAT
65 CTTCCAGAAGATGCTAT
464099 AAATACATTC
Statistics
Matches: 314, Mismatches: 15, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
83 269 0.86
84 45 0.14
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:465269 original size:7 final size:7
Alignment explanation
Indices: 465257--465308 Score: 50
Period size: 7 Copynumber: 6.9 Consensus size: 7
465247 ACCCCCCTTT
465257 TTTTTTC
1 TTTTTTC
465264 TTTTTTC
1 TTTTTTC
465271 TTTTTTTTTC
1 ---TTTTTTC
465281 TTTTTTC
1 TTTTTTC
465288 TTTTTTTC
1 -TTTTTTC
* *
465296 TCTTCTC
1 TTTTTTC
465303 TTTTTT
1 TTTTTT
465309 TTTCTTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
7 23 0.62
8 7 0.19
10 7 0.19
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTTTC
Found at i:465275 original size:17 final size:17
Alignment explanation
Indices: 465253--465314 Score: 92
Period size: 17 Copynumber: 3.8 Consensus size: 17
465243 CTTGACCCCC
465253 CTTTTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTT
465270 CTTTTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTT
* *
465287 C--TTTTTTTCTCTTCT
1 CTTTTTTTTTCTTTTTT
465302 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
465315 CAAGCATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
15 13 0.32
17 27 0.68
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
CTTTTTTTTTCTTTTTT
Found at i:465276 original size:15 final size:15
Alignment explanation
Indices: 465256--465309 Score: 72
Period size: 15 Copynumber: 3.5 Consensus size: 15
465246 GACCCCCCTT
465256 TTTTTTTCTTTTTTC
1 TTTTTTTCTTTTTTC
465271 TTTTTTTTTCTTTTTTC
1 --TTTTTTTCTTTTTTC
* *
465288 TTTTTTTCTCTTCTC
1 TTTTTTTCTTTTTTC
465303 TTTTTTT
1 TTTTTTT
465310 TTCTTCAAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 20 0.57
17 15 0.43
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTCTTTTTTC
Found at i:471068 original size:83 final size:83
Alignment explanation
Indices: 470924--471666 Score: 1179
Period size: 83 Copynumber: 8.9 Consensus size: 83
470914 TCTCCTATGA
*
470924 GCAAGTTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
470989 TTCCAGAAGATGCTATTG
66 TTCCAGAAGATGCTATTG
*
471007 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
*
471072 TTCCAGAAAATGCTATTG
66 TTCCAGAAGATGCTATTG
* * * *
471090 GCAAATTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
*
471154 CTTCCAGAAGATGCTATTA
65 CTTCCAGAAGATGCTATTG
* * *
471173 GCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
471238 CTTCCAGAAGATGCTA-TG
65 CTTCCAGAAGATGCTATTG
* *
471256 AGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
471321 CTTCCAGAAGATGCTATTG
65 CTTCCAGAAGATGCTATTG
*
471340 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACAC
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
*
471405 TTCCAGAAAATGCTATTG
66 TTCCAGAAGATGCTATTG
* * * *
471423 GCAAATTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
*
471487 CTTCCAGAAGATGCTATTA
65 CTTCCAGAAGATGCTATTG
* * *
471506 GCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACA
1 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACA
471571 CTTCCAGAAGATGCTA-TG
65 CTTCCAGAAGATGCTATTG
* *
471589 AGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
1 -GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACA
471654 CTTCCAGAAGATG
65 CTTCCAGAAGATG
471667 TTATAAATAC
Statistics
Matches: 618, Mismatches: 35, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
83 468 0.76
84 150 0.24
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (83 bp):
GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACAC
TTCCAGAAGATGCTATTG
Found at i:471686 original size:250 final size:250
Alignment explanation
Indices: 470918--471666 Score: 1227
Period size: 250 Copynumber: 3.0 Consensus size: 250
470908 CTTATTTCTC
* * * * *
470918 CTATGAGCAAGTTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
*
470982 AGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
66 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
* * * *
471047 TCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTA
131 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
* *
471112 ATAATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
196 ATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
471167 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
* * *
471232 AGAACACTTCCAGAAGATGCTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
66 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
471297 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
131 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
* *
471362 ATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAAATG
196 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
471417 CTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
* * *
471481 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAA
66 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAA
* *
471546 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGTACATTCATCTTCCAAATT
130 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCAAATT
471610 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
194 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
471667 TTATAAATAC
Statistics
Matches: 467, Mismatches: 29, Indels: 7
0.93 0.06 0.01
Matches are distributed among these distances:
249 114 0.24
250 353 0.76
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (250 bp):
CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:471688 original size:333 final size:333
Alignment explanation
Indices: 470929--471666 Score: 1476
Period size: 333 Copynumber: 2.2 Consensus size: 333
470919 TATGAGCAAG
470929 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
470994 GAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATA
66 GAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATA
471059 ACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCT
131 ACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCT
471124 GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
196 GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
471189 AATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
261 AATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
471254 TGAGTACA
326 TGAGTACA
471262 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
471327 GAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATA
