Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold277
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: 582610
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
File 4 of 4
Found at i:476381 original size:32 final size:32
Alignment explanation
Indices: 476328--476392 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
476318 AATTATATTT
*
476328 ATTTTAAAAATTAAATTAATAAAA-TAAATAAA
1 ATTTTAAAAATTAAATAAATAAAATTAAA-AAA
*
476360 ATTTTAAAATTTTAAA-AAATAAAATTAAAAAA
1 ATTTTAAAA-ATTAAATAAATAAAATTAAAAAA
476392 A
1 A
476393 GTGAAAGAGC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 20 0.69
33 9 0.31
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (32 bp):
ATTTTAAAAATTAAATAAATAAAATTAAAAAA
Found at i:476617 original size:11 final size:11
Alignment explanation
Indices: 476601--476679 Score: 60
Period size: 11 Copynumber: 7.5 Consensus size: 11
476591 TTTACTCCAT
476601 ATAAAAATATA
1 ATAAAAATATA
476612 ATAAAAATA-A
1 ATAAAAATATA
*
476622 TTAAAAA-ATA
1 ATAAAAATATA
*
476632 ATATAAAAGATA
1 ATA-AAAATATA
*
476644 AT-ATAATATA
1 ATAAAAATATA
*
476654 A-AAATAATTTA
1 ATAAA-AATATA
*
476665 ATATAAATAT-
1 ATAAAAATATA
476675 ATAAA
1 ATAAA
476680 TAAATATATT
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 1 0.02
10 22 0.42
11 23 0.43
12 7 0.13
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.30
Consensus pattern (11 bp):
ATAAAAATATA
Found at i:476666 original size:16 final size:17
Alignment explanation
Indices: 476629--476671 Score: 70
Period size: 16 Copynumber: 2.6 Consensus size: 17
476619 TAATTAAAAA
476629 ATAATATAAAAGATAAT
1 ATAATATAAAAGATAAT
476646 ATAATATAAAA-ATAAT
1 ATAATATAAAAGATAAT
*
476662 TTAATATAAA
1 ATAATATAAA
476672 TATATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
ATAATATAAAAGATAAT
Found at i:476686 original size:39 final size:38
Alignment explanation
Indices: 476605--476692 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 38
476595 CTCCATATAA
476605 AAATAT-A-ATAAAAATAATTAAAAAATAATATAAAAG
1 AAATATAATATAAAAATAATTAAAAAATAATATAAAAG
*
476641 ATAATATAATATAAAAATAATTTAATATAAAT-ATAT-AAAT
1 A-AATATAATATAAAAATAA-TTAA-A-AAATAATATAAAAG
*
476681 AAATATATTATA
1 AAATATAATATA
476693 TTTTATATAA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
36 1 0.02
37 5 0.11
38 1 0.02
39 20 0.45
40 8 0.18
41 5 0.11
42 4 0.09
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (38 bp):
AAATATAATATAAAAATAATTAAAAAATAATATAAAAG
Found at i:477144 original size:23 final size:25
Alignment explanation
Indices: 477111--477158 Score: 82
Period size: 24 Copynumber: 2.0 Consensus size: 25
477101 TTGAATACTA
477111 ACCGTTTGATTA-GTCAGTATTTTG
1 ACCGTTTGATTACGTCAGTATTTTG
477135 ACCG-TTGATTACGTCAGTATTTTG
1 ACCGTTTGATTACGTCAGTATTTTG
477159 GGATTAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.44
Consensus pattern (25 bp):
ACCGTTTGATTACGTCAGTATTTTG
Found at i:477769 original size:10 final size:9
Alignment explanation
Indices: 477754--477793 Score: 53
Period size: 10 Copynumber: 4.1 Consensus size: 9
477744 AATAAAATTA
477754 TTTTTATTCT
1 TTTTTATT-T
477764 TTTTTATTT
1 TTTTTATTT
477773 TTATTTATTT
1 TT-TTTATTT
477783 ATTTTTATTT
1 -TTTTTATTT
477793 T
1 T
477794 ATGAATAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 4 0.14
10 22 0.79
11 2 0.07
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (9 bp):
TTTTTATTT
Found at i:491579 original size:33 final size:33
Alignment explanation
Indices: 491542--491608 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
491532 TTCAACGATT
491542 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
491575 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
491608 T
1 T
491609 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:491580 original size:13 final size:13
Alignment explanation
Indices: 491562--491586 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
491552 CATAAAATGT
491562 TGTATCGATACAA
1 TGTATCGATACAA
491575 TGTATCGATACA
1 TGTATCGATACA
491587 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:491667 original size:13 final size:13
Alignment explanation
Indices: 491649--491673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
491639 ATTACTCAAA
491649 TGTATCGATACAT
1 TGTATCGATACAT
491662 TGTATCGATACA
1 TGTATCGATACA
491674 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:491837 original size:52 final size:51
Alignment explanation
Indices: 491682--491856 Score: 314
Period size: 51 Copynumber: 3.4 Consensus size: 51
491672 CACTGATCTT
491682 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
491733 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
* *
491784 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
*
491836 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
491857 CTTTTCATAT
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 72 0.60
52 48 0.40
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:496007 original size:10 final size:10
Alignment explanation
Indices: 495992--496018 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
495982 TGCTAACTAA
495992 GTTTTTGTTT
1 GTTTTTGTTT
496002 GTTTTTGTTT
1 GTTTTTGTTT
496012 GTTTTTG
1 GTTTTTG
496019 CTTGATACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (10 bp):
GTTTTTGTTT
Found at i:505713 original size:1 final size:1
Alignment explanation
Indices: 505707--505819 Score: 91
Period size: 1 Copynumber: 113.0 Consensus size: 1
505697 GGCGTCCTCC
* ** ** **
