Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015316.1 Kokia drynarioides strain JFW-HI SEQ_130361, 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: 577508
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 343 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:389587 original size:43 final size:43
Alignment explanation
Indices: 389494--389616 Score: 135
Period size: 43 Copynumber: 2.9 Consensus size: 43
389484 CATTGTCTTT
* *
389494 ATGGTCTTTAGTGGCGCTTTT-AC-CATAACGCCGCTAAAAAAC
1 ATGGTCTTTAGTGGCGTTTTTCACACA-AACGCCACTAAAAAAC
* * * *
389536 ATGGTCTTTAATGGCGTTTTTCACACAAACGTCACTACAGAAC
1 ATGGTCTTTAGTGGCGTTTTTCACACAAACGCCACTAAAAAAC
* *
389579 ATGGTCTTTAGCGGCGTTTTTCTCACAAA-GACCACTAA
1 ATGGTCTTTAGTGGCGTTTTTCACACAAACG-CCACTAA
389617 CATTAACATA
Statistics
Matches: 67, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
42 20 0.30
43 45 0.67
44 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (43 bp):
ATGGTCTTTAGTGGCGTTTTTCACACAAACGCCACTAAAAAAC
Found at i:392774 original size:40 final size:41
Alignment explanation
Indices: 392730--392807 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 41
392720 GAAAACGTCG
*
392730 CTATTACTTAATCATTAGCGGCACTCTTC-CATAAACATTT
1 CTATTACTTAACCATTAGCGGCACTCTTCTCATAAACATTT
* * * * *
392770 CTATTGCTTAACCTTTAGTGGCATTTTTCTCATAAACA
1 CTATTACTTAACCATTAGCGGCACTCTTCTCATAAACA
392808 CCGTTACTGC
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
40 23 0.74
41 8 0.26
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (41 bp):
CTATTACTTAACCATTAGCGGCACTCTTCTCATAAACATTT
Found at i:406326 original size:30 final size:30
Alignment explanation
Indices: 406252--406476 Score: 167
Period size: 30 Copynumber: 7.4 Consensus size: 30
406242 GTTTTATTTA
* * *
406252 AAAATTACATTTTAACTCCC-AAACTTTT-A
1 AAAATTATATTTTGAC-CCCTAAACTTTTCC
* *
406281 AAAATTGCAT-TTTTGAGCCCTAAAATTTTCC
1 AAAATT--ATATTTTGACCCCTAAACTTTTCC
*
406312 AAAATTATGTTTTGACCCCATAAACTTTTCC
1 AAAATTATATTTTGACCCC-TAAACTTTTCC
* * *
406343 AAAATTACATTTTAACCCCTAAACTTTCCC
1 AAAATTATATTTTGACCCCTAAACTTTTCC
* *
406373 AAAATTATATTTT-ATCCCCCCCAAACTTTTCT
1 AAAATTATATTTTGA---CCCCTAAACTTTTCC
* * *
406405 AAAATCACATTTTGA-CCCTAGAACTTTTCT
1 AAAATTATATTTTGACCCCTA-AACTTTTCC
* *
406435 AAAATCATATTTTGA-CCCTAAA-TTTCCTC
1 AAAATTATATTTTGACCCCTAAACTTTTC-C
*
406464 AAAATTACATTTT
1 AAAATTATATTTT
406477 TTACTCGAAA
Statistics
Matches: 161, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
28 4 0.02
29 29 0.18
30 71 0.44
31 33 0.20
32 23 0.14
33 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAACTTTTCC
Found at i:406354 original size:62 final size:59
Alignment explanation
Indices: 406252--406476 Score: 199
Period size: 62 Copynumber: 3.7 Consensus size: 59
406242 GTTTTATTTA
* * * * *
406252 AAAATTACATTTTAACTCCC-AAACTTTT-AAAAATTGCATTTTTGAGCCCTAAAATTTTCC
1 AAAATTATATTTTGAC-CCCTAAACTTTTCCAAAATTACA-TTTTGA-CCCTAAACTTTTCC
* * *
406312 AAAATTATGTTTTGACCCCATAAACTTTTCCAAAATTACATTTTAACCCCTAAACTTTCCC
1 AAAATTATATTTTGACCCC-TAAACTTTTCCAAAATTACATTTTGA-CCCTAAACTTTTCC
* * * *
406373 AAAATTATATTTT-ATCCCCCCCAAACTTTTCTAAAATCACATTTTGACCCTAGAACTTTTCT
1 AAAATTATATTTTGA---CCCCTAAACTTTTCCAAAATTACATTTTGACCCTA-AACTTTTCC
* *
406435 AAAATCATATTTTGA-CCCTAAA-TTTCCTCAAAATTACATTTT
1 AAAATTATATTTTGACCCCTAAACTTTTC-CAAAATTACATTTT
406477 TTACTCGAAA
Statistics
Matches: 135, Mismatches: 21, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
58 4 0.03
59 21 0.16
60 14 0.10
61 42 0.31
62 49 0.36
63 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.04, T:0.38
Consensus pattern (59 bp):
AAAATTATATTTTGACCCCTAAACTTTTCCAAAATTACATTTTGACCCTAAACTTTTCC
Found at i:410467 original size:18 final size:17
Alignment explanation
Indices: 410444--410480 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
410434 ATTTATTTAT
410444 TTAAATAAATAAATTAAA
1 TTAAATAAATAAA-TAAA
*
410462 TTAAATTAATAAATAAA
1 TTAAATAAATAAATAAA
410479 TT
1 TT
410481 TGGGCCTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAATAAATAAATAAA
Found at i:410574 original size:15 final size:15
Alignment explanation
Indices: 410556--410586 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
410546 ATAAAATAAT
410556 AAATAAAAAAACAAA
1 AAATAAAAAAACAAA
410571 AAATAAAAAAACAAA
1 AAATAAAAAAACAAA
410586 A
1 A
410587 TTGGGCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.87, C:0.06, G:0.00, T:0.06
Consensus pattern (15 bp):
AAATAAAAAAACAAA
Found at i:411282 original size:39 final size:40
Alignment explanation
Indices: 411218--411361 Score: 170
Period size: 40 Copynumber: 3.6 Consensus size: 40
411208 CTCATAGCTT
* *
411218 TAGGGATAAAAGATTGGATTG-CTTCAATCTGCCC-ATGG
1 TAGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
* * * *
411256 TAGGGGTAAGAGATAGGATGGTCTTCAATCTTCCCTCTGG
1 TAGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
*
411296 TTA-GGGTAAAAGATTGGATTG-CTTTCAATCTGCCCTATGG
1 -TAGGGGTAAAAGATTGGATGGTC-TTCAATCTGCCCTATGG
*
411336 TCGGGGTAAAAGATTGGATGGTCTTC
1 TAGGGGTAAAAGATTGGATGGTCTTC
411362 GCTCCATTTC
Statistics
Matches: 87, Mismatches: 13, Indels: 10
0.79 0.12 0.09
Matches are distributed among these distances:
38 17 0.20
39 14 0.16
40 53 0.61
41 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.28, T:0.31
Consensus pattern (40 bp):
TAGGGGTAAAAGATTGGATGGTCTTCAATCTGCCCTATGG
Found at i:411534 original size:50 final size:50
Alignment explanation
Indices: 411371--411535 Score: 206
Period size: 50 Copynumber: 3.3 Consensus size: 50
411361 CGCTCCATTT
* * ** *
411371 CAGCTTCAGGAGTATAAGATTCATCTTTG-GGACTTCAATCTGCCCCTCTA
1 CAGCTTTAGGTGTATAAGATTCGCCATTGCGG-CTTCAATCTGCCCCTCTA
** *
411421 CAGCTTTAGGTAAATGAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTA
1 CAGCTTTAGGTGTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTA
* * *
411471 TAGCTTTAGGTGTATAAGATTTGTCATTGCGGCTTCAATCTGCCCCTCTA
1 CAGCTTTAGGTGTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTA
*
411521 CAGCTTTATGTGTAT
1 CAGCTTTAGGTGTAT
411536 GAGACTCGTC
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
50 96 0.98
51 2 0.02
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (50 bp):
CAGCTTTAGGTGTATAAGATTCGCCATTGCGGCTTCAATCTGCCCCTCTA
Found at i:422647 original size:2 final size:2
Alignment explanation
Indices: 422640--422664 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
422630 AAAGCGTGAA
422640 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
422665 GGATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:422763 original size:30 final size:30
Alignment explanation
Indices: 422708--422821 Score: 167
Period size: 30 Copynumber: 3.8 Consensus size: 30
422698 AAATTTGAAT
* *
422708 TTTTGGAAAAATTTAGGGGTCAAATTCAAAA
1 TTTTGG-AAAGTTTAGGGGTTAAATTCAAAA
*
422739 TTTTGGAAAGTTTGGGGGTTAAATTCAAAA
1 TTTTGGAAAGTTTAGGGGTTAAATTCAAAA
422769 TTTTGGAAAGTTTAGGGGTTAAATTCAAAA
1 TTTTGGAAAGTTTAGGGGTTAAATTCAAAA
*
422799 TTTTAGAAAGTTT-GAGGGTTAAA
1 TTTTGGAAAGTTTAG-GGGTTAAA
422822 ACACTATTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
29 1 0.01
30 70 0.91
31 6 0.08
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTTAGGGGTTAAATTCAAAA
Found at i:422793 original size:60 final size:61
Alignment explanation
Indices: 422708--422821 Score: 185
Period size: 60 Copynumber: 1.9 Consensus size: 61
422698 AAATTTGAAT
* *
422708 TTTTGGAAAAATTTAGGGGTCAAATTCAAAATTTTGGAAAGTTTGGGGGTTAAATTCAAAA
1 TTTTGGAAAAATTTAGGGGTCAAATTCAAAATTTTAGAAAGTTTGAGGGTTAAATTCAAAA
* *
422769 TTTTGG-AAAGTTTAGGGGTTAAATTCAAAATTTTAGAAAGTTTGAGGGTTAAA
1 TTTTGGAAAAATTTAGGGGTCAAATTCAAAATTTTAGAAAGTTTGAGGGTTAAA
422822 ACACTATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 43 0.88
61 6 0.12
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.36
Consensus pattern (61 bp):
TTTTGGAAAAATTTAGGGGTCAAATTCAAAATTTTAGAAAGTTTGAGGGTTAAATTCAAAA
Found at i:424031 original size:13 final size:12
Alignment explanation
Indices: 423995--424038 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
423985 TATTTATTTA
423995 TAAATAATAAAT
1 TAAATAATAAAT
*
424007 TAATTAATTAAAT
1 TAAATAA-TAAAT
424020 TAAATGAATAAA-
1 TAAAT-AATAAAT
424032 TAAATAA
1 TAAATAA
424039 ATTTGAGCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 2 0.07
12 11 0.39
13 13 0.46
14 2 0.07
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
TAAATAATAAAT
Found at i:424129 original size:19 final size:20
Alignment explanation
Indices: 424093--424132 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
424083 ATTTATATTT
424093 ATAAAATAATAAATAAATAA
1 ATAAAATAATAAATAAATAA
424113 ATAAATATAA-AAA-AAATAA
1 ATAAA-ATAATAAATAAATAA
424132 A
1 A
424133 AACAAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
ATAAAATAATAAATAAATAA
Found at i:424716 original size:28 final size:28
Alignment explanation
Indices: 424666--424732 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
424656 GTTAGCTTTT
* * *
424666 ATATATGGTCGAATCTGCTGCCTGAATG
1 ATATATGGTCGAATCTACCGCCTGAATA
*
424694 ATATATGGTCGACTCTACCGCCTGAATA
1 ATATATGGTCGAATCTACCGCCTGAATA
424722 ATATATGGTCG
1 ATATATGGTCG
424733 GCACTGCTGC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (28 bp):
ATATATGGTCGAATCTACCGCCTGAATA
Found at i:424747 original size:28 final size:28
Alignment explanation
Indices: 424666--424754 Score: 90
Period size: 28 Copynumber: 3.2 Consensus size: 28
424656 GTTAGCTTTT
* *
424666 ATATATGGTC-GAATCTGCTGCCTGAATG
1 ATATATGGTCGGCA-CTGCTGCCTGAATA
* * * *
424694 ATATATGGTCGACTCTACCGCCTGAATA
1 ATATATGGTCGGCACTGCTGCCTGAATA
*
424722 ATATATGGTCGGCACTGCTGCTTGAATA
1 ATATATGGTCGGCACTGCTGCCTGAATA
*
424750 CTATA
1 ATATA
424755 GTACATTAAA
Statistics
Matches: 48, Mismatches: 12, Indels: 2
0.77 0.19 0.03
Matches are distributed among these distances:
28 48 1.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (28 bp):
ATATATGGTCGGCACTGCTGCCTGAATA
Found at i:425482 original size:14 final size:13
Alignment explanation
Indices: 425463--425493 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
425453 TGTTAAGAAA
425463 TGTTTTTGATAAAG
1 TGTTTTTGA-AAAG
425477 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
425490 TGTT
1 TGTT
425494 ATGGGAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:426305 original size:14 final size:14
Alignment explanation
Indices: 426286--426315 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
426276 ATCTTAAAAA
*
426286 ATAAAAAAATTTAT
1 ATAAAAAAATTAAT
426300 ATAAAAAAATTAAT
1 ATAAAAAAATTAAT
426314 AT
1 AT
426316 TATGCTATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATAAAAAAATTAAT
Found at i:426380 original size:18 final size:19
Alignment explanation
Indices: 426353--426390 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
426343 TTTGTTTTGC
*
426353 TTTTTAAAATTAAATTTTA
1 TTTTTAAAATTAAAATTTA
426372 TTTTT-AAATTAAAATTTA
1 TTTTTAAAATTAAAATTTA
426390 T
1 T
426391 ATGATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTAAAATTAAAATTTA
Found at i:426960 original size:4 final size:4
Alignment explanation
Indices: 426928--426972 Score: 53
Period size: 4 Copynumber: 12.2 Consensus size: 4
426918 AAAAAAAAGA
*
426928 AAGG AAGG AAGG AAGG AA-G AA-G AAAG AAGG AA-G AAGG AA-G AAGG
1 AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG AAGG
426972 A
1 A
426973 GAATGAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
3 12 0.32
4 25 0.68
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (4 bp):
AAGG
Found at i:426971 original size:7 final size:7
Alignment explanation
Indices: 426931--426972 Score: 66
Period size: 7 Copynumber: 5.9 Consensus size: 7
426921 AAAAAGAAAG
426931 GAAGGAA
1 GAAGGAA
426938 GGAAGGAA
1 -GAAGGAA
*
426946 GAAGAAA
1 GAAGGAA
426953 GAAGGAA
1 GAAGGAA
426960 GAAGGAA
1 GAAGGAA
426967 GAAGGA
1 GAAGGA
426973 GAATGAGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
7 25 0.78
8 7 0.22
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (7 bp):
GAAGGAA
Found at i:427145 original size:18 final size:18
Alignment explanation
Indices: 427122--427156 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
427112 GGAAGAAAAA
427122 TAAGTTTGATTAATTTTT
1 TAAGTTTGATTAATTTTT
*
427140 TAAGTTTGGTTAATTTT
1 TAAGTTTGATTAATTTT
427157 AAATTTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (18 bp):
TAAGTTTGATTAATTTTT
Found at i:431451 original size:35 final size:35
Alignment explanation
Indices: 431403--431686 Score: 146
Period size: 36 Copynumber: 7.9 Consensus size: 35
431393 GGTGTTGACA
* *
431403 TAGATAAGGTTTATCCAATTTTTTTAAGGTTGTCT
1 TAGACAAGGTTTATCCAACTTTTTTAAGGTTGTCT
* * * * *
431438 TAGACAATGTTTATTTCAACCTTTTTAAAGTTGTCA
1 TAGACAAGGTTTA-TCCAACTTTTTTAAGGTTGTCT
* ** *
431474 TAGAC-GGGTTTATTTTAACTTTTTTAAGGTTGTAT
1 TAGACAAGGTTTA-TCCAACTTTTTTAAGGTTGTCT
** * *
431509 TAGATGA-GTTTATCTTAATCATTTTTAGAGGTTGTCT
1 TAGACAAGGTTTATC-CAA-CTTTTTTA-AGGTTGTCT
** * *
431546 TAGACAAAATCTATCTCAACCTTTTTAAGGTTG-CTT
1 TAGACAAGGTTTATC-CAACTTTTTTAAGGTTGTC-T
** * * * *
431582 TAGATGA-CTCTATCTCAATCTTTTTTAAAGGTTGCCA
1 TAGACAAGGTTTATC-CAA-CTTTTTT-AAGGTTGTCT
* * * *
431619 TATACAAGGTTTATTTCAACTTTTTTGAGGTTGTTT
1 TAGACAAGGTTTA-TCCAACTTTTTTAAGGTTGTCT
*
431655 TAGAC-AGGTTTATCCCAATTTTTTTTAAGGTT
1 TAGACAAGGTTTAT-CCAA-CTTTTTTAAGGTT
431687 AATTTATCTA
Statistics
Matches: 191, Mismatches: 44, Indels: 27
0.73 0.17 0.10
Matches are distributed among these distances:
34 2 0.01
35 67 0.35
36 68 0.36
37 38 0.20
38 15 0.08
39 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.15, T:0.46
Consensus pattern (35 bp):
TAGACAAGGTTTATCCAACTTTTTTAAGGTTGTCT
Found at i:431471 original size:36 final size:35
Alignment explanation
Indices: 431423--431667 Score: 161
Period size: 36 Copynumber: 6.8 Consensus size: 35
431413 TTATCCAATT
431423 TTTTTAAGGTTGTCTTAGACAATGTTTATTTCAACC
1 TTTTTAAGGTTGTCTTAGACAA-GTTTATTTCAACC
* * ** * *
431459 TTTTTAAAGTTGTCATAGACGGGTTTATTTTAACT
1 TTTTTAAGGTTGTCTTAGACAAGTTTATTTCAACC
* ** *
431494 TTTTTAAGGTTGTATTAGATGAGTTTATCTT-AATCA
1 TTTTTAAGGTTGTCTTAGACAAGTTTAT-TTCAA-CC
* * *
431530 TTTTTAGAGGTTGTCTTAGACAAAATCTATCTCAACC
1 TTTTTA-AGGTTGTCTTAGAC-AAGTTTATTTCAACC
** * * * *
431567 TTTTTAAGGTTG-CTTTAGATGACTCTATCTCAATCT
1 TTTTTAAGGTTGTC-TTAGACAAGTTTATTTCAA-CC
* * * *
431603 TTTTTAAAGGTTGCCATATACAAGGTTTATTTCAACT
1 TTTTT-AAGGTTGTCTTAGACAA-GTTTATTTCAACC
* * *
431640 TTTTTGAGGTTGTTTTAGACAGGTTTAT
1 TTTTTAAGGTTGTCTTAGACAAGTTTAT
431668 CCCAATTTTT
Statistics
Matches: 163, Mismatches: 36, Indels: 21
0.74 0.16 0.10
Matches are distributed among these distances:
35 54 0.33
36 55 0.34
37 38 0.23
38 16 0.10
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (35 bp):
TTTTTAAGGTTGTCTTAGACAAGTTTATTTCAACC
Found at i:431657 original size:73 final size:73
Alignment explanation
Indices: 431396--431658 Score: 228
Period size: 73 Copynumber: 3.6 Consensus size: 73
431386 TATGTAAGGT
* * * * * ** * * * *
431396 GTTGACATAGATAAGGTTTA-TCCAATTTTTTTAAGGTTGTCTTAGACAATGTTTATTTCAA-CC
1 GTTGTCATAGACAAGGTTTATTTCAACTTTTTTAAGGTTGTTTTAGATGA-CTCTATCTCAATCA
431459 TTTTTAAA-
65 TTTTTAAAG
* * * * * *
431467 GTTGTCATAGAC-GGGTTTATTTTAACTTTTTTAAGGTTGTATTAGATGAGTTTATCTTAATCAT
1 GTTGTCATAGACAAGGTTTATTTCAACTTTTTTAAGGTTGTTTTAGATGACTCTATCTCAATCAT
*
431531 TTTTAGAG
66 TTTTAAAG
* ** * * * * *
431539 GTTGTCTTAGACAAAATCTATCTCAACCTTTTTAAGGTTGCTTTAGATGACTCTATCTCAATCTT
