Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 10 of 97
Found at i:4829109 original size:2 final size:2
Alignment explanation
Indices: 4829104--4829143 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
4829094 AATATATCTC
*
4829104 AT AT AT TT AT AT AT AT AT AT AT -T A- 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
4829144 TCAGTTATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:4829125 original size:16 final size:16
Alignment explanation
Indices: 4829089--4829141 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
4829079 TGTAAATCTT
*
4829089 TATTTAATATATCTCATA
1 TATTT-ATATATAT-ATA
4829107 TATTTATATATATATA
1 TATTTATATATATATA
*
4829123 TATTAATATATATATA
1 TATTTATATATATATA
4829139 TAT
1 TAT
4829142 ATTCAGTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
16 21 0.64
17 7 0.21
18 5 0.15
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (16 bp):
TATTTATATATATATA
Found at i:4836819 original size:15 final size:16
Alignment explanation
Indices: 4836788--4836829 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 16
4836778 CTCCTTTAAG
4836788 CTCTCTTCTCTCACTC
1 CTCTCTTCTCTCACTC
*
4836804 CTCTCTT-TCTCTCTC
1 CTCTCTTCTCTCACTC
*
4836819 CTCTCTCCTCT
1 CTCTCTTCTCT
4836830 ATCCTGTCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (16 bp):
CTCTCTTCTCTCACTC
Found at i:4839637 original size:215 final size:214
Alignment explanation
Indices: 4839266--4839695 Score: 684
Period size: 215 Copynumber: 2.0 Consensus size: 214
4839256 TAATTGATCT
* * * **
4839266 CGTATTTCATTTCAAATCTTAAAGTTTTAATATTCATAAAATGAAACAGTACGATTTTTTATTAT
1 CGTATTTCATTTCAAATCTTAAAATTTTAACATTCATAAAATAAAACAGTAAAATTTTTTATTAT
* *
4839331 GATATATCTCGCATATCATTTCAAATCTTTATGATTCAAAAGTAAATATATTTATTTAACATCTA
66 GATATATCTCGCATAACATTTCAAATCTTTATGATTCAAAAGTAAATACATTTATTTAACATCTA
*
4839396 ATCAAAAAGTTAAATCTAAAAGTTTTATTTGATGGAAGCTATTTC-CATGTCATCGAACAGATTA
131 ATCAAAAAGTTAAATCTAAAAGTTTTATTTGATGGAAACTA-TTCACATGTCATCGAACAGATTA
* * *
4839460 TAATTTTTTTTTCTTGTTATG
195 GAA-TTTCTTTTCTTGCTATG
*
4839481 CGTATTTCATTTCAAATCTTAAAATTTTAACATTTATAAAATAAAACAGTAAAATTTTTTATTAT
1 CGTATTTCATTTCAAATCTTAAAATTTTAACATTCATAAAATAAAACAGTAAAATTTTTTATTAT
* * *
4839546 GATTTATCTCGCATAACATTTTAAAT-TCTTATGATTCAAAAGTAAATACATTTGTTTAACATCT
66 GATATATCTCGCATAACATTTCAAATCT-TTATGATTCAAAAGTAAATACATTTATTTAACATCT
4839610 AATCAAAAAGTTAAATCTAAAAGTTTTATTTGATGGAAACTATTCACATGTCATCGAACAGATTA
130 AATCAAAAAGTTAAATCTAAAAGTTTTATTTGATGGAAACTATTCACATGTCATCGAACAGATTA
4839675 GAATTTCTTTTCTTGCTATG
195 GAATTTCTTTTCTTGCTATG
4839695 C
1 C
4839696 TACATGGTTT
Statistics
Matches: 198, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
214 20 0.10
215 178 0.90
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (214 bp):
CGTATTTCATTTCAAATCTTAAAATTTTAACATTCATAAAATAAAACAGTAAAATTTTTTATTAT
GATATATCTCGCATAACATTTCAAATCTTTATGATTCAAAAGTAAATACATTTATTTAACATCTA
ATCAAAAAGTTAAATCTAAAAGTTTTATTTGATGGAAACTATTCACATGTCATCGAACAGATTAG
AATTTCTTTTCTTGCTATG
Found at i:4857122 original size:29 final size:29
Alignment explanation
Indices: 4857076--4857196 Score: 118
Period size: 29 Copynumber: 4.2 Consensus size: 29
4857066 TCCTTTCTTG
* * * * *
4857076 TTCTCATATACTTGTTCACATACACCTTC
1 TTCTCTTATACCTATTCACGTACAACTTC
* * *
4857105 TTCTCTTATGCCTATTCACGTATAGCTTC
1 TTCTCTTATACCTATTCACGTACAACTTC
* * *
4857134 TTCTCTTATATCTATTTACGTATAACTTC
1 TTCTCTTATACCTATTCACGTACAACTTC
* *
4857163 TTCTCTTGTACCTGTTCACGTACAACTT-
1 TTCTCTTATACCTATTCACGTACAACTTC
4857191 TTCTCT
1 TTCTCT
4857197 ATTAGCTCCT
Statistics
Matches: 76, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
28 6 0.08
29 70 0.92
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.46
Consensus pattern (29 bp):
TTCTCTTATACCTATTCACGTACAACTTC
Found at i:4893193 original size:2 final size:2
Alignment explanation
Indices: 4893181--4893221 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
4893171 CAACAGATAA
4893181 AT AT A- 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
4893222 TGTTTCTGAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4895289 original size:2 final size:2
Alignment explanation
Indices: 4895282--4895306 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4895272 CAGAAGTTGA
4895282 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
4895307 TTCTTGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:4903436 original size:25 final size:25
Alignment explanation
Indices: 4903408--4903458 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
4903398 AGCTTGTAAG
4903408 AAGAAAAAAAAAAAAGGGAAAAATA
1 AAGAAAAAAAAAAAAGGGAAAAATA
* * *
4903433 AAGAAAAAACAGAAAGGGAACAATA
1 AAGAAAAAAAAAAAAGGGAAAAATA
4903458 A
1 A
4903459 GCGAACATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.75, C:0.04, G:0.18, T:0.04
Consensus pattern (25 bp):
AAGAAAAAAAAAAAAGGGAAAAATA
Found at i:4918241 original size:23 final size:22
Alignment explanation
Indices: 4918185--4918241 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 22
4918175 TGAATTTATG
*
4918185 AATAATTAC-CAACAATTACAA
1 AATAATTACACAACAAATACAA
** * *
4918206 AATAAGAAAACAATAAATAGCAA
1 AATAATTACACAACAAATA-CAA
4918229 AATAATTACACAA
1 AATAATTACACAA
4918242 AAACTCTAAG
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
21 6 0.23
22 7 0.27
23 13 0.50
ACGTcount: A:0.63, C:0.14, G:0.04, T:0.19
Consensus pattern (22 bp):
AATAATTACACAACAAATACAA
Found at i:4919628 original size:26 final size:24
Alignment explanation
Indices: 4919585--4919643 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
4919575 AAACCTTATT
* *
4919585 TTTTTATTATCTTCAATCAAGTAACTA
1 TTTTTA-TATCTTAAATCAAATAA--A
*
4919612 TTTTTATATTTTAAATCAAATAAA
1 TTTTTATATCTTAAATCAAATAAA
4919636 TTTTTATA
1 TTTTTATA
4919644 ATTAATAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 9 0.31
26 14 0.48
27 6 0.21
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (24 bp):
TTTTTATATCTTAAATCAAATAAA
Found at i:4919656 original size:24 final size:24
Alignment explanation
Indices: 4919611--4919656 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4919601 TCAAGTAACT
* *
4919611 ATTTTTATATTTTAAATCAAATAA
1 ATTTTTATAATTAAAATCAAATAA
4919635 ATTTTTATAATTAATAAT-AAAT
1 ATTTTTATAATTAA-AATCAAAT
4919657 TAACTACCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
ATTTTTATAATTAAAATCAAATAA
Found at i:4929122 original size:2 final size:2
Alignment explanation
Indices: 4929110--4929141 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4929100 ATTTTAAATT
*
4929110 TA TA AA 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
4929142 ACATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:4930633 original size:28 final size:28
Alignment explanation
Indices: 4930579--4930642 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
4930569 ATGTTTATAC
4930579 AATTAATATGATTGAAACAATTAAATTA
1 AATTAATATGATTGAAACAATTAAATTA
*
4930607 AATTAATATGTATTTAAA-ATATTAATTATTA
1 AATTAATATG-ATTGAAACA-ATTAA--ATTA
4930638 AATTA
1 AATTA
4930643 TAATAAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
28 11 0.35
29 11 0.35
31 9 0.29
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.42
Consensus pattern (28 bp):
AATTAATATGATTGAAACAATTAAATTA
Found at i:4930670 original size:16 final size:16
Alignment explanation
Indices: 4930646--4930677 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4930636 TAAATTATAA
*
4930646 TAAACTATTAATATTT
1 TAAAATATTAATATTT
4930662 TAAAATATTAATATTT
1 TAAAATATTAATATTT
4930678 AAATTATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAAATATTAATATTT
Found at i:4930907 original size:16 final size:16
Alignment explanation
Indices: 4930886--4930917 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4930876 TAATAATTAT
*
4930886 TTTATTTTATTCTTAC
1 TTTATTCTATTCTTAC
4930902 TTTATTCTATTCTTAC
1 TTTATTCTATTCTTAC
4930918 ATAATAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.16, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTATTCTATTCTTAC
Found at i:4931413 original size:25 final size:22
Alignment explanation
Indices: 4931370--4931414 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 22
4931360 TATCTAGTTA
*
4931370 ATTATAATAGTTATATTAGAAT
1 ATTATAATAGTTAGATTAGAAT
4931392 ATTATTAATTAGTTAGAGTTAGA
1 ATTA-TAA-TAGTTAGA-TTAGA
4931415 TTATAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 3 0.16
24 7 0.37
25 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.44
Consensus pattern (22 bp):
ATTATAATAGTTAGATTAGAAT
Found at i:4933530 original size:11 final size:11
Alignment explanation
Indices: 4933514--4933546 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
4933504 ATCATTAAAA
4933514 TATTAATAATT
1 TATTAATAATT
*
4933525 TATTAATAA-A
1 TATTAATAATT
4933535 TATTAATAATT
1 TATTAATAATT
4933546 T
1 T
4933547 CCTATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
TATTAATAATT
Found at i:4933537 original size:21 final size:22
Alignment explanation
Indices: 4933509--4933564 Score: 78
Period size: 21 Copynumber: 2.6 Consensus size: 22