505707 AAAAAAACAAAAAAAAAAAAAAAAAAAAACGAAAAAAAATGAAAAACCAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * * *
505772 AGGAAAAAAAAAACAAAAACAATAAAAAAAACAAACAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
505820 GGGGGTCCGG
Statistics
Matches: 88, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
1 88 1.00
ACGTcount: A:0.87, C:0.08, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:505752 original size:39 final size:37
Alignment explanation
Indices: 505709--505819 Score: 134
Period size: 37 Copynumber: 2.9 Consensus size: 37
505699 CGTCCTCCAA
*
505709 AAAAACAAAAAAAAAAAAAAAAAAAAACGAAAAAAAATG
1 AAAAACAAAAAAAAAAAAAAAAAAAAAC-AAAAAAAA-C
*
505748 AAAAACCAAAAAAAAAAAAAAAAAAGGAA-AAAAAAAAC
1 AAAAA-CAAAAAAAAAAAAAAAAAA-AAACAAAAAAAAC
* * *
505786 AAAAACAATAAAAAAAACAAACAAAAACAAAAAA
1 AAAAACAAAAAAAAAAAAAAAAAAAAACAAAAAA
505820 GGGGGTCCGG
Statistics
Matches: 63, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
36 2 0.03
37 22 0.35
38 5 0.08
39 13 0.21
40 19 0.30
41 2 0.03
ACGTcount: A:0.86, C:0.08, G:0.04, T:0.02
Consensus pattern (37 bp):
AAAAACAAAAAAAAAAAAAAAAAAAAACAAAAAAAAC
Found at i:505779 original size:49 final size:47
Alignment explanation
Indices: 505705--505821 Score: 143
Period size: 47 Copynumber: 2.5 Consensus size: 47
505695 ACGGCGTCCT
505705 CCAAAAAAACAAAAAAAAAAA--AAAAAAAAAACGAAAAAAAATGAAAAA
1 CCAAAAAAA-AAAAAAAAAAAGGAAAAAAAAAAC-AAAAAAAAT-AAAAA
*
505753 CCAAAAAAAAAAAAAAAAAAGGAAAAAAAAAACAAAAACAATAAAAA
1 CCAAAAAAAAAAAAAAAAAAGGAAAAAAAAAACAAAAAAAATAAAAA
*
505800 --AAACAAACAAAAACAAAAAAGG
1 CCAAA-AAA-AAAAAAAAAAAAGG
505822 GGGTCCGGAT
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
45 3 0.05
46 3 0.05
47 29 0.46
48 17 0.27
49 11 0.17
ACGTcount: A:0.84, C:0.09, G:0.05, T:0.02
Consensus pattern (47 bp):
CCAAAAAAAAAAAAAAAAAAGGAAAAAAAAAACAAAAAAAATAAAAA
Found at i:507300 original size:30 final size:30
Alignment explanation
Indices: 507260--507340 Score: 128
Period size: 30 Copynumber: 2.7 Consensus size: 30
507250 TCACCCTTCA
*
507260 AAAGTCCACAAGTCAGTGGCATTTTTTTTC-
1 AAAGCCCACAAGTCAGTGGCA-TTTTTTTCG
*
507290 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCATTTTTTTCG
507320 AAAGCCCACAAGTCAGTGGCA
1 AAAGCCCACAAGTCAGTGGCA
507341 ACCTTCAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 8 0.17
30 39 0.83
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.27
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCATTTTTTTCG
Found at i:507362 original size:27 final size:27
Alignment explanation
Indices: 507320--507414 Score: 93
Period size: 27 Copynumber: 3.3 Consensus size: 27
507310 ATTTTTTTCG
*
507320 AAAGCCCACAAGTCAGTGGCAACCTTC
1 AAAGCCCACAAATCAGTGGCAACCTTC
507347 AAAGCCCACAAATCAGTGGC-ACCATTTTCC
1 AAAGCCCACAAATCAGTGGCAACC---TT-C
*
507377 AAAGCCCACACAAGTCGGTGGCAACCCTTC
1 AAAGCCCACA-AA-TCAGTGGCAA-CCTTC
*
507407 TAAGCCCA
1 AAAGCCCA
507415 ATATAGCTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
26 3 0.05
27 19 0.33
29 2 0.04
30 19 0.33
31 4 0.07
32 7 0.12
33 1 0.02
34 2 0.04
ACGTcount: A:0.33, C:0.35, G:0.17, T:0.16
Consensus pattern (27 bp):
AAAGCCCACAAATCAGTGGCAACCTTC
Found at i:507366 original size:57 final size:60
Alignment explanation
Indices: 507287--507414 Score: 163
Period size: 57 Copynumber: 2.2 Consensus size: 60
507277 GGCATTTTTT
* * *** *
507287 TTCAAAGCCCACAAGTCGGTGGCATTTTTTTCGAAAG-CC-CACAAGTCAGTGGCAA-CC
1 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
507344 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCGGTGGCAACCC
1 TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
*
507404 TTCTAAGCCCA
1 TTCAAAGCCCA
507415 ATATAGCTGG
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 31 0.52
58 2 0.03
59 15 0.25
60 12 0.20
ACGTcount: A:0.30, C:0.32, G:0.18, T:0.20
Consensus pattern (60 bp):
TTCAAAGCCCACAAATCAGTGGCACCATTTTCCAAAGCCCACACAAGTCAGTGGCAACCC
Found at i:507382 original size:30 final size:30
Alignment explanation
Indices: 507260--507386 Score: 127
Period size: 30 Copynumber: 4.3 Consensus size: 30
507250 TCACCCTTCA
* ** *
507260 AAAGTCCACAAGTCAGTGGCATTTTTTTTC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
* ** *
507290 AAAGCCCACAAGTCGGTGGCATTTTTTTCG
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
507320 AAAGCCCACAAGTCAGTGGCAACC---TT-C
1 AAAGCCCACAAGTCAGTGGC-ACCTTTTTCC
* *
507347 AAAGCCCACAAATCAGTGGCACCATTTTCC
1 AAAGCCCACAAGTCAGTGGCACCTTTTTCC
507377 AAAGCCCACA
1 AAAGCCCACA
507387 CAAGTCGGTG
Statistics
Matches: 83, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
26 3 0.04
27 19 0.23
28 2 0.02
29 2 0.02
30 56 0.67
31 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (30 bp):
AAAGCCCACAAGTCAGTGGCACCTTTTTCC
Found at i:507412 original size:30 final size:30
Alignment explanation
Indices: 507326--507414 Score: 96
Period size: 30 Copynumber: 3.0 Consensus size: 30
507316 TTCGAAAGCC
507326 CACAAGTCAGTGGCAA-CCTTCAAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
*
507355 CA-AA-TCAGTGGC-ACCATTTTCCAAAGCCCA
1 CACAAGTCAGTGGCAACC--CTT-CAAAGCCCA
* *
507385 CACAAGTCGGTGGCAACCCTTCTAAGCCCA
1 CACAAGTCAGTGGCAACCCTTCAAAGCCCA
507415 ATATAGCTGG
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
26 1 0.02
27 9 0.18
28 2 0.04
29 4 0.08
30 19 0.39
31 4 0.08
32 7 0.14
33 3 0.06
ACGTcount: A:0.31, C:0.35, G:0.17, T:0.17
Consensus pattern (30 bp):
CACAAGTCAGTGGCAACCCTTCAAAGCCCA
Found at i:507469 original size:49 final size:49
Alignment explanation