66 GAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATA
471392 ACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCT
131 ACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCT
471457 GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
196 GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
471522 AATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
261 AATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
471587 TGAGTACA
326 TGAGTACA
471595 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
1 TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
471660 GAAGATG
66 GAAGATG
471667 TTATAAATAC
Statistics
Matches: 405, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
333 405 1.00
ACGTcount: A:0.37, C:0.22, G:0.13, T:0.28
Consensus pattern (333 bp):
TTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCA
GAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATA
ACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCT
GTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTA
AATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
TGAGTACA
Found at i:472842 original size:7 final size:7
Alignment explanation
Indices: 472830--472880 Score: 57
Period size: 7 Copynumber: 6.9 Consensus size: 7
472820 CCCCCCCTTT
472830 TTTTTTC
1 TTTTTTC
472837 TTTTTTC
1 TTTTTTC
472844 TTTTTTTTTC
1 ---TTTTTTC
472854 TTTTTTC
1 TTTTTTC
472861 TTTTTTC
1 TTTTTTC
* *
472868 TCTTCTC
1 TTTTTTC
472875 TTTTTT
1 TTTTTT
472881 TTTCTTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 30 0.81
10 7 0.19
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTTTTC
Found at i:472848 original size:17 final size:17
Alignment explanation
Indices: 472826--472886 Score: 83
Period size: 17 Copynumber: 3.8 Consensus size: 17
472816 TTGACCCCCC
472826 CTTTTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTT
472843 CTTTTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTT
* *
472860 C---TTTTTTCTCTTCT
1 CTTTTTTTTTCTTTTTT
472874 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
472887 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
14 12 0.32
17 26 0.68
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (17 bp):
CTTTTTTTTTCTTTTTT
Found at i:472857 original size:24 final size:24
Alignment explanation
Indices: 472826--472886 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
472816 TTGACCCCCC
*
472826 CTTTTTTTTTCTTTTTTCT-TTTT
1 CTTTTTTTTTCTTTTTTCTCTTCT
*
472849 TTTTCTTTTTTCTTTTTTCTCTTCT
1 CTTT-TTTTTTCTTTTTTCTCTTCT
472874 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
472887 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 3 0.09
24 24 0.73
25 6 0.18
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (24 bp):
CTTTTTTTTTCTTTTTTCTCTTCT
Found at i:479005 original size:250 final size:250
Alignment explanation
Indices: 478474--479223 Score: 1208
Period size: 250 Copynumber: 3.0 Consensus size: 250
478464 CTTATTTCTC
* * * *
478474 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAA-CAGATCAGATAACTC-A
1 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
*
478536 AGAACACTTCCAGAAGATGCTATG-GCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAA
66 AGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
* * * * *
478600 TCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAACTCATCTTCTAAATTTA
131 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
* *
478665 ATAATTGATTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
196 ATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
478720 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
* *
478785 AGAACACTTCCAGAAGATGCTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
66 AGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
478850 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
131 CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
* *
478915 ATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAAATG
196 ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* *
478970 CTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
* * * *
479034 AGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAA
66 AGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAA
* *
479099 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGTACATTCATCTTCCAAATT
130 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCAAATT
479163 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
194 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
479220 CTAT
1 CTAT
479224 AAATATATTC
Statistics
Matches: 469, Mismatches: 28, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
246 37 0.08
247 5 0.01
248 15 0.03
249 103 0.22
250 309 0.66
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (250 bp):
CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
AGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA
CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCA
ATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:479077 original size:333 final size:333
Alignment explanation
Indices: 478474--479223 Score: 1443
Period size: 333 Copynumber: 2.3 Consensus size: 333
478464 CTTATTTCTC
* *
478474 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA-CAGATCAGATAACTC-AA
1 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
478537 GAACACTTCCAGAAGATGCTA-TGGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAAT
66 GAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAAT
478601 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAACTCATCTTCTAAATTTAA
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAACTCATCTTCTAAATTTAA
478666 TAATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA
196 TAATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA
478731 TTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCC
261 TTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCC
478796 AGAAGATG
326 AGAAGATG
478804 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
478869 GAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAAT
66 GAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAAT
*
478934 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAATTCATCTTCTAAATTTAA
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAACTCATCTTCTAAATTTAA
478999 TAATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA
