Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold350
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: 1036165
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 8
Found at i:415478 original size:52 final size:51
Alignment explanation
Indices: 415393--415516 Score: 205
Period size: 52 Copynumber: 2.4 Consensus size: 51
415383 ATATGAAAAG
* *
415393 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
415444 TTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACA-TTTAATAATGTATCGATACATCTGGGCAAA
415496 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
415517 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 21 0.30
52 43 0.62
53 5 0.07
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:415529 original size:51 final size:50
Alignment explanation
Indices: 415393--415536 Score: 177
Period size: 52 Copynumber: 2.8 Consensus size: 50
415383 ATATGAAAAG
* *
415393 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--AAATAGTGTATCGATACATCTGGGCAAAT
415445 TTGCCTGCATGTATCGATACATTTTAAA-A-TGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA----AAATAGTGTATCGATACATCTGGGCAAAT
415496 TTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACAAA-AT-AGTGTATCGATACA
415537 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 2, Indels: 13
0.85 0.02 0.13
Matches are distributed among these distances:
47 2 0.02
48 1 0.01
50 1 0.01
51 33 0.39
52 42 0.50
53 1 0.01
54 4 0.05
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (50 bp):
TTGCCTGCATGTATCGATACAAAATAGTGTATCGATACATCTGGGCAAAT
Found at i:415543 original size:13 final size:13
Alignment explanation
Indices: 415525--415549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
415515 CAAAGATCAG
415525 TGTATCGATACAA
1 TGTATCGATACAA
415538 TGTATCGATACA
1 TGTATCGATACA
415550 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:415631 original size:13 final size:13
Alignment explanation
Indices: 415613--415637 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
415603 AAAAAAAATA
415613 TGTATCGATACAT
1 TGTATCGATACAT
415626 TGTATCGATACA
1 TGTATCGATACA
415638 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:418528 original size:52 final size:52
Alignment explanation
Indices: 418443--418567 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
418433 ATATGAAAAG
* *
418443 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
* *
418495 TTGCCTGCATGTATCGATACATTTTATAATGTATTGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
418547 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
418568 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:418580 original size:52 final size:51
Alignment explanation
Indices: 418443--418587 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
418433 ATATGAAAAG
*
418443 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
418495 TTGCCTGCATGTATCGATACATTTTATAATGTATTGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
418547 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
418588 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:418594 original size:13 final size:13
Alignment explanation
Indices: 418576--418600 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
418566 CAAAGATCAG
418576 TGTATCGATACAA
1 TGTATCGATACAA
418589 TGTATCGATACA
1 TGTATCGATACA
418601 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:418678 original size:33 final size:33
Alignment explanation
Indices: 418641--418707 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
418631 AGTAGCTTAA
418641 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
418674 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
418707 A
1 A
418708 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:418681 original size:13 final size:13
Alignment explanation
Indices: 418663--418687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
418653 CAAAAAAATA
418663 TGTATCGATACAT
1 TGTATCGATACAT
418676 TGTATCGATACA
1 TGTATCGATACA
418688 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:419592 original size:67 final size:68
Alignment explanation
Indices: 419470--419596 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
419460 ATTGGGTTTT
* * *
419470 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
419535 AGA
66 AGA
* * * *
419538 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
419597 GAAAAAAGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:419818 original size:49 final size:49
Alignment explanation
Indices: 419609--420952 Score: 1802
Period size: 49 Copynumber: 27.8 Consensus size: 49
419599 AAAAAGATGT
* *
419609 CAATGTGCTCATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
419661 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
419704 CAA-GATGCTGATTCAAGGCCAGCTACCTTGGACTTAAAGGTG-AGGTGC
1 CAATG-TGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
419752 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
419801 CAATGTGCTGAGTCAAGGCCAGCTACATT-GTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
419849 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
419898 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTA-TTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGG-ACTTAAAGATGAAGGTGC
* * * *
419947 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
419996 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
420045 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
420094 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
420142 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* ** *
420191 CAATGTGCTGAGTCAAGGCCAGCTACATTGTTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * ** * *
420240 TAATATGCTGATTCAAGGCCAGCTGTATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420289 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
420338 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420387 CGATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
420436 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
420485 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
420534 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420583 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAATATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
420632 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
420681 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* * * *
420733 CAATATGCTGATTCCAGGCCAGCTATATTAGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
420776 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420819 CAATGTGCTGATTCAATGCCAGCTACATTGGACTTAAAGGTGTA-GTG-
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
**** * *
420866 TTGGGAGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
420915 CAATATGCTGATTCAGGGCCAGCTATATTGGACTTAAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
420953 AGGGTTGCCA
Statistics
Matches: 1133, Mismatches: 135, Indels: 51
0.86 0.10 0.04
Matches are distributed among these distances:
43 118 0.10
47 35 0.03
48 142 0.13
49 768 0.68
50 2 0.00
52 68 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:419983 original size:98 final size:98
Alignment explanation
Indices: 419543--420952 Score: 2051
Period size: 98 Copynumber: 14.5 Consensus size: 98
419533 TGAGAAAAGT
* * * * * * *
419543 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAAGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G----AAGGTG
* * * *
419608 TCAATGTGCTCATTCAAGGCCAGCTACATTGAACTTAAA
60 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
419647 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
* *
419706 A-GATGCTGATTCAAGGCCAGCTACCTTGGACTTAAA
63 ATG-TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * *
419742 GGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
419806 TGCTGAGTCAAGGCCAGCTACATT-GTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
419838 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
419903 TGCTGAGTCAAGGCCAGCTACATTGGTA-TTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGG-ACTTAAA
* *
419936 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
420001 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
420034 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
* *
420099 TGCTGATTCAAGGCCAGCTACGTTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * *
420132 GGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
**
420196 TGCTGAGTCAAGGCCAGCTACATTGTTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * *
420229 GATAAAGGTGCTAATATGCTGATTCAAGGCCAGCTGTATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
420294 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
*
420327 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
420392 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
420425 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
420490 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
420523 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
420588 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
*
420621 TATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