1 GTTGTCATAGACAAGGTTTATTTCAACTTTTTTAAGGTTGTTTTAGATGACTCTATCTCAATCAT
431604 TTTTAAAG
66 TTTTAAAG
* * *
431612 GTTGCCATATACAAGGTTTATTTCAACTTTTTTGAGGTTGTTTTAGA
1 GTTGTCATAGACAAGGTTTATTTCAACTTTTTTAAGGTTGTTTTAGA
431659 CAGGTTTATC
Statistics
Matches: 150, Mismatches: 38, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
70 15 0.10
71 41 0.27
72 11 0.07
73 83 0.55
ACGTcount: A:0.27, C:0.12, G:0.16, T:0.46
Consensus pattern (73 bp):
GTTGTCATAGACAAGGTTTATTTCAACTTTTTTAAGGTTGTTTTAGATGACTCTATCTCAATCAT
TTTTAAAG
Found at i:432127 original size:60 final size:60
Alignment explanation
Indices: 432038--432319 Score: 248
Period size: 60 Copynumber: 4.6 Consensus size: 60
432028 TTTGTCAGAT
* * ** * *
432038 AAAAATTCAATTTTTTTGGTGTTGTTCATGTC-ATGGTCGACACCCCTTATTTATTTGATA
1 AAAAAATCAAATTTTTTGGTGTTGGCCATG-CAATGGCCGACACCCCTTATTTATCTGATA
* * * * * ** *
432098 AAAAAATCAAATTTTTTGGTGTTGGTCATGCAATGACCGATACTCCTTTTTTGCCAGATA
1 AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTATTTATCTGATA
*
432158 AAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCTCTTATTTATCTGATA
1 AAAAAA--TC-AAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTATTTATCTGATA
* * * **
432221 AAAAAATCAAATTTTTTGGTGTTGGCCATGTAA-GAGTCGACATCCCCTT-TTTGTCAAATA
1 AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATG-GCCGACA-CCCCTTATTTATCTGATA
*
432281 AAAAAATTTTAAAATTTTTTTGGTGTT-GCTCATGCAATG
1 AAAAAA---TCAAA-TTTTTTGGTGTTGGC-CATGCAATG
432320 ATTGACACCA
Statistics
Matches: 181, Mismatches: 29, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
59 2 0.01
60 96 0.53
61 7 0.04
62 2 0.01
63 55 0.30
64 18 0.10
65 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.16, T:0.39
Consensus pattern (60 bp):
AAAAAATCAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCTTATTTATCTGATA
Found at i:432184 original size:63 final size:60
Alignment explanation
Indices: 431999--432320 Score: 237
Period size: 60 Copynumber: 5.3 Consensus size: 60
431989 AAAAATTTAA
* * * *
431999 GTTGGCCATTGC-ATGACTGACATTTCC-TTTTTGTCAGAT-AAAAATTCAATTTTTTTGGT
1 GTTGGCCA-TGCAATGACCGACA-CTCCTTTTTTGTCAGATAAAAAAATCAAATTTTTTGGT
** ** * * * **
432058 GTTGTTCATGTC-ATGGTCGACACCCCTTATTTATTTGATAAAAAAATCAAATTTTTTGGT
1 GTTGGCCATG-CAATGACCGACACTCCTTTTTTGTCAGATAAAAAAATCAAATTTTTTGGT
* * *
432118 GTTGGTCATGCAATGACCGATACTCCTTTTTTGCCAGATAAAAAAATTTCAAAATTTTTTGGT
1 GTTGGCCATGCAATGACCGACACTCCTTTTTTGTCAGATAAAAAAA--TC-AAATTTTTTGGT
* * * *
432181 GTTGGCCATGCAATGGCCGACAC-CTCTTATTTATCTGATAAAAAAATCAAATTTTTTGGT
1 GTTGGCCATGCAATGACCGACACTC-CTTTTTTGTCAGATAAAAAAATCAAATTTTTTGGT
* * * * *
432241 GTTGGCCATGTAA-GAGTCGACA-TCCCCTTTTTGTCAAATAAAAAAATTTTAAAATTTTTTTGG
1 GTTGGCCATGCAATGA-CCGACACT-CCTTTTTTGTCAGATAAAAAAA---TCAAA-TTTTTTGG
432304 T
60 T
432305 GTT-GCTCATGCAATGA
1 GTTGGC-CATGCAATGA
432321 TTGACACCAT
Statistics
Matches: 206, Mismatches: 40, Indels: 28
0.75 0.15 0.10
Matches are distributed among these distances:
58 4 0.02
59 24 0.12
60 97 0.47
61 3 0.01
62 3 0.01
63 55 0.27
64 18 0.09
65 2 0.01
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (60 bp):
GTTGGCCATGCAATGACCGACACTCCTTTTTTGTCAGATAAAAAAATCAAATTTTTTGGT
Found at i:432220 original size:123 final size:123
Alignment explanation
Indices: 432024--432319 Score: 365
Period size: 123 Copynumber: 2.4 Consensus size: 123
432014 ACTGACATTT
* ** *
432024 CCTTTTTGTCAGAT--AAAAA-TTC-AATTTTTTTGGTGTTGTTCATGTC-ATGGTCGACACCCC
1 CCTTTTTGTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATG-CAATGGCCGACACCCC
* * *
432084 TTATTTATTTGATAAAAAAATCAAATTTTTTGGTGTTGGTCATGCAATGA-CCGATA-CTC
65 TTATTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCCATGCAA-GAGCCGACATC-C
* * *
432143 CTTTTTTGCCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCTCT
1 CCTTTTTGTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT
* *
432208 TATTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCCATGTAAGAGTCGACATCC
66 TATTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCCATGCAAGAGCCGACATCC
* *
432266 CCTTTTTGTCAAATAAAAAAATTTTAAAATTTTTTTGGTGTT-GCTCATGCAATG
1 CCTTTTTGTCAGATAAAAAAATTTCAAAA-TTTTTTGGTGTTGGC-CATGCAATG
432320 ATTGACACCA
Statistics
Matches: 152, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
119 12 0.08
121 5 0.03
122 6 0.04
123 107 0.70
124 22 0.14
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (123 bp):
CCTTTTTGTCAGATAAAAAAATTTCAAAATTTTTTGGTGTTGGCCATGCAATGGCCGACACCCCT
TATTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGCCATGCAAGAGCCGACATCC
Found at i:432348 original size:123 final size:123
Alignment explanation
Indices: 431999--432376 Score: 326
Period size: 123 Copynumber: 3.1 Consensus size: 123
431989 AAAAATTTAA
* * * * * *
431999 GTTGGCCATTGC-ATGACTGACATTTCCTTTTTGTCAGAT--AAAAA-TTC-AATTTTTTTGGTG
1 GTTGGCCA-TGCAATGACCGACACTCCCTTTTTGCCAAATAAAAAAATTTCAAAATTTTTTGGTG
** ** * ** *
432059 TTGTTCATGTC-ATGGTCGACACCCCTTATTTATTTGATAAAAAAATCAAATTTTTTGGT
65 TTGGCCATG-CAATGACCGACACCTCTTACCTATATGATAAAAAAATCAAATTTTTTGGT
* * * *
432118 GTTGGTCATGCAATGACCGATACTCCTTTTTTGCCAGATAAAAAAATTTCAAAATTTTTTGGTGT
1 GTTGGCCATGCAATGACCGACACTCCCTTTTTGCCAAATAAAAAAATTTCAAAATTTTTTGGTGT
* ** *
432183 TGGCCATGCAATGGCCGACACCTCTTATTTATCTGATAAAAAAATCAAATTTTTTGGT
66 TGGCCATGCAATGACCGACACCTCTTACCTATATGATAAAAAAATCAAATTTTTTGGT
* * * *
432241 GTTGGCCATGTAA-GAGTCGACA-TCCCCTTTTTGTCAAATAAAAAAATTTTAAAATTTTTTTGG
1 GTTGGCCATGCAATGA-CCGACACT-CCCTTTTTGCCAAATAAAAAAATTTCAAAA-TTTTTTGG
** *
432304 TGTT-GCTCATGCAATGATTGACACCATCTT-CCTATATGATAAAAAAAATGTAAATTTTTTTGG
63 TGTTGGC-CATGCAATGACCGACACC-TCTTACCTATATGAT-AAAAAAAT-CAAA-TTTTTTGG
432367 T
123 T
*
432368 GTTGACCAT
1 GTTGGCCAT
432377 ACATTAGTCG
Statistics
Matches: 216, Mismatches: 29, Indels: 20
0.82 0.11 0.08
Matches are distributed among these distances:
118 3 0.01
119 28 0.13
121 5 0.02
122 7 0.03
123 107 0.50
124 34 0.16
125 12 0.06
126 3 0.01
127 17 0.08
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (123 bp):
GTTGGCCATGCAATGACCGACACTCCCTTTTTGCCAAATAAAAAAATTTCAAAATTTTTTGGTGT
TGGCCATGCAATGACCGACACCTCTTACCTATATGATAAAAAAATCAAATTTTTTGGT
Found at i:433240 original size:30 final size:30
Alignment explanation
Indices: 433201--433288 Score: 106
Period size: 30 Copynumber: 2.9 Consensus size: 30
433191 AATTAGAACG
* *
433201 TACAGGAAATTAGAAATTAAAATTAAAATA
1 TACAAGAAATTAGAAATTAAATTTAAAATA
*
433231 TACAAGAAATTAGAAATTGAATTTAAAATA
1 TACAAGAAATTAGAAATTAAATTTAAAATA
* * *
433261 -AAAACGAAATTACAAACTAAATTTAAAA
1 TACAA-GAAATTAGAAATTAAATTTAAAA
433289 AGTAAACGGA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 3 0.06
30 47 0.94
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (30 bp):
TACAAGAAATTAGAAATTAAATTTAAAATA
Found at i:433897 original size:62 final size:62
Alignment explanation
Indices: 433800--433984 Score: 239
Period size: 61 Copynumber: 3.0 Consensus size: 62
433790 AGCTCGTCCG
433800 TGGGTGTCGGACATTGCATGACCAACACAAAAAAAAAATTGAATTTTTTATCTGACAAAAAA
1 TGGGTGTCGGACATTGCATGACCAACACAAAAAAAAAATTGAATTTTTTATCTGACAAAAAA
* * * * *
433862 TGGGTGTCGAACATTGCACGATCAACAC-AAAAAAAAATTG-ATTTTTTATCAGATAAAAAA
1 TGGGTGTCGGACATTGCATGACCAACACAAAAAAAAAATTGAATTTTTTATCTGACAAAAAA
* * * * * *
433922 GGGGTTGTTGGCCATGGCATGACCAACACAAAAAGAAAATTTGACTTTTTTATCTGACAAAAA
1 TGGG-TGTCGGACATTGCATGACCAACACAAAAA-AAAAATTGAATTTTTTATCTGACAAAAA
433985 GGGTATCGGC
Statistics
Matches: 103, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
60 21 0.20
61 30 0.29
62 29 0.28
63 7 0.07
64 16 0.16
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.26
Consensus pattern (62 bp):
TGGGTGTCGGACATTGCATGACCAACACAAAAAAAAAATTGAATTTTTTATCTGACAAAAAA
Found at i:434017 original size:63 final size:61
Alignment explanation
Indices: 433816--434106 Score: 199
Period size: 61 Copynumber: 4.8 Consensus size: 61
433806 TCGGACATTG
* * * * **
433816 CATGACCAACACAAAAAAAAAATTGAATTTTTTATCTGACAAAAAATGGG-TGTCGAACATTG-
1 CATGACCAACAC-AAAAAAAAATTG-ATTTTTTATCAGATAAAAAAGGGGTTATCGGCCA-TGA
* * * * *
433878 CACGATCAACACAAAAAAAAATTGATTTTTTATCAGATAAAAAAGGGGTTGTTGGCCATGG
1 CATGACCAACACAAAAAAAAATTGATTTTTTATCAGATAAAAAAGGGGTTATCGGCCATGA
* *
433939 CATGACCAACACAAAAAGAAAATTTGACTTTTTTATCTGA-CAAAAA-GGG-TATCGGCCATGA
1 CATGACCAACACAAAAA-AAAA-TTGA-TTTTTTATCAGATAAAAAAGGGGTTATCGGCCATGA
* ** ** * * * *
434000 CATGGCCAACAC-CCAAAATTTTGATTTTTTATTCAAAT-AAAATGGGG-TGTCGGCCATGG
1 CATGACCAACACAAAAAAAAATTGATTTTTTA-TCAGATAAAAAAGGGGTTATCGGCCATGA
* **
434059 CATGGCCAACAC--CTAAAAATCTGATTTTTTATTCAGAT-AAAAAGGGGT
1 CATGACCAACACAAAAAAAAAT-TGATTTTTTA-TCAGATAAAAAAGGGGT
434107 GTCGACAATG
Statistics
Matches: 189, Mismatches: 30, Indels: 22
0.78 0.12 0.09
Matches are distributed among these distances:
57 7 0.04
58 16 0.08
59 51 0.27
60 25 0.13
61 53 0.28
62 17 0.09
63 9 0.05
64 11 0.06
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (61 bp):
CATGACCAACACAAAAAAAAATTGATTTTTTATCAGATAAAAAAGGGGTTATCGGCCATGA
Found at i:434064 original size:59 final size:58
Alignment explanation
Indices: 433893--434299 Score: 318
Period size: 59 Copynumber: 6.9 Consensus size: 58
433883 TCAACACAAA
* * * *
433893 AAAAAATTGATTTTTTA-TCAGATAAAAAAGGGGTTGTTGGCCATGGCATGACCAACACAAAA
1 AAAAATTTGATTTTTTATTCAGAT-AAAAAGGGG-TGTCGGCCATGGCATGGCCAACAC---C
* * * *
433955 AGAAAATTTGACTTTTTTA-TCTGACAAAAA-GGGTATCGGCCATGACATGGCCAACACCC
1 A-AAAATTTGA-TTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGGCATGGCCAACA-CC
* * *
434014 AAAATTTTGATTTTTTATTCAAATAAAATGGGGTGTCGGCCATGGCATGGCCAACACC
1 AAAAATTTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGGCATGGCCAACACC
* * * *
434072 TAAAAATCTGATTTTTTATTCAGATAAAAAGGGGTGTCGACAAT-GCAATTGCCAACA--
1 -AAAAATTTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGGC-ATGGCCAACACC
* * * *
434129 AAAAATTTAATTTTTT-TATCAGATAAAAAAGGGGTGTAGGTCATGGCATGACCAACACC
1 AAAAATTTGATTTTTTAT-TCAGAT-AAAAAGGGGTGTCGGCCATGGCATGGCCAACACC
* * * * *
434188 AAAAGATTTGAATTTTTTATCTAACA-AAAAAGAGGTGTCGTCCATGGTATGGCCAACACC
1 AAAA-ATTTG-ATTTTTTAT-TCAGATAAAAAGGGGTGTCGGCCATGGCATGGCCAACACC
* * *
434248 --AAATTT--TTTTTT-TGTCAGATAAAAAAGAGGATGTTGGCCATGGCATAGCCAA
1 AAAAATTTGATTTTTTAT-TCAGAT-AAAAAG-GGGTGTCGGCCATGGCATGGCCAA
434300 TACAATTTTT
Statistics
Matches: 278, Mismatches: 49, Indels: 42
0.75 0.13 0.11
Matches are distributed among these distances:
53 4 0.01
54 6 0.02
55 7 0.03
56 38 0.14
57 34 0.12
58 23 0.08
59 75 0.27
60 32 0.12
61 26 0.09
62 9 0.03
63 13 0.05
64 11 0.04
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (58 bp):
AAAAATTTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGGCATGGCCAACACC
Found at i:434163 original size:116 final size:112
Alignment explanation
Indices: 433893--434293 Score: 346
Period size: 116 Copynumber: 3.4 Consensus size: 112
433883 TCAACACAAA
* *
433893 AAAAAATTGA-TTTTTTATCAGATAAAAAAGGGGTTGTTGGCCATGGCATGACCAACACAAAAAG
1 AAAAAATTTATTTTTTTATCAGATAAAAAAGGGG-TGTTGGCCATGGCATGACCAACAC---CA-
* * *
433957 AAAATTTGACTTTTTTA-TCTGACAAAAA-GGGTATCGGCCATGACATGGCCAAC
61 AAAATTTGA-TTTTTTATTCAGA-AAAAAGGGGTGTCGACCATGA-ATGGCCAAC
* * * * *
434010 ACCCAAAATTT-TGATTTTTTATTCAAAT-AAAATGGGGTGTCGGCCATGGCATGGCCAACACCT
1 A--AAAAATTTAT--TTTTTTA-TCAGATAAAAAAGGGGTGTTGGCCATGGCATGACCAACACC-
* * *
434073 AAAAATCTGATTTTTTATTCAGATAAAAAGGGGTGTCGACAATGCAATTGCCAAC
60 AAAAATTTGATTTTTTATTCAGA-AAAAAGGGGTGTCGACCATG-AATGGCCAAC
* *
434128 AAAAAATTTAATTTTTTTATCAGATAAAAAAGGGGTGTAGGTCATGGCATGACCAACACCAAAAG
1 AAAAAATTT-ATTTTTTTATCAGATAAAAAAGGGGTGTTGGCCATGGCATGACCAACACCAAAA-
* * * * *
434193 ATTTGAATTTTTTATCTAACAAAAAAGAGGTGTCGTCCATGGTATGGCCAAC
64 ATTTG-ATTTTTTAT-TCAGAAAAAAGGGGTGTCGACCAT-GAATGGCCAAC
** * *
434245 ACCAAATTT-TTTTTTTGTCAGATAAAAAAGAGGATGTTGGCCATGGCAT
1 AAAAAATTTATTTTTTTATCAGATAAAAAAG-GGGTGTTGGCCATGGCAT
434294 AGCCAATACA
Statistics
Matches: 232, Mismatches: 34, Indels: 37
0.77 0.11 0.12
Matches are distributed among these distances:
115 29 0.12
116 70 0.30
117 58 0.25
118 26 0.11
119 7 0.03
120 22 0.09
121 15 0.06
122 5 0.02
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.29
Consensus pattern (112 bp):
AAAAAATTTATTTTTTTATCAGATAAAAAAGGGGTGTTGGCCATGGCATGACCAACACCAAAAAT
TTGATTTTTTATTCAGAAAAAAGGGGTGTCGACCATGAATGGCCAAC
Found at i:441604 original size:2 final size:2
Alignment explanation
Indices: 441599--441637 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
441589 TACTTCCCCC
441599 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT -T CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
441638 AATGCTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:448280 original size:29 final size:28
Alignment explanation
Indices: 448211--448280 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
448201 GGCGTCCTTC
*
448211 ACAGAATCAGCCACATAGGCTTACTTTA
1 ACAGAATCAGCCACATAGACTTACTTTA
*
448239 ACA-AATTCGGCCACGA-AGACTTCACTTTA
1 ACAGAA-TCAGCCAC-ATAGACTT-ACTTTA
448268 ACAGAATCAGCCA
1 ACAGAATCAGCCA
448281 TAAAGGCTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 2 0.06
28 15 0.43
29 16 0.46
30 2 0.06
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.21
Consensus pattern (28 bp):
ACAGAATCAGCCACATAGACTTACTTTA
Found at i:448954 original size:96 final size:96
Alignment explanation
Indices: 448770--448961 Score: 257
Period size: 96 Copynumber: 2.0 Consensus size: 96
448760 ATTTTTGCAA
** *
448770 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
448835 GAATCGAAGATAAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* *
448866 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTC
1 AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATA-TTTC
*
448930 -GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
448962 TTTTAAAGCT
Statistics
Matches: 85, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
95 3 0.04
96 77 0.91
97 5 0.06
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:449259 original size:29 final size:29
Alignment explanation
Indices: 449220--449320 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
449210 TTAGAGTTTA
449220 AAAATGG-AATTTTTAGACATTCGGGGGT
1 AAAATGGTAATTTTTAGACATTCGGGGGT
* * ** *
449248 AAAAGGGTAATTTTGAGAGTTTC-GAGGT
1 AAAATGGTAATTTTTAGACATTCGGGGGT
* * *
449276 CAAAAATGG-AGTTTTTGGACATCCGGGGGT
1 --AAAATGGTAATTTTTAGACATTCGGGGGT
449306 AAAATGGTAATTTTT
1 AAAATGGTAATTTTT
449321 GGAAGTTTTA
Statistics
Matches: 54, Mismatches: 14, Indels: 9
0.70 0.18 0.12
Matches are distributed among these distances:
28 17 0.31
29 27 0.50
30 10 0.19
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTAGACATTCGGGGGT
Found at i:449321 original size:29 final size:28
Alignment explanation
Indices: 449220--449323 Score: 86
Period size: 28 Copynumber: 3.6 Consensus size: 28
449210 TTAGAGTTTA
*
449220 AAAATGGAATTTTTAGACATTCGGGGGT
1 AAAATGGAATTTTTGGACATTCGGGGGT
* ** *
449248 AAAAGGGTAA-TTTTGAGAGTTTC-GAGGT
1 AAAATGG-AATTTTTG-GACATTCGGGGGT
* *
449276 CAAAAATGGAGTTTTTGGACATCCGGGGGT
1 --AAAATGGAATTTTTGGACATTCGGGGGT
449306 AAAATGGTAATTTTTGGA
1 AAAATGG-AATTTTTGGA
449324 AGTTTTAGGG
Statistics
Matches: 57, Mismatches: 12, Indels: 13
0.70 0.15 0.16
Matches are distributed among these distances:
28 21 0.37
29 21 0.37
30 15 0.26
ACGTcount: A:0.32, C:0.07, G:0.30, T:0.32
Consensus pattern (28 bp):
AAAATGGAATTTTTGGACATTCGGGGGT
Found at i:449334 original size:29 final size:29
Alignment explanation
Indices: 449302--449746 Score: 331
