Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004114.1 Hibiscus syriacus cultivar Beakdansim tig00009003_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: 1048340
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:338608 original size:146 final size:147
Alignment explanation
Indices: 338366--338654 Score: 411
Period size: 146 Copynumber: 2.0 Consensus size: 147
338356 GAATACCATG
* *
338366 AGTGGCACCTTTTATGTCAATAATGCACCGTTATGCATTTAACTATCATTAATGGCACCTTTTAT
1 AGTGGCACCTTTTATGCCAATAATGCACCGTTATACATTTAACTATCATTAATGGCACCTTTTAT
* * * * * *
338431 GCCGAAATGCACTATTATGCATTTAAGTTTCATTAGTGGCACCTTTTATG-TGAAATGCACCATT
66 GCCAAAATGCACCATTATGCATTCAACTTTCATTAGTGGCACCTTTTATGCCGAAATACACCATT
338495 ATGCATTTAATTTTCATT
131 ATGCATTT-ATTTTCATT
* * * * * *
338513 AGTGGTACCTTTTATGCCGA-AATGCACTGTTATATATTTAACTTTCATTAGTGGCACCTTTTAT
1 AGTGGCACCTTTTATGCCAATAATGCACCGTTATACATTTAACTATCATTAATGGCACCTTTTAT
* *
338577 GCCAAAATGTACCATTATGCATTCAACTTTCATTAGTGGCACCTTTTATGCCGAAATATACCATT
66 GCCAAAATGCACCATTATGCATTCAACTTTCATTAGTGGCACCTTTTATGCCGAAATACACCATT
338642 ATGCATTTATTTT
131 ATGCATTTATTTT
338655 GGCAACATCG
Statistics
Matches: 125, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
146 89 0.71
147 36 0.29
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.40
Consensus pattern (147 bp):
AGTGGCACCTTTTATGCCAATAATGCACCGTTATACATTTAACTATCATTAATGGCACCTTTTAT
GCCAAAATGCACCATTATGCATTCAACTTTCATTAGTGGCACCTTTTATGCCGAAATACACCATT
ATGCATTTATTTTCATT
Found at i:348028 original size:13 final size:13
Alignment explanation
Indices: 348012--348036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
348002 GACAAACATT
348012 GTTTTCAAAAATA
1 GTTTTCAAAAATA
348025 GTTTTCAAAAAT
1 GTTTTCAAAAAT
348037 TGCCCATTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
GTTTTCAAAAATA
Found at i:349318 original size:20 final size:20
Alignment explanation
Indices: 349293--349330 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
349283 TTTTATTTAG
*
349293 GGATGTATTGATACACACTT
1 GGATGTATCGATACACACTT
349313 GGATGTATCGATACACAC
1 GGATGTATCGATACACAC
349331 CAAACATCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (20 bp):
GGATGTATCGATACACACTT
Found at i:357473 original size:12 final size:11
Alignment explanation
Indices: 357447--357485 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
357437 CACAATCGTA
*
357447 ATATATT-TAC
1 ATATATTATAT
357457 ATATATTATAT
1 ATATATTATAT
357468 ACTATATTATAT
1 A-TATATTATAT
357480 ATATAT
1 ATATAT
357486 ATAGAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 7 0.27
11 8 0.31
12 11 0.42
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATATTATAT
Found at i:361236 original size:37 final size:35
Alignment explanation
Indices: 361186--361287 Score: 123
Period size: 37 Copynumber: 2.8 Consensus size: 35
361176 TCGGATCAAA
* *
361186 GTCGGATAGAGGATATATATTTTTCGGGTCGAGTCAG
1 GTCGGATGGAGGATATATA-TTTTCGGGTAGAGTC-G
*
361223 GTCGGATGGAGGATATATAATTTTCTGGTAGAGTCG
1 GTCGGATGGAGGATATAT-ATTTTCGGGTAGAGTCG
* *
361259 GTTCGGGTGGAGGATACATATTTTCGGGT
1 G-TCGGATGGAGGATATATATTTTCGGGT
361288 TGGGTCGAGT
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
36 11 0.19
37 45 0.79
38 1 0.02
ACGTcount: A:0.23, C:0.10, G:0.34, T:0.33
Consensus pattern (35 bp):
GTCGGATGGAGGATATATATTTTCGGGTAGAGTCG
Found at i:362543 original size:3 final size:3
Alignment explanation
Indices: 362535--362637 Score: 206
Period size: 3 Copynumber: 34.3 Consensus size: 3
362525 TTGCCCACAA
362535 TAT TAT TAT TAT TAT TAT TAT TAT 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
362583 TAT TAT TAT TAT TAT TAT TAT TAT 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
362631 TAT TAT T
1 TAT TAT T
362638 GAGATGATGC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:363030 original size:19 final size:19
Alignment explanation
Indices: 363006--363042 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
362996 ATGTTCAAGT
363006 TTGAGTTTCACCTTAAACA
1 TTGAGTTTCACCTTAAACA
363025 TTGAGTTTCACCTTAAAC
1 TTGAGTTTCACCTTAAAC
363043 CCAGATATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (19 bp):
TTGAGTTTCACCTTAAACA
Found at i:370038 original size:2 final size:2
Alignment explanation
Indices: 370031--370060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
370021 TATAGTTTAT
370031 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
370061 AATGTATAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:370659 original size:20 final size:22
Alignment explanation
Indices: 370614--370659 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
370604 GTGTCACAAT
*
370614 TTAATTGAATATTAAATTTATT
1 TTAATTGAATATTAAATTTATA
370636 TTAATT-AA-ATTAAA-TTATGA
1 TTAATTGAATATTAAATTTAT-A
370656 TTAA
1 TTAA
370660 ATTTATAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 4 0.18
20 10 0.45
21 2 0.09
22 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (22 bp):
TTAATTGAATATTAAATTTATA
Found at i:374101 original size:2 final size:2
Alignment explanation
Indices: 374094--374121 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
374084 TATTCCAATG
374094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
374122 ATGATTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:376886 original size:89 final size:89
Alignment explanation
Indices: 376735--376917 Score: 267
Period size: 89 Copynumber: 2.1 Consensus size: 89
376725 AATTAAAGAA
* * *
376735 AGAAGCTGAAATCAGTACAGTGAAAGCCTATTCAGCTAGTCGTAGGGCTTAGCCTTCTAGGATGA
1 AGAAGCTGAAATCAATACAGTGAAAGCCTATTCAGCTAGTCATAGGGCTGAGCCTTCTAGGATGA
*
376800 TCCGAGAAAAGAGTCCCCATACTC
66 TCCAAGAAAAGAGTCCCCATACTC
* * ** *
376824 AGAAGCTGAAATCAATACAGTGGAAGCCTATTCAGTTTTTCATAGGGCTGAGCCTTCTAGGATGG
1 AGAAGCTGAAATCAATACAGTGAAAGCCTATTCAGCTAGTCATAGGGCTGAGCCTTCTAGGATGA
*
376889 TCCAATAAAAGAGTCCCCATACTC
66 TCCAAGAAAAGAGTCCCCATACTC
*
376913 TGAAG
1 AGAAG
376918 GCTACGATGT
Statistics
Matches: 83, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.24
Consensus pattern (89 bp):
AGAAGCTGAAATCAATACAGTGAAAGCCTATTCAGCTAGTCATAGGGCTGAGCCTTCTAGGATGA
TCCAAGAAAAGAGTCCCCATACTC
Found at i:377934 original size:42 final size:42
Alignment explanation
Indices: 377767--378159 Score: 385
Period size: 42 Copynumber: 9.1 Consensus size: 42
377757 AACAAAAAAT
*
377767 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTGTTCCTTGGAAAAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCG--T-TT--TTGGAACAAAC
* * * *
377815 GCCGTAAAAGGTTGACATCTATAGCGACG-TTTTGAGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTG-GAACAAAC
* * * * * *
377858 GCCACAAAAGGTTGACATCTACAGTGGCATTTTTGGAACAAAC
1 GCCGCAAAAGG-TCAGATCTATAGCGGCGTTTTTGGAACAAAC
*
377901 GCCGCAGAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * *
377943 CCCGCAAAAGGTCAGATCTATTGCAGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * ** *
377985 GCCGTAAAAGATCAAGATCTATAATGACG-TTTTGGAACAAAC
1 GCCGCAAAAGGTC-AGATCTATAGCGGCGTTTTTGGAACAAAC
** * *
378027 GCCATAAAAGGTCAAATCTATAGCGGCGTTTTTTGATACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
* *
378070 GCCGCAAAAGGTTAGATCTATAGCGGCGTTTCTGGAACAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
* * * * *
378112 ACCGCAAAAGGTCAAATCTATAACGGCGTTTTTTGATATAAAC
1 GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGA-ACAAAC
378155 GCCGC
1 GCCGC
378160 TAATTACCTT
Statistics
Matches: 287, Mismatches: 51, Indels: 19
0.80 0.14 0.05
Matches are distributed among these distances:
41 11 0.04
42 143 0.50
43 102 0.36
44 7 0.02
48 23 0.08
49 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (42 bp):
GCCGCAAAAGGTCAGATCTATAGCGGCGTTTTTGGAACAAAC
Found at i:378124 original size:85 final size:83
Alignment explanation
Indices: 377767--378159 Score: 390
Period size: 85 Copynumber: 4.6 Consensus size: 83
377757 AACAAAAAAT
* * * *
377767 GCCGCAAAAGGTCGAGATCTATAGCGGCGTTTGTTCCTTGGAAAAAACGCCGTAAAAGGTTGACA
1 GCCGCAAAAGGTC-AAATCTATAGCGGCG-TT-TT--TT-GAACAAACGCCGCAAAAGGTT-AGA
377832 TCTATAGCGACGTTTTGAGAACAAAC
59 TCTATAGCGACGTTTTG-GAACAAAC
* * * * * * * * *
377858 GCCACAAAAGGTTGACATCTACAGTGGCATTTTTGGAACAAACGCCGCAGAAGGTCAGATCTATA
1 GCCGCAAAAGG-TCAAATCTATAGCGGCGTTTTTTGAACAAACGCCGCAAAAGGTTAGATCTATA
*
377923 GCGGCGTTTTTGGAACAAAC
65 GCGACG-TTTTGGAACAAAC
* * * * * * * *
377943 CCCGCAAAAGGTCAGATCTATTGCAGCGTTTTTGGAACAAACGCCGTAAAAGATCAAGATCTATA
1 GCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGAACAAACGCCGCAAAAGGT-TAGATCTATA
**
378008 ATGACGTTTTGGAACAAAC
65 GCGACGTTTTGGAACAAAC
**
378027 GCCATAAAAGGTCAAATCTATAGCGGCGTTTTTTGATACAAACGCCGCAAAAGGTTAGATCTATA
1 GCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGA-ACAAACGCCGCAAAAGGTTAGATCTATA
*
378092 GCGGCGTTTCTGGAACAAAC
65 GCGACGTTT-TGGAACAAAC
* * *
378112 ACCGCAAAAGGTCAAATCTATAACGGCGTTTTTTGATATAAACGCCGC
1 GCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGA-ACAAACGCCGC
378160 TAATTACCTT
Statistics
Matches: 250, Mismatches: 47, Indels: 16
0.80 0.15 0.05
Matches are distributed among these distances:
84 90 0.36
85 111 0.44
86 22 0.09
87 1 0.00
89 2 0.01
90 2 0.01
91 21 0.08
92 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.24
Consensus pattern (83 bp):
GCCGCAAAAGGTCAAATCTATAGCGGCGTTTTTTGAACAAACGCCGCAAAAGGTTAGATCTATAG
CGACGTTTTGGAACAAAC
Found at i:381792 original size:82 final size:82
Alignment explanation
Indices: 381706--381982 Score: 324
Period size: 82 Copynumber: 3.4 Consensus size: 82
381696 TGAGTCTTTA
* * * * *
381706 GCGGCGTTTGTATAGAAACGCCGCTAAAGTACTATTATGTTGTGGCGTTTATTGAAAAACGCCAC
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTATTAAAAAACGCCAC
* *
381771 TATAGGTAAATACTATT
66 TATAGGTGAATCCTATT
* * * *
381788 GCGGCGTTTGTTTAAAAACGCCGCTAAAGTTCTAATCTGTTGCGGCATTTATTAAAAAAATGCCA
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTATT-AAAAAACGCCA
*
381853 CTATAAGTGAATCCTATT
65 CTATAGGTGAATCCTATT
* * * *
381871 GCGGCGTTTGTATAAAAACGACGCTAAA-TACTAATCTATTGCGGCGTTTGTCAAAAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTAT-TAAAAAACGCCA
* *
381935 CTATAGATGAACCCTATT
65 CTATAGGTGAATCCTATT
* * *
381953 ACGGCATTTATA-AATAAACGCCGCTAAAGT
1 GCGGCGTTTGTATAA-AAACGCCGCTAAAGT
381983 TACCATTTTG
Statistics
Matches: 164, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
81 2 0.01
82 111 0.68
83 51 0.31
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (82 bp):
GCGGCGTTTGTATAAAAACGCCGCTAAAGTACTAATCTGTTGCGGCGTTTATTAAAAAACGCCAC
TATAGGTGAATCCTATT
Found at i:381874 original size:42 final size:42
Alignment explanation
Indices: 381760--381982 Score: 131
Period size: 41 Copynumber: 5.4 Consensus size: 42
381750 GCGTTTATTG
* * * * * *
381760 AAAAACGCCACTATAGGTAAATACTATTGCGGCGTTTGTT-T
1 AAAAACGCCACTATAAGTGAATCCTATTGCGGCATTTATTAA
* * *
381801 AAAAACGCCGCTA-AAGTTCTAAT-CTGTTGCGGCATTTATTAA
1 AAAAACGCCACTATAAG-T-GAATCCTATTGCGGCATTTATTAA
* * * *
381843 AAAAATGCCACTATAAGTGAATCCTATTGCGGCGTTT-GTAT
1 AAAAACGCCACTATAAGTGAATCCTATTGCGGCATTTATTAA
* * * * * * *
381884 AAAAACGACGCTAAATACT-AAT-CTATTGCGGCGTTTGTCAA
1 AAAAACGCCACTATA-AGTGAATCCTATTGCGGCATTTATTAA
* *
381925 AAAAACGCCACTAT-AGATGAACCCTATTACGGCATTTA-TAA
1 AAAAACGCCACTATAAG-TGAATCCTATTGCGGCATTTATTAA
* *
381966 ATAAACGCCGCTA-AAGT
1 AAAAACGCCACTATAAGT
381983 TACCATTTTG
Statistics
Matches: 138, Mismatches: 33, Indels: 23
0.71 0.17 0.12
Matches are distributed among these distances:
39 1 0.01
40 18 0.13
41 75 0.54
42 41 0.30
43 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (42 bp):
AAAAACGCCACTATAAGTGAATCCTATTGCGGCATTTATTAA
Found at i:381917 original size:40 final size:40
Alignment explanation
Indices: 381706--381933 Score: 147
Period size: 41 Copynumber: 5.5 Consensus size: 40
381696 TGAGTCTTTA
* * * * *
381706 GCGGCGTTTGTATAGAAACGCCGCTAAAGTACTATTATGTT
1 GCGGCGTTTGTAAAAAAACGCCGCTAAA-TACTAATCTATT
* * ** * *
381747 GTGGCGTTTATTGAAAAACGCCACT--ATAGGTAAATACTATT
1 GCGGCGTTTGTAAAAAAACGCCGCTAAATA-CT-AAT-CTATT
** * *
381788 GCGGCGTTTGTTTAAAAACGCCGCTAAAGTTCTAATCTGTT
1 GCGGCGTTTGTAAAAAAACGCCGCTAAA-TACTAATCTATT
* * * * * *
381829 GCGGCATTTATTAAAAAAATGCCACTATA-AGTGAATCCTATT
1 GCGGCGTTT-GTAAAAAAACGCCGCTAAATACT-AAT-CTATT
* *
381871 GCGGCGTTTGTATAAAAACGACGCTAAATACTAATCTATT
1 GCGGCGTTTGTAAAAAAACGCCGCTAAATACTAATCTATT
381911 GCGGCGTTTGTCAAAAAAACGCC
1 GCGGCGTTTGT-AAAAAAACGCC
381934 ACTATAGATG
Statistics
Matches: 139, Mismatches: 37, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 19 0.14
41 83 0.60
42 30 0.22
43 2 0.01
44 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTGTAAAAAAACGCCGCTAAATACTAATCTATT
Found at i:382515 original size:12 final size:12
Alignment explanation
Indices: 382500--382569 Score: 71
Period size: 11 Copynumber: 6.2 Consensus size: 12
382490 AGATCACATC
382500 AAAGCAAAGAAA
1 AAAGCAAAGAAA
382512 AAAGCAAAG-AA
1 AAAGCAAAGAAA
*
382523 AAAGTAAAG-AA
1 AAAGCAAAGAAA
382534 AAAG---A-AAA
1 AAAGCAAAGAAA
382542 AAAGCAAAGAAA
1 AAAGCAAAGAAA
*
382554 AAAACAAAAGAAA
