Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 17 of 352
Found at i:5423763 original size:42 final size:42
Alignment explanation
Indices: 5423717--5423797 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
5423707 TAGAAAAGTT
*
5423717 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGATAGAAAGACTA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
*
5423759 ACAGAGAGCAAACGTGAGAAAGAAAGAAGGAAAGAAAGA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGA
5423798 AAGAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.05
Consensus pattern (42 bp):
ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
Found at i:5429285 original size:42 final size:42
Alignment explanation
Indices: 5429239--5429319 Score: 144
Period size: 42 Copynumber: 1.9 Consensus size: 42
5429229 TAGAAAAGTT
*
5429239 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGATAGAAAGACTA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
*
5429281 ACAGAGAGCAAACGTGAGAAAGAAAGAAGGAAAGAAAGA
1 ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGA
5429320 AATAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.58, C:0.09, G:0.28, T:0.05
Consensus pattern (42 bp):
ACAGAGAGCAAACGTGAGAAAGAAAGAAAGAAAGAAAGACTA
Found at i:5438906 original size:19 final size:20
Alignment explanation
Indices: 5438869--5438911 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
5438859 AATAATTTTT
* *
5438869 TTATAATAATTAATTATTAA
1 TTATAATAACTAATCATTAA
5438889 TTATAAT-ACTAATCATTAA
1 TTATAATAACTAATCATTAA
5438908 TTAT
1 TTAT
5438912 TACTTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTATAATAACTAATCATTAA
Found at i:5441664 original size:13 final size:14
Alignment explanation
Indices: 5441626--5441656 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
5441616 AAATTCTATT
*
5441626 ATATATTATTTCTA
1 ATATATTATTTTTA
5441640 ATATATTATTTTTA
1 ATATATTATTTTTA
5441654 ATA
1 ATA
5441657 GTTATTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
ATATATTATTTTTA
Found at i:5441760 original size:21 final size:22
Alignment explanation
Indices: 5441722--5441766 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
5441712 CCGATGTTTC
5441722 TAATCTCACTACTATAGT-ATT
1 TAATCTCACTACTATAGTAATT
*
5441743 TAATCTCA-TCACTGTAGTAATT
1 TAATCTCACT-ACTATAGTAATT
5441765 TA
1 TA
5441767 TATCGCCACC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 15 0.71
22 5 0.24
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.42
Consensus pattern (22 bp):
TAATCTCACTACTATAGTAATT
Found at i:5442768 original size:38 final size:38
Alignment explanation
Indices: 5442726--5442801 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
5442716 ATTGATCATC
*
5442726 ATGTCATGTTATCACATAGG-TTCAGATATTTACATATT
1 ATGTCATGCTATCACAT-GGATTCAGATATTTACATATT
*
5442764 ATGTCATGCTATCACATGGATTTAGATATTTACATATT
1 ATGTCATGCTATCACATGGATTCAGATATTTACATATT
5442802 TTTAATTGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
37 2 0.06
38 33 0.94
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (38 bp):
ATGTCATGCTATCACATGGATTCAGATATTTACATATT
Found at i:5445461 original size:26 final size:26
Alignment explanation
Indices: 5445431--5445506 Score: 82
Period size: 27 Copynumber: 2.9 Consensus size: 26
5445421 TTAATAAACC
5445431 TACTATATTATTTTATTATTTTTATA
1 TACTATATTATTTTATTATTTTTATA
* *
5445457 TACTATAGTT-TTTTATCGATTTTTTTA
1 TACTATA-TTATTTTAT-TATTTTTATA
* * *
5445484 TACTAAATTATTTTTTTTTTTTT
1 TACTATATTATTTTATTATTTTT
5445507 CTTTTTTTCT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
26 20 0.49
27 21 0.51
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.67
Consensus pattern (26 bp):
TACTATATTATTTTATTATTTTTATA
Found at i:5445511 original size:8 final size:8
Alignment explanation
Indices: 5445494--5445522 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5445484 TACTAAATTA
5445494 TTTTTT-T
1 TTTTTTCT
5445501 TTTTTTCT
1 TTTTTTCT
5445509 TTTTTTCT
1 TTTTTTCT
5445517 TTTTTT
1 TTTTTT
5445523 TTCGCTTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 6 0.29
8 15 0.71
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (8 bp):
TTTTTTCT
Found at i:5447471 original size:53 final size:53
Alignment explanation
Indices: 5447315--5447480 Score: 212
Period size: 53 Copynumber: 3.1 Consensus size: 53
5447305 GACGAAAAAT
* * **
5447315 ATGTGATAAGTGTG-C-CCGTTTAAGACCGTAGCTGGGCTATGGCATCGGTGCA
1 ATGTGATAA-TGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
5447367 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
1 ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
* * *
5447420 ATGTGATAATGTGATTCCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGA
1 ATGTGATAATGTGACTCCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A
5447474 TATGTGA
1 -ATGTGA
5447481 ACCGTGTAAG
Statistics
Matches: 102, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
51 4 0.04
52 11 0.11
53 80 0.78
54 1 0.01
55 6 0.06
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.30
Consensus pattern (53 bp):
ATGTGATAATGTGACTCCGTATAAGACCATAGCTGGGCTATGGCATCGGTATA
Found at i:5452768 original size:135 final size:135
Alignment explanation
Indices: 5452532--5453019 Score: 684
Period size: 135 Copynumber: 3.6 Consensus size: 135
5452522 CAGATATCAT
* *
5452532 CAGCCTTATCTTCACTGAGCAGGAGTGGAACAGGCTAAA-A-ACCAGATCTTATCTTCACTGAGT
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
* * * *
5452595 AGGAGTGAAGCAGATCGAATTTTGATG-AA-TCTTATCTCCACGTACCGGCGATGGAGCAGATTC
66 AGGAGTGAAGCAGATCAAATTTTG--GCAAGTCTTATCTCCACGTATCGGCAATGGAGCAGATTT
* *
5452658 CAATCAT
129 CAACCAC
* *
5452665 CAGCCTTATCTTCACTGAGGAGGAGTGGAGCAGGCTAAACATACCAGATCTTATATTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
* * * *
5452730 AGGAGTGAAGCAGGTCAAATTTTGGCAAGTCTTCTCTCCATC-TATCGACAATAGAGCAGATTTC
66 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCA-CGTATCGGCAATGGAGCAGATTTC
*
5452794 AGCCAC
130 AACCAC
*
5452800 CAACCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
* *
5452865 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCATGTATCGGCAATGGAGCAGATTTTA
66 AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCACGTATCGGCAATGGAGCAGATTTCA
*
5452930 GCCAC
131 ACCAC
* * **
5452935 CAGCCTTATCTTCACTGAGCAGGAGTGAAGCAGGCTAAACATA-CAGATCTTATCTTCGCTGATT
1 CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
5452999 AGGAGT-AGAGCAGATCAAATT
66 AGGAGTGA-AGCAGATCAAATT
5453020 ACAGCAGACC
Statistics
Matches: 319, Mismatches: 29, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
133 39 0.12
134 40 0.13
135 239 0.75
136 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (135 bp):
CAGCCTTATCTTCACTGAGCAGGAGTGGAGCAGGCTAAACATACCAGATCTTATCTTCACTGAGC
AGGAGTGAAGCAGATCAAATTTTGGCAAGTCTTATCTCCACGTATCGGCAATGGAGCAGATTTCA
ACCAC
Found at i:5462717 original size:22 final size:22
Alignment explanation
Indices: 5462675--5462717 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5462665 ATAAAGTATG
*
5462675 TTATATATTATTTTTTATAATA
1 TTATATATTATATTTTATAATA
5462697 TTATATATTATGATTTT-TAAT
1 TTATATATTAT-ATTTTATAAT
5462718 TCATATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATATATTATATTTTATAATA
Found at i:5462832 original size:26 final size:25
Alignment explanation
Indices: 5462799--5462849 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
5462789 AATTATTTAT
*
5462799 TTTTATTAAAATATATTTAACAATAA
1 TTTTATTAAAATATA-ATAACAATAA
*
5462825 TTTTATTAAAATTTAATAACAATAA
1 TTTTATTAAAATATAATAACAATAA
5462850 GAATAATCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (25 bp):
TTTTATTAAAATATAATAACAATAA
Found at i:5463004 original size:16 final size:15
Alignment explanation
Indices: 5462968--5463010 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
5462958 GGTTATAGTT
*
5462968 TTATTCTATTACAAC
1 TTATTCAATTACAAC
5462983 TCTATTCAATTACAAC
1 T-TATTCAATTACAAC
*
5462999 ATTATTCCATTA
1 -TTATTCAATTA
5463011 TAGTGAACCA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 1 0.04
16 22 0.92
17 1 0.04
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (15 bp):
TTATTCAATTACAAC
Found at i:5465773 original size:16 final size:16
Alignment explanation
Indices: 5465752--5465798 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
5465742 AATATATAAA
5465752 TTAAATTATTTATTTT
1 TTAAATTATTTATTTT
5465768 TTAAATT-TCTT-TTTT
1 TTAAATTAT-TTATTTT
*
5465783 TTGAAATAATTTATTT
1 TT-AAATTATTTATTT
5465799 ATCAATATCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 7 0.27
16 15 0.58
17 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTAAATTATTTATTTT
Found at i:5467487 original size:20 final size:19
Alignment explanation
Indices: 5467455--5467495 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
5467445 AAAATTTTAA
5467455 ATTAAAAAATATAAAAATT
1 ATTAAAAAATATAAAAATT
5467474 ATTAAAAAAGTATAAAAATT
1 ATTAAAAAA-TATAAAAATT
5467494 AT
1 AT
5467496 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
ATTAAAAAATATAAAAATT
Found at i:5470877 original size:28 final size:28
Alignment explanation
Indices: 5470845--5470902 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
5470835 GGTTAAAGTA
5470845 ATCAATTATTGAGGTTCATGTAAAATCG
1 ATCAATTATTGAGGTTCATGTAAAATCG
5470873 ATCAATTATTGAGGTTCATGTAAAATCG
1 ATCAATTATTGAGGTTCATGTAAAATCG
5470901 AT
1 AT
5470903 GTATGTGGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (28 bp):
ATCAATTATTGAGGTTCATGTAAAATCG
Found at i:5473602 original size:33 final size:33
Alignment explanation