Period size: 30 Copynumber: 15.1 Consensus size: 29
449292 GGACATCCGG
449302 GGGT-AAAATGGTAATTTTTGGAAGTTTTA
1 GGGTAAAAATGG-AATTTTTGGAAGTTTTA
*
449331 GGGTAAAAAAT-GATATATTTGGAAG-TTT-
1 GGGT-AAAAATGGA-ATTTTTGGAAGTTTTA
* * *
449359 GGGCCTAAAAATGGAAATTTTGAAAGTTTCGA
1 GGG--TAAAAATGGAATTTTTGGAAGTTT-TA
* *
449391 GGGTAAGAATGAAATTTTTGGAAGTTTT-
1 GGGTAAAAATGGAATTTTTGGAAGTTTTA
* ***
449419 GGGTCAAAAATGGGATTTTTGGAAGTTCGG
1 GGGT-AAAAATGGAATTTTTGGAAGTTTTA
** *
449449 GGGTAAAAATAAAATTTTTGGAAG-TTTC
1 GGGTAAAAATGGAATTTTTGGAAGTTTTA
* *
449477 GAGGTCAAAAATGGTATTTTTGGAAGTTTGA
1 G-GGT-AAAAATGGAATTTTTGGAAGTTTTA
* ** *
449508 GGCTAAAAATGGAATTTTTAAAAGTTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTT-A
* * *
449538 GGGTAAGAATGGAATTTTTGGTAGTTTTGG
1 GGGTAAAAATGGAATTTTTGGAAGTTTT-A
***
449568 GGGTTAAAAAT-GAGATTTTTGGAAGTTCGG
1 GGG-TAAAAATGGA-ATTTTTGGAAGTTTTA
* *
449598 GGGCAAAAATGGGATTTTTGGAAGTTTT-
1 GGGTAAAAATGGAATTTTTGGAAGTTTTA
**
449626 GGGATTAAAAAT-GAGATATTTT-GAAG-TTCG
1 GGG--TAAAAATGGA-AT-TTTTGGAAGTTTTA
*
449656 GGGTAAAAATAGAATTTTTGGAAGTTTTA
1 GGGTAAAAATGGAATTTTTGGAAGTTTTA
*
449685 GGGTCAAAAAT-GAGATTTTTGGAAGTTTGA
1 GGGT-AAAAATGGA-ATTTTTGGAAGTTTTA
*
449715 GGGTAAAAATGAAATTTTTGGATAG-TTTA
1 GGGTAAAAATGGAATTTTTGGA-AGTTTTA
449744 GGG
1 GGG
449747 ACCTTCAAGG
Statistics
Matches: 333, Mismatches: 53, Indels: 60
0.75 0.12 0.13
Matches are distributed among these distances:
27 4 0.01
28 25 0.08
29 134 0.40
30 137 0.41
31 30 0.09
32 3 0.01
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.35
Consensus pattern (29 bp):
GGGTAAAAATGGAATTTTTGGAAGTTTTA
Found at i:449353 original size:59 final size:58
Alignment explanation
Indices: 449210--449342 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 58
449200 TTTAGGAAAA
* * * * *
449210 TTAGAGTTTAAAAATGGAATTTTTAGACATTCGGGGGTAAAAGGGTAATTTTGAGAGT
1 TTAGAGGTAAAAAATGGAGTTTTTGGACATCCGGGGGTAAAAGGGTAATTTTGAGAGT
* * *
449268 TTCGAGGTCAAAAATGGAGTTTTTGGACATCCGGGGGTAAAATGGTAATTTTTG-GAAGTT
1 TTAGAGGTAAAAAATGGAGTTTTTGGACATCCGGGGGTAAAAGGGTAA-TTTTGAG-AG-T
449328 TTAG-GGTAAAAAATG
1 TTAGAGGTAAAAAATG
449343 ATATATTTGG
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
58 42 0.67
59 17 0.27
60 4 0.06
ACGTcount: A:0.33, C:0.05, G:0.29, T:0.33
Consensus pattern (58 bp):
TTAGAGGTAAAAAATGGAGTTTTTGGACATCCGGGGGTAAAAGGGTAATTTTGAGAGT
Found at i:449368 original size:59 final size:56
Alignment explanation
Indices: 449305--449746 Score: 343
Period size: 59 Copynumber: 7.5 Consensus size: 56
449295 CATCCGGGGG
* *
449305 TAAAATGGTAATTTTTGGAAGTTTTAGGGTAAAAAATGATATATTTGGAAGTTTGGGCC
1 TAAAATGG-AATTTTTGGAAGTTTTAGGGT-AAAAATGAGATTTTTGGAAGTTTGGG-C
* * * * *
449364 TAAAAATGGAAATTTTGAAAGTTTCGAGGGTAAGAATGAAATTTTTGGAAGTTTTGGGTC
1 T-AAAATGGAATTTTTGGAAGTTT-TAGGGTAAAAATGAGATTTTTGGAAG-TTTGGG-C
* * *** * *
449424 AAAAATGGGATTTTTGGAAGTTCGGGGGTAAAAATAAAATTTTTGGAAGTTTCGAGGTC
1 TAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGAGATTTTTGGAAGTTT-G-GG-C
* * * * ** *
449483 AAAAATGGTATTTTTGGAAGTTTGAGGCTAAAAATG-GAATTTTTAAAAGTTTTGGGGG
1 TAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGAG-ATTTTTGGAAG-TTT-GGGC
* * *
449541 TAAGAATGGAATTTTTGGTAGTTTTGGGGGTTAAAAATGAGATTTTTGGAAGTTCGGGGGC
1 TAA-AATGGAATTTTTGGAAGTTTT-AGGG-TAAAAATGAGATTTTTGGAAGTT--TGGGC
* * * *
449602 AAAAATGGGATTTTTGGAAGTTTT-GGGATTAAAAATGAGATATTTT-GAAGTTCGGGG
1 TAAAATGGAATTTTTGGAAGTTTTAGGG--TAAAAATGAGAT-TTTTGGAAGTTTGGGC
* *
449659 TAAAAATAGAATTTTTGGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTGAGGG
1 T-AAAATGGAATTTTTGGAAGTTTTAGGGT-AAAAATGAGATTTTTGGAAGTTTG-GGC
*
449718 TAAAAATGAAATTTTTGGATAG-TTTAGGG
1 T-AAAATGGAATTTTTGGA-AGTTTTAGGG
449747 ACCTTCAAGG
Statistics
Matches: 316, Mismatches: 46, Indels: 42
0.78 0.11 0.10
Matches are distributed among these distances:
57 11 0.03
58 68 0.22
59 162 0.51
60 52 0.16
61 22 0.07
62 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (56 bp):
TAAAATGGAATTTTTGGAAGTTTTAGGGTAAAAATGAGATTTTTGGAAGTTTGGGC
Found at i:451552 original size:17 final size:17
Alignment explanation
Indices: 451512--451544 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
451502 ATTGGACATT
*
451512 TTAAATTTAAAATAAAC
1 TTAATTTTAAAATAAAC
451529 TTAATTTTAAAATAAA
1 TTAATTTTAAAATAAA
451545 TTCAATTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAATTTTAAAATAAAC
Found at i:456162 original size:34 final size:34
Alignment explanation
Indices: 456119--456189 Score: 142
Period size: 34 Copynumber: 2.1 Consensus size: 34
456109 TATGCATAGT
456119 TGACCTATCAATCAACAGAACTTGAAGTAACTTG
1 TGACCTATCAATCAACAGAACTTGAAGTAACTTG
456153 TGACCTATCAATCAACAGAACTTGAAGTAACTTG
1 TGACCTATCAATCAACAGAACTTGAAGTAACTTG
456187 TGA
1 TGA
456190 GCCTTGAGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (34 bp):
TGACCTATCAATCAACAGAACTTGAAGTAACTTG
Found at i:457453 original size:2 final size:2
Alignment explanation
Indices: 457446--457472 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
457436 GTGAGTGAGT
457446 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
457473 GGTCTCATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:466197 original size:5 final size:6
Alignment explanation
Indices: 466165--466211 Score: 64
Period size: 6 Copynumber: 8.2 Consensus size: 6
466155 TTTTAAAACA
466165 ATATTT ATATTT ATATTT ATATTT ATA-TT ATA-TT AT-TTT AATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT -ATATTT
466211 A
1 A
466212 ATAATTTTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
5 11 0.29
6 24 0.63
7 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
ATATTT
Found at i:466209 original size:28 final size:28
Alignment explanation
Indices: 466165--466232 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
466155 TTTTAAAACA
466165 ATAT-TTATATTT-ATATTT-AT-ATTTAT
1 ATATATTAT-TTTAATATTTAATAATTT-T
466191 ATTATATTATTTTAATATTTAATAATTTT
1 A-TATATTATTTTAATATTTAATAATTTT
*
466220 ATATATTTTTTTA
1 ATATATTATTTTA
466233 TTTATTGAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 1 0.03
27 6 0.17
28 21 0.58
29 4 0.11
30 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
ATATATTATTTTAATATTTAATAATTTT
Found at i:475000 original size:17 final size:18
Alignment explanation
Indices: 474968--475001 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
474958 TTATTTACCA
*
474968 AAAAATTACATAATATAT
1 AAAAATAACATAATATAT
474986 AAAAATAACAT-ATATA
1 AAAAATAACATAATATA
475002 AAGTACTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAACATAATATAT
Found at i:476077 original size:31 final size:32
Alignment explanation
Indices: 476042--476112 Score: 110
Period size: 31 Copynumber: 2.3 Consensus size: 32
476032 AACTTAACAG
*
476042 TTCAATGACTTGAATAAAAACTTTTAAAT-GT
1 TTCAATGACTTAAATAAAAACTTTTAAATAGT
*
476073 TTCAATGACTTAAATGAAAACTTTTAAATAGT
1 TTCAATGACTTAAATAAAAACTTTTAAATAGT
476105 TT-AATGAC
1 TTCAATGAC
476113 CAAATTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 33 0.89
32 4 0.11
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (32 bp):
TTCAATGACTTAAATAAAAACTTTTAAATAGT
Found at i:478472 original size:16 final size:16
Alignment explanation
Indices: 478430--478477 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
478420 TTTTATGAAC
478430 TTTTTATATATTTTTAA
1 TTTTT-TATATTTTTAA
* ** *
478447 TGTTAAATATTTTTTA
1 TTTTTTATATTTTTAA
478463 TTTTTTATATTTTTA
1 TTTTTTATATTTTTA
478478 CAATTATTTG
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTTTATATTTTTAA
Found at i:479010 original size:30 final size:32
Alignment explanation
Indices: 478947--479026 Score: 101
Period size: 30 Copynumber: 2.6 Consensus size: 32
478937 GGACCACAAA
*
478947 AAGTTTAAGTACCAACTTAAAAACAAGGTGTC
1 AAGTTTAAGTACCAAATTAAAAACAAGGTGTC
**
478979 AAGTTTAAGTACCAAATTAGGAA-AA-GTGTC
1 AAGTTTAAGTACCAAATTAAAAACAAGGTGTC
* *
479009 AAGTTTGAGTATCAAATT
1 AAGTTTAAGTACCAAATT
479027 GGACCCAGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 21 0.49
31 2 0.05
32 20 0.47
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.29
Consensus pattern (32 bp):
AAGTTTAAGTACCAAATTAAAAACAAGGTGTC
Found at i:485530 original size:21 final size:21
Alignment explanation
Indices: 485480--485530 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
485470 GGAGTTTTTA
* *
485480 GTATCGATAGAAGCATGACTT
1 GTATCGATAAAAGCATCACTT
* * *
485501 GTTTTGATAAAAGCTTCACTT
1 GTATCGATAAAAGCATCACTT
485522 GTATCGATA
1 GTATCGATA
485531 GAACTGTCAC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.14, G:0.20, T:0.35
Consensus pattern (21 bp):
GTATCGATAAAAGCATCACTT
Found at i:492014 original size:26 final size:26
Alignment explanation
Indices: 491971--492026 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
491961 GTATACTGGT
491971 TAAACTCTATCTAGGCTCGTAAGAGC
1 TAAACTCTATCTAGGCTCGTAAGAGC
*
491997 TAAACTCTGTCT-GAGCTCGTAAGAGC
1 TAAACTCTATCTAG-GCTCGTAAGAGC
492023 TAAA
1 TAAA
492027 AATTTTGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 1 0.04
26 27 0.96
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (26 bp):
TAAACTCTATCTAGGCTCGTAAGAGC
Found at i:495723 original size:13 final size:13
Alignment explanation
Indices: 495705--495731 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
495695 CAAAAGGGAC
495705 ACTTGTCCAATTT
1 ACTTGTCCAATTT
495718 ACTTGTCCAATTT
1 ACTTGTCCAATTT
495731 A
1 A
495732 AAGGAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (13 bp):
ACTTGTCCAATTT
Found at i:498660 original size:52 final size:52
Alignment explanation
Indices: 498504--498649 Score: 213
Period size: 52 Copynumber: 2.8 Consensus size: 52
498494 GCCATAAACG
* *
498504 AAGAGGTCCGTTGACTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
1 AAGAGGTCCGATGACTTAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* *
498556 AAGAGGTCCAATGA-TTAAGTGTCATCGTGAGTATATGAATCTTTTACGGATT
1 AAGAGGTCCGATGACTT-AGTGTCATCGTGAGTATATGAATCCTTTACGGATT
* * *
498608 AAGAGGTCTGATGACTTTGTGTCATCGCGAGTATATGAATCC
1 AAGAGGTCCGATGACTTAGTGTCATCGTGAGTATATGAATCC
498650 CTTGCAGATT
Statistics
Matches: 83, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 1 0.01
52 80 0.96
53 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.25, T:0.33
Consensus pattern (52 bp):
AAGAGGTCCGATGACTTAGTGTCATCGTGAGTATATGAATCCTTTACGGATT
Found at i:500551 original size:2 final size:2
Alignment explanation
Indices: 500546--500607 Score: 106
Period size: 2 Copynumber: 31.0 Consensus size: 2
500536 ATATATATAC
500546 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
* *
500588 GT GT GT TT AT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT
500608 ATGTATTATT
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.52
Consensus pattern (2 bp):
GT
Found at i:501142 original size:38 final size:39
Alignment explanation
Indices: 501059--501142 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 39
501049 TGAGTCTATT
* *
501059 TAGAATTGCGCCCAGAATTGTCACTGCATGATAATGTCC
1 TAGAATTGCGCCCAAAATTGTCACTGCATGAGAATGTCC
* *
501098 -AAAATTGCGCCCAAAATTGTCACTGCATGAGCATG-CC
1 TAGAATTGCGCCCAAAATTGTCACTGCATGAGAATGTCC
501135 TAGAATTG
1 TAGAATTG
501143 TCGTTGCAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
37 2 0.05
38 37 0.95
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (39 bp):
TAGAATTGCGCCCAAAATTGTCACTGCATGAGAATGTCC
Found at i:504233 original size:38 final size:38
Alignment explanation
Indices: 504150--504234 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
504140 TGAGTCTATT
* * *
504150 CAGAATTGCGCCCAGAATTGTCACTGCATGACGATGTC
1 CAGAATTGTGCCCAAAATTGTCACTGCATGACGATGCC
*
504188 CAAAATTGTGCCCAAAATTGTCACTGCATGA-GCATGCC
1 CAGAATTGTGCCCAAAATTGTCACTGCATGACG-ATGCC
504226 CAGAATTGT
1 CAGAATTGT
504235 CGCTACAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 1 0.02
38 40 0.98
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.25
Consensus pattern (38 bp):
CAGAATTGTGCCCAAAATTGTCACTGCATGACGATGCC
Found at i:505108 original size:20 final size:20
Alignment explanation
Indices: 505083--505127 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
505073 TTTGTCATAT
*
505083 TTTATAAACTGCATAGGATG
1 TTTATAAACTGCATAGGATA
505103 TTTATAAACTGCATAGGATA
1 TTTATAAACTGCATAGGATA
505123 TTTAT
1 TTTAT
505128 CTATAACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.40
Consensus pattern (20 bp):
TTTATAAACTGCATAGGATA
Found at i:509017 original size:5 final size:5
Alignment explanation
Indices: 509007--509031 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
508997 GAAATTTTTT
509007 GACTC GACTC GACTC GACTC GACTC
1 GACTC GACTC GACTC GACTC GACTC
509032 AATCGAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.40, G:0.20, T:0.20
Consensus pattern (5 bp):
GACTC
Found at i:510798 original size:123 final size:123
Alignment explanation
Indices: 510579--510828 Score: 500
Period size: 123 Copynumber: 2.0 Consensus size: 123
510569 AACACTAACA
510579 CATACTATTTAGAATGAACCAACATTGATAAGTACGTTCCATAAATTCCTCATATTTTTTCTCTT
1 CATACTATTTAGAATGAACCAACATTGATAAGTACGTTCCATAAATTCCTCATATTTTTTCTCTT
510644 AATTTTCTAATTTGTTTCGAATTGGTCTATGATTGTTCCTAACTTATTTTTAAGGCCT
66 AATTTTCTAATTTGTTTCGAATTGGTCTATGATTGTTCCTAACTTATTTTTAAGGCCT
510702 CATACTATTTAGAATGAACCAACATTGATAAGTACGTTCCATAAATTCCTCATATTTTTTCTCTT
1 CATACTATTTAGAATGAACCAACATTGATAAGTACGTTCCATAAATTCCTCATATTTTTTCTCTT
510767 AATTTTCTAATTTGTTTCGAATTGGTCTATGATTGTTCCTAACTTATTTTTAAGGCCT
66 AATTTTCTAATTTGTTTCGAATTGGTCTATGATTGTTCCTAACTTATTTTTAAGGCCT
510825 CATA
1 CATA
510829 GGCTCGACTT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 127 1.00
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.44
Consensus pattern (123 bp):
CATACTATTTAGAATGAACCAACATTGATAAGTACGTTCCATAAATTCCTCATATTTTTTCTCTT
AATTTTCTAATTTGTTTCGAATTGGTCTATGATTGTTCCTAACTTATTTTTAAGGCCT
Found at i:512362 original size:13 final size:13
Alignment explanation
Indices: 512340--512364 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
512330 TATTTTTCAC
512340 AACACTTTTCAAA
1 AACACTTTTCAAA
512353 AACACTTTTCAA
1 AACACTTTTCAA
512365 TCTTAATGAT
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:0.24, G:0.00, T:0.32
Consensus pattern (13 bp):
AACACTTTTCAAA
Found at i:516945 original size:7 final size:7
Alignment explanation
Indices: 516933--517018 Score: 172
Period size: 7 Copynumber: 12.3 Consensus size: 7
516923 CATTTGTATC
516933 GAAAACG
1 GAAAACG
516940 GAAAACG
1 GAAAACG
516947 GAAAACG
1 GAAAACG
516954 GAAAACG
1 GAAAACG
516961 GAAAACG
1 GAAAACG
516968 GAAAACG
1 GAAAACG
516975 GAAAACG
1 GAAAACG
516982 GAAAACG
1 GAAAACG
516989 GAAAACG
1 GAAAACG
516996 GAAAACG
1 GAAAACG
517003 GAAAACG
1 GAAAACG
517010 GAAAACG
1 GAAAACG
517017 GA
1 GA
517019 GAGTATGAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 79 1.00
ACGTcount: A:0.57, C:0.14, G:0.29, T:0.00
Consensus pattern (7 bp):
GAAAACG
Found at i:526018 original size:479 final size:479
Alignment explanation
Indices: 525121--526142 Score: 1857
Period size: 479 Copynumber: 2.1 Consensus size: 479
525111 AAATTTGCTG
*
525121 AGTATTTTTATACTTACCTTAATTTTTATTTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGTA
1 AGTATTTTTATACTTACCTTAATTTTTATGTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGTA
* * *
525186 GGTTAGATTATCGGAGCATACATATCTTCTTACGTTCCTCTTCGGTAGATATTGATGTCTTGAAT
66 GGTTAGATCATCGAAGCATACACATCTTCTTACGTTCCTCTTCGGTAGATATTGATGTCTTGAAT