4933499 CTGCCATCAT
*
4933509 TAAAATATTAATAATTTATTAA
1 TAAAATATTAATAATTTACTAA
* *
4933531 T-AAATATTAATAATTTCCTAT
1 TAAAATATTAATAATTTACTAA
4933552 TAAAATATTAATA
1 TAAAATATTAATA
4933565 TGAATTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 18 0.60
22 12 0.40
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAAATATTAATAATTTACTAA
Found at i:4933925 original size:22 final size:22
Alignment explanation
Indices: 4933900--4933968 Score: 86
Period size: 22 Copynumber: 3.1 Consensus size: 22
4933890 TTTTTATCTT
* *
4933900 TTAATTTCTTATTAACATATTA
1 TTAATTTATTATTAAAATATTA
* *
4933922 TTAATTTAATAATAAAATAATTA
1 TTAATTTATTATTAAAAT-ATTA
4933945 TT-ATTTATTATTAAAATATTA
1 TTAATTTATTATTAAAATATTA
4933966 TTA
1 TTA
4933969 TGATATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 6 0.15
22 27 0.69
23 6 0.15
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAATTTATTATTAAAATATTA
Found at i:4942985 original size:2 final size:2
Alignment explanation
Indices: 4942980--4943030 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
4942970 TTTTTTTTTA
4942980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
4943021 AT AT AT AT AT
1 AT AT AT AT AT
4943031 TTTGCCACTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4945568 original size:46 final size:46
Alignment explanation
Indices: 4945510--4945599 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
4945500 CTCATATTGT
* * *
4945510 TGAAATTTATTTCTGCACTGTTCCTGAGCAAGACGTTCTCATAGTA
1 TGAAATATATTTCTGCACTGATCCTGAACAAGACGTTCTCATAGTA
* *
4945556 TGAAATATATTTCTGCACTGATCCTTAACAAGACTTTCTCATAG
1 TGAAATATATTTCTGCACTGATCCTGAACAAGACGTTCTCATAG
4945600 CTCCCAATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (46 bp):
TGAAATATATTTCTGCACTGATCCTGAACAAGACGTTCTCATAGTA
Found at i:4947508 original size:30 final size:30
Alignment explanation
Indices: 4947472--4947533 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
4947462 TCTGTCCAGG
4947472 GATTTTCCCAGTGATGGCCAGAGTCATGTA
1 GATTTTCCCAGTGATGGCCAGAGTCATGTA
4947502 GATTTTCCCAGTGATGGCCAGAGTCATGTA
1 GATTTTCCCAGTGATGGCCAGAGTCATGTA
4947532 GA
1 GA
4947534 AACTACAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (30 bp):
GATTTTCCCAGTGATGGCCAGAGTCATGTA
Found at i:4955089 original size:29 final size:27
Alignment explanation
Indices: 4955019--4955092 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 27
4955009 GTCTCTCAAA
* *
4955019 ATTTTTAAAATTTTTATAACAATATTT
1 ATTTTTAAAAATTTTACAACAATATTT
4955046 ATTTTTACAATAATTTTACAA-AATATTCTT
1 ATTTTTA-AA-AATTTTACAACAATA-T-TT
4955076 ATTTTTTAAAAATTTTA
1 A-TTTTTAAAAATTTTA
4955093 TAATTTTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
27 7 0.17
28 6 0.15
29 16 0.40
30 5 0.12
31 6 0.15
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (27 bp):
ATTTTTAAAAATTTTACAACAATATTT
Found at i:4959324 original size:2 final size:2
Alignment explanation
Indices: 4959319--4959358 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
4959309 TTTCTCAAGT
4959319 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4959359 ATCTTCTGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:4959852 original size:21 final size:22
Alignment explanation
Indices: 4959810--4959852 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
4959800 TAATAAATTA
* *
4959810 TTAAAATAATAAATGTTTTAAT
1 TTAAAATAATAAATATTATAAT
*
4959832 TTAAAA-ATTAAATATTATAAT
1 TTAAAATAATAAATATTATAAT
4959853 AAAAAGCATA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (22 bp):
TTAAAATAATAAATATTATAAT
Found at i:4972664 original size:30 final size:30
Alignment explanation
Indices: 4972628--4972698 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
4972618 TAAGAGTTGA
*
4972628 TGTTGAATTTTGCTATTATACTTTTAATTT
1 TGTTGAATTTTGCTAGTATACTTTTAATTT
* * *
4972658 TGTTGAATTTTGTTAGTATATTTTTAGTTT
1 TGTTGAATTTTGCTAGTATACTTTTAATTT
4972688 TGTTGAATTTT
1 TGTTGAATTTT
4972699 TAATATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.21, C:0.03, G:0.14, T:0.62
Consensus pattern (30 bp):
TGTTGAATTTTGCTAGTATACTTTTAATTT
Found at i:4973165 original size:2 final size:2
Alignment explanation
Indices: 4973154--4973202 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
4973144 GCTACATTTC
4973154 AT AT -T 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
4973195 AT AT AT AT
1 AT AT AT AT
4973203 CTTTCTTCCA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:4974806 original size:2 final size:2
Alignment explanation
Indices: 4974801--4974881 Score: 67
Period size: 2 Copynumber: 41.0 Consensus size: 2
4974791 AAAAAAAAAT
* * * *
4974801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA NA TT TC T- TCA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * * *
4974843 AA AA AA T- TA AA 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 TA TA
4974882 CTAATTTACC
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:4983062 original size:23 final size:23
Alignment explanation
Indices: 4983036--4983098 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 23
4983026 ATATAAACAA
*
4983036 TATTAATAATTTAAATTATCAAT
1 TATTAATAATTTAAATTACCAAT
*
4983059 TATTAATATTTAAATAAATTACCAAT
1 TATTAATAATT---TAAATTACCAAT
4983085 TATTAAT-ATTTAAA
1 TATTAATAATTTAAA
4983099 AAAATAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 4 0.12
23 10 0.29
25 2 0.06
26 18 0.53
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (23 bp):
TATTAATAATTTAAATTACCAAT
Found at i:4983084 original size:26 final size:26
Alignment explanation
Indices: 4983047--4983103 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
4983037 ATTAATAATT
*
4983047 TAAATTATCAATTATTAATATTTAAA
1 TAAATTACCAATTATTAATATTTAAA
4983073 TAAATTACCAATTATTAATATTTAAA
1 TAAATTACCAATTATTAATATTTAAA
*
4983099 AAAAT
1 TAAAT
4983104 AAAATAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATTACCAATTATTAATATTTAAA
Found at i:4983139 original size:116 final size:108
Alignment explanation
Indices: 4982920--4983218 Score: 284
Period size: 111 Copynumber: 2.7 Consensus size: 108
4982910 TTATACCAAT
* * * **
4982920 AAAATAATATTATTTAAATTATCAATTATTAACA---AAATAAATTATAAATTATTCCTATTTAA
1 AAAATATTAATATTTAAATTATCAATTATTAATATTTAAATAAATTATAAATTATTAATATTTAA
* *
4982982 AACAAAATAAATTAAAAATAAATAAACATAATATCATTTAAATTATATA
66 AA-AAAATAAAATAAAAATAAATAAACAT-A-AT-A--TAAATTAAATA
**
4983031 AACAATATTAATAATTTAAATTATCAATTATTAATATTTAAATAAATTACCAATTATTAATATTT
1 AA-AATATTAAT-ATTTAAATTATCAATTATTAATATTTAAATAAATTATAAATTATTAATATTT
* *
4983096 -AAAAAAATAAAATAAAAATTAATCATA-ATAATATTTAAATTAAATA
64 AAAAAAAATAAAATAAAAATAAAT-AAACATAATA--TAAATTAAATA
* * * * *
4983142 CAAATATTAATATTTAAATGATCCATCATTAATATTTTAAATAAAAATATAAATTATTAATATTT
1 AAAATATTAATATTTAAATTATCAATTATTAATA-TTTAAAT-AAATTATAAATTATTAATATTT
*
4983207 CAAAATAAATAA
64 -AAAAAAAATAA
4983219 NAAATATTAA
Statistics
Matches: 159, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
109 20 0.13
110 16 0.10
111 35 0.22
112 9 0.06
113 32 0.20
114 20 0.13
115 5 0.03
116 22 0.14
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (108 bp):
AAAATATTAATATTTAAATTATCAATTATTAATATTTAAATAAATTATAAATTATTAATATTTAA
AAAAAATAAAATAAAAATAAATAAACATAATATAAATTAAATA
Found at i:4983204 original size:111 final size:113
Alignment explanation
Indices: 4982954--4983218 Score: 315
Period size: 111 Copynumber: 2.3 Consensus size: 113
4982944 ATTATTAACA
** *
4982954 AAATAAATTATAAATTATTCCTATTTAAAACAAAATAAATTAAAAATAAATAAACATAATATCAT
1 AAATAAATTATAAATTATTAATATTTAAAA-AAAATAAAATAAAAAT--ATAAACATAATATCAT
* * *
4983019 TTAAATTATATAAACAATATTAATAATTTAAATTATCAATTATTAATATTT
63 TTAAATTAAATAAACAATATTAATAATTTAAATGATCAATCATTAATATTT
** *
4983070 AAATAAATTACCAATTATTAATATTT-AAAAAAATAAAATAAAAAT-TAATCATAATAAT-ATTT
1 AAATAAATTATAAATTATTAATATTTAAAAAAAATAAAATAAAAATATAAACATAAT-ATCATTT
* *
4983132 AAATTAAATACA-AATATTAAT-ATTTAAATGATCCATCATTAATATTTT
65 AAATTAAATAAACAATATTAATAATTTAAATGATCAATCATTAATA-TTT
* *
4983180 AAATAAAAATATAAATTATTAATATTTCAAAATAAATAA
1 AAAT-AAATTATAAATTATTAATATTT-AAAAAAAATAA
4983219 NAAATATTAA
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
109 20 0.16
110 16 0.12
111 42 0.33
112 2 0.02
113 9 0.07
114 15 0.12
115 3 0.02
116 22 0.17
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (113 bp):
AAATAAATTATAAATTATTAATATTTAAAAAAAATAAAATAAAAATATAAACATAATATCATTTA
AATTAAATAAACAATATTAATAATTTAAATGATCAATCATTAATATTT
Found at i:4983223 original size:28 final size:27
Alignment explanation
Indices: 4983169--4983235 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
4983159 ATGATCCATC
*
4983169 ATTAATATTTTAAATAAAAATATAAATT
1 ATTAATATTTAAAATAAAAATATAAA-T
* *
4983197 ATTAATATTTCAAAATAAATA-ANAAAT
1 ATTAATATTT-AAAATAAAAATATAAAT
4983224 ATTAATAATTTA
1 ATTAAT-ATTTA
4983236 TAATTTATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 8 0.24
28 18 0.53
29 8 0.24
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTAATATTTAAAATAAAAATATAAAT
Found at i:4983226 original size:27 final size:28
Alignment explanation