196 TAATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA
479064 TTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCC
261 TTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCC
479129 AGAAGATG
326 AGAAGATG
479137 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
479202 GAACACTTCCAGAAGATGCTAT
66 GAACACTTCCAGAAGATGCTAT
479224 AAATATATTC
Statistics
Matches: 413, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
330 44 0.11
331 15 0.04
332 23 0.06
333 331 0.80
ACGTcount: A:0.38, C:0.22, G:0.13, T:0.28
Consensus pattern (333 bp):
CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAAT
CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGGCAAACTCATCTTCTAAATTTAA
TAATTGATTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAA
TTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAAAGAACACTTCC
AGAAGATG
Found at i:479234 original size:83 final size:83
Alignment explanation
Indices: 478474--479241 Score: 1150
Period size: 83 Copynumber: 9.3 Consensus size: 83
478464 CTTATTTCTC
*
478474 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAA-CAGATCAGATAACTC-AA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
478537 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * *
478555 CTA-TGGCAAATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAATCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
478619 GAACACTTCCAGAAAATG
66 GAACACTTCCAGAAGATG
* * * * * *
478637 CTATTGGCAAACTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
478701 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
478720 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
478785 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
478804 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
478869 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
478887 CTATTGGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
*
478952 GAACACTTCCAGAAAATG
66 GAACACTTCCAGAAGATG
* * * * *
478970 CTATTGGCAAATTCATCTTCTAAATTTAATAATTGATTCTGTCC-AACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
479034 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
479053 CTATTAGCAAATTCATCTTCTAAATTCAATAATTGATTCTGTCCAAACCAGATCAGATAACTCAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAA
479118 AGAACACTTCCAGAAGATG
65 AGAACACTTCCAGAAGATG
* * *
479137 CTATGAGTACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
479202 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* ** *
479220 CTATAAATATATTCATCTTCCA
1 CTATTAGCAAATTCATCTTCCA
479242 GTTAATGTTT
Statistics
Matches: 636, Mismatches: 44, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
80 39 0.06
81 18 0.03
82 22 0.03
83 405 0.64
84 152 0.24
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (83 bp):
CTATTAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:480395 original size:7 final size:7
Alignment explanation
Indices: 480383--480433 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
480373 CCCCCCCTTT
480383 TTTTTTC
1 TTTTTTC
480390 TTTTTTC
1 TTTTTTC
480397 --TTTT-
1 TTTTTTC
480401 TTTTTT-
1 TTTTTTC
480407 TTTTTTC
1 TTTTTTC
480414 TTTTTTC
1 TTTTTTC
* *
480421 TCTTCTC
1 TTTTTTC
480428 TTTTTT
1 TTTTTT
480434 TTTCTTCAAG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
5 4 0.11
6 10 0.27
7 23 0.62
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:480401 original size:17 final size:17
Alignment explanation
Indices: 480379--480439 Score: 74
Period size: 15 Copynumber: 3.8 Consensus size: 17
480369 TGACCCCCCC
480379 CTTTTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTT
480396 C-TTTTTTTT-TTTTTT
1 CTTTTTTTTTCTTTTTT
* * *
480411 -TTCTTTTTTCTCTTCT
1 CTTTTTTTTTCTTTTTT
480427 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
480440 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
15 13 0.36
16 12 0.33
17 11 0.31
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (17 bp):
CTTTTTTTTTCTTTTTT
Found at i:480407 original size:24 final size:24
Alignment explanation
Indices: 480379--480439 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
480369 TGACCCCCCC
* *
480379 CTTTTTTTTTCTTTTTTCTTTTTT
1 CTTTTTTTTTCTTTTTTCTCTTCT
*
480403 TTTTTTTTTTCTTTTTTCTCTTCT
1 CTTTTTTTTTCTTTTTTCTCTTCT
480427 CTTTTTTTTTCTT
1 CTTTTTTTTTCTT
480440 CAAGCATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
CTTTTTTTTTCTTTTTTCTCTTCT
Found at i:480436 original size:1 final size:1
Alignment explanation
Indices: 480380--480419 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
480370 GACCCCCCCC
* * *
480380 TTTTTTTTTCTTTTTTCTTTTTTTTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
480420 CTCTTCTCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:494958 original size:22 final size:22
Alignment explanation
Indices: 494919--494981 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
494909 GTCTTTATGT
* *
494919 CACGTTTATCTCTGCCTTTGTAG
1 CACGTTT-GCTCTACCTTTGTAG
* *
494942 CACGTTTGCTCTACCTTTTTGG
1 CACGTTTGCTCTACCTTTGTAG
494964 CACGTTTGCTCTACCTTT
1 CACGTTTGCTCTACCTTT
494982 TGGTAGTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 29 0.81
23 7 0.19
ACGTcount: A:0.11, C:0.29, G:0.16, T:0.44
Consensus pattern (22 bp):
CACGTTTGCTCTACCTTTGTAG
Found at i:494984 original size:21 final size:22
Alignment explanation
Indices: 494941--494982 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
494931 TGCCTTTGTA
494941 GCACGTTTGCTCTACCTTTTTG
1 GCACGTTTGCTCTACCTTTTTG
494963 GCACGTTTGCTCTACCTTTT
1 GCACGTTTGCTCTACCTTTT
494983 GGTAGTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.10, C:0.29, G:0.17, T:0.45
Consensus pattern (22 bp):
GCACGTTTGCTCTACCTTTTTG
Found at i:497648 original size:3 final size:3
Alignment explanation
Indices: 497640--497709 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
497630 GTTGAAGAAT
497640 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
497688 AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA A
497710 ACATTTAATA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:498320 original size:18 final size:19
Alignment explanation
Indices: 498299--498345 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
498289 ATATTTAATC
*
498299 ATATTTAATATATAT-TTT
1 ATATTTAATATATATGTTG
*
498317 ATATGTAA-ATATATGTTG
1 ATATTTAATATATATGTTG
498335 ATATGTTAATA
1 ATAT-TTAATA