Indices: 5473560--5473628 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
5473550 TCATAAGCTG
5473560 TTTGTGACAGCAATGCCTGACCTTATTTTTGGT
1 TTTGTGACAGCAATGCCTGACCTTATTTTTGGT
*
5473593 TTTGTGACAGCAGTGCCTGACCTTATTTTTGGT
1 TTTGTGACAGCAATGCCTGACCTTATTTTTGGT
5473626 TTT
1 TTT
5473629 CTTTCTCTTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.16, C:0.17, G:0.22, T:0.45
Consensus pattern (33 bp):
TTTGTGACAGCAATGCCTGACCTTATTTTTGGT
Found at i:5482030 original size:18 final size:19
Alignment explanation
Indices: 5481995--5482030 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5481985 CAATTTAATT
*
5481995 TTTTCTTTTTATTTCTTTA
1 TTTTCCTTTTATTTCTTTA
5482014 TTTTCCTTTTA-TTCTTT
1 TTTTCCTTTTATTTCTTT
5482031 CCCTTTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.08, C:0.14, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTCCTTTTATTTCTTTA
Found at i:5495734 original size:25 final size:28
Alignment explanation
Indices: 5495706--5495763 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
5495696 ATTTTTATAA
*
5495706 AAAAGCTTTA-GATG-AA-TGGTAAATT
1 AAAAGCTTTACAATGCAATTGGTAAATT
*
5495731 AAAAGTTTTACTAATGCAATTGGTAAATT
1 AAAAGCTTTAC-AATGCAATTGGTAAATT
5495760 AAAA
1 AAAA
5495764 AGATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 9 0.33
27 3 0.11
28 2 0.07
29 13 0.48
ACGTcount: A:0.47, C:0.05, G:0.16, T:0.33
Consensus pattern (28 bp):
AAAAGCTTTACAATGCAATTGGTAAATT
Found at i:5499522 original size:87 final size:87
Alignment explanation
Indices: 5499386--5499563 Score: 338
Period size: 87 Copynumber: 2.0 Consensus size: 87
5499376 CCAGCAGCAG
5499386 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
1 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
*
5499451 GTACCTCTCTCCTGTCCAGTTC
66 GTACCTCTCTCCTGTCCAGCTC
*
5499473 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCATTGAA
1 CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
5499538 GTACCTCTCTCCTGTCCAGCTC
66 GTACCTCTCTCCTGTCCAGCTC
5499560 CAGC
1 CAGC
5499564 TCCAGCCCCA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 89 1.00
ACGTcount: A:0.16, C:0.36, G:0.16, T:0.31
Consensus pattern (87 bp):
CAGCAGCATAACTCCGTCGTCCTTTCTCTTTATCACTCTCGTGTTCGGCCTTAGACGCCACTGAA
GTACCTCTCTCCTGTCCAGCTC
Found at i:5502495 original size:14 final size:14
Alignment explanation
Indices: 5502476--5502505 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5502466 GGAGTCTAGC
5502476 TAGTACCACAGTAG
1 TAGTACCACAGTAG
*
5502490 TAGTACCTCAGTAG
1 TAGTACCACAGTAG
5502504 TA
1 TA
5502506 AGCATCTAAG
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:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (14 bp):
TAGTACCACAGTAG
Found at i:5506512 original size:16 final size:15
Alignment explanation
Indices: 5506471--5506500 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5506461 CAATTAATTT
5506471 ATATTAATTTATGAG
1 ATATTAATTTATGAG
5506486 ATATTAATTTATGAG
1 ATATTAATTTATGAG
5506501 TCAATTAATT
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:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (15 bp):
ATATTAATTTATGAG
Found at i:5517096 original size:27 final size:27
Alignment explanation
Indices: 5517064--5517118 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
5517054 GGATAATTCA
5517064 GAGGAGAAACTGGTTTCTGAGTCAGTT
1 GAGGAGAAACTGGTTTCTGAGTCAGTT
*
5517091 GAGGAGAAAGTGGTTTCTGAGTCAGTT
1 GAGGAGAAACTGGTTTCTGAGTCAGTT
5517118 G
1 G
5517119 GGGTTTCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.25, C:0.09, G:0.36, T:0.29
Consensus pattern (27 bp):
GAGGAGAAACTGGTTTCTGAGTCAGTT
Found at i:5519548 original size:3 final size:3
Alignment explanation
Indices: 5519542--5519567 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5519532 ATCATCATCA
5519542 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
5519568 CTCTCTCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:5528664 original size:59 final size:59
Alignment explanation
Indices: 5528567--5528748 Score: 215
Period size: 67 Copynumber: 2.9 Consensus size: 59
5528557 CAGCTCCAAT
* *
5528567 ATTAC-CAAAACATTACAAAAGCTGTAATAATTTGTGTAATTGGATAATGTTTTGT-ATA
1 ATTACACAAAACATTAC-AAAGTTGTAATAATTTGTGTAATTGGGTAATGTTTTGTCATA
5528625 ATTACACAAAACATTACGAAAGTTGTAATAATTTGTGTAATTGGGTAATGCTTTGTGGGATTGCA
1 ATTACACAAAACATTAC-AAAGTTGTAATAATTTGTGTAATTGGGTAATG-TTT-T--G--T-CA
5528690 TA
58 TA
* *
5528692 ATTACACAATACATTACAAATGTTGTAATAATTTGTATAATTGGGTAATTGTTTTGT
1 ATTACACAAAACATTACAAA-GTTGTAATAATTTGTGTAATTGGGTAA-TGTTTTGT
5528749 GTAGTAGAAG
Statistics
Matches: 108, Mismatches: 5, Indels: 18
0.82 0.04 0.14
Matches are distributed among these distances:
58 5 0.05
59 41 0.38
60 3 0.03
61 1 0.01
62 1 0.01
63 1 0.01
64 1 0.01
65 1 0.01
66 4 0.04
67 48 0.44
68 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (59 bp):
ATTACACAAAACATTACAAAGTTGTAATAATTTGTGTAATTGGGTAATGTTTTGTCATA
Found at i:5547025 original size:32 final size:32
Alignment explanation
Indices: 5546985--5547050 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
5546975 CTAATTAAAA
5546985 TGATAATAAAAATTTTTAAGAATTGTAAGCAC
1 TGATAATAAAAATTTTTAAGAATTGTAAGCAC
5547017 TGATAATAAAAATTTTTAAGAATTGTAAGCAC
1 TGATAATAAAAATTTTTAAGAATTGTAAGCAC
5547049 TG
1 TG
5547051 TTAAAATTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (32 bp):
TGATAATAAAAATTTTTAAGAATTGTAAGCAC
Found at i:5549047 original size:30 final size:30
Alignment explanation
Indices: 5549011--5549068 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
5549001 TGGCAAGAAG
5549011 AATTTCCTCAGAAAGCTTATCACTTTGAAC
1 AATTTCCTCAGAAAGCTTATCACTTTGAAC
*
5549041 AATTTCCTCAGAAAGCTTATCAGTTTGA
1 AATTTCCTCAGAAAGCTTATCACTTTGA
5549069 CATTTACCAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (30 bp):
AATTTCCTCAGAAAGCTTATCACTTTGAAC
Found at i:5558868 original size:15 final size:14
Alignment explanation
Indices: 5558848--5558889 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
5558838 CGATGAATTT
5558848 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
*
5558863 ATTGAAATTATTTTG
1 ATTG-AATTATATTG
5558878 ATTGAATTATAT
1 ATTGAATTATAT
5558890 AATATATATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 7 0.29
15 15 0.62
16 2 0.08
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:5559292 original size:23 final size:23
Alignment explanation
Indices: 5559262--5559348 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
5559252 ACTTTATCAA
* *
5559262 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
5559285 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
5559306 TCAGGCACCTCGTGTGTC--ATT
1 TCAGGCACCTCATGTGTCGTATT
* * *
5559327 TTAGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
5559349 ACTGATCAGG
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
19 1 0.02
21 32 0.60
23 20 0.38
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:5559309 original size:21 final size:22
Alignment explanation
Indices: 5559274--5559323 Score: 84
Period size: 21 Copynumber: 2.3 Consensus size: 22
5559264 AGGCACTTTA
5559274 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA-TTCAGGCACCTCG
5559297 TGTGTCGTA-TCAGGCACCTCG
1 TGTGTCGTATTCAGGCACCTCG
5559318 TGTGTC
1 TGTGTC
5559324 ATTTTAGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 18 0.67
23 9 0.33
ACGTcount: A:0.12, C:0.26, G:0.28, T:0.34
Consensus pattern (22 bp):
TGTGTCGTATTCAGGCACCTCG
Found at i:5576236 original size:11 final size:11
Alignment explanation
Indices: 5576216--5576246 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5576206 ACCTAATTAC
*
5576216 ATCAATCATGA
1 ATCAAACATGA
5576227 ATCAAACATGA
1 ATCAAACATGA
5576238 ATCAAACAT
1 ATCAAACAT
5576247 AGTTCTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (11 bp):
ATCAAACATGA
Found at i:5582473 original size:23 final size:23
Alignment explanation
Indices: 5582443--5582529 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
5582433 GCTTTACTGA
* *
5582443 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
5582466 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
5582487 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
5582509 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
5582530 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:5584949 original size:73 final size:73
Alignment explanation
Indices: 5584862--5585009 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
5584852 CATACAATGT
5584862 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
1 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
5584927 AACCCCAC
66 AACCCCAC
5584935 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
1 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
5585000 AACCCCAC
66 AACCCCAC
5585008 TG
1 TG
5585010 GACACTTATC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Consensus pattern (73 bp):
TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
AACCCCAC
Found at i:5589111 original size:32 final size:30
Alignment explanation
Indices: 5589038--5589112 Score: 73
Period size: 32 Copynumber: 2.4 Consensus size: 30
5589028 AATTGGGGTC
5589038 TAATT-AAATTTTTAAATTTTTTTGTGAGAT
1 TAATTAAAATTTTTAAATTTTTTTGT-AGAT
* * *
5589068 TAATGAGAATTTTTAAATATTTTAATTGT-GTT
1 TAATTAAAATTTTTAAAT-TTTT--TTGTAGAT
5589100 TAATTAAAATTTT
1 TAATTAAAATTTT
5589113 CAAAATAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
30 4 0.11
31 11 0.31
32 17 0.47
34 4 0.11
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (30 bp):