Indices: 4983169--4983230 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
4983159 ATGATCCATC
* *
4983169 ATTAATATTTTAAATAAAAATATAAATT
1 ATTAATATTTCAAATAAAAATATAAAAT
*
4983197 ATTAATATTTCAAA-ATAAATA-ANAAAT
1 ATTAATATTTCAAATAAAAATATA-AAAT
4983224 ATTAATA
1 ATTAATA
4983231 ATTTATAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 16 0.53
28 13 0.43
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (28 bp):
ATTAATATTTCAAATAAAAATATAAAAT
Found at i:4983329 original size:25 final size:26
Alignment explanation
Indices: 4983248--4983367 Score: 89
Period size: 27 Copynumber: 4.3 Consensus size: 26
4983238 ATTTATTTAA
4983248 AATATTTATGATTTATAATTTAAACATT
1 AATATTT-TG-TTTATAATTTAAACATT
* *
4983276 AATATGATTATTTCATTTAATTTGAAACATT
1 AATAT-TTTGTTT-A--TAATTT-AAACATT
4983307 AATATTTTGTTTATAATTT-AACATT
1 AATATTTTGTTTATAATTTAAACATT
* ** * *
4983332 ATTATGATTAATTTATAGTTTAAATATT
1 AATAT--TTTGTTTATAATTTAAACATT
4983360 AATATTTT
1 AATATTTT
4983368 AAATTATTAA
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
25 10 0.14
26 2 0.03
27 20 0.27
28 16 0.22
29 2 0.03
30 11 0.15
31 12 0.16
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.53
Consensus pattern (26 bp):
AATATTTTGTTTATAATTTAAACATT
Found at i:4983370 original size:15 final size:16
Alignment explanation
Indices: 4983350--4983386 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
4983340 TAATTTATAG
4983350 TTTAAA-TATTAATAT
1 TTTAAATTATTAATAT
4983365 TTTAAATTATTAATAT
1 TTTAAATTATTAATAT
4983381 TTTAAA
1 TTTAAA
4983387 AATCTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTAAATTATTAATAT
Found at i:4985205 original size:15 final size:16
Alignment explanation
Indices: 4985178--4985210 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
4985168 TATTTTTTTT
*
4985178 ATATATAAAATTTGAA
1 ATATATAAAATTTAAA
4985194 ATATAT-AAATTTAAA
1 ATATATAAAATTTAAA
4985209 AT
1 AT
4985211 TTTATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
ATATATAAAATTTAAA
Found at i:4992277 original size:26 final size:26
Alignment explanation
Indices: 4992248--4992327 Score: 72
Period size: 26 Copynumber: 3.0 Consensus size: 26
4992238 TTGAAATATC
* * *
4992248 TTGGGCGCTTCCACGTTAGGAACACG
1 TTGGGCACTTCCACCTTCGGAACACG
* * *
4992274 TTGGAGCTA-TTCCGCTTTCGGAACACC
1 TTGG-GC-ACTTCCACCTTCGGAACACG
*
4992301 CTGGGCACTTCCACCTTCGGAACACG
1 TTGGGCACTTCCACCTTCGGAACACG
4992327 T
1 T
4992328 GCTTCTACGC
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
25 1 0.02
26 21 0.51
27 19 0.46
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (26 bp):
TTGGGCACTTCCACCTTCGGAACACG
Found at i:4994280 original size:97 final size:97
Alignment explanation
Indices: 4994084--4994294 Score: 260
Period size: 97 Copynumber: 2.2 Consensus size: 97
4994074 TTGAAAGCAG
* * ** * * *
4994084 AAAGGGTAAAACCGTGAGACAATGAGAGTGGAGATGGAATATTAGAAGTGCTTGGAAGGGCAGTG
1 AAAGGGTGAGACCGTGAGATGATGAGAGTGGAGATGGAAGACTAGAAGTGCTTGGAAGAGCAGTG
** *
4994149 ATCGATCGACAGTCGGCAAAAGTAGAAATAAA
66 ATCGATCGACAGTCGGCAAAACCAAAAATAAA
* *
4994181 AAAGGGTGAGACTGTGAGATGATGAGAGTGGAGATGGAAGACTAGAAGTGCTTGGAAGAGTAGTG
1 AAAGGGTGAGACCGTGAGATGATGAGAGTGGAGATGGAAGACTAGAAGTGCTTGGAAGAGCAGTG
** * * * *
4994246 ATCGATCGGTATTTGGCAGAACCAAAAATCAA
66 ATCGATCGACAGTCGGCAAAACCAAAAATAAA
4994278 AAAGGGTGAGACCGTGA
1 AAAGGGTGAGACCGTGA
4994295 TAATGGAGAT
Statistics
Matches: 95, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
97 95 1.00
ACGTcount: A:0.38, C:0.10, G:0.34, T:0.18
Consensus pattern (97 bp):
AAAGGGTGAGACCGTGAGATGATGAGAGTGGAGATGGAAGACTAGAAGTGCTTGGAAGAGCAGTG
ATCGATCGACAGTCGGCAAAACCAAAAATAAA
Found at i:4994503 original size:14 final size:15
Alignment explanation
Indices: 4994486--4994533 Score: 73
Period size: 14 Copynumber: 3.3 Consensus size: 15
4994476 CCGAATTAAT
4994486 CGAATC-GAACTAAC
1 CGAATCTGAACTAAC
4994500 CGAACTCTGAACTAAC
1 CGAA-TCTGAACTAAC
4994516 CGAA-CTGAACTAAC
1 CGAATCTGAACTAAC
4994530 CGAA
1 CGAA
4994534 CTCAATTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 18 0.56
15 2 0.06
16 12 0.38
ACGTcount: A:0.42, C:0.29, G:0.15, T:0.15
Consensus pattern (15 bp):
CGAATCTGAACTAAC
Found at i:4995888 original size:21 final size:21
Alignment explanation
Indices: 4995862--4995907 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 21
4995852 GGTAATGTAG
4995862 TTGAATTAT-ACATTATTGTGC
1 TTGAATT-TGACATTATTGTGC
4995883 TTGAATTTGGAACATTATTGTGC
1 TTGAATTT-G-ACATTATTGTGC
4995906 TT
1 TT
4995908 TTAATTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 1 0.05
21 7 0.32
23 14 0.64
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (21 bp):
TTGAATTTGACATTATTGTGC
Found at i:4997140 original size:382 final size:382
Alignment explanation
Indices: 4996431--4997194 Score: 1492
Period size: 382 Copynumber: 2.0 Consensus size: 382
4996421 CGTGCCCCTG
*
4996431 CAGTATTTCTAACCTTATTTTTTATGTATAAACATTGAGCAGTATTCAGCATTTTTCACTATTGT
1 CAGTATTTCTAACCTTATTTTTTATGTATAAACATTGAGCAGTATTCAGAATTTTTCACTATTGT
4996496 ATTGATCGTTGGATAGTATATTTGGTTTCTTATGTGTGAAGCCATAGTTTTTATAAGAGTATTAA
66 ATTGATCGTTGGATAGTATATTTGGTTTCTTATGTGTGAAGCCATAGTTTTTATAAGAGTATTAA
4996561 CAATGTTAAATGGTCTTAAATTCAGGCCATTGGAAAATCAATTAAGGTTGAGATTTAAGTGAATG
131 CAATGTTAAATGGTCTTAAATTCAGGCCATTGGAAAATCAATTAAGGTTGAGATTTAAGTGAATG
4996626 GCTTTTGTTTGATGTCGACCTTTTGCCTTTGAACTTATCCATGTGCTTCTCATTTCCCAATTGCC
196 GCTTTTGTTTGATGTCGACCTTTTGCCTTTGAACTTATCCATGTGCTTCTCATTTCCCAATTGCC
*
4996691 TAGATGAAAACTTACATCCCTTGATAGTTTTGGTTTTGGTAATTCTTCTCTTCTTTTTTGCTGAA
261 TAGATGAAAACTTACATCCCTTGATAGTTTTGGTTTTGATAATTCTTCTCTTCTTTTTTGCTGAA
4996756 ATGTACAAATATATATACAATACAAGATGTAGCAAGAGACCAAAAAGAAAGAGATAA
326 ATGTACAAATATATATACAATACAAGATGTAGCAAGAGACCAAAAAGAAAGAGATAA
*
4996813 CAGTATTTCTAACCTTATTTTTTATGTATAAACATTGAGCAGTATTCATAATTTTTCACTATTGT
1 CAGTATTTCTAACCTTATTTTTTATGTATAAACATTGAGCAGTATTCAGAATTTTTCACTATTGT
4996878 ATTGATCGTTGGATAGTATATTTGGTTTCTTATGTGTGAAGCCATAGTTTTTATAAGAGTATTAA
66 ATTGATCGTTGGATAGTATATTTGGTTTCTTATGTGTGAAGCCATAGTTTTTATAAGAGTATTAA
4996943 CAATGTTAAATGGTCTTAAATTCAGGCCATTGGAAAATCAATTAAGGTTGAGATTTAAGTGAATG
131 CAATGTTAAATGGTCTTAAATTCAGGCCATTGGAAAATCAATTAAGGTTGAGATTTAAGTGAATG
4997008 GCTTTTGTTTGATGTCGACCTTTTGCCTTTGAACTTATCCATGTGCTTCTCATTTCCCAATTGCC
196 GCTTTTGTTTGATGTCGACCTTTTGCCTTTGAACTTATCCATGTGCTTCTCATTTCCCAATTGCC
*
4997073 TAGATGAAAACTTACATCCCTTGATAGTTTTGGTTTTGATAATTCTTCTCTTCTTTTTTGTTGAA
261 TAGATGAAAACTTACATCCCTTGATAGTTTTGGTTTTGATAATTCTTCTCTTCTTTTTTGCTGAA
4997138 ATGTACAAATATATATACAATACAAGATGTAGCAAGAGACCAAAAAGAAAGAGATAA
326 ATGTACAAATATATATACAATACAAGATGTAGCAAGAGACCAAAAAGAAAGAGATAA
4997195 GGTGCTTCTT
Statistics
Matches: 378, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
382 378 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (382 bp):
CAGTATTTCTAACCTTATTTTTTATGTATAAACATTGAGCAGTATTCAGAATTTTTCACTATTGT
ATTGATCGTTGGATAGTATATTTGGTTTCTTATGTGTGAAGCCATAGTTTTTATAAGAGTATTAA
CAATGTTAAATGGTCTTAAATTCAGGCCATTGGAAAATCAATTAAGGTTGAGATTTAAGTGAATG
GCTTTTGTTTGATGTCGACCTTTTGCCTTTGAACTTATCCATGTGCTTCTCATTTCCCAATTGCC
TAGATGAAAACTTACATCCCTTGATAGTTTTGGTTTTGATAATTCTTCTCTTCTTTTTTGCTGAA
ATGTACAAATATATATACAATACAAGATGTAGCAAGAGACCAAAAAGAAAGAGATAA
Found at i:5009746 original size:42 final size:42
Alignment explanation
Indices: 5009687--5009771 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
5009677 ATCCATAAAA
5009687 TACATATGAAAGAATTTGAATCCATCCTAAAAGAAAGACATG
1 TACATATGAAAGAATTTGAATCCATCCTAAAAGAAAGACATG
*
5009729 TACATATGAAAGAATTTGAATCCATCCTAAAAGAAGGACATG
1 TACATATGAAAGAATTTGAATCCATCCTAAAAGAAAGACATG
5009771 T
1 T
5009772 TTACTGCATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.25
Consensus pattern (42 bp):
TACATATGAAAGAATTTGAATCCATCCTAAAAGAAAGACATG
Found at i:5014537 original size:19 final size:20
Alignment explanation
Indices: 5014500--5014537 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5014490 GGAGGGGAAG
*
5014500 GAGGTGGGAGGATAAGGTTT
1 GAGGTGGGAGGAGAAGGTTT
*
5014520 GAGGT-GGAGGAGACGGTT
1 GAGGTGGGAGGAGAAGGTT
5014538 GACGTTGGCG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.24, C:0.03, G:0.53, T:0.21
Consensus pattern (20 bp):
GAGGTGGGAGGAGAAGGTTT
Found at i:5028914 original size:60 final size:58
Alignment explanation
Indices: 5028806--5028917 Score: 136
Period size: 60 Copynumber: 1.9 Consensus size: 58
5028796 CAAAAAGAAA
* *
5028806 AACGTTTAAGCATTTTGAGTATTTTAGAGTAGTTTTTAATACACGAAGAAAATCTATG
1 AACGTTTAAGCATTTTAAGCATTTTAGAGTAGTTTTTAATACACGAAGAAAATCTATG
* * * *
5028864 AACGTTTTAAGCATTTTTAAGCATTTTGGAGT-GATTTTTTATATATGAAGAAAA
1 AACG-TTTAAGCA-TTTTAAGCATTTTAGAGTAG-TTTTTAATACACGAAGAAAA
5028918 ACTTTTGAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.09
59 9 0.20
60 32 0.71
ACGTcount: A:0.36, C:0.07, G:0.17, T:0.40
Consensus pattern (58 bp):
AACGTTTAAGCATTTTAAGCATTTTAGAGTAGTTTTTAATACACGAAGAAAATCTATG
Found at i:5029122 original size:21 final size:21
Alignment explanation
Indices: 5029066--5029125 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
5029056 ATGACTAGTT
5029066 TTTAGGCATTACGTGACTGAC
1 TTTAGGCATTACGTGACTGAC
*