Indices: 507407--507658 Score: 281
Period size: 49 Copynumber: 5.0 Consensus size: 49
507397 GCAACCCTTC
* *
507407 TAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
* *
507456 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCACCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
507505 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTT
* * * * *
507557 TAAGTTCAATGTAGCTGGCCTTAAATCAGCACATTGACATCCTTTTTCTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC---TT-T-ATCTT
* * * * *
507612 TAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCAACTTTATC
1 TAAGTCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTTATC
507659 ACTTCTCTCA
Statistics
Matches: 174, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
49 89 0.51
50 3 0.02
51 2 0.01
52 38 0.22
53 2 0.01
54 2 0.01
55 37 0.21
56 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.33
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
Found at i:507637 original size:107 final size:99
Alignment explanation
Indices: 507402--507655 Score: 296
Period size: 107 Copynumber: 2.5 Consensus size: 99
507392 CGGTGGCAAC
*
507402 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCACCATATTGGCACC-TTTATCTTTAAGTCCAAT
1 CCTT-TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAAT
* * *
507466 ATAGCTGGCCTTGAATCAGCATATTGGCACCTTCA
65 ATAGCTGGCCTTAAATCAGCACATTGACACCTTCA
* *
507501 CCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAA
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTT--ATCTTTAAGTCCAA
*
507566 TGTAGCTGGCCTTAAATCAGCACATTGACATCCTTTTTCTCA
64 TATAGCTGGCCTTAAATCAGCACATTGACA-CC----T-TCA
* * * * *
507608 TCTTTAAGCCCAATATCGTTGGCCGTGAATC-GACATATTGGCAACTTT
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAG-CATATTGGCACCTTT
507656 ATCACTTCTC
Statistics
Matches: 132, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
98 39 0.30
99 7 0.05
101 39 0.30
102 2 0.02
106 2 0.02
107 43 0.33
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (99 bp):
CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTATCTTTAAGTCCAATA
TAGCTGGCCTTAAATCAGCACATTGACACCTTCA
Found at i:508472 original size:33 final size:33
Alignment explanation
Indices: 508435--508501 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
508425 TTCAACGATT
508435 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
508468 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
508501 T
1 T
508502 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:508473 original size:13 final size:13
Alignment explanation
Indices: 508455--508479 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
508445 CATAAAATGT
508455 TGTATCGATACAA
1 TGTATCGATACAA
508468 TGTATCGATACA
1 TGTATCGATACA
508480 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:508560 original size:13 final size:13
Alignment explanation
Indices: 508542--508566 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
508532 ATTACTCAAA
508542 TGTATCGATACAT
1 TGTATCGATACAT
508555 TGTATCGATACA
1 TGTATCGATACA
508567 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:508730 original size:52 final size:51
Alignment explanation
Indices: 508575--508749 Score: 314
Period size: 51 Copynumber: 3.4 Consensus size: 51
508565 CACTGATCTT
508575 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
508626 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
* *
508677 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACATTATAAAA
*
508729 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
508750 CTTTTCATAT
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
51 72 0.60
52 48 0.40
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (51 bp):
TGTATCGATACATGCAGGCAATTTGCCCAGATGTATCGATACATTATAAAA
Found at i:513723 original size:27 final size:27
Alignment explanation
Indices: 513692--513743 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
513682 TTTTAATCAA
*
513692 AGTCAAAGT-TAACAATTAATAGTCAGC
1 AGTCAAAGTCAAACAATTAA-AGTCAGC
513719 AGTCAAAGTCAAACAATTAAAGTCA
1 AGTCAAAGTCAAACAATTAAAGTCA
513744 ATTATCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.23
Consensus pattern (27 bp):
AGTCAAAGTCAAACAATTAAAGTCAGC
Found at i:513757 original size:20 final size:20
Alignment explanation
Indices: 513734--513774 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
513724 AAGTCAAACA
513734 ATTAAAGTCAATTATCAACT
1 ATTAAAGTCAATTATCAACT
*
513754 ATTAAAGTCAATTGTCAACT
1 ATTAAAGTCAATTATCAACT
513774 A
1 A
513775 AGGTCGAAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (20 bp):
ATTAAAGTCAATTATCAACT
Found at i:515142 original size:38 final size:38
Alignment explanation
Indices: 515095--515192 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 38
515085 TGTCATAATA
*
515095 TTATGTTAAATAATAATTAAAAATTATTAAAAATATAT
1 TTATATTAAATAATAATTAAAAATTATTAAAAATATAT
* * *
515133 TTATATTAAATAACAATCAATAAAATTATTAAAATTATAT
1 TTATATTAAATAATAAT-TA-AAAATTATTAAAAATATAT
* *
515173 ATATTTTAAA-AATAAATTAA
1 TTATATTAAATAAT-AATTAA
515193 TAAAATAGAT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
38 16 0.33
39 4 0.08
40 29 0.59
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (38 bp):
TTATATTAAATAATAATTAAAAATTATTAAAAATATAT
Found at i:515195 original size:40 final size:40
Alignment explanation
Indices: 515114--515198 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
515104 ATAATAATTA
* *
515114 AAAATTATTAAAAATATATTTATATTAAATAACAATCAAT