1 AAAGC-AAAGAAA
382567 AAA
1 AAA
382570 AAAACACAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 11
0.79 0.03 0.17
Matches are distributed among these distances:
8 7 0.14
11 17 0.34
12 16 0.32
13 10 0.20
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (12 bp):
AAAGCAAAGAAA
Found at i:382526 original size:11 final size:11
Alignment explanation
Indices: 382500--382555 Score: 73
Period size: 11 Copynumber: 5.3 Consensus size: 11
382490 AGATCACATC
382500 AAAGCAAAGAAA
1 AAAGCAAAG-AA
382512 AAAGCAAAGAA
1 AAAGCAAAGAA
*
382523 AAAGTAAAGAA
1 AAAGCAAAGAA
382534 AAAG--AA-AA
1 AAAGCAAAGAA
382542 AAAGCAAAGAA
1 AAAGCAAAGAA
382553 AAA
1 AAA
382556 AACAAAAGAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
8 6 0.15
9 2 0.05
10 2 0.05
11 21 0.52
12 9 0.22
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAGCAAAGAA
Found at i:382545 original size:19 final size:17
Alignment explanation
Indices: 382521--382573 Score: 63
Period size: 19 Copynumber: 3.0 Consensus size: 17
382511 AAAAGCAAAG
382521 AAAAAGTAAAGAAAAAGAA
1 AAAAAG-AAAGAAAAA-AA
382540 AAAAAGCAAAGAAAAAAA
1 AAAAAG-AAAGAAAAAAA
*
382558 CAAAAGAAA-AAAAAAA
1 AAAAAGAAAGAAAAAAA
382574 CACAGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
16 7 0.22
17 3 0.09
18 7 0.22
19 15 0.47
ACGTcount: A:0.83, C:0.04, G:0.11, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAGAAAAAAA
Found at i:382552 original size:13 final size:13
Alignment explanation
Indices: 382500--382570 Score: 74
Period size: 13 Copynumber: 5.2 Consensus size: 13
382490 AGATCACATC
382500 AAAGCAAAG-AAA
1 AAAGCAAAGAAAA
382512 AAAGCAAAGAAAAA
1 AAAGCAAAG-AAAA
*
382526 GTAAAGAAAAAGAAAA
1 --AAAG-CAAAGAAAA
382542 AAAGCAAAGAAAA
1 AAAGCAAAGAAAA
382555 AAA-CAAAAGAAAA
1 AAAGC-AAAGAAAA
382568 AAA
1 AAA
382571 AAACACAGAG
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
12 10 0.20
13 22 0.43
14 7 0.14
16 8 0.16
17 4 0.08
ACGTcount: A:0.79, C:0.06, G:0.14, T:0.01
Consensus pattern (13 bp):
AAAGCAAAGAAAA
Found at i:382572 original size:30 final size:30
Alignment explanation
Indices: 382500--382596 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
382490 AGATCACATC
* *
382500 AAAGCAAAGAAAAAAGCAAAGAAAAAGTAAA
1 AAAGAAAAAAAAAAAGCAAAGAAAAAG-AAA
* *
382531 GAA-AAAGAAAAAAAGCAAAGAAAAA-AACA
1 AAAGAAAAAAAAAAAGCAAAGAAAAAGAA-A
*
382560 AAAGAAAAAAAAAACA-CAGAGAAAAAGAGAA
1 AAAGAAAAAAAAAA-AGCAAAGAAAAAGA-AA
*
382591 CAAGAA
1 AAAGAA
382597 GCACATGCAA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
28 2 0.04
29 3 0.06
30 37 0.70
31 10 0.19
32 1 0.02
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.01
Consensus pattern (30 bp):
AAAGAAAAAAAAAAAGCAAAGAAAAAGAAA
Found at i:384051 original size:36 final size:36
Alignment explanation
Indices: 383990--384082 Score: 116
Period size: 36 Copynumber: 2.6 Consensus size: 36
383980 CATCTCACTA
* * * *
383990 GAGACAATTTTTCTTAAAAACAAATTTTGTCTCGGTT
1 GAGACAATTTCTC-TCAAAACAAATTTCGTCTCGCTT
384027 GAGACAATTTCTCTCAAAACAAATTTCGTCTCGCTT
1 GAGACAATTTCTCTCAAAACAAATTTCGTCTCGCTT
* *
384063 AAGACATTTTC-CTCAAAACA
1 GAGACAATTTCTCTCAAAACA
384083 CTAAATTTAA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
35 9 0.18
36 29 0.58
37 12 0.24
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (36 bp):
GAGACAATTTCTCTCAAAACAAATTTCGTCTCGCTT
Found at i:384203 original size:65 final size:65
Alignment explanation
Indices: 384122--384441 Score: 502
Period size: 65 Copynumber: 5.0 Consensus size: 65
384112 AAACCCTAAA
* ** *
384122 ATCTTTGAGATTGTTTCCCTTGAAACGAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAATATC
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
* * *
384187 ATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTCTTAAGATA-TTTCTCTTGAAACATC
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
* * * *
384251 ATCTTTGATATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTATCTTAAAACAAC
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
384316 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
* *
384381 ATCTTTGAGATCGTTTCCCTTGAAATGAA-TTT-TCTCTCTTAAGACAGTTTCTCTTGAAACA
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
384442 AATCCTTAAA
Statistics
Matches: 234, Mismatches: 20, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
63 28 0.12
64 62 0.26
65 144 0.62
ACGTcount: A:0.25, C:0.20, G:0.13, T:0.41
Consensus pattern (65 bp):
ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
Found at i:384277 original size:129 final size:128
Alignment explanation
Indices: 384122--384442 Score: 500
Period size: 129 Copynumber: 2.5 Consensus size: 128
384112 AAACCCTAAA
* * *
384122 ATCTTTGAGATTGTTTCCCTTGAAACGAATTTCATCTCTCTTGAGACAGTTTCTCTTGAAATATC
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTT--TCTCTCTTGAGACAGTTTCTCTTGAAACAAC
* *
384187 ATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCTCTTAAGATA-TTTCTCTTGAAACATC
64 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACATC
* * *
384251 ATCTTTGATATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTATCTTAAAACAAC
1 ATCTTTGAGATCGTTTCCCTTGAAACGAA-TTT-TCTCTCTTGAGACAGTTTCTCTTGAAACAAC
*
384316 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACATC
64 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACATC
* *
384381 ATCTTTGAGATCGTTTCCCTTGAAATGAATTTTCTCTCTTAAGACAGTTTCTCTTGAAACAA
1 ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTCTCTCTTGAGACAGTTTCTCTTGAAACAA
384443 ATCCTTAAAG
Statistics
Matches: 175, Mismatches: 15, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
128 27 0.15
129 102 0.58
130 46 0.26
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (128 bp):
ATCTTTGAGATCGTTTCCCTTGAAACGAATTTTCTCTCTTGAGACAGTTTCTCTTGAAACAACAT
CTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCTCTTAAGACAGTTTCTCTTGAAACATC
Found at i:384341 original size:29 final size:29
Alignment explanation
Indices: 384309--384405 Score: 81
Period size: 29 Copynumber: 3.1 Consensus size: 29
384299 GTTTATCTTA
384309 AAACAACATCTTTGAGATCGTTTCCCTTG
1 AAACAACATCTTTGAGATCGTTTCCCTTG
*
384338 AAACGAATTTTGTC-TCTCTTGAGA-CAGTTTCTCTTG
1 AAAC-AA------CATCT-TTGAGATC-GTTTCCCTTG
*
384374 AAACATCATCTTTGAGATCGTTTCCCTTG
1 AAACAACATCTTTGAGATCGTTTCCCTTG
384403 AAA
1 AAA
384406 TGAATTTTCT
Statistics
Matches: 54, Mismatches: 3, Indels: 22
0.68 0.04 0.28
Matches are distributed among these distances:
29 23 0.43
30 6 0.11
35 5 0.09
36 20 0.37
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (29 bp):
AAACAACATCTTTGAGATCGTTTCCCTTG
Found at i:384774 original size:134 final size:130
Alignment explanation
Indices: 384443--384785 Score: 384
Period size: 130 Copynumber: 2.6 Consensus size: 130
384433 CTTGAAACAA
* * *
384443 ATCCTTAAAGATGGCCAGCCGTCCTCATCACGTAGGAACTGTGTTATCCACCGACCAGACCTCCT
1 ATCCTTAAAGATGGTCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
* * ** * *
384508 CATCACTTAGGAGTTGTGTCACCTTAGATAACTAGCCGTCCTTATCACGTAGGAACTGTGTTATC
66 CATCACGTAAGAGCCGTGTCACCCTAGATAACTAGCCGTCCTCATCACGTAGGAACTGTGTTATC
* * * * * *
384573 ATCCCTAAAGATGGTCTGCCATCCTCATCATGTAGGAACCATGTCATCCACTC-ACCAGACCTAC
1 ATCCTTAAAGATGGTCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCAC-CGACCAGACCTCC
* *
384637 TCATCACGTAAGAGCCGTGTCACCCCTAGATAACTAGTCGTCCTCATCACGTAGTAA-TAGTGTT
65 TCATCACGTAAGAGCCGTGTCA-CCCTAGATAACTAGCCGTCCTCATCACGTAGGAACT-GTGTT
*
384701 GTCAC
128 AT--C
* * ** * * *
384706 TATTCTTAAATATGGTCAGCCGTCCTCATTGCGTAAGAACCGTGTCATCCACCGACTAGATCTCC
1 -ATCCTTAAAGATGGTCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCC
*
384771 TCATCACGTATGAGC
65 TCATCACGTAAGAGC
384786 AGCGTCATCA
Statistics
Matches: 174, Mismatches: 32, Indels: 10
0.81 0.15 0.05
Matches are distributed among these distances:
130 72 0.41
131 37 0.21
133 2 0.01
134 63 0.36
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (130 bp):
ATCCTTAAAGATGGTCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGACCTCCT
CATCACGTAAGAGCCGTGTCACCCTAGATAACTAGCCGTCCTCATCACGTAGGAACTGTGTTATC
Found at i:384971 original size:3 final size:3
Alignment explanation
Indices: 384965--385004 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
384955 TGGCTAAAAA
* *
384965 TAT TAT TAA TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
385005 TTAACAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:392786 original size:33 final size:33
Alignment explanation
Indices: 392733--392805 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
392723 TGTGACCAAA
* *
392733 TAGATCCCGTAAAAATGGTTGAAATAGATACCTC
1 TAGA-CCCATAAAAACGGTTGAAATAGATACCTC
* *
392767 TAGACCCATAAAAACGGTTGAATTTGATACCTC
1 TAGACCCATAAAAACGGTTGAAATAGATACCTC
392800 TAGACC
1 TAGACC
392806 GTACTCCAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
33 31 0.89
34 4 0.11
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (33 bp):
TAGACCCATAAAAACGGTTGAAATAGATACCTC
Found at i:394687 original size:34 final size:34
Alignment explanation
Indices: 394644--394713 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
394634 CCGTCCGGCG
*
394644 TTATTATATAGAAAAGCCTCCATTAATTATTTTT
1 TTATTATATAGAAAAACCTCCATTAATTATTTTT
394678 TTATTATATAGAAAAACCTCCATTAATTATTTTT
1 TTATTATATAGAAAAACCTCCATTAATTATTTTT
394712 TT
1 TT
394714 GAGAAATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.49
Consensus pattern (34 bp):
TTATTATATAGAAAAACCTCCATTAATTATTTTT
Found at i:396443 original size:75 final size:77
Alignment explanation
Indices: 396294--396497 Score: 317
Period size: 75 Copynumber: 2.7 Consensus size: 77
396284 TAGCAGAATA
396294 TTTAGACCAATTTCATTCATCCATTAC-TAGCAGCATTATACCAATTGTTATA-AGCCCTTTTTC
1 TTTAGACCAATTTCATTCAT-CATTACTTA-CAGCATTATACCAATTGTTATAGAGCCCTTTTTC
396357 GATCTTCCTGTATG
64 GATCTTCCTGTATG
* *
396371 TTTAGACCAATTTCATTCATCATTACTTACAACATTATACCGATTG-TATAGA-CCCTTTTTCGA
1 TTTAGACCAATTTCATTCATCATTACTTACAGCATTATACCAATTGTTATAGAGCCCTTTTTCGA
396434 TCTTCCTGTATG
66 TCTTCCTGTATG
* * *
396446 TTTAGTCCAATTTCATTCATCATTACTTACAGCATTATGCCTATTGTTATAG
1 TTTAGACCAATTTCATTCATCATTACTTACAGCATTATACCAATTGTTATAG
396498 GCTTTTTTTT
Statistics
Matches: 118, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
75 69 0.58
76 27 0.23
77 22 0.19
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (77 bp):
TTTAGACCAATTTCATTCATCATTACTTACAGCATTATACCAATTGTTATAGAGCCCTTTTTCGA
TCTTCCTGTATG
Found at i:398384 original size:22 final size:20
Alignment explanation
Indices: 398340--398397 Score: 57
Period size: 22 Copynumber: 2.9 Consensus size: 20
398330 ATATATATAT
398340 ATTT-AATTTTTTTTT-GTA
1 ATTTAAATTTTTTTTTAGTA
398358 ATTTAAATTTTGTTTTTAGTA
1 ATTTAAATTTT-TTTTTAGTA
* *
398379 TTTTTATATTTATTTTTTA
1 -ATTTAAATTT-TTTTTTA
398398 ATTATTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 4 0.12
19 6 0.18
20 5 0.15
21 3 0.09
22 14 0.42
23 1 0.03
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (20 bp):
ATTTAAATTTTTTTTTAGTA
Found at i:398412 original size:16 final size:17
Alignment explanation
Indices: 398382--398414 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
398372 TTTAGTATTT
*
398382 TTATATTTATTTTTTAA
1 TTATATTTATATTTTAA
398399 TTAT-TTTATATTTTAA
1 TTATATTTATATTTTAA
398415 ATGTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATATTTATATTTTAA
Found at i:398432 original size:22 final size:22
Alignment explanation
Indices: 398377--398434 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
398367 TTGTTTTTAG
** * *
398377 TATTTTTATATTTATTTTTTAAT
1 TATTTTTAT-TTTAAATGTTAAA
398400 TATTTTATATTTTAAATGTTAAA
1 TATTTT-TATTTTAAATGTTAAA
398423 TATTTTTATTTT
1 TATTTTTATTTT
398435 TCTAAAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 6 0.20
23 21 0.70
24 3 0.10
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (22 bp):
TATTTTTATTTTAAATGTTAAA
Found at i:398976 original size:20 final size:19
Alignment explanation
Indices: 398953--398999 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
398943 CGATATACCA
398953 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
398973 GGTAACAAAATGATAAAATC
1 GGTAA-AAAATGATAAAACC
398993 GGTAAAA
1 GGTAAAA
399000 CGTTACCGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.80
21 3 0.12
ACGTcount: A:0.55, C:0.09, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:399033 original size:163 final size:162
Alignment explanation
Indices: 398761--399212 Score: 517
Period size: 163 Copynumber: 2.7 Consensus size: 162
398751 ATCCAAATTA
* * ***
398761 AAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATAA
* * *
398826 AACCGGTAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTCG
66 AACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTCG
398891 TGAATTTAAAAGAGAAGCAGTTTTAAATCCTAT
130 TGAATTTAAAAGAGAAGCAGTTTTAAATCCTAT
* *
398924 AAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATAA
1 AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATAA
* * * * *
398989 AATCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTGT
66 AACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
*
399054 GAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTT
131 GAATTTAAAAGAGAAGCAG-TTT------TA-AA----TC----CTAT
* * * *
399102 AAAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAA--TGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGAT
* * * *
399167 AAAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATACTTT
64 AAAACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTT
399213 CGTAAGTACG
Statistics
Matches: 248, Mismatches: 23, Indels: 19
0.86 0.08 0.07
Matches are distributed among these distances:
162 39 0.16
163 98 0.40
169 2 0.01
170 2 0.01
174 2 0.01
178 7 0.03
180 98 0.40
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.26
Consensus pattern (162 bp):
AAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGGTAACAAAATGATAA
AACCGGTAAAACGCTACCAGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCGT
GAATTTAAAAGAGAAGCAGTTTTAAATCCTAT
Found at i:399156 original size:20 final size:19
Alignment explanation
Indices: 399133--399179 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
399123 CGATATAACA
399133 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
399153 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
399173 GGTAAAA
1 GGTAAAA
399180 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:399181 original size:17 final size:19
Alignment explanation
Indices: 399142--399184 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
399132 AGGTAAAAAT
399142 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
399162 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
399179 ATGATA
1 ATGATA
399185 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:401425 original size:21 final size:21
Alignment explanation
Indices: 401399--401463 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
401389 AAGACAATCA
* * *
401399 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGATACACTTGAG
401420 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATACACTTGAG
401441 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGATACACTTGAG
401462 AG
1 AG
401464 GCATAAGGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.40, C:0.12, G:0.29, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGATACACTTGAG
Found at i:401539 original size:33 final size:33
Alignment explanation
Indices: 401497--401562 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
401487 AAATAGATGG
*
401497 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
* *
401530 AGTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
401563 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:403376 original size:19 final size:19
Alignment explanation
Indices: 403352--403400 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
403342 AATGTAGGGT
403352 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
403371 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
403390 TAATTTTGTAT
1 TAATTTTGTAT
403401 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:404196 original size:202 final size:200
Alignment explanation
Indices: 403513--404278 Score: 1338
Period size: 200 Copynumber: 3.8 Consensus size: 200
403503 AATTTACAAT
403513 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCA-AAAGCA
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAA-CA
*
403577 TCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
65 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
403642 TATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
130 TATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCA
403707 GAATGA
195 GAATGA
*
403713 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
*
403778 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* *
403843 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAT
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
403908 AATGA
196 AATGA
* *
403913 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
403978 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
*
404043 ATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTTAGTTTGTGTCGATATTTTTGGTCC
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACAC--TTTTTTAGTTTGTGTCGATATTTTTGGTCC
404108 AGAATGA
194 AGAATGA
* *
404115 ATGGAAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
* * *
404180 CGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATATCGGTTTT
66 CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
* * *
404245 ATGAGAGAATTGGTATATAAT-ATGTATCGACACT
131 ATGAGAGAATAGGTCTA-AATAATGTGTCGACACT
404279 GTTTAATGTT
Statistics
Matches: 541, Mismatches: 21, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
200 352 0.65
201 3 0.01
202 183 0.34
203 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (200 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACAT
CGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGA
Found at i:404277 original size:402 final size:400
Alignment explanation
Indices: 403513--404278 Score: 1356
Period size: 402 Copynumber: 1.9 Consensus size: 400
403503 AATTTACAAT
403513 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAGCAT
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAGCAT
403578 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
66 CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
403643 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
131 ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
* **
403708 AATGAATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
196 AATGAATGGAAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
*
403773 AACATCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCG
261 AACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAATATACCG
* *
403838 GTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
326 GTTTTATGAGAGAATAGGTATAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
403903 TCCATAATGA
391 TCCATAATGA
* *
403913 ATGGCAAACAGGGTGCAACCGTAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCGTAAA-CA
1 ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC-AAAAGCA
*
403977 TCGAAACCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
65 TCGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTT
*
404042 TATGAGATAATAGGTCTAAATAATGTGTCGACACTTTTTTTTAGTTTGTGTCGATATTTTTGGTC
130 TATGAGAGAATAGGTCTAAATAATGTGTCGACAC--TTTTTTAGTTTGTGTCGATATTTTTGGTC
404107 CAGAATGAATGGAAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC
193 CAGAATGAATGGAAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC
* *
404172 ATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATA
258 ATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAATATA
* *
404237 TCGGTTTTATGAGAGAATTGGTATATAAT-ATGTATCGACACT
323 CCGGTTTTATGAGAGAATAGGTATA-AATAATGTATCGACACT
404279 GTTTAATGTT
Statistics
Matches: 348, Mismatches: 14, Indels: 6
0.95 0.04 0.02
Matches are distributed among these distances:
400 155 0.45
401 3 0.01
402 187 0.54
403 3 0.01
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (400 bp):
ATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAGCAT
CGAAAACCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTT
ATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAG
AATGAATGGAAAACAGGGTGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATA
AACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTACAAATATACCG
GTTTTATGAGAGAATAGGTATAAATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGG
TCCATAATGA
Found at i:405785 original size:6 final size:6
Alignment explanation
Indices: 405774--405885 Score: 80
Period size: 6 Copynumber: 18.7 Consensus size: 6
405764 CAAGCGGTCA
** * * * * *
405774 ATGAAG ATGAAG CCGACG ATGAAG ATGACG ATGAAG ATGACG ACGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * * *
405822 ATGATG ATGAAG CTGACG ATGAAG ATGACG ATGAAG ATGATG ACGATG
1 ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* *
405870 ATGATG ATGATG ATGA
1 ATGAAG ATGAAG ATGA
405886 TCCAAACAAG
Statistics
Matches: 84, Mismatches: 22, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 84 1.00
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.20
Consensus pattern (6 bp):
ATGAAG
Found at i:405824 original size:3 final size:3
Alignment explanation
Indices: 405791--405886 Score: 84
Period size: 3 Copynumber: 32.0 Consensus size: 3
405781 TGAAGCCGAC
* * * * * * * *
405791 GAT GAA GAT GAC GAT GAA GAT GAC GAC GAT GAT GAT GAT GAA GCT GAC
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* * * *
405839 GAT GAA GAT GAC GAT GAA GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
405887 CCAAACAAGT
Statistics
Matches: 71, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.38, C:0.07, G:0.33, T:0.22
Consensus pattern (3 bp):
GAT
Found at i:405840 original size:48 final size:48
Alignment explanation
Indices: 405774--405879 Score: 185
Period size: 48 Copynumber: 2.2 Consensus size: 48
405764 CAAGCGGTCA
*
405774 ATGAAGATGAAGCCGACGATGAAGATGACGATGAAGATGACGACGATG
1 ATGATGATGAAGCCGACGATGAAGATGACGATGAAGATGACGACGATG
* *
405822 ATGATGATGAAGCTGACGATGAAGATGACGATGAAGATGATGACGATG
1 ATGATGATGAAGCCGACGATGAAGATGACGATGAAGATGACGACGATG
405870 ATGATGATGA
1 ATGATGATGA
405880 TGATGATCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.39, C:0.09, G:0.33, T:0.19
Consensus pattern (48 bp):
ATGATGATGAAGCCGACGATGAAGATGACGATGAAGATGACGACGATG
Found at i:405886 original size:12 final size:12
Alignment explanation
Indices: 405774--405885 Score: 116
Period size: 12 Copynumber: 9.3 Consensus size: 12
405764 CAAGCGGTCA
*
405774 ATGAAGATGAAG
1 ATGACGATGAAG
**
405786 CCGACGATGAAG
1 ATGACGATGAAG
405798 ATGACGATGAAG
1 ATGACGATGAAG
* *
405810 ATGACGACGATG
1 ATGACGATGAAG
*
405822 ATGATGATGAAG
1 ATGACGATGAAG
*
405834 CTGACGATGAAG
1 ATGACGATGAAG
405846 ATGACGATGAAG
1 ATGACGATGAAG
* * *
405858 ATGATGACGATG
1 ATGACGATGAAG
* *
405870 ATGATGATGATG
1 ATGACGATGAAG
405882 ATGA
1 ATGA
405886 TCCAAACAAG
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 83 1.00
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.20
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:407404 original size:183 final size:183
Alignment explanation
Indices: 407096--407483 Score: 731
Period size: 183 Copynumber: 2.1 Consensus size: 183
407086 CAAAGTTTTC
* * *
407096 ACACTTTTTAATATTGTGTCTGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTAATTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
407161 CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATAT
407226 AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
407279 ACACTTTTTAATATTGTGTCGGTAATTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTAATTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
407344 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATAT
*
407409 AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTGTACAACCTATATCG
131 AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
407462 ACACTTTTTAATATTGTGTCGG
1 ACACTTTTTAATATTGTGTCGG
407484 CACTTTACAA
Statistics
Matches: 200, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
183 200 1.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTAATTTATCTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:410313 original size:23 final size:23
Alignment explanation
Indices: 410282--410354 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
410272 ATAGGTAAAA
*
410282 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
410305 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
410328 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
410351 ATAT
1 ATAT
410355 TGTAAAGTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.34, C:0.05, G:0.22, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:410750 original size:23 final size:23
Alignment explanation
Indices: 410719--410791 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
410709 ATAGGTAAAA
* *
410719 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
* *
410742 ATATAATGTAATATGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
410765 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
410788 ATAT
1 ATAT
410792 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:410838 original size:437 final size:438
Alignment explanation
Indices: 410020--410901 Score: 1660
Period size: 437 Copynumber: 2.0 Consensus size: 438
410010 ATATTATTAT
410020 TAAATTAAAAACAATAAACATATAAATTACATATTTATTATTATATTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATAAATTACATATTTATTATTATATTTGGTTAATATTGTTAAAT
*
410085 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
410150 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
410215 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
*
410280 AAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTA
261 AAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTA
* *
410345 GTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTTTTCACTGTGGAAAA
326 GTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAA
* *
410410 CATTAATTTAAGGTTATCTTTTTAGTGAGTTTTAAGATATTAATTTAG
391 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAG
* *
410458 TAAATTAAAAACAATAAACATATATATTACATATTTATTATTATCTTTGGTTAATATTGTTAAAT
1 TAAATTAAAAACAATAAACATATAAATTACATATTTATTATTATATTTGGTTAATATTGTTAAAT
410523 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
66 TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
410588 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATT-AAAAAAATTGAAACATAAATTAC
131 TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
410652 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
196 ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
*
410717 AAATATGATGTAATAGGTAGCACTTATATAATGTAATATGTAGCGTTTATATAATGTAATAGGTA
261 AAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTA
410782 GTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAA
326 GTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAA
*
410847 CATTAATTTAAGGTTATCTTTTGATTGAGTTTTAAGATATCAATTTAG
391 CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAG
410895 T-AATTAA
1 TAAATTAA
410902 TGTATCTAAT
Statistics
Matches: 434, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
436 6 0.01
437 260 0.60
438 168 0.39
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.39
Consensus pattern (438 bp):
TAAATTAAAAACAATAAACATATAAATTACATATTTATTATTATATTTGGTTAATATTGTTAAAT
TTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATAAAAT
TATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTAC
ATAACTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAA
AAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTA
GTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGGAAAA
CATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAG
Found at i:411295 original size:23 final size:23
Alignment explanation
Indices: 411266--411313 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
411256 AAATAGGTCA
*
411266 ATATAAGCGCTACCTATTATATT
1 ATATAAGCGCTACCTAGTATATT
*
411289 ATATAAGCGCTACCTAGTATGTT
1 ATATAAGCGCTACCTAGTATATT
411312 AT
1 AT
411314 TGTACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAGTATATT
Found at i:419563 original size:41 final size:41
Alignment explanation
Indices: 419518--420076 Score: 416
Period size: 41 Copynumber: 13.6 Consensus size: 41
419508 CTTGATTTAA
* * *
419518 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATG
1 ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
*
419559 ATTGAATTGAATCGAATTG-TGAATTATTGCACT-CTACCATG
1 ATTGAATTGAATCGAA-TGATGAATTATTGCA-TGCTGCCATG
* * * * * * *
419600 A-TCAAATCAATTTGAATGTTGAATTATTGTATGATGCCATG
1 ATTGAATTGAA-TCGAATGATGAATTATTGCATGCTGCCATG
* ** ** *
419641 ATTGAATTGAATCGAATGATGAACTATTGCATATTGTAAAG
1 ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
* * * * *** *
419682 ATTCAACTGAATTGAATTATGAATTATTATGTGCTACCATG
1 ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
* * * * *
419723 ATTGAA-TCAAGTTGAATGTTGAATTATTGTATACTGCCATG
1 ATTGAATTGAA-TCGAATGATGAATTATTGCATGCTGCCATG
* * * * *
419764 ATCGAATCGAATCGAATGATGAACTATTTCATGCTGTCATG
1 ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
*
419805 ATTGAATTGAATCGAATTG-TGAATTATTGCATGCTACCATG
1 ATTGAATTGAATCGAA-TGATGAATTATTGCATGCTGCCATG
* * * * * *
419846 ATCGAA-TCAAGTTGAATGTTGAATTATTGTATGATGCCATG
1 ATTGAATTGAA-TCGAATGATGAATTATTGCATGCTGCCATG
* * * **
419887 ATTGAATTGAATCGAATGGTGAACTATTGCATGTTTTCATG
1 ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
* * *
419928 ATTGAATTGAATCGAATTATGAATTATTTCATGCTACCATG
1 ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
* * * * * ** *
419969 ATCGAA-TAAAGTTGAATGTTAAATTATTATATGTTGCCATG
1 ATTGAATTGAA-TCGAATGATGAATTATTGCATGCTGCCATG
* * *
420010 ATTGAATTGAATC-AAGTGATGAATTATTGCATGTTGTCATT
1 ATTGAATTGAATCGAA-TGATGAATTATTGCATGCTGCCATG
*
420051 ATTGAATCGAATCGAATTG-TGAATTA
1 ATTGAATTGAATCGAA-TGATGAATTA
420077 GTAACTGGAT
Statistics
Matches: 399, Mismatches: 103, Indels: 32
0.75 0.19 0.06
Matches are distributed among these distances:
40 22 0.06
41 354 0.89
42 23 0.06
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (41 bp):
ATTGAATTGAATCGAATGATGAATTATTGCATGCTGCCATG
Found at i:420108 original size:123 final size:122
Alignment explanation
Indices: 419518--420076 Score: 773
Period size: 123 Copynumber: 4.5 Consensus size: 122
419508 CTTGATTTAA
* *
419518 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTGTGAAT
1 ATTGAATTGAATCGAATGATGAACTATTGCATGTTGTCATGATTGAATTGAATCGAATTGTGAAT
* *
419583 TATTGCACT-CTACCATGATCAAATCAATTTGAATGTTGAATTATTGTATGATGCCATG
66 TATT--ACTGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGATGCCATG
* * * * * * *
419641 ATTGAATTGAATCGAATGATGAACTATTGCATATTGTAAAGATTCAACTGAATTGAATTATGAAT
1 ATTGAATTGAATCGAATGATGAACTATTGCATGTTGTCATGATTGAATTGAATCGAATTGTGAAT
* *
419706 TATTATGTGCTACCATGATTGAATCAAGTTGAATGTTGAATTATTGTAT-ACTGCCATG
66 TATTA-CTGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGA-TGCCATG
* * * *
419764 ATCGAATCGAATCGAATGATGAACTATTTCATGCTGTCATGATTGAATTGAATCGAATTGTGAAT
1 ATTGAATTGAATCGAATGATGAACTATTGCATGTTGTCATGATTGAATTGAATCGAATTGTGAAT
*
419829 TATTGCATGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGATGCCATG
66 TATTAC-TGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGATGCCATG
* * *
419887 ATTGAATTGAATCGAATGGTGAACTATTGCATGTTTTCATGATTGAATTGAATCGAATTATGAAT
1 ATTGAATTGAATCGAATGATGAACTATTGCATGTTGTCATGATTGAATTGAATCGAATTGTGAAT
* * * * *
419952 TATTTCATGCTACCATGATCGAATAAAGTTGAATGTTAAATTATTATATGTTGCCATG
66 TATTAC-TGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGATGCCATG
* * *
420010 ATTGAATTGAATC-AAGTGATGAATTATTGCATGTTGTCATTATTGAATCGAATCGAATTGTGAA
1 ATTGAATTGAATCGAA-TGATGAACTATTGCATGTTGTCATGATTGAATTGAATCGAATTGTGAA
420074 TTA
65 TTA
420077 GTAACTGGAT
Statistics
Matches: 385, Mismatches: 45, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
121 1 0.00
122 4 0.01
123 379 0.98
124 1 0.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (122 bp):
ATTGAATTGAATCGAATGATGAACTATTGCATGTTGTCATGATTGAATTGAATCGAATTGTGAAT
TATTACTGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGATGCCATG
Found at i:424387 original size:19 final size:19
Alignment explanation
Indices: 424365--424413 Score: 54
Period size: 14 Copynumber: 2.8 Consensus size: 19
424355 AAACAAAGTT
424365 GGATTAATTGAATTGCATA
1 GGATTAATTGAATTGCATA
424384 GGA-T-A---AATTGCATA
1 GGATTAATTGAATTGCATA
*
424398 GGATAAATTGAATTGC
1 GGATTAATTGAATTGC
424414 CTAAGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 10
0.69 0.03 0.29
Matches are distributed among these distances:
14 12 0.50
16 1 0.04
17 1 0.04
18 1 0.04
19 9 0.38
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (19 bp):
GGATTAATTGAATTGCATA
Found at i:424394 original size:14 final size:14
Alignment explanation
Indices: 424375--424407 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
424365 GGATTAATTG
424375 AATTGCATAGGATA
1 AATTGCATAGGATA
424389 AATTGCATAGGATA
1 AATTGCATAGGATA
424403 AATTG
1 AATTG
424408 AATTGCCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.30
Consensus pattern (14 bp):
AATTGCATAGGATA
Found at i:426130 original size:20 final size:20
Alignment explanation
Indices: 426105--426150 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
426095 TGGAACTTAA
426105 AATTAAGGGAAAGAAAGATT
1 AATTAAGGGAAAGAAAGATT
426125 AATTAAGGGAAAGAAAGATT
1 AATTAAGGGAAAGAAAGATT
426145 AATTAA
1 AATTAA
426151 AGGCTATAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (20 bp):
AATTAAGGGAAAGAAAGATT
Found at i:426287 original size:41 final size:41
Alignment explanation
Indices: 426218--426768 Score: 412
Period size: 41 Copynumber: 13.6 Consensus size: 41
426208 CTTGATTTAA
* * *
426218 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* * * *
426259 ATTTAATTGAATCAAATTATGAATTATTGCATGCTGTCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* * * ** *
426300 ATCGAA-TCAAGTTGAATAT-TGAATTATTTTATGTTGCCATG
1 ATTGAATTGAA-TCGAAT-TGTGAATTATTGCATGCTGCCATG
* * * ** *
426341 ATTGATTTGAATCGAATGGTGAACTATTGCATGCTATCACG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* * *
426382 ATTGAATTGAATCGAATTTTGAATTATTGGATGCTACCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* ** * * *
426423 ATCGAATCAAATTGAA-TGTTGAATTATTGTATGCTTCCATG
1 ATTGAATTGAATCGAATTG-TGAATTATTGCATGCTGCCATG
* * * * *
426464 ATTGAAATGAATCGAA-TGATGAACTATAGCATACTACCATG
1 ATTGAATTGAATCGAATTG-TGAATTATTGCATGCTGCCATG
** *
426505 ATTGAATTGAATCGAATAATGAATTATTGCATGCTACCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* *
426546 A-T-CA---AATC-AA--GTGAATTATTGTATGCTGCCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* * * * *
426579 ATTGAATTGAATCGAATGGTGAACTACTGCATGTTGTCATG
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
* * * *
426620 ATTGAATTGAATTGAATTGTGAATTATTACATGTTAG-CATT
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCT-GCCATG
* * * *
426661 ATCGAA-TCAAGTTGAA-TGTTGAATTATTGTATGCTGCCATG
1 ATTGAATTGAA-TCGAATTG-TGAATTATTGCATGCTGCCATG
* * * * * *
426702 ATTGAATTGAAACGAATGGTGAACTATTGCATGTTGTCATT
1 ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
*
426743 ATTGAATTGAATTGAATTGTGAATTA
1 ATTGAATTGAATCGAATTGTGAATTA
426769 ATACCTGCTG
Statistics
Matches: 397, Mismatches: 93, Indels: 40
0.75 0.18 0.08
Matches are distributed among these distances:
33 21 0.05
34 1 0.00
35 3 0.01
36 4 0.01
38 4 0.01
39 3 0.01
40 11 0.03
41 341 0.86
42 9 0.02
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (41 bp):
ATTGAATTGAATCGAATTGTGAATTATTGCATGCTGCCATG
Found at i:426369 original size:123 final size:123
Alignment explanation
Indices: 426218--426768 Score: 731
Period size: 123 Copynumber: 4.5 Consensus size: 123
426208 CTTGATTTAA
* *
426218 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTTAATTGAATCAAATTATGAAT
1 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTATGAAT
** * * *
426283 TATTGCATGCTGTCATGATCGAATCAAGTTGAATATTGAATTATTTTATGTTGCCATG
66 TATTGCATGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGCTGCCATG
* * * *
426341 ATTGATTTGAATCGAATGGTGAACTATTGCATGCTATCACGATTGAATTGAATCGAATTTTGAAT
1 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTATGAAT
* * *
426406 TATTGGATGCTACCATGATCGAATCAAATTGAATGTTGAATTATTGTATGCTTCCATG
66 TATTGCATGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGCTGCCATG
* * * * ** *
426464 ATTGAAATGAATCGAATGATGAACTATAGCATACTACCATGATTGAATTGAATCGAATAATGAAT
1 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTATGAAT
*
426529 TATTGCATGCTACCATGATC--A--AA--TCAA-G-TGAATTATTGTATGCTGCCATG
66 TATTGCATGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGCTGCCATG
* * * *
426579 ATTGAATTGAATCGAATGGTGAACTACTGCATGTTGTCATGATTGAATTGAATTGAATTGTGAAT
1 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTATGAAT
* * * *
426644 TATTACATGTTAGCATTATCGAATCAAGTTGAATGTTGAATTATTGTATGCTGCCATG
66 TATTGCATGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGCTGCCATG
* * * * *
426702 ATTGAATTGAAACGAATGGTGAACTATTGCATGTTGTCATTATTGAATTGAATTGAATTGTGAAT
1 ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTATGAAT
426767 TA
66 TA
426769 ATACCTGCTG
Statistics
Matches: 375, Mismatches: 45, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
115 91 0.24
116 1 0.00
117 4 0.01
119 4 0.01
121 4 0.01
122 1 0.00
123 270 0.72
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (123 bp):
ATTGAATTGAATCGAATGGTGAACTATTGCATGCTGTCATGATTGAATTGAATCGAATTATGAAT
TATTGCATGCTACCATGATCGAATCAAGTTGAATGTTGAATTATTGTATGCTGCCATG
Found at i:427419 original size:92 final size:92
Alignment explanation
Indices: 427262--427446 Score: 228
Period size: 92 Copynumber: 2.0 Consensus size: 92
427252 GTTTCCTTCT
* * * *
427262 TGTTCGAATAGAGGAATGAATGATATACATATTGAATTGTTTAATCTTATTGCCATAAAGATTGC
1 TGTTCAAATAGAGGAAAGAATGATATACATATTGAATTGCTTAATCGTATTGCCATAAAGATTGC
* ** *
427327 ATTAATATGTATGTAATGAAATGTTCC
66 ATGAATACATATGCAATGAAATGTTCC
* * * * *
427354 TGTTCAAATAGAGGAAAGAATGTTATACCTATTGAATTGCTTAATCCGT-TTGTCTTATAGATTG
1 TGTTCAAATAGAGGAAAGAATGATATACATATTGAATTGCTTAAT-CGTATTGCCATAAAGATTG
*
427418 CATGAATACATATGCAGTGAAATGTTCC
65 CATGAATACATATGCAATGAAATGTTCC
427446 T
1 T
427447 TTCGAGTGGA
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
92 76 0.97
93 2 0.03
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (92 bp):
TGTTCAAATAGAGGAAAGAATGATATACATATTGAATTGCTTAATCGTATTGCCATAAAGATTGC
ATGAATACATATGCAATGAAATGTTCC
Found at i:429958 original size:143 final size:143
Alignment explanation
Indices: 429699--430314 Score: 722
Period size: 143 Copynumber: 4.3 Consensus size: 143
429689 TAGTTCAACA
* * ** * * *
429699 AATTCATATCATAAAAATATGCATTTCTAAAAGGCAAAATAATGCACCATGGTAGAAACTTTTCA