5029087 TTT-GGACATTACGTGATTGAC
1 TTTAGG-CATTACGTGACTGAC
* *
5029108 TTTAGGTATTGCGTGACT
1 TTTAGGCATTACGTGACT
5029126 AATTTTTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
20 2 0.06
21 29 0.88
22 2 0.06
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (21 bp):
TTTAGGCATTACGTGACTGAC
Found at i:5029166 original size:23 final size:24
Alignment explanation
Indices: 5029135--5029199 Score: 80
Period size: 23 Copynumber: 2.8 Consensus size: 24
5029125 TAATTTTTGA
*
5029135 TAAGGCATTACGTGACTTA-TTAG
1 TAAGACATTACGTGACTTAGTTAG
*
5029158 TAAGACATTACGTGAC-TAGTTGG
1 TAAGACATTACGTGACTTAGTTAG
**
5029181 TAAGACATTGTGTGACTTA
1 TAAGACATTACGTGACTTA
5029200 AGCATTACTT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
22 2 0.06
23 32 0.89
24 2 0.06
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.34
Consensus pattern (24 bp):
TAAGACATTACGTGACTTAGTTAG
Found at i:5029278 original size:21 final size:21
Alignment explanation
Indices: 5029233--5029278 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
5029223 GCAATGCTTA
* *
5029233 AAAACCAATCACGCAATGTCT
1 AAAACCAATCACGCAATGCCC
* *
5029254 AAAACCAATCATGTAATGCCC
1 AAAACCAATCACGCAATGCCC
5029275 AAAA
1 AAAA
5029279 ATTAATCACG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.26, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAACCAATCACGCAATGCCC
Found at i:5047425 original size:29 final size:29
Alignment explanation
Indices: 5047389--5047455 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
5047379 TATAAAAAAA
* * *
5047389 AATA-TTTTTGAATATGTCGTATAACAAC
1 AATATTTTTTCAACATGACGTATAACAAC
* *
5047417 AATATTTTTTCAACATGACGTGTAACAAT
1 AATATTTTTTCAACATGACGTATAACAAC
*
5047446 AATTTTTTTT
1 AATATTTTTT
5047456 TTTCAATATG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 4 0.12
29 28 0.88
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (29 bp):
AATATTTTTTCAACATGACGTATAACAAC
Found at i:5047645 original size:114 final size:114
Alignment explanation
Indices: 5047518--5047723 Score: 297
Period size: 114 Copynumber: 1.8 Consensus size: 114
5047508 ATTTTTTTCA
* * *
5047518 ACATGGCGTGTAACAACCTAACCATGACTTATCACAGGTTTTTGTATAT-GACGTGTAACAAGCT
1 ACATGGCATGTAACAACCTAACCATGACTTATCACAGATTTTTGTACATAG-CGTGTAACAAGCT
*
5047582 AACTATAGCTTGTCACAGGTTTTTGTACTTAACTTGTTACATATTTTTAT
65 AACCATAGCTTGTCACAGGTTTTTGTACTTAACTTGTTACATATTTTTAT
* * * * * *
5047632 ACATGGCATGTAACAAGCTAATCATGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGCTA
1 ACATGGCATGTAACAACCTAACCATGACTTATCACAGATTTTTGTACATAGCGTGTAACAAGCTA
*
5047697 ACCATGGCTTGTCACAGGTTTTTGTAC
66 ACCATAGCTTGTCACAGGTTTTTGTAC
5047724 ATGGCGTGTA
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
114 79 0.99
115 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (114 bp):
ACATGGCATGTAACAACCTAACCATGACTTATCACAGATTTTTGTACATAGCGTGTAACAAGCTA
ACCATAGCTTGTCACAGGTTTTTGTACTTAACTTGTTACATATTTTTAT
Found at i:5047680 original size:45 final size:45
Alignment explanation
Indices: 5047614--5047771 Score: 208
Period size: 45 Copynumber: 3.5 Consensus size: 45
5047604 TTGTACTTAA
* * * *
5047614 CTTGTTACATATTTTTATACATGGCATGTAACAAGCTAATCATGG
1 CTTGTCACAGATTTTTGTACATGGCGTGTAACAAGCTAATCATGG
* * * *
5047659 CTTGTCACATATTTTTGTACATAGCGTGTAACACGCTAACCATGG
1 CTTGTCACAGATTTTTGTACATGGCGTGTAACAAGCTAATCATGG
* **
5047704 CTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAATCATAA
1 CTTGTCACAGATTTTTGTACATGGCGTGTAACAAGCTAATCATGG
*
5047749 CTTGTCACAGGTTTTTGTACATG
1 CTTGTCACAGATTTTTGTACATG
5047772 ACTTGTCACA
Statistics
Matches: 100, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (45 bp):
CTTGTCACAGATTTTTGTACATGGCGTGTAACAAGCTAATCATGG
Found at i:5047777 original size:114 final size:114
Alignment explanation
Indices: 5047654--5047887 Score: 326
Period size: 114 Copynumber: 2.1 Consensus size: 114
5047644 ACAAGCTAAT
* * * * *
5047654 CATGGCTTGTCACATATTTTTGTACAT-AGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTT
1 CATGACTTGTCACATATTTTTATACATGA-CATGTAACAAGCTAACCATGGCTTGTCACAGATTT
* *
5047718 TTGTACATGGCGTGTAACAAGCTAATCATAACTTGTCACAGGTTTTTGTA
65 TTGTACATAGCGTGTAACAAGCTAATCATAACTTGTCACAAGTTTTTGTA
* * *
5047768 CATGACTTGTCACATATTTTTATACATGACATGTAACAAGCTAACTATGGTTTGTCACATATTTT
1 CATGACTTGTCACATATTTTTATACATGACATGTAACAAGCTAACCATGGCTTGTCACAGATTTT
* * **
5047833 TGTACATAGCGTGTAACACGTTAATCATGGCTTGTCACAAGTTTTTGTA
66 TGTACATAGCGTGTAACAAGCTAATCATAACTTGTCACAAGTTTTTGTA
5047882 CATGAC
1 CATGAC
5047888 GTGTAACAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
114 104 0.99
115 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (114 bp):
CATGACTTGTCACATATTTTTATACATGACATGTAACAAGCTAACCATGGCTTGTCACAGATTTT
TGTACATAGCGTGTAACAAGCTAATCATAACTTGTCACAAGTTTTTGTA
Found at i:5047780 original size:24 final size:24
Alignment explanation
Indices: 5047748--5047797 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
5047738 GCTAATCATA
* *
5047748 ACTTGTCACAGGTTTTTGTACATG
1 ACTTGTCACAGATTTTTATACATG
*
5047772 ACTTGTCACATATTTTTATACATG
1 ACTTGTCACAGATTTTTATACATG
5047796 AC
1 AC
5047798 ATGTAACAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.42
Consensus pattern (24 bp):
ACTTGTCACAGATTTTTATACATG
Found at i:5047801 original size:159 final size:158
Alignment explanation
Indices: 5047518--5048220 Score: 752
Period size: 159 Copynumber: 4.3 Consensus size: 158
5047508 ATTTTTTTCA
* * *
5047518 ACATGGCGTGTAACAAC-CTAACCATGACTTATCACAGGTTTTTGTATATGACGTGTAACAAGCT
1 ACATAGCGTGTAAC-ACGCTAACCATGACTTGTCACAGGTTTTTGTACATGACGTGTAACAAGCT
* * * * *
5047582 AACTATAGCTTGTCACAGGTTTTTGTACTTAACTTGTTACATATTTTTATACATGGCATGTAACA
65 AAC-ATAACTTGTCACAGGTTTTTGTACATGACTTGTCACATATTTTTATACATGACATGTAACA
5047647 AGCTAA-TCATGGCTTGTCACATATTTTTGT
129 AGCTAACT-ATGGCTTGTCACATATTTTTGT
* *
5047677 ACATAGCGTGTAACACGCTAACCATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTA
1 ACATAGCGTGTAACACGCTAACCATGACTTGTCACAGGTTTTTGTACATGACGTGTAACAAGCTA
5047742 ATCATAACTTGTCACAGGTTTTTGTACATGACTTGTCACATATTTTTATACATGACATGTAACAA
66 A-CATAACTTGTCACAGGTTTTTGTACATGACTTGTCACATATTTTTATACATGACATGTAACAA
*
5047807 GCTAACTATGGTTTGTCACATATTTTTGT
130 GCTAACTATGGCTTGTCACATATTTTTGT
* * * * *
5047836 ACATAGCGTGTAACACGTTAATCATGGCTTGTCACAAGTTTTTGTACATGACGTGTAACAAACTA
1 ACATAGCGTGTAACACGCTAACCATGACTTGTCACAGGTTTTTGTACATGACGTGTAACAAGCTA
* * * *
5047901 AC-TACAGCTTGTCACAGGTTTTTGTACATGACTTGTCATATATTTTTGTATATGGCATGTAACA
66 ACATA-A-CTTGTCACAGGTTTTTGTACATGACTTGTCACATATTTTTATACATGACATGTAACA
*
5047965 AGCTAACTATGGCTTGTCACATATTTTTAT
129 AGCTAACTATGGCTTGTCACATATTTTTGT
* * ** * ** *
5047995 ATAT-GACATGTAACAAACT-ACCATAACTTGTCACATATTTTTGTACATAACGTGTAACACA-C
1 ACATAG-CGTGTAACACGCTAACCATGACTTGTCACAGGTTTTTGTACATGACGTGTAACA-AGC
* * * * *
5048057 TAACCATGACTTGTCATAGATTTTTGTACATGGCGTGTAACAAGCTAACTATAGCTTGTCACATA
64 TAA-CATAACTTGTCACAGGTTTTTGTACATGAC-T-T-----G-TCAC-ATA---T-T----T-
*
5048122 TTTTTATACATGACATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGT
110 ---TTATACATGACATGTAACAAGCTAACTATGGCTTGTCACATATTTTTGT
* * *
5048174 ACATAGCGTGTAACACGTTAATCATAACTTGTCACAGGTTTTTGTAC
1 ACATAGCGTGTAACACGCTAACCATGACTTGTCACAGGTTTTTGTAC
5048221 GTGGCATGTC
Statistics
Matches: 460, Mismatches: 52, Indels: 43
0.83 0.09 0.08
Matches are distributed among these distances:
157 2 0.00
158 65 0.14
159 299 0.65
160 4 0.01
165 1 0.00
166 2 0.00
167 3 0.01
170 1 0.00
171 1 0.00
175 1 0.00
179 56 0.12
180 25 0.05
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (158 bp):
ACATAGCGTGTAACACGCTAACCATGACTTGTCACAGGTTTTTGTACATGACGTGTAACAAGCTA
ACATAACTTGTCACAGGTTTTTGTACATGACTTGTCACATATTTTTATACATGACATGTAACAAG
CTAACTATGGCTTGTCACATATTTTTGT
Found at i:5047823 original size:69 final size:69
Alignment explanation
Indices: 5047699--5047839 Score: 167
Period size: 69 Copynumber: 2.0 Consensus size: 69
5047689 ACACGCTAAC
* * * * * *
5047699 CATGGCTTGTCACAGGTTTTTGTACATGGCGTGTAACAAGCTAATCATAACTTGTCACAGGTTTT
1 CATGACTTGTCACAGATTTTTATACATGACATGTAACAAGCTAATCATAACTTGTCACAGATTTT
5047764 TGTA
66 TGTA
* *** *
5047768 CATGACTTGTCACATATTTTTATACATGACATGTAACAAGCTAA-CTATGGTTTGTCACATATTT
1 CATGACTTGTCACAGATTTTTATACATGACATGTAACAAGCTAATC-ATAACTTGTCACAGATTT
5047832 TTGTA
65 TTGTA
5047837 CAT
1 CAT
5047840 AGCGTGTAAC
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
68 1 0.02
69 59 0.98
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (69 bp):
CATGACTTGTCACAGATTTTTATACATGACATGTAACAAGCTAATCATAACTTGTCACAGATTTT
TGTA
Found at i:5047839 original size:45 final size:45
Alignment explanation
Indices: 5047773--5047932 Score: 182
Period size: 45 Copynumber: 3.6 Consensus size: 45
5047763 TTGTACATGA
* *
5047773 CTTGTCACATATTTTTATACATGACATGTAACAAGCTAACTATGG
1 CTTGTCACATATTTTTGTACATGACGTGTAACAAGCTAACTATGG
* * *
5047818 TTTGTCACATATTTTTGTACAT-AGCGTGTAACACGTTAA-TCATGG
1 CTTGTCACATATTTTTGTACATGA-CGTGTAACAAGCTAACT-ATGG
* **
5047863 CTTGTCACA-AGTTTTTGTACATGACGTGTAACAAACTAACTACAG
1 CTTGTCACATA-TTTTTGTACATGACGTGTAACAAGCTAACTATGG
**
5047908 CTTGTCACAGGTTTTTGTACATGAC
1 CTTGTCACATATTTTTGTACATGAC