TAATTAAAATTTTTAAATTTTTTTGTAGAT
Found at i:5590054 original size:20 final size:21
Alignment explanation
Indices: 5590029--5590068 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5590019 CATCGTCCGG
*
5590029 TTTTCTTTTTCTTTT-TTTGC
1 TTTTCTATTTCTTTTCTTTGC
*
5590049 TTTTCTATTTGTTTTCTTTG
1 TTTTCTATTTCTTTTCTTTG
5590069 TTTCCGGCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.03, C:0.12, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTCTATTTCTTTTCTTTGC
Found at i:5590754 original size:16 final size:16
Alignment explanation
Indices: 5590733--5590767 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5590723 CAACATTTTC
5590733 TTTAATATATTTAAAT
1 TTTAATATATTTAAAT
5590749 TTTAATATATTTAAAT
1 TTTAATATATTTAAAT
5590765 TTT
1 TTT
5590768 TTAAGTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTAATATATTTAAAT
Found at i:5590953 original size:19 final size:18
Alignment explanation
Indices: 5590926--5591013 Score: 67
Period size: 17 Copynumber: 4.9 Consensus size: 18
5590916 TAAAATTAGT
*
5590926 TATACTTAACAAATTTTAA
1 TATATTTAA-AAATTTTAA
5590945 TATATTT-AAAATTTTAA
1 TATATTTAAAAATTTTAA
***
5590962 TATATTTAATTTTTTTAA
1 TATATTTAAAAATTTTAA
*
5590980 GT-T-TTTTAAAATTTTAA
1 -TATATTTAAAAATTTTAA
5590997 -ATATATTAAGAAATTTT
1 TATAT-TTAA-AAATTTT
5591014 TTTTGTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
16 1 0.02
17 27 0.50
18 12 0.22
19 14 0.26
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.53
Consensus pattern (18 bp):
TATATTTAAAAATTTTAA
Found at i:5590958 original size:17 final size:17
Alignment explanation
Indices: 5590936--5591013 Score: 77
Period size: 17 Copynumber: 4.4 Consensus size: 17
5590926 TATACTTAAC
5590936 AAATTTTAATATATTTA
1 AAATTTTAATATATTTA
5590953 AAATTTTAATATATTTA
1 AAATTTTAATATATTTA
** *
5590970 ATTTTTTTAAGT-TTTTTA
1 A-AATTTTAA-TATATTTA
*
5590988 AAATTTTAAATATATTAA
1 AAATTTT-AATATATTTA
5591006 GAAATTTT
1 -AAATTTT
5591014 TTTTGTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
17 23 0.47
18 18 0.37
19 8 0.16
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AAATTTTAATATATTTA
Found at i:5590960 original size:62 final size:62
Alignment explanation
Indices: 5590839--5590961 Score: 174
Period size: 62 Copynumber: 2.0 Consensus size: 62
5590829 TAAAATATTG
* * *** * **
5590839 AATATATTAAAATTTTAAAATTAGTTATATTTAACTTTTTTTAATATTTTTAATTTTTTAAA
1 AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAAA
5590901 AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAA
1 AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAA
5590962 TATATTTAAT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (62 bp):
AATAAATTAAAATTTTAAAATTAGTTATACTTAACAAATTTTAATATATTTAAAATTTTAAA
Found at i:5591088 original size:18 final size:17
Alignment explanation
Indices: 5591042--5591080 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5591032 AAAATATATA
* *
5591042 TTAAGTATATTAAAATT
1 TTAAATATATTAAACTT
5591059 TTAAATATATTAAACTT
1 TTAAATATATTAAACTT
5591076 TTAAA
1 TTAAA
5591081 ATTAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAACTT
Found at i:5594558 original size:40 final size:40
Alignment explanation
Indices: 5594503--5594584 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
5594493 AGGAGAATTC
5594503 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
1 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
5594543 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
1 TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
5594583 TA
1 TA
5594585 TAACGAGATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.26
Consensus pattern (40 bp):
TAGCAACCTGCCAAAAACAAAGTGTGCAACTTATATGTCT
Found at i:5597561 original size:75 final size:75
Alignment explanation
Indices: 5597471--5597619 Score: 289
Period size: 75 Copynumber: 2.0 Consensus size: 75
5597461 CATACAATGT
5597471 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
1 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
5597536 AACCCCACTC
66 AACCCCACTC
*
5597546 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTTTAATTTGACT
1 TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
5597611 AACCCCACT
66 AACCCCACT
5597620 GGACACTTAT
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (75 bp):
TGTGTTACAGCCTGCCATAGGTGTAAACTAGTGGAATTTAAATTTAATGAAATTGTAATTTGACT
AACCCCACTC
Found at i:5603038 original size:27 final size:26
Alignment explanation
Indices: 5602955--5603045 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 26
5602945 AACCCCAAAC
5602955 TCGAGGTTCAA-AGTTCA-AGTTTGAGGT
1 TCGAGGTTCAATA-TT-AGAGTTT-AGGT
* * * *
5602982 TCAAGGTCCAATGTTAGGGTTTAGGGT
1 TCGAGGTTCAATATTAGAGTTTA-GGT
5603009 TCGAGGTTCAATATTAGAGTTTAGGAT
1 TCGAGGTTCAATATTAGAGTTTAGG-T
*
5603036 TCGAGATTCA
1 TCGAGGTTCA
5603046 TGATTTAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
26 4 0.08
27 47 0.92
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (26 bp):
TCGAGGTTCAATATTAGAGTTTAGGT
Found at i:5608474 original size:25 final size:25
Alignment explanation
Indices: 5608445--5608496 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
5608435 AAGAATAATT
**
5608445 TGAATATTGGATATTGCCTAATAAA
1 TGAATATCCGATATTGCCTAATAAA
* *
5608470 TGAATATCCGATATTGCTTAGTAAA
1 TGAATATCCGATATTGCCTAATAAA
5608495 TG
1 TG
5608497 TCAAGCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (25 bp):
TGAATATCCGATATTGCCTAATAAA
Found at i:5609464 original size:38 final size:39
Alignment explanation
Indices: 5609358--5609464 Score: 92
Period size: 38 Copynumber: 2.7 Consensus size: 39
5609348 CTTCGACCTT
* * *
5609358 GAGTTGATGAGACACTGGGTGTCACTATTTTACTTCGGATA
1 GAGTCGATGAGACACTGGGTGTCA--ACTTTACTCCGGATA
* * ** * * *
5609399 GATTCGATAAGGTACTGGGT-ACCACTTTACTCCGGCTA
1 GAGTCGATGAGACACTGGGTGTCAACTTTACTCCGGATA
5609437 G-GTCGATGAGACACTGGGTGTCAACTTT
1 GAGTCGATGAGACACTGGGTGTCAACTTT
5609465 GCTTCGAACT
Statistics
Matches: 49, Mismatches: 16, Indels: 5
0.70 0.23 0.07
Matches are distributed among these distances:
37 14 0.29
38 19 0.39
40 1 0.02
41 15 0.31
ACGTcount: A:0.23, C:0.19, G:0.27, T:0.31
Consensus pattern (39 bp):
GAGTCGATGAGACACTGGGTGTCAACTTTACTCCGGATA
Found at i:5609810 original size:12 final size:12
Alignment explanation
Indices: 5609793--5609817 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5609783 AAAGTAAAAT
5609793 TATGAATTGAAA
1 TATGAATTGAAA
5609805 TATGAATTGAAA
1 TATGAATTGAAA
5609817 T
1 T
5609818 TGAGATATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (12 bp):
TATGAATTGAAA
Found at i:5619362 original size:20 final size:19
Alignment explanation
Indices: 5619338--5619384 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
5619328 TCTTTTTTTA
5619338 CTTTTTTATT-AACTTTTGT
1 CTTTTTT-TTAAACTTTTGT
* *
5619357 CTTTTTCTTTAAATTTTTTT
1 CTTTTT-TTTAAACTTTTGT
5619377 CTTTTTTT
1 CTTTTTTT
5619385 GAGTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (19 bp):
CTTTTTTTTAAACTTTTGT
Found at i:5619436 original size:23 final size:24
Alignment explanation
Indices: 5619393--5619439 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5619383 TTGAGTTTTA
*
5619393 TATTTTTTCTTATTTTATTTTGTT
1 TATTTCTTCTTATTTTATTTTGTT
5619417 TATTTCTT-TTATTTCT-TTTTGTT
1 TATTTCTTCTTATTT-TATTTTGTT
5619440 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (24 bp):
TATTTCTTCTTATTTTATTTTGTT
Found at i:5619513 original size:23 final size:24
Alignment explanation
Indices: 5619464--5619534 Score: 82
Period size: 22 Copynumber: 3.2 Consensus size: 24
5619454 ATTTGAAATG
*
5619464 TTTTATAATATATATTTTTAAA-AA
1 TTTTATAATAT-TATTTTTAAATTA
5619488 TTTTA-AATATTATTTTTAAATTA
1 TTTTATAATATTATTTTTAAATTA
5619511 -TTTATAA-A--ATTTTTAAATTA
1 TTTTATAATATTATTTTTAAATTA
5619531 TTTT
1 TTTT
5619535 TAAAATGTTG
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
20 12 0.28
21 3 0.07
22 15 0.35
23 8 0.19
24 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
TTTTATAATATTATTTTTAAATTA
Found at i:5619522 original size:20 final size:20
Alignment explanation
Indices: 5619499--5619554 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5619489 TTTAAATATT
5619499 ATTTTTAAATTATTTATAAA
1 ATTTTTAAATTATTTATAAA
*
5619519 ATTTTTAAATTATTTTTAAA
1 ATTTTTAAATTATTTATAAA
* *
5619539 ATGTTGAATATTATTT
1 ATTTTTAA-ATTATTT
5619555 TTTAAATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 25 0.78
21 7 0.22
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
ATTTTTAAATTATTTATAAA
Found at i:5619534 original size:31 final size:31
Alignment explanation
Indices: 5619480--5619538 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5619470 AATATATATT
5619480 TTTAAAAATTTTAAATATTATTTTTAAATTA
1 TTTAAAAATTTTAAATATTATTTTTAAATTA
*
5619511 TTTATAAAATTTTTAA-ATTATTTTTAAA
1 TTTA-AAAATTTTAAATATTATTTTTAAA
5619539 ATGTTGAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (31 bp):
TTTAAAAATTTTAAATATTATTTTTAAATTA
Found at i:5619553 original size:21 final size:20
Alignment explanation
Indices: 5619505--5619561 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
5619495 TATTATTTTT
* * *
5619505 AAATTATTTATAAAATTTTT
1 AAATTATTTTTAAAATGTTG
5619525 AAATTATTTTTAAAATGTTG
1 AAATTATTTTTAAAATGTTG
*
5619545 AATATTATTTTTTAAAT
1 AA-ATTATTTTTAAAAT
5619562 TATGTCTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 19 0.59
21 13 0.41
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (20 bp):
AAATTATTTTTAAAATGTTG
Found at i:5619640 original size:14 final size:14