1 AATTCATATAAGAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGTAACTTTTCA
* * *
429764 ATGCCCAATTACTCATCTAT-AGCAACCTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTC
66 GTGCCCAATTACTCATCT-TCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTC
*
429828 AGTCG-TGATATATC
130 AAT-GTTGATATATC
* * * * *
429842 AATTCATATAAGAAAAATGTGCATTTTTCATAGGCAAAATAATGCGCCATTCTAGTAACTTTTCA
1 AATTCATATAAGAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGTAACTTTTCA
* * *
429907 GTGCCCAATTTA-TCATCTTCAACAACTTTTCATTGATATGTCAACTTATTTCAGAAAACTTTTC
66 GTGCCCAA-TTACTCATCTTCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTC
*
429971 AATGTTGATACATC
130 AATGTTGATATATC
* * *
429985 ACTTCATA-ACATAAAAACGTGCATTTATCAAAGGCAAAATAATGCACCATGCTA-TAAACTTTT
1 AATTCATATA-AGAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGT-AACTTTT
* *
430048 CAGTGCCCCATTACTCATATTCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTT
64 CAGTGCCCAATTACTCATCTTCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTT
*
430113 TAATAG-TGATATATC
129 CAAT-GTTGATATATC
* * * * * * ** *
430128 AATGCATATAAGAAAAACGTGCATTTTTCATAGGCAAAATAATACACCATTCCAACAACTTTTTA
1 AATTCATATAAGAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGTAACTTTTCA
* ** * * *
430193 GTGCCCAATTACTCATCTTTAGTAACTTTTCAGTGATATGTCAACTCATTTTAGAAAACTTTTTA
66 GTGCCCAATTACTCATCTTCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCA
*
430258 GTGTTGATATATC
131 ATGTTGATATATC
* * **
430271 AGTTCATATAAGAAAAACGTGTATTTCTCAACTGCAAAATAATG
1 AATTCATATAAGAAAAACGTGCATTTCTCAAAGGCAAAATAATG
430315 TACATGGCAA
Statistics
Matches: 405, Mismatches: 58, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
142 8 0.02
143 392 0.97
144 5 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (143 bp):
AATTCATATAAGAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGTAACTTTTCA
GTGCCCAATTACTCATCTTCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCA
ATGTTGATATATC
Found at i:430222 original size:286 final size:286
Alignment explanation
Indices: 429701--430314 Score: 847
Period size: 286 Copynumber: 2.1 Consensus size: 286
429691 GTTCAACAAA
* ** * *
429701 TTCATATCATAAAAATATGCATTTCTAAAAGGCAAAATAATGCACCATGGTAGAAACTTTTCAAT
1 TTCATAACATAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGAAACTTTTCAAT
* * *
429766 GCCCAATTACTCATCTATAGCAACCTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAGT
66 GCCCAATTACTCATATATAACAACCTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAAT
* * * * * *
429831 CGTGATATATCAATTCATATAAGAAAAATGTGCATTTTTCATAGGCAAAATAATGCGCCATTCTA
131 AGTGATATATCAATGCATATAAGAAAAACGTGCATTTTTCATAGGCAAAATAATACACCATTCCA
** * *
429896 GTAACTTTTCAGTGCCCAATTTATCATCTTCAACAACTTTTCATTGATATGTCAACTTATTTCAG
196 ACAACTTTTCAGTGCCCAATTTATCATCTTCAACAACTTTTCAGTGATATGTCAACTCATTTCAG
429961 AAAACTTTTCAATGTTGATACATCAC
261 AAAACTTTTCAATGTTGATACATCAC
* * *
429987 TTCATAACATAAAAACGTGCATTTATCAAAGGCAAAATAATGCACCATGCTATAAACTTTTCAGT
1 TTCATAACATAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGAAACTTTTCAAT
* * *
430052 GCCCCATTACTCATAT-TCAACAACTTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTTAA
66 GCCCAATTACTCATATAT-AACAACCTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAA
430116 TAGTGATATATCAATGCATATAAGAAAAACGTGCATTTTTCATAGGCAAAATAATACACCATTCC
130 TAGTGATATATCAATGCATATAAGAAAAACGTGCATTTTTCATAGGCAAAATAATACACCATTCC
* * ** *
430181 AACAACTTTTTAGTGCCCAA-TTACTCATCTTTAGTAACTTTTCAGTGATATGTCAACTCATTTT
195 AACAACTTTTCAGTGCCCAATTTA-TCATCTTCAACAACTTTTCAGTGATATGTCAACTCATTTC
* * * *
430245 AGAAAACTTTTTAGTGTTGATATATCAG
259 AGAAAACTTTTCAATGTTGATACATCAC
* * **
430273 TTCATATA-AGAAAAACGTGTATTTCTCAACTGCAAAATAATG
1 TTCATA-ACATAAAAACGTGCATTTCTCAAAGGCAAAATAATG
430315 TACATGGCAA
Statistics
Matches: 287, Mismatches: 38, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
285 4 0.01
286 282 0.98
287 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (286 bp):
TTCATAACATAAAAACGTGCATTTCTCAAAGGCAAAATAATGCACCATGCTAGAAACTTTTCAAT
GCCCAATTACTCATATATAACAACCTTTCAGTGATATATCAACTCATTTCAGAAAACTTTTCAAT
AGTGATATATCAATGCATATAAGAAAAACGTGCATTTTTCATAGGCAAAATAATACACCATTCCA
ACAACTTTTCAGTGCCCAATTTATCATCTTCAACAACTTTTCAGTGATATGTCAACTCATTTCAG
AAAACTTTTCAATGTTGATACATCAC
Found at i:440068 original size:30 final size:30
Alignment explanation
Indices: 440026--440089 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
440016 TAGTTGACAT
440026 AAAT-ACTCTAGGTACCTATTTTGACCAAA
1 AAATAACTCTAGGTACCTATTTTGACCAAA
* ** *
440055 AAATAACTTTAGGTATTTATTTTGACCAAG
1 AAATAACTCTAGGTACCTATTTTGACCAAA
440085 AAATA
1 AAATA
440090 GGCTTTCGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (30 bp):
AAATAACTCTAGGTACCTATTTTGACCAAA
Found at i:441351 original size:22 final size:23
Alignment explanation
Indices: 441321--441368 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
441311 TAATTGAGAG
*
441321 AGAATGAAAGTAGAAAAAGATAA
1 AGAATGAAAGTAGAAAAAGAAAA
* *
441344 AGAA-GAAATTAGAAGAAGAAAA
1 AGAATGAAAGTAGAAAAAGAAAA
441366 AGA
1 AGA
441369 CACAAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.67, C:0.00, G:0.23, T:0.10
Consensus pattern (23 bp):
AGAATGAAAGTAGAAAAAGAAAA
Found at i:441388 original size:13 final size:13
Alignment explanation
Indices: 441343--441389 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
441333 GAAAAAGATA
**
441343 AAGAAGAAATTAG
1 AAGAAGAAAAAAG
441356 AAGAAG-AAAAAG
1 AAGAAGAAAAAAG
*
441368 ACACAAGAAAAAAG
1 A-AGAAGAAAAAAG
441382 AAGAAGAA
1 AAGAAGAA
441390 GAAGAGTTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 5 0.18
13 16 0.57
14 7 0.25
ACGTcount: A:0.70, C:0.04, G:0.21, T:0.04
Consensus pattern (13 bp):
AAGAAGAAAAAAG
Found at i:452110 original size:45 final size:42
Alignment explanation
Indices: 452046--452268 Score: 163
Period size: 45 Copynumber: 5.5 Consensus size: 42
452036 TTAAAAGAAT
*
452046 AATGCATATGAGTGCATTATTGGCATGTAAGGATGCCATAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGTAAGGATGCCA-AG-T-A
* * *
452091 AATGCATATGGGTGCATTATCGACA--TAA--AAG--AA-T-
1 AATGCATATGGGTGCATTATTGGCATGTAAGGATGCCAAGTA
* *
452125 AATGCATATGGGGGCATTATTGGCATGAAAGGATGCCATAGCTAA
1 AATGCATATGGGTGCATTATTGGCATGTAAGGATGCCA-AG-T-A
* * *
452170 AATGCATATGGGTGCATTATCGACA--TAA--AAG--AA-T-
1 AATGCATATGGGTGCATTATTGGCATGTAAGGATGCCAAGTA
*
452204 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGTAAGGATGCC-AAG-T-A
452249 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
452269 CAACATAAAT
Statistics
Matches: 138, Mismatches: 18, Indels: 44
0.69 0.09 0.22
Matches are distributed among these distances:
34 45 0.33
36 6 0.04
38 6 0.04
39 2 0.01
40 1 0.01
41 7 0.05
43 7 0.05
45 64 0.46
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.28
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGTAAGGATGCCAAGTA
Found at i:452129 original size:34 final size:34
Alignment explanation
Indices: 452091--452223 Score: 140
Period size: 34 Copynumber: 3.6 Consensus size: 34
452081 CCATAGTTGA
452091 AATGCATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGACATAAAAGAAT
* * *
452125 AATGCATATGGGGGCATTATTGGCATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGACAT-AAA--A-G--A-A--T
452168 AAAATGCATATGGGTGCATTATCGACATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGACATAAAAGAAT
452204 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
452224 TGGCATGAAA
Statistics
Matches: 82, Mismatches: 6, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
34 43 0.52
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.04
45 23 0.28
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGACATAAAAGAAT
Found at i:452173 original size:79 final size:79
Alignment explanation
Indices: 452037--452277 Score: 419
Period size: 79 Copynumber: 3.1 Consensus size: 79
452027 AACGAATTGT
* *
452037 TAAAAGAATAATGCATATGAGTGCATTATTGGCATGTAAGGATGCCATAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGG
452102 GTGCATTATCGACA
66 GTGCATTATCGACA
* * *
452116 TAAAAGAATAATGCATATGGGGGCATTATTGGCATGAAAGGATGCCATAGCTAAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGG
452181 GTGCATTATCGACA
66 GTGCATTATCGACA
*
452195 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGG
*
452260 GTGCATTATCAACA
66 GTGCATTATCGACA
452274 TAAA
1 TAAA
452278 TATGCTATAA
Statistics
Matches: 152, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 152 1.00
ACGTcount: A:0.37, C:0.12, G:0.24, T:0.27
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGTTGAAATGCATATGG
GTGCATTATCGACA
Found at i:458343 original size:20 final size:19
Alignment explanation
Indices: 458318--458370 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
458308 TGATTGAATC
*
458318 AGTATCGATACCAAAGGGGG
1 AGTATCGATACCAAA-GGGA
* *
458338 AGTATCAATACCGAAGGGA
1 AGTATCGATACCAAAGGGA
458357 AGGTATCGATACCA
1 A-GTATCGATACCA
458371 TTTTGAAACA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.38, C:0.17, G:0.28, T:0.17
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:458858 original size:45 final size:45
Alignment explanation
Indices: 458794--458937 Score: 175
Period size: 45 Copynumber: 3.4 Consensus size: 45
458784 TCATAAGAAT
* *
458794 AATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
*
458839 AATGCATATGGGTGCATTATCGACAT-AAA--A-G--A-A--T--
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
458873 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
*
458918 AATGCATATGGGTGTATTAT
1 AATGCATATGGGTGCATTAT
458938 CGGTATAAAA
Statistics
Matches: 83, Mismatches: 5, Indels: 22
0.75 0.05 0.20
Matches are distributed among these distances:
34 25 0.30
35 3 0.04
36 1 0.01
37 1 0.01
38 2 0.02
39 1 0.01
40 1 0.01
41 2 0.02
42 1 0.01
43 1 0.01
44 3 0.04
45 42 0.51
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
Found at i:458878 original size:34 final size:34
Alignment explanation
Indices: 458839--459055 Score: 139
Period size: 34 Copynumber: 5.8 Consensus size: 34
458829 CCATAGCTGA
*
458839 AATGCATATGGGTGCATTATCGACATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
458873 AATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G--A-A--T
* *
458916 GAAATGCATATGGGTGTATTATCGGTATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
458952 AATGCATAT-AGTGAATTATTGGCATGAAAGGATGCCAAAGTT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G---AA--T
*
458994 GAAATGCATATGGGTGCATTATCGGCATAAAAGAGT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
*
459030 AATGCATATGGGTGCATTATTGGCAT
1 AATGCATATGGGTGCATTATCGGCAT
459056 GAAATGATGC
Statistics
Matches: 146, Mismatches: 14, Indels: 46
0.71 0.07 0.22
Matches are distributed among these distances:
33 12 0.08
34 62 0.42
35 3 0.02
36 3 0.02
37 2 0.01
38 3 0.02
39 1 0.01
40 3 0.02
41 3 0.02
42 3 0.02
43 1 0.01
44 15 0.10
45 35 0.24
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.29
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:458919 original size:79 final size:79
Alignment explanation
Indices: 458788--459105 Score: 476
Period size: 79 Copynumber: 4.0 Consensus size: 79
458778 GAATGATCAT
* *
458788 AAGAATAATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
458853 CATTATCGACATAA
66 CATTATCGACATAA
* *
458867 AAGAATAATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
* **
458932 TATTATCGGTATAA
66 CATTATCGACATAA
* * *
458946 AAGAATAATGCATAT-AGTGAATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATGGGTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
*
459010 CATTATCGGCATAA
66 CATTATCGACATAA
* * * * *
459024 AAGAGTAATGCATATGGGTGCATTATTGGCATGAAATGATGCGAAAGTTGAAATGCATGTGGGTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
*
459089 CATTATCAACATAA
66 CATTATCGACATAA
459103 AAG
1 AAG
459106 TATGCTATAA
Statistics
Matches: 218, Mismatches: 20, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 70 0.32
79 148 0.68
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (79 bp):
AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
CATTATCGACATAA
Found at i:459095 original size:157 final size:158
Alignment explanation
Indices: 458788--459095 Score: 492
Period size: 157 Copynumber: 2.0 Consensus size: 158
458778 GAATGATCAT
* * *
458788 AAGAATAATGCATATGGATGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
1 AAGAATAATGCATATAGATGAATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
*
458853 CATTATCGACATAAAAGAATAATGCATATGGGTGCATTATTGACATGAAAGGATGCCATAGCTGA
66 CATTATCGACATAAAAGAATAATGCATATGGGTGCATTATTGACATGAAAGGATGCCAAAGCTGA
*
458918 AATGCATATGGGTGTATTATCGGTATAA
131 AATGCATATGGGTGCATTATCGGTATAA
*
458946 AAGAATAATGCATATAG-TGAATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATGGGTG
1 AAGAATAATGCATATAGATGAATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
* * * * * *
459010 CATTATCGGCATAAAAGAGTAATGCATATGGGTGCATTATTGGCATGAAATGATGCGAAAGTTGA
66 CATTATCGACATAAAAGAATAATGCATATGGGTGCATTATTGACATGAAAGGATGCCAAAGCTGA
*
459075 AATGCATGTGGGTGCATTATC