1 AAAATTATTAAAAATATATATATATTAAATAAAAATCAAT
* * *
515154 AAAATTATTAAAATTATATATATTTTAAA-AATAAATTAAT
1 AAAATTATTAAAAATATATATATATTAAATAA-AAATCAAT
515194 AAAAT
1 AAAAT
515199 AGATAAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 2 0.05
40 37 0.95
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (40 bp):
AAAATTATTAAAAATATATATATATTAAATAAAAATCAAT
Found at i:515232 original size:15 final size:14
Alignment explanation
Indices: 515180--515243 Score: 53
Period size: 15 Copynumber: 4.5 Consensus size: 14
515170 TATATATTTT
515180 AAAAAT-AAATTAA
1 AAAAATAAAATTAA
* *
515193 TAAAAT-AGA-TAA
1 AAAAATAAAATTAA
515205 AAAAAGTTAAAAATTAA
1 AAAAA--T-AAAATTAA
515222 AATAAATAAAATTAA
1 AA-AAATAAAATTAA
515237 AAAAATA
1 AAAAATA
515244 CAAAAGCTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
12 7 0.17
13 7 0.17
14 6 0.15
15 10 0.24
16 3 0.07
17 5 0.12
18 3 0.07
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAATAAAATTAA
Found at i:515572 original size:28 final size:28
Alignment explanation
Indices: 515535--515599 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
515525 AATAAATATG
* * *
515535 ATAAAAATAA-TTAAAAGTTGATATAAA
1 ATAAATATAATTTAAAAATTAATATAAA
*
515562 ATTAAATATAATTTAAAAATTAATATAAT
1 A-TAAATATAATTTAAAAATTAATATAAA
515591 ATAAATATA
1 ATAAATATA
515600 TAAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 1 0.03
28 16 0.50
29 15 0.47
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (28 bp):
ATAAATATAATTTAAAAATTAATATAAA
Found at i:515586 original size:17 final size:18
Alignment explanation
Indices: 515555--515610 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
515545 TTAAAAGTTG
515555 ATAT-AAAATTAAATATA
1 ATATAAAAATTAAATATA
*
515572 ATTTAAAAATT-AATATA
1 ATATAAAAATTAAATATA
*
515589 ATATAAATATATAAATA-A
1 ATATAAAAAT-TAAATATA
515607 ATAT
1 ATAT
515611 TTCATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
17 17 0.52
18 12 0.36
19 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
ATATAAAAATTAAATATA
Found at i:516286 original size:25 final size:26
Alignment explanation
Indices: 516258--516328 Score: 108
Period size: 25 Copynumber: 2.8 Consensus size: 26
516248 AATAAATCTC
* * *
516258 TTTTAATCAAAACCATGTAACATT-T
1 TTTTAATCAAAACCAAGAAACATTGG
516283 TTTTAATCAAAACCAAGAAACATTGG
1 TTTTAATCAAAACCAAGAAACATTGG
516309 TTTTAATCAAAACCAAGAAA
1 TTTTAATCAAAACCAAGAAA
516329 TGTTTCAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 22 0.52
26 20 0.48
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.31
Consensus pattern (26 bp):
TTTTAATCAAAACCAAGAAACATTGG
Found at i:521629 original size:2 final size:2
Alignment explanation
Indices: 521624--521680 Score: 64
Period size: 2 Copynumber: 29.0 Consensus size: 2
521614 TCTCTCTCTC
* * *
521624 TA TA TA AA TA TT TA TA TA TGA -A AA TA -A TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
521665 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
521681 AACATATAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
1 2 0.04
2 44 0.94
3 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:522818 original size:21 final size:21
Alignment explanation
Indices: 522788--522830 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
522778 AATATCAACC
522788 ATTGACTATGTCAGTAGTTTG
1 ATTGACTATGTCAGTAGTTTG
* *
522809 ATTGATTATGTCAGTATTTTG
1 ATTGACTATGTCAGTAGTTTG
522830 A
1 A
522831 GTCTAAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (21 bp):
ATTGACTATGTCAGTAGTTTG
Found at i:523930 original size:172 final size:172
Alignment explanation
Indices: 523644--523990 Score: 685
Period size: 172 Copynumber: 2.0 Consensus size: 172
523634 GTCTTATTTT
*
523644 TTAAATATTTTGTATTTATTTTAATAAAGCCTTAATCCAATGATGAGAACTTAGTTATTGATTTA
1 TTAAATATTTTGTATTTATTTTAATAAAGCCCTAATCCAATGATGAGAACTTAGTTATTGATTTA
523709 TCTTGACAATTGAAAAAATATAAGCTTGATTTGAATTTGAGTTAAATTATTTTATTAGTCTCATT
66 TCTTGACAATTGAAAAAATATAAGCTTGATTTGAATTTGAGTTAAATTATTTTATTAGTCTCATT
523774 GTTAAGATGTGAACTTCAATATTTGAGCACATAATTTTTTAC
131 GTTAAGATGTGAACTTCAATATTTGAGCACATAATTTTTTAC
523816 TTAAATATTTTGTATTTATTTTAATAAAGCCCTAATCCAATGATGAGAACTTAGTTATTGATTTA
1 TTAAATATTTTGTATTTATTTTAATAAAGCCCTAATCCAATGATGAGAACTTAGTTATTGATTTA
523881 TCTTGACAATTGAAAAAATATAAGCTTGATTTGAATTTGAGTTAAATTATTTTATTAGTCTCATT
66 TCTTGACAATTGAAAAAATATAAGCTTGATTTGAATTTGAGTTAAATTATTTTATTAGTCTCATT
523946 GTTAAGATGTGAACTTCAATATTTGAGCACATAATTTTTTAC
131 GTTAAGATGTGAACTTCAATATTTGAGCACATAATTTTTTAC
523988 TTA
1 TTA
523991 GATTTGCATT
Statistics
Matches: 174, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
172 174 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (172 bp):
TTAAATATTTTGTATTTATTTTAATAAAGCCCTAATCCAATGATGAGAACTTAGTTATTGATTTA
TCTTGACAATTGAAAAAATATAAGCTTGATTTGAATTTGAGTTAAATTATTTTATTAGTCTCATT
GTTAAGATGTGAACTTCAATATTTGAGCACATAATTTTTTAC
Found at i:524178 original size:2 final size:2
Alignment explanation
Indices: 524171--524212 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
524161 ACATACATAC
524171 AT AT AT AT AT AT 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 AT AT AT AT AT AT
524213 CTTTAGTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526100 original size:14 final size:14
Alignment explanation
Indices: 526077--526110 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
526067 TATTTATTTT
526077 AAAAAAT-AAATTA
1 AAAAAATAAAATTA
526090 AAAAAATTAAAATTA
1 AAAAAA-TAAAATTA
526105 AAAAAA
1 AAAAAA