498346 GACCATGATA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 3 0.13
20 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (19 bp):
ATATTTAATATATATGTTG
Found at i:498338 original size:29 final size:28
Alignment explanation
Indices: 498268--498338 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
498258 TTAATTATTC
*
498268 ATATATTTG-TATTATATTTATATATTTA
1 ATATATTTGATA-TATATTTATATATTAA
*
498296 ATCATATTTAATATATATTT-TATATGTAA
1 AT-ATATTTGATATATATTTATATAT-TAA
498325 ATATATGTTGATAT
1 ATATAT-TTGATAT
498339 GTTAATAGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
28 11 0.31
29 23 0.64
30 2 0.06
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.55
Consensus pattern (28 bp):
ATATATTTGATATATATTTATATATTAA
Found at i:506105 original size:202 final size:206
Alignment explanation
Indices: 505752--507558 Score: 2146
Period size: 202 Copynumber: 8.6 Consensus size: 206
505742 ACTTCGATAA
** *
505752 AATGAATAACTAACATAAAAAATGGTCAAATTTCAGGATAAATATATGTCTAACCCTATACCCGA
1 AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGA
* * * * *
505817 TTTACATTCACAAATCTTTATAAAGTGTCTTTATCGTATCCTTGATTGAACTTATGATAATAAAT
66 TTTACATGCGCTAATCTTTATAAA-TGTCTTTATCGTATACTTGATCGAACTTATGATAATAAAT
* *
505882 TAGTATTATTATGAATCAAATTAACGGATCAGATCTTTTTACACATCCCTAATTGATATAATAAA
130 TAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAATAAA
505947 A-TT-T-CAA-G
195 ATTTATACAACG
* * * *
505955 -ATGAACAACTAACATAAAAGGGGGTTAAATATCAGGATAAATATGTGTCTAACCCTATACCCGA
1 AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGA
*
506019 TTTACATGCGTTAATCTTTATATAATGTCTTTATCGTATACTTGATCGAACTTATGATAATAAAT
66 TTTACATGCGCTAATCTTTATA-AATGTCTTTATCGTATACTTGATCGAACTTATGATAATAAAT
* ** * * *
506084 TAGTATTATTATGAATCAAATTAACAGATCAAATCTTTTTACACATCTCTAACTGATATAATAAA
130 TAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAATAAA
506149 ATTT-T---A-G
195 ATTTATACAACG
* * * *
506156 GATGAACAACT-ACAATAAAAAGGGGTCAAATTTCATGATAAATATGTGTCTAACCCTATACCTG
1 AATGAATAACTAAC-ATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCG
*
506220 ATTTACATGCGCAAATCTTTATAAAGTGTCTTTATCGTATACTTGATCGAACTTATGATAATAAA
65 ATTTACATGCGCTAATCTTTATAAA-TGTCTTTATCGTATACTTGATCGAACTTATGATAATAAA
* * *
506285 TTAGTATTATTATGAATCAAATTAACAGATCGGATCTTTTTACACATCCCTAACTGATATAATAA
129 TTAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAATAA
506350 AA-TT-T-CAA-G
194 AATTTATACAACG
*
506359 -ATGAACAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGA
1 AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGA
* *
506423 TTTACATGTGCTAATCTTTATATAATGTCTTTATCGTATACTTGATTGAACTTATGATAATAAAT
66 TTTACATGCGCTAATCTTTATA-AATGTCTTTATCGTATACTTGATCGAACTTATGATAATAAAT
* * *
506488 TAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCTCTAACTGATATAATAAA
130 TAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAATAAA
506553 A-TT-T-C-A-G
195 ATTTATACAACG
* * * * *
506560 GATAAACAACTAACATAAAAAGGGGTCAAATTTTAGGATAAATATATGTCTAACCCTATACCCGA
1 AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGA
* * *
506625 TTTACATGCCCTAATCTTTATACAGTGTCTTTATCGTATACTTGATCCCAACTTATGATAATAAA
66 TTTACATGCGCTAATCTTTATA-AATGTCTTTATCGTATACTTGAT-CGAACTTATGATAATAAA
* * * * * *
506690 TTGGTATTATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATTCCTAATGGATACAATAA
129 TTAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAATAA
506755 AATTTCAGGATGAACAACTTCG
194 AATTT----AT--ACAA---CG
*
506777 ATAAAATGAATAACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATAC
1 ----AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATAC
* * *
506842 CCGATCTACATGCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTATGATAGT
62 CCGATTTACATGCGCTAATCTTTATA-AATGTCTTTATCGTATACTTGATCGAACTTATGATAAT
* * * * *
506907 AAATTGGTATTATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAA
126 AAATTAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAA
506972 TAAAATTTTAGGATGAACAACTTCG
191 TAAAA-TTT---AT--ACAA---CG
*
506997 ATAAAATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCTTATAC
1 ----AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATAC
* * *
507062 CCGATCTACATGCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTTTGATAAT
62 CCGATTTACATGCGCTAATCTTTATA-AATGTCTTTATCGTATACTTGATCGAACTTATGATAAT
* * * * *
507127 AAATTGGTATTATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAA
126 AAATTAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAA
507192 TAAAATTTCAGGATGAACAACTTCG
191 TAAAATTT----AT--ACAA---CG
* *
507217 ATAAAATGAATAACTAACATAAAAATGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATAC
1 ----AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATAC
* *
507282 CCAATTTACATGCGCTAATCTTTATAAAGTGTCTTTATCGTATACTTGATCCAACTTATGATAAT
62 CCGATTTACATGCGCTAATCTTTATAAA-TGTCTTTATCGTATACTTGATCGAACTTATGATAAT
* * * * * *
507347 AAATTGGTATTATTCTCAATCAAATTAACGGTTTGGATCTTTTTGCACATCCCTAA-TGTATACA
126 AAATTAGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTG-ATACA
507411 ATAAAATTTCAGGATGAACAACTTCG
190 ATAAAATTT----AT--ACAA---CG
* * *
507437 ATAAAATGAATAACTAACATAAAAAGGCGTGAAATTTCAGGATAAATATGTTTCTAACCCTATAC
1 ----AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATAC
* *
507502 CCTATTTACACGCGCTAATCTTTATAAATTGTCTTTATCGTATACTTGATCGAACTT
62 CCGATTTACATGCGCTAATCTTTATAAA-TGTCTTTATCGTATACTTGATCGAACTT
507559 GATAGAAGAA
Statistics
Matches: 1487, Mismatches: 84, Indels: 49
0.92 0.05 0.03
Matches are distributed among these distances:
201 11 0.01
202 643 0.43
203 85 0.06
204 2 0.00
209 1 0.00
212 1 0.00
213 1 0.00
217 1 0.00
219 6 0.00
220 631 0.42
221 105 0.07
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (206 bp):
AATGAATAACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGA
TTTACATGCGCTAATCTTTATAAATGTCTTTATCGTATACTTGATCGAACTTATGATAATAAATT
AGTATTATTATGAATCAAATTAACGGATCGGATCTTTTTACACATCCCTAATTGATACAATAAAA
TTTATACAACG
Found at i:506994 original size:220 final size:220
Alignment explanation
Indices: 506567--507558 Score: 1727
Period size: 220 Copynumber: 4.5 Consensus size: 220
506557 CAGGATAAAC
* * *
506567 AACTAACATAAAAAGGGGTCAAATTTTAGGATAAATATATGTCTAACCCTATACCCGATTTACAT
1 AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATTTACAT
* *
506632 GCCCTAATCTTTATACAGTGTCTTTATCGTATACTTGATCCCAACTTATGATAATAAATTGGTAT
66 GCGCTAATCTTTATACAATGTCTTTATCGTATACTTGAT-CCAACTTATGATAATAAATTGGTAT
*