131 AATGCATATGGGTGCATTATC
459096 AACATAAAAG
Statistics
Matches: 137, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
157 121 0.88
158 16 0.12
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.28
Consensus pattern (158 bp):
AAGAATAATGCATATAGATGAATTATTGGCATGAAAGGATGCCAAAGCTGAAATGCATATGGGTG
CATTATCGACATAAAAGAATAATGCATATGGGTGCATTATTGACATGAAAGGATGCCAAAGCTGA
AATGCATATGGGTGCATTATCGGTATAA
Found at i:471435 original size:82 final size:81
Alignment explanation
Indices: 471281--471442 Score: 200
Period size: 82 Copynumber: 2.0 Consensus size: 81
471271 TGACCACTTT
* * * ** *
471281 GGTATCGATACTCACCTGAGTATCGATACCAAAATTAGCTTCGATGTTTTGAAAAATAACTTGGT
1 GGTATCGATACTCACCTGAGTATCAATACCAAAATTAGCTTCAATGTTTTCAAAAATAACTCAGC
471346 ATCGATATTCTACCCTG
66 ATCGATATT-TACCCTG
* * **
471363 GGTATCGATACTC-CCATGAGTATCAATACCAAATTTGGCTTCAATGTTTTCAAAAATGCCTCAG
1 GGTATCGATACTCACC-TGAGTATCAATACCAAAATTAGCTTCAATGTTTTCAAAAATAACTCAG
*
471427 CATTGATATTTACCCT
65 CATCGATATTTACCCT
471443 CTCAATATCA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
81 8 0.12
82 60 0.88
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (81 bp):
GGTATCGATACTCACCTGAGTATCAATACCAAAATTAGCTTCAATGTTTTCAAAAATAACTCAGC
ATCGATATTTACCCTG
Found at i:474892 original size:78 final size:77
Alignment explanation
Indices: 474800--475048 Score: 247
Period size: 78 Copynumber: 3.2 Consensus size: 77
474790 TGTGCCAAAG
* * * *
474800 AATGTCATGGTTCACTAAGAAATAGATTGCGATATGGAATGTTAATATTTTTATTAAATAAAATG
1 AATGTCATGATTCACTAAGAAATAGGTTGCTATATGGAATGTTAATATTTTTATT-AATAAAATA
474865 GGTTGGCCCTAAA
65 GGTTGGCCCTAAA
* *
474878 AATGACATGATTCACTAA-AATATAGGTTG-TAGTATGGAATATTAATATTTTTATTAATAAAAT
1 AATGTCATGATTCACTAAGAA-ATAGGTTGCTA-TATGGAATGTTAATATTTTTATTAATAAAAT
*
474941 AGGTTAAG-CCT-AA
64 AGGTT-GGCCCTAAA
* * * *
474954 AATGTTATGGTTCACTAAGAAAGTAGGTTACGATCTATAATGTAATGTTAATATTTTTTTTAATA
1 AATGTCATGATTCACTAAGAAA-TAGGTT--G--CTAT-ATGGAATGTTAATATTTTTATTAATA
* *
475019 AAATTGGTTGCGCCC-AAG
60 AAATAGGTTG-GCCCTAAA
475037 AATGTCATGATT
1 AATGTCATGATT
475049 TTGAATATAA
Statistics
Matches: 139, Mismatches: 18, Indels: 23
0.77 0.10 0.13
Matches are distributed among these distances:
76 18 0.13
77 26 0.19
78 46 0.33
79 1 0.01
81 1 0.01
82 34 0.24
83 13 0.09
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.37
Consensus pattern (77 bp):
AATGTCATGATTCACTAAGAAATAGGTTGCTATATGGAATGTTAATATTTTTATTAATAAAATAG
GTTGGCCCTAAA
Found at i:475311 original size:151 final size:150
Alignment explanation
Indices: 475010--475396 Score: 497
Period size: 151 Copynumber: 2.5 Consensus size: 150
475000 GTTAATATTT
* * * *
475010 TTTTTAATAAAAT-TGGTTGCGCCCAAGAATGTCATGATTTTGAATATAACTAAGTTGTGATATG
1 TTTTTAATAAAATAT-GTTGCACCCAAGAATGTCATGATTTTGAATAAAAATAGGTTGTGATATG
* * * * *
475074 TTATATTAATATTTTTAATAAAATAGGTAGCGCCCAAGAATATCATGATTTTGAATAGAAATAGG
65 TTATATTAATATTTTTAACAAAATAGATAGCGCCCAAGAAAACCATGATTTTGAATAGAAATAAG
475139 TTGCGATATGTTATGTTAATA
130 TTGCGATATGTTATGTTAATA
* * *
475160 TTTTTAATAAAATATGTTACACCCAAGAATATCATGTTTTTGAATAAAAATAGGTTGTGATATGT
1 TTTTTAATAAAATATGTTGCACCCAAGAATGTCATGATTTTGAATAAAAATAGGTTGTGATATGT
* * *
475225 TATGTTAATATTTTTTAACAAAATAGATTGCGCCCAAGAAAACCATGGTTTTGAATAGAAATAAG
66 TATATTAATA-TTTTTAACAAAATAGATAGCGCCCAAGAAAACCATGATTTTGAATAGAAATAAG
**
475290 TTGTTATATGTTATGTTAATA
130 TTGCGATATGTTATGTTAATA
* * * *
475311 TTTTCATCAGTAAAATAGGTTGCACCCAAGAATGTCATGGTTTTGAATAGAAATAGGTTGTGATA
1 TTTT--T-AATAAAATATGTTGCACCCAAGAATGTCATGATTTTGAATAAAAATAGGTTGTGATA
* * *
475376 TATTATTATCAATACTTTTAA
63 TGTTA-TATTAATATTTTTAA
475397 ATATAGAAAT
Statistics
Matches: 204, Mismatches: 27, Indels: 8
0.85 0.11 0.03
Matches are distributed among these distances:
150 65 0.32
151 71 0.35
153 1 0.00
154 61 0.30
155 6 0.03
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.39
Consensus pattern (150 bp):
TTTTTAATAAAATATGTTGCACCCAAGAATGTCATGATTTTGAATAAAAATAGGTTGTGATATGT
TATATTAATATTTTTAACAAAATAGATAGCGCCCAAGAAAACCATGATTTTGAATAGAAATAAGT
TGCGATATGTTATGTTAATA
Found at i:475360 original size:78 final size:75
Alignment explanation
Indices: 475010--475381 Score: 483
Period size: 75 Copynumber: 4.9 Consensus size: 75
475000 GTTAATATTT
* * * * *
475010 TTTTTAATAAAATTGGTTGCGCCCAAGAATGTCATGATTTTGAATATAACTAAGTTGTGATATGT
1 TTTTTAATAAAATAGGTTGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGTGATATGT
*
475075 TATATTAATA
66 TATGTTAATA
* *
475085 TTTTTAATAAAATAGGTAGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGCGATATGT
1 TTTTTAATAAAATAGGTTGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGTGATATGT
475150 TATGTTAATA
66 TATGTTAATA
* * * * *
475160 TTTTTAATAAAATATGTTACACCCAAGAATATCATGTTTTTGAATAAAAATAGGTTGTGATATGT
1 TTTTTAATAAAATAGGTTGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGTGATATGT
475225 TATGTTAATA
66 TATGTTAATA
* * * * * * *
475235 TTTTTTAACAAAATAGATTGCGCCCAAGAAAACCATGGTTTTGAATAGAAATAAGTTGTTATATG
1 -TTTTTAATAAAATAGGTTGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGTGATATG
475300 TTATGTTAATA
65 TTATGTTAATA
* * * *
475311 TTTTCATCAGTAAAATAGGTTGCACCCAAGAATGTCATGGTTTTGAATAGAAATAGGTTGTGATA
1 TTTT--T-AATAAAATAGGTTGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGTGATA
*
475376 TATTAT
63 TGTTAT
475382 TATCAATACT
Statistics
Matches: 257, Mismatches: 36, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
75 139 0.54
76 64 0.25
77 1 0.00
78 53 0.21
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (75 bp):
TTTTTAATAAAATAGGTTGCGCCCAAGAATATCATGATTTTGAATAGAAATAGGTTGTGATATGT
TATGTTAATA
Found at i:475917 original size:101 final size:101
Alignment explanation
Indices: 475703--476070 Score: 388
Period size: 101 Copynumber: 3.6 Consensus size: 101
475693 CACTACTTAC
* *
475703 AATGTTATACTTATAAATCA-ATTTTGT-TTACTTTTGCATAATATAAAA-GGATTCAAACATAT
1 AATGTTATACTTATAAA-CATGTTTTGTCTTACTTTTGCATAATA-AAAACGGTTTCAAACATAT
* **
475765 AACATAGACAATTGACGATTAAAAAAGGCGTC-ACCTAT
64 AACATAAACAATTGAAAATTAAAAAAGGCG-CAACCTAT
* *
475803 AATGTTATACTTATAAACATGTTTTGTCTTACTTTTGCATAATAAAAATGGTTTCAAAGA-ATAA
1 AATGTTATACTTATAAACATGTTTTGTCTTACTTTTGCATAATAAAAACGGTTTCAAACATATAA
* *** *
475867 CCTAAATGGTTGAAAATTAAAAATAGGTGCAACCTAT
66 CATAAACAATTGAAAATTAAAAA-AGGCGCAACCTAT
* ** * *
475904 AATGTTA-AGCTTATAAACCTGTTTTGTCTTGTTTTTTCATAATAAAAACGATTTCAAACATATA
1 AATGTTATA-CTTATAAACATGTTTTGTCTTACTTTTGCATAATAAAAACGGTTTCAAACATATA
* * * * * * *
475968 ATATAAACAATTGACAATTTTAAAAAGACACAACTTAG
65 ACATAAACAATTGA-AAATTAAAAAAGGCGCAACCTAT
* * * *
476006 AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTTCATAATATAAACGGTTTCAAACATATAA
1 AATGTTATACTTATAAACATGTTTTGTCTTACTTTTGCATAATAAAAACGGTTTCAAACATATAA
476071 TGTAAACGAC
Statistics
Matches: 225, Mismatches: 34, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
99 2 0.01
100 49 0.22
101 86 0.38
102 79 0.35
103 9 0.04
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.36
Consensus pattern (101 bp):
AATGTTATACTTATAAACATGTTTTGTCTTACTTTTGCATAATAAAAACGGTTTCAAACATATAA
CATAAACAATTGAAAATTAAAAAAGGCGCAACCTAT
Found at i:476034 original size:102 final size:102
Alignment explanation
Indices: 475703--476096 Score: 377
Period size: 102 Copynumber: 3.9 Consensus size: 102
475693 CACTACTTAC
* * ** *
475703 AATGTTATACTTATAAATCAATTTTGT-TTACTTTTGCATAATATAAAAGGA-TTCAAACATATA
1 AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTGCATAATA-AAAACGATTTCAAACATATA
* * * *
475766 ACATAGACAATTGACGA-TTAAAAAAGGCGTC-ACCTAT
65 ACATAAACAATTGACAATTTAAAAAAGAC-ACAACCTAT
* * * * *
475803 AATGTTATACTTATAAACATGTTTTGTCTTACTTTTGCATAATAAAAATGGTTTCAAAGA-ATAA
1 AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTGCATAATAAAAACGATTTCAAACATATAA
* *** * ***
475867 CCTAAATGGTTGA-AAATTAAAAATAGGTGCAACCTAT
66 CATAAACAATTGACAATTTAAAAA-AGACACAACCTAT
* ** *
475904 AATGTTAAGCTTATAAACCTGTTTTGTCTTGTTTTTTCATAATAAAAACGATTTCAAACATATAA
1 AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTGCATAATAAAAACGATTTCAAACATATAA
* * * *
475969 TATAAACAATTGACAATTTTAAAAAGACACAACTTAG
66 CATAAACAATTGACAATTTAAAAAAGACACAACCTAT
* * *
476006 AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTTCATAATATAAACGGTTTCAAACATATAA
1 AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTGCATAATAAAAACGATTTCAAACATATAA
** * * *
476071 TGTAAACGACTGATAATTTAAAAAAG
66 CATAAACAATTGACAATTTAAAAAAG
476097 TATATGGATA
Statistics
Matches: 241, Mismatches: 46, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
99 1 0.00
100 48 0.20
101 83 0.34
102 101 0.42
103 8 0.03
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (102 bp):
AATGTTAAACTTATAAACCTGTTTTGTCTTACTTTTGCATAATAAAAACGATTTCAAACATATAA
CATAAACAATTGACAATTTAAAAAAGACACAACCTAT
Found at i:476406 original size:77 final size:77
Alignment explanation
Indices: 476310--476608 Score: 399
Period size: 77 Copynumber: 3.9 Consensus size: 77
476300 CATTTAAATT
* * * * * *
476310 TTTTAATTAATAAAAATATTAACATTCCAAATCGCAACCTATTTCCTAGTGAACCATGATA-TTC
1 TTTT-ATTAATGAAAATATTAACATTCCAGATCACAACCTATTTCTTAGCGAACCATGACATTTC
476374 TTGG-GCATGACCCA
65 TTGGTGCA--ACCCA
* * * * *
476388 TTTTATTAAT-AAACATATTAATATTCCATATCGCAACCTATTTCTTAGCAAACCATGACATTTT
1 TTTTATTAATGAAA-ATATTAACATTCCAGATCACAACCTATTTCTTAGCGAACCATGACATTTC
476452 TTGGTGCAACCCA
65 TTGGTGCAACCCA
* *
476465 TTTTATTAATGAAAATAGTAACATTCCAGATCACAACCTATTTCTTAGCGAACCATGACATTTTT
1 TTTTATTAATGAAAATATTAACATTCCAGATCACAACCTATTTCTTAGCGAACCATGACATTTCT
476530 TGGTGCAACCCA
66 TGGTGCAACCCA
* *
476542 TTTTATTAATGAAAATATTAACATTCCAGATCACAATCTATTTCTTAGTGAACCATGACA-TTCT
1 TTTTATTAATGAAAATATTAACATTCCAGATCACAACCTATTTCTTAGCGAACCATGACATTTCT
476606 TGG
66 TGG
476609 GCGCAACTAT
Statistics
Matches: 201, Mismatches: 16, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
76 9 0.04
77 176 0.88
78 13 0.06
79 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (77 bp):
TTTTATTAATGAAAATATTAACATTCCAGATCACAACCTATTTCTTAGCGAACCATGACATTTCT
TGGTGCAACCCA
Found at i:476566 original size:40 final size:39
Alignment explanation
Indices: 476445--476566 Score: 88
Period size: 40 Copynumber: 3.1 Consensus size: 39
476435 GCAAACCATG
476445 ACATTTTTTGGTGCAACCCATTTTATTAATGAAAATAGTA
1 ACATTTTTTGGTGCAACCCATTTTATTAATGAAAATA-TA
*** * * * * ** ** *
476485 ACA-TTCCAGATCACAACCTA-TTTCTTAGCG-AACCATG
1 ACATTTTTTGGT-GCAACCCATTTTATTAATGAAAATATA
476522 ACATTTTTTGGTGCAACCCATTTTATTAATGAAAATATTA
1 ACATTTTTTGGTGCAACCCATTTTATTAATGAAAATA-TA
476562 ACATT
1 ACATT
476567 CCAGATCACA
Statistics
Matches: 53, Mismatches: 24, Indels: 10
0.61 0.28 0.11
Matches are distributed among these distances:
37 10 0.19
38 14 0.26
39 14 0.26
40 15 0.28
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (39 bp):
ACATTTTTTGGTGCAACCCATTTTATTAATGAAAATATA
Found at i:485142 original size:46 final size:46
Alignment explanation
Indices: 485033--485203 Score: 229
Period size: 46 Copynumber: 3.7 Consensus size: 46
485023 CAGTTATGCC
* * * * *
485033 GTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGTTCAT-T
1 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGCTTCT
485078 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGCTTCT
1 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGCTTCT
* *
485124 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATG-TATCC
1 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGCT-TCT
* * *
485170 GTTCATGCATTTTAGTTATGGCATCCTTTCATGC
1 GTTCATGCACTTTAATTATGACATCCTTTCATGC
485204 ATTTTAGTTA
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
45 40 0.35
46 74 0.65
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (46 bp):
GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGCTTCT
Found at i:485152 original size:91 final size:92
Alignment explanation
Indices: 485033--485203 Score: 247
Period size: 91 Copynumber: 1.9 Consensus size: 92
485023 CAGTTATGCC
* * * * *
485033 GTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGT-TCAT-TGTTCATGCACTTTAATTA
1 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGT-ATCCGTTCATGCACTTTAATTA
485096 TGACATCCTTTCATGCCTTAGTGCTTCT
65 TGACATCCTTTCATGCCTTAGTGCTTCT
* *
485124 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTAGTTAT
1 GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGTATCCGTTCATGCACTTTAATTAT
*
485189 GGCATCCTTTCATGC
66 GACATCCTTTCATGC
485204 ATTTTAGTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
91 38 0.54
92 32 0.46
ACGTcount: A:0.20, C:0.22, G:0.14, T:0.44
Consensus pattern (92 bp):
GTTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGTATCCGTTCATGCACTTTAATTAT
GACATCCTTTCATGCCTTAGTGCTTCT
Found at i:485201 original size:72 final size:72
Alignment explanation
Indices: 485125--485399 Score: 223
Period size: 72 Copynumber: 3.9 Consensus size: 72
485115 AGTGCTTCTG
* * * *
485125 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTAGTTATG
1 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGAATCCATTCATGCACTTTAATTATG
* *