525251 TTTTGGTTAATTTTGGCATGTATTTAGGATGTTATTTTGTAAAGGTATAATTATGTCTTAGAATT
131 TTTTGGTTAATTTTGGCATGTATTTAGGATGTTATTTTGTAAAGGTATAATTATGTCTTAGAATT
525316 TAATTTTGTATAAACTTGGTGCTTGGACAAATTGGCCAAGGTGGGTCTTTTGCAATTGTACATAT
196 TAATTTTGTATAAACTTGGTGCTTGGACAAATTGGCCAAGGTGGGTCTTTTGCAATTGTACATAT
* * *
525381 ATGATATAATTTGATGCCTAAATTGAGTAATTTTAGTTGTTTTGGTATGATTTGGATAGGTTTTG
261 ATGATATAATTTCATGCCTAAATTGAGTAATTTTAATTGTTTTGGTATGATTTGGAGAGGTTTTG
525446 AATGTGTTTTAATCATAGGAATTCATAAGGATATGCATTAGTAAAGTTTAAGCAAATGGCTTGTT
326 AATGTGTTTTAATCATAGGAATTCATAAGGATATGCATTAGTAAAGTTTAAGCAAATGGCTTGTT
* * *
525511 TTATGAGCTTTTTGTTGTGTACACGGGTTGGCATATGGTCTGGTCACACGATCATGTGACACTAT
391 TCATGAGCTTTTTGTTGTGTACACGGGTTGGCATACGGTCTGGTCACACAATCATGTGACACTAT
*
525576 TCATTTTAGGTTCAGGGTTTACTA
456 TCATTTTAGGTGCAGGGTTTACTA
525600 AGTATTTTTATACTTACCTTAATTTTTATGTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGTA
1 AGTATTTTTATACTTACCTTAATTTTTATGTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGTA
* * *
525665 GGTTAGATCATCGAAGTATACACATCTTCTTACGTTCCT-TCTCGGTTGATATTGATGTCTTGAT
66 GGTTAGATCATCGAAGCATACACATCTTCTTACGTTCCTCT-TCGGTAGATATTGATGTCTTGAA
*
525729 TTTTTGGTTAATTTTGGCATGTATTTAGGATGTTATTTTGTAAAGGTATGATTATGTCTTAGAAT
130 TTTTTGGTTAATTTTGGCATGTATTTAGGATGTTATTTTGTAAAGGTATAATTATGTCTTAGAAT
* *
525794 TTAATTTTGTATAAGCTTGGTGCTTGGACAAATTGGCCAAGTTGGGTCTTTTGCAATTGTACATA
195 TTAATTTTGTATAAACTTGGTGCTTGGACAAATTGGCCAAGGTGGGTCTTTTGCAATTGTACATA
525859 TATGATATAATTTCATGCCTAAATTGAGTAATTTTAATTGTTTTGGTATGATTTGGAGAGGTTTT
260 TATGATATAATTTCATGCCTAAATTGAGTAATTTTAATTGTTTTGGTATGATTTGGAGAGGTTTT
* *
525924 GAATGTGTTTTAATCATAGGAATTCATAAGGATATGCATTAGTGATGTTTAAGCAAATGGCTTGT
325 GAATGTGTTTTAATCATAGGAATTCATAAGGATATGCATTAGTAAAGTTTAAGCAAATGGCTTGT
525989 TTCATGAGCTTTTTGTTGTGTACACGGGTTGGCATACGGTCTGGTCACACAATCATGTGACACTA
390 TTCATGAGCTTTTTGTTGTGTACACGGGTTGGCATACGGTCTGGTCACACAATCATGTGACACTA
526054 TTCATTTTAGGTGCAGGGTTTACTA
455 TTCATTTTAGGTGCAGGGTTTACTA
526079 AGTATTTTTATACTTACCTTAATTTTTATGTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGT
1 AGTATTTTTATACTTACCTTAATTTTTATGTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGT
526143 GTGACCCTTT
Statistics
Matches: 523, Mismatches: 19, Indels: 2
0.96 0.03 0.00
Matches are distributed among these distances:
478 1 0.00
479 522 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.44
Consensus pattern (479 bp):
AGTATTTTTATACTTACCTTAATTTTTATGTCCTTTGTAAATTTTGAACTTTTTGAGAATTCGTA
GGTTAGATCATCGAAGCATACACATCTTCTTACGTTCCTCTTCGGTAGATATTGATGTCTTGAAT
TTTTGGTTAATTTTGGCATGTATTTAGGATGTTATTTTGTAAAGGTATAATTATGTCTTAGAATT
TAATTTTGTATAAACTTGGTGCTTGGACAAATTGGCCAAGGTGGGTCTTTTGCAATTGTACATAT
ATGATATAATTTCATGCCTAAATTGAGTAATTTTAATTGTTTTGGTATGATTTGGAGAGGTTTTG
AATGTGTTTTAATCATAGGAATTCATAAGGATATGCATTAGTAAAGTTTAAGCAAATGGCTTGTT
TCATGAGCTTTTTGTTGTGTACACGGGTTGGCATACGGTCTGGTCACACAATCATGTGACACTAT
TCATTTTAGGTGCAGGGTTTACTA
Found at i:526668 original size:36 final size:36
Alignment explanation
Indices: 526622--526693 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
526612 AACCTCAACC
*
526622 ATACATTACACAGCTCAACCTCAACCATACCATCTT
1 ATACAATACACAGCTCAACCTCAACCATACCATCTT
526658 ATACAATACACAGCTCAACCTCAACCATACCATCTT
1 ATACAATACACAGCTCAACCTCAACCATACCATCTT
526694 CATATCACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.36, G:0.03, T:0.24
Consensus pattern (36 bp):
ATACAATACACAGCTCAACCTCAACCATACCATCTT
Found at i:529110 original size:42 final size:42
Alignment explanation
Indices: 529063--529157 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
529053 TATCTCAATT
529063 AGAAATGATAGACAAAGGAACCCCATAAAGACGAACTATATC
1 AGAAATGATAGACAAAGGAACCCCATAAAGACGAACTATATC
*
529105 AGAAATGATAGACAAAGGAACCCCATAAAGACGAACTATCTC
1 AGAAATGATAGACAAAGGAACCCCATAAAGACGAACTATATC
*
529147 CGAAATG-TAGA
1 AGAAATGATAGA
529158 GTCGGACTAA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
41 4 0.08
42 47 0.92
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.15
Consensus pattern (42 bp):
AGAAATGATAGACAAAGGAACCCCATAAAGACGAACTATATC
Found at i:534467 original size:7 final size:7
Alignment explanation
Indices: 534457--534539 Score: 62
Period size: 7 Copynumber: 11.6 Consensus size: 7
534447 AACCTAAAAC
534457 TCAATGG
1 TCAATGG
*
534464 TCAACGG
1 TCAATGG
*
534471 TCATTGG
1 TCAATGG
**
534478 TCAATCA
1 TCAATGG
*
534485 TCAACGG
1 TCAATGG
534492 TCAACT-G
1 TCAA-TGG
534499 TCAATGG
1 TCAATGG
534506 TCAATGG
1 TCAATGG
534513 TCAACACT-G
1 TC-A-A-TGG
534522 TCAATGG
1 TCAATGG
*
534529 TCAACGG
1 TCAATGG
534536 TCAA
1 TCAA
534540 AGGGTTTAAG
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
6 2 0.03
7 50 0.85
8 2 0.03
9 4 0.07
10 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (7 bp):
TCAATGG
Found at i:534501 original size:21 final size:21
Alignment explanation
Indices: 534457--534539 Score: 96
Period size: 21 Copynumber: 3.9 Consensus size: 21
534447 AACCTAAAAC
*
534457 TCAATGGTCAACGGTC-ATTGG
1 TCAATGGTCAACGGTCAACT-G
**
534478 TCAATCATCAACGGTCAACTG
1 TCAATGGTCAACGGTCAACTG
*
534499 TCAATGGTCAATGGTCAACACTG
1 TCAATGGTCAACGGTC-A-ACTG
534522 TCAATGGTCAACGGTCAA
1 TCAATGGTCAACGGTCAA
534540 AGGGTTTAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
21 29 0.56
22 4 0.08
23 19 0.37
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (21 bp):
TCAATGGTCAACGGTCAACTG
Found at i:534525 original size:23 final size:23
Alignment explanation
Indices: 534485--534539 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
534475 TGGTCAATCA
534485 TCAACGGTC-A-ACTGTCAATGG
1 TCAACGGTCAACACTGTCAATGG
*
534506 TCAATGGTCAACACTGTCAATGG
1 TCAACGGTCAACACTGTCAATGG
534529 TCAACGGTCAA
1 TCAACGGTCAA
534540 AGGGTTTAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.27
22 1 0.03
23 21 0.70
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
TCAACGGTCAACACTGTCAATGG
Found at i:537598 original size:27 final size:27
Alignment explanation
Indices: 537547--537598 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
537537 ATTTAAAAAG
**
537547 TTATATTAAATTATATTTTATTTATCA
1 TTATATTAAATTATATTAAATTTATCA
537574 TTATATTAAATTAT-TTAAATATTAT
1 TTATATTAAATTATATTAAAT-TTAT
537599 TTATAAATGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TTATATTAAATTATATTAAATTTATCA
Found at i:540270 original size:227 final size:227
Alignment explanation
Indices: 539875--540322 Score: 833
Period size: 227 Copynumber: 2.0 Consensus size: 227
539865 CAGCTCATAG
*
539875 TAATCTAAGGCTTGCGAGAATTATTGCTAAGTTCCTCCTTGAAACAGAGCAAAATAATCCTTCAG
1 TAATCTAAGGCTTGCGAGAATTATTGCTAAGTTCCTCCTTGAAACAGAACAAAATAATCCTTCAG
* *
539940 TTTATGTGCTTTTGTCAAATACTTATGCAGCTGCTGGGCAATGGGAAGAAGCAGCTAGAGTGAGG
66 TTTATGTGCTTTTGTCAAATACTTATGCAGCTGATGGGCAATGGGAAGAAACAGCTAGAGTGAGG
* *
540005 GAATCCATGAAAAATGTTGGGGTGATGAAGCAACCTGGCTCAAGTTGGATCAGTATGTAGATCCC
131 GAATCCATGAAAAATGTTGGGGTGATGAAGCAACCTGGCTCAAGTTGGATCAGGATATAGATCCC
540070 TTCTGATGCCATCTTCCCTCTTCCCTCTTCCC
196 TTCTGATGCCATCTTCCCTCTTCCCTCTTCCC
*
540102 TAATCTAAGGCTTGCGAGAATTATTGCTAAGTTCCTCCTTGACACAGAACAAAATAATCCTTCAG
1 TAATCTAAGGCTTGCGAGAATTATTGCTAAGTTCCTCCTTGAAACAGAACAAAATAATCCTTCAG
540167 TTTATGTGCTTTTGTCAAATACTTATGCAGCTGATGGGCAATGGGAAGAAACAGCTAGAGTGAGG
66 TTTATGTGCTTTTGTCAAATACTTATGCAGCTGATGGGCAATGGGAAGAAACAGCTAGAGTGAGG
540232 GAATCCATGAAAAATGTTGGGGTGATGAAGCAACCTGGCTCAAGTTGGATCAGGATATAGATCCC
131 GAATCCATGAAAAATGTTGGGGTGATGAAGCAACCTGGCTCAAGTTGGATCAGGATATAGATCCC
*
540297 TTCTGATGCCATCTTCTCTCTTCCCT
196 TTCTGATGCCATCTTCCCTCTTCCCT
540323 GTAGAGCAAA
Statistics
Matches: 214, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
227 214 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.29
Consensus pattern (227 bp):
TAATCTAAGGCTTGCGAGAATTATTGCTAAGTTCCTCCTTGAAACAGAACAAAATAATCCTTCAG
TTTATGTGCTTTTGTCAAATACTTATGCAGCTGATGGGCAATGGGAAGAAACAGCTAGAGTGAGG
GAATCCATGAAAAATGTTGGGGTGATGAAGCAACCTGGCTCAAGTTGGATCAGGATATAGATCCC
TTCTGATGCCATCTTCCCTCTTCCCTCTTCCC
Found at i:542584 original size:19 final size:20
Alignment explanation
Indices: 542542--542584 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
542532 CTTTTCTAAG
*
542542 TTTTTAATATATTATATTTGA
1 TTTTTAATATATTATA-TTAA
*
542563 TTTTTTATATATTATA-TAA
1 TTTTTAATATATTATATTAA
542582 TTT
1 TTT
542585 ATAACACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
21 15 0.75
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTTAATATATTATATTAA
Found at i:544054 original size:16 final size:15
Alignment explanation
Indices: 544031--544061 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
544021 ATTATAAAAC
544031 TAAATAATATATTAT
1 TAAATAATATATTAT
544046 TAAATTAATATATTAT
1 TAAA-TAATATATTAT
544062 ATATTTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATAATATATTAT
Found at i:545284 original size:18 final size:19
Alignment explanation
Indices: 545258--545297 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
545248 CAATCAGGGC
* *
545258 ATTATGGACTTGA-ATTTG
1 ATTAGGGACTTCAGATTTG
545276 ATTAGGGACTTCAGATTTG
1 ATTAGGGACTTCAGATTTG
545295 ATT
1 ATT
545298 GCCAGTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (19 bp):
ATTAGGGACTTCAGATTTG
Found at i:546868 original size:102 final size:104
Alignment explanation
Indices: 546683--546885 Score: 322
Period size: 102 Copynumber: 2.0 Consensus size: 104
546673 ATCAATCTTT
* *
546683 TTTTTTTTTTCAAATTGCTTTCTTTCACAGATTTGATGAAATTACAGTAAAAAAAAATTAATGAG
1 TTTTTTTTTT-AAATTACTTTCTTTAACAGATTTGATGAAATTACAGTAAAAAAAAATTAATGAG
546748 ATGATGTGAAATATTTTTAATGAGATTAATTCATTATTTG
65 ATGATGTGAAATATTTTTAATGAGATTAATTCATTATTTG
* *
546788 TTTTTTTTTT-AATTATTTTCTTTAACAGATTTGATGAAATTA-ACGT-AAAAAAAATTAATGGG
1 TTTTTTTTTTAAATTACTTTCTTTAACAGATTTGATGAAATTACA-GTAAAAAAAAATTAATGAG
*
546850 ATGATGTGGAATATTTTTAATGAGATTAATTCATTA
65 ATGATGTGAAATATTTTTAATGAGATTAATTCATTA
546886 CTTAAATAAC
Statistics
Matches: 92, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
102 51 0.55
103 31 0.34
105 10 0.11
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.45
Consensus pattern (104 bp):
TTTTTTTTTTAAATTACTTTCTTTAACAGATTTGATGAAATTACAGTAAAAAAAAATTAATGAGA
TGATGTGAAATATTTTTAATGAGATTAATTCATTATTTG
Found at i:550276 original size:229 final size:226
Alignment explanation
Indices: 549870--550323 Score: 649
Period size: 229 Copynumber: 2.0 Consensus size: 226
549860 TCCTTGCCTT
*
549870 TGTCAAAACGTTTATTTTTGAGGAAAACAAATAAGTCTCGAACAATATTTAAAAATAAAAAAATG
1 TGTCAAAACGTTTATTTTTGAGGAAAACAAACAAGTCTCGAACAATATTTAAAAATAAAAAAATG
** ** *
549935 AGTATTTTAAATGATAAAAAAATGGGAGTCGCCACCAATTTTTTTATATGGTGTGATTGGATCAC
66 AGTATTTTAAATGATAAAAAAATAAGAGTAACCACCAATATTTTTATATGGTGTGATTGGATCAC
* ** *
550000 CACAAAACGTTTAAAATCCGTTTTGAAAAATGTTTTGGTCCTCGAAATCCAGAAAACAGATTCGG
131 CACAAAACATTTAAAATCCGTTTTGAAAAAAATTTTGGTCCTCGAAATCCAAAAAACAGATTCGG
*
550065 GAGTCGGTTACGCATGAGGAAGGATTAGCAC
196 GAGTCGATTACGCATGAGGAAGGATTAGCAC
* * * ** *
550096 TGTCGAAACGTTTATTTTTTG-GGAAAACATACATGTCTCGAACAATATTTTAAAAATCGAAATA
1 TGTCAAAACGTTTA-TTTTTGAGGAAAACAAACAAGTCTCGAACAATA-TTTAAAAATAAAAAAA
*
550160 TGGGTATTTTAAATGATTGAAAAAAATAAGAGTAACCACCAATATTTTTATATGGTGTGATTGGA
64 TGAGTATTTTAAATGA-T-AAAAAAATAAGAGTAACCACCAATATTTTTATATGGTGTGATTGGA
* * ** *
550225 TCACCACAAAACATTTAAAATCCGTTTTGAAAAAAATTTTGGTCTTCGAAATCTAAAAAATGGGT
127 TCACCACAAAACATTTAAAATCCGTTTTGAAAAAAATTTTGGTCCTCGAAATCCAAAAAACAGAT
*
550290 TCGGGAGTCGATTACGTATGAGGAAGGATTAGCA
192 TCGGGAGTCGATTACGCATGAGGAAGGATTAGCA
550324 GCCCCACACG
Statistics
Matches: 200, Mismatches: 24, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
226 36 0.18
227 34 0.17
228 1 0.00
229 129 0.64
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (226 bp):
TGTCAAAACGTTTATTTTTGAGGAAAACAAACAAGTCTCGAACAATATTTAAAAATAAAAAAATG
AGTATTTTAAATGATAAAAAAATAAGAGTAACCACCAATATTTTTATATGGTGTGATTGGATCAC
CACAAAACATTTAAAATCCGTTTTGAAAAAAATTTTGGTCCTCGAAATCCAAAAAACAGATTCGG
GAGTCGATTACGCATGAGGAAGGATTAGCAC
Found at i:551292 original size:27 final size:29
Alignment explanation
Indices: 551254--551323 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 29
551244 ATTCGAGGGT
551254 AAAATGGT-ATTTTTAGACA-CTCG-GGGGA
1 AAAAT-GTAATTTTTAGACATC-CGAGGGGA
* *
551282 AAAA-GTAATTTTTGGACATCCGAGGGTA
1 AAAATGTAATTTTTAGACATCCGAGGGGA
551310 AAAATGTAATTTTT
1 AAAATGTAATTTTT
551324 GGAAAGTTCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 2 0.06
27 12 0.33
28 13 0.36
29 9 0.25
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.33
Consensus pattern (29 bp):
AAAATGTAATTTTTAGACATCCGAGGGGA
Found at i:551321 original size:29 final size:29
Alignment explanation
Indices: 551246--551326 Score: 91
Period size: 27 Copynumber: 2.9 Consensus size: 29
551236 TCTCGAAGAT
*
551246 TCGAGGGT-AAAATGGT-ATTTTTAGACAC
1 TCGAGGGTAAAAAT-GTAATTTTTGGACAC
*
551274 TCG-GGGGAAAAA-GTAATTTTTGGACA-
1 TCGAGGGTAAAAATGTAATTTTTGGACAC
551300 TCCGAGGGTAAAAATGTAATTTTTGGA
1 T-CGAGGGTAAAAATGTAATTTTTGGA
551327 AAGTTCAAGG
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 3 0.07
27 15 0.33
28 15 0.33
29 12 0.27
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.31
Consensus pattern (29 bp):
TCGAGGGTAAAAATGTAATTTTTGGACAC
Found at i:551429 original size:30 final size:28
Alignment explanation
Indices: 551281--551585 Score: 178
Period size: 29 Copynumber: 10.5 Consensus size: 28
551271 CACTCGGGGG
*
551281 AAAAA-GTAATTTTTGGACA-TCCGAGGGT
1 AAAAATGTAATTTTTGGA-AGTTC-AGGGT
*
551309 AAAAATGTAATTTTTGGAAAGTTCAAGGT
1 AAAAATGTAATTTTTGG-AAGTTCAGGGT
* **
551338 CAAAAAAT-CAATTTTTGGAAGTTTGGGGGT
1 --AAAAATGTAATTTTTGGAAG-TTCAGGGT
** *
551368 -AAAATGGTAATTTTTAAAAAGTTCAGAGT
1 AAAAAT-GTAATTTTT-GGAAGTTCAGGGT
551397 AAAAAATGTAATTTTTGGAAGTTCAAGGGT
1 -AAAAATGTAATTTTTGGAAGTTC-AGGGT
* * *
551427 -AAAATGGTAGTTTTTGGAAGGT--GGGAC
1 AAAAAT-GTAATTTTTGGAAGTTCAGGG-T
* *
551454 AAAAATGTAATTTTTGTAAAGTTCAGGGG
1 AAAAATGTAATTTTTG-GAAGTTCAGGGT
* * *
551483 CAAAATGGTAATTTTTGAAAAGTTCAGGAT
1 AAAAAT-GTAATTTTTG-GAAGTTCAGGGT
*
551513 CAAAAATG-ATATTTTTGGTAGTTCAAGGGT
1 -AAAAATGTA-ATTTTTGGAAGTTC-AGGGT
*
551543 -AAAATGGTAATTTTTGGAAAGTTTAGGGT
1 AAAAAT-GTAATTTTTGG-AAGTTCAGGGT
* * *
551572 CAAAACGTGATTTT
1 AAAAATGTAATTTT
551586 CGAATAGTTC
Statistics
Matches: 217, Mismatches: 34, Indels: 51
0.72 0.11 0.17
Matches are distributed among these distances:
26 3 0.01
27 14 0.06
28 24 0.11
29 83 0.38
30 77 0.35
31 16 0.07
ACGTcount: A:0.37, C:0.05, G:0.24, T:0.34
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAGTTCAGGGT
Found at i:551575 original size:59 final size:59
Alignment explanation
Indices: 551281--551576 Score: 302
Period size: 59 Copynumber: 5.1 Consensus size: 59
551271 CACTCGGGGG
* * *
551281 AAAAA-GTAATTTTTGGACA-TCCGAGGGTAAAAAT-GTAATTTTTGGAAAGTTCAAGGTC
1 AAAAATGTAATTTTTGGA-AGTTCAAGGGT-AAAATGGTAATTTTTGGAAAGTTCAGGGTC
* *** ** * *
551339 AAAAAAT-CAATTTTTGGAAGTTTGGGGGTAAAATGGTAATTTTTAAAAAGTTCAGAGTA
1 -AAAAATGTAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTC
* * *
551398 AAAAATGTAATTTTTGGAAGTTCAAGGGTAAAATGGTAGTTTTTGG-AAGGT--GGGAC
1 AAAAATGTAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTC
* * * * *
551454 AAAAATGTAATTTTTGTAAAGTTCAGGGGCAAAATGGTAATTTTTGAAAAGTTCAGGATC
1 AAAAATGTAATTTTTG-GAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTC
* *
551514 AAAAATG-ATATTTTTGGTAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTC
1 AAAAATGTA-ATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTC
551573 AAAA
1 AAAA
551577 CGTGATTTTC
Statistics
Matches: 193, Mismatches: 35, Indels: 18
0.78 0.14 0.07
Matches are distributed among these distances:
56 18 0.09
57 25 0.13
58 20 0.10
59 113 0.59
60 17 0.09
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (59 bp):
AAAAATGTAATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTC
Found at i:551594 original size:29 final size:28
Alignment explanation
Indices: 551554--551609 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
551544 AAATGGTAAT
* *
551554 TTTTGGAAAGTTTAGGGTCAAAACGTGA
1 TTTTCGAAAGTTCAGGGTCAAAACGTGA
*
551582 TTTTCGAATAGTTCGGGGTCAAAACGTG
1 TTTTCGAA-AGTTCAGGGTCAAAACGTG
551610 GTATTTTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.29, C:0.11, G:0.29, T:0.32
Consensus pattern (28 bp):
TTTTCGAAAGTTCAGGGTCAAAACGTGA
Found at i:553363 original size:18 final size:17
Alignment explanation
Indices: 553330--553421 Score: 121
Period size: 17 Copynumber: 5.3 Consensus size: 17
553320 AACTTTTGAT
*
553330 TAAATTTTAATTTAAAA
1 TAAATTTAAATTTAAAA
553347 TAAATTTAAATTTTAAAA
1 TAAATTTAAA-TTTAAAA
553365 TAAATTTAAACTTTAAAA
1 TAAATTTAAA-TTTAAAA
* *
553383 TAAATTTGAACTTAAAA
1 TAAATTTAAATTTAAAA
*
553400 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
*
553417 AAAAT
1 TAAAT
553422 CCAAAATTGG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
17 33 0.50
18 33 0.50
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:553379 original size:7 final size:6
Alignment explanation
Indices: 553329--553415 Score: 56
Period size: 6 Copynumber: 14.8 Consensus size: 6
553319 CAACTTTTGA
* * *
553329 TTAAAT TTTAAT TTAAA- ATAAAT TTAAATT TTAAA- ATAAAT TTAAACT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TTAAAT TTAAA-T
* * * * *
553377 TTAAA- ATAAAT TTGAAC TTAAA- ATAAAT TAAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
553416 AAAAATCCAA
Statistics
Matches: 60, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
5 16 0.27
6 32 0.53
7 12 0.20
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (6 bp):
TTAAAT
Found at i:554121 original size:208 final size:208
Alignment explanation
Indices: 553762--554459 Score: 943
Period size: 208 Copynumber: 3.3 Consensus size: 208
553752 TTTGTGTTTG
* * * *
553762 GTTTCATTGATTTGGTCTATTTCTCAGTATCTTATCATGAAGATGACCGCATCGCTTGTTTTGAT
1 GTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCG-TTGTTTTGAT
* * * * *
553827 CCACTTCTCTGTGTCTCATCAGGAAGACGAATCTGGTTTACTTCTCTGTATCTCATCAGGAAGAT
65 CCACTTCTTTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGT
553892 AACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGC
130 AACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGC
553957 TCACTTTGAGCCTA
195 TCACTTTGAGCCTA
***********
553971 GTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCNNNNNNNNNNNCGCCTCGTTGTTTTGATC
1 GTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCGTTGTTTTGATC
* *
554036 CACTTCTTTGTATCTCATCGGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTA
66 CACTTCTTTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTA
** * *
554101 ACTACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGC-TGAGGTTCAAAGATTTGC
131 ACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTG-GGTTCGAAGATTTGC
554165 TCACTTTGAGCCTA
195 TCACTTTGAGCCTA
* * * * * *
554179 GTTTCATTGATTTAGTCCACTTTTTAGTATCTCATTAGGAAGATGACCGCCTCGTTATTTTGATC
1 GTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCGTTGTTTTGATC
* *
554244 CACTTCTTTGTATCTCATCAGGAAGACAGATCTGG-TCTACTACTCTGTATCTCATCAGGAAGGT
66 CACTTCTTTGTATCTCATCAGGAAGACGGATCTGGTTC-ACTTCTCTGTATCTCATCAGGAAGGT
*
554308 AACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGC
130 AACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGC
554373 TCACTTTGAGCCT-
195 TCACTTTGAGCCTA
** * * * * * *
554386 GATTTTGTTGATTTGGTCTACTTCCCAGTATCTCATTAGAAAAATGACCGCATCACTTGTTTTGA
1 G-TTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTC-GTTGTTTTGA
554451 TCCACTTCT
64 TCCACTTCT
554460 CTATGTCTCA
Statistics
Matches: 421, Mismatches: 63, Indels: 10
0.85 0.13 0.02
Matches are distributed among these distances:
207 5 0.01
208 358 0.85
209 58 0.14
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.37
Consensus pattern (208 bp):
GTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCGTTGTTTTGATC
CACTTCTTTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTA
ACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTGGGTTCGAAGATTTGCT
CACTTTGAGCCTA
Found at i:554590 original size:172 final size:172
Alignment explanation
Indices: 554301--554642 Score: 560
Period size: 172 Copynumber: 2.0 Consensus size: 172
554291 TATCTCATCA
* *
554301 GGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAA
1 GGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAA
** *
554366 GATTTGCTCACTTTGAGCCTGATTTTGTTGATTTGGTCTACTTCCCAGTATCTCAT-TAGAAAAA
66 GATTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTACTTCCCAGTATCTCATCAAG-AAAA
554430 TGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATTT
130 TGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATTT
*
554473 GGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTAGGTTCAAA
1 GGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAA
* ** *
554538 GATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTTAGTATCTCATCAAGAAGAT
66 GATTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTACTTCCCAGTATCTCATCAAGAAAAT
* *
554603 GACCGTATCACTTGTTTTGATCCACTTTTCTATGTCTCAT
131 GACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCAT
554643 CAGGAAGACG
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
172 155 0.99
173 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.19, T:0.38
Consensus pattern (172 bp):
GGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAA
GATTTGCTCACTTTGAGCCTGATTTCATTGATTTGGTCTACTTCCCAGTATCTCATCAAGAAAAT
GACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATTT
Found at i:554780 original size:381 final size:380
Alignment explanation
Indices: 554094--554850 Score: 1149
Period size: 381 Copynumber: 2.0 Consensus size: 380
554084 ATCTCATCAA
* *
554094 GAAGGTAACTACTTTATTGCTTCGACCTGCTTCTTAGTATCTCATCAGGAAGCTGAGGTTCAAAG
1 GAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAAG
* * *
554159 ATTTGCTCACTTTGAGCCTAGTTTCATTGATTTAGTCCACTTTTTAGTATCTCATTAGGAAGATG
66 ATTTGCTCACTTTGAGCCTAGTTTCATTGATTTAGTCCACTTCTTAGTATCTCATCAAGAAGATG
* * * ** *
554224 ACCGCCTCGTTATTTTGATCCACTTCTTTGTATCTCATCAGGAAGACAGATCTGGTCTACTACTC
131 ACCGCATCCTTATTTTGATCCACTTCTTTATATCTCATCAGGAAGACAGATCTGACCCACTACTC
* * *
554289 TGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAG
196 AGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGCATCTCATCAGGAAG
* ** *
554354 CTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGATTTTGTTGATTTGGTCTACTTCCCAGTATCT
261 CTGGGGTTCGAAGATTTGCTCAATTTGAGCCTGATTTCATTGATTTGGTATACTTCCCAGTATCT
*
554419 CAT-TAGAAAAATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATTTG
326 CATCAAG-AAAATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATTTG
* *
554474 GAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTTAGGTTCAAAG
1 GAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAAG
* * *
554539 ATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTCTACTTCTTAGTATCTCATCAAGAAGATG
66 ATTTGCTCACTTTGAGCCTAGTTTCATTGATTTAGTCCACTTCTTAGTATCTCATCAAGAAGATG
* * * * * *
554604 ACCGTATCACTTGTTTTGATCCACTT-TTCTATGTCTCATCAGGAAGACGGATTTGACCCACTTC
131 ACCGCATC-CTTATTTTGATCCACTTCTT-TATATCTCATCAGGAAGACAGATCTGACCCACTAC
554668 TCAGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGCATCTCATCAGGA
194 TCAGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGCATCTCATCAGGA
* *
554733 AGCTGGGGTTCGAAGATTTGCTCAATTTGAGCCTGGTTTCATTGATTTGGTATACTTCTCAGTAT
259 AGCTGGGGTTCGAAGATTTGCTCAATTTGAGCCTGATTTCATTGATTTGGTATACTTCCCAGTAT
* * * *
554798 CTCATCAAGAAGATGATCGCATCACTTGTTTTGATCCACTTTTCTGTGTCTCA
324 CTCATCAAGAAAATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCA
554851 ACAGGAAGAC
Statistics
Matches: 338, Mismatches: 36, Indels: 5
0.89 0.09 0.01
Matches are distributed among these distances:
380 128 0.38
381 208 0.62
382 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.19, T:0.37
Consensus pattern (380 bp):
GAAGGTAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCAAAG
ATTTGCTCACTTTGAGCCTAGTTTCATTGATTTAGTCCACTTCTTAGTATCTCATCAAGAAGATG
ACCGCATCCTTATTTTGATCCACTTCTTTATATCTCATCAGGAAGACAGATCTGACCCACTACTC
AGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGCATCTCATCAGGAAG
CTGGGGTTCGAAGATTTGCTCAATTTGAGCCTGATTTCATTGATTTGGTATACTTCCCAGTATCT
CATCAAGAAAATGACCGCATCACTTGTTTTGATCCACTTCTCTATGTCTCATTTG
Found at i:554812 original size:209 final size:209
Alignment explanation
Indices: 554446--554992 Score: 835
Period size: 209 Copynumber: 2.6 Consensus size: 209
554436 CATCACTTGT
* * **
554446 TTTGATCCACTTCTCTA-TGTCTCATTTGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCA
1 TTTGACCCACTTCTC-AGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCA
** *
554510 GTATCTCATCAGGAAGCTTAGGTTCAAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGT
65 GTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGT
* * *
554575 CTACTTCTTAGTATCTCATCAAGAAGATGACCGTATCACTTGTTTTGATCCACTTTTCTATGTCT
130 ATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTCTATGTCT
*
554640 CATCAGGAAGACGGA
195 CAACAGGAAGACGGA
*
554655 TTTGACCCACTTCTCAGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAG
1 TTTGACCCACTTCTCAGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAG
* *
554720 CATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAATTTGAGCCTGGTTTCATTGATTTGGTA
66 TATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTA
* *
554785 TACTTCTCAGTATCTCATCAAGAAGATGATCGCATCACTTGTTTTGATCCACTTTTCTGTGTCTC
131 TACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTCTATGTCTC
554850 AACAGGAAGACGGA
196 AACAGGAAGACGGA
* *
554864 TCTGACCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAG
1 TTTGACCCACTTCTCAGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAG
* * * * * * * *
554929 TATCTCATCAAGCAGCTGGGGTTTGAAGATTCGCTCACGTCGAGCTTTGGCTTCATTGATTTGG
66 TATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC-CTGGTTTCATTGATTTGG
554993 AGTCCTCCTT
Statistics
Matches: 307, Mismatches: 29, Indels: 3
0.91 0.09 0.01
Matches are distributed among these distances:
208 1 0.00
209 290 0.94
210 16 0.05
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (209 bp):
TTTGACCCACTTCTCAGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAG
TATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTGGTTTCATTGATTTGGTA
TACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTCTATGTCTC
AACAGGAAGACGGA
Found at i:560454 original size:208 final size:208
Alignment explanation
Indices: 560096--561025 Score: 1283
Period size: 208 Copynumber: 4.5 Consensus size: 208
560086 CGAATTCTAG
* * * *
560096 TGAGCCTAGTTTTATTGATTTGGTCTACTTCTCAGTATCTTATTAGAAAGATGACCAG-CTCATT
1 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACC-GCCTCATT
* * * *
560160 ATTTTGATCCACTTCTCTGTATCTCATCGGGAAGACGGATCTTGTTCACTTCTCTGTATCTCATT
65 GTTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATC
* * *
560225 AAGAAGGTAACAGCTTTATTGCTTCGACCTGTTTCTTAGTATCTCATCAGGAAGCTGTGGTTCAA
130 AAGAAGGTAACAGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAA
560290 AGATTTGCTCACTT
195 AGATTTGCTCACTT
* * * ** *
560304 TGAGCCTGGTTTCATTGATTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGAGCGCCTTGTTA
1 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTG
* * * *
560369 TTTTGATCCACTTCTCTGTATCTTATCAAGAAGACGGATCTGGTTTACTTCTTTGTATCTCATCA
66 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCA
* * *
560434 AGAAGGTAACCGCTTTATTGCTTCG-CCTTGCTTCTCAGTATCTCATCAGGAAGATGGGGTTCGA
131 AGAAGGTAACAGCTTTATTGCTTCGACC-TGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAA
*
560498 AGATTTGCTCAGTT
195 AGATTTGCTCACTT
** * * * * * *
560512 TGAGTTTGGTTTCATTGATTTGGTATACTTCTCAATATCTCATCAGAAAGATGATCGCCTCGTTG
1 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTG
* *
560577 TTTTGTTCCACTTCTCTGTATCTCATCGGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCA
66 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCA
* * * * * *
560642 GGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTTGTGTTCAGA
131 AGAAGGTAACAGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAA
*
560707 GATTTGCTCACAT
196 GATTTGCTCACTT
* * * *
560720 TAAGCCTAGTTTCATTAATTTGGTCTACTTCTCAGTATCTCATCATGAAGATGATCGCCTCATTG
1 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTG
* * * * * *
560785 TTTGGATCCAATTCTCTGTATCTCATCAAGAAGAC-GATTCTAGTTCACTTCTTTGTATCTTATC
66 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGA-TCTGGTTCACTTCTCTGTATCTCATC
*
560849 -AGAAAGGTAACAGCTTTATCGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCA
130 AAG-AAGGTAACAGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCA
560913 AAGATTTGCTCACTT
194 AAGATTTGCTCACTT
* **
560928 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATATCATCAGGAAGATGACCGCCTTTTTG
1 TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTG
*
560993 TTTTGATTCACTTCTCTGTATCTCATCAGGAAG
66 TTTTGATCCACTTCTCTGTATCTCATCAGGAAG
561026 GTGACCGCTT
Statistics
Matches: 633, Mismatches: 84, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
207 6 0.01
208 625 0.99
209 2 0.00
ACGTcount: A:0.22, C:0.21, G:0.19, T:0.38
Consensus pattern (208 bp):
TGAGCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAGGAAGATGACCGCCTCATTG
TTTTGATCCACTTCTCTGTATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCA
AGAAGGTAACAGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAA
GATTTGCTCACTT
Found at i:561019 original size:48 final size:48
Alignment explanation
Indices: 560953--561068 Score: 146
Period size: 48 Copynumber: 2.4 Consensus size: 48
560943 TGATTTGGTC
* * *
560953 TACTTCTCAGTATATCATCAGGAAGATGACCGCCTTT-TTGTTTTGA-T
1 TACTTCTCAGTATCTCATCAGGAAGATGACCG-CTTTATTGCTTTAACT
* *
561000 TCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTAACT
1 T-ACTTCTCAGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACT
*
561049 TGCTTCTCAGTATCTCATCA
1 TACTTCTCAGTATCTCATCA
561069 AGTAGCTTGG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
47 5 0.08
48 52 0.88
49 2 0.03
ACGTcount: A:0.22, C:0.23, G:0.16, T:0.40
Consensus pattern (48 bp):
TACTTCTCAGTATCTCATCAGGAAGATGACCGCTTTATTGCTTTAACT
Found at i:561118 original size:171 final size:171
Alignment explanation
Indices: 560828--561196 Score: 522
Period size: 171 Copynumber: 2.2 Consensus size: 171
560818 ACGATTCTAG
* * *
560828 TTCACTTCTTTGTATCTTATCAGAAAGGTAACAGCTTTATCGCTTCGACCTGCTTCTCAGTATCT
1 TTCACTTCTTTGTATCTCATCAGGAAGGTAACAGCTTTATCGCTTCAACCTGCTTCTCAGTATCT
* *
560893 CATCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTT
66 CATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATTGAGCCTAGTTTCATTGATTTGGTCTACTT
* **
560958 CTCAGTATATCATCAGGAAGATGACCGCCTTTTTGTTTTGA
131 CTCAGTATATCATCAGGAAGAGGACCGCCTCATTGTTTTGA
* * * * * *
560999 TTCACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTAACTTGCTTCTCAGTATCT
1 TTCACTTCTTTGTATCTCATCAGGAAGGTAACAGCTTTATCGCTTCAACCTGCTTCTCAGTATCT
* * * *