5047933 TTGTCATATA
Statistics
Matches: 97, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
44 3 0.03
45 92 0.95
46 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (45 bp):
CTTGTCACATATTTTTGTACATGACGTGTAACAAGCTAACTATGG
Found at i:5047937 original size:114 final size:113
Alignment explanation
Indices: 5047819--5048042 Score: 283
Period size: 114 Copynumber: 2.0 Consensus size: 113
5047809 TAACTATGGT
* * * *
5047819 TTGTCACATATTTTTGTACATAGCGTGTAACACGTTAA-TCATGGCTTGTCACA-AGTTTTTGTA
1 TTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACT-ATGGCTTGTCACATA-TTTTTATA
* *
5047882 CATGACGTGTAACAAACTAAC-TACAGCTTGTCACAGGTTTTTGTACATGAC
64 CATGACATGTAACAAACTAACATA-A-CTTGTCACAGATTTTTGTACATGAC
* * * *
5047933 TTGTCATATATTTTTGTATATGGCATGTAACAAGCTAACTATGGCTTGTCACATATTTTTATATA
1 TTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACTATGGCTTGTCACATATTTTTATACA
* *
5047998 TGACATGTAACAAACTACCATAACTTGTCACATATTTTTGTACAT
66 TGACATGTAACAAACTAACATAACTTGTCACAGATTTTTGTACAT
5048043 AACGTGTAAC
Statistics
Matches: 95, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
113 20 0.21
114 71 0.75
115 4 0.04
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (113 bp):
TTGTCACATATTTTTGTACATAGCATGTAACAAGCTAACTATGGCTTGTCACATATTTTTATACA
TGACATGTAACAAACTAACATAACTTGTCACAGATTTTTGTACATGAC
Found at i:5047998 original size:45 final size:45
Alignment explanation
Indices: 5047927--5048177 Score: 299
Period size: 45 Copynumber: 5.6 Consensus size: 45
5047917 GGTTTTTGTA
* * * *
5047927 CATGACTTGTCATATATTTTTGTATATGGCATGTAACAAGCTAAC
1 CATGGCTTGTCACATATTTTTGTACATGACATGTAACAAGCTAAC
* * * *
5047972 TATGGCTTGTCACATATTTTTATATATGACATGTAACAAACT-AC
1 CATGGCTTGTCACATATTTTTGTACATGACATGTAACAAGCTAAC
** * *
5048016 CATAACTTGTCACATATTTTTGTACATAACGTGTAACACA-CTAAC
1 CATGGCTTGTCACATATTTTTGTACATGACATGTAACA-AGCTAAC
* * * * *
5048061 CATGACTTGTCATAGATTTTTGTACATGGCGTGTAACAAGCTAAC
1 CATGGCTTGTCACATATTTTTGTACATGACATGTAACAAGCTAAC
* * *
5048106 TATAGCTTGTCACATATTTTTATACATGACATGTAACAAGCTAAC
1 CATGGCTTGTCACATATTTTTGTACATGACATGTAACAAGCTAAC
5048151 CATGGCTTGTCACATATTTTTGTACAT
1 CATGGCTTGTCACATATTTTTGTACAT
5048178 AGCGTGTAAC
Statistics
Matches: 174, Mismatches: 29, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
44 36 0.21
45 138 0.79
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.37
Consensus pattern (45 bp):
CATGGCTTGTCACATATTTTTGTACATGACATGTAACAAGCTAAC
Found at i:5048142 original size:90 final size:89
Alignment explanation
Indices: 5047931--5048229 Score: 330
Period size: 90 Copynumber: 3.3 Consensus size: 89
5047921 TTTGTACATG
* * * * *
5047931 ACTTGTCATATATTTTTGTATATGGCATGTAACAAGCTAACTATGGCTTGTCACATATTTTTATA
1 ACTTGTCACATATTTTTGTACATGACATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
* * *
5047996 TATGACATGTAACAAACTACCATA
66 CATGGCGTGTAACAAACTACCATA
* * * * *
5048020 ACTTGTCACATATTTTTGTACATAACGTGTAACACA-CTAACCATGACTTGTCATAGATTTTTGT
1 ACTTGTCACATATTTTTGTACATGACATGTAACA-AGCTAACCATGGCTTGTCACATATTTTTGT
* *
5048084 ACATGGCGTGTAACAAGCTAACTATA
65 ACATGGCGTGTAACAAACT-ACCATA
* *
5048110 GCTTGTCACATATTTTTATACATGACATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
1 ACTTGTCACATATTTTTGTACATGACATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
* *** *
5048175 CATAGCGTGTAACACGTTAATCATA
66 CATGGCGTGTAACAAACT-ACCATA
** * *
5048200 ACTTGTCACAGGTTTTTGTACGTGGCATGT
1 ACTTGTCACATATTTTTGTACATGACATGT
5048230 CACATATTTT
Statistics
Matches: 174, Mismatches: 33, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
89 68 0.39
90 106 0.61
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (89 bp):
ACTTGTCACATATTTTTGTACATGACATGTAACAAGCTAACCATGGCTTGTCACATATTTTTGTA
CATGGCGTGTAACAAACTACCATA
Found at i:5048186 original size:45 final size:44
Alignment explanation
Indices: 5047927--5048229 Score: 288
Period size: 45 Copynumber: 6.8 Consensus size: 44
5047917 GGTTTTTGTA
* *
5047927 CATGACTTGTCATATATTTTTGTATATGGCATGTAACAAGCTAAC
1 CATGACTTGTCACATATTTTTGTACAT-GCATGTAACAAGCTAAC
* * * * *
5047972 TATGGCTTGTCACATATTTTTATATATGACATGTAACAAACT-AC
1 CATGACTTGTCACATATTTTTGTACATG-CATGTAACAAGCTAAC
* * *
5048016 CATAACTTGTCACATATTTTTGTACATAACGTGTAACACA-CTAAC
1 CATGACTTGTCACATATTTTTGTACAT-GCATGTAACA-AGCTAAC
* * *
5048061 CATGACTTGTCATAGATTTTTGTACATGGCGTGTAACAAGCTAAC
1 CATGACTTGTCACATATTTTTGTACAT-GCATGTAACAAGCTAAC
* *
5048106 TAT-AGCTTGTCACATATTTTTATACATGACATGTAACAAGCTAAC
1 CATGA-CTTGTCACATATTTTTGTACATG-CATGTAACAAGCTAAC
* * * * *
5048151 CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGTTAAT
1 CATGACTTGTCACATATTTTTGTACAT-GCATGTAACAAGCTAAC
* ** *
5048196 CATAACTTGTCACAGGTTTTTGTACGTGGCATGT
1 CATGACTTGTCACATATTTTTGTACAT-GCATGT
5048230 CACATATTTT
Statistics
Matches: 213, Mismatches: 36, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
44 38 0.18
45 174 0.82
46 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (44 bp):
CATGACTTGTCACATATTTTTGTACATGCATGTAACAAGCTAAC
Found at i:5048459 original size:24 final size:24
Alignment explanation
Indices: 5048410--5048460 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
5048400 AACCATAATT
* *
5048410 TGTCACAAGTTTTTGTACACAGCG
1 TGTCACAAGTTTTTATACACAACG
*
5048434 TGTCACATA-TTTTTATACATAACG
1 TGTCACA-AGTTTTTATACACAACG
5048458 TGT
1 TGT
5048461 AACACGCTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 22 0.96
25 1 0.04
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (24 bp):
TGTCACAAGTTTTTATACACAACG
Found at i:5048505 original size:69 final size:69
Alignment explanation
Indices: 5048151--5048510 Score: 387
Period size: 69 Copynumber: 5.2 Consensus size: 69
5048141 ACAAGCTAAC
* * * * * *
5048151 CATGGCTTGTCACATATTTTTGTACATAGCGTGTAACACGTTAATCATAACTTGTCACAGGTTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
5048216 TGTA
66 TGTA
* * * * * *
5048220 CGTGGCATGTCACATATTTTTATATATAGCATGTAACACGTTAACTATGACTTGTCACAAGTTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
5048285 TGTA
66 TGTA
* ** * ***
5048289 TATGGTATGTCACATATTTTTATACATAGCGTGTAACACGCTAATCATGACTTGTCATGGGTTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
*
5048354 TATA
66 TGTA
* * ** * * * * *
5048358 AATGGTGTGTCACAGGTTTTTATATATGGTGTGTAACACGCTAACCATAATTTGTCACAAGTTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
5048423 TGTA
66 TGTA
** * * * *
5048427 CACAGCGTGTCACATATTTTTATACATAACGTGTAACACGCTAACCATGATTTATCACAAATTTT
1 CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
5048492 TGTA
66 TGTA
* *
5048496 CATGACGTGTAACAT
1 CATGGCGTGTCACAT
5048511 CATAGTGTGT
Statistics
Matches: 239, Mismatches: 52, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
69 239 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.38
Consensus pattern (69 bp):
CATGGCGTGTCACATATTTTTATACATAGCGTGTAACACGCTAACCATGACTTGTCACAAGTTTT
TGTA
Found at i:5061964 original size:13 final size:13
Alignment explanation
Indices: 5061946--5061970 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5061936 ATAATAATAT
5061946 TATATATATTATA
1 TATATATATTATA
5061959 TATATATATTAT
1 TATATATATTAT
5061971 TTGTGGCAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATATATATTATA
Found at i:5064919 original size:2 final size:2
Alignment explanation
Indices: 5064912--5064948 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5064902 ATGTATCATC
*
5064912 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT TT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
5064949 GTGTGATTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:5067234 original size:3 final size:3
Alignment explanation
Indices: 5067226--5067282 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
5067216 TTGAATAAAT
* * * * * *
5067226 GCA GCA GCA ACA GCA TCA ACA GCA ACA ACA ACA GCA GCA GCA GCA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
*
5067274 GCA CCA GCA
1 GCA GCA GCA
5067283 TCATAAACTG
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.42, C:0.35, G:0.21, T:0.02
Consensus pattern (3 bp):
GCA
Found at i:5067676 original size:17 final size:17
Alignment explanation
Indices: 5067654--5067686 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5067644 AAAGAAATGC
5067654 ACGTAGCTATCATCGCT
1 ACGTAGCTATCATCGCT
5067671 ACGTAGCTATCATCGC
1 ACGTAGCTATCATCGC
5067687 CACAAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.27
Consensus pattern (17 bp):
ACGTAGCTATCATCGCT
Found at i:5068788 original size:22 final size:20
Alignment explanation
Indices: 5068749--5068793 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 20
5068739 TGTTGGAAAG
5068749 AAAGAGAAAGAACAAAAGGAA
1 AAAGAGAAAGAACAAAA-GAA
5068770 AAAGAAGAAAGAA-AGAAAGAA
1 AAAG-AGAAAGAACA-AAAGAA
5068791 AAA
1 AAA
5068794 CAAAGAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AAAGAGAAAGAACAAAAGAA
Found at i:5068798 original size:14 final size:15
Alignment explanation
Indices: 5068745--5068807 Score: 56
Period size: 15 Copynumber: 3.9 Consensus size: 15
5068735 TCCATGTTGG
5068745 AAAGAAAGAGAAAGAAC
1 AAAGAAA-AGAAA-AAC
*
5068762 AAAAGGAAAAAGAAGAAAG