Alignment explanation
Indices: 5619623--5619651 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5619613 TTTAAATTTT
5619623 AAATATATTTTTAA
1 AAATATATTTTTAA
5619637 AAATATATTTTTAA
1 AAATATATTTTTAA
5619651 A
1 A
5619652 CAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAATATATTTTTAA
Found at i:5619691 original size:19 final size:20
Alignment explanation
Indices: 5619663--5619700 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
5619653 AAAATAAAAC
5619663 AATTTCAAAAATAT-TTTTA
1 AATTTCAAAAATATATTTTA
*
5619682 AATTTTAAAAATATATTTT
1 AATTTCAAAAATATATTTT
5619701 TGAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
AATTTCAAAAATATATTTTA
Found at i:5619720 original size:36 final size:34
Alignment explanation
Indices: 5619676--5619773 Score: 139
Period size: 36 Copynumber: 2.9 Consensus size: 34
5619666 TTCAAAAATA
5619676 TTTTTAAATTTTAAAAATATATTTTTGAAATTAT
1 TTTTTAAATTTTAAAAATATATTTTTGAAATTAT
*
5619710 TTCTTATAAATTTTAAAAATATATTTTAGAAATTAT
1 TT-TT-TAAATTTTAAAAATATATTTTTGAAATTAT
*
5619746 TTTTT-AATTTTAAATAT-TATTTTT-AAAT
1 TTTTTAAATTTTAAAAATATATTTTTGAAAT
5619774 ATTAAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
31 4 0.07
32 6 0.10
33 11 0.19
34 3 0.05
35 4 0.07
36 31 0.53
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (34 bp):
TTTTTAAATTTTAAAAATATATTTTTGAAATTAT
Found at i:5619757 original size:20 final size:20
Alignment explanation
Indices: 5619732--5619782 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
5619722 TTAAAAATAT
5619732 ATTTTAGAA-ATTATTTTTTA
1 ATTTTA-AATATTATTTTTTA
*
5619752 ATTTTAAATATTATTTTTAA
1 ATTTTAAATATTATTTTTTA
*
5619772 ATATTAAATAT
1 ATTTTAAATAT
5619783 ATATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 2 0.07
20 26 0.93
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTTTAAATATTATTTTTTA
Found at i:5619771 original size:13 final size:13
Alignment explanation
Indices: 5619753--5619777 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5619743 TATTTTTTAA
5619753 TTTTAAATATTAT
1 TTTTAAATATTAT
5619766 TTTTAAATATTA
1 TTTTAAATATTA
5619778 AATATATATA
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTTAAATATTAT
Found at i:5619804 original size:26 final size:22
Alignment explanation
Indices: 5619741--5619805 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 22
5619731 TATTTTAGAA
5619741 ATTATTTTT-TAAT-TTTAAAT
1 ATTATTTTTATAATATTTAAAT
5619761 ATTATTTTTA-AATA-TTAAAT
1 ATTATTTTTATAATATTTAAAT
5619781 ATATATATATTTAATAATATTTAAA
1 AT-TAT-T-TTT-ATAATATTTAAA
5619806 CATTTAAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
20 20 0.54
21 3 0.08
22 1 0.03
23 3 0.08
24 1 0.03
25 4 0.11
26 5 0.14
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
ATTATTTTTATAATATTTAAAT
Found at i:5619824 original size:25 final size:24
Alignment explanation
Indices: 5619765--5619824 Score: 57
Period size: 26 Copynumber: 2.4 Consensus size: 24
5619755 TTAAATATTA
* *
5619765 TTTTTAAATATTAAATATATATAT
1 TTTTTAAATATTAAACATATAAAT
* * *
5619789 ATTTAATAATATTTAAACATTTAAAT
1 TTTTTA-AATA-TTAAACATATAAAT
5619815 TTTTTAAATA
1 TTTTTAAATA
5619825 AAATTATTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
24 4 0.15
25 8 0.30
26 15 0.56
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (24 bp):
TTTTTAAATATTAAACATATAAAT
Found at i:5619891 original size:13 final size:13
Alignment explanation
Indices: 5619873--5619898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5619863 TAAAAAATCA
5619873 TAATTTCAAAAAT
1 TAATTTCAAAAAT
5619886 TAATTTCAAAAAT
1 TAATTTCAAAAAT
5619899 AAAGAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATTTCAAAAAT
Found at i:5619962 original size:31 final size:33
Alignment explanation
Indices: 5619901--5619972 Score: 121
Period size: 31 Copynumber: 2.2 Consensus size: 33
5619891 TCAAAAATAA
5619901 AGAAAAATAATATATTTTAAAATTTTAAAATTT
1 AGAAAAATAATATATTTTAAAATTTTAAAATTT
*
5619934 ATAAAAATAATATA-TTTAAAA-TTTAAAATTT
1 AGAAAAATAATATATTTTAAAATTTTAAAATTT
5619965 AGAAAAAT
1 AGAAAAAT
5619973 TAATTTCAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
31 17 0.46
32 7 0.19
33 13 0.35
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (33 bp):
AGAAAAATAATATATTTTAAAATTTTAAAATTT
Found at i:5620000 original size:36 final size:34
Alignment explanation
Indices: 5619924--5620076 Score: 154
Period size: 36 Copynumber: 4.6 Consensus size: 34
5619914 ATTTTAAAAT
* ** *
5619924 TTTAAAATTTATAAAAATAA--T-ATATTTAAAA
1 TTTAAAATTTATAAAAATAATTTCAAAAATAATA
* *
5619955 TTTAAAATTTAGAAAAATTAATTTCAAAAATATATT
1 TTTAAAATTTATAAAAA-TAATTTCAAAAATA-ATA
* *
5619991 TTTAAAATTTATAAGACATAATTTAAAAAATAATA
1 TTTAAAATTTATAA-AAATAATTTCAAAAATAATA
*
5620026 TTCAAAATTT-TAAAAATAATTTC-AAAATAATA
1 TTTAAAATTTATAAAAATAATTTCAAAAATAATA
*
5620058 TTTAAAATTTTTAAAAATA
1 TTTAAAATTTATAAAAATA
5620077 TATATTATAA
Statistics
Matches: 101, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
31 16 0.16
32 21 0.21
33 16 0.16
34 4 0.04
35 15 0.15
36 27 0.27
37 2 0.02
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.41
Consensus pattern (34 bp):
TTTAAAATTTATAAAAATAATTTCAAAAATAATA
Found at i:5620049 original size:20 final size:21
Alignment explanation
Indices: 5620010--5620053 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
5620000 TATAAGACAT
5620010 AATTTAAAAAATAATATTCAA
1 AATTTAAAAAATAATATTCAA
*
5620031 AATTTTAAAAATAAT-TTCAA
1 AATTTAAAAAATAATATTCAA
5620051 AAT
1 AAT
5620054 AATATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (21 bp):
AATTTAAAAAATAATATTCAA
Found at i:5620081 original size:23 final size:22
Alignment explanation
Indices: 5620049--5620115 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
5620039 AAATAATTTC
5620049 AAAATA-ATATTTAAAATTTTT
1 AAAATATATATTTAAAATTTTT
**
5620070 AAAAATATATATTATAAAACATTT
1 -AAAATATATATT-TAAAATTTTT
* * *
5620094 CAAATATACATTTCAAATTTTT
1 AAAATATATATTTAAAATTTTT
5620116 TAATATTAAT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
22 13 0.36
23 15 0.42
24 8 0.22
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATATATTTAAAATTTTT
Found at i:5620158 original size:24 final size:24
Alignment explanation
Indices: 5620131--5620182 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
5620121 TTAATAACAA
*
5620131 AAAATAAATAAAAAATAAAATAAG
1 AAAATAAATAAAAAATAAAAAAAG
* **
5620155 AAAATATATAAAACTTAAAAAAAG
1 AAAATAAATAAAAAATAAAAAAAG
5620179 AAAA
1 AAAA
5620183 AGATTTAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.77, C:0.02, G:0.04, T:0.17
Consensus pattern (24 bp):
AAAATAAATAAAAAATAAAAAAAG
Found at i:5620165 original size:12 final size:11
Alignment explanation
Indices: 5620129--5620167 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 11
5620119 TATTAATAAC
5620129 AAAAAATAAAT
1 AAAAAATAAAT
5620140 AAAAAATAAAAT
1 AAAAAAT-AAAT
*
5620152 AAGAAAATATAT
1 AA-AAAATAAAT
5620164 AAAA
1 AAAA
5620168 CTTAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 9 0.36
12 11 0.44
13 5 0.20
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
AAAAAATAAAT
Found at i:5620215 original size:19 final size:18
Alignment explanation
Indices: 5620171--5620234 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 18
5620161 TATAAAACTT
5620171 AAAAAAAGAAAAAGATTTA
1 AAAAAAAGAAAAAGA-TTA
5620190 AAGAAAAAGACAAAAG-TTA
1 AA-AAAAAGA-AAAAGATTA
5620209 ATAAAAAAGTAAAAAGA--A
1 A-AAAAAAG-AAAAAGATTA
5620227 AAAAAAAG
1 AAAAAAAG
5620235 TGAAAGAAGG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
17 7 0.17
18 2 0.05
19 17 0.43
20 9 0.22
21 5 0.12
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.11
Consensus pattern (18 bp):
AAAAAAAGAAAAAGATTA
Found at i:5620530 original size:27 final size:27
Alignment explanation
Indices: 5620498--5620550 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
5620488 TATAGTTGAA
5620498 TGGTTATTTAGTGTTTAATTAAGTGAT
1 TGGTTATTTAGTGTTTAATTAAGTGAT
5620525 TGGTTATTTAGTGTTTAATTAAGTGA
1 TGGTTATTTAGTGTTTAATTAAGTGA
5620551 AGTAGCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (27 bp):
TGGTTATTTAGTGTTTAATTAAGTGAT
Found at i:5631956 original size:10 final size:10
Alignment explanation
Indices: 5631938--5631970 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
5631928 TATTTTAGTC
*
5631938 TTTTATTTAT
1 TTTTTTTTAT
5631948 TTTTTTTTA-
1 TTTTTTTTAT
5631957 TTTTTTTTAT
1 TTTTTTTTAT
5631967 TTTT
1 TTTT
5631971 AAAAATTATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTTTTAT
Found at i:5647597 original size:21 final size:20
Alignment explanation
Indices: 5647555--5647608 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
5647545 ATTCGAAATA
5647555 TTATATTTTAGTTAGTTATG
1 TTATATTTTAGTTAGTTATG
* * *
5647575 TTATGTTTTATGTTATTTTTG
1 TTATATTTTA-GTTAGTTATG
*
5647596 TTA-ATTTTTGTTA
1 TTATATTTTAGTTA
5647609 ACAGTAAGCT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 4 0.14
20 13 0.46
21 11 0.39
ACGTcount: A:0.20, C:0.00, G:0.13, T:0.67
Consensus pattern (20 bp):
TTATATTTTAGTTAGTTATG
Found at i:5660432 original size:28 final size:27
Alignment explanation
Indices: 5660392--5660468 Score: 86
Period size: 25 Copynumber: 2.9 Consensus size: 27
5660382 AATTCTTTCT
5660392 ATTTTTTATAGTTTATATATATATTAGA
1 ATTTTTTATAGTTTATATATAT-TTAGA
* * *
5660420 TTTTTTTCTAGTTT-TAT-TATTTATA
1 ATTTTTTATAGTTTATATATATTTAGA
* *
5660445 ATTTTTTAAAATTTATATATATTT
1 ATTTTTTATAGTTTATATATATTT
5660469 TTAGTAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
25 14 0.35
26 6 0.15
27 8 0.20
28 12 0.30