506697 TATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATTCCTAATGGATACAATAAAATTTCA
130 TATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTCA
506762 GGATGAACAACTTCGATAAAATGAAT
195 GGATGAACAACTTCGATAAAATGAAT
*
506788 AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATCTACAT
1 AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATTTACAT
*
506853 GCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTATGATAGTAAATTGGTATT
66 GCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTATGATAATAAATTGGTATT
*
506918 ATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTTAG
131 ATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTCAG
506983 GATGAACAACTTCGATAAAATGAAT
196 GATGAACAACTTCGATAAAATGAAT
* * *
507008 AACTAACATAAAAAGGGGTCAAATTTCAGGATAAATATGTGTCTAACCTTATACCCGATCTACAT
1 AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATTTACAT
*
507073 GCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTTTGATAATAAATTGGTATT
66 GCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTATGATAATAAATTGGTATT
507138 ATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTCAG
131 ATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTCAG
507203 GATGAACAACTTCGATAAAATGAAT
196 GATGAACAACTTCGATAAAATGAAT
* *
507228 AACTAACATAAAAATGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCAATTTACAT
1 AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATTTACAT
507293 GCGCTAATCTTTATA-AAGTGTCTTTATCGTATACTTGATCCAACTTATGATAATAAATTGGTAT
66 GCGCTAATCTTTATACAA-TGTCTTTATCGTATACTTGATCCAACTTATGATAATAAATTGGTAT
* * *
507357 TATTCTCAATCAAATTAACGGTTTGGATCTTTTTGCACATCCCTAATGTATACAATAAAATTTCA
130 TATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTCA
507422 GGATGAACAACTTCGATAAAATGAAT
195 GGATGAACAACTTCGATAAAATGAAT
* * * * *
507448 AACTAACATAAAAAGGCGTGAAATTTCAGGATAAATATGTTTCTAACCCTATACCCTATTTACAC
1 AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATTTACAT
*
507513 GCGCTAATCTTTATA-AATTGTCTTTATCGTATACTTGATCGAACTT
66 GCGCTAATCTTTATACAA-TGTCTTTATCGTATACTTGATCCAACTT
507559 GATAGAAGAA
Statistics
Matches: 739, Mismatches: 31, Indels: 3
0.96 0.04 0.00
Matches are distributed among these distances:
219 2 0.00
220 639 0.86
221 98 0.13
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (220 bp):
AACTAACATAAAAAGGAGTCAAATTTCAGGATAAATATGTGTCTAACCCTATACCCGATTTACAT
GCGCTAATCTTTATACAATGTCTTTATCGTATACTTGATCCAACTTATGATAATAAATTGGTATT
ATTCTGAATCAAATTAACGGATTGGATCTTTTTGCACATCCCTAATGGATACAATAAAATTTCAG
GATGAACAACTTCGATAAAATGAAT
Found at i:514016 original size:59 final size:59
Alignment explanation
Indices: 513807--514002 Score: 374
Period size: 59 Copynumber: 3.3 Consensus size: 59
513797 AGTACTCAAA
*
513807 CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTATGCTACTTTGTTGAGTACCCGG
1 CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTGTGCTACTTTGTTGAGTACCCGG
*
513866 CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTGTGCTACTTTGTTGATTACCCGG
1 CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTGTGCTACTTTGTTGAGTACCCGG
513925 CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTGTGCTACTTTGTTGAGTACCCGG
1 CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTGTGCTACTTTGTTGAGTACCCGG
513984 CTATTAAAAGTTACAAAAT
1 CTATTAAAAGTTACAAAAT
514003 GGTCATCCGA
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 134 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (59 bp):
CTATTAAAAGTTACAAAATAATTTTCTAATTATAGTGTGCTACTTTGTTGAGTACCCGG
Found at i:514302 original size:58 final size:58
Alignment explanation
Indices: 514235--514386 Score: 225
Period size: 59 Copynumber: 2.6 Consensus size: 58
514225 CACCATCTTG
* * *
514235 TAATTTTTAATAGTCGAGGACTCAGCAAAATAACGTCTTATAATC-AGGGGTTATTTTA
1 TAATTTTTAATAGTCGAGGACTCAACAAAATAACGTCTTATAATCGA-AGGTTATTCTA
*
514293 TAATTTTTAATAGTCGGAAGACTCAACAAAATAACGTCTTATAATCGAAGGTTATTCTA
1 TAATTTTTAATAGTC-GAGGACTCAACAAAATAACGTCTTATAATCGAAGGTTATTCTA
*
514352 TAATTTTTAATAGTCGAGTGACTGAACAAAATAAC
1 TAATTTTTAATAGTCGAG-GACTCAACAAAATAAC
514387 ATATCATTTG
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
58 17 0.20
59 67 0.79
60 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.34
Consensus pattern (58 bp):
TAATTTTTAATAGTCGAGGACTCAACAAAATAACGTCTTATAATCGAAGGTTATTCTA
Found at i:516666 original size:37 final size:36
Alignment explanation
Indices: 516624--516694 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 36
516614 TCGACTTGAT
*
516624 CTGAAAATATATATCATTCATCCGACTTGACTCGAAC
1 CTGAAAATATATATCATTCATCC-ACCTGACTCGAAC
*
516661 CTGAAAATATATATCCTTCATCCACCTGACTCGA
1 CTGAAAATATATATCATTCATCCACCTGACTCGA
516695 TCTAAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 10 0.31
37 22 0.69
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.30
Consensus pattern (36 bp):
CTGAAAATATATATCATTCATCCACCTGACTCGAAC
Found at i:517841 original size:4 final size:4
Alignment explanation
Indices: 517832--517866 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
517822 AAAGGTAAGC
517832 AATA AATA AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AATA AAT
517867 TAAAATGAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:517911 original size:15 final size:15
Alignment explanation
Indices: 517888--517923 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
517878 AAAAACAAAT
*
517888 TAAATAAAAGATAAGA
1 TAAA-AAAAGAAAAGA
517904 TAAAAAAAGAAAAGA
1 TAAAAAAAGAAAAGA
517919 TAAAA
1 TAAAA
517924 TAATAAGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (15 bp):
TAAAAAAAGAAAAGA
Found at i:517959 original size:51 final size:52
Alignment explanation
Indices: 517898--518063 Score: 143
Period size: 52 Copynumber: 3.2 Consensus size: 52
517888 TAAATAAAAG
* *
517898 ATAAGATAAAAAAAGAAAAGAT-AAAATAATA-AGTA-AAATAAAAAAAATAT
1 ATAAAATAAAAAAAGAAAAGATAAAAATAATATA-TATAAATAAAAAAAATAA
* * *
517948 AT-ATATATAAAAAAGAAAAAGATGAAAA-AATATATATAAATAAAACAAATAA
1 ATAAAATA-AAAAAAG-AAAAGATAAAAATAATATATATAAATAAAAAAAATAA
* * *
518000 ATAAAATAATAATAAA-AAAA-ATAAAAATAATATATGTATATAAAATAAAT--
1 ATAAAATAA-AA-AAAGAAAAGATAAAAATAATATATATAAATAAAAAAAATAA
518050 ATAAACATAAAAAA
1 ATAAA-ATAAAAAA
518064 TAGTAAATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
49 6 0.06
50 16 0.16
51 23 0.23
52 44 0.45
53 6 0.06
54 3 0.03
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (52 bp):
ATAAAATAAAAAAAGAAAAGATAAAAATAATATATATAAATAAAAAAAATAA