420686 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
420719 GATGGAAAAGGTGCCAATATGCTGATTCCAGGCCAGCTATATTAGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
*
420778 ATGTGCTGATTCAAGGCCAGCTACATTGGAC-T---
63 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * * * ****
420810 --TAAAGGTGCCAATGTGCTGATTCAATGCCAGCTACATTGGACTTAAAGGTGTA-GTG-TTGGG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
420871 AGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
420904 GATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGACTTAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
420953 AGGGTTGCCA
Statistics
Matches: 1199, Mismatches: 76, Indels: 70
0.89 0.06 0.05
Matches are distributed among these distances:
86 38 0.03
89 1 0.00
90 27 0.02
91 43 0.04
92 1 0.00
94 2 0.00
95 80 0.07
96 51 0.04
97 203 0.17
98 671 0.56
101 41 0.03
103 1 0.00
104 3 0.00
107 37 0.03
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
Found at i:421085 original size:34 final size:34
Alignment explanation
Indices: 420991--421390 Score: 468
Period size: 34 Copynumber: 11.8 Consensus size: 34
420981 AGAGAGTGAT
* * *
420991 TGCCACCGACTTGTGGAC-TTAAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTTAAAA-GGAAAAAG-G
*
421026 TGCCACGAAGTTGTGGGCTTTAAAA-GAAAAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGG
421059 TGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-G
421096 TGCCACGGAGTTGTGGGCTTTAAAA-GAAAAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGG
*
421129 TGCCATGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-G
* *
421166 TGCCACGGAGTTGTGGGCTCTAAAAAGAAAAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGG
421200 TGCCACGGAGTTGTGGGCTTTAAAA-GAAAAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGG
*
421233 TGCCACGGAGTTGTTGGCTTTGAAAAGGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-G
* *
421270 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAGG
1 TGCCACGGAGTTGTGGGCTTTAAA-AGGAAAAAGG
421304 TGCCACGGAGTTGTGGGC-TTAAAA-G-----GG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGG
* * *
421331 TGCCACGGAGTTGTGGAC-TTAAAGATGAAAAAAG
1 TGCCACGGAGTTGTGGGCTTTAAA-AGGAAAAAGG
421365 TGCCACGGAGTTGTGGGC-TTAAAAGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGG
421391 GTGCTACGGA
Statistics
Matches: 325, Mismatches: 19, Indels: 44
0.84 0.05 0.11
Matches are distributed among these distances:
27 24 0.07
28 1 0.00
29 1 0.00
32 1 0.00
33 73 0.22
34 97 0.30
35 31 0.10
36 38 0.12
37 59 0.18
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
TGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGG
Found at i:421099 original size:70 final size:69
Alignment explanation
Indices: 420991--421389 Score: 499
Period size: 70 Copynumber: 5.9 Consensus size: 69
420981 AGAGAGTGAT
* * * *
420991 TGCCACCGACTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAA
1 TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
421055 AAGG
66 AAGG
421059 TGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
1 TGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
421124 AAAGG
65 AAAGG
* *
421129 TGCCATGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTCTAAAAAGA
1 TGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT-TTAAAAGA
421194 AAAAGG
64 AAAAGG
*
421200 TGCCACGGAGTTGTGGGCTTTAAAA--GAAAAAG-GTGCCACGGAGTTGTTGGCTTTGAAAAGGG
1 TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA--G
421262 AAAAAGAG
63 AAAAAG-G
* *
421270 TGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAAG-GTGCCACGGAGTTGTGGGC-TTAAAAG--
1 TGCCACGGAGTTGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAA
421329 ---GG
65 AAAGG
* *
421331 TGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAA-AGTGCCACGGAGTTGTGGGC-TTAAAAG
1 TGCCACGGAGTTGTGGGCTTTAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
421390 GGTGCTACGG
Statistics
Matches: 309, Mismatches: 11, Indels: 29
0.89 0.03 0.08
Matches are distributed among these distances:
61 59 0.19
62 1 0.00
66 1 0.00
67 24 0.08
68 25 0.08
69 15 0.05
70 126 0.41
71 58 0.19
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (69 bp):
TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAA
AAGG
Found at i:421211 original size:104 final size:101
Alignment explanation
Indices: 420991--421388 Score: 494
Period size: 104 Copynumber: 3.9 Consensus size: 101
420981 AGAGAGTGAT
* * * *
420991 TGCCACCGACTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAA--GAA
1 TGCCACGGAGTTGTGGGCTTAAAA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAA
*
421054 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAG
63 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-AGAAAAAG-G
*
421096 TGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCATGGAGTTGTGGGCTTTGAAAAGGGAAA
1 TGCCACGGAGTTGTGGGC-TTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAA
421161 AAGAGTGCCACGGAGTTGTGGGCTCTAAAAAGAAAAAGG
64 AAGAGTGCCACGGAGTTGTGGGCT-TAAAAAGAAAAAGG
*
421200 TGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTTGGCTTTGAAAAGGGAAA
1 TGCCACGGAGTTGTGGGC-TTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAAA
* *
421265 AAGAGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAGG
64 AAGAGTGCCACGGAGTTGTGGGCTTAAA-AAGAAAAAGG
* *
421304 TGCCACGGAGTTGTGGGCTTAAAAG-----GGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAA
1 TGCCACGGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAG-GGAAAA
421362 A-AGTGCCACGGAGTTGTGGGCTTAAAA
65 AGAGTGCCACGGAGTTGTGGGCTTAAAA
421389 GGGTGCTACG
Statistics
Matches: 271, Mismatches: 14, Indels: 27
0.87 0.04 0.09
Matches are distributed among these distances:
94 1 0.00
95 28 0.10
96 6 0.02
97 2 0.01
98 18 0.07
103 31 0.11
104 125 0.46
105 22 0.08
106 18 0.07
107 20 0.07
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (101 bp):
TGCCACGGAGTTGTGGGCTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAA
GAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGG
Found at i:421335 original size:27 final size:27
Alignment explanation
Indices: 421297--421402 Score: 113
Period size: 27 Copynumber: 3.7 Consensus size: 27
421287 CTTAAAGATG
*
421297 AAAAAGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
421324 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
*
421351 AAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAA-A-G-----GGTGCCACGGAGTTGTGGGCTT
*
421385 AAAAGGGTGCTACGGAGT
1 AAAAGGGTGCCACGGAGT
421403 CATGGACTTT
Statistics
Matches: 66, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
27 39 0.59
28 1 0.02
29 1 0.02
32 1 0.02
33 1 0.02
34 23 0.35
ACGTcount: A:0.30, C:0.13, G:0.36, T:0.21
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTT
Found at i:421358 original size:61 final size:61
Alignment explanation
Indices: 421263--421411 Score: 253
Period size: 61 Copynumber: 2.4 Consensus size: 61
421253 TGAAAAGGGA
* *
421263 AAAAGAGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
421324 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
* **
421385 AAAAGGGTGCTACGGAGTCATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
421412 TGAAGAAAAG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 83 1.00
ACGTcount: A:0.31, C:0.13, G:0.34, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
Found at i:421435 original size:32 final size:32
Alignment explanation
Indices: 421385--421446 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
421375 TTGTGGGCTT
* *
421385 AAAAGGGTGCTACGGAGTCATGGACTTTGAAG
1 AAAAGGATGCCACGGAGTCATGGACTTTGAAG
* *
421417 AAAAGGATGCCACTGAGTCGTGGACTTTGA
1 AAAAGGATGCCACGGAGTCATGGACTTTGA
421447 GAAGAGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.32, T:0.23
Consensus pattern (32 bp):
AAAAGGATGCCACGGAGTCATGGACTTTGAAG
Found at i:421580 original size:16 final size:17
Alignment explanation
Indices: 421549--421586 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
421539 GATGTAAATA
* *
421549 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
421566 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
421582 ATGAT
1 ATGAT
421587 TATAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:427242 original size:49 final size:49
Alignment explanation
Indices: 427168--428258 Score: 1617
Period size: 49 Copynumber: 22.3 Consensus size: 49
427158 CCTTATGGTT
* * * *
427168 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTAGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* *
427217 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGTC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * **
427266 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTGTATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * * *
427315 TTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGTC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
427364 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
427413 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
427462 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
427511 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * * *
427560 TTAAAGATAAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
427609 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * * *
427658 TTAAAGATAAAGGTGCCAATATGCTGATTGAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
427707 TTAATGTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
427756 TTAAAGGTG-AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* *
427804 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGTC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * **
427853 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTGTATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * * * *
427902 TTAATGGTGAAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGTC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
427951 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
428000 TTAAAGATGAAGGAGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAA
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
428049 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
428098 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
428147 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
*
428196 TTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* *
428245 TTTAAGATAAAGGT
1 TTAAAGATGAAGGT
428259 CGAATCCTCC
Statistics
Matches: 925, Mismatches: 116, Indels: 2
0.89 0.11 0.00
Matches are distributed among these distances:
48 46 0.05
49 879 0.95
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
Found at i:427287 original size:98 final size:98
Alignment explanation
Indices: 427168--428258 Score: 1950
Period size: 98 Copynumber: 11.1 Consensus size: 98
427158 CCTTATGGTT
*
427168 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTAGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
427233 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
* * *
427266 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTGTATTGGACTTAATGGTGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
427331 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
427364 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
427429 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
427462 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
427527 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
*
427560 TTAAAGATAAAGGTGCCAATATGTTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
427625 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
* * *
427658 TTAAAGATAAAGGTGCCAATATGCTGATTGAAGGCCAGCTATATTGGACTTAATGTTGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
427723 CAATGTGCTGATTCAAGGCCAGCTACGTTGGAC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
* * * *
427756 TTAAAGGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
427820 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
* * *
427853 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTGTATTGGACTTAATGGTGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
* *
427918 CAATGTGCTGAGTCAAGGCTAGCTACATTGGTC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
*
427951 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGAGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
*
428016 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAA
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
428049 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
428114 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
428147 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
428212 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
66 CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
*
428245 TTTAAGATAAAGGT
1 TTAAAGATAAAGGT
428259 CGAATCCTCC
Statistics
Matches: 949, Mismatches: 43, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
97 87 0.09
98 862 0.91
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (98 bp):
TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
CAATGTGCTGAGTCAAGGCCAGCTACATTGGAC
Found at i:429095 original size:13 final size:13
Alignment explanation
Indices: 429077--429102 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
429067 CAATTTTTTG
429077 TGTATCGATACAT
1 TGTATCGATACAT
429090 TGTATCGATACAT
1 TGTATCGATACAT
429103 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:429117 original size:32 final size:33
Alignment explanation
Indices: 429057--429120 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
429047 TACAAGCCAA
** *
429057 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
429090 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
429121 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:429842 original size:21 final size:21
Alignment explanation
Indices: 429801--429844 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
429791 CTCCCCTTTA
* *
429801 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
429822 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
429843 TC
1 TC
429845 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:431665 original size:13 final size:13
Alignment explanation
Indices: 431647--431724 Score: 147
Period size: 13 Copynumber: 6.0 Consensus size: 13
431637 ATAATCACCC
431647 TGTATCGATACAA
1 TGTATCGATACAA
431660 TGTATCGATACAA
1 TGTATCGATACAA
431673 TGTATCGATACAA
1 TGTATCGATACAA
431686 TGTATCGATACAA
1 TGTATCGATACAA
431699 TGTATCGATACAA
1 TGTATCGATACAA
*
431712 TGTATCAATACAA
1 TGTATCGATACAA
431725 AGAAAAATGT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
13 64 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:433823 original size:15 final size:15
Alignment explanation
Indices: 433803--433833 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
433793 ATTTCGTTTG
*
433803 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
433818 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
433833 G
1 G
433834 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:437894 original size:13 final size:13
Alignment explanation
Indices: 437876--437901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
437866 CAATTTTTTG
437876 TGTATCGATACAT
1 TGTATCGATACAT
437889 TGTATCGATACAT
1 TGTATCGATACAT
437902 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:437916 original size:32 final size:33
Alignment explanation
Indices: 437856--437919 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
437846 TACAAGCCAA
** *
437856 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
437889 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
437920 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:440453 original size:2 final size:2
Alignment explanation
Indices: 440441--440474 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
440431 GTGAGCTATG
*
440441 AT AT AT TT 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
440475 GTAAAAACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:442439 original size:23 final size:22
Alignment explanation
Indices: 442412--442462 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 22
442402 AAACTCATGA
* *
442412 AAAAAACAAAACATAAAGATAATT
1 AAAAAA-ATAACATAAAAATAA-T
442436 AAAAAAATAACATAAAAATAAT
1 AAAAAAATAACATAAAAATAAT
442458 AAAAA
1 AAAAA
442463 TACGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.24
23 13 0.52
24 6 0.24
ACGTcount: A:0.76, C:0.06, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAAAATAACATAAAAATAAT
Found at i:443519 original size:34 final size:34
Alignment explanation
Indices: 443481--443582 Score: 177
Period size: 34 Copynumber: 3.0 Consensus size: 34
443471 CTTTGTTAAG
443481 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
443515 TGTATTTGGTGAGAATGTTAGGTGTATTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
* *
443549 TGTGTTAGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
443583 GAATGTTAGG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 64 1.00
ACGTcount: A:0.22, C:0.00, G:0.38, T:0.40
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:443577 original size:22 final size:22
Alignment explanation
Indices: 443549--443604 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
443539 TATTAGGTGA
443549 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
443571 TGTGTTAGGTGAGAATGTTAGG
1 TGTGTTAGGTGAGAATGTTAGG
443593 TGTGTTAGGTGA
1 TGTGTTAGGTGA
443605 TGTATTTGGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.21, C:0.00, G:0.41, T:0.38
Consensus pattern (22 bp):
TGTGTTAGGTGAGAATGTTAGG
Found at i:443582 original size:56 final size:56
Alignment explanation
Indices: 443522--443633 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
443512 TGATGTATTT
* *
443522 GGTGAGAATGTTAGGTGTATTAGGTGATGTGTTAGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTATTAGGTGATGTATTAGGTGAGAATGTTAGGTATGTTA
* *
443578 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTATGTTA
1 GGTGAGAATGTTAGGTGTATTAGGTGATGTATTAGGTGAGAATGTTAGGTATGTTA
443634 ACATGTATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.23, C:0.00, G:0.38, T:0.38
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTATTAGGTGATGTATTAGGTGAGAATGTTAGGTATGTTA
Found at i:448315 original size:34 final size:34