561064 CATCAAGTAGCTTGGGTTCGAAGATTTGCTCACATTGAGCCTAGTTTTATTGATTTGGTCTACTT
66 CATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATTGAGCCTAGTTTCATTGATTTGGTCTACTT
* * **
561129 CTCAGTTTCTCATTTGGAAGAGGACCGCCTCATTGTTTTGA
131 CTCAGTATATCATCAGGAAGAGGACCGCCTCATTGTTTTGA
* *
561170 TCCACTTCTTTGTATCTCATCGGGAAG
1 TTCACTTCTTTGTATCTCATCAGGAAG
561197 ACGGGTCTAG
Statistics
Matches: 173, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
171 173 1.00
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (171 bp):
TTCACTTCTTTGTATCTCATCAGGAAGGTAACAGCTTTATCGCTTCAACCTGCTTCTCAGTATCT
CATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATTGAGCCTAGTTTCATTGATTTGGTCTACTT
CTCAGTATATCATCAGGAAGAGGACCGCCTCATTGTTTTGA
Found at i:561128 original size:379 final size:374
Alignment explanation
Indices: 560622--561773 Score: 1466
Period size: 379 Copynumber: 3.1 Consensus size: 374
560612 GGATCTGGTT
560622 CACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
* * *
560687 TCAAGAAGCTTGTGTTC-AGAGATTTGCTCACATTAAGCCTAGTTTCATTAATTTGGTCTACTTC
66 TCAAGAAGCTTGGGTTCGA-AGATTTGCTCACATTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * *
560751 TCAGTATCTCATCATGAAGATGATCGCCTCATTGTTTGGATCCAATTCTCTGTATCTCATCAAGA
130 TCAGTATCTCATCATGAAGATGACCGCCTCATTGTTTTGATCCACTTCTCTGTATCTCATC-AGA
* * * *
560816 AGACGATTCTAGTTCACTTCTTTGTATCTTATCAGAAAGGTAACAGCTTTATCGCTTCGACCTGC
194 AGACGATTCTAGTTCACTTCTCTGTATCTCATCAG-AAGGTAACCGCTTTATTGCTTCGACCTGC
*
560881 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACTTTGAGCCTAGTTTCATTGA
258 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGA
*
560946 TTTGGTCTACTTCTCAGTATATCATCAGGAAGATGACCGCCTTTTTGTTTTGATT
323 TTTGGTCTACTTCTCAGTATATCATCAGGAAGATGA-CGCC--TTTGTTTTGATC
* ** *
561001 CACTTCTCTGTATCTCATCAGGAAGGTGACCGCTTTATTGCTTTAACTTGCTTCTCAGTATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
* *
561066 TCAAGTAGCTTGGGTTCGAAGATTTGCTCACATTGAGCCTAGTTTTATTGATTTGGTCTACTTCT
66 TCAAGAAGCTTGGGTTCGAAGATTTGCTCACATTGAGCCTAGTTTCATTGATTTGGTCTACTTCT
* * * * *
561131 CAGTTTCTCAT-TTGGAAGAGGACCGCCTCATTGTTTTGATCCACTTCTTTGTATCTCATCGGGA
131 CAGTATCTCATCAT-GAAGATGACCGCCTCATTGTTTTGATCCACTTCTCTGTATCTCATC-AGA
** ** *
561195 AGACGGGTCTAGTTCACTTCTCTGTATCTCATCACGAAGGTAACCTTTTTATTGCTTAGACCTGC
194 AGACGATTCTAGTTCACTTCTCTGTATCTCATCA-GAAGGTAACCGCTTTATTGCTTCGACCTGC
* * * * *
561260 TTCTCAATTTCTCATCAGGAAGCTAGGGTTTCGAAGATTTGCCCACTTTGAGCCTAATTTCATTG
258 TTCTCAGTATCTCATCAGGAAGCT-GGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTG
* * ** * * * *
561325 ATTTGGTTTACTTTTCA--ATATC-TCATCAAGAAGACG-----ATTCTGACC
322 ATTTGGTCTACTTCTCAGTATATCATCAGGAAGATGACGCCTTTGTTTTGATC
* * *
561370 CACTTCTCTGTATCTCATCAAGAAGGTAACAGCTTTATTGCTTCGACCTGCTTCTCAGCATCTCA
1 CACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
* * * * * *
561435 TCAGGAAGCTTGGGTTTGAAGAGTTGC-CTACTTTGAGCCTAGTTTCGTTGTTTTGGTCTACTTC
66 TCAAGAAGCTTGGGTTCGAAGATTTGCTC-ACATTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * * * *
561499 TTAGTATCTCATCAGGAAGATGACCACCTCGTTGTTTTGATCCACTTCTCTGTATTTCATCAGTA
130 TCAGTATCTCATCATGAAGATGACCGCCTCATTGTTTTGATCCACTTCTCTGTATCTCATCAG-A
* * *
561564 AGACGAATT-TGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTTTTGCTTCGACCTA
194 AGACG-ATTCTAGTTCACTTCTCTGTATCTCATCA-GAAGGTAACCGCTTTATTGCTTCGACCTG
* * *
561628 CTTTTCAGTATCTCTTCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTG
257 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTG
* *
561693 ATTTGGTCTACTTCTCAGTATCTCATC-GAGAAGATGATCACCTCGTTGTTTTGATC
322 ATTTGGTCTACTTCTCAGTATATCATCAG-GAAGATGA-CGCCT--TTGTTTTGATC
* *
561749 CACTTCTTTGTATCTCATCGGGAAG
1 CACTTCTCTGTATCTCATCAGGAAG
561774 ACGGATCTGG
Statistics
Matches: 656, Mismatches: 97, Indels: 40
0.83 0.12 0.05
Matches are distributed among these distances:
368 53 0.08
369 243 0.37
370 5 0.01
371 8 0.01
372 1 0.00
376 2 0.00
377 9 0.01
378 6 0.01
379 276 0.42
380 53 0.08
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (374 bp):
CACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCA
TCAAGAAGCTTGGGTTCGAAGATTTGCTCACATTGAGCCTAGTTTCATTGATTTGGTCTACTTCT
CAGTATCTCATCATGAAGATGACCGCCTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGAAG
ACGATTCTAGTTCACTTCTCTGTATCTCATCAGAAGGTAACCGCTTTATTGCTTCGACCTGCTTC
TCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTT
GGTCTACTTCTCAGTATATCATCAGGAAGATGACGCCTTTGTTTTGATC
Found at i:561360 original size:161 final size:160
Alignment explanation
Indices: 561158--561518 Score: 438
Period size: 161 Copynumber: 2.2 Consensus size: 160
561148 GAGGACCGCC
* * * ** * * **
561158 TCATTGTTTTGATCCACTTCTTTGTATCTCATCGGGAAGACGGGTCT-AGTTCACTTCTCTGTAT
1 TCATTGATTTGGTCTACTTCTTAATATCTCATCAGGAAGACGAGTCTGA-CCCACTTCTCTGTAT
* *** **
561222 CTCATCACGAAGGTAACCTTTTTATTGCTTAGACCTGCTTCTCAATTTCTCATCAGGAAGCTAGG
65 CTCATCAAGAAGGTAACAGCTTTATTGCTTAGACCTGCTTCTCAACATCTCATCAGGAAGCTAGG
*
561287 GTTTCGAAGATTTGCCCACTTTGAGCCTAATT
130 GTTT-GAAGAGTTGCCCACTTTGAGCCTAATT
* * *
561319 TCATTGATTTGGTTTACTT-TTCAATATCTCATCAAGAAGACGATTCTGACCCACTTCTCTGTAT
1 TCATTGATTTGGTCTACTTCTT-AATATCTCATCAGGAAGACGAGTCTGACCCACTTCTCTGTAT
* * *
561383 CTCATCAAGAAGGTAACAGCTTTATTGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTTGG
65 CTCATCAAGAAGGTAACAGCTTTATTGCTTAGACCTGCTTCTCAACATCTCATCAGGAAGCTAGG
* *
561448 GTTTGAAGAGTTGCCTACTTTGAGCCTAGTT
130 GTTTGAAGAGTTGCCCACTTTGAGCCTAATT
* * *
561479 TCGTTGTTTTGGTCTACTTCTTAGTATCTCATCAGGAAGA
1 TCATTGATTTGGTCTACTTCTTAATATCTCATCAGGAAGA
561519 TGACCACCTC
Statistics
Matches: 168, Mismatches: 29, Indels: 7
0.82 0.14 0.03
Matches are distributed among these distances:
160 58 0.35
161 109 0.65
162 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.37
Consensus pattern (160 bp):
TCATTGATTTGGTCTACTTCTTAATATCTCATCAGGAAGACGAGTCTGACCCACTTCTCTGTATC
TCATCAAGAAGGTAACAGCTTTATTGCTTAGACCTGCTTCTCAACATCTCATCAGGAAGCTAGGG
TTTGAAGAGTTGCCCACTTTGAGCCTAATT
Found at i:561715 original size:208 final size:208
Alignment explanation
Indices: 561343--562599 Score: 1599
Period size: 208 Copynumber: 6.0 Consensus size: 208
561333 TACTTTTCAA
* *** * *
561343 TATCTCATCAAGAAGAC-GATTCTGACCCACTTCTCTGTATCTCATCAAGAAGGTAACAGCTTTA
1 TATCTCATCAGGAAGACGGA-TCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTA
* * *
561407 TTGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTTGGGTTTGAAGAGTTGC-CTACTTTGA
65 TTGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTC-ACTTTGA
* * * *
561471 GCCTAGTTTCGTTGTTTTGGTCTACTTCTTAGTATCTCATCAGGAAGATGACCACCTCGTTGTTT
129 GCCTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCACCTCGTTGTTT
561536 TGATCCACTTCTCTG
194 TGATCCACTTCTCTG
* * * * *
561551 TATTTCATCAGTAAGACGAATTTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTTT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
* * * * *
561616 TGCTTCGACCTACTTTTCAGTATCTCTTCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
* *
561681 CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCGAGAAGATGATCACCTCGTTGTTTTG
131 CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCACCTCGTTGTTTTG
*
561746 ATCCACTTCTTTG
196 ATCCACTTCTCTG
* * * **
561759 TATCTCATCGGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATTAAGAAGGTAACTACTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
* * * * *
561824 TGCTTCGACCTGCTTCTCAGTATCTTATTAGGAAGCTGAGGTTCAAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
* * ** *
561889 CTAGTTTCATTGATTTAGTCCACTTCTCAGTATCTCAT-AAGGAAGATGACTGCCTCGTTATTTT
131 CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAA-GAAGATGACCACCTCGTTGTTTT
561953 GATCCACTTCTCTG
195 GATCCACTTCTCTG
* * *
561967 TATCTCATCATGAAGACGGATCTGGTTAACTTTTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
* *
562032 TGCTTCGACCTGCTTCTCAGTATCTCATCAAGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
* * * * *
562097 CTGGTTTCATTGATTTGGTCTACTTCTCAATATCTCATCAAAAAGATGACCGTATCAC-TTGTTT
131 CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACC--ACCTCGTTGTTT
*
562161 TGATCCACTTTTCTG
194 TGATCCACTTCTCTG
* * *** * *
562176 TGTCTCATCAGGAAGACGAATCTGACCCACTTCTTTGTATCTCATCAGGAAGGTAATCGCTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
* *
562241 TCCTTCGACATGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
66 TGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
* * * * * * *
562306 TTGGTTTCGTTTATTTGGTATACTTCTCAGTATCTCATCAAGAAGATAACTACATCTC-TTGTTT
131 CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAC--CACCTCGTTGTTT
* *
562370 TGATCCACTTTTATG
194 TGATCCACTTCTCTG
* *** * *
562385 TGTCTCATCAGGAAGACGGATCTGACCCACTTCTCAGTATCTCATCAGGAAGGTAACCGTTTTAT
1 TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
* * * *
562450 TGCTTCGACCTACTTCTCAACATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCAGTTTGAGC
66 TGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
* * * * *
562515 CTGGTTTCATTGATTTGGTATACTTCTCAGTATCTCACCAAGAAGATGACTGCATCAC-TTGTTT
131 CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGAC--CACCTCGTTGTTT
* *
562579 TGACCCACTTTTCTG
194 TGATCCACTTCTCTG
*
562594 TGTCTC
1 TATCTC
562600 TGTTTCTCAT
Statistics
Matches: 924, Mismatches: 117, Indels: 15
0.88 0.11 0.01
Matches are distributed among these distances:
207 1 0.00
208 519 0.56
209 401 0.43
210 2 0.00
211 1 0.00
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (208 bp):
TATCTCATCAGGAAGACGGATCTGGTTCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTAT
TGCTTCGACCTGCTTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGC
CTAGTTTCATTGATTTGGTCTACTTCTCAGTATCTCATCAAGAAGATGACCACCTCGTTGTTTTG
ATCCACTTCTCTG
Found at i:565719 original size:208 final size:209
Alignment explanation
Indices: 565256--567228 Score: 2619
Period size: 208 Copynumber: 9.5 Consensus size: 209
565246 CTGTTTTGAT
* * ** ** * * *
565256 TCACTTCTCTGTATCTCATCAAGAAGGTAATCGCTTTATTGCTTTAATTTTCTTCTCAGTAACTT
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * *
565321 ATCAGGTAGCTTCGGTTCGAAGATTTGCTTACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
66 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * * *
565386 TCAGTATCTCATCAAGAAGATGATCGCATCACTTATTTTGATCCACTTTTCTGTGTCTCATCAGG
131 TCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGG
* *
565451 AAGACGAATCTGAC
196 AAGACGGATCTGGC
* * ** **
565465 CCACTTCTCTGTATCTCATCAAGAAGGTAATAGCTTTATTGCTTCGACCTGCTTCTCAACATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * * *
565530 ATCAGGAAGCTTGGGTTCGAAGAGTTGCCCACTTTAAGCCTAGTTTCATTGTTTTGGTCTACTTC
66 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * * * * *
565595 TTAGTATCTCATCAGGAAGATGACCACCTCA-TTGTTTTGATCCACTTCTCTGTATTTCATCAGT
131 TCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGG
* * *
565659 AAGACGAATTTGGT
196 AAGACGGATCTGGC
* * *
565673 TCACTTCTCTGTATCTCATCAGGAAGGTAACCTCTTTTTTGCTTCGACCTACTTCTCAGTATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
565738 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
66 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * * * * *
565803 TCAGTATCTCATC-GAGAAGATGATCGCCTC-GTTGTTTTGATCCACTTCTTTGTATCTCATCGG
131 TCAGTATCTCATCAG-GAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAG
*
565866 GAAGACGGATCTGGT
195 GAAGACGGATCTGGC
* ** *
565881 TCACTTCTCTGTATCTCATCAAGAAGGTAACTACTTTATTGCTTCGACCTGCTTCTTAGTATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * * *
565946 ATCAGGATGC-TGAGGTTCAAAGATTTGCTCACTTTAAGCCTAGTTTCATTGATTTAGTCCT-CT
66 ATCAGGAAGCTTG-GGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGT-CTACT
* * * * * * * * *
566009 TCTCAATATCTCATAAGGAAAATGACCGCCTC-GTTATTTTGATCCACTTATTTGTATCTCATCA
129 TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCA
566073 GGAAGACGGATCTGG-
194 GGAAGACGGATCTGGC
*
566088 TCTACTACTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCT
1 TC-ACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCT
* * *
566153 CATCAGGAAG-ATGGGTTCAAAGATTTGCTCACTTTGAGCCTAATTTCATTGATTTGGTCTACTT
65 CATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTT
* *
566217 CTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTAATCCACTTCTCTGTGTCTCATCAG
130 CTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAG
566282 GAAGACGGATCTGG-
195 GAAGACGGATCTGGC
* *
566296 TCTACTACTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTTGACCTGCTTCTCAGTATCT
1 TC-ACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCT
* * *
566361 CATTAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCT-GATTTAATTGATTTGGTCTACT
65 CATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAG-TTTCATTGATTTGGTCTACT
* * *
566425 TCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTAGATCCACTTCTCTTTGTCTCATCA
129 TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCA
566490 GGAAGACGGATCTGGTC
194 GGAAGACGGATCTGG-C
* *
566507 TC-CTTCTCTGTATCTCATCAGGAAGGTAATCGCTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * * * *
566571 ATTAGGAAG-TTGGGGTTCGAAGATTTGCTAAATTTGAGCCTGGTTTCATTGATTTGGCCTACTT
66 ATCAGGAAGCTT-GGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTT
* * * *
566635 CTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTT-TCTGTGTCTTACCAG
130 CTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAG
*** *
566699 GAAGAAAAATCTGAC
195 GAAGACGGATCTGGC
* * *
566714 CCATTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGCATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * * *
566779 ATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTGAG-CTTGATTTCATTGATTTGGTATACTT
66 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAG-TTTCATTGATTTGGTCTACTT
* * *
566843 CTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTCTATGTCTCATCAG
130 CTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAG
*
566908 GAAGACGGATCTGAC
195 GAAGACGGATCTGGC
* * * *
566923 CCACTTCT-TAGTATCTCATCTGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGCATCT
1 TCACTTCTCT-GTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCT
* * *
566987 CATCAGGAAG-TTGGGGTTCGAAGATTTGATCACTTTGAGCCTGGTTTCATTGATTTGGTATACT
65 CATCAGGAAGCTT-GGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACT
* * * * *
567051 TCTCAGTATCTCATCAAGAAGATGACTGCATCAGTTGTTTTGATCCACTTTTCTGTGTCTCAACA
129 TCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCA
567116 GGAAGACGGATCTGGC
194 GGAAGACGGATCTGGC
* * * *
567132 CCACTTCTCTGTATCTCATCAGGAAGGTAATCGTTTTATTGCTTCGACTTGCTTCTCAGTATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
* * * *
567197 ATCAAGCAGCTGGGGTTCGAAGATTCGCTCAC
66 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCAC
567229 GTCGAGCTTT
Statistics
Matches: 1580, Mismatches: 160, Indels: 48
0.88 0.09 0.03
Matches are distributed among these distances:
206 2 0.00
207 83 0.05
208 768 0.49
209 719 0.46
210 6 0.00
211 2 0.00
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (209 bp):
TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
TCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCCACTTCTCTGTGTCTCATCAGG
AAGACGGATCTGGC
Found at i:566726 original size:417 final size:417
Alignment explanation
Indices: 565256--567228 Score: 2683
Period size: 417 Copynumber: 4.7 Consensus size: 417
565246 CTGTTTTGAT
* * ** ** * * *
565256 TCACTTCTCTGTATCTCATCAAGAAGGTAATCGCTTTATTGCTTTAATTTTCTTCTCAGTAACTT
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTC
* * *