Found at i:518043 original size:43 final size:43
Alignment explanation
Indices: 517918--518126 Score: 134
Period size: 44 Copynumber: 4.9 Consensus size: 43
517908 AAAAGAAAAG
517918 ATAAAATAATAAGTAAAATAA-AA-AAAATATATATATATAAA-AA
1 ATAAAATAATAA-TAAAA-AATAATAAAA-ATATATATATAAATAA
* * * *
517961 AGAAAA-AGAT--GAAAAAATATATATAAATA-A-A-ACAAATAA
1 ATAAAATA-ATAATAAAAAATA-ATAAAAATATATATATAAATAA
* *
518000 ATAAAATAATAATAAAAAA-AATAAAAATAATATATGTATATAAA
1 ATAAAATAATAATAAAAAATAATAAAAAT-ATATATATAAAT-AA
* * *
518044 ATAAATATAA-ACATAAAAAATAGTAAATATATATATATAAATTA
1 ATAAA-ATAATA-ATAAAAAATAATAAAAATATATATATAAATAA
* * * *
518088 ATAAAACAGATAATAAAAAATAACATATATATATATATA
1 ATAAAATA-ATAATAAAAAATAATAAAAATATATATATA
518127 TATGTAATCT
Statistics
Matches: 129, Mismatches: 19, Indels: 35
0.70 0.10 0.19
Matches are distributed among these distances:
38 4 0.03
39 19 0.15
40 9 0.07
41 11 0.09
42 5 0.04
43 12 0.09
44 39 0.30
45 23 0.18
46 7 0.05
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.26
Consensus pattern (43 bp):
ATAAAATAATAATAAAAAATAATAAAAATATATATATAAATAA
Found at i:518062 original size:85 final size:83
Alignment explanation
Indices: 517922--518167 Score: 217
Period size: 85 Copynumber: 2.8 Consensus size: 83
517912 GAAAAGATAA
** *
517922 AATAATAAGTAAAATAAAAAAAATATATATATATAAAA-AAGAAAAAGATGAAAAAATATATATA
1 AATAATAAAAAAAATAAAAATAATATATATATATAAAATAA-AAAAA-AT-AAAAAATATATATA
*
517986 AATAAAACAAATAAATAAAAT
63 AATAAAACAAATAAATAAAAC
* *
518007 AATAATAAAAAAAATAAAAATAATATATGTATATAAAATAAATATAAACATAAAAAATAGTAAAT
1 AATAATAAAAAAAATAAAAATAATATATATATATAAAATAAA-A-AAA-ATAAAAAATA-TATAT
* * * *
518072 ATATATATATAAATTAATAAAAC
62 AAATA-AAACAAATAAATAAAAC
* * * * **
518095 AGATAATAAAAAATAACATATATATATATATATATGTAATCTAAAAAAAAT-AAAAATATATACT
1 A-ATAATAAAAAA-AATAAAAATA-ATATATATATATAAAATAAAAAAAATAAAAAATATATA-T
518159 AAAGTAAAA
62 AAA-TAAAA
518168 AAGAAAATGC
Statistics
Matches: 130, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
85 35 0.27
86 14 0.11
87 25 0.19
88 18 0.14
89 14 0.11
90 8 0.06
91 16 0.12
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (83 bp):
AATAATAAAAAAAATAAAAATAATATATATATATAAAATAAAAAAAATAAAAAATATATATAAAT
AAAACAAATAAATAAAAC
Found at i:518811 original size:36 final size:37
Alignment explanation
Indices: 518683--518830 Score: 208
Period size: 37 Copynumber: 4.0 Consensus size: 37
518673 ATGCTTGTGG
* * *
518683 ATCCTATTTTTAGGAGTTTGAATTATAGTAGAACTTT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* * *
518720 ATCTTATTTTTAGGAATTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
*
518757 ATCATATTTTTAGGAGTTTGAATCATAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
* *
518794 ATCCTA-TTTTAAGAGTTTGAATCCTAGTAAAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
518830 A
1 A
518831 AAGTTATATT
Statistics
Matches: 99, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
36 29 0.29
37 70 0.71
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGTAAAACTCT
Found at i:521089 original size:2 final size:2
Alignment explanation
Indices: 521072--521167 Score: 84
Period size: 2 Copynumber: 52.5 Consensus size: 2
521062 AATTACAAAT
* *
521072 TA TA -A TA TA TA CA TA TA TA TA -A TA T- TA TA TA -A TG T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
521109 TA AA T- TA TA AA T- TA TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
521148 TA -A TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
521168 GTTTTATTTA
Statistics
Matches: 76, Mismatches: 9, Indels: 18
0.74 0.09 0.17
Matches are distributed among these distances:
1 9 0.12
2 67 0.88
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (2 bp):
TA
Found at i:521166 original size:10 final size:10
Alignment explanation
Indices: 521072--521167 Score: 84
Period size: 9 Copynumber: 10.5 Consensus size: 10
521062 AATTACAAAT
521072 TATA-ATATA
1 TATATATATA
*
521081 TACATATATA
1 TATATATATA
521091 TA-ATAT-TA
1 TATATATATA
*
521099 TATA-ATGT-
1 TATATATATA
*
521107 TATAAAT-TA
1 TATATATATA
*
521116 TAAAT-TATA
1 TATATATATA
521125 -ATATATATA
1 TATATATATA
521134 TATATATATA
1 TATATATATA
521144 TATATA-ATA
1 TATATATATA
*
521153 TATATATATG
1 TATATATATA
521163 TATAT
1 TATAT
521168 GTTTTATTTA
Statistics
Matches: 73, Mismatches: 5, Indels: 17
0.77 0.05 0.18
Matches are distributed among these distances:
8 15 0.21
9 29 0.40
10 29 0.40
ACGTcount: A:0.50, C:0.01, G:0.02, T:0.47
Consensus pattern (10 bp):
TATATATATA
Found at i:522421 original size:156 final size:156
Alignment explanation
Indices: 522255--522574 Score: 631
Period size: 156 Copynumber: 2.1 Consensus size: 156
522245 ATTTAGACCC
522255 TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
1 TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
522320 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAATTATTCTTATGATCATTTCTTTA
66 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAATTATTCTTATGATCATTTCTTTA
522385 TTTTATTACTATGTCTTATAATCGTA
131 TTTTATTACTATGTCTTATAATCGTA
*
522411 TATATATAATTATTACGTTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
1 TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
522476 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAATTATTCTTATGATCATTTCTTTA
66 TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAATTATTCTTATGATCATTTCTTTA
522541 TTTTATTACTATGTCTTATAATCGTA
131 TTTTATTACTATGTCTTATAATCGTA
522567 TATATATA
1 TATATATA
522575 TATATATATA
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
156 163 1.00
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.57
Consensus pattern (156 bp):
TATATATAATTATTACATTTTAATCCTTATATTGTATATTACTTTATATTATTTATTTTGTTATA
TGCGTATTTTTTGTATATATTTTATTTGTACATAATTCTTAATTATTCTTATGATCATTTCTTTA
TTTTATTACTATGTCTTATAATCGTA
Found at i:522687 original size:29 final size:26
Alignment explanation
Indices: 522612--522687 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 26
522602 TTCTTTACTA
*
522612 TTATATTAT-ATTATTTTATTTACCT
1 TTATATTATAATTATTTTTTTTACCT
522637 TTATATCTATACATTATCTTTTTTTACCT
1 TTATAT-TATA-ATTAT-TTTTTTTACCT
522666 CTATATATATATAATTATTTTT
1 -T-TATAT-TATAATTATTTTT
522688 GTTTTTACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
25 6 0.14
26 3 0.07
28 5 0.12
29 14 0.33
30 6 0.14
31 9 0.21
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATATTATAATTATTTTTTTTACCT
Found at i:540213 original size:18 final size:18