1 -AAA-G-AAAAGAA-AAAC
5068781 AAAG-AAAGAAAAAC
1 AAAGAAAAGAAAAAC
5068795 AAAGAAAAGAAAA
1 AAAGAAAAGAAAA
5068808 CCAGGAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
14 7 0.18
15 14 0.36
17 1 0.03
18 6 0.15
19 7 0.18
20 4 0.10
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAC
Found at i:5068799 original size:22 final size:21
Alignment explanation
Indices: 5068743--5068816 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
5068733 AGTCCATGTT
*
5068743 GGAAAGAAAGAGAAAGAACAAAA
1 GGAAA-AAAAAGAAAGAA-AAAA
*
5068766 GGAAAAAGAAGAAAGAAAGAAA
1 GGAAAAAAAAGAAAGAAA-AAA
*
5068788 -GAAAAACAAAGAAAAGAAAACCA
1 GGAAAAA-AAAG-AAAGAAAA-AA
5068811 GGAAAA
1 GGAAAA
5068817 GGCTGCTCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
21 7 0.17
22 17 0.40
23 13 0.31
24 5 0.12
ACGTcount: A:0.72, C:0.05, G:0.23, T:0.00
Consensus pattern (21 bp):
GGAAAAAAAAGAAAGAAAAAA
Found at i:5079918 original size:15 final size:17
Alignment explanation
Indices: 5079897--5079939 Score: 63
Period size: 15 Copynumber: 2.6 Consensus size: 17
5079887 AATATTGGAA
5079897 ATGGTGGAGGCG-TTGG
1 ATGGTGGAGGCGTTTGG
5079913 -TGGTGGAGGCGTTTGG
1 ATGGTGGAGGCGTTTGG
5079929 ATTGGTGGAGG
1 A-TGGTGGAGG
5079940 AATCAACAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 11 0.46
16 4 0.17
18 9 0.38
ACGTcount: A:0.12, C:0.05, G:0.56, T:0.28
Consensus pattern (17 bp):
ATGGTGGAGGCGTTTGG
Found at i:5087701 original size:14 final size:15
Alignment explanation
Indices: 5087668--5087701 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5087658 TAGGAAACAT
*
5087668 AAAAAAATAATCAGC
1 AAAAAAATAATAAGC
*
5087683 AAAAAAATATTAAGC
1 AAAAAAATAATAAGC
5087698 AAAA
1 AAAA
5087702 GCAACCATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.71, C:0.09, G:0.06, T:0.15
Consensus pattern (15 bp):
AAAAAAATAATAAGC
Found at i:5098109 original size:3 final size:3
Alignment explanation
Indices: 5098095--5098132 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5098085 ATGTACTGTT
*
5098095 TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5098133 TAATTATCTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5112702 original size:22 final size:22
Alignment explanation
Indices: 5112677--5112728 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
5112667 TAATGAAATC
5112677 ATTTGATACAATT-AATAT-TTTT
1 ATTT-ATA-AATTGAATATATTTT
5112699 ATTTATAAATTGAATATATTTT
1 ATTTATAAATTGAATATATTTT
*
5112721 ACTTATAA
1 ATTTATAA
5112729 TTATAACACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 4 0.15
21 8 0.30
22 15 0.56
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (22 bp):
ATTTATAAATTGAATATATTTT
Found at i:5113311 original size:18 final size:17
Alignment explanation
Indices: 5113285--5113318 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5113275 ATTCAAAGGA
5113285 TATTATTTAAAAGTTTTT
1 TATTATTTAAAA-TTTTT
*
5113303 TATTTTTTAAAATTTT
1 TATTATTTAAAATTTT
5113319 AATGCCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TATTATTTAAAATTTTT
Found at i:5125295 original size:32 final size:32
Alignment explanation
Indices: 5125249--5125311 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
5125239 AGTAGAAAGT
5125249 CATGTAATTATGTATAATTGCATTTGTGTAAG
1 CATGTAATTATGTATAATTGCATTTGTGTAAG
*
5125281 CATGTAATTGTGTATAATTGCATTTGTGTAA
1 CATGTAATTATGTATAATTGCATTTGTGTAA
5125312 TCTTTGCGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.44
Consensus pattern (32 bp):
CATGTAATTATGTATAATTGCATTTGTGTAAG
Found at i:5125307 original size:16 final size:16
Alignment explanation
Indices: 5125259--5125310 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
5125249 CATGTAATTA
5125259 TGTATAATTGCATTTG
1 TGTATAATTGCATTTG
* *
5125275 TGTA-AGCA-TGTAATTG
1 TGTATA--ATTGCATTTG
5125291 TGTATAATTGCATTTG
1 TGTATAATTGCATTTG
5125307 TGTA
1 TGTA
5125311 ATCTTTGCGG
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 2 0.07
16 24 0.86
17 2 0.07
ACGTcount: A:0.27, C:0.06, G:0.21, T:0.46
Consensus pattern (16 bp):
TGTATAATTGCATTTG
Found at i:5129504 original size:24 final size:25
Alignment explanation
Indices: 5129473--5129520 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5129463 TTGTCCAATT
*
5129473 ATATAACCATAA-A-ATATAGTGAA
1 ATATAACCAAAATATATATAGTGAA
5129496 ATATGAACCAAAATATATATAGTGA
1 ATAT-AACCAAAATATATATAGTGA
5129521 GTTTAATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 7 0.33
25 1 0.05
26 9 0.43
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.27
Consensus pattern (25 bp):
ATATAACCAAAATATATATAGTGAA
Found at i:5133338 original size:6 final size:6
Alignment explanation
Indices: 5133327--5133351 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5133317 TTAAATTATG
5133327 TTAAAT TTAAAT TTAAAT TTAAAT T
1 TTAAAT TTAAAT TTAAAT TTAAAT T
5133352 ATTAATTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:5133377 original size:17 final size:17
Alignment explanation
Indices: 5133355--5133388 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5133345 TTAAATTATT
*
5133355 AATTTGGATATACAAAA
1 AATTTGGAAATACAAAA
*
5133372 AATTTGTAAATACAAAA
1 AATTTGGAAATACAAAA
5133389 TAAAATTATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.09, T:0.29
Consensus pattern (17 bp):
AATTTGGAAATACAAAA
Found at i:5138114 original size:27 final size:27
Alignment explanation
Indices: 5138082--5138134 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5138072 AAATGGTAAA
*
5138082 CAGTCACAAGAAATTGTTGCAAAACAG
1 CAGTCACAAGAAATTGTTACAAAACAG
*
5138109 CAGTCACAAGAGATTGTTACAAAACA
1 CAGTCACAAGAAATTGTTACAAAACA
5138135 AAACTTAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.45, C:0.19, G:0.17, T:0.19
Consensus pattern (27 bp):
CAGTCACAAGAAATTGTTACAAAACAG
Found at i:5155891 original size:2 final size:2
Alignment explanation
Indices: 5155871--5155925 Score: 83
Period size: 2 Copynumber: 27.0 Consensus size: 2
5155861 TCCCTTGTGT
* *
5155871 TA TA TA CA TA CA TA CTA 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 TA TA TA
5155914 TA TA TA TA TA TA
1 TA TA TA TA TA TA
5155926 AATTTTCATC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5163312 original size:2 final size:2
Alignment explanation
Indices: 5163305--5163341 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5163295 TTCGAAAAGA
*
5163305 TC TC TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
5163342 ATTGTTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:5166755 original size:2 final size:2
Alignment explanation
Indices: 5166748--5166776 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5166738 TATAATTATT
5166748 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
5166777 TACTTAATTA
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:5166815 original size:59 final size:56
Alignment explanation
Indices: 5166750--5166866 Score: 191
Period size: 59 Copynumber: 2.0 Consensus size: 56
5166740 TAATTATTTA
5166750 TATATATATATATATATATATATATATTACTTAATT-AGTAGTTTAAACTAAACCTCTC
1 TATATATATATATATATATATATATATTACTTAATTGAGT--TTTAAAC-AAACCTCTC
5166808 NTATATATATATATATATATATATATATTACTTAATTGAGTTTTAAACAAACCTCTC
1 -TATATATATATATATATATATATATATTACTTAATTGAGTTTTAAACAAACCTCTC
5166865 TA
1 TA
5166867 GTATCTTATA
Statistics
Matches: 57, Mismatches: 0, Indels: 5
0.92 0.00 0.08
Matches are distributed among these distances:
56 2 0.04
57 9 0.16
58 7 0.12
59 36 0.63
60 3 0.05
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.44
Consensus pattern (56 bp):
TATATATATATATATATATATATATATTACTTAATTGAGTTTTAAACAAACCTCTC
Found at i:5166816 original size:2 final size:2
Alignment explanation
Indices: 5166809--5166835 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5166799 AAACCTCTCN
5166809 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 T
5166836 TACTTAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5175485 original size:3 final size:3
Alignment explanation
Indices: 5175477--5175510 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
5175467 TATGTAGCAT
5175477 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5175511 AAGTTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5194652 original size:18 final size:19
Alignment explanation
Indices: 5194631--5194673 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
5194621 AATATTGAAG
*
5194631 TTCTTATCA-AGGTAAATT
1 TTCTTATAATAGGTAAATT
*
5194649 TTCTT-TAATAGGTAATTT
1 TTCTTATAATAGGTAAATT
5194667 TTCTTAT
1 TTCTTAT
5194674 TAGATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.86
19 1 0.05
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.53
Consensus pattern (19 bp):
TTCTTATAATAGGTAAATT
Found at i:5205290 original size:45 final size:47
Alignment explanation
Indices: 5205188--5205293 Score: 128
Period size: 46 Copynumber: 2.3 Consensus size: 47
5205178 ATATACAACC
* * * * **
5205188 GATGTGAGATTCAT-ACCTCTTCTTTGGGACTATGACATCCTCCCTT
1 GATGTGAGATTAATGACCTCTTCATTGAGACCATGACATCCTCCCAA
*
5205234 GATGTGAGATTAATGA-CTTTTCATTGAGACCATGACATCCT-CCAA
1 GATGTGAGATTAATGACCTCTTCATTGAGACCATGACATCCTCCCAA