565321 ATCAGGTAGCTTCGGTTCGAAGATTTGCTTACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
66 ATCAGGAAG-TTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* *
565386 TCAGTATCTCATCAAGAAGATGATCGCATCACTTATTTTGATCCACTTTTCTGTGTCTCATCAGG
130 TCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCAC-TTTCTGTGTCTCATCAGG
* * * **
565451 AAGACGAATCTGACCCACTTCTCTGTATCTCATCAAGAAGGTAATAGCTTTATTGCTTCGACCTG
194 AAGACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTG
** * * *
565516 CTTCTCAACATCTCATCAGGAAGCTTGGGTTCGAAGAGTTGCCCACTTTAAGCCTAGTTTCATTG
259 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTAAGCCTAGTTTCATTG
* * * * *
565581 TTTTGGTCTACTTCTTAGTATCTCATCAGGAAGATGACCACCTCA-TTGTTTTGATCCACTTCTC
324 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTGATCCACTTCTC
* * * * *
565645 TGTATTTCATCAGTAAGACGAATTTGGT-
389 TTTATCTCATCAGGAAGACGGATCTGGTC
* *
565673 TCACTTCTCTGTATCTCATCAGGAAGGTAACCTCTTTTTTGCTTCGACCTACTTCTCAGTATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTC
565738 ATCAGGAAGCTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
66 ATCAGGAAG-TTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * * * * * *
565803 TCAGTATCTCATCGAGAAGATGATCGCCTC-GTTGTTTTGATCCACTTCTTTGTATCTCATCGGG
130 TCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTT-TCTGTGTCTCATCAGG
** * **
565867 AAGACGGATCTGGTTCACTTCTCTGTATCTCATCAAGAAGGTAACTACTTTATTGCTTCGACCTG
194 AAGACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTG
* * * *
565932 CTTCTTAGTATCTCATCAGGATGCTGAGGTTCAAAGATTTGCTCACTTTAAGCCTAGTTTCATTG
259 CTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTAAGCCTAGTTTCATTG
* * * * * * *
565997 ATTTAGTCCT-CTTCTCAATATCTCATAAGGAAAATGACCGCCTC-GTTATTTTGATCCACTTAT
324 ATTTGGT-CTACTTCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTGATCCACTTCT
566060 -TTGTATCTCATCAGGAAGACGGATCTGGTC
388 CTT-TATCTCATCAGGAAGACGGATCTGGTC
* *
566090 T-ACTACTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTC
* * *
566154 ATCAGGAAGATGGGTTCAAAGATTTGCTCACTTTGAGCCTAATTTCATTGATTTGGTCTACTTCT
66 ATCAGGAAGTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCT
* * *
566219 CAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTAATCCACTTCTCTGTGTCTCATCAGGA
131 CAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTT-TCTGTGTCTCATCAGGA
* * * *
566284 AGACGGATCTGGTCTACTACTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTTGACCTGC
195 AGACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGC
* * *
566349 TTCTCAGTATCTCATTAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTGAGCCT-GATTTAATTG
260 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTAAGCCTAG-TTTCATTG
*
566413 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTAGATCCACTTCTC
324 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTGATCCACTTCTC
*
566478 TTTGTCTCATCAGGAAGACGGATCTGGTC
389 TTTATCTCATCAGGAAGACGGATCTGGTC
* * *
566507 TC-CTTCTCTGTATCTCATCAGGAAGGTAATCGCTTTATTGCTTCGACCTGCTTCTCAGTGTCTC
1 TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTC
* * * * *
566571 ATTAGGAAGTTGGGGTTCGAAGATTTGCTAAATTTGAGCCTGGTTTCATTGATTTGGCCTACTTC
66 ATCAGGAAGTT-GGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTC
* * *
566636 TCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTCTGTGTCTTACCAGGA
130 TCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTCTGTGTCTCATCAGGA
*** * *
566701 AGAAAAATCTGACCCATTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGC
195 AGACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGC
* * * *
566766 TTCTCAGCATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTTACTTTGAG-CTTGATTTCATTG
260 TTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTAAGCCTAG-TTTCATTG
* * * *
566830 ATTTGGTATACTTCTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTTC
324 ATTTGGTCTACTTCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTGATCCACTTCTC
* * *
566895 TATGTCTCATCAGGAAGACGGATCT-GAC
389 TTTATCTCATCAGGAAGACGGATCTGGTC
* * *
566923 CCACTTCT-TAGTATCTCATCTGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGCATCT
1 TCACTTCTCT-GTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCT
* * *
566987 CATCAGGAAGTTGGGGTTCGAAGATTTGATCACTTTGAGCCTGGTTTCATTGATTTGGTATACTT
65 CATCAGGAAGTT-GGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTT
* * *
567052 CTCAGTATCTCATCAAGAAGATGACTGCATCAGTTGTTTTGATCCACTTTTCTGTGTCTCAACAG
129 CTCAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCAC-TTTCTGTGTCTCATCAG
* * *
567117 GAAGACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAATCGTTTTATTGCTTCGACTT
193 GAAGACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCT
* * *
567182 GCTTCTCAGTATCTCATCAAGCAGCTGGGGTTCGAAGATTCGCTCAC
258 GCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCAC
567229 GTCGAGCTTT
Statistics
Matches: 1382, Mismatches: 158, Indels: 31
0.88 0.10 0.02
Matches are distributed among these distances:
415 83 0.06
416 466 0.34
417 626 0.45
418 207 0.15
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.36
Consensus pattern (417 bp):
TCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTACTTCTCAGTATCTC
ATCAGGAAGTTGGGTTCGAAGATTTGCTCACTTTGAGCCTAGTTTCATTGATTTGGTCTACTTCT
CAGTATCTCATCAAGAAGATGACCGCATCACTTGTTTTGATCCACTTTCTGTGTCTCATCAGGAA
GACGGATCTGGCCCACTTCTCTGTATCTCATCAGGAAGGTAACCGCTTTATTGCTTCGACCTGCT
TCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACTTTAAGCCTAGTTTCATTGAT
TTGGTCTACTTCTCAGTATCTCATCAGGAAAATGACCGCATCACTTGTTTTGATCCACTTCTCTT
TATCTCATCAGGAAGACGGATCTGGTC
Found at i:568771 original size:39 final size:39
Alignment explanation
Indices: 568720--568975 Score: 162
Period size: 39 Copynumber: 6.6 Consensus size: 39
568710 TTATGATATA
568720 CCCCATGG-TCGGGGTAAAAGATCAAATGACTGCAATCTG
1 CCCCA-GGCTCGGGGTAAAAGATCAAATGACTGCAATCTG
* * * ** *
568759 CCTCAGGCTCGGGGTAAGAGAT-AGATTGA-TAGTGATTTG
1 CCCCAGGCTCGGGGTAAAAGATCA-AATGACT-GCAATCTG
* * *
568798 CCCCATGCTCGGGGTAAAAGATCGAATGACTGCAATCTA
1 CCCCAGGCTCGGGGTAAAAGATCAAATGACTGCAATCTG
* * ** * ** *
568837 CCCCAGGCTCGAGGTAAGAGATTGACTGA-TGGTGATTTG
1 CCCCAGGCTCGGGGTAAAAGATCAAATGACT-GCAATCTG
* * * *
568876 CCTCAAGCTCGGGGTAAAATATCAAATGGC-GACAATCTG
1 CCCCAGGCTCGGGGTAAAAGATCAAATGACTG-CAATCTG
* * * * **
568915 CCCTAGGCTCGGGGTAAGAGATCAAATGATTACAATCAA
1 CCCCAGGCTCGGGGTAAAAGATCAAATGACTGCAATCTG
* * *
568954 CCCCAAGCTCGAGGTAAGAGAT
1 CCCCAGGCTCGGGGTAAAAGAT
568976 TGGCTGATAG
Statistics
Matches: 159, Mismatches: 49, Indels: 18
0.70 0.22 0.08
Matches are distributed among these distances:
38 6 0.04
39 152 0.96
40 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.27, T:0.22
Consensus pattern (39 bp):
CCCCAGGCTCGGGGTAAAAGATCAAATGACTGCAATCTG
Found at i:568803 original size:78 final size:77
Alignment explanation
Indices: 568720--568936 Score: 292
Period size: 78 Copynumber: 2.8 Consensus size: 77
568710 TTATGATATA
* *
568720 CCCCATGGTCGGGGTAAAAGATCAAATGACTGCAATCTGCCTCAGGCTCGGGGTAAGAGATAGAT
1 CCCCATGCTCGGGGTAAAAGATCAAATGACTGCAATCTGCC-CAGGCTCGGGGTAAGAGATAGAC
568785 TGATAGTGATTTG
65 TGATAGTGATTTG
* * * *
568798 CCCCATGCTCGGGGTAAAAGATCGAATGACTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGAC
1 CCCCATGCTCGGGGTAAAAGATCAAATGACTGCAATCT-GCCCAGGCTCGGGGTAAGAGATAGAC
*
568863 TGATGGTGATTTG
65 TGATAGTGATTTG
* * * *
568876 CCTCAAGCTCGGGGTAAAATATCAAATGGC-GACAATCTGCCCTAGGCTCGGGGTAAGAGAT
1 CCCCATGCTCGGGGTAAAAGATCAAATGACTG-CAATCTGCCC-AGGCTCGGGGTAAGAGAT
568937 CAAATGATTA
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
77 4 0.03
78 116 0.95
79 2 0.02
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.23
Consensus pattern (77 bp):
CCCCATGCTCGGGGTAAAAGATCAAATGACTGCAATCTGCCCAGGCTCGGGGTAAGAGATAGACT
GATAGTGATTTG
Found at i:568886 original size:117 final size:117
Alignment explanation
Indices: 568757--569060 Score: 317
Period size: 117 Copynumber: 2.6 Consensus size: 117
568747 GACTGCAATC
* * * *
568757 TGCCTCAGGCTCGGGGTAAGAGATAGATTGATAGTGATTTGCCCCATGCTCGGGGTAAAAGATCG
1 TGCCTCAGGCTCGGGGTAAAAGATAAATTGATAGTGATTTGCCCTAAGCTCGGGGTAAAAGATCG
* * * * *
568822 AATGACTGCAATCTACCCCAGGCTCGAGGTAAGAGATTGACTGATGGTGATT
66 AATGACTACAATCAACCCCAAGCTCGAGGTAAGAGATTGACTGATAGTGACT
* * * ** ** * * *
568874 TGCCTCAAGCTCGGGGTAAAATATCAAATGGCGA-CAATCTGCCCTAGGCTCGGGGTAAGAGATC
1 TGCCTCAGGCTCGGGGTAAAAGAT-AAATTGATAGTGATTTGCCCTAAGCTCGGGGTAAAAGATC
* * *
568938 AAATGATTACAATCAACCCCAAGCTCGAGGTAAGAGATTGGCTGATAGTGACT
65 GAATGACTACAATCAACCCCAAGCTCGAGGTAAGAGATTGACTGATAGTGACT
* * * * *
568991 TGCCCCAGGCTTGAGGTAAAAGAT-CATCTGAT-GATGATTTGCCCTAAACTCGGGGTAAAAGAT
1 TGCCTCAGGCTCGGGGTAAAAGATAAAT-TGATAG-TGATTTGCCCTAAGCTCGGGGTAAAAGAT
569054 CGAATGA
64 CGAATGA
569061 TTATGATCTG
Statistics
Matches: 146, Mismatches: 37, Indels: 8
0.76 0.19 0.04
Matches are distributed among these distances:
115 2 0.01
116 1 0.01
117 138 0.95
118 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (117 bp):
TGCCTCAGGCTCGGGGTAAAAGATAAATTGATAGTGATTTGCCCTAAGCTCGGGGTAAAAGATCG
AATGACTACAATCAACCCCAAGCTCGAGGTAAGAGATTGACTGATAGTGACT
Found at i:569061 original size:117 final size:117
Alignment explanation
Indices: 568791--569063 Score: 321
Period size: 117 Copynumber: 2.3 Consensus size: 117
568781 AGATTGATAG
* * * * * *
568791 TGATTTGCCCCATGCTCGGGGTAAAAGATCGAATGACTGCAATCTACCCCAGGCTCGAGGTAAGA
1 TGATTTGCCCTAAGCTCGGGGTAAAAGATCGAATGATTACAATCAACCCCAAGCTCGAGGTAAGA
* * * * * *
568856 GATTGACTGATGGTGATTTGCCTCAAGCTCGGGGTAAAATATCAAATGGCGA
66 GATTGACTGATAGTGACTTGCCCCAAGCTCGAGGTAAAAGATCAAATGACGA
** * * * *
568908 CAATCTGCCCTAGGCTCGGGGTAAGAGATCAAATGATTACAATCAACCCCAAGCTCGAGGTAAGA
1 TGATTTGCCCTAAGCTCGGGGTAAAAGATCGAATGATTACAATCAACCCCAAGCTCGAGGTAAGA
* * * ** *
568973 GATTGGCTGATAGTGACTTGCCCCAGGCTTGAGGTAAAAGATCATCTGATGA
66 GATTGACTGATAGTGACTTGCCCCAAGCTCGAGGTAAAAGATCAAATGACGA
*
569025 TGATTTGCCCTAAACTCGGGGTAAAAGATCGAATGATTA
1 TGATTTGCCCTAAGCTCGGGGTAAAAGATCGAATGATTA
569064 TGATCTGTCC
Statistics
Matches: 126, Mismatches: 30, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
117 126 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (117 bp):
TGATTTGCCCTAAGCTCGGGGTAAAAGATCGAATGATTACAATCAACCCCAAGCTCGAGGTAAGA
GATTGACTGATAGTGACTTGCCCCAAGCTCGAGGTAAAAGATCAAATGACGA
Found at i:569178 original size:41 final size:41
Alignment explanation
Indices: 569081--569185 Score: 149
Period size: 41 Copynumber: 2.6 Consensus size: 41
569071 TCCAAGGCTC
* *
569081 TAATTAAGGGTAAAAAACTAGAATCTCCAATATGCCCTTCT
1 TAATTAAGGGTAAAAGATTAGAATCTCCAATATGCCCTTCT
* * *
569122 TAATCAAGGGTAAAAGATTAGAATCTTCAATCTGCCCTTCT
1 TAATTAAGGGTAAAAGATTAGAATCTCCAATATGCCCTTCT
*
569163 TGATTAAGGGTAAAAGATT-GAAT
1 TAATTAAGGGTAAAAGATTAGAAT
569186 GATGATGTAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
40 4 0.07
41 53 0.93
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.30
Consensus pattern (41 bp):
TAATTAAGGGTAAAAGATTAGAATCTCCAATATGCCCTTCT
Found at i:569555 original size:50 final size:49
Alignment explanation
Indices: 569418--570062 Score: 360
Period size: 50 Copynumber: 13.1 Consensus size: 49
569408 TCATCTTGTT
* * *
569418 TTCTAAGGTACCGGGTTCGTCGTTACGGCCTCAACCTTTCCCATCACAT-
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* * * * *
569467 TTC-ATGGTACCAGATTCG-CTGTTGCGACCTCAATCTTTCCTATCACATC
1 TTCTA-GGTACCAGGTTCGTC-ATTGCGGCCTCAACCTTTCCCATCACATC
* * *
569516 TTCTGAGGTACCAGGTTCGTCATTGTGGCCTTAACCTTTCCCATCACATT
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
**
569566 TTCTAAGGTACTGGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACAT-
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* * * ** *
569615 ATC-ATGGTACC-GGATTC-ACTGTTGCGGCCTCAATATTTCCTATCACATC
1 TTCTA-GGTACCAGG-TTCGTC-ATTGCGGCCTCAACCTTTCCCATCACATC
* * *
569664 TTTTGAGGTACCAGGTTCGCCATTGCGGCCTTAACCTTTCCCATCACATC
1 TTCT-AGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* * ** *
569714 TTTTAAGGTATC-GGATTCACCGTTGCGGCCTCAATCC-TT-CCATCATC-TC
1 TTCT-AGGTACCAGG-TTCGTCATTGCGGCCTCAA-CCTTTCCCATCA-CATC
* * ** * * *
569763 TTC-ATGGTATCAGGCTCACCGTTGCGGCCTTAACCTTTCCCATCAAATC
1 TTCTA-GGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* * ** * * * * *
569812 TTCTTAGGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCTTTACATC
1 TTC-TAGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* * * * *
569862 TT-TATGGTATCGGGTTCGTCGTTACGGCCTCAACCTTTCTCATCACATC
1 TTCTA-GGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* *
569911 TTCTAAGGTA-CTGGATTCACCGTCA-T--GGCCTCAATCC-TTCCCTTCATC-TC
1 TTCT-AGGTACCAGG-TT---CGTCATTGCGGCCTCAA-CCTTTCCCATCA-CATC
* * * * * *
569961 TTC-ATGGTATCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTACATC
1 TTCTA-GGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
* * ** * *
570010 TTC-ATGGTATCGGGTTCACCATTGCGGTCTCAACCTTTCCCATCACATA
1 TTCTA-GGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
570059 TTCT
1 TTCT
570063 TAGGAACTGA
Statistics
Matches: 484, Mismatches: 71, Indels: 81
0.76 0.11 0.13
Matches are distributed among these distances:
46 3 0.01
47 10 0.02
48 98 0.20
49 147 0.30
50 208 0.43
51 13 0.03
52 1 0.00
53 4 0.01
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (49 bp):
TTCTAGGTACCAGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATC
Found at i:569624 original size:98 final size:97
Alignment explanation
Indices: 569423--570062 Score: 329
Period size: 98 Copynumber: 6.5 Consensus size: 97
569413 TTGTTTTCTA
* * *
569423 AGGTACCGGGTTCGTCGTTACGGCCTCAACCTTTCCCATCACA-TTTC-ATGGTACCAGATTCGC
1 AGGTACC-GGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTTCTAAGGTACCAGGTTCGC
* * * * *
569486 TGTTGCGACCTCAATCTTTCCTATCACATCTTCT
65 -ATTGCGGCCTCAACCTTTCCCATCACATCATCT
* * * **
569520 GAGGTACCAGGTTCGTCATTGTGGCCTTAACCTTTCCCATCACATTTTCTAAGGTACTGGGTTCG
1 -AGGTACC-GGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTTCTAAGGTACCAGGTTCG
569585 TCATTGCGGCCTCAACCTTTCCCATCACAT-ATC-
64 -CATTGCGGCCTCAACCTTTCCCATCACATCATCT
* ** * *
569618 ATGGTACCGGATTC-ACTGTTGCGGCCTCAATATTTCCTATCACATCTTT-TGAGGTACCAGGTT
1 A-GGTACCGG-TTCGTC-GTTGCGGCCTCAACCTTTCCCATCACAT-TTTCTAAGGTACCAGGTT
* * *
569681 CGCCATTGCGGCCTTAACCTTTCCCATCACATCTTTT
62 CG-CATTGCGGCCTCAACCTTTCCCATCACATCATCT
* ** * * * *
569718 AAGGTATCGGATTCACCGTTGCGGCCTCAATCC-TT-CCATCATC-TCTTC-ATGGTATCAGGCT
1 -AGGTACCGG-TTCGTCGTTGCGGCCTCAA-CCTTTCCCATCA-CATTTTCTAAGGTACCAGGTT
* * * * *
569779 CACCGTTGCGGCCTTAACCTTTCCCATCAAATCTTCTT
62 C-GCATTGCGGCCTCAACCTTTCCCATCACATCATC-T
* ** * * * * * * * *
569817 AGGTATCGGGTTCACCGTTACGACCTCAACCTTTCCCTTTACATCTT-TATGGTATCGGGTTCGT
1 AGGTA-CCGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTTCTAAGGTACCAGGTTCG-
* * * *
569881 CGTTACGGCCTCAACCTTTCTCATCACATCTTCT
64 CATTGCGGCCTCAACCTTTCCCATCACATCATCT
* ** *** * * * * *
569915 AAGGTACTGGATTCACCGTCATGGCCTCAATCC-TTCCCTTCATC-TCTTC-ATGGTATCGGGTT
1 -AGGTACCGG-TTCGTCGTTGCGGCCTCAA-CCTTTCCCATCA-CATTTTCTAAGGTACCAGGTT
* * * *
569977 CGCCGTTGCGGCCTCAACCTTTCCCTTTACATCTTC-
62 CG-CATTGCGGCCTCAACCTTTCCCATCACATCATCT
* ** * * *
570013 ATGGTATCGGGTTCACCATTGCGGTCTCAACCTTTCCCATCACATATTCT
1 A-GGTA-CCGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTTCT
570063 TAGGAACTGA
Statistics
Matches: 437, Mismatches: 73, Indels: 63
0.76 0.13 0.11
Matches are distributed among these distances:
97 10 0.02
98 211 0.48
99 148 0.34
100 65 0.15
101 3 0.01
ACGTcount: A:0.18, C:0.31, G:0.17, T:0.34
Consensus pattern (97 bp):
AGGTACCGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTTCTAAGGTACCAGGTTCGCA
TTGCGGCCTCAACCTTTCCCATCACATCATCT
Found at i:569688 original size:148 final size:148
Alignment explanation
Indices: 569416--570199 Score: 608
Period size: 148 Copynumber: 5.3 Consensus size: 148
569406 TTTCATCTTG
* * *
569416 TTTTCTAAGGTACCGGGTTCGTCGTTACGGCCTCAACCTTTCCCATCACATTTCATGGTACCAGA
1 TTTTCTAAGGTATCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGA
* * * * * *
569481 TTCGCTGTTGCGACCTCAATCTTTCCTATCACATCTTCTGAGGTACCAGGTTCGTCATTGTGGCC
66 TTCACCGTTGCGGCCTCAATCTTTCCTATCACATCTTTTGAGGTACCAGGTTCGCCATTGCGGCC
*
569546 TTAACCTTTCCCATCACA
131 TCAACCTTTCCCATCACA
* *
569564 TTTTCTAAGGTA-CTGGGTTCGTCATTGCGGCCTCAACCTTTCCCATCACATATCATGGTACCGG
1 TTTTCTAAGGTATC-GGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGG
* *
569628 ATTCACTGTTGCGGCCTCAATATTTCCTATCACATCTTTTGAGGTACCAGGTTCGCCATTGCGGC
65 ATTCACCGTTGCGGCCTCAATCTTTCCTATCACATCTTTTGAGGTACCAGGTTCGCCATTGCGGC
*
569693 CTTAACCTTTCCCATCACA
130 CTCAACCTTTCCCATCACA
* **
569712 TCTTT-TAAGGTATCGGATTCACCGTTGCGGCCTCAATCC-TT-CCATCATC-TCTTCATGGTAT
1 T-TTTCTAAGGTATCGGGTTCGTCGTTGCGGCCTCAA-CCTTTCCCATCA-CAT-TTCATGGTA-
* * * * * * * * * *
569773 CAGG-CTCACCGTTGCGGCCTTAACCTTTCCCATCAAATCTTCTT-AGGTATCGGGTTCACCGTT
61 CCGGATTCACCGTTGCGGCCTCAATCTTTCCTATCACATCTT-TTGAGGTACCAGGTTCGCCATT
* * * *
569836 ACGACCTCAACCTTTCCCTTTACA
125 GCGGCCTCAACCTTTCCCATCACA
* * * * * *
569860 TCTT-TATGGTATCGGGTTCGTCGTTACGGCCTCAACCTTTCTCATCACATCTTCTAAGGTACTG
1 TTTTCTAAGGTATCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACAT-TTC-ATGGTACCG
*** * * * * * *
569924 GATTCACCGTCATGGCCTCAATCCTTCCCT-T--CATCTCTTCATGGTATCGGGTTCGCCGTTGC
64 GATTCACCGTTGCGGCCTCAAT-CTTTCCTATCACATCTTTTGA-GGTACCAGGTTCGCCATTGC
* *
569986 GGCCTCAACCTTTCCCTTTACA
127 GGCCTCAACCTTTCCCATCACA
* * ** * * * * *
570008 TCTTC-ATGGTATCGGGTTCACCATTGCGGTCTCAACCTTTCCCATCACATATTCTTAGGAACTG
1 TTTTCTAAGGTATCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACAT-TTCAT-GGTACCG
* ** ** * *** * ** * *
570072 AATTTTCCGTCACGGCATCAATCTTTCCCT-TTGTATC-TTTGTGGTACTGGGTTCACCGTTGCG
64 GATTCACCGTTGCGGCCTCAATCTTT-CCTATCACATCTTTTGAGGTACCAGGTTCGCCATTGCG
* * *
570135 GCCTTAACCCTTCCTATCACA
128 GCCTCAACCTTTCCCATCACA
* * * * *
570156 TCTTCTTAGGTA-CTGGGTTCGCCGTTGCGGTCTCAATCTTTCCC
1 TTTTCTAAGGTATC-GGGTTCGTCGTTGCGGCCTCAACCTTTCCC
570200 TTCAATCTTT
Statistics
Matches: 526, Mismatches: 87, Indels: 45
0.80 0.13 0.07
Matches are distributed among these distances:
146 4 0.01
147 47 0.09
148 403 0.77
149 64 0.12
150 8 0.02
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (148 bp):
TTTTCTAAGGTATCGGGTTCGTCGTTGCGGCCTCAACCTTTCCCATCACATTTCATGGTACCGGA
TTCACCGTTGCGGCCTCAATCTTTCCTATCACATCTTTTGAGGTACCAGGTTCGCCATTGCGGCC
TCAACCTTTCCCATCACA
Found at i:570239 original size:99 final size:100
Alignment explanation
Indices: 569438--570237 Score: 536
Period size: 99 Copynumber: 8.1 Consensus size: 100
569428 CCGGGTTCGT
* * * ** * * * *
569438 CGTTACGGCCTCAACCTTTCCCATCACAT-TTCAT-GGTACCAGATTCGCTGTTGCGACCTCAAT
1 CGTTGCGGCCTCAACCTTTCCTATCACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAAC
* * * * **
569501 CTTTCCTATCACATCTTCTGAGGTACCAGG-TTCGT
66 CTTTCCCATCACATCTTTTAAGGTATC-GGATTCAC
* * * * * * * *
569536 CATTGTGGCCTTAACCTTTCCCATCACATTTTCTAAGGTACTGGGTTCGTCATTGCGGCCTCAAC
1 CGTTGCGGCCTCAACCTTTCCTATCACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAAC
* * * *
569601 CTTTCCCATCACA--TATCATGGTACCGGATTCAC
66 CTTTCCCATCACATCTTTTAAGGTATCGGATTCAC
* ** ** * *
569634 TGTTGCGGCCTCAATATTTCCTATCACATCTT-TTGAGGTACCAGGTTCGCCATTGCGGCCTTAA
1 CGTTGCGGCCTCAACCTTTCCTATCACATCTTCTT-AGGTACTGGGTTCGCCGTTGCGGCCTCAA
569698 CCTTTCCCATCACATCTTTTAAGGTATCGGATTCAC
65 CCTTTCCCATCACATCTTTTAAGGTATCGGATTCAC
* * * * *
569734 CGTTGCGGCCTCAATCC-TTCC-ATCATC-TCTTCAT-GGTA-TCAGGCTCACCGTTGCGGCCTT
1 CGTTGCGGCCTCAA-CCTTTCCTATCA-CATCTTCTTAGGTACT-GGGTTCGCCGTTGCGGCCTC
* *
569794 AACCTTTCCCATCAAATCTTCTT-AGGTATCGGGTTCAC
63 AACCTTTCCCATCACATCTT-TTAAGGTATCGGATTCAC
* * * * *
569832 CGTTACGACCTCAACCTTTCCCT-TTACATC-T-TTATGGTA-TCGGGTTCGTCGTTACGGCCTC
1 CGTTGCGGCCTCAACCTTT-CCTATCACATCTTCTTA-GGTACT-GGGTTCGCCGTTGCGGCCTC
* *
569893 AACCTTTCTCATCACATCTTCTAAGGTA-CTGGATTCAC
63 AACCTTTCCCATCACATCTTTTAAGGTATC-GGATTCAC
*** * *
569931 CGTCATGGCCTCAATCCTTCCCT-TCATC-TCTTCAT-GGTA-TCGGGTTCGCCGTTGCGGCCTC
1 CGTTGCGGCCTCAA-CCTTTCCTATCA-CATCTTCTTAGGTACT-GGGTTCGCCGTTGCGGCCTC
* * * * *
569992 AACCTTTCCCTTTACATC-TTCATGGTATCGGGTTCAC
63 AACCTTTCCCATCACATCTTTTAAGGTATCGGATTCAC
* * * * * ** ** ** * *
570029 CATTGCGGTCTCAACCTTTCCCATCACATATTCTTAGGAACTGAATTTTCCGTCACGGCATCAAT
1 CGTTGCGGCCTCAACCTTTCCTATCACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAAC
* *** *
570094 CTTTCCCTTTGTATCTTTGT--GGTA-CTGGGTTCAC
66 CTTTCCCATCACATCTTT-TAAGGTATC-GGATTCAC
* * * *
570128 CGTTGCGGCCTTAACCCTTCCTATCACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGTCTCAAT
1 CGTTGCGGCCTCAACCTTTCCTATCACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAAC
* * *
570193 CTTTCCCTTCA-ATCTTTTAAGGTATAGGATTCGC
66 CTTTCCCATCACATCTTTTAAGGTATCGGATTCAC
570227 CGTTGCGGCCT
1 CGTTGCGGCCT
570238 TATTCATTCC
Statistics
Matches: 549, Mismatches: 119, Indels: 67
0.75 0.16 0.09
Matches are distributed among these distances:
97 14 0.03
98 207 0.38
99 250 0.46
100 77 0.14
101 1 0.00
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.34
Consensus pattern (100 bp):
CGTTGCGGCCTCAACCTTTCCTATCACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAAC
CTTTCCCATCACATCTTTTAAGGTATCGGATTCAC
Found at i:570250 original size:247 final size:246
Alignment explanation
Indices: 569596--570251 Score: 651
Period size: 247 Copynumber: 2.7 Consensus size: 246
569586 CATTGCGGCC
* * * * * * * **
569596 TCAACCTTTCCCATCACAT-ATCATGGTACCGGATTCACTGTTGCGGCCTCAATATTTCCTATCA
1 TCAACCTTTCCCTTTACATCTTTATGGTACTGGGTTCACCGTTGCGGCCTCAA-CCTTCCTATCA
** * * * *
569660 CATCTT-TTGAGGTACCAGGTTCGCCATTGCGGCCTTAACCTTTCCCATCACATCTTTTAAGGTA
65 CATCTTCTT-AGGTACTGGGTTCGCCGTTGCGGCCTCAATCTTTCCCTTCA-ATCTTTTAAGGTA
* * * * *
569724 TCGGATTCACCGTTGCGGCCTCAATCCTT-CCATCATCTCTTCATGGTATCAGGCTCACCGTTGC
128 TCGGATTCGCCGTTGCGGCCTCAATCATTCCCTTTATCTCTTCATGGTATCAGGCTCACCATTGC
* * * ** * *
569788 GGCCTTAACCTTTCCCATCAAATCTTCTTAGGTATCGGGTTCACCGTTACGACC
193 GGCCTCAACCTTTCCCATCAAATATTCTTAGGAATCGAATTCACCGTCACGACA
** * *
569842 TCAACCTTTCCCTTTACATCTTTATGGTA-TCGGGTTCGTCGTTACGGCCTCAACCTTTCTCATC
1 TCAACCTTTCCCTTTACATCTTTATGGTACT-GGGTTCACCGTTGCGGCCTCAACCTTCCT-ATC
* * * *** * * *
569906 ACATCTTCTAAGGTACTGGATTCACCGTCATGGCCTCAATCCTTCCCTTC-ATCTCTTCATGGTA
64 ACATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAATCTTTCCCTTCAATCT-TTTAAGGTA
* * * * *
569970 TCGGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTTA-CATCTTCATGGTATCGGGTTCACCATTG
128 TCGGATTCGCCGTTGCGGCCTCAATCATTCCCTTTATC-TCTTCATGGTATCAGGCTCACCATTG
* * ** *
570034 CGGTCTCAACCTTTCCCATCACATATTCTTAGGAA-CTGAATTTTCCGTCACGGCA
192 CGGCCTCAACCTTTCCCATCAAATATTCTTAGGAATC-GAATTCACCGTCACGACA
* ** * *
570089 TCAATCTTTCCCTTTGTATCTTTGTGGTACTGGGTTCACCGTTGCGGCCTTAACCCTTCCTATCA
1 TCAACCTTTCCCTTTACATCTTTATGGTACTGGGTTCACCGTTGCGGCCTCAA-CCTTCCTATCA
* *
570154 CATCTTCTTAGGTACTGGGTTCGCCGTTGCGGTCTCAATCTTTCCCTTCAATCTTTTAAGGTATA
65 CATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAATCTTTCCCTTCAATCTTTTAAGGTATC
* *
570219 GGATTCGCCGTTGCGGCCTTATTCATTCCCTTT
130 GGATTCGCCGTTGCGGCCTCAATCATTCCCTTT
570252 CAAACCTGTA
Statistics
Matches: 325, Mismatches: 74, Indels: 21
0.77 0.18 0.05
Matches are distributed among these distances:
245 4 0.01
246 55 0.17
247 254 0.78
248 12 0.04
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (246 bp):
TCAACCTTTCCCTTTACATCTTTATGGTACTGGGTTCACCGTTGCGGCCTCAACCTTCCTATCAC
ATCTTCTTAGGTACTGGGTTCGCCGTTGCGGCCTCAATCTTTCCCTTCAATCTTTTAAGGTATCG
GATTCGCCGTTGCGGCCTCAATCATTCCCTTTATCTCTTCATGGTATCAGGCTCACCATTGCGGC
CTCAACCTTTCCCATCAAATATTCTTAGGAATCGAATTCACCGTCACGACA
Found at i:576416 original size:29 final size:30
Alignment explanation
Indices: 576384--576440 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
576374 AGGAAATTAT
* *
576384 GGATCAAAATTGAA-TTTTTTGAAAATTTA
1 GGATCAAAATCGAACTTTTTGGAAAATTTA
*
576413 GGATTAAAATCGAACTTTTTGGAAAATT
1 GGATCAAAATCGAACTTTTTGGAAAATT
576441 GAGGGTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (30 bp):
GGATCAAAATCGAACTTTTTGGAAAATTTA
Found at i:576449 original size:29 final size:29
Alignment explanation
Indices: 576389--576463 Score: 73
Period size: 30 Copynumber: 2.6 Consensus size: 29
576379 ATTATGGATC
* * * *
576389 AAAATTGAATTTTTTGAAAATTTAGGATT
1 AAAATCGAATTTTTGGAAAATTGAGGAGT
576418 AAAATCGAACTTTTTGGAAAATTGAGG-GT
1 AAAATCGAA-TTTTTGGAAAATTGAGGAGT
*
576447 -AAATGGTAATTTTTGGA
1 AAAATCG-AATTTTTGGA
576464 TGCTCAGGTG
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 13 0.33
29 11 0.28
30 15 0.38
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.39
Consensus pattern (29 bp):
AAAATCGAATTTTTGGAAAATTGAGGAGT
Found at i:576505 original size:29 final size:29
Alignment explanation
Indices: 576475--576669 Score: 191
Period size: 29 Copynumber: 6.7 Consensus size: 29
576465 GCTCAGGTGT
*
576475 AAAATGGTGATTTTTGAAAGTTTGAGGGTA
1 AAAAT-GTAATTTTTGAAAGTTTGAGGGTA
*
576505 AAAATGTAATTTTTAAGAAGTTTG-GGGTA
1 AAAATGTAATTTTTGA-AAGTTTGAGGGTA
* **
576534 AAAGTGTAATTTTTGAAAGTACGAGGGTA
1 AAAATGTAATTTTTGAAAGTTTGAGGGTA
* * ** *
576563 AAAATGTGATTTTTGGAAG-TACAAGG-A
1 AAAATGTAATTTTTGAAAGTTTGAGGGTA
* * *
576590 AAAATGTGATTTTGGGAAGTTTGAGGGTA
1 AAAATGTAATTTTTGAAAGTTTGAGGGTA
* *
576619 AAAATGTATTTTTTGAGAAGTTT-AGGGTC
1 AAAATGTAATTTTTGA-AAGTTTGAGGGTA
576648 AAAATGTAATTTTTGGAAAGTT
1 AAAATGTAATTTTT-GAAAGTT
576670 CGGGGGTCAA
Statistics
Matches: 136, Mismatches: 23, Indels: 13
0.79 0.13 0.08
Matches are distributed among these distances:
27 19 0.14
28 12 0.09
29 85 0.62
30 20 0.15
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTGAGGGTA
Found at i:576546 original size:58 final size:56
Alignment explanation
Indices: 576439--576757 Score: 227
Period size: 56 Copynumber: 5.6 Consensus size: 56
576429 TTTTGGAAAA
* * * * *
576439 TTGAGGGT--AAATGGTAATTTTTGGATGCTCAGGTGTAAAATGGTGATTTTTGAAAGT
1 TTGAGGGTAAAAAT-GTAATTTTTAGAAGTTTAGG-GTAAAAT-GTAATTTTTGAAAGT
*
576496 TTGAGGGTAAAAATGTAATTTTTAAGAAGTTTGGGGTAAAAGTGTAATTTTTGAAAGT
1 TTGAGGGTAAAAATGTAATTTTT-AGAAGTTTAGGGTAAAA-TGTAATTTTTGAAAGT
** * * ** * * * * *
576554 ACGAGGGTAAAAATGTGATTTTTGGAAGTACAAGGAAAAATGTGATTTTGGGAAGT
1 TTGAGGGTAAAAATGTAATTTTTAGAAGTTTAGGGTAAAATGTAATTTTTGAAAGT
*
576610 TTGAGGGTAAAAATGTATTTTTTGAGAAGTTTAGGGTCAAAATGTAATTTTTGGAAAGT
1 TTGAGGGTAAAAATGTAATTTTT-AGAAGTTTAGGGT-AAAATGTAATTTTT-GAAAGT
* * * * * *
576669 TCGGGGGTCAAAAT-T--TTTTCACGAAGTTTAGGTTCAAAATATAATTTTGGTG-AAGT
1 TTGAGGGTAAAAATGTAATTTTTA-GAAGTTTAGGGT-AAAATGTAATTTT--TGAAAGT
* * * *
576725 TTAAGGGTCAAAATATAATTTTATAAAAGTTTA
1 TTGAGGGTAAAAATGTAATTTT-TAGAAGTTTA
576758 AGGACTTTTA
Statistics
Matches: 207, Mismatches: 41, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
55 1 0.00
56 75 0.36
57 29 0.14
58 63 0.30
59 38 0.18
60 1 0.00
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.37
Consensus pattern (56 bp):
TTGAGGGTAAAAATGTAATTTTTAGAAGTTTAGGGTAAAATGTAATTTTTGAAAGT
Found at i:576632 original size:114 final size:116
Alignment explanation
Indices: 576475--576682 Score: 314
Period size: 114 Copynumber: 1.8 Consensus size: 116
576465 GCTCAGGTGT
* *
576475 AAAATGGTGATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTGGGGT-AAAAGT
1 AAAATGGTGATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGTCAAAA-T
576539 GTAATTTTT-GAAAGTACGAGGGTAAAAATGTGATTTTTGGAAGTACAAGGA
65 GTAATTTTTGGAAAGTACGAGGGTAAAAATGTGATTTTTGGAAGTACAAGGA
* * *
576590 AAAAT-GTGATTTTGGGAAGTTTGAGGGTAAAAATGTATTTTTTGAGAAGTTTAGGGTCAAAATG
1 AAAATGGTGATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGTCAAAATG
* * *
576654 TAATTTTTGGAAAGTTCGGGGGTCAAAAT
66 TAATTTTTGGAAAGTACGAGGGTAAAAAT
576683 TTTTTCACGA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
114 57 0.69
115 26 0.31
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.35
Consensus pattern (116 bp):
AAAATGGTGATTTTGGAAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGTCAAAATG
TAATTTTTGGAAAGTACGAGGGTAAAAATGTGATTTTTGGAAGTACAAGGA
Found at i:576708 original size:114 final size:113
Alignment explanation
Indices: 576475--576757 Score: 288
Period size: 114 Copynumber: 2.5 Consensus size: 113
576465 GCTCAGGTGT
* * *
576475 AAAATGGTGATTTTTGAAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTGGGGTAAAAGTG
1 AAAAT-GTGATTTTGGGAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGTAAAAGTG
**
576540 TAATTTTTGAAAGTACGAGGGTAAAAATGTGATTTTTGGAAGTACAAGGA
65 TAATTTTTGAAAGTACGAGGGTAAAAATGT-ATTTTACGAAGTACAAGGA
* *
576590 AAAATGTGATTTTGGGAAGTTTGAGGGTAAAAATGTATTTTTTGAGAAGTTTAGGGTCAAAA-TG
1 AAAATGTGATTTTGGGAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGT-AAAAGTG
* * * ** *
576654 TAATTTTTGGAAAGTTCGGGGGTCAAAAT-T-TTTTCACGAAGT-TTAGGTTC
65 TAATTTTT-GAAAGTACGAGGGTAAAAATGTATTTT-ACGAAGTACAAGG--A
* * * * *
576704 AAAATATAATTTTGGTGAAGTTTAAGGGTCAAAATATAATTTTATAA-AAGTTTA
1 AAAATGTGATTTTGG-GAAGTTTGAGGGTAAAAATGTAATTTT-TAAGAAGTTTA
576758 AGGACTTTTA
Statistics
Matches: 141, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
112 7 0.05
113 5 0.04
114 71 0.50
115 56 0.40
116 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.36
Consensus pattern (113 bp):
AAAATGTGATTTTGGGAAGTTTGAGGGTAAAAATGTAATTTTTAAGAAGTTTAGGGTAAAAGTGT
AATTTTTGAAAGTACGAGGGTAAAAATGTATTTTACGAAGTACAAGGA
Found at i:576738 original size:30 final size:28
Alignment explanation
Indices: 576598--576746 Score: 115
Period size: 30 Copynumber: 5.2 Consensus size: 28
576588 GAAAAATGTG
* *
576598 ATTTTGGGAAGTTTGAGGGTAAAAATGTA
1 ATTTTGGGAAGTTT-AGGGTCAAAATATA
* * *
576627 TTTTTTGAGAAGTTTAGGGTCAAAATGTA
1 -ATTTTGGGAAGTTTAGGGTCAAAATATA
* **
576656 ATTTTTGGAAAGTTCGGGGGTCAAAAT-T-
1 A-TTTTGGGAAGTT-TAGGGTCAAAATATA
** *
576684 -TTTTCACGAAGTTTAGGTTCAAAATATA
1 ATTTT-GGGAAGTTTAGGGTCAAAATATA
576712 ATTTTGGTGAAGTTTAAGGGTCAAAATATA
1 ATTTTGG-GAAGTTT-AGGGTCAAAATATA
576742 ATTTT
1 ATTTT
576747 ATAAAAGTTT
Statistics
Matches: 94, Mismatches: 17, Indels: 16
0.74 0.13 0.13
Matches are distributed among these distances:
26 13 0.14
27 6 0.06
29 35 0.37
30 40 0.43
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.39
Consensus pattern (28 bp):
ATTTTGGGAAGTTTAGGGTCAAAATATA
Found at i:576755 original size:30 final size:30
Alignment explanation
Indices: 576692--576760 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
576682 TTTTTTCACG
* * *
576692 AAGTTT-AGGTTCAAAATATAATTTTGGTG
1 AAGTTTAAGGGTCAAAATATAATTTTGATA
576721 AAGTTTAAGGGTCAAAATATAATTTT-ATAA
1 AAGTTTAAGGGTCAAAATATAATTTTGAT-A
576751 AAGTTTAAGG
1 AAGTTTAAGG
576761 ACTTTTAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 28 0.80
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.38
Consensus pattern (30 bp):
AAGTTTAAGGGTCAAAATATAATTTTGATA
Found at i:577486 original size:2 final size:2
Alignment explanation
Indices: 577479--577508 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
577469 ATGTATTTAA
577479 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
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):
AT
Done.