Alignment explanation
Indices: 448277--448446 Score: 331
Period size: 34 Copynumber: 5.0 Consensus size: 34
448267 CTTTGTTAAG
448277 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
448311 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
448345 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
448379 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
*
448413 TGTGTTTGGTGAGAATGTTAGGTGTGTTAGGTGA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
448447 GAATGTTAGG
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
34 135 1.00
ACGTcount: A:0.20, C:0.00, G:0.39, T:0.41
Consensus pattern (34 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
Found at i:448330 original size:25 final size:25
Alignment explanation
Indices: 448301--448402 Score: 80
Period size: 25 Copynumber: 4.4 Consensus size: 25
448291 ATGTTAGGTG
448301 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
* *
448326 TGTTAGGTG-TG--TTAGGTGATGTA
1 TGTTAGGTGATGTATTTGGTGA-GAA
*
448349 T-TT-GGTGA-GAATGTTAGGT--G--
1 TGTTAGGTGATGTAT-TT-GGTGAGAA
448369 TGTTAGGTGATGTATTTGGTGAGAA
1 TGTTAGGTGATGTATTTGGTGAGAA
448394 TGTTAGGTG
1 TGTTAGGTG
448403 TGTTAGGTGA
Statistics
Matches: 60, Mismatches: 4, Indels: 26
0.67 0.04 0.29
Matches are distributed among these distances:
20 1 0.02
21 10 0.17
22 17 0.28
23 8 0.13
24 3 0.05
25 21 0.35
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (25 bp):
TGTTAGGTGATGTATTTGGTGAGAA
Found at i:448453 original size:56 final size:56
Alignment explanation
Indices: 448386--448497 Score: 215
Period size: 56 Copynumber: 2.0 Consensus size: 56
448376 TGATGTATTT
*
448386 GGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
448442 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
1 GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
448498 ACATGTATAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 55 1.00
ACGTcount: A:0.21, C:0.00, G:0.40, T:0.39
Consensus pattern (56 bp):
GGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTA
Found at i:448480 original size:68 final size:66
Alignment explanation
Indices: 448277--448497 Score: 327
Period size: 68 Copynumber: 3.4 Consensus size: 66
448267 CTTTGTTAAG
448277 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGT-AG-ATGTTAGGTGTGTTAGG
448342 TGA
64 TGA
448345 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGT-AG-ATGTTAGGTGTGTTAGG
448410 TGA
64 TGA
*
448413 TGTGTTTGGTGAGAATGTTAGGTGTGTTA-G-G-TG-A----G-A-ATGTTAGGTGTGTTAGGTG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTAGATGTTAGGTGTGTTAGGTG
448468 A
66 A
448469 TGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTA
448498 ACATGTATAT
Statistics
Matches: 151, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
56 48 0.32
58 1 0.01
60 1 0.01
64 1 0.01
65 2 0.01
66 1 0.01
67 1 0.01
68 96 0.64
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.41
Consensus pattern (66 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTAGATGTTAGGTGTGTTAGGTG
A
Found at i:448480 original size:102 final size:100
Alignment explanation
Indices: 448277--448497 Score: 336
Period size: 102 Copynumber: 2.3 Consensus size: 100
448267 CTTTGTTAAG
448277 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
*
448342 TGATGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGA
66 TGATGAATTTGGT-AG-ATGTTAGGTGTGTTAGGTGA
*
448379 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTGTTTGGTGAGAATGTTAGGTGTGTTA-G
1 TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
448443 -G-TG-A----G-A-ATGTTAGGTGTGTTAGGTGA
66 TGATGAATTTGGTAGATGTTAGGTGTGTTAGGTGA
448469 TGTATTTGGTGAGAATGTTAGGTGTGTTA
1 TGTATTTGGTGAGAATGTTAGGTGTGTTA
448498 ACATGTATAT
Statistics
Matches: 118, Mismatches: 1, Indels: 12
0.90 0.01 0.09
Matches are distributed among these distances:
90 49 0.42
92 1 0.01
94 1 0.01
98 1 0.01
99 2 0.02
100 1 0.01
101 1 0.01
102 62 0.53
ACGTcount: A:0.20, C:0.00, G:0.38, T:0.41
Consensus pattern (100 bp):
TGTATTTGGTGAGAATGTTAGGTGTGTTAGGTGATGTATTTGGTGAGAATGTTAGGTGTGTTAGG
TGATGAATTTGGTAGATGTTAGGTGTGTTAGGTGA
Found at i:448958 original size:27 final size:28
Alignment explanation
Indices: 448905--448974 Score: 79
Period size: 27 Copynumber: 2.4 Consensus size: 28
448895 TTATCTCTAT
* * *
448905 ATATTTTATTATATTATAATTATATTTAAG
1 ATATTTTA-TAT-TTATAATAAAATTTAAA
448935 ATATTTTATATTTAT-ATAAAATTTAAA
1 ATATTTTATATTTATAATAAAATTTAAA
448962 ATATTTATATATT
1 ATATTT-TATATT
448975 CGTATATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
27 15 0.42
28 10 0.28
29 3 0.08
30 8 0.22
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (28 bp):
ATATTTTATATTTATAATAAAATTTAAA
Found at i:448966 original size:36 final size:36
Alignment explanation
Indices: 448926--448994 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
448916 TATTATAATT
*
448926 ATATTTAAGATATT-TTATATTTATATAAAATTTAAA
1 ATATTT-AGATATTCGTATATTTATATAAAATTTAAA
* *
448962 ATATTTATATATTCGTATATTTATATAATATTT
1 ATATTTAGATATTCGTATATTTATATAAAATTT
448995 TTAATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 6 0.21
36 23 0.79
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (36 bp):
ATATTTAGATATTCGTATATTTATATAAAATTTAAA
Found at i:450189 original size:20 final size:20
Alignment explanation
Indices: 450145--450218 Score: 67
Period size: 21 Copynumber: 3.6 Consensus size: 20
450135 TTCTATAATT
* * *
450145 TGTATTGATACAAACAGTAAA
1 TGTATCGATACATA-AGTGAA
450166 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
* ***
450186 TGTAACGATACATCCCTGAAA
1 TGTATCGATACATAAGTG-AA
450207 TGTATCGATACA
1 TGTATCGATACA
450219 AAACCATACT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 19 0.43
21 25 0.57
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Found at i:450411 original size:19 final size:19
Alignment explanation
Indices: 450387--450437 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
450377 TTACAAGCCA
450387 ATGTATCGATACATCTTGT
1 ATGTATCGATACATCTTGT
450406 ATGTATCGATACATCTTGT
1 ATGTATCGATACATCTTGT
450425 ATGTATCGATACA
1 ATGTATCGATACA
450438 AACAGTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (19 bp):
ATGTATCGATACATCTTGT
Found at i:453013 original size:32 final size:33
Alignment explanation
Indices: 452977--453041 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
452967 TATCAGTTTT
452977 ATGTATCGATACCAAG-AACATGTATCAATACA
1 ATGTATCGATACCAAGCAACATGTATCAATACA
* * *
453009 ATGTATCGATACTAAGCAATATGTATCGATACA
1 ATGTATCGATACCAAGCAACATGTATCAATACA
453042 TTTGGGTGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
ATGTATCGATACCAAGCAACATGTATCAATACA
Found at i:453502 original size:23 final size:22
Alignment explanation
Indices: 453468--453532 Score: 60
Period size: 23 Copynumber: 2.9 Consensus size: 22
453458 ATTTATTTAA
453468 ATTAAAAGAATATATTAACGAAT
1 ATTAAAA-AATATATTAACGAAT
* *
453491 ATTAAATAAATATATTTATGAAT
1 ATTAAA-AAATATATTAACGAAT
* *
453514 AATAAACAAACA-ATTAACG
1 ATTAAA-AAATATATTAACG
453533 TCTTAGTAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 5 0.15
23 28 0.82
24 1 0.03
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (22 bp):
ATTAAAAAATATATTAACGAAT
Found at i:453630 original size:33 final size:33
Alignment explanation
Indices: 453579--453651 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
453569 AATTTTAAAT
*
453579 ATAAAAT-AAAAATAAAAAT-ATAATTATGAATAA
1 ATAAAATAAAAAATAAAAATCATAA-AAT-AATAA
*
453612 ATAAAATAAAAAAT-AAAATCATAAAATCATAA
1 ATAAAATAAAAAATAAAAATCATAAAATAATAA
453644 ATAAAATA
1 ATAAAATA
453652 TAATCAAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
32 12 0.33
33 14 0.39
34 10 0.28
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (33 bp):
ATAAAATAAAAAATAAAAATCATAAAATAATAA
Found at i:453637 original size:20 final size:19
Alignment explanation
Indices: 453575--453654 Score: 62
Period size: 20 Copynumber: 4.4 Consensus size: 19
453565 TTTTAATTTT
453575 AAATATAAAAT-AAAAATA
1 AAATATAAAATAAAAAATA
* * **
453593 AAA-ATATAATTATGAAT-
1 AAATATAAAATAAAAAATA
453610 -AA-ATAAAATAAAAAATA
1 AAATATAAAATAAAAAATA
* *
453627 AAATCATAAAATCATAAATA
1 AAAT-ATAAAATAAAAAATA
453647 AAATATAA
1 AAATATAA
453655 TCAAATAATA
Statistics
Matches: 48, Mismatches: 9, Indels: 9
0.73 0.14 0.14
Matches are distributed among these distances:
16 12 0.25
17 6 0.12
18 9 0.19
19 4 0.08
20 17 0.35
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (19 bp):
AAATATAAAATAAAAAATA
Found at i:458411 original size:78 final size:78
Alignment explanation
Indices: 458302--458449 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 78
458292 ACATAATCTT
* * * *
458302 AGACTCACTTTTAAGGTACCATTATCGAAATGACCTTAATGGACATGTTTTGACACAAAGGTTCA
1 AGACTCACTTTTAAGGTACCATTACCGAAATGACCCTAATGGACATATTATGACACAAAGGTTCA
458367 CACATAACCCTAA
66 CACATAACCCTAA
* * ** * *
458380 AGACTCAGTTTTAAGGTGCTTTTACCTAAATGACCCTAATGGACATATTATGACACAAAGGTTCT
1 AGACTCACTTTTAAGGTACCATTACCGAAATGACCCTAATGGACATATTATGACACAAAGGTTCA
458445 CACAT
66 CACAT
458450 GATCCTAGAC
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 60 1.00
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (78 bp):