485190 GCATCCT
66 ACATCCA
* * * *
485197 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGTGAATCCATTCATGCACTTTAATTATG
1 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGAATCCATTCATGCACTTTAATTATG
485262 ACATCCA
66 ACATCCA
* * * * *
485269 TTCATGC-C-TT-A--ATG-CATCCGTTCATGCATTTTATTTATGGCATCCTTTGATGC-C-TT-
1 TTCATGCACTTTAATTATGACATCCTTTCATGC--CTTA---AT-GAATCCATTCATGCACTTTA
* *
485325 A--GTG-CATCCG
60 ATTATGACATCCA
* * * *
485335 TTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGTGCATCCATTCATGCACTTTAACTATG
1 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGAATCCATTCATGCACTTTAATTATG
485400 GATTCAATTT
Statistics
Matches: 160, Mismatches: 26, Indels: 35
0.72 0.12 0.16
Matches are distributed among these distances:
66 36 0.22
67 8 0.05
68 7 0.04
69 3 0.02
70 7 0.04
71 7 0.04
72 92 0.57
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.41
Consensus pattern (72 bp):
TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAATGAATCCATTCATGCACTTTAATTATG
ACATCCA
Found at i:485215 original size:118 final size:118
Alignment explanation
Indices: 485079--485321 Score: 387
Period size: 118 Copynumber: 2.1 Consensus size: 118
485069 TAGTTCATTG
** **
485079 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGCTTCTGTTCATGCACTTTAATTATG
1 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGAATCCATTCATGCACTTTAATTATG
* *
485144 ACATCCTTTCATGCCTTAATGTATCCGTTCATGCATTTTAGTTATGGCATCCT
66 ACATCCATTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
* * *
485197 TTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGTGAATCCATTCATGCACTTTAATTATG
1 TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGAATCCATTCATGCACTTTAATTATG
*
485262 ACATCCATTCATGCCTTAATGCATCCGTTCATGCATTTTATTTATGGCATCCT
66 ACATCCATTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
*
485315 TTGATGC
1 TTCATGC
485322 CTTAGTGCAT
Statistics
Matches: 114, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
118 114 1.00
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (118 bp):
TTCATGCACTTTAATTATGACATCCTTTCATGCCTTAGTGAATCCATTCATGCACTTTAATTATG
ACATCCATTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
Found at i:485246 original size:20 final size:20
Alignment explanation
Indices: 485218--485295 Score: 66
Period size: 20 Copynumber: 3.6 Consensus size: 20
485208 TAGTTATGGC
* *
485218 ATCCTTTCATGCCTTAGTGA
1 ATCCATTCATGCCTTAATGA
485238 ATCCATTCATGCACTTTAATTATGA
1 ATCCATTCATGC-C-TT-A--ATGA
*
485263 CATCCATTCATGCCTTAATGC
1 -ATCCATTCATGCCTTAATGA
*
485284 ATCCGTTCATGC
1 ATCCATTCATGC
485296 ATTTTATTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
20 22 0.46
21 4 0.08
22 2 0.04
23 2 0.04
24 2 0.04
25 4 0.08
26 12 0.25
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.37
Consensus pattern (20 bp):
ATCCATTCATGCCTTAATGA
Found at i:485247 original size:46 final size:46
Alignment explanation
Indices: 485190--485400 Score: 305
Period size: 46 Copynumber: 4.6 Consensus size: 46
485180 TTTAGTTATG
* * *
485190 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAGT
1 GCATCCATTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGT
* * * *
485236 GAATCCATTCATGCACTTTAATTATGACATCCATTCATGCCTTAAT
1 GCATCCATTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGT
* * * *
485282 GCATCCGTTCATGCATTTTATTTATGGCATCCTTTGATGCCTTAGT
1 GCATCCATTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGT
*
485328 GCATCCGTTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGT
1 GCATCCATTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGT
*
485374 GCATCCATTCATGCACTTTAACTATGG
1 GCATCCATTCATGCACTTTAATTATGG
485401 ATTCAATTTA
Statistics
Matches: 145, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 145 1.00
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
GCATCCATTCATGCACTTTAATTATGGCATCCTTTCATGCCTTAGT
Found at i:485333 original size:20 final size:20
Alignment explanation
Indices: 485308--485387 Score: 70
Period size: 20 Copynumber: 3.7 Consensus size: 20
485298 TTTATTTATG
*
485308 GCATCCTTTGATGCCTTAGT
1 GCATCCTTTCATGCCTTAGT
* *
485328 GCATCCGTTCATGCACTTTAATTAT
1 GCATCCTTTCATGC-C-TT-A--GT
485353 GGCATCCTTTCATGCCTTAGT
1 -GCATCCTTTCATGCCTTAGT
*
485374 GCATCCATTCATGC
1 GCATCCTTTCATGC
485388 ACTTTAACTA
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 25 0.52
21 2 0.04
22 2 0.04
23 2 0.04
24 2 0.04
25 2 0.04
26 13 0.27
ACGTcount: A:0.19, C:0.28, G:0.16, T:0.38
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAGT
Found at i:502493 original size:20 final size:21
Alignment explanation
Indices: 502468--502508 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
502458 CTCTTTAGAC
502468 TTGCAAGAAAAATAT-TTCCT
1 TTGCAAGAAAAATATGTTCCT
*
502488 TTGCAAGATAAATATGTTCCT
1 TTGCAAGAAAAATATGTTCCT
502509 CACTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.37
Consensus pattern (21 bp):
TTGCAAGAAAAATATGTTCCT
Found at i:503437 original size:34 final size:34
Alignment explanation
Indices: 503393--503472 Score: 133
Period size: 34 Copynumber: 2.4 Consensus size: 34
503383 ACTATTAGAA
* *
503393 GGTATAGATACCATTGATAATAGAATGCAAAACT
1 GGTATCGATACCATTGATAATAGAATGCAAAAAT
503427 GGTATCGATACCATTGATAATAGAATGCAAAAAT
1 GGTATCGATACCATTGATAATAGAATGCAAAAAT
*
503461 GGCATCGATACC
1 GGTATCGATACC
503473 GTATTAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (34 bp):
GGTATCGATACCATTGATAATAGAATGCAAAAAT
Found at i:503526 original size:20 final size:22
Alignment explanation
Indices: 503480--503532 Score: 74
Period size: 20 Copynumber: 2.5 Consensus size: 22
503470 ACCGTATTAA
*
503480 AGTATCGATACCATAGTGTAGT
1 AGTATCGATACCATAGTGTAGG
503502 AGTATCGATACCAT-G-GTAGG
1 AGTATCGATACCATAGTGTAGG
*
503522 GGTATCGATAC
1 AGTATCGATAC
503533 TATTGAGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 14 0.48
21 1 0.03
22 14 0.48
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
AGTATCGATACCATAGTGTAGG
Found at i:503952 original size:55 final size:55
Alignment explanation
Indices: 503858--504197 Score: 463
Period size: 55 Copynumber: 6.2 Consensus size: 55
503848 CTAAGTGTAC
* * * *
503858 TACAAGCACTATGTGTGGAAATCCACGGAATTCAACATGAGTTGATGAATAATCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
** *
503913 TACATACACTATGTGTGCAAATCCACTGAATTCATCATGAGTTGATGAAT-ACCTG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACC-G
* *
503968 TACAGGCACTATGTGTGCAAATCCATGGAATTTATCATGAGTTGATGAATAACCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
504023 TAC-GCGTACTATGTGTGAAAATCCACGGAATTCATCATGAGTTGATGAACAACCG
1 TACAG-GCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* *
504078 TACAGGCACTAAGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCA
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
* * *
504133 TATAGGCACTATGTGTGC-AACCCACGAAATTCATCATGAGTTGATGAACT-ACCG
1 TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAA-TAACCG
*
504187 TATAGGCACTA
1 TACAGGCACTA
504198 CATGTGCATC
Statistics
Matches: 254, Mismatches: 26, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
54 45 0.18
55 205 0.81
56 4 0.02
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (55 bp):
TACAGGCACTATGTGTGCAAATCCACGGAATTCATCATGAGTTGATGAATAACCG
Found at i:507133 original size:17 final size:17
Alignment explanation
Indices: 507108--507141 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
507098 CTTTATCTAA
*
507108 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
507125 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
507142 TTATGTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:510067 original size:15 final size:16
Alignment explanation
Indices: 510020--510067 Score: 50
Period size: 15 Copynumber: 3.1 Consensus size: 16
510010 ATTATTTTAA
510020 TTTTTCATTTG-TTATT
1 TTTTTC-TTTGATTATT
510036 TTTTTC--TGATTTATT
1 TTTTTCTTTGA-TTATT
510051 TTTTTCTTTGATT-TT
1 TTTTTCTTTGATTATT
510066 TT
1 TT
510068 AGGTATGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
13 2 0.07
15 15 0.54
16 8 0.29
17 3 0.11
ACGTcount: A:0.10, C:0.06, G:0.06, T:0.77
Consensus pattern (16 bp):
TTTTTCTTTGATTATT
Found at i:512837 original size:4 final size:4
Alignment explanation
Indices: 512828--512865 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
512818 CTTTATCTCA
*
512828 ATTT ATTT ATTTT ATTT ATTT GTTT ATTT ATTT -TTT AT
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT ATTT ATTT AT
512866 CTCATTATTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 23 0.77
5 4 0.13
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (4 bp):
ATTT
Found at i:515302 original size:68 final size:68
Alignment explanation
Indices: 515193--515328 Score: 238
Period size: 68 Copynumber: 2.0 Consensus size: 68
515183 TTTGCTATTC
515193 ACTTTAATTCCATATCAATCACTATATTCAACCAAACTCATAATACTTTCAAACTAG-TACAACA
1 ACTTTAATTCCATATCAATCACTATATTCAACCAAACTCATAATACTTTCAAACT-GTTACAACA
515257 ACAT
65 ACAT
* *
515261 ACTTTAATTCCATATCAATCACTATATTTAACCAATCTCATAATACTTTCAAACTGTTACAACAA
1 ACTTTAATTCCATATCAATCACTATATTCAACCAAACTCATAATACTTTCAAACTGTTACAACAA
515326 CAT
66 CAT
515329 TGCATATTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 1 0.02
68 64 0.98
ACGTcount: A:0.41, C:0.24, G:0.01, T:0.33
Consensus pattern (68 bp):
ACTTTAATTCCATATCAATCACTATATTCAACCAAACTCATAATACTTTCAAACTGTTACAACAA
CAT
Found at i:516890 original size:46 final size:46
Alignment explanation
Indices: 516818--516911 Score: 170
Period size: 46 Copynumber: 2.0 Consensus size: 46
516808 CATTTTCCTC
516818 TTCAAAAACCTGAAAATCATCATCTCATGAATTTATCAAAACCATG
1 TTCAAAAACCTGAAAATCATCATCTCATGAATTTATCAAAACCATG
* *
516864 TTCAGAAACCTGAAAATCATCATCTCATGATTTTATCAAAACCATG
1 TTCAAAAACCTGAAAATCATCATCTCATGAATTTATCAAAACCATG
516910 TT
1 TT
516912 AATCAAGATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.31
Consensus pattern (46 bp):
TTCAAAAACCTGAAAATCATCATCTCATGAATTTATCAAAACCATG
Found at i:519274 original size:37 final size:37
Alignment explanation
Indices: 519221--519296 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
519211 CATTAAAATA
*
519221 TCCCATAGTCAAAGATGAACCA-ACTTGAAGTTGACTT
1 TCCCATAGTCAAAGATGAA-CATACTTGAAGTTGAATT
*
519258 TCCCATAGTCATAGATGAACATACTTGAAGTTGAATT
1 TCCCATAGTCAAAGATGAACATACTTGAAGTTGAATT
519295 TC
1 TC
519297 TACTTTAGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (37 bp):
TCCCATAGTCAAAGATGAACATACTTGAAGTTGAATT
Found at i:527171 original size:13 final size:13
Alignment explanation
Indices: 527149--527178 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
527139 ACTAAACACC
527149 TTTC-ACATACCT
1 TTTCAACATACCT
527161 TTTCAACATACCT
1 TTTCAACATACCT
527174 TTTCA
1 TTTCA
527179 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:529832 original size:23 final size:24
Alignment explanation
Indices: 529796--529841 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
529786 TTTTTCTTCC
*
529796 TTTTTGAGTTCTTTCAATTTCTTA
1 TTTTTGAGTGCTTTCAATTTCTTA
* *
529820 TTTTT-AGTGCTTTGATTTTCTT
1 TTTTTGAGTGCTTTCAATTTCTT
529842 TGTTGGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.13, C:0.11, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTTTGAGTGCTTTCAATTTCTTA
Found at i:532259 original size:21 final size:21
Alignment explanation
Indices: 532233--532400 Score: 113
Period size: 21 Copynumber: 7.9 Consensus size: 21
532223 TATATAAAAT
* **
532233 TGTCCCTAAGGACCTTATATA
1 TGTCCCAAAGGACCACATATA
* *
532254 TGTCCCGAATGACCACATATA
1 TGTCCCAAAGGACCACATATA
532275 TGTCCCAAAGGACCACATATAA
1 TGTCCCAAAGGACCACATAT-A
**
532297 T-TCTACTTAAGGACCACATATA
1 TGTC--CCAAAGGACCACATATA
* * * * *
532319 TATTCCAAATGACCAAATATG
1 TGTCCCAAAGGACCACATATA
* * *
532340 TGGCCCAAAGAACCGCATATA
1 TGTCCCAAAGGACCACATATA
* **
532361 TGTTCCAAAGGATTACATATA
1 TGTCCCAAAGGACCACATATA
***
532382 TGTCTTGAAGGACCACATA
1 TGTCCCAAAGGACCACATA
532401 GAACCCTCAA
Statistics
Matches: 109, Mismatches: 34, Indels: 8
0.72 0.23 0.05
Matches are distributed among these distances:
21 90 0.83
22 4 0.04
23 15 0.14
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.26
Consensus pattern (21 bp):
TGTCCCAAAGGACCACATATA
Found at i:532318 original size:65 final size:65
Alignment explanation
Indices: 532239--532360 Score: 154
Period size: 65 Copynumber: 1.9 Consensus size: 65
532229 AAATTGTCCC
** * * * * *
532239 TAAGGACCTTATATATGTCCCGAATGACCACATATATGTCCCAAAGGACCACATATAATTCTACT
1 TAAGGACCACATATATATCCCAAATGACCAAATATATGGCCCAAAGAACCACATATAATTCTACT
* * *
532304 TAAGGACCACATATATATTCCAAATGACCAAATATGTGGCCCAAAGAACCGCATATA
1 TAAGGACCACATATATATCCCAAATGACCAAATATATGGCCCAAAGAACCACATATA
532361 TGTTCCAAAG
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
65 47 1.00
ACGTcount: A:0.39, C:0.24, G:0.13, T:0.25
Consensus pattern (65 bp):
TAAGGACCACATATATATCCCAAATGACCAAATATATGGCCCAAAGAACCACATATAATTCTACT
Found at i:539384 original size:21 final size:21
Alignment explanation
Indices: 539345--539407 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