5205279 GATGTGAGATTAATG
1 GATGTGAGATTAATG
5205294 GCTCTCTACT
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 17 0.33
46 34 0.65
47 1 0.02
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (47 bp):
GATGTGAGATTAATGACCTCTTCATTGAGACCATGACATCCTCCCAA
Found at i:5209527 original size:95 final size:96
Alignment explanation
Indices: 5209363--5209551 Score: 256
Period size: 95 Copynumber: 2.0 Consensus size: 96
5209353 CAAATATAAA
* ** * * *
5209363 AGGGGAATTACCTTGTCAAAGGGGGTGGAAGGTTATACAATTGACGACGGCCATAAATCTTCAAC
1 AGGGGAATCACCCGGTCAAAGGGGGTGGAAGATTATACAATCGACGACGACCATAAATCTTCAAC
*
5209428 AACAAAA-AGGGATTAGTGGGACTGGAGTAAT
66 AACAAAATA-GGATTAGTGGGACTCGAGTAAT
* * *
5209459 AGGGGAATCACCCGGTCAAAGGGGGTGGAA-ATTATACAGTCGTCGACGACCATAAATCTTCAGC
1 AGGGGAATCACCCGGTCAAAGGGGGTGGAAGATTATACAATCGACGACGACCATAAATCTTCAAC
*
5209523 AACAAAATAGGATTAGTGGGGCTCGAGTA
66 AACAAAATAGGATTAGTGGGACTCGAGTA
5209552 GTGATTGTTA
Statistics
Matches: 81, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
95 53 0.65
96 28 0.35
ACGTcount: A:0.34, C:0.16, G:0.29, T:0.21
Consensus pattern (96 bp):
AGGGGAATCACCCGGTCAAAGGGGGTGGAAGATTATACAATCGACGACGACCATAAATCTTCAAC
AACAAAATAGGATTAGTGGGACTCGAGTAAT
Found at i:5211702 original size:17 final size:17
Alignment explanation
Indices: 5211680--5211722 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
5211670 AGTCTTAATC
* *
5211680 GAAATTTTTAACCTAAG
1 GAAATTCTTAACCTAAA
5211697 GAAATTCTTAACCTAAA
1 GAAATTCTTAACCTAAA
5211714 GAAATTCTT
1 GAAATTCTT
5211723 TCGAAATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (17 bp):
GAAATTCTTAACCTAAA
Found at i:5211851 original size:18 final size:18
Alignment explanation
Indices: 5211828--5211872 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
5211818 AGGTCTTATT
* * *
5211828 TTTTTATTTTTTATTTTA
1 TTTTTATTTATTAATTGA
5211846 TTTTTATTTATTAATTGA
1 TTTTTATTTATTAATTGA
5211864 TTTTT-TTTA
1 TTTTTATTTA
5211873 AAACCAAACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (18 bp):
TTTTTATTTATTAATTGA
Found at i:5212360 original size:13 final size:13
Alignment explanation
Indices: 5212342--5212379 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
5212332 CCCTGCTGGC
5212342 TTCTTCTTTCTTT
1 TTCTTCTTTCTTT
5212355 TTCTTCTTTC--T
1 TTCTTCTTTCTTT
*
5212366 TTCTCCTTTCTTT
1 TTCTTCTTTCTTT
5212379 T
1 T
5212380 CTCTCTCCCC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTCTTCTTTCTTT
Found at i:5212382 original size:54 final size:54
Alignment explanation
Indices: 5212298--5212438 Score: 196
Period size: 54 Copynumber: 2.6 Consensus size: 54
5212288 CTACTTCTAT
* ** *
5212298 TTTTTTTTC-CTCTTTCTCACTTTCCCTTCTCTCTCCCTGCTGGCTTCTTCTTTC
1 TTTTTCTTCTCTCTTTCTC-CTTTCTTTTCTCTCTCCCCGCTGGCTTCTTCTTTC
*
5212352 TTTTTCTTCTTTCTTTCTCCTTTCTTTTCTCTCTCCCCGCTGGCTTCTTCTTTC
1 TTTTTCTTCTCTCTTTCTCCTTTCTTTTCTCTCTCCCCGCTGGCTTCTTCTTTC
*
5212406 TTTTTCTTCTCTATTTCTCC-TTCTCTTTCTCTC
1 TTTTTCTTCTCTCTTTCTCCTTTCT-TTTCTCTC
5212439 CTTTCTCCCT
Statistics
Matches: 78, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
53 4 0.05
54 66 0.85
55 8 0.10
ACGTcount: A:0.01, C:0.35, G:0.04, T:0.59
Consensus pattern (54 bp):
TTTTTCTTCTCTCTTTCTCCTTTCTTTTCTCTCTCCCCGCTGGCTTCTTCTTTC
Found at i:5212491 original size:16 final size:16
Alignment explanation
Indices: 5212467--5212497 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5212457 CACACCTTTC
5212467 TCCTCTTCTCTCTCCT
1 TCCTCTTCTCTCTCCT
*
5212483 TCCTTTTCTCTCTCC
1 TCCTCTTCTCTCTCC
5212498 CAGCCGATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (16 bp):
TCCTCTTCTCTCTCCT
Found at i:5212963 original size:10 final size:10
Alignment explanation
Indices: 5212923--5212967 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
5212913 CGTACACTTA
5212923 ATTTTTTATT
1 ATTTTTTATT
*
5212933 A-TTATTATT
1 ATTTTTTATT
5212942 -TTATTTTA-T
1 ATT-TTTTATT
5212951 ATTTTTTATT
1 ATTTTTTATT
5212961 ATTTTTT
1 ATTTTTT
5212968 TTGAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
9 14 0.48
10 15 0.52
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (10 bp):
ATTTTTTATT
Found at i:5212980 original size:22 final size:22
Alignment explanation
Indices: 5212934--5212978 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
5212924 TTTTTTATTA
5212934 TTATTATTTTATTTTATATTTT
1 TTATTATTTTATTTTATATTTT
5212956 TTATTATTTT-TTTTGA-ATTTT
1 TTATTATTTTATTTT-ATATTTT
5212977 TT
1 TT
5212979 TAGATGTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (22 bp):
TTATTATTTTATTTTATATTTT
Found at i:5220682 original size:31 final size:32
Alignment explanation
Indices: 5220634--5220695 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
5220624 CGCGACTCCA
*
5220634 TCCTTTTCTCAAAAAGTTACCTTGATGAAGTT
1 TCCTTTTCTCAAAAAGTTAACTTGATGAAGTT
* *
5220666 TCCTTTT-TCGAAAAGTTAACTTGATTAAGT
1 TCCTTTTCTCAAAAAGTTAACTTGATGAAGT
5220696 CTGCAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.74
32 7 0.26
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.42
Consensus pattern (32 bp):
TCCTTTTCTCAAAAAGTTAACTTGATGAAGTT
Found at i:5226508 original size:23 final size:22
Alignment explanation
Indices: 5226486--5226529 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
5226476 TTTTCAAATA
5226486 ATAATT-ATATATAAAATATAAT
1 ATAATTAATATATAAAAT-TAAT
* *
5226508 ATATTTAATGTATAAAATTAAT
1 ATAATTAATATATAAAATTAAT
5226530 TGTTTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
ATAATTAATATATAAAATTAAT
Found at i:5228475 original size:34 final size:34
Alignment explanation
Indices: 5228415--5228485 Score: 81
Period size: 35 Copynumber: 2.1 Consensus size: 34
5228405 GTCTTGCTTT
* * *
5228415 CTTTTTCCGATAGTTGGG-AATGGGGGATTTTAA
1 CTTTTTCCGATAGTTGGGAAAAGGGGAATTTGAA
* *
5228448 CTTTTTCTGAATAGTTGGTAAAAGGGGAATTTGAA
1 CTTTTTCCG-ATAGTTGGGAAAAGGGGAATTTGAA
5228483 CTT
1 CTT
5228486 GTGACCTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
33 8 0.26
34 8 0.26
35 15 0.48
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.39
Consensus pattern (34 bp):
CTTTTTCCGATAGTTGGGAAAAGGGGAATTTGAA
Found at i:5271867 original size:27 final size:27
Alignment explanation
Indices: 5271828--5271879 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5271818 TAAAGACCAA
*
5271828 GTTACACAACATGTGGAAAAAAAAATT
1 GTTACACAACATGTGAAAAAAAAAATT
* *
5271855 GTTACACACCATGTTAAAAAAAAAA
1 GTTACACAACATGTGAAAAAAAAAA
5271880 AAGTTATTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.54, C:0.13, G:0.12, T:0.21
Consensus pattern (27 bp):
GTTACACAACATGTGAAAAAAAAAATT
Found at i:5271885 original size:27 final size:27
Alignment explanation
Indices: 5271826--5271885 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
5271816 AATAAAGACC
*
5271826 AAGTTACACAACATGTGGAAAAAAAAA
1 AAGTTACACAACATGTGAAAAAAAAAA
** * *
5271853 TTGTTACACACCATGTTAAAAAAAAAA
1 AAGTTACACAACATGTGAAAAAAAAAA
5271880 AAGTTA
1 AAGTTA
5271886 TTACACACCA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (27 bp):
AAGTTACACAACATGTGAAAAAAAAAA
Found at i:5272003 original size:34 final size:34
Alignment explanation
Indices: 5271943--5272009 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
5271933 AAAGCAAAAG
* *
5271943 ATATTACACGTCAAAGTCAAAACTTCAATACCAA
1 ATATTACAAGTCAAAGCCAAAACTTCAATACCAA
* *
5271977 ATATTACAAGTTAAAGCCAAAGCTTCAATACCA
1 ATATTACAAGTCAAAGCCAAAACTTCAATACCA
5272010 GATGTTATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.24
Consensus pattern (34 bp):
ATATTACAAGTCAAAGCCAAAACTTCAATACCAA
Found at i:5297822 original size:26 final size:26
Alignment explanation
Indices: 5297800--5297968 Score: 157
Period size: 26 Copynumber: 6.7 Consensus size: 26
5297790 ATATGACTGA
5297800 TTTTTTATAAGGCATTGCGTGACTAG
1 TTTTTTATAAGGCATTGCGTGACTAG
*
5297826 ---TTAAT-AGGCATTGCGTGACTAG
1 TTTTTTATAAGGCATTGCGTGACTAG
* *
5297848 TTTTTTATAAAGTATTGCGTGACTAG
1 TTTTTTATAAGGCATTGCGTGACTAG
* *
5297874 TTTTTTATAAGACATTGCGTAACTAG
1 TTTTTTATAAGGCATTGCGTGACTAG
* * * ** *
5297900 TTTATGAGAAAACATTACGTGACTAG
1 TTTTTTATAAGGCATTGCGTGACTAG
* * * *
5297926 TTTCTGAAAAGGTATTGCGTGACTAG
1 TTTTTTATAAGGCATTGCGTGACTAG
* *
5297952 TTTCTGATAAGGCATTG
1 TTTTTTATAAGGCATTG
5297969 TATGATTAGT
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
22 17 0.15
23 4 0.03
25 4 0.03
26 92 0.79
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (26 bp):
TTTTTTATAAGGCATTGCGTGACTAG
Found at i:5297950 original size:78 final size:74
Alignment explanation
Indices: 5297800--5297968 Score: 205
Period size: 78 Copynumber: 2.2 Consensus size: 74
5297790 ATATGACTGA
* * * * *
5297800 TTTTTTATAAGGCATTGCGTGACTAGTTAATAGGCATTGCGTGACTAGTTTTTTATAAAGTATTG
1 TTTTTTATAAGGCATTGCGTAACTAGTTAATAGACATTACGTGACTAGTTTCTGATAAAGTATTG
5297865 CGTGACTAG
66 CGTGACTAG
* *
5297874 TTTTTTATAAGACATTGCGTAACTAGTTTATGAGAAAACATTACGTGACTAGTTTCTGA-AAAGG
1 TTTTTTATAAGGCATTGCGTAACTAGTTAAT-AG---ACATTACGTGACTAGTTTCTGATAAA-G
5297938 TATTGCGTGACTAG
61 TATTGCGTGACTAG
* *
5297952 TTTCTGATAAGGCATTG
1 TTTTTTATAAGGCATTG
5297969 TATGATTAGT
Statistics