AGACTCACTTTTAAGGTACCATTACCGAAATGACCCTAATGGACATATTATGACACAAAGGTTCA
CACATAACCCTAA
Found at i:458883 original size:18 final size:17
Alignment explanation
Indices: 458845--458884 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
458835 GTAATGGTCC
**
458845 CTAAATCATGAAAATTC
1 CTAAATCATGAAAATGA
458862 CTAAATCATGAAAAATGA
1 CTAAATCATG-AAAATGA
458880 CTAAA
1 CTAAA
458885 ATGGTCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (17 bp):
CTAAATCATGAAAATGA
Found at i:459047 original size:59 final size:58
Alignment explanation
Indices: 458861--459116 Score: 254
Period size: 58 Copynumber: 4.4 Consensus size: 58
458851 CATGAAAATT
* * *
458861 CCTAAATCATGAAAAATGACTAAAATGGTCTTAAAATGAATTAAA-TCACATAAT-AGTC
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAAGT-ACATAATGA-TC
* * * * * *
458919 CCTTAATTATCG-AAAATGAC-AAGAATAGTCCT-AAATACATGAAATTACATAATGGTC
1 CCTAAATCAT-GAAAAATGACTAA-AATAGTCTTAAAATGCATGAAAGTACATAATGATC
* * * *
458976 CTTAAATTATGAAAAATAACTAAAATAGTCTTAAAATGCATGAAAAGTACATAATGACC
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATG-AAAGTACATAATGATC
** * * *
459035 CCTAAATCATGAAAAATGACTAAAAGGGTTTTAAAATGCATG-AAGTTACATAATGGTA
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAAG-TACATAATGATC
459093 CCTAAATCATGAAAAATGACTAAA
1 CCTAAATCATGAAAAATGACTAAA
459117 TTGACCTAAA
Statistics
Matches: 164, Mismatches: 25, Indels: 18
0.79 0.12 0.09
Matches are distributed among these distances:
56 1 0.01
57 46 0.28
58 67 0.41
59 50 0.30
ACGTcount: A:0.48, C:0.13, G:0.12, T:0.27
Consensus pattern (58 bp):
CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAAGTACATAATGATC
Found at i:459110 original size:58 final size:58
Alignment explanation
Indices: 458861--459166 Score: 296
Period size: 57 Copynumber: 5.3 Consensus size: 58
458851 CATGAAAATT
* * * * *
458861 CCTAAATCATGAAAAATGACTAAAATGGTCTTAAAATGAATTAAATCACATAATAGTC
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAATTACATAATGGTC
* * * *
458919 CCTTAATTATCG-AAAATGAC-AAGAATAGTCCT-AAATACATGAAATTACATAATGGTC
1 CCTAAATCAT-GAAAAATGACTAA-AATAGTCTTAAAATGCATGAAATTACATAATGGTC
* * * * **
458976 CTTAAATTATGAAAAATAACTAAAATAGTCTTAAAATGCATGAAAAGTACATAATGACC
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATG-AAATTACATAATGGTC
** * * *
459035 CCTAAATCATGAAAAATGACTAAAAGGGTTTTAAAATGCATGAAGTTACATAATGGTA
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAATTACATAATGGTC
* * * * * *
459093 CCTAAATCATGAAAAATGACT-AAATTGACCTAAAATGTATGAAGTTACATAATAGTC
1 CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAATTACATAATGGTC
*
459150 CTTAATATGCATGAAAA
1 CCTAA-AT-CATGAAAA
459167 CATGGTGGAA
Statistics
Matches: 203, Mismatches: 37, Indels: 15
0.80 0.15 0.06
Matches are distributed among these distances:
56 1 0.00
57 77 0.38
58 67 0.33
59 58 0.29
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.28
Consensus pattern (58 bp):
CCTAAATCATGAAAAATGACTAAAATAGTCTTAAAATGCATGAAATTACATAATGGTC
Found at i:459791 original size:18 final size:17
Alignment explanation
Indices: 459756--459800 Score: 54
Period size: 18 Copynumber: 2.6 Consensus size: 17
459746 TTTCCAAAAC
*
459756 TTTTTTTTCTTTATTTT
1 TTTTTTTTCTTTACTTT
*
459773 TATTTTTTTCTTTCCTTT
1 T-TTTTTTTCTTTACTTT
*
459791 TTTCTTTTCT
1 TTTTTTTTCT
459801 AGTTTCCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.04, C:0.13, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTTCTTTACTTT
Found at i:462996 original size:163 final size:164
Alignment explanation
Indices: 462796--463439 Score: 606
Period size: 163 Copynumber: 3.9 Consensus size: 164
462786 TTCAAACATC
* * * * *
462796 AAAATTCTTCGAATATTATCATTTAATTC-TCATTAAATCAGTTTTCAAAAATTAATTCATCTTC
1 AAAATTCATCAAATATTATCATTTATTTCAT-ATTAAATCAATTTTCAAAAATTAATTCATTTTC
* * *
462860 ATGAGTTTTTAAATTTTTTCTTGAAA-TTTTTTTTTTC-GAAATATGATGTTTTCTACGCCGAAA
65 ATGAGTTTTT-AATTTTTTCTTGAAACTTTTTTTTTTCTAAAATACGATGTTTTCTACTCCGAAA
* * *
462923 ATGTTTTCGAGAGATTTTTCTTGGTTTTTAATTTCT
129 ATTTTTTCGAGAGATTTTTCTTGGTTTTCAATTTTT
* * * *
462959 AAATTTAATCAAATATTATCATTTATTTCATATTAAATCAGCTTTT-AAAAATTCATTCATTTTC
1 AAAATTCATCAAATATTATCATTTATTTCATATTAAATCA-ATTTTCAAAAATTAATTCATTTTC
* * * * * * * *
463023 ATGAGTTTTTGATTTTTTCCTTAAAACTCTATTTTTTCTAAAATATGATATTTTCTACTTCGTAA
65 ATGAGTTTTTAATTTTTT-CTTGAAACTTTTTTTTTTCTAAAATACGATGTTTTCTACTCCGAAA
463088 ATTTTTTCGA-ATGGATTTTTCTTGGTTTTCAATTTTT
129 ATTTTTTCGAGA--GATTTTTCTTGGTTTTCAATTTTT
* *
463125 AAAATTCATC--A-A--ATCATTTATTTCATATTAATTCAACTTTCAAAAATGT-ATTCATTTT-
1 AAAATTCATCAAATATTATCATTTATTTCATATTAAATCAATTTTCAAAAAT-TAATTCATTTTC
* * * *
463183 ATTGAGTTTTTTATTTTTTTCGTGAAACTTTCTTTTTTTCTAAAATACAATGTTTTCTACT-CTA
65 A-TGAG-TTTTTAATTTTTTCTTGAAACTTT-TTTTTTTCTAAAATACGATGTTTTCTACTCCGA
* * * *
463247 TAA-TTTTTAGAGGGGA-TTTTCTCGGTTTTCAATTTTT
127 AAATTTTTTCGA-GAGATTTTTCTTGGTTTTCAATTTTT
* * * * * *
463284 AAAATTCATCAAACATCATTATTTGA-TTCATATTAATTCAATTTTAAAAAATTAATTCATTTTT
1 AAAATTCATCAAATATTATCATTT-ATTTCATATTAAATCAATTTTCAAAAATTAATTCATTTTC
* * * *
463348 ATGAGTTTTTTATTTTTTGTTGAAA-TTTTATTTTTTCTGAAAA-ACCGA-GTTTTCAACTCCGT
65 ATGAGTTTTTAATTTTTTCTTGAAACTTTT-TTTTTTCT-AAAATA-CGATGTTTTCTACTCCGA
* *
463410 AAATTTTTTCGGGGAAATTTTTCTTGGTTT
127 AAATTTTTTC-GAGAGATTTTTCTTGGTTT
463440 AGAATTTTAC
Statistics
Matches: 395, Mismatches: 57, Indels: 56
0.78 0.11 0.11
Matches are distributed among these distances:
159 30 0.08
160 13 0.03
161 54 0.14
162 66 0.17
163 92 0.23
164 66 0.17
165 44 0.11
166 30 0.08
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (164 bp):
AAAATTCATCAAATATTATCATTTATTTCATATTAAATCAATTTTCAAAAATTAATTCATTTTCA
TGAGTTTTTAATTTTTTCTTGAAACTTTTTTTTTTCTAAAATACGATGTTTTCTACTCCGAAAAT
TTTTTCGAGAGATTTTTCTTGGTTTTCAATTTTT
Found at i:463388 original size:17 final size:18
Alignment explanation
Indices: 463355--463389 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
463345 TTTATGAGTT
*
463355 TTTTATTTTTTGTTGAAA
1 TTTTATTTTTTGCTGAAA
463373 TTTTATTTTTT-CTGAAA
1 TTTTATTTTTTGCTGAAA
463390 AACCGAGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.09, T:0.66
Consensus pattern (18 bp):
TTTTATTTTTTGCTGAAA
Found at i:463432 original size:324 final size:323
Alignment explanation
Indices: 462838--463439 Score: 704
Period size: 325 Copynumber: 1.9 Consensus size: 323
462828 TTAAATCAGT
* *
462838 TTTCAAAAATTAATTCATCTTCATGAGTTTTTAAATTTTTTCTTGAAATTTTTTTTTTCGAAATA
1 TTTCAAAAATTAATTCATCTTCATGAGTTTTTAAATTTTTTCGTGAAATTTTTTTTTTCAAAATA
** * * * *
462903 TGATGTTTTCTACGCCGAAAATGTTTTCGAGAGATTTTTCTTGGTTTTTAATTTCTAAATTTAAT
66 CAATGTTTTCTACGCCGAAAATGTTTTAGAGAGATTTTTCTCGGTTTTCAATTTCTAAAATTAAT
* * * *
462968 CAAATATTATCATTTATTTCATATTAAATCAGCTTTTAAAAATTCATTCATTTTCATGAGTTTTT
131 CAAACATCATCATTTATTTCATATTAAATCAGATTTTAAAAATTAATTCATTTTCATGAGTTTTT
* * *
463033 GATTTTTTCCTTAAAACTCTATTTTTTCTAAAATATGATATTTTCTACTTCGTAAATTTTTTCGA
196 GATTTTTTCCTTAAAACTCTATTTTTTCTAAAATACGATATTTTCAACTCCGTAAATTTTTTCG-
*
463098 ATGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAATCATTTATTTCATATTAATTCAAC
260 AGGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAATCATTTATTTCATATTAATTCAAC
* * *
463162 TTTCAAAAATGT-ATTCAT-TTTATTGAGTTTTTTATTTTTTTCGTGAAACTTTCTTTTTTTCTA
1 TTTCAAAAAT-TAATTCATCTTCA-TGAGTTTTTAAATTTTTTCGTGAAA-TTT-TTTTTTTC-A
* * * * *
463225 AAATACAATGTTTTCTAC-TCTATAAT-TTTTAGAGGGGA-TTTTCTCGGTTTTCAATTTTTAAA
61 AAATACAATGTTTTCTACGCCGAAAATGTTTTAGA-GAGATTTTTCTCGGTTTTCAATTTCTAAA
* * * *
463287 ATTCATCAAACATCATTATTTGA-TTCATATTAATTCA-ATTTTAAAAAATTAATTCATTTTTAT
125 ATTAATCAAACATCATCATTT-ATTTCATATTAAATCAGATTTT-AAAAATTAATTCATTTTCAT
* * * * * *
463350 GAGTTTTTTATTTTTT-GTTGAAATTTTATTTTTTCTGAAAA-ACCGA-GTTTTCAACTCCGTAA
188 GAGTTTTTGATTTTTTCCTTAAAACTCTATTTTTTCT-AAAATA-CGATATTTTCAACTCCGTAA
463412 ATTTTTTCG-GGGAAATTTTTCTTGGTTT
251 ATTTTTTCGAGGG--ATTTTTCTTGGTTT
463440 AGAATTTTAC
Statistics
Matches: 232, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
322 2 0.01
323 3 0.01
324 95 0.41
325 99 0.43
326 17 0.07
327 16 0.07
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (323 bp):
TTTCAAAAATTAATTCATCTTCATGAGTTTTTAAATTTTTTCGTGAAATTTTTTTTTTCAAAATA
CAATGTTTTCTACGCCGAAAATGTTTTAGAGAGATTTTTCTCGGTTTTCAATTTCTAAAATTAAT
CAAACATCATCATTTATTTCATATTAAATCAGATTTTAAAAATTAATTCATTTTCATGAGTTTTT
GATTTTTTCCTTAAAACTCTATTTTTTCTAAAATACGATATTTTCAACTCCGTAAATTTTTTCGA
GGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAATCATTTATTTCATATTAATTCAAC
Found at i:463484 original size:324 final size:322
Alignment explanation
Indices: 462838--463484 Score: 674
Period size: 324 Copynumber: 2.0 Consensus size: 322
462828 TTAAATCAGT
* *
462838 TTTCAAAAATTAATTCATCTTCATGAGTTTTTAAATTTTTTCTTGAAATTTTTTTTTTCGAAATA
1 TTTCAAAAATTAATTCATCTTCATGAGTTTTTAAATTTTTTCGTGAAATTTTTTTTTTCAAAATA
** * * * *
462903 TGATGTTTTCTACGCCGAAAATGTTTTCGAGAGATTTTTCTTGGTTTTTAATTTCTAAATTTAAT
66 CAATGTTTTCTACGCCGAAAATGTTTTAGAGAGATTTTTCTCGGTTTTCAATTTCTAAAATTAAT
* * * *
462968 CAAATATTATCATTTATTTCATATTAAATCAGCTTTTAAAAATTCATTCATTTTCATGAGTTTTT
131 CAAACATCATCATTTATTTCATATTAAATCAGATTTTAAAAATTAATTCATTTTCATGAGTTTTT
* * *
463033 GATTTTTTCCTTAAAACTCTATTTTTTCTAAAATATGATATTTTCTACTTCGTAAATTTTTTCGA