526111 AGTGAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 1 0.05
15 12 0.63
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
AAAAAATAAAATTA
Found at i:526381 original size:22 final size:23
Alignment explanation
Indices: 526354--526396 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
526344 TACTCCATAT
526354 AAAAATATAATA-AAAATAATTA
1 AAAAATATAATATAAAATAATTA
*
526376 AAAAATATTATATAAAATAAT
1 AAAAATATAATATAAAATAAT
526397 ATAATATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
AAAAATATAATATAAAATAATTA
Found at i:526385 original size:10 final size:11
Alignment explanation
Indices: 526351--526400 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
526341 CTTTACTCCA
526351 TATAAAAATAT
1 TATAAAAATAT
*
526362 AATAAAAATAAT
1 TATAAAAAT-AT
526374 TA-AAAAATAT
1 TATAAAAATAT
*
526384 TATATAAAATAA
1 TATA-AAAATAT
526396 TATAA
1 TATAA
526401 TATAAATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 4 0.12
11 16 0.48
12 13 0.39
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
TATAAAAATAT
Found at i:526401 original size:37 final size:38
Alignment explanation
Indices: 526350--526456 Score: 103
Period size: 37 Copynumber: 2.7 Consensus size: 38
526340 ACTTTACTCC
*
526350 ATATAAA-AATATAATAAAAATAATTAA-AAA-ATATT
1 ATATAAATAATATAATAAAAATAATAAATAAATATATT
*
526385 ATATAAAATAATATAATATAAATACATAAATAAATATATT
1 ATAT-AAATAATATAATAAAAATA-ATAAATAAATATATT
526425 ATATTTTAAATAAATTATAATAAAAAATAATA
1 ATA---TAAAT-AA-TATAAT-AAAAATAATA
526457 TATATGATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
35 4 0.07
36 3 0.05
37 14 0.24
38 4 0.07
39 3 0.05
40 8 0.14
42 4 0.07
43 3 0.05
44 9 0.16
45 6 0.10
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (38 bp):
ATATAAATAATATAATAAAAATAATAAATAAATATATT
Found at i:526493 original size:27 final size:25
Alignment explanation
Indices: 526437--526499 Score: 63
Period size: 27 Copynumber: 2.4 Consensus size: 25
526427 ATTTTAAATA
* * *
526437 AATTATAATAAAAAATAATATATAT
1 AATTTTAATAAAAAATAATAAACAT
*
526462 GATTTTAATATAAAAATAATTAAACAT
1 AATTTTAATA-AAAAATAA-TAAACAT
526489 AATTTGTAATA
1 AATTT-TAATA
526500 CTCATGAACG
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
25 8 0.27
26 8 0.27
27 9 0.30
28 5 0.17
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (25 bp):
AATTTTAATAAAAAATAATAAACAT
Found at i:527770 original size:27 final size:26
Alignment explanation
Indices: 527713--527770 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
527703 ATGAAAATTT
527713 TAATATTATATAAACATTTTTAAAAC
1 TAATATTATATAAACATTTTTAAAAC
* * *
527739 AAATATTATAATATATATTTTTATAAA-
1 TAATATTAT-ATAAACATTTTTA-AAAC
527766 TAATA
1 TAATA
527771 AAGGTCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 8 0.31
27 15 0.58
28 3 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (26 bp):
TAATATTATATAAACATTTTTAAAAC
Found at i:527809 original size:35 final size:34
Alignment explanation
Indices: 527745--527818 Score: 82
Period size: 35 Copynumber: 2.2 Consensus size: 34
527735 AAACAAATAT
* *
527745 TATAATATATATTTTTATAAATAATAAAGGTCAAA
1 TATAATATATATTTTGATAAATAAAAAAGGT-AAA
527780 TATAATATA-ATTTATGATGAAA-AAAAAAGGTAAA
1 TATAATATATATTT-TGAT-AAATAAAAAAGGTAAA
527814 T-TAAT
1 TATAAT
527819 TAGATAATCC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
33 4 0.11
34 8 0.23
35 20 0.57
36 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.36
Consensus pattern (34 bp):
TATAATATATATTTTGATAAATAAAAAAGGTAAA
Found at i:529994 original size:27 final size:27
Alignment explanation
Indices: 529922--530022 Score: 100
Period size: 27 Copynumber: 3.9 Consensus size: 27
529912 AAAATTAGCT
* * *
529922 ACAAATTTTGACAAA-AC-AACAAGCC
1 ACAATTTTTGACAAATACAAAGAAACC
* * *
529947 ATAATTTTTGATAAATA-AAAGAAATC
1 ACAATTTTTGACAAATACAAAGAAACC
*
529973 ACAATTTTTGACAAATACAAAGTAACC
1 ACAATTTTTGACAAATACAAAGAAACC
* *
530000 ACCATTTTTGACAAACACAAAGA
1 ACAATTTTTGACAAATACAAAGA
530023 GTGGCTTTTG
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
25 12 0.20
26 21 0.35
27 27 0.45
ACGTcount: A:0.50, C:0.17, G:0.08, T:0.25
Consensus pattern (27 bp):
ACAATTTTTGACAAATACAAAGAAACC
Found at i:534527 original size:27 final size:27
Alignment explanation
Indices: 534494--534566 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
534484 ACAAGCCACA
* *
534494 ATTTTTGATAAACAAAAAGGAATCATC
1 ATTTTTGACAAACAAAAAGGAACCATC
* * *
534521 ATTTTTGACAAATACAAAGTAACCATC
1 ATTTTTGACAAACAAAAAGGAACCATC
534548 ATTTTTGACAAACACAAAA
1 ATTTTTGACAAACA-AAAA
534567 TGTGACTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
27 35 0.92
28 3 0.08
ACGTcount: A:0.48, C:0.15, G:0.08, T:0.29
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCATC
Found at i:539763 original size:87 final size:87
Alignment explanation
Indices: 539608--539867 Score: 479
Period size: 87 Copynumber: 3.0 Consensus size: 87
539598 ATGCACGAGA
539608 ATAACCATT-AATAAAGCACATAACCTAGGATTAAACAACTAGAAAGGTACTTTGCCATGCTAAA
1 ATAACCATTCAATAAAGCACATAACCTAGGATTAAACAACTAGAAAGGTACTTTGCCATGCTAAA
539672 AACTGGAACCCTGTTCATACAG
66 AACTGGAACCCTGTTCATACAG
539694 ATAACCATTCAATAAAGCACATAACCTAGGATTAAACAACTAGAAAGGTACTTTGCCATGCTAAA
1 ATAACCATTCAATAAAGCACATAACCTAGGATTAAACAACTAGAAAGGTACTTTGCCATGCTAAA
539759 AACTGGAACCCTGTTCATACAG
66 AACTGGAACCCTGTTCATACAG
539781 ATAACCATTCAATAAAGCACATAACCTAGGATTAAACAACTA-AAAGGGTACTTTGCCATGCTAA
1 ATAACCATTCAATAAAGCACATAACCTAGGATTAAACAACTAGAAA-GGTACTTTGCCATGCTAA
* *
539845 AAACTAGAACCTTGTTCATACAG
65 AAACTGGAACCCTGTTCATACAG