539335 CATATAAAAT
* * *
539345 TATCCCTAAGGACCTCATATA
1 TATCCCGAAGAACCACATATA
*
539366 TGTCCCGAAGAACCACATATA
1 TATCCCGAAGAACCACATATA
*
539387 TATCCCGAAGGACCACATATA
1 TATCCCGAAGAACCACATATA
539408 ATTCTCATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.22
Consensus pattern (21 bp):
TATCCCGAAGAACCACATATA
Found at i:539480 original size:21 final size:21
Alignment explanation
Indices: 539447--539505 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
539437 AAATGACCAA
* **
539447 ATATGTGTCCCAAAGAATTGT
1 ATATATGTCCCAAAGAATTAC
* *
539468 ATATATGTTCCAAAGGATTAC
1 ATATATGTCCCAAAGAATTAC
*
539489 ATATATGTCCCGAAGAA
1 ATATATGTCCCAAAGAA
539506 CCATATAAAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (21 bp):
ATATATGTCCCAAAGAATTAC
Found at i:546038 original size:22 final size:22
Alignment explanation
Indices: 546007--546062 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
545997 ATTGATACCA
*
546007 TATAGGGGTATCGGTACC-ATAG
1 TATA-GGGTATCGATACCTATAG
*
546029 TATAGTGGTATCGATACCTATGG
1 TATAG-GGTATCGATACCTATAG
546052 TA-AGGGTATCG
1 TATAGGGTATCG
546063 CTACGGGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
21 8 0.27
22 17 0.57
23 5 0.17
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.30
Consensus pattern (22 bp):
TATAGGGTATCGATACCTATAG
Found at i:546061 original size:21 final size:21
Alignment explanation
Indices: 545994--546062 Score: 63
Period size: 19 Copynumber: 3.3 Consensus size: 21
545984 ACCTAATTTT
* *
545994 GGTATTGATACCATA-TA-GG
1 GGTATCGATACCATAGTATAG
*
546013 GGTATCGGTACCATAGTATAG
1 GGTATCGATACCATAGTATAG
*
546034 TGGTATCGATACCTATGGTA-AG
1 -GGTATCGATACC-ATAGTATAG
546056 GGTATCG
1 GGTATCG
546063 CTACGGGGCC
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 8 0.20
22 13 0.32
23 5 0.12
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.30
Consensus pattern (21 bp):
GGTATCGATACCATAGTATAG
Found at i:546086 original size:96 final size:94
Alignment explanation
Indices: 545920--546161 Score: 247
Period size: 96 Copynumber: 2.5 Consensus size: 94
545910 GATTCAATTA
* * * * * *
545920 GTATCGGTACC-TAATGAAGTGGTATCAATACCATGGTGAGGGTATCGATATAGGGTAACATCGA
1 GTATCGGTACCATAGT-AAGTGGTATCGATACCATGGTAAGGGTATCGATACAGGGCAACATCAA
545984 ACCTAATTTTGGTATTGATACCAT-ATA-GGG
65 ACCTAATTTTGGTATTGATA-C-TGATAGGGG
* * * *
546014 GTATCGGTACCATAGTATAGTGGTATCGATACCTATGGTAAGGGTATCGCTACGGGGCCATATCA
1 GTATCGGTACCATAGTA-AGTGGTATCGATACC-ATGGTAAGGGTATCGATACAGGGCAACATCA
* *
546079 AATCTAATTTTGGTATTGATACTGGTAGGGG
64 AACCTAATTTTGGTATTGATACTGATAGGGG
* * * * * *
546110 GTATCGATACCATAGTAGGGTAGTATAGATACCATAGTAAGGGTATTGATAC
1 GTATCGGTACCATAGTA-AGTGGTATCGATACCATGGTAAGGGTATCGATAC
546162 TGAAGGGCCA
Statistics
Matches: 123, Mismatches: 20, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
94 13 0.11
95 36 0.29
96 74 0.60
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (94 bp):
GTATCGGTACCATAGTAAGTGGTATCGATACCATGGTAAGGGTATCGATACAGGGCAACATCAAA
CCTAATTTTGGTATTGATACTGATAGGGG
Found at i:546140 original size:22 final size:23
Alignment explanation
Indices: 546110--546154 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
546100 CTGGTAGGGG
*
546110 GTATCGATACCATAGT-AGGGTA
1 GTATAGATACCATAGTAAGGGTA
546132 GTATAGATACCATAGTAAGGGTA
1 GTATAGATACCATAGTAAGGGTA
546155 TTGATACTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.27
Consensus pattern (23 bp):
GTATAGATACCATAGTAAGGGTA
Found at i:546160 original size:20 final size:19
Alignment explanation
Indices: 546108--546161 Score: 63
Period size: 22 Copynumber: 2.6 Consensus size: 19
546098 TACTGGTAGG
*
546108 GGGTATCGATACCATAGTA
1 GGGTATTGATACCATAGTA
546127 GGGTAGTATAGATACCATAGTAA
1 GGGTA-T-T-GATACCATAGT-A
546150 GGGTATTGATAC
1 GGGTATTGATAC
546162 TGAAGGGCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 5 0.17
20 6 0.20
21 1 0.03
22 12 0.40
23 6 0.20
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (19 bp):
GGGTATTGATACCATAGTA
Found at i:546658 original size:45 final size:45
Alignment explanation
Indices: 546609--546938 Score: 430
Period size: 45 Copynumber: 7.4 Consensus size: 45
546599 AAATGATGCC
* *
546609 ATAGTTGAAATGTATATGGGTACATTATAAACAGAAAAGTATACG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
546654 ATAGTTGAAATGTATATGAGTACATTATCAACAGAAAAATATACA
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * * *
546699 ATAGTTTAAATGCATATGGGTGCATTGTCAACATAAAAGTATGCT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * *
546744 AGAGTTGAAATGTATATGGGTACATTATCAACTGAAAAGTATAAT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
546789 ATAGTTGAAATGTATATGGGTACATTATCAACAG-AAAGCATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* *
546833 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
* * * * **
546878 ATAGTTGAAATGTTTATGGGTGCATTTTCAACAGAAAAATATGTT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
*
546923 ATAGTTTAAA-GTATAT
1 ATAGTTGAAATGTATAT
546939 AGTGGTGTAT
Statistics
Matches: 247, Mismatches: 37, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
44 45 0.18
45 202 0.82
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.32
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:546762 original size:135 final size:134
Alignment explanation
Indices: 546611--546915 Score: 457
Period size: 134 Copynumber: 2.3 Consensus size: 134
546601 ATGATGCCAT
* *
546611 AGTTGAAATGTATATGGGTACATTATAAACAGAAAAGTATACGATAGTTGAAATGTATATGAGTA
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAAGATAGTTGAAATGTATATGAGTA
* * * *
546676 CATTATCAACAGAAAAATATACAATAGTTTAAATGCATATGGGTGCATTGTCAACATAAAAGTAT
66 CATTATCAACAG-AAAACATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTAT
*
546741 GCTAG
130 ACTAG
* * *
546746 AGTTGAAATGTATATGGGTACATTATCAACTGAAAAGTATAATATAGTTGAAATGTATATGGGTA
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAAGATAGTTGAAATGTATATGAGTA
* *
546811 CATTATCAACAGAAAGCATACTATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATA
66 CATTATCAACAGAAAACATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATA
*
546876 CTAT
131 CTAG
* * *
546880 AGTTGAAATGTTTATGGGTGCATTTTCAACAGAAAA
1 AGTTGAAATGTATATGGGTACATTATCAACAGAAAA
546916 ATATGTTATA
Statistics
Matches: 153, Mismatches: 17, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
134 81 0.53
135 72 0.47
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.30
Consensus pattern (134 bp):
AGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAAGATAGTTGAAATGTATATGAGTA
CATTATCAACAGAAAACATACAATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATA
CTAG
Found at i:547544 original size:2 final size:2
Alignment explanation
Indices: 547537--547568 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
547527 TGAAGGGAGG
547537 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
547569 CAACAAGGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:550857 original size:3 final size:3
Alignment explanation
Indices: 550849--550873 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
550839 TATTTCTACA
550849 CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT C
550874 ACGTACGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:551597 original size:96 final size:95
Alignment explanation
Indices: 551447--551646 Score: 215
Period size: 96 Copynumber: 2.1 Consensus size: 95
551437 AATGAAGTCA
* ** * *
551447 TATCGATACCGGGTAACATCAAACCTAATTTTGGTATCGATACCATATAGGGGTATCGGTATCAT
1 TATCGATACGGGGCCACATCAAACCTAATTTTGGTATCGATACCATATAGGGGTATCGATACCAT
* ** *
551512 AGTATAGTGGTATCGATACCTATGGTAAGGG
66 AGTAGAGTAATATCGATACC-ATAGTAAGGG
* * * * *
551543 TATTGATACGGGGCCACATCGAATCTAATTTTGGTATTGATA-C-TGGTAGTGGGTATCGATACC
1 TATCGATACGGGGCCACATCAAACCTAATTTTGGTATCGATACCAT-ATAG-GGGTATCGATACC
* *
551606 ATAGTAGGGTAATATCGATACCATAGTAGGGG
64 ATAGTAGAGTAATATCGATACCATAGTAAGGG
551638 TATCGATAC
1 TATCGATAC
551647 TGAAGGGCCA
Statistics
Matches: 85, Mismatches: 17, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
94 1 0.01
95 20 0.24
96 64 0.75
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.30
Consensus pattern (95 bp):
TATCGATACGGGGCCACATCAAACCTAATTTTGGTATCGATACCATATAGGGGTATCGATACCAT
AGTAGAGTAATATCGATACCATAGTAAGGG
Found at i:551643 original size:20 final size:20
Alignment explanation
Indices: 551588--551646 Score: 82
Period size: 22 Copynumber: 2.8 Consensus size: 20
551578 ATTGATACTG
551588 GTAGTGGGTATCGATACCATA
1 GTAG-GGGTATCGATACCATA
*
551609 GTAGGGTAATATCGATACCATA
1 GTAGGG--GTATCGATACCATA
551631 GTAGGGGTATCGATAC
1 GTAGGGGTATCGATAC
551647 TGAAGGGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 11 0.32
21 4 0.12
22 19 0.56
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.27
Consensus pattern (20 bp):
GTAGGGGTATCGATACCATA
Found at i:552143 original size:45 final size:45
Alignment explanation
Indices: 552094--552405 Score: 461
Period size: 45 Copynumber: 7.0 Consensus size: 45
552084 AAAGGATGTC
*
552094 ATAGTTGAAATGTATATGGGTACATTATGAACAGAAAAGTATACG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
552139 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
*
552184 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACA
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
* * *
552229 ATAGTTGAAATGCATATGGGTGCATTGTCAACAGAAAAGTAT--G
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
* * **
552272 CTAGATTTAAATGTATATGGGTACATTATCAACTA-AAAAGTATATT
1 ATAG-TTGAAATGTATATGGGTACATTATCAAC-AGAAAAGTATACG
* *
552318 ATAGTTGTAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
* *
552363 A-AGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAC
1 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAC
552406 TATCAACAGA
Statistics
Matches: 243, Mismatches: 19, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
43 3 0.01
44 72 0.30
45 165 0.68
46 3 0.01
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (45 bp):
ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACG
Found at i:552322 original size:89 final size:89
Alignment explanation
Indices: 552098--552405 Score: 442
Period size: 89 Copynumber: 3.4 Consensus size: 89
552088 GATGTCATAG
* *
552098 TTGAAATGTATATGGGTACATTATGAACAGAAAAGTATACGATAGTTGAAATGTATATGGGTACA
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGTATATGGGTACA
*
552163 TTATCAACAGAAAAGTATACGATAG-
66 TTATCAACAGAAAAGTAT--GCTAGA
* *
552188 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGCATATGGGTGCA
1 TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGTATATGGGTACA
*
552253 TTGTCAACAGAAAAGTATGCTAGA
66 TTATCAACAGAAAAGTATGCTAGA
* ** *
552277 TTTAAATGTATATGGGTACATTATCAACTA-AAAAGTATATTATAGTTGTAATGTATATGGGTAC
1 TTGAAATGTATATGGGTACATTATCAAC-AGAAAAGTATACAATAGTTGAAATGTATATGGGTAC
*
552341 ATTATCAACAGAAAAGTATACTA-A
65 ATTATCAACAGAAAAGTATGCTAGA
* *
552365 GTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATAC
1 -TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATAC
552406 TATCAACAGA
Statistics
Matches: 196, Mismatches: 18, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
88 6 0.03
89 111 0.57
90 79 0.40
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.30
Consensus pattern (89 bp):
TTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACAATAGTTGAAATGTATATGGGTACA
TTATCAACAGAAAAGTATGCTAGA
Found at i:554643 original size:15 final size:15
Alignment explanation
Indices: 554623--554651 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
554613 CTTTAGATTA
554623 TTTATTTAATTATTT
1 TTTATTTAATTATTT
554638 TTTATTTAATTATT
1 TTTATTTAATTATT
554652 ATCTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTATTTAATTATTT
Found at i:554658 original size:18 final size:19
Alignment explanation
Indices: 554620--554662 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
554610 TCTCTTTAGA
* *
554620 TTATTTATTTAATTATTTT
1 TTATTTAATTAATTATCTT
554639 TTATTTAATT-ATTATCTT
1 TTATTTAATTAATTATCTT
554657 TTATTT
1 TTATTT
554663 TAAAAACAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (19 bp):
TTATTTAATTAATTATCTT
Found at i:554792 original size:15 final size:16
Alignment explanation
Indices: 554768--554797 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
554758 TTCCCCACTT
554768 TTTTTATTTTATTTTG
1 TTTTTATTTTATTTTG
554784 TTTTT-TTTTATTTT
1 TTTTTATTTTATTTT
554798 CTCTTTTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.00, G:0.03, T:0.87
Consensus pattern (16 bp):
TTTTTATTTTATTTTG
Found at i:554906 original size:10 final size:11
Alignment explanation
Indices: 554874--554906 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
554864 TTATTTTTTC
554874 TTTTAACATTT
1 TTTTAACATTT
554885 TTTATAACATTT
1 TTT-TAACATTT
554897 TTTTAA-ATTT
1 TTTTAACATTT
554907 AATTTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.19
11 6 0.29
12 11 0.52
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (11 bp):
TTTTAACATTT
Done.