196 GATTTTTTCCTTAAAACTCTATTTTTTCTAAAATACGATATTTTCAACTCCGTAAATTTTTTCG-
* * * * *
463098 ATGGATTTTTCTTGGTTTTCAATTTTTAAAATTCATCAAATCATTTATTTCATATTAATTCAAC
260 AGGGATTTTTCTTGGTTTACAATTTTCAAAATCCATCAAATCATTTATTGCATA-TAATTCAAC
* * *
463162 TTTCAAAAATGT-ATTCAT-TTTATTGAGTTTTTTATTTTTTTCGTGAAACTTTCTTTTTTTCTA
1 TTTCAAAAAT-TAATTCATCTTCA-TGAGTTTTTAAATTTTTTCGTGAAA-TTT-TTTTTTTC-A
* * * * *
463225 AAATACAATGTTTTCTAC-TCTATAAT-TTTTAGAGGGGA-TTTTCTCGGTTTTCAATTTTTAAA
61 AAATACAATGTTTTCTACGCCGAAAATGTTTTAGA-GAGATTTTTCTCGGTTTTCAATTTCTAAA
* * * *
463287 ATTCATCAAACATCATTATTTGA-TTCATATTAATTCA-ATTTTAAAAAATTAATTCATTTTTAT
125 ATTAATCAAACATCATCATTT-ATTTCATATTAAATCAGATTTT-AAAAATTAATTCATTTTCAT
* * * * * *
463350 GAGTTTTTTATTTTTT-GTTGAAATTTTATTTTTTCTGAAAA-ACCGA-GTTTTCAACTCCGTAA
188 GAGTTTTTGATTTTTTCCTTAAAACTCTATTTTTTCT-AAAATA-CGATATTTTCAACTCCGTAA
* *
463412 ATTTTTTCG-GGGAAATTTTTCTTGGTTTAGAATTTTACAAAACTCCCATTAAATCAGTTT-TTG
251 ATTTTTTCGAGGG--ATTTTTCTTGGTTTACAATTTT-CAAAA-T-CCATCAAATCA-TTTATTG
463475 CA-A-AATTCAA
310 CATATAATTCAA
463485 TTTATTTTTT
Statistics
Matches: 267, Mismatches: 40, Indels: 32
0.79 0.12 0.09
Matches are distributed among these distances:
322 2 0.01
323 3 0.01
324 108 0.40
325 103 0.39
326 19 0.07
327 29 0.11
328 3 0.01
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.50
Consensus pattern (322 bp):
TTTCAAAAATTAATTCATCTTCATGAGTTTTTAAATTTTTTCGTGAAATTTTTTTTTTCAAAATA
CAATGTTTTCTACGCCGAAAATGTTTTAGAGAGATTTTTCTCGGTTTTCAATTTCTAAAATTAAT
CAAACATCATCATTTATTTCATATTAAATCAGATTTTAAAAATTAATTCATTTTCATGAGTTTTT
GATTTTTTCCTTAAAACTCTATTTTTTCTAAAATACGATATTTTCAACTCCGTAAATTTTTTCGA
GGGATTTTTCTTGGTTTACAATTTTCAAAATCCATCAAATCATTTATTGCATATAATTCAAC
Found at i:466273 original size:20 final size:20
Alignment explanation
Indices: 466250--466298 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 20
466240 CTGGACATGT
*
466250 TAAATATGCATGAAACATAA
1 TAAAAATGCATGAAACATAA
466270 TAAAAAAAATGCATGAAACATAA
1 T---AAAAATGCATGAAACATAA
466293 TAAAAA
1 TAAAAA
466299 AAATGCATGG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 6 0.24
23 19 0.76
ACGTcount: A:0.63, C:0.08, G:0.08, T:0.20
Consensus pattern (20 bp):
TAAAAATGCATGAAACATAA
Found at i:466285 original size:23 final size:23
Alignment explanation
Indices: 466255--466307 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
466245 CATGTTAAAT
466255 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
466278 ATGCATGAAACATAATAAAAAAA
1 ATGCATGAAACATAATAAAAAAA
466301 ATGCATG
1 ATGCATG
466308 GTCAAAGGCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.60, C:0.09, G:0.11, T:0.19
Consensus pattern (23 bp):
ATGCATGAAACATAATAAAAAAA
Found at i:467265 original size:20 final size:20
Alignment explanation
Indices: 467218--467292 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
467208 AAAAAGACAT
*
467218 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
467237 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
467258 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
467278 AATGTATCGATACAT
1 AATGTATCGATACAT
467293 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:467286 original size:40 final size:39
Alignment explanation
Indices: 467215--467292 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
467205 GGTAAAAAGA
* *
467215 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
467254 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
467293 CAGGGTATGA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.35
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:469417 original size:156 final size:154
Alignment explanation
Indices: 468876--469613 Score: 558
Period size: 157 Copynumber: 4.7 Consensus size: 154
468866 TCATAGAGGT
* * * * * * * * * *
468876 ATTTTTGTAATTTTTTAGAACCAACTCCTAGGTTATCACCGAGTCCACTTTCATGTCGAAAGTAG
1 ATTTTCGTAATTTCTTAGAACCAAGTCCTAGGTTGTCACCGGGTCCGCTTTTATGCCGAAGGTGG
* * * * ** * * * *
468941 GTATTTAGGATAGGTTCATCCTATTTCTA-TCCTTTTTAAGTGTCACTAGGGGTACCGAGATATT
66 GCATTTAGGATAGGTTCATCCCATCTCTAGT-CTTTTTAAGT-CCTTTAGGAGTATCGGGATA-C
* * * * *
469005 TTTATGTCGAAAGTATACCCCTAGGGGT
128 TTTACGTCAAAAGTAT-CCCTTATGGGC
* * * * * ** * * **
469033 ATTTTGGTAATTTTTTAGAATCAATTCTTAGGTCATCATCGGGTTCAG-TTTTATGTTGAAGGTG
1 ATTTTCGTAATTTCTTAGAACCAAGTCCTAGGTTGTCACCGGG-TCCGCTTTTATGCCGAAGGTG
* * * * * * ** *
469097 AGCGTTTAGGATAGGTTCATCTCTTTTATGAGTCTTTTTAAGTCCTTTAGG-GTCGCCGAGATAC
65 GGCATTTAGGATAGGTTCATCCCATCTCT-AGTCTTTTTAAGTCCTTTAGGAGT-ATCGGGATAC
* *
469161 TTTTACGTCAAAAGTATGCCCATAGGGGC
128 -TTTACGTCAAAAGTAT-CCCTTATGGGC
* * * * *
469190 ATTTTCGTAATTTCTTAGAATCGAGTCCTAAGTTGTCACCGGGTTCGCTTTTATGCCGAAGGTGA
1 ATTTTCGTAATTTCTTAGAACCAAGTCCTAGGTTGTCACCGGGTCCGCTTTTATGCCGAAGGTGG
* * * * *
469255 GAATTTAGGATAGGTTTATCCCATCTCTAGATCTTTTCTAGGTCCTTTAGGGGTATTGGG-TACT
66 GCATTTAGGATAGGTTCATCCCATCTCTAG-TCTTTT-TAAGTCCTTTAGGAGTATCGGGATACT
*
469319 TCTACATCAAAAGTATCCCTTATGGGC
129 T-TACGTCAAAAGTATCCCTTATGGGC
* * * * * *
469346 ATTTTCATAATTT-TCTAAAACCAAGTCCTAGGTTATCACCGAGTCCACTTTTATGCCGAATGTG
1 ATTTTCGTAATTTCT-TAGAACCAAGTCCTAGGTTGTCACCGGGTCCGCTTTTATGCCGAAGGTG
* * * *
469410 GGCATTTAGGAT-GGTTCATCCCTTATGTAGTCTTTTTAAGTCTTTTAGGAGTATCGGGATACTT
65 GGCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAGTCCTTTAGGAGTATCGGGATACTT
* *
469474 TCACGT-AGAAGGTATCTCTT-TGGGGC
130 T-ACGTCA-AAAGTATCCCTTAT-GGGC
* * *
469500 ATTTTCGTAATTTCTTAGAACCAATTCCTAGGTCGTCACCGGGTCCGCTTTTATGCTGAAGGTGG
1 ATTTTCGTAATTTCTTAGAACCAAGTCCTAGGTTGTCACCGGGTCCGCTTTTATGCCGAAGGTGG
* * * * *
469565 ACATTTAGAATAGGTTCATCTCATCTCT-GGCTTTTTTAAGTCCATTAGG
66 GCATTTAGGATAGGTTCATCCCATCTCTAGTC-TTTTTAAGTCCTTTAGG
469614 GATACCAAGA
Statistics
Matches: 464, Mismatches: 99, Indels: 38
0.77 0.16 0.06
Matches are distributed among these distances:
153 21 0.05
154 93 0.20
155 43 0.09
156 79 0.17
157 198 0.43
158 27 0.06
159 3 0.01
ACGTcount: A:0.23, C:0.18, G:0.21, T:0.38
Consensus pattern (154 bp):
ATTTTCGTAATTTCTTAGAACCAAGTCCTAGGTTGTCACCGGGTCCGCTTTTATGCCGAAGGTGG
GCATTTAGGATAGGTTCATCCCATCTCTAGTCTTTTTAAGTCCTTTAGGAGTATCGGGATACTTT
ACGTCAAAAGTATCCCTTATGGGC
Found at i:469774 original size:72 final size:72
Alignment explanation
Indices: 469678--469823 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 72
469668 TTCTTAAACT
* * *
469678 TAGCCTTTTAAAGTTATCGGGTACCTTAGTATCAATGGTAAGCTTTAAGAATAATTTGATCGAGT
1 TAGCCCTTTAAAGTTATCGAGTACCTTAGTATCAATGGTAAGCTTTAAAAATAATTTGATCGAGT
469743 CCTAAGC
66 CCTAAGC
*
469750 TAGCCCTTTAGAGTTATCGAGTACCTTAGTATCAATGGTAAGCTTTAAAAATAATTTGATCGAGT
1 TAGCCCTTTAAAGTTATCGAGTACCTTAGTATCAATGGTAAGCTTTAAAAATAATTTGATCGAGT
469815 CCTAAGC
66 CCTAAGC
469822 TA
1 TA
469824 TTATCAGGTA
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (72 bp):
TAGCCCTTTAAAGTTATCGAGTACCTTAGTATCAATGGTAAGCTTTAAAAATAATTTGATCGAGT
CCTAAGC
Found at i:482484 original size:13 final size:13
Alignment explanation
Indices: 482462--482496 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
482452 TTCCCCAGAG
*
482462 GATTTATGATTCT
1 GATTTGTGATTCT
*
482475 GATTTGTGATTGT
1 GATTTGTGATTCT
482488 GATTTGTGA
1 GATTTGTGA
482497 ATTGTGATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.51
Consensus pattern (13 bp):
GATTTGTGATTCT
Found at i:484160 original size:7 final size:7
Alignment explanation
Indices: 484148--484200 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
484138 TGGATTTGAA
484148 TTTAAAT
1 TTTAAAT
484155 TTTAAAAT
1 TTT-AAAT
484163 TTTAAAAT
1 TTT-AAAT
484171 TTTAAAT
1 TTTAAAT
*
484178 TTGAAAT
1 TTTAAAT
* *
484185 TAATAATT
1 T-TTAAAT
484193 TTTAAAT
1 TTTAAAT
484200 T
1 T
484201 CATGATTTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
7 19 0.50
8 19 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (7 bp):
TTTAAAT
Found at i:484164 original size:8 final size:8
Alignment explanation
Indices: 484151--484176 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
484141 ATTTGAATTT
484151 AAATTTTA
1 AAATTTTA
484159 AAATTTTA
1 AAATTTTA
484167 AAATTTTA
1 AAATTTTA
484175 AA
1 AA
484177 TTTGAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (8 bp):
AAATTTTA
Found at i:484168 original size:15 final size:14
Alignment explanation
Indices: 484148--484200 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
484138 TGGATTTGAA
484148 TTTAAATTTTAAAAT
1 TTTAAATTTT-AAAT
484163 TTTAAAATTTTAAAT
1 TTT-AAATTTTAAAT
* * *
484178 TTGAAATTAATAATT
1 TTTAAATT-TTAAAT
484193 TTTAAATT
1 TTTAAATT
484201 CATGATTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 20 0.62
16 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTAAATTTTAAAT
Found at i:484336 original size:18 final size:19
Alignment explanation
Indices: 484288--484336 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
484278 AACAACATAC
*
484288 AAAATAATTAAATGAAACT
1 AAAATAAATAAATGAAACT
* *
484307 AAAATACA-AAATGCAACT
1 AAAATAAATAAATGAAACT
484325 AAAA-AAATAAAT
1 AAAATAAATAAAT
484337 TTTATTCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 2 0.08
18 17 0.68
19 6 0.24
ACGTcount: A:0.67, C:0.08, G:0.04, T:0.20
Consensus pattern (19 bp):
AAAATAAATAAATGAAACT
Found at i:484514 original size:13 final size:13