539868 CTTGATCACT
Statistics
Matches: 170, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
86 12 0.07
87 158 0.93
ACGTcount: A:0.42, C:0.21, G:0.13, T:0.23
Consensus pattern (87 bp):
ATAACCATTCAATAAAGCACATAACCTAGGATTAAACAACTAGAAAGGTACTTTGCCATGCTAAA
AACTGGAACCCTGTTCATACAG
Found at i:542171 original size:42 final size:42
Alignment explanation
Indices: 542112--542196 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
542102 TTAAGAAACA
542112 TACCTTTGTTTTCATGCCATGCATGATAACTGATACATTCTT
1 TACCTTTGTTTTCATGCCATGCATGATAACTGATACATTCTT
542154 TACCTTTGTTTTCATGCCATGCATGATAACTGATACATTCTT
1 TACCTTTGTTTTCATGCCATGCATGATAACTGATACATTCTT
542196 T
1 T
542197 TTTCTTATGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.24, C:0.21, G:0.12, T:0.44
Consensus pattern (42 bp):
TACCTTTGTTTTCATGCCATGCATGATAACTGATACATTCTT
Found at i:542311 original size:17 final size:17
Alignment explanation
Indices: 542285--542317 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
542275 ATTCATAACT
542285 TCTTTATTTTTTTCTTG
1 TCTTTATTTTTTTCTTG
*
542302 TCTTTCTTTTTTTCTT
1 TCTTTATTTTTTTCTT
542318 TTAAGGTGGT
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:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (17 bp):
TCTTTATTTTTTTCTTG
Found at i:544924 original size:40 final size:39
Alignment explanation
Indices: 544847--544951 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 39
544837 TGTCGTGGTA
* * *
544847 TTATGTTAAATAATAATTA-AAAATTATTAAAAATATAT
1 TTATATTAAATAATAATAATAAAATTATCAAAAATATAT
*
544885 TTATATTAAATAATAATCAATAAAATTATCAAAATTATAT
1 TTATATTAAATAATAAT-AATAAAATTATCAAAAATATAT
* *
544925 TTATTTTAAAAAATAAATTAATAAAAT
1 TTATATTAAATAAT-AA-TAATAAAAT
544952 AAATAAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
38 16 0.28
39 1 0.02
40 29 0.51
41 10 0.18
42 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.41
Consensus pattern (39 bp):
TTATATTAAATAATAATAATAAAATTATCAAAAATATAT
Found at i:545326 original size:17 final size:16
Alignment explanation
Indices: 545300--545348 Score: 64
Period size: 17 Copynumber: 3.0 Consensus size: 16
545290 AAAAATAATT
545300 AAAAAT-TAATATAAA
1 AAAAATATAATATAAA
*
545315 ATAAAATATAATCTAAA
1 A-AAAATATAATATAAA
545332 AAATAATATAATATAAA
1 AAA-AATATAATATAAA
545349 TATTTAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 7 0.24
17 21 0.72
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAAATATAATATAAA
Found at i:545347 original size:29 final size:28
Alignment explanation
Indices: 545268--545348 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 28
545258 AACTTTACCT
*
545268 ATTAAAATATAATA-AATATGATAAAAATA
1 ATTAAAAAATAATATAATAT-A-AAAAATA
* * *
545297 ATTAAAAATTAATATAAAATAAAATATA
1 ATTAAAAAATAATATAATATAAAAAATA
545325 ATCTAAAAAATAATATAATATAAA
1 AT-TAAAAAATAATATAATATAAA
545349 TATTTAAATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 8 0.18
29 32 0.73
30 4 0.09
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (28 bp):
ATTAAAAAATAATATAATATAAAAAATA
Found at i:554858 original size:2 final size:2
Alignment explanation
Indices: 554853--554929 Score: 104
Period size: 2 Copynumber: 39.0 Consensus size: 2
554843 TCTCTCTCTC
* * *
554853 TA TA TA TA AA TA TT TA TA TA TGA -A AA T- TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA
554894 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
554930 CACCCATACG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
1 2 0.03
2 64 0.96
3 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:563592 original size:23 final size:25
Alignment explanation
Indices: 563542--563592 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 25
563532 ATATTTTTTA
* * *
563542 TTTTTTAAAACAAATAAAGATCATT
1 TTTTTTAAAACAAATAAACATAAAT
563567 TTTTTTAAAA-AAA-AAACATAAAT
1 TTTTTTAAAACAAATAAACATAAAT
563590 TTT
1 TTT
563593 GAACTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 3 0.13
25 10 0.43
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.41
Consensus pattern (25 bp):
TTTTTTAAAACAAATAAACATAAAT
Found at i:564139 original size:10 final size:10
Alignment explanation
Indices: 564126--564155 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
564116 CCATTTCATA
564126 TTTTTTCTTT
1 TTTTTTCTTT
564136 TTTTTTCTTT
1 TTTTTTCTTT
*
564146 TTCTTTCTTT
1 TTTTTTCTTT
564156 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:564148 original size:16 final size:17
Alignment explanation
Indices: 564127--564161 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
564117 CATTTCATAT
*
564127 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
564143 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
564160 TT
1 TT
564162 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:565462 original size:32 final size:32
Alignment explanation
Indices: 565407--565881 Score: 783
Period size: 32 Copynumber: 14.8 Consensus size: 32
565397 AAAATGGTGA
* * *
565407 TTTGAAAAGGGTTGCCACTGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* * *
565439 TTTTAAATGGGTTACCACCGACTTGCGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
565471 TTTTAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
** *
565503 TTTGAAAAAGGTTACCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
565535 TTTGAAATGGGTTGCCACCTACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
565567 TTT-AGAATGGGTTGCCACCGACCTGTGTGGGC
1 TTTGA-AATGGGTTGCCACCGACTTGTGTGGGC
565599 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