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.64
Consensus pattern (27 bp):
ATTTTTTATAGTTTATATATATTTAGA
Found at i:5664151 original size:51 final size:51
Alignment explanation
Indices: 5664071--5664227 Score: 196
Period size: 51 Copynumber: 3.1 Consensus size: 51
5664061 GACGAAGCTC
* * * *
5664071 CTGCTGCCGCTGAAGTTCCAACTGCCGTTGATGCTGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
5664122 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
* * * *
5664173 CTGCTGCCACTGATGCTCCAACTG-C--TGCTGCCT-CTGAAGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACAGACGTTGATG-CTGCTGAAGCTCCAACTG
*
5664221 ATGCTGC
1 CTGCTGC
5664228 TGCCGTTGTA
Statistics
Matches: 96, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
48 25 0.26
49 2 0.02
50 1 0.01
51 68 0.71
ACGTcount: A:0.18, C:0.32, G:0.24, T:0.25
Consensus pattern (51 bp):
CTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTG
Found at i:5664189 original size:12 final size:13
Alignment explanation
Indices: 5664166--5664227 Score: 60
Period size: 12 Copynumber: 5.1 Consensus size: 13
5664156 TGCTGAAGCT
*
5664166 CCAACTGCTGCTG
1 CCAACTGATGCTG
5664179 CC-ACTGATGCT-
1 CCAACTGATGCTG
*
5664190 CCAACTGCTGCTG
1 CCAACTGATGCTG
* *
5664203 CC-TCTGAAGCT-
1 CCAACTGATGCTG
5664214 CCAACTGATGCTG
1 CCAACTGATGCTG
5664227 C
1 C
5664228 TGCCGTTGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 4 0.11
12 29 0.76
13 5 0.13
ACGTcount: A:0.18, C:0.37, G:0.21, T:0.24
Consensus pattern (13 bp):
CCAACTGATGCTG
Found at i:5664190 original size:24 final size:24
Alignment explanation
Indices: 5664071--5664254 Score: 161
Period size: 24 Copynumber: 7.3 Consensus size: 24
5664061 GACGAAGCTC
*
5664071 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
* * *
5664095 CCGTTGATGCTGCTGAAGTTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
*
5664122 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGAAGCTCCAACTG
* *
5664146 ACGTTGATGCTGCTGAAGCTCCAACTG
1 -C--TGCTGCCGCTGAAGCTCCAACTG
* *
5664173 CTGCTGCCACTGATGCTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
5664197 CTGCTGCCTCTGAAGCTCCAACTGATG
1 CTGCTGCCGCTGAAGCTCCAAC---TG
* * *
5664224 CTGCTGCCGTTGTAGTTCCAACTG
1 CTGCTGCCGCTGAAGCTCCAACTG
*
5664248 CCGCTGC
1 CTGCTGC
5664255 TGTTCAAATT
Statistics
Matches: 131, Mismatches: 20, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
24 66 0.50
25 2 0.02
26 2 0.02
27 61 0.47
ACGTcount: A:0.17, C:0.33, G:0.24, T:0.26
Consensus pattern (24 bp):
CTGCTGCCGCTGAAGCTCCAACTG
Found at i:5664244 original size:75 final size:75
Alignment explanation
Indices: 5664114--5664254 Score: 192
Period size: 75 Copynumber: 1.9 Consensus size: 75
5664104 CTGCTGAAGT
* * *
5664114 TCCAACTGCTGCTGCCGCTGAAGCTCCAACAGACGTTGATGCTGCTGAAGCTCCAACTGCTGCTG
1 TCCAACTGCTGCTGCCGCTGAAGCTCCAACAGACGCTGATGCCGCTGAAGCTCCAACTGCCGCTG
5664179 CCACTGATGC
66 CCACTGATGC
* * * * * * *
5664189 TCCAACTGCTGCTGCCTCTGAAGCTCCAACTGATGCTGCTGCCGTTGTAGTTCCAACTGCCGCTG
1 TCCAACTGCTGCTGCCGCTGAAGCTCCAACAGACGCTGATGCCGCTGAAGCTCCAACTGCCGCTG
5664254 C
66 C
5664255 TGTTCAAATT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 56 1.00
ACGTcount: A:0.18, C:0.34, G:0.23, T:0.25
Consensus pattern (75 bp):
TCCAACTGCTGCTGCCGCTGAAGCTCCAACAGACGCTGATGCCGCTGAAGCTCCAACTGCCGCTG
CCACTGATGC
Found at i:5664253 original size:27 final size:27
Alignment explanation
Indices: 5664071--5664256 Score: 117
Period size: 27 Copynumber: 7.2 Consensus size: 27
5664061 GACGAAGCTC
* * *
5664071 CTGCTGCCGCTGAAGTTCCAACTGCCG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* * *
5664098 TTGATG-CTGCTGAAGTTCCAACT---G
1 CTGCTGCCT-CTGAAGCTCCAACTGACG
* *
5664122 CTGCTGCCGCTGAAGCTCCAACAGACG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* *
5664149 TTGATG-CTGCTGAAGCTCCAACT---G
1 CTGCTGCCT-CTGAAGCTCCAACTGACG
* *
5664173 CTGCTGCCACTGATGCTCCAACT---G
1 CTGCTGCCTCTGAAGCTCCAACTGACG
*
5664197 CTGCTGCCTCTGAAGCTCCAACTGATG
1 CTGCTGCCTCTGAAGCTCCAACTGACG
* * *
5664224 CTGCTGCCGT-TGTAGTTCCAACTGCCG
1 CTGCTGCC-TCTGAAGCTCCAACTGACG
5664251 CTGCTG
1 CTGCTG
5664257 TTCAAATTGA
Statistics
Matches: 126, Mismatches: 22, Indels: 22
0.74 0.13 0.13
Matches are distributed among these distances:
24 57 0.45
25 2 0.02
26 2 0.02
27 64 0.51
28 1 0.01
ACGTcount: A:0.17, C:0.32, G:0.25, T:0.26
Consensus pattern (27 bp):
CTGCTGCCTCTGAAGCTCCAACTGACG
Found at i:5675591 original size:46 final size:45
Alignment explanation
Indices: 5675539--5675858 Score: 369
Period size: 46 Copynumber: 7.0 Consensus size: 45
5675529 GCTATCTGAA
* *
5675539 ATGAAATATGTAAGATCATGGTTGAAAGATACCATGGCAACATGAT
1 ATGAAATA-GTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * *
5675585 ATGAAATGTGTAAGACCATGGTTGAAAGATATCATGGCAACGTGAC
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
5675631 ATGAAA-AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATAG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
5675677 GA-GAAATGAATAAGACCATAGTTGAAAGATACCATGGCAGCGTGAC
1 -ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
5675723 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGGAACATGAC
1 ATGAAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
5675769 ATGAAA-AGAATAAGACCATGGTTGAAAGATACCATGGTAACATGAC
1 ATGAAATAG--TAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* * * *
5675815 A-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 ATG-AAAT-AGTAAGACCATGGTTGAAAGATACCATGGCAACATG
5675859 TCAAAGATAA
Statistics
Matches: 239, Mismatches: 23, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
44 2 0.01
45 2 0.01
46 231 0.97
47 1 0.00
48 3 0.01
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.21
Consensus pattern (45 bp):
ATGAAATAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:5675701 original size:92 final size:92
Alignment explanation
Indices: 5675549--5675858 Score: 435
Period size: 92 Copynumber: 3.4 Consensus size: 92
5675539 ATGAAATATG
* * **
5675549 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
*
5675614 TATCATGGCAACGTGACATGAAAAGAA
66 TACCATGGCAACGTGACATGAAAAGAA
*
5675641 TAAGACCATGGTTGAAAGATACCATGGCAACATGACGA-GAAATGAATAAGACCATAGTTGAAAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-ATGAAATGAATAAGACCATGGTTGAAAG
* *
5675705 ATACCATGGCAGCGTGACATGAAATGAA
65 ATACCATGGCAACGTGACATGAAAAGAA
* *
5675733 TAAGACCATGGTTGAAAGATACCATGGGAACATGACATGAAAAGAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* * *
5675798 TACCATGGTAACATGACA-GAAAATGAG
66 TACCATGGCAACGTGACATGAAAA-GAA
* * * *
5675825 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATG
5675859 TCAAAGATAA
Statistics
Matches: 194, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
91 5 0.03
92 188 0.97
93 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (92 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACGTGACATGAAAAGAA
Found at i:5675789 original size:138 final size:138
Alignment explanation
Indices: 5675549--5675858 Score: 469
Period size: 138 Copynumber: 2.2 Consensus size: 138
5675539 ATGAAATATG
* * * **
5675549 TAAGATCATGGTTGAAAGATACCATGGCAACATGATATGAAATGTGTAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* *
5675614 TATCATGGCAACGTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC-G
66 TACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
5675678 AGAAATGAA
131 A-AAATGAA
* *
5675687 TAAGACCATAGTTGAAAGATACCATGGCAGCGTGACATGAAATGAATAAGACCATGGTTGAAAGA
1 TAAGACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
* *
5675752 TACCATGGGAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGTAACATGACAG
66 TACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
*
5675817 AAAATGAG
131 AAAATGAA
* * *
5675825 TAAGACCATAGTTGAAAGACACTATGGCATCATG
1 TAAGACCATAGTTGAAAGATACCATGGCAACATG
5675859 TCAAAGATAA
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
138 153 0.99
139 2 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (138 bp):
TAAGACCATAGTTGAAAGATACCATGGCAACATGACATGAAATGAATAAGACCATGGTTGAAAGA
TACCATGGCAACATGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACAG
AAAATGAA
Found at i:5677806 original size:46 final size:46
Alignment explanation
Indices: 5677631--5677806 Score: 178
Period size: 46 Copynumber: 3.8 Consensus size: 46
5677621 TGTAACCCAC
* * * * *
5677631 CCATAAGCGAGCTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
* *
5677677 CCATAAGTGAACTCGGACTCAACTTAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* ** * *
5677723 ACATATCTCGAACTTGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
5677770 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
5677807 TGCCCAAATA
Statistics
Matches: 106, Mismatches: 17, Indels: 14
0.77 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 66 0.62
47 31 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:5677825 original size:46 final size:44
Alignment explanation
Indices: 5677682--5677825 Score: 105
Period size: 46 Copynumber: 3.1 Consensus size: 44
5677672 CGCATCCATA
* * * *
5677682 AGTGAACTCGGACTCAACTTAACGAGCTCGGATGCCTAGT-TACAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA-TAT-CCT
* * * *
5677727 ATCTCGAACTTGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 A-GT-GAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATATCC-T
5677774 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC--ATATCCT
5677821 AGTGA
1 AGTGA
5677826 CATGTCACTT
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
44 4 0.05
45 1 0.01
46 34 0.45
47 29 0.38