Alignment explanation
Indices: 540171--540216 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 18
540161 CGACTGCTTG
540171 CTTAGCTTTCTTCTTCTT
1 CTTAGCTTTCTTCTTCTT
540189 CTT---TTTCTTGC-TCTT
1 CTTAGCTTTCTT-CTTCTT
540204 CTTAGCTTTCTTC
1 CTTAGCTTTCTTC
540217 CCGTGGTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
15 13 0.54
16 1 0.04
17 1 0.04
18 9 0.38
ACGTcount: A:0.04, C:0.28, G:0.07, T:0.61
Consensus pattern (18 bp):
CTTAGCTTTCTTCTTCTT
Found at i:544839 original size:20 final size:20
Alignment explanation
Indices: 544814--544854 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
544804 GTTCATGCAA
544814 CCTAACTATGTTAAGATGTT
1 CCTAACTATGTTAAGATGTT
544834 CCTAACTATGTTAAGATGTT
1 CCTAACTATGTTAAGATGTT
544854 C
1 C
544855 AAAAATCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
CCTAACTATGTTAAGATGTT
Found at i:545168 original size:18 final size:18
Alignment explanation
Indices: 545147--545181 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
545137 TAATTGAGAT
*
545147 GGAGGATATATTTGAGGA
1 GGAGGATACATTTGAGGA
545165 GGAGGATACATTTGAGG
1 GGAGGATACATTTGAGG
545182 TTGATATGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.40, T:0.26
Consensus pattern (18 bp):
GGAGGATACATTTGAGGA
Found at i:552267 original size:29 final size:30
Alignment explanation
Indices: 552188--552268 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
552178 ATAAATTTTT
*
552188 AAAATTATATTTCTAGTCCCTAAACTTTTCA
1 AAAATTATATTT-TAGTCACTAAACTTTTCA
** * * **
552219 AACTTTATACTTCAACCACTAAAC-TTTCA
1 AAAATTATATTTTAGTCACTAAACTTTTCA
552248 AAAATTATATTTTAGTCACTA
1 AAAATTATATTTTAGTCACTA
552269 GTTAAAATTT
Statistics
Matches: 37, Mismatches: 13, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
29 20 0.54
30 8 0.22
31 9 0.24
ACGTcount: A:0.38, C:0.20, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTATATTTTAGTCACTAAACTTTTCA
Found at i:559882 original size:2 final size:2
Alignment explanation
Indices: 559875--559903 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
559865 GATTTTGTTT
559875 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
559904 TTTTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:561725 original size:25 final size:25
Alignment explanation
Indices: 561675--561725 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
561665 CATATGTTCC
*
561675 AAACTCATTTTTGGGACATTAAAAA
1 AAACTCATTTTTGGGACATGAAAAA
* *
561700 AAACTCATTTTTGGGATATGATAAA
1 AAACTCATTTTTGGGACATGAAAAA
561725 A
1 A
561726 CTTGATCCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (25 bp):
AAACTCATTTTTGGGACATGAAAAA
Found at i:563415 original size:15 final size:15
Alignment explanation
Indices: 563391--563422 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
563381 TGGCAGATCC
*
563391 AAATCCAGAACGGGA
1 AAATCAAGAACGGGA
563406 AAATCAAGAACGGGA
1 AAATCAAGAACGGGA
563421 AA
1 AA
563423 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.16, G:0.25, T:0.06
Consensus pattern (15 bp):
AAATCAAGAACGGGA
Found at i:569667 original size:46 final size:46
Alignment explanation
Indices: 569617--569716 Score: 137
Period size: 46 Copynumber: 2.2 Consensus size: 46
569607 ATCTAAACCA
*
569617 AAACCAACCCGAATTGACCTAAAAATCTAAAGGTTGATCCGAATCG
1 AAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGATCCGAATCG
* * * * * *
569663 AAACCAATCTGAATTGACCCGAAAATCTAAAGTTTGATTCGAGTCG
1 AAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGATCCGAATCG
569709 AAACCAAC
1 AAACCAAC
569717 TGATTCGATA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.41, C:0.23, G:0.15, T:0.21
Consensus pattern (46 bp):
AAACCAACCCGAATTGACCCAAAAATCTAAAGGTTGATCCGAATCG
Found at i:570148 original size:13 final size:13
Alignment explanation
Indices: 570130--570159 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
570120 AGACTATTAT
570130 AATAATTTTAAAC
1 AATAATTTTAAAC
*
570143 AATAATTTTAAAG
1 AATAATTTTAAAC
570156 AATA
1 AATA
570160 TTAAGGTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (13 bp):
AATAATTTTAAAC
Found at i:576431 original size:17 final size:18
Alignment explanation
Indices: 576388--576428 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
576378 AAATTATATT
576388 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
576405 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
576423 ATTAAA
1 AGTAAA
576429 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:578463 original size:3 final size:3
Alignment explanation
Indices: 578455--578518 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
578445 AATGGTGATT
* * *
578455 TGA TGA TGA TGA TG- TCGA TGA TGA TGA CGA TGG TGA TGG TGA TG-
1 TGA TGA TGA TGA TGA T-GA TGA TGA TGA TGA TGA TGA TGA TGA TGA
*
578499 TCGA TGA TGA TGA TGG TGA T
1 T-GA TGA TGA TGA TGA TGA T
578519 TGATAGATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 2 0.04
3 45 0.92
4 2 0.04
ACGTcount: A:0.25, C:0.05, G:0.38, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:582858 original size:27 final size:28
Alignment explanation
Indices: 582794--582861 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
582784 TAGAATGTGG
582794 CAAGGAAAGTTTCCAAATTTTGAAACTT
1 CAAGGAAAGTTTCCAAATTTTGAAACTT
* *
582822 CAAGGGAAGTTTCC-AATTTTCTAAACTT
1 CAAGGAAAGTTTCCAAATTTT-GAAACTT
*
582850 C-TGGAAAGTTTC
1 CAAGGAAAGTTTC
582862 AAAACTTAGC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
27 15 0.43
28 20 0.57
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (28 bp):
CAAGGAAAGTTTCCAAATTTTGAAACTT
Found at i:585514 original size:16 final size:16
Alignment explanation
Indices: 585493--585523 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
585483 ATAAATAAAT
585493 GAACATAAACAAACAC
1 GAACATAAACAAACAC
*
585509 GAACATAAACGAACA
1 GAACATAAACAAACA
585524 AATTTTTTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.23, G:0.10, T:0.06
Consensus pattern (16 bp):
GAACATAAACAAACAC
Found at i:585612 original size:16 final size:16
Alignment explanation
Indices: 585594--585651 Score: 98
Period size: 16 Copynumber: 3.6 Consensus size: 16
585584 TAAATAAACG
*
585594 AACATAAACGAACACG
1 AACATAAACGAACACA
585610 AACATAAACGAACACA
1 AACATAAACGAACACA
*
585626 AACATAAATGAACACA
1 AACATAAACGAACACA
585642 AACATAAACG
1 AACATAAACG
585652 TTGGAGACCC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.60, C:0.22, G:0.09, T:0.09
Consensus pattern (16 bp):