Alignment explanation
Indices: 484498--484522 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
484488 ATTTTAAAAA
484498 TAAATTTAAATTT
1 TAAATTTAAATTT
484511 TAAATTTAAATT
1 TAAATTTAAATT
484523 ACAGGTTGGA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TAAATTTAAATTT
Found at i:486246 original size:17 final size:18
Alignment explanation
Indices: 486226--486259 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
486216 ATATATTTAT
486226 TTAATAT-TTTAAATAAA
1 TTAATATATTTAAATAAA
*
486243 TTAATATATTTATATAA
1 TTAATATATTTAAATAA
486260 TAATTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTAATATATTTAAATAAA
Found at i:486266 original size:20 final size:19
Alignment explanation
Indices: 486229--486267 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
486219 TATTTATTTA
486229 ATATTTTAAATAAATTAAT
1 ATATTTTAAATAAATTAAT
486248 ATATTTATATAAT-AATTAAT
1 ATATTT-TA-AATAAATTAAT
486268 TAATTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 9 0.50
21 3 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATATTTTAAATAAATTAAT
Found at i:488743 original size:18 final size:19
Alignment explanation
Indices: 488709--488758 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
488699 TATTAATAAA
488709 AATAAATATATAATACATC
1 AATAAATATATAATACATC
*
488728 AATAATTATA-AATACAT-
1 AATAAATATATAATACATC
*
488745 AA-AAGTATATAATA
1 AATAAATATATAATA
488759 GATAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.21
17 6 0.21
18 7 0.25
19 9 0.32
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (19 bp):
AATAAATATATAATACATC
Found at i:488763 original size:17 final size:17
Alignment explanation
Indices: 488715--488764 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
488705 TAAAAATAAA
*
488715 TATATAATACATCAATAAT
1 TATATAATACAT-AA-AAG
488734 TATA-AATACATAAAAG
1 TATATAATACATAAAAG
*
488750 TATATAATAGATAAA
1 TATATAATACATAAA
488765 TTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.21
17 11 0.39
18 7 0.25
19 4 0.14
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (17 bp):
TATATAATACATAAAAG
Found at i:489856 original size:24 final size:24
Alignment explanation
Indices: 489824--489871 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
489814 CTCCTACACC
489824 TTCTCTCTCTCTCTACCACTATAT
1 TTCTCTCTCTCTCTACCACTATAT
*
489848 TTCTCTCTCTTTCTACCACTATAT
1 TTCTCTCTCTCTCTACCACTATAT
489872 ATGGCAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.17, C:0.35, G:0.00, T:0.48
Consensus pattern (24 bp):
TTCTCTCTCTCTCTACCACTATAT
Found at i:490410 original size:14 final size:14
Alignment explanation
Indices: 490391--490418 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
490381 TATATGTAAA
490391 TATACTCTAAAATT
1 TATACTCTAAAATT
490405 TATACTCTAAAATT
1 TATACTCTAAAATT
490419 GATAAGTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (14 bp):
TATACTCTAAAATT
Found at i:491233 original size:16 final size:17
Alignment explanation
Indices: 491191--491269 Score: 58
Period size: 16 Copynumber: 4.8 Consensus size: 17
491181 ATACTGAAAA
*
491191 AATATTAAATATATTAT
1 AATAATAAATATATTAT
* *
491208 ATTAAAAAATATA-TAT
1 AATAATAAATATATTAT
*
491224 AATAATAAATA-ATTAA
1 AATAATAAATATATTAT
* **
491240 AAGTTATATTTATATTA-
1 AA-TAATAAATATATTAT
491257 AATAATAAA-ATAT
1 AATAATAAATATAT
491270 AAATTAAAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 8
0.70 0.18 0.12
Matches are distributed among these distances:
15 5 0.11
16 20 0.43
17 18 0.38
18 4 0.09
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (17 bp):
AATAATAAATATATTAT
Found at i:491241 original size:26 final size:26
Alignment explanation
Indices: 491212--491276 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
491202 TATTATATTA
491212 AAAAATATATA-TAATAATAAATAATT
1 AAAAATATATATTAATAATAAATAA-T
* * *
491238 AAAAGT-TATATTTATATTAAATAAT
1 AAAAATATATATTAATAATAAATAAT
*
491263 -AAAATATAAATTAA
1 AAAAATATATATTAA
491277 AAACATATTA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
24 4 0.13
25 11 0.35
26 16 0.52
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (26 bp):
AAAAATATATATTAATAATAAATAAT
Found at i:491294 original size:17 final size:18
Alignment explanation
Indices: 491272--491312 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
491262 TAAAATATAA
491272 ATTAAAAACATA-TTAA-T
1 ATTAAAAA-ATAGTTAATT
*
491289 ATTAAATAATAGTTAATT
1 ATTAAAAAATAGTTAATT
491307 ATTAAA
1 ATTAAA
491313 TTATATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 3 0.14
17 11 0.52
18 7 0.33
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
ATTAAAAAATAGTTAATT
Found at i:491299 original size:69 final size:65
Alignment explanation
Indices: 491215--491384 Score: 159
Period size: 69 Copynumber: 2.5 Consensus size: 65
491205 TATATTAAAA
491215 AATATATATAATAATAAATAATTAAAAGTTATATTTATATTAAATAATAAAATATAAATTAAAAA
1 AATAT-TA-AATAATAAATAATTAAAA-TTATATTTATATTAAA-AATAAAAT-T--ATTAAAAA
491280 -CATATT
59 TCATATT
** * * *
491286 AATATTAAATAATAGTTAATTATTAAATTATATTTATTTTAAAAATTAAATTATTAAAAATTATA
1 AATATTAAATAATAAATAATTA--AAATTATATTTATATTAAAAATAAAATTATTAAAAATCATA
491351 TT
64 TT
* *
491353 GACATTAAA-AATAAATTAA-TAAAATTA-ATTTA
1 AATATTAAATAATAAA-TAATTAAAATTATATTTA
491385 AATAACCCTT
Statistics
Matches: 86, Mismatches: 9, Indels: 16
0.77 0.08 0.14
Matches are distributed among these distances:
63 5 0.06
64 6 0.07
66 14 0.16
67 15 0.17
68 1 0.01
69 20 0.23
70 17 0.20
71 8 0.09
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (65 bp):
AATATTAAATAATAAATAATTAAAATTATATTTATATTAAAAATAAAATTATTAAAAATCATATT
Found at i:491344 original size:15 final size:15
Alignment explanation
Indices: 491324--491380 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
491314 TATATTTATT
491324 TTAAAAATTAAATTA
1 TTAAAAATTAAATTA
*
491339 TTAAAAATTATATTGACA
1 TTAAAAATTAAATT---A
491357 TTAAAAA-TAAATTA
1 TTAAAAATTAAATTA
*
491371 AT-AAAATTAA
1 TTAAAAATTAA
491381 TTTAAATAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
13 4 0.11
14 5 0.14
15 13 0.37
17 5 0.14
18 8 0.23
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (15 bp):
TTAAAAATTAAATTA
Found at i:491352 original size:33 final size:34
Alignment explanation
Indices: 491224--491384 Score: 124
Period size: 33 Copynumber: 4.9 Consensus size: 34
491214 AAATATATAT
* *
491224 AATAA-TAAATAATTAAAAGTTATATTTATATTA
1 AATAATTAAATTATTAAAAATTATATTTATATTA
* * *
491257 AATAATAAAATATAAATTAAAAA-CATATTAATATTA
1 AATAATTAAAT-T--ATTAAAAATTATATTTATATTA
* *
491293 AATAATAGTTAATTATT--AAATTATATTTATTTTA
1 AATAAT--TAAATTATTAAAAATTATATTTATATTA
* *
491327 AA-AATTAAATTATTAAAAATTATATTGACATTA
1 AATAATTAAATTATTAAAAATTATATTTATATTA
*
491360 AA-AA-TAAATTAAT-AAAATTA-ATTTA
1 AATAATTAAATTATTAAAAATTATATTTA
491385 AATAACCCTT
Statistics
Matches: 103, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
30 4 0.04
31 15 0.15
32 8 0.08
33 29 0.28
34 16 0.16
35 3 0.03
36 17 0.17
37 8 0.08
38 3 0.03
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (34 bp):
AATAATTAAATTATTAAAAATTATATTTATATTA
Found at i:494455 original size:2 final size:2
Alignment explanation
Indices: 494448--494474 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
494438 TTATGTTCCA
494448 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
494475 AGATAGTTGC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:495674 original size:18 final size:17
Alignment explanation
Indices: 495651--495697 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
495641 CACGAAATCA
*
495651 ATTTAATTTAAATTTAAG
1 ATTTAATAT-AATTTAAG
495669 ATTTAATATAATTTAA-
1 ATTTAATATAATTTAAG
*
495685 TTTTAATAATAAT
1 ATTTAAT-ATAAT
495698 ATTTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 6 0.23
17 12 0.46
18 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTTAATATAATTTAAG
Found at i:495681 original size:28 final size:26
Alignment explanation
Indices: 495650--495722 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 26
495640 ACACGAAATC
495650 AATTTAATTTAAATTTAAGATTTAATAT
1 AATTTAATTTAAATTTAAGATTT-A-AT
* * *
495678 AATTTAATTTTAATAATAATATTTAAT
1 AATTTAATTTAAAT-TTAAGATTTAAT
495705 AATTTAAATTTTAAATTT
1 AATTT-AA-TTTAAATTT
495723 TAATAATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
27 7 0.19
28 17 0.46
29 13 0.35
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (26 bp):
AATTTAATTTAAATTTAAGATTTAAT
Found at i:495726 original size:29 final size:28
Alignment explanation
Indices: 495650--495745 Score: 83
Period size: 29 Copynumber: 3.4 Consensus size: 28
495640 ACACGAAATC
*
495650 AATTTAA-TTTAAA-TTTAAGATTTAATAT
1 AATTTAATTTTAAATTTTAATATTT-A-AT
**
495678 AATTTAATTTT-AATAATAATATTTAAT
1 AATTTAATTTTAAATTTTAATATTTAAT
*
495705 AATTTAAATTTTAAATTTTAATAATTTTAT
1 AATTT-AATTTTAAATTTTAAT-ATTTAAT
495735 -ATTTATATTTT
1 AATTTA-ATTTT
495746 TATATTTTTA
Statistics
Matches: 56, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
27 7 0.12
28 17 0.30
29 26 0.46
30 6 0.11
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
AATTTAATTTTAAATTTTAATATTTAAT
Found at i:495744 original size:22 final size:22
Alignment explanation
Indices: 495682--495755 Score: 62