48 5 0.07
49 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATCCT
Found at i:5679523 original size:14 final size:14
Alignment explanation
Indices: 5679504--5679609 Score: 68
Period size: 13 Copynumber: 8.1 Consensus size: 14
5679494 GTACAATCAC
5679504 TTCATATAACT-ATT
1 TTCATATAACTCA-T
5679518 TTCATATAA-TCAT
1 TTCATATAACTCAT
5679531 TTCATAT-ACTCAT
1 TTCATATAACTCAT
*
5679544 TT-ATATAAC-AAT
1 TTCATATAACTCAT
** *
5679556 TTTGTAT-ACCCAT
1 TTCATATAACTCAT
* *
5679569 CTCATATTAC-CAT
1 TTCATATAACTCAT
* *
5679582 TTCGTAGAA-TCAT
1 TTCATATAACTCAT
5679595 TTCATATAAC-CAT
1 TTCATATAACTCAT
5679608 TT
1 TT
5679610 TGAGTAACCA
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
12 11 0.15
13 49 0.68
14 12 0.17
ACGTcount: A:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (14 bp):
TTCATATAACTCAT
Found at i:5679583 original size:26 final size:26
Alignment explanation
Indices: 5679546--5679625 Score: 72
Period size: 26 Copynumber: 3.1 Consensus size: 26
5679536 ATACTCATTT
* * *
5679546 ATATAACAATTTTGTATACCCATCTC
1 ATATAACCATTTTGTAGAACCATCTC
* * * *
5679572 ATATTACCATTTCGTAGAATCATTTC
1 ATATAACCATTTTGTAGAACCATCTC
*
5679598 ATATAACCATTTTG-AGTAACCATTTC
1 ATATAACCATTTTGTAG-AACCATCTC
5679624 AT
1 AT
5679626 TTTACACATT
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
25 2 0.05
26 41 0.95
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (26 bp):
ATATAACCATTTTGTAGAACCATCTC
Found at i:5680085 original size:17 final size:18
Alignment explanation
Indices: 5680059--5680104 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5680049 TTTTCAACAT
*
5680059 AATCATAATTTAGT-CAA
1 AATCACAATTTAGTACAA
*
5680076 TATCACAATTTAGTACAA
1 AATCACAATTTAGTACAA
5680094 AATCACCAATT
1 AATCA-CAATT
5680105 GTCATTTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 12 0.50
18 7 0.29
19 5 0.21
ACGTcount: A:0.46, C:0.17, G:0.04, T:0.33
Consensus pattern (18 bp):
AATCACAATTTAGTACAA
Found at i:5685035 original size:24 final size:24
Alignment explanation
Indices: 5684735--5685028 Score: 417
Period size: 24 Copynumber: 12.0 Consensus size: 24
5684725 GATGAAGCTC
* *
5684735 CTGCTGCCGCTGAAGTTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
* * * *
5684759 TCTTTGATGCTGCTGAAGTTCCAACTG
1 -C--TGCTGCCGCTGATGCTCCAACTG
* *
5684786 CTGCTGCCGCTGAAGCTCCAACAG
1 CTGCTGCCGCTGATGCTCCAACTG
* *
5684810 ACGTTGCTGCTGCTGAAGCTCCAACTG
1 -C--TGCTGCCGCTGATGCTCCAACTG
*
5684837 CTGCTGCCGCTGATGCTCCAATTG
1 CTGCTGCCGCTGATGCTCCAACTG
5684861 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5684885 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5684909 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5684933 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5684957 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5684981 CTGCTGCCGCTGATGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
* *
5685005 CTGCTGCCTCTGAAGCTCCAACTG
1 CTGCTGCCGCTGATGCTCCAACTG
5685029 ACGCTGCTGG
Statistics
Matches: 250, Mismatches: 14, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
24 204 0.82
25 2 0.01
26 2 0.01
27 42 0.17
ACGTcount: A:0.15, C:0.35, G:0.24, T:0.26
Consensus pattern (24 bp):
CTGCTGCCGCTGATGCTCCAACTG
Found at i:5692545 original size:15 final size:15
Alignment explanation
Indices: 5692510--5692561 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
5692500 TTAAGAATTT
*
5692510 TATTAAATTAT-ATA
1 TATTTAATTATAATA
5692524 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
5692538 TATTTAATAATAAT-
1 TATTTAATTATAATA
5692552 TATGTTAATT
1 TAT-TTAATT
5692562 TATATTTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:5692587 original size:120 final size:120
Alignment explanation
Indices: 5692385--5692682 Score: 483
Period size: 120 Copynumber: 2.5 Consensus size: 120
5692375 AATTATTTTA
* * *
5692385 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTAT-TTCAAATTTTCTTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AAATTTTATTT
*
5692449 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
5692505 AATTTTATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTT-AATTTATATTT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTT-TATTT
* *
5692569 TACAGTATTATATATTATGATTTGAGTAAATTCATATGAGAATATTAATTATTAAG
65 TACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
*
5692625 AATTTTATTAAATTATATATTTTAATTAAAATATGTTTAATAATAATTATGTTTAAAT
1 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
5692683 ATGATTAAAA
Statistics
Matches: 165, Mismatches: 9, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
119 5 0.03
120 153 0.93
121 4 0.02
122 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.50
Consensus pattern (120 bp):
AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTTTATTTT
ACAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTAATTATTAAG
Found at i:5692618 original size:66 final size:62
Alignment explanation
Indices: 5692423--5692621 Score: 166
Period size: 66 Copynumber: 3.2 Consensus size: 62
5692413 AAATATATTT
* *
5692423 AATATTAATTATTTCAAATTTTCTTTTATAGTATCATATATTATGATTTGAGTAAATTCATATAA
1 AATATTAATTATTT--AATTTTATTTTA-AGTATTATATATTATGATTTGAGTAAATTCATAT-A
5692488 G
62 G
* * * **
5692489 AATATTAATTATTAAGAATTTTA--TTAA--ATTATATATT-TTAATT-A-T-AA-T-ATATTT
1 AATATTAATTATT--TAATTTTATTTTAAGTATTATATATTATGATTTGAGTAAATTCATATAG
*
5692543 AATAATAATTATGTTAATTTATATTTTACAGTATTATATATTATGATTTGAGTAAATTCATATGA
1 AATATTAATTAT-TTAATTT-TATTTTA-AGTATTATATATTATGATTTGAGTAAATTCATAT-A
5692608 G
62 G
5692609 AATATTAATTATT
1 AATATTAATTATT
5692622 AAGAATTTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 33
0.69 0.09 0.22
Matches are distributed among these distances:
53 5 0.05
54 13 0.13
55 5 0.05
56 4 0.04
57 3 0.03
58 1 0.01
59 11 0.11
60 8 0.08
61 10 0.10
62 1 0.01
63 3 0.03
64 4 0.04
65 5 0.05
66 30 0.29
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (62 bp):
AATATTAATTATTTAATTTTATTTTAAGTATTATATATTATGATTTGAGTAAATTCATATAG
Found at i:5692917 original size:16 final size:16
Alignment explanation
Indices: 5692896--5692947 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
5692886 GATTTGCTAT
5692896 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
5692912 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
5692928 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
5692944 TACA
1 TACA
5692948 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:5695013 original size:13 final size:13
Alignment explanation
Indices: 5694995--5695058 Score: 74
Period size: 13 Copynumber: 4.9 Consensus size: 13
5694985 AGTTCTTTAT
5694995 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
5695008 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
* *
5695021 TGTTGTGGAAAAG
1 TGTTTTTGAAAAG
** *
5695034 TACTTTTGAGAAG
1 TGTTTTTGAAAAG
*
5695047 TGTTTTGGAAAA
1 TGTTTTTGAAAA
5695059 ATTTAAGTGT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.41
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:5695024 original size:26 final size:26
Alignment explanation
Indices: 5694995--5695058 Score: 83
Period size: 26 Copynumber: 2.5 Consensus size: 26
5694985 AGTTCTTTAT
* **
5694995 TGTTTTTGAAAAGTGTTTTTGAAAAG
1 TGTTTTGGAAAAGTACTTTTGAAAAG
* *
5695021 TGTTGTGGAAAAGTACTTTTGAGAAG
1 TGTTTTGGAAAAGTACTTTTGAAAAG
5695047 TGTTTTGGAAAA
1 TGTTTTGGAAAA
5695059 ATTTAAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.31, C:0.02, G:0.27, T:0.41
Consensus pattern (26 bp):
TGTTTTGGAAAAGTACTTTTGAAAAG
Found at i:5695342 original size:21 final size:19
Alignment explanation
Indices: 5695286--5695346 Score: 70
Period size: 19 Copynumber: 3.1 Consensus size: 19
5695276 TAATTATTTA
5695286 TTAAATT-TAATTAGAATAT
1 TTAAATTATAATTA-AATAT
* *
5695305 ATAAATTATATTTAAATAT
1 TTAAATTATAATTAAATAT
5695324 TTAAATATAATAATTAAATAT
1 TTAAAT-T-ATAATTAAATAT
5695345 TT
1 TT
5695347 GTAATTAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
19 16 0.46
20 6 0.17
21 13 0.37
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (19 bp):
TTAAATTATAATTAAATAT
Found at i:5701358 original size:26 final size:26
Alignment explanation
Indices: 5701328--5701379 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
5701318 ATAGCTTGTT
*
5701328 GCTGATTGCAGTAATTGGTTTGACCA
1 GCTGATTGCAGTAATTGATTTGACCA
** *
5701354 GCTGATTTTATTAATTGATTTGACCA
1 GCTGATTGCAGTAATTGATTTGACCA
5701380 AGTGATTCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (26 bp):
GCTGATTGCAGTAATTGATTTGACCA
Found at i:5701385 original size:26 final size:26
Alignment explanation
Indices: 5701339--5701393 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
5701329 CTGATTGCAG
* *
5701339 TAATTGGTTTGACCAGCTGATTTTAT
1 TAATTGATTTGACCAGCTGATTCTAT
5701365 TAATTGATTTGACCAAG-TGATTCTAT
1 TAATTGATTTGACC-AGCTGATTCTAT
5701391 TAA
1 TAA
5701394 CTGTTTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.29, C:0.11, G:0.16, T:0.44
Consensus pattern (26 bp):
TAATTGATTTGACCAGCTGATTCTAT
Found at i:5703927 original size:22 final size:22
Alignment explanation
Indices: 5703902--5703945 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
5703892 AGCACATCAG
5703902 ATTGCTTCCTTGCTGCACGTTT
1 ATTGCTTCCTTGCTGCACGTTT
5703924 ATTGCTTCCTTGCTGCACGTTT
1 ATTGCTTCCTTGCTGCACGTTT
5703946 GTGAGCAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.27, G:0.18, T:0.45
Consensus pattern (22 bp):
ATTGCTTCCTTGCTGCACGTTT
Found at i:5704491 original size:44 final size:45
Alignment explanation