565631 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
565663 TTTGAAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTG-AAATGGGTTGCCACCGACTTGTGTGGGC
565696 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
565728 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
565760 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
565792 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
*
565824 TTTGGAATGGGTTGCCACCGACTTGTGTGGGC
1 TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
* *
565856 TTTGAAATGGG-TGCCACAGAGTTGTG
1 TTTGAAATGGGTTGCCACCGACTTGTG
565882 GATTAAAAGG
Statistics
Matches: 419, Mismatches: 21, Indels: 7
0.94 0.05 0.02
Matches are distributed among these distances:
31 14 0.03
32 372 0.89
33 33 0.08
ACGTcount: A:0.17, C:0.19, G:0.33, T:0.31
Consensus pattern (32 bp):
TTTGAAATGGGTTGCCACCGACTTGTGTGGGC
Found at i:565924 original size:27 final size:27
Alignment explanation
Indices: 565864--566659 Score: 1215
Period size: 27 Copynumber: 29.1 Consensus size: 27
565854 GCTTTGAAAT
*
565864 GGGTGCCACAGAGTTGTGGA-TTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
** *
565890 GGACGCCACGGAGTTGTGGAGTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
565917 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
565944 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
565971 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
565999 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
566026 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
566054 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
566081 GGGTGCCACGGAGTTGTGGTCTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
566108 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
566135 GGGTGCCACAGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
566162 GGGTGCCACGGAGTTGTGGACTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
*
566190 GGGTGCCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
566217 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
566245 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
566272 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
566299 GGGTGCCACGGAGTTGTGGTCTTTAAAA
1 GGGTGCCACGGAGTTGTGGAC-TTAAAA
566327 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
566354 GGGTGCCACGGAGTTGTGGACTAAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
566381 GGGTGCCACGGAGTTGTAGGACTTTAAA
1 GGGTGCCACGGAGTTGT-GGACTTAAAA
* *
566409 GGG-GGCACAGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
* *
566435 GAGATGCCACGGAGTTATGGACTTAAAA
1 G-GGTGCCACGGAGTTGTGGACTTAAAA
566463 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
566490 GGGTGCCACGGAG-TGTGGACTT-AAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
566515 GGGTGCCACGGGAGTTGTGGTCTTTAAAA
1 GGGTGCCAC-GGAGTTGTGGAC-TTAAAA
566544 GGGTGCCACGGAGTTGTGGACTT-AAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
566570 GGGTGCCACGGAGTTGTGGACTTAAAA
1 GGGTGCCACGGAGTTGTGGACTTAAAA
*
566597 GGGTGCCACGGAGTTTGTGGACCTAAAAA
1 GGGTGCCACGGAG-TTGTGGA-CTTAAAA
566626 GGGTGCCACGGAGTGTGTGGACTTTAAAAA
1 GGGTGCCACGGAGT-TGTGGAC-TT-AAAA
566656 GGGT
1 GGGT
566660 CACAGTACTA
Statistics
Matches: 705, Mismatches: 46, Indels: 34
0.90 0.06 0.04
Matches are distributed among these distances:
25 12 0.02
26 66 0.09
27 403 0.57
28 178 0.25
29 38 0.05
30 8 0.01
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (27 bp):
GGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:566083 original size:164 final size:163
Alignment explanation
Indices: 565864--566659 Score: 1228
Period size: 164 Copynumber: 4.9 Consensus size: 163
565854 GCTTTGAAAT
* ** *
565864 GGGTGCCACAGAGTTGTGGA-TTAAAAGGACGCCACGGAGTTGTGGAGTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* *
565928 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
*
565993 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAA
131 TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* *
566026 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
* *
566091 GAGTTGTGGTCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC
65 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
*
566156 -TAAAAAGGGTGCCACGGAGTTGTGGACTTTAAAA
130 TTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAA
* * *
566190 GGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACG
1 GGGTGCCACGGAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
*
566255 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTC
65 GAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
566320 TTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
130 TTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
* * * *
566354 GGGTGCCACGGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTAGGACTTTAAAGGG-GGCACA
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGT-GGACTTAAAAGGGTGCCACG
* *
566418 GAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGA
65 GAGTTGTGGACTTAAAAG-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGA
566483 C-TTAAAAGGGTGCCACGGAG-TGTGGACTT-AAA
129 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
*
566515 GGGTGCCACGGGAGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTT-AAAGGGTGCCAC
1 GGGTGCCAC-GGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCAC
*
566579 GGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTTGTGGACCTAAAAAGGGTGCCACGGAGTGTGT