AACATAAACGAACACA
Found at i:585841 original size:16 final size:16
Alignment explanation
Indices: 585811--585841 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
585801 TGAAACTTGA
*
585811 CTCGAACTCGAAAAAG
1 CTCGAACTCAAAAAAG
585827 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
585842 AATTTAAGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.26, G:0.13, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:585880 original size:24 final size:25
Alignment explanation
Indices: 585850--585914 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 25
585840 AAAATTTAAG
585850 AGCTCGATTAAAACTCGAGATTC-A
1 AGCTCGATTAAAACTCGAGATTCTA
* * *
585874 AGCTCGATTGAATCTC--GATTCTG
1 AGCTCGATTAAAACTCGAGATTCTA
*
585897 AGCTCGATTAAAATTCGA
1 AGCTCGATTAAAACTCGA
585915 TTTTGAGCTC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 5 0.16
23 13 0.41
24 14 0.44
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (25 bp):
AGCTCGATTAAAACTCGAGATTCTA
Found at i:585904 original size:23 final size:23
Alignment explanation
Indices: 585849--585928 Score: 83
Period size: 23 Copynumber: 3.4 Consensus size: 23
585839 AAAAATTTAA
*
585849 GAGCTCGATTAAAACTCGAGATTC-
1 GAGCTCGATTAAAATTC--GATTCT
* *
585873 AAGCTCGATT-GAATCTCGATTCT
1 GAGCTCGATTAAAAT-TCGATTCT
*
585896 GAGCTCGATTAAAATTCGATTTT
1 GAGCTCGATTAAAATTCGATTCT
585919 GAGCTCGATT
1 GAGCTCGATT
585929 CAAGCTCAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
22 5 0.11
23 28 0.60
24 14 0.30
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (23 bp):
GAGCTCGATTAAAATTCGATTCT
Found at i:587068 original size:45 final size:45
Alignment explanation
Indices: 587013--587133 Score: 224
Period size: 45 Copynumber: 2.7 Consensus size: 45
587003 TGCATTGCTT
587013 GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA
587058 GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA
**
587103 GTGCATCGATTTATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
587134 CAATTTATTC
Statistics
Matches: 74, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (45 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCAA
Found at i:587071 original size:64 final size:64
Alignment explanation
Indices: 586949--587071 Score: 151
Period size: 64 Copynumber: 1.9 Consensus size: 64
586939 GGAACACTTA
** * *
586949 GTGCATCGATGAATAAAATGCATTCGATGTTTGAAAATAGACTGAGTGCATTGGTGCATTGCTT
1 GTGCATCGATGAATAAAATGCATTCGATGTTTGAAAATAGACCAAGTGCATCGATGCATTGCTT
* * *
587013 GTGCATCGATGCATGAAATGCATTCGATGTTTTAATAA-A-ACCCAAGTGCATCGATGCAT
1 GTGCATCGATGAATAAAATGCATTCGATGTTTGAA-AATAGA-CCAAGTGCATCGATGCAT
587072 GAAATGCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
63 1 0.02
64 47 0.94
65 2 0.04
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGAATAAAATGCATTCGATGTTTGAAAATAGACCAAGTGCATCGATGCATTGCTT
Found at i:589833 original size:44 final size:44
Alignment explanation
Indices: 589738--589834 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
589728 GCTCTTGTGC
* * *
589738 ATTGATACACATTCAAGGGCGTGCATCGGTGCATCAGCTGATGT
1 ATTGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
* * *
589782 ATCGATGCACATTCAAAGGG-ATGCATCGGTGCA-CTGTTAAGTGT
1 ATTGATGCACATTC-AAGGGCATGCATCGGTGCATCAGCTAA-TGT
589826 ATTGATGCA
1 ATTGATGCA
589835 TTAAGCACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
43 4 0.09
44 35 0.80
45 5 0.11
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.28
Consensus pattern (44 bp):
ATTGATGCACATTCAAGGGCATGCATCGGTGCATCAGCTAATGT
Found at i:595673 original size:64 final size:62
Alignment explanation
Indices: 595604--595782 Score: 189
Period size: 64 Copynumber: 2.8 Consensus size: 62
595594 TGGAACACTT
** * **
595604 AGTGCATCGGTGCACCAAGTGTGCATCGATGCAAAAAATGCATTCGATGTTTGAA-AATAGCCTG
1 AGTGCATCGGTGCA--AAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAA-AACCCA
** * *
595668 AGTGCATCGGTGCATTGCTCGTGTATCGATGCATGAAATGCATTCGATGTTTTAATAAAACCCA
1 AGTGCATCGGTGCAAAG-T-GTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
* *
595732 AGTGCATCGATGCATAGAGAGTGCATCGATGCATGAAATGCATTCGATGTT
1 AGTGCATCGGTGCA-A-AGTGTGCATCGATGCATGAAATGCATTCGATGTT
595783 CAATTTATTC
Statistics
Matches: 96, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 91 0.95
65 2 0.02
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (62 bp):
AGTGCATCGGTGCAAAGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAATAAAACCCA
Found at i:596657 original size:14 final size:14
Alignment explanation
Indices: 596640--596696 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
596630 GAATGAACAT
596640 AAACGAACATAACC
1 AAACGAACATAACC
596654 AAACGAAC--AA--
1 AAACGAACATAACC
596664 AAACGAACATAACC
1 AAACGAACATAACC
* *
596678 GAACGAATATAACC
1 AAACGAACATAACC
*
596692 GAACG
1 AAACG
596697 TTCACGAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
12 4 0.11
14 25 0.68
ACGTcount: A:0.56, C:0.25, G:0.12, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:596661 original size:24 final size:24
Alignment explanation
Indices: 596634--596695 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 24
596624 ATAAATGAAT
596634 GAACATAAACGAACATAACCAAAC
1 GAACATAAACGAACATAACCAAAC
* *
596658 GAACAAAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCAAAC
* *
596682 GAATATAACCGAAC
1 GAACATAAACGAAC
596696 GTTCACGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.56, C:0.24, G:0.11, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCAAAC
Found at i:625019 original size:17 final size:17
Alignment explanation
Indices: 624959--625019 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
624949 AGCCAAAAGA
**
624959 CTTTCTTTCCTTCTTC-
1 CTTTCTTTTTTTCTTCT
*
624975 CTATTCTATTTTTCTTTCT
1 CT-TTCTTTTTTTC-TTCT
* *
624994 CCTTATTTTTTTCTTCT
1 CTTTCTTTTTTTCTTCT
625011 CTTTCTTTT
1 CTTTCTTTT
625020 CATAAGGATG
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
16 2 0.06
17 19 0.56
18 12 0.35
19 1 0.03
ACGTcount: A:0.05, C:0.26, G:0.00, T:0.69
Consensus pattern (17 bp):
CTTTCTTTTTTTCTTCT
Found at i:633238 original size:18 final size:18
Alignment explanation
Indices: 633215--633249 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
633205 AAAGAAATAG
*
633215 AAAATAACAGAAAATAAT
1 AAAATAAAAGAAAATAAT
*
633233 AAAATAAAATAAAATAA
1 AAAATAAAAGAAAATAA
633250 AAAGAAAGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAATAAAAGAAAATAAT
Done.