Indices: 5704414--5704510 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 45
5704404 CAAGCTGAAG
* * *
5704414 TGGCGGACAATCTAAATGCAAGCCTGAGTGGGTGCAAGCCAAAAA
1 TGGCAGACAATCTAAATGCAAGCCTAAGAGGGTGCAAGCCAAAAA
*
5704459 -GGCAGACAATCTAAATGTAAG-CTCAAGAGGGTGCAAGCCAAAAA
1 TGGCAGACAATCTAAATGCAAGCCT-AAGAGGGTGCAAGCCAAAAA
5704503 TGGCAGAC
1 TGGCAGAC
5704511 TAAAGGCAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
43 2 0.04
44 37 0.80
45 7 0.15
ACGTcount: A:0.38, C:0.20, G:0.28, T:0.14
Consensus pattern (45 bp):
TGGCAGACAATCTAAATGCAAGCCTAAGAGGGTGCAAGCCAAAAA
Found at i:5707871 original size:23 final size:23
Alignment explanation
Indices: 5707845--5707895 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
5707835 TACTATTTCA
5707845 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5707868 TATTTAAGCTTTATTCACCAAAG
1 TATTTAAGCTTTATTCACCAAAG
5707891 TATTT
1 TATTT
5707896 GAAATATCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTTAAGCTTTATTCACCAAAG
Found at i:5708151 original size:42 final size:42
Alignment explanation
Indices: 5708090--5708251 Score: 191
Period size: 42 Copynumber: 3.7 Consensus size: 42
5708080 TCGTTTTCTC
** *
5708090 GATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAAT
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAAT
* *
5708132 GATGCCATAGCCCAGCTATGGTCTTACACATATTCATAT-AT
1 GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAAT
*
5708173 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATATT
1 -GATGCCATAGCCCAGCTATGGTCTTACAC---AT--C-T-TCACATAAT
5708223 GATGCCATAGCCCAGCTATGGTCTTACAC
1 GATGCCATAGCCCAGCTATGGTCTTACAC
5708252 GAATCACATA
Statistics
Matches: 103, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
41 2 0.02
42 63 0.61
45 2 0.02
48 1 0.01
49 34 0.33
50 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (42 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATCTTCACATAAT
Found at i:5708344 original size:47 final size:46
Alignment explanation
Indices: 5708173--5708341 Score: 194
Period size: 47 Copynumber: 3.6 Consensus size: 46
5708163 ATTCATATAT
* *
5708173 CGATGCCATAGCCCAGCTATGGTCTTACACGTAATCACATATCACATAT
1 CGATGCCATAGCCCAGATATGGTCTTACACGT-ATCACATATCAC--AC
* * * *
5708222 TGATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCAC
1 CGATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACAC
* * * * *
5708268 TGATGCCATATCCCAGATATGGTCTTATACAGTAGCATATATCACAC
1 CGATGCCATAGCCCAGATATGGTCTTACAC-GTATCACATATCACAC
*
5708315 CGATGCCATATCCCAGATATGGTCTTA
1 CGATGCCATAGCCCAGATATGGTCTTA
5708342 TACGGAAATC
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
46 28 0.26
47 38 0.36
48 11 0.10
49 30 0.28
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (46 bp):
CGATGCCATAGCCCAGATATGGTCTTACACGTATCACATATCACAC
Found at i:5708353 original size:95 final size:94
Alignment explanation
Indices: 5708132--5708341 Score: 236
Period size: 95 Copynumber: 2.3 Consensus size: 94
5708122 TTCACATAAT
* * * *
5708132 GATGCCATAGCCCAGCTATGGTCTTACAC-ATAT-TCATATAT--C-GATGCCATAGCCCAGCTA
1 GATGCCATAGCCCAGATATGGTCTTACACGA-ATCACATATCTCACTGATGCCATAGCCCAGATA
* **
5708192 TGGTCTTACACGTAATCACATATCACATATT
65 TGGTCTTACACGTAAGCACATATCACA-ACC
* *
5708223 GATGCCATAGCCCAGCTATGGTCTTACACGAATCACATATCTCACTGATGCCATATCCCAGATAT
1 GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
* *
5708288 GGTCTTATACAGT-AGCATATATCAC-ACC
66 GGTCTTACAC-GTAAGCACATATCACAACC
*
5708316 GATGCCATATCCCAGATATGGTCTTA
1 GATGCCATAGCCCAGATATGGTCTTA
5708342 TACGGAAATC
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
91 31 0.30
92 7 0.07
93 25 0.25
94 1 0.01
95 36 0.35
96 2 0.02
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (94 bp):
GATGCCATAGCCCAGATATGGTCTTACACGAATCACATATCTCACTGATGCCATAGCCCAGATAT
GGTCTTACACGTAAGCACATATCACAACC
Found at i:5708398 original size:31 final size:31
Alignment explanation
Indices: 5708363--5708480 Score: 175
Period size: 31 Copynumber: 3.8 Consensus size: 31
5708353 CTTGTCATTT
*
5708363 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
5708394 GTAGCC-AGAGCTACCATTTTTCACTGATTAG
1 GTAGCCGA-AGCTACCACTTTTCACTGATCAG
*
5708425 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
5708456 GTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
5708481 TGTTATTTGT
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 1 0.01
31 76 0.99
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:5708460 original size:62 final size:62
Alignment explanation
Indices: 5708363--5708480 Score: 193
Period size: 62 Copynumber: 1.9 Consensus size: 62
5708353 CTTGTCATTT
*
5708363 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCCAG-AGCTACCATTTTTCACTGATTAG
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAG-CAGAAGCTACCACTTTTCACTGATTAG
* *
5708425 GTAGCCGGAGCTACCACTTTTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACT
5708481 TGTTATTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
61 3 0.06
62 49 0.94
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.27
Consensus pattern (62 bp):
GTAGCCGAAGCTACCACTATTCACTGATCAGGTAGCAGAAGCTACCACTTTTCACTGATTAG
Found at i:5708560 original size:50 final size:50
Alignment explanation
Indices: 5708456--5708638 Score: 231
Period size: 56 Copynumber: 3.5 Consensus size: 50
5708446 CACTGATCAG
* * * * *
5708456 GTAGCAGAAGCTACCACTTTTCACTTGTTATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
*
5708507 GTAGCCGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGTGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAA--GT
* *
5708559 AGCCGTAGCCGAAGCTTTTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 ----GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
5708613 GTAGCCGAAGCTATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
5708639 GTTGCCATGG
Statistics
Matches: 115, Mismatches: 11, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
50 43 0.37
51 23 0.20
52 2 0.02
54 2 0.02
56 45 0.39
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.36
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:5711191 original size:2 final size:2
Alignment explanation
Indices: 5711186--5711213 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5711176 AAATCAACAC
5711186 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
5711214 TAGATACTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5711523 original size:19 final size:19
Alignment explanation
Indices: 5711499--5711543 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
5711489 AAAGAAAGAT
5711499 GAAGATGTGTGTAGAGAGA
1 GAAGATGTGTGTAGAGAGA
5711518 GAAGATGTGTGTAGAGAGA
1 GAAGATGTGTGTAGAGAGA
5711537 GAAGATG
1 GAAGATG
5711544 AAAGGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (19 bp):
GAAGATGTGTGTAGAGAGA
Found at i:5713510 original size:68 final size:65
Alignment explanation
Indices: 5713424--5713644 Score: 214
Period size: 67 Copynumber: 3.4 Consensus size: 65
5713414 TAATACGGGA
* * * *
5713424 TGTATACCATGTGTACAAGAGAGTTACGAGACATTATGAGGTAGCTAGGTTGCATGGGTGATACT
1 TGTACACCATGTATACAAGAGAGCTACGAGA-A-TA-GAAGTAGCTAGGTTGCATGGGTGATACT
5713489 ATG
63 ATG
* * * * * *
5713492 TGTACACCATGTATACAAGAGAGCTACAAG-ATAGATGTAGCTAGGTTGCATGTGTGGTTCCAGG
1 TGTACACCATGTATACAAGAGAGCTACGAGAATAGAAGTAGCTAGGTTGCATGGGTGATACTA--
5713556 TG
64 TG
* * * * **
5713558 AAGGACACCATGTAAACAAGAGAGCTACGAG-ATA-AAGTGGCTAGGTCACATGGGTGATACTAT
1 -TGTACACCATGTATACAAGAGAGCTACGAGAATAGAAGTAGCTAGGTTGCATGGGTGATACTAT
5713621 G
65 G
*
5713622 TGTACACCATGTGTACAAGAGAG
1 TGTACACCATGTATACAAGAGAG
5713645 ACAAAATTTT
Statistics
Matches: 125, Mismatches: 25, Indels: 11
0.78 0.16 0.07
Matches are distributed among these distances:
63 19 0.15
64 26 0.21
65 2 0.02
66 23 0.18
67 29 0.23
68 26 0.21
ACGTcount: A:0.32, C:0.14, G:0.29, T:0.25
Consensus pattern (65 bp):
TGTACACCATGTATACAAGAGAGCTACGAGAATAGAAGTAGCTAGGTTGCATGGGTGATACTATG
Found at i:5723860 original size:23 final size:23
Alignment explanation
Indices: 5723834--5723885 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
5723824 TATAATTTTA
5723834 TAAAA-ATTCAAAATCCTAAATTC
1 TAAAATATT-AAAATCCTAAATTC
* *
5723857 TAAAATATTAAAATCCTAGATTT
1 TAAAATATTAAAATCCTAAATTC
5723880 TAAAAT
1 TAAAAT
5723886 TATCTTTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.35
Consensus pattern (23 bp):
TAAAATATTAAAATCCTAAATTC
Found at i:5729744 original size:114 final size:114
Alignment explanation
Indices: 5729602--5729829 Score: 359
Period size: 114 Copynumber: 2.0 Consensus size: 114
5729592 TTTTTTTTAA
* *
5729602 AATTTAAATAAACAACTATTTATGATTTTTTTATATGTTATATTTTAGATTTTAGATTTGAATTT
1 AATTTAAATAAACAACTATTTATGATTTTTTCATATGTTATACTTTAGATTTTAGATTTGAATTT
* * * * *
5729667 TTTAAGATATATTTGTAAATGATAAAATTTTGAAGAGTTTTGTAAGTGC
66 TTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAAGTGC
* *
5729716 AATTTAAATAAACAAC-GTTTATGCATTTTTTCATATGTTATACTTTGGATTTTAGATTTGAATT
1 AATTTAAATAAACAACTATTTATG-ATTTTTTCATATGTTATACTTTAGATTTTAGATTTGAATT
5729780 TTTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAAGTGC
65 TTTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAAGTGC
5729830 TTTAAAAGGA
Statistics
Matches: 104, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 6 0.06
114 98 0.94
ACGTcount: A:0.36, C:0.05, G:0.13, T:0.46
Consensus pattern (114 bp):
AATTTAAATAAACAACTATTTATGATTTTTTCATATGTTATACTTTAGATTTTAGATTTGAATTT
TTAAAGACACATTTGTAAATGATAAAATTTTGAAAAGCTTTGTAAGTGC
Found at i:5734318 original size:29 final size:30
Alignment explanation