64 GGAGTTGTGGACTTAAAAGGGTGCCACGGAG-TTGTGGA-CTTAAAAGGGTGCCACGGAGT-TGT
566644 GGACTTTAAAAAGGGT
126 GGACTTT-AAAAGGGT
566660 CACAGTACTA
Statistics
Matches: 581, Mismatches: 38, Indels: 26
0.90 0.06 0.04
Matches are distributed among these distances:
161 29 0.05
162 55 0.09
163 162 0.28
164 299 0.51
165 28 0.05
166 8 0.01
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (163 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACT
TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAA
Found at i:566187 original size:191 final size:189
Alignment explanation
Indices: 565864--566659 Score: 1215
Period size: 191 Copynumber: 4.2 Consensus size: 189
565854 GCTTTGAAAT
* ** *
565864 GGGTGCCACAGAGTTGTGGA-TTAAAAGGACGCCACGGAGTTGTGGAGTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
565928 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGAC-
565993 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAA
130 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GATGCCACGGAGTTATGGACTTAAAA
*
566054 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGTCTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
566119 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
66 AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGAC-
566184 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGAGATGCCACGGAGTTATGGACTTAAAA
130 TTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAG-GATGCCACGGAGTTATGGACTTAAAA
566245 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
1 GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
* * *
566310 AGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC
66 AGTTGTGGAC-TTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGAC
* * * * * * *
566375 TAAAAAGGGTGCCACGGAGTTGTAGGACTTTAAAGG-GGGCACAGAGTTGTGGACTTAAAA
130 TTAAAAGGGTGCCACAGAGTTGT-GGACTTAAAAGGATGCCACGGAGTTATGGACTTAAAA
* *
566435 GAGATGCCACGGAGTTATGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
1 G-GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACG
* * *
566500 GAG-TGTGGACTT-AAAGGGTGCCACGGGAGTTGTGGTCTTTAAAAGGGTGCCACGGAGTTGTGG
65 GAGTTGTGGACTTAAAAGGGTGCCAC-AGAGTTGTGGAC-TAAAAAGGGTGCCACGGAGTTGTGG
* * * *
566563 ACTT-AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTTGTGGACCTAAAAA
128 ACTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAG-TTATGGA-CTTAAAA
566626 GGGTGCCACGGAGTGTGTGGACTTTAAAAAGGGT
1 GGGTGCCACGGAGT-TGTGGAC-TT-AAAAGGGT
566660 CACAGTACTA
Statistics
Matches: 566, Mismatches: 28, Indels: 21
0.92 0.05 0.03
Matches are distributed among these distances:
188 23 0.04
189 40 0.07
190 93 0.16
191 338 0.60
192 64 0.11
193 8 0.01
ACGTcount: A:0.28, C:0.14, G:0.36, T:0.22
Consensus pattern (189 bp):
GGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGACTAAAAAGGGTGCCACGGAGTTGTGGACT
TAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTATGGACTTAAAA
Found at i:567692 original size:15 final size:15
Alignment explanation
Indices: 567674--567703 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
567664 TTGGTGAAAA
567674 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
567689 GGTTTTTTTTTTTTT
1 GGTTTTTTTTTTTTT
567704 AGGATTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (15 bp):
GGTTTTTTTTTTTTT
Found at i:574447 original size:10 final size:10
Alignment explanation
Indices: 574434--574463 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
574424 CCATTTCATA
574434 TTTTTTCTTT
1 TTTTTTCTTT
574444 TTTTTTCTTT
1 TTTTTTCTTT
*
574454 TTCTTTCTTT
1 TTTTTTCTTT
574464 CTTCTTCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTTCTTT
Found at i:574456 original size:16 final size:17
Alignment explanation
Indices: 574435--574469 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
574425 CATTTCATAT
*
574435 TTTTTCTTT-TTTTTTC
1 TTTTTCTTTCTTTCTTC
574451 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
574468 TT
1 TT
574470 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:577310 original size:25 final size:25
Alignment explanation
Indices: 577259--577310 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
577249 ATATTTTTTA
* * * * *
577259 TTTTTAAAACAAATAAAGATCATTT
1 TTTTTAAAAAAAAAAAACATAAATT
577284 TTTTTAAAAAAAAAAAACATAAATT
1 TTTTTAAAAAAAAAAAACATAAATT
577309 TT
1 TT
577311 GAACTTTTCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (25 bp):
TTTTTAAAAAAAAAAAACATAAATT
Found at i:577864 original size:15 final size:17
Alignment explanation
Indices: 577844--577877 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
577834 CCATTTCATA
577844 TTTTTCTTT-TTT-TTC
1 TTTTTCTTTCTTTCTTC
577859 TTTTTCTTTCTTTCTTC
1 TTTTTCTTTCTTTCTTC
577876 TT
1 TT
577878 CATCTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTCTTTCTTTCTTC
Found at i:579345 original size:2 final size:2
Alignment explanation
Indices: 579338--579366 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
579328 TCATTTCCAT
579338 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
579367 TTAAAAAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:582425 original size:16 final size:16
Alignment explanation
Indices: 582404--582436 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
582394 CTAAAACCAA
582404 CATTAAGTTACCTATC
1 CATTAAGTTACCTATC
*
582420 CATTAAGTTCCCTATC
1 CATTAAGTTACCTATC
582436 C
1 C
582437 TACCGCAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.30, G:0.06, T:0.36
Consensus pattern (16 bp):
CATTAAGTTACCTATC
Done.