Matches: 80, Mismatches: 10, Indels: 6
0.83 0.10 0.06
Matches are distributed among these distances:
74 28 0.35
75 2 0.03
77 3 0.04
78 47 0.59
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.38
Consensus pattern (74 bp):
TTTTTTATAAGGCATTGCGTAACTAGTTAATAGACATTACGTGACTAGTTTCTGATAAAGTATTG
CGTGACTAG
Found at i:5298429 original size:35 final size:34
Alignment explanation
Indices: 5298371--5298690 Score: 420
Period size: 35 Copynumber: 9.3 Consensus size: 34
5298361 CAGGGAGAGT
*
5298371 TAAAAGCTGGTT-TTTGCCTCCGGTTAGGAGGAG
1 TAAAAGCTGGTTGTTTGCCGCCGGTTAGGAGGAG
5298404 TAAAAGCTGGTTTGTTTGCCGCCGGTTAGGAGGAG
1 TAAAAGCTGG-TTGTTTGCCGCCGGTTAGGAGGAG
*
5298439 TAAAAGCTGGTTTGTTTGCCGCCGGTTAGGAAGAG
1 TAAAAGCTGG-TTGTTTGCCGCCGGTTAGGAGGAG
5298474 TTAAAAGCTGGTT-TTTGCCGCCGGTTAGGAGGAG
1 -TAAAAGCTGGTTGTTTGCCGCCGGTTAGGAGGAG
5298508 TAAAAGCTGGGTTGTTTGCCGCCGGTTAGG-GAGAG
1 TAAAAGCT-GGTTGTTTGCCGCCGGTTAGGAG-GAG
5298543 TTAAAAGCTGGGTT-TTTGCCGCCGGTTAGGAGGAG
1 -TAAAAGCT-GGTTGTTTGCCGCCGGTTAGGAGGAG
*
5298578 TAAAAGTTGGGTTGTTTGCCGCCGGTTAGG-GAGAG
1 TAAAAGCT-GGTTGTTTGCCGCCGGTTAGGAG-GAG
* *
5298613 TTAAAGCTGGATGTTTGCCGCCGGTTAGG-GAGAG
1 TAAAAGCTGGTTGTTTGCCGCCGGTTAGGAG-GAG
* *
5298647 TTAAAGCTGGATGTTTGCCGCCGGTTAGG-GAGAG
1 TAAAAGCTGGTTGTTTGCCGCCGGTTAGGAG-GAG
*
5298681 TTAAAGCTGG
1 TAAAAGCTGG
5298691 GTTATCTGCT
Statistics
Matches: 270, Mismatches: 7, Indels: 19
0.91 0.02 0.06
Matches are distributed among these distances:
33 18 0.07
34 109 0.40
35 119 0.44
36 24 0.09
ACGTcount: A:0.21, C:0.14, G:0.37, T:0.28
Consensus pattern (34 bp):
TAAAAGCTGGTTGTTTGCCGCCGGTTAGGAGGAG
Found at i:5298561 original size:104 final size:104
Alignment explanation
Indices: 5298366--5298690 Score: 466
Period size: 104 Copynumber: 3.1 Consensus size: 104
5298356 GGGTGCAGGG
* *
5298366 AGAGTTAAAAGCTGGTTTTTGCCTCCGGTTAGGAGGAGTAAAAGCTGGTTTGTTTGCCGCCGGTT
1 AGAGTTAAAAGCTGGTTTTTGCCGCCGGTTAGGAGGAGTAAAAGCTGGGTTGTTTGCCGCCGGTT
*
5298431 A-GGAGGAG-TAAAAGCTGGTTTGTTTGCCGCCGGTTAGGA
66 AGGGA-GAGTTAAAAGCTGGATT-TTTGCCGCCGGTTAGGA
5298470 AGAGTTAAAAGCTGGTTTTTGCCGCCGGTTAGGAGGAGTAAAAGCTGGGTTGTTTGCCGCCGGTT
1 AGAGTTAAAAGCTGGTTTTTGCCGCCGGTTAGGAGGAGTAAAAGCTGGGTTGTTTGCCGCCGGTT
*
5298535 AGGGAGAGTTAAAAGCTGGGTTTTTGCCGCCGGTTAGGA
66 AGGGAGAGTTAAAAGCTGGATTTTTGCCGCCGGTTAGGA
* * * *
5298574 GGAG-TAAAAGTTGGGTTGTTTGCCGCCGGTTAGG-GAGAGTTAAAGCT-GGATGTTTGCCGCCG
1 AGAGTTAAAAGCT-GGTT-TTTGCCGCCGGTTAGGAG-GAGTAAAAGCTGGGTTGTTTGCCGCCG
* *
5298636 GTTAGGGAGAGTT-AAAGCTGGATGTTTGCCGCCGGTTAGGG
63 GTTAGGGAGAGTTAAAAGCTGGATTTTTGCCGCCGGTTAGGA
5298677 AGAGTT-AAAGCTGG
1 AGAGTTAAAAGCTGG
5298691 GTTATCTGCT
Statistics
Matches: 203, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
102 2 0.01
103 40 0.20
104 120 0.59
105 41 0.20
ACGTcount: A:0.21, C:0.14, G:0.37, T:0.28
Consensus pattern (104 bp):
AGAGTTAAAAGCTGGTTTTTGCCGCCGGTTAGGAGGAGTAAAAGCTGGGTTGTTTGCCGCCGGTT
AGGGAGAGTTAAAAGCTGGATTTTTGCCGCCGGTTAGGA
Found at i:5299531 original size:10 final size:10
Alignment explanation
Indices: 5299518--5299550 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
5299508 ATAGAGATAA
5299518 ATAAATAAAT
1 ATAAATAAAT
5299528 ATAAATAAAT
1 ATAAATAAAT
*
5299538 ATAAACAAAT
1 ATAAATAAAT
5299548 ATA
1 ATA
5299551 TTATATTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.27
Consensus pattern (10 bp):
ATAAATAAAT
Found at i:5299973 original size:4 final size:4
Alignment explanation
Indices: 5299964--5299999 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
5299954 TACATGACAT
5299964 TAAA TAAA TAAA TAAA TAAA T-AA T-AA T-AA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
5300000 CTAATTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 9 0.29
4 22 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:5300179 original size:16 final size:16
Alignment explanation
Indices: 5300160--5300190 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5300150 AATAAAAAAT
5300160 ATAAAAAATACATAAA
1 ATAAAAAATACATAAA
*
5300176 ATAAAAAATATATAA
1 ATAAAAAATACATAA
5300191 TTTTTGTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
ATAAAAAATACATAAA
Found at i:5300347 original size:12 final size:13
Alignment explanation
Indices: 5300323--5300352 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
5300313 TAAGAATAGG
5300323 AAATATGATAATA
1 AAATATGATAATA
5300336 AAATAT-ATAATA
1 AAATATGATAATA
5300348 AAATA
1 AAATA
5300353 AAAATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAATATGATAATA
Found at i:5300358 original size:18 final size:19
Alignment explanation
Indices: 5300335--5300387 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
5300325 ATATGATAAT
*
5300335 AAAATATATAATAA-AATA
1 AAAATATATAATAATAACA
5300353 AAAATA-ATTAATAATAACA
1 AAAATATA-TAATAATAACA
*
5300372 AAAAAATATAGATAAT
1 AAAATATATA-ATAAT
5300388 TGCATTAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 12 0.41
19 10 0.34
20 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAATATATAATAATAACA
Found at i:5300425 original size:16 final size:17
Alignment explanation
Indices: 5300401--5300433 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
5300391 ATTAGCATAG
*
5300401 CATATATGT-ATTGCAT
1 CATACATGTCATTGCAT
5300417 CATACATGTCATTGCAT
1 CATACATGTCATTGCAT
5300434 ATAAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.39
Consensus pattern (17 bp):
CATACATGTCATTGCAT
Found at i:5301322 original size:22 final size:21
Alignment explanation
Indices: 5301297--5301356 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
5301287 AATCAGTCAT
5301297 GTAATGTATAAAAACTAATCAC
1 GTAATG-ATAAAAACTAATCAC
* *
5301319 GTAATGCCT-AAAACCAATCAC
1 GTAATG-ATAAAAACTAATCAC
5301340 GTAATGACTAAAAACTA
1 GTAATGA-TAAAAACTA
5301357 GTCATACTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.23
Consensus pattern (21 bp):
GTAATGATAAAAACTAATCAC
Found at i:5301337 original size:21 final size:21
Alignment explanation
Indices: 5301307--5301352 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
5301297 GTAATGTATA
* *
5301307 AAAACTAATCACGTAATGCCT
1 AAAACCAATCACGTAATGACT
5301328 AAAACCAATCACGTAATGACT
1 AAAACCAATCACGTAATGACT
5301349 AAAA
1 AAAA
5301353 ACTAGTCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.20
Consensus pattern (21 bp):
AAAACCAATCACGTAATGACT
Found at i:5306642 original size:2 final size:2
Alignment explanation
Indices: 5306637--5306671 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5306627 GTTGATAGAT
5306637 TA TA TA 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 TA TA TA T
5306672 GGATAAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5310821 original size:33 final size:33
Alignment explanation
Indices: 5310779--5310846 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
5310769 TACGGAAAAC
* *
5310779 TTGCCGTTGGTCTCTGTAGTCATCCTCTATAAA
1 TTGCCGTTGGCCTCTGTAGTCATCCACTATAAA
*
5310812 TTGCCGTTGGCCTCTGTAGTCATCCACTGTAAA
1 TTGCCGTTGGCCTCTGTAGTCATCCACTATAAA
5310845 TT
1 TT
5310847 CTCATCTCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (33 bp):
TTGCCGTTGGCCTCTGTAGTCATCCACTATAAA
Found at i:5314765 original size:22 final size:23
Alignment explanation
Indices: 5314740--5314782 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5314730 TATTAAATAT
5314740 ATTTAAGTAA-TAA-ACTTTTTAA
1 ATTTAA-TAACTAACACTTTTTAA
5314762 ATTTAATAACTAACACTTTTT
1 ATTTAATAACTAACACTTTTT
5314783 TTAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 3 0.16
22 9 0.47
23 7 0.37
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (23 bp):
ATTTAATAACTAACACTTTTTAA
Found at i:5320819 original size:7 final size:7
Alignment explanation
Indices: 5320807--5320831 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5320797 AGTGATAGAA
5320807 AAACCAT
1 AAACCAT
5320814 AAACCAT
1 AAACCAT
5320821 AAACCAT
1 AAACCAT
5320828 AAAC
1 AAAC
5320832 TTAAAGGGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.28, G:0.00, T:0.12
Consensus pattern (7 bp):
AAACCAT
Found at i:5321878 original size:27 final size:26
Alignment explanation
Indices: 5321824--5321892 Score: 76
Period size: 27 Copynumber: 2.8 Consensus size: 26
5321814 TTAAATAAAA
*
5321824 TATTAATATTTAAAT---T-ATCTAT
1 TATTAATATTTAAATAAATAATCAAT
*
5321846 TGTTAATATTTTAAATAAATAATCAAT
1 TATTAATA-TTTAAATAAATAATCAAT
5321873 TATTAATATTTAAA-AAATAA
1 TATTAATATTTAAATAAATAA
5321893 AAAATAATTG
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 7 0.18
23 7 0.18
25 6 0.15
26 7 0.18
27 12 0.31
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.46
Consensus pattern (26 bp):
TATTAATATTTAAATAAATAATCAAT
Found at i:5321927 original size:16 final size:18
Alignment explanation
Indices: 5321908--5321954 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 18
5321898 AATTGATCAT
5321908 AATAATATTTAA-A-TTA
1 AATAATATTTAATATTTA
5321924 AATAATATATTAATATTTA
1 AATAATAT-TTAATATTTA
5321943 AA-AATA-TTAATA
1 AATAATATTTAATA
5321955 ATCAAATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 5 0.18
19 5 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAATATTTAATATTTA
Done.