Indices: 5734259--5734316 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
5734249 TCCGAGCCTT
*
5734259 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
5734289 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
5734317 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:5734546 original size:13 final size:13
Alignment explanation
Indices: 5734528--5734559 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5734518 TTTCCAGCAA
5734528 TTATGAATTTATT
1 TTATGAATTTATT
5734541 TTATGAATTTATT
1 TTATGAATTTATT
*
5734554 TGATGA
1 TTATGA
5734560 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:5734767 original size:50 final size:50
Alignment explanation
Indices: 5734654--5734895 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
5734644 ATTTGGGTAA
* * *
5734654 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
5734710 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5734760 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
5734810 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
5734860 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
5734896 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:5734843 original size:100 final size:103
Alignment explanation
Indices: 5734654--5734903 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
5734644 ATTTGGGTAA
5734654 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
5734719 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
5734760 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
5734822 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
5734860 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
5734904 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:5741036 original size:15 final size:15
Alignment explanation
Indices: 5741000--5741048 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5740990 CGAAAATCTA
*
5741000 AATAAAATAA-ACAT
1 AATAAAATAATAAAT
5741014 AA-ACAAATAAGT-AAT
1 AATA-AAATAA-TAAAT
5741029 AATAAAATAATAAAT
1 AATAAAATAATAAAT
5741044 AATAA
1 AATAA
5741049 TAGAATAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
13 1 0.03
14 9 0.31
15 18 0.62
16 1 0.03
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.22
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:5741040 original size:18 final size:18
Alignment explanation
Indices: 5741019--5741069 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
5741009 AACATAAACA
*
5741019 AATAAGTAATAATAAAAT
1 AATAAATAATAATAAAAT
*
5741037 AATAAATAATAATAGAAT
1 AATAAATAATAATAAAAT
5741055 AA-ACAA-AATAATAAA
1 AATA-AATAATAATAAA
5741070 GTGGCTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (18 bp):
AATAAATAATAATAAAAT
Found at i:5742235 original size:27 final size:27
Alignment explanation
Indices: 5742195--5742263 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
5742185 GTTTTTTGTT
*
5742195 TTGGGTT-TTGGGCTGAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
5742221 TTGGGTTATTGGGCTAAGGGTAGGCTA
1 TTGGGTTATTGGGCTAAGGGTAGGCTA
5742248 TTGGGTTATTGGGCTA
1 TTGGGTTATTGGGCTA
5742264 GTGGTTCTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
26 7 0.17
27 34 0.83
ACGTcount: A:0.14, C:0.07, G:0.42, T:0.36
Consensus pattern (27 bp):
TTGGGTTATTGGGCTAAGGGTAGGCTA
Found at i:5742646 original size:43 final size:42
Alignment explanation
Indices: 5742562--5742663 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 42
5742552 CTCTACTGCC
* * *
5742562 ACTTCAGAGAGATAAGATTTTTTTTTAATCCGCTCCACTGTA
1 ACTTCAGGGAGATAAGATTTGTCTTTAATCCGCTCCACTGTA
* * *
5742604 ACTTCAGGGAGATAGGATTATGTCTTTAATCTGCTCCGCTGTA
1 ACTTCAGGGAGATAAGATT-TGTCTTTAATCCGCTCCACTGTA
*
5742647 ACCTCA-GGAGATAAGAT
1 ACTTCAGGGAGATAAGAT
5742664 CTGCAATTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 27 0.53
43 24 0.47
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (42 bp):
ACTTCAGGGAGATAAGATTTGTCTTTAATCCGCTCCACTGTA
Found at i:5742783 original size:85 final size:85
Alignment explanation
Indices: 5742686--5742962 Score: 243
Period size: 85 Copynumber: 3.2 Consensus size: 85
5742676 GTCTACTCCG
* *
5742686 CTGTAACCTCAGGGAAATAAGACCTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATC
1 CTGTAACTTCAGGGAAATAAGACTTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATC
*
5742751 CTTTATTTTAATCCGTTCCA
66 CTTTATTTTAATCCATTCCA
* * * * * * ** * *
5742771 CTGTAACTTCAGGGAGATAGGATAGTGACTTCGCTTCCATCTATTCCATTACAACTTTAG-GGGA
1 CTGTAACTTCA-GG-GA-A--ATA-AGACTT-GATGCGATCTACTCTATTGTAACTTCAGAGAG-
* * *
5742835 ATAAGATTCGTTT-TTTCAATCTATTCCA
58 ATAAGA-TCCTTTATTTTAATCCATTCCA
* * * ** *
5742863 CTGCATCTTCAGGGAAATAAGACTTGATGCGACCTACTCTGCTGTAACCTCAGAGAGATAAGATC
1 CTGTAACTTCAGGGAAATAAGACTTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATC
*
5742928 CTTTATTTTAATCCACTCCA
66 CTTTATTTTAATCCATTCCA
*
5742948 CTGTAACTTCGGGGA
1 CTGTAACTTCAGGGA
5742963 GATAGGATAG
Statistics
Matches: 142, Mismatches: 39, Indels: 22
0.70 0.19 0.11
Matches are distributed among these distances:
84 5 0.04
85 56 0.39
86 9 0.06
87 5 0.04
88 1 0.01
89 1 0.01
90 5 0.04
91 8 0.06
92 47 0.33
93 5 0.04
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (85 bp):
CTGTAACTTCAGGGAAATAAGACTTGATGCGATCTACTCTATTGTAACTTCAGAGAGATAAGATC
CTTTATTTTAATCCATTCCA
Found at i:5743006 original size:43 final size:44
Alignment explanation
Indices: 5742943--5743228 Score: 144
Period size: 44 Copynumber: 6.7 Consensus size: 44
5742933 TTTTAATCCA
* * * * * *
5742943 CTCCACTGTAACTTCGGGGAGATAGGAT-AGTGTCTTCGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATCTG
* * *
5742986 CTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATCTG
* * * ***
5743030 CTCCACTGTAACCTCAGGGAAATAAGATCTGAAAT-TCTTTGGTCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATC---ACTGGCTTCAATCTG
* * * * *
5743076 TTCCACTGTAATCTCAGGGAGATAAGA-C-CT-GATGT-GATCTT
1 CTCCACTGTAACCTCAGGGAGATAAGATCACTGGCT-TCAATCTG
* * * * *
5743117 CTCTACTGTAACTTCAGAGAGATACGATC-CT---TT-AATCCG
1 CTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATCTG
* * * * * * **
5743156 CTCCATTGTAATCTCAAGGAGATAGGATTACTGTCTTTGATCTG
1 CTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATCTG
* *
5743200 CTCCGCTGTAATCTCAGGGAGATAAGATC
1 CTCCACTGTAACCTCAGGGAGATAAGATC
5743229 TGAAATTCTT
Statistics
Matches: 182, Mismatches: 50, Indels: 21
0.72 0.20 0.08
Matches are distributed among these distances:
39 25 0.14
40 3 0.02
41 27 0.15
42 4 0.02
43 25 0.14
44 65 0.36
45 1 0.01
46 31 0.17
47 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.31
Consensus pattern (44 bp):
CTCCACTGTAACCTCAGGGAGATAAGATCACTGGCTTCAATCTG
Found at i:5743039 original size:44 final size:42
Alignment explanation
Indices: 5742980--5743272 Score: 195
Period size: 46 Copynumber: 6.8 Consensus size: 42
5742970 TAGTGTCTTC
*
5742980 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCT-GCTT
* * * * *
5743023 CAATCTGCTCCACTGTAACCTCAGGGAAATAAGATCTGAAATTCTTT
1 -GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTGC-TT
* * *
5743070 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-C-CTGATGT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGCT-T
* * * *
5743111 GATCTTCTCTACTGTAA-CTTCAGAGAGATACGATC-CT--TT
1 GATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTCTGCTT
* * * * *
5743150 AATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-TACTGTCTTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-CTG-C-TT
* * *
5743194 GATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTT
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTGC-TT
* *
5743240 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 GATCTGCTCCACTGTAATCTCAGGGAGATAAGA
5743273 CCTGTATTAT
Statistics
Matches: 193, Mismatches: 39, Indels: 32
0.73 0.15 0.12
Matches are distributed among these distances:
39 25 0.13
40 6 0.03
41 27 0.14
42 3 0.02
44 62 0.32
45 2 0.01
46 63 0.33
47 5 0.03
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (42 bp):
GATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTGCTT
Found at i:5743093 original size:46 final size:45
Alignment explanation
Indices: 5742975--5743272 Score: 221
Period size: 44 Copynumber: 6.8 Consensus size: 45
5742965 TAGGATAGTG
* * *
5742975 TCTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCT--CT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* ** * *
5743018 GGCTTCAATCTGCTCCACTGTAACCTCAGGGAAATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* * *
5743065 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGACCTG-A-
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
* * * *
5743108 --TGTGATCTTCTCTACTGTAA-CTTCAGAGAGAT---A-C-G-AT
1 TCTTTGATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTGAAT
* * * * * * *
5743145 CCTTTAATCCGCTCCATTGTAATCTCAAGGAGATAGGAT-T-ACT
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
*
5743188 GTCTTTGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAAT
1 -TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTG-AAT
* *
5743235 TCTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGA
5743273 CCTGTATTAT
Statistics
Matches: 196, Mismatches: 40, Indels: 34
0.73 0.15 0.13
Matches are distributed among these distances:
36 2 0.01
37 1 0.01
38 1 0.01
39 22 0.11
40 2 0.01
41 24 0.12
42 1 0.01
43 1 0.01
44 69 0.35
45 1 0.01
46 69 0.35
47 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (45 bp):
TCTTTGATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTGAAT
Done.