Period size: 22 Copynumber: 3.4 Consensus size: 22
495672 TAATATAATT
* *
495682 TAATTTTAATAATAATA-TTTAA
1 TAATTTT-ATATTTATATTTTAA
* *
495704 TAA-TTTAAATTTTAAATTTTAA
1 TAATTTTATA-TTTATATTTTAA
*
495726 TAATTTTATATTTATATTTTTA
1 TAATTTTATATTTATATTTTAA
*
495748 TATTTTTA
1 TAATTTTA
495756 AAATACAATC
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
20 2 0.05
21 6 0.15
22 28 0.68
23 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (22 bp):
TAATTTTATATTTATATTTTAA
Found at i:499443 original size:14 final size:14
Alignment explanation
Indices: 499426--499467 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
499416 TAGATAAATT
499426 AACAAAAATAATAA
1 AACAAAAATAATAA
* *
499440 AACAATAATAACAA
1 AACAAAAATAATAA
499454 AACACAAAA-AATAA
1 AACA-AAAATAATAA
499468 TGAAAAAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 20 0.87
15 3 0.13
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (14 bp):
AACAAAAATAATAA
Found at i:502680 original size:20 final size:20
Alignment explanation
Indices: 502655--502708 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
502645 AAAACCCTTG
*
502655 AATGTATCGATACACACCCT
1 AATGTATCGATACACACCCA
502675 AATGTATCGATACACACCCA
1 AATGTATCGATACACACCCA
502695 AATGTATCGATACA
1 AATGTATCGATACA
502709 TTATGCTTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (20 bp):
AATGTATCGATACACACCCA
Found at i:502759 original size:20 final size:19
Alignment explanation
Indices: 502720--502769 Score: 73
Period size: 20 Copynumber: 2.6 Consensus size: 19
502710 TATGCTTTGC
**
502720 ATCGATACATGTTCATTGT
1 ATCGATACATGGACATTGT
502739 ATCGATACATGGACAATTGT
1 ATCGATACATGGAC-ATTGT
502759 ATCGATACATG
1 ATCGATACATG
502770 AAATTAGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (19 bp):
ATCGATACATGGACATTGT
Found at i:502842 original size:33 final size:33
Alignment explanation
Indices: 502798--502866 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
502788 CTACCACTGT
*
502798 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
* *
502831 TTGTATGGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
502864 TTG
1 TTG
502867 CTTGTAACGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 31 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:509026 original size:13 final size:13
Alignment explanation
Indices: 509008--509034 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
508998 ACAACATTCC
509008 TTGTATCGATACA
1 TTGTATCGATACA
509021 TTGTATCGATACA
1 TTGTATCGATACA
509034 T
1 T
509035 GGGTTACTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:510714 original size:58 final size:58
Alignment explanation
Indices: 510624--510741 Score: 218
Period size: 58 Copynumber: 2.0 Consensus size: 58
510614 CGAGCATCAT
510624 TCCTCGACTAACTCTAGTGACAACAAGTCTTAGAGTTTAGTCTTCTTATTAGGATTAG
1 TCCTCGACTAACTCTAGTGACAACAAGTCTTAGAGTTTAGTCTTCTTATTAGGATTAG
* *
510682 TCCTCGACTAACTCTAGTGACGACAAGTCTTAGATTTTAGTCTTCTTATTAGGATTAG
1 TCCTCGACTAACTCTAGTGACAACAAGTCTTAGAGTTTAGTCTTCTTATTAGGATTAG
510740 TC
1 TC
510742 ATACTTCTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.37
Consensus pattern (58 bp):
TCCTCGACTAACTCTAGTGACAACAAGTCTTAGAGTTTAGTCTTCTTATTAGGATTAG
Found at i:511571 original size:19 final size:19
Alignment explanation
Indices: 511528--511599 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
511518 CACACCCAGA
*
511528 TGTATCGATACAT-TATGCTT
1 TGTATCGATACATGT-T-CAT
511548 TGTATCGATACATGTTCAT
1 TGTATCGATACATGTTCAT
**
511567 TGTATCGATACATGGACAAT
1 TGTATCGATACATGTTC-AT
511587 TGTATCGATACAT
1 TGTATCGATACAT
511600 TAAATTAGCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
19 17 0.36
20 29 0.62
21 1 0.02
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (19 bp):
TGTATCGATACATGTTCAT
Found at i:511655 original size:20 final size:20
Alignment explanation
Indices: 511630--511682 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
511620 TACCACTGTT
*
511630 TGTATCGATACATGGT-ACAA
1 TGTATCGATACATGATGA-AA
*
511650 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAA
511670 TGTATCGATACAT
1 TGTATCGATACAT
511683 TGCTTGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:517811 original size:52 final size:49
Alignment explanation
Indices: 517712--518001 Score: 200
Period size: 52 Copynumber: 5.8 Consensus size: 49
517702 TAATATTGGG
* * * ** *
517712 CTTAAGGATGTAAAGAATGTCAATGTGCTGATTCACGATCAGCGACATTAGA
1 CTTAA-GATGTAAAG-ATGCCAATATGCTGATTCAAGGCCAACGACATT-GA
* * * *
517764 CTTGAAGATGAAAAGAATGCCAATGTGCTGATTCAAGGCCAATGACATTGG
1 CTT-AAGATGTAAAG-ATGCCAATATGCTGATTCAAGGCCAACGACATTGA
* * *
517815 GTTAAGGAATGTTAAAGATGCCAATATGCTGATTCAAGGCCAACGATATCGGA
1 CTTAA-G-ATG-TAAAGATGCCAATATGCTGATTCAAGGCCAACGACAT-TGA
* * *
517868 CTTAAAGATG-AAAG-TGCCAATATGCTGATTCAAGGCTAGCGACATTGGT
1 CTT-AAGATGTAAAGATGCCAATATGCTGATTCAAGGCCAACGACATT-GA
* * * * *
517917 CTTAA-A-G-ACAAGGTGCCAATATGCTAATTCAAGGCTAGCGACATTGGT
1 CTTAAGATGTA-AAGATGCCAATATGCTGATTCAAGGCCAACGACATT-GA
*
517965 CTTAA-A-G-ACAAGGTGCCAATATGCTGATTCAAGGCCA
1 CTTAAGATGTA-AAGATGCCAATATGCTGATTCAAGGCCA
518002 GCGATATTAG
Statistics
Matches: 205, Mismatches: 24, Indels: 22
0.82 0.10 0.09
Matches are distributed among these distances:
46 2 0.01
47 4 0.02
48 71 0.35
49 32 0.16
50 6 0.03
51 4 0.02
52 74 0.36
53 10 0.05
54 2 0.01
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (49 bp):
CTTAAGATGTAAAGATGCCAATATGCTGATTCAAGGCCAACGACATTGA
Found at i:517952 original size:48 final size:48
Alignment explanation
Indices: 517833--518110 Score: 288
Period size: 48 Copynumber: 5.9 Consensus size: 48
517823 ATGTTAAAGA
* * * * * *
517833 TGCCAATATGCTGATTCAAGGCCAACGATATCGGACTTAAAGATGAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGG
*
517882 TGCCAATATGCTGATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
* *
517930 TGCCAATATGCTAATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
*
517978 TGCCAATATGCTGATTCAAGGCCAGCGATATTAGG-CTT---------G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATT-GGTCTTAAAGACAAGG
* *
518017 TGCCAATGTGCTGATTCAAGGCCAGCTGACATTGGTCTTAAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGC-GACATTGGTCTTAAAGA-CAAGG
* * * * *
518067 TGCTAATATGTTGTTTCAAGGCCAGCGATATTGGACTTAGAAGA
1 TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTA-AAGA
518111 AGACGCCACC
Statistics
Matches: 196, Mismatches: 19, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
39 28 0.14
40 8 0.04
48 82 0.42
49 51 0.26
50 27 0.14
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (48 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGG
Found at i:518085 original size:89 final size:87
Alignment explanation
Indices: 517929--518098 Score: 259
Period size: 89 Copynumber: 1.9 Consensus size: 87
517919 TAAAGACAAG
* *
517929 GTGCCAATATGCTAATTCAAGGCTAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATT
1 GTGCCAATATGCTAATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCTGATT
517994 CAAGGCCAGCGATATTAGGCTT
66 CAAGGCCAGCGATATTAGGCTT
* * * * *
518016 GTGCCAATGTGCTGATTCAAGGCCAGCTGACATTGGTCTTAAAGATAAAGGTGCTAATATGTTGT
1 GTGCCAATATGCTAATTCAAGGCCAGC-GACATTGGTCTTAAAGA-AAAGGTGCCAATATGCTGA
518081 TTCAAGGCCAGCGATATT
64 TTCAAGGCCAGCGATATT
518099 GGACTTAGAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
87 24 0.32
88 17 0.23
89 33 0.45
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (87 bp):
GTGCCAATATGCTAATTCAAGGCCAGCGACATTGGTCTTAAAGAAAAGGTGCCAATATGCTGATT
CAAGGCCAGCGATATTAGGCTT
Found at i:518185 original size:28 final size:28
Alignment explanation
Indices: 518127--518257 Score: 111
Period size: 28 Copynumber: 4.6 Consensus size: 28
518117 CACCAACTTG
**
518127 TGTGGGCTTTTGAAAGGGTTG-CACCAACT
1 TGTGGGCTTTTG-AA-GGTTGCCACTGACT
* *
518156 TGTGTGCTTTTGAAGGTTACCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
* * * *
518184 TGTGGGCTTTTAAAAGGGGTGCCACGGAGT
1 TGTGGGCTTTT-GAA-GGTTGCCACTGACT
* * *
518214 TATGGGCTTTTGACGATTGCCACTGACT
1 TGTGGGCTTTTGAAGGTTGCCACTGACT
*
518242 TGTAGGCTTTTGAAGG
1 TGTGGGCTTTTGAAGG
518258 GTGAGGAATG
Statistics
Matches: 78, Mismatches: 21, Indels: 7
0.74 0.20 0.07
Matches are distributed among these distances:
27 4 0.05
28 40 0.51
29 14 0.18
30 20 0.26
ACGTcount: A:0.19, C:0.16, G:0.31, T:0.34
Consensus pattern (28 bp):
TGTGGGCTTTTGAAGGTTGCCACTGACT
Found at i:519740 original size:17 final size:17
Alignment explanation
Indices: 519710--519752 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
519700 CTTTTTGTTA
*
519710 TTTTTTTATTTGTT-TT
1 TTTTTTTGTTTGTTCTT
519726 TTTTGTTTGTTTGTTCTT
1 TTTT-TTTGTTTGTTCTT
519744 TTTTTTTGT
1 TTTTTTTGT
519753 CTCTATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 14 0.58
18 6 0.25
ACGTcount: A:0.02, C:0.02, G:0.12, T:0.84
Consensus pattern (17 bp):
TTTTTTTGTTTGTTCTT
Found at i:533630 original size:20 final size:20
Alignment explanation
Indices: 533577--533631 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
533567 AAATTCCCAG
**
533577 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
533597 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
533617 ATGTATCGATACATT
1 ATGTATCGATACATT
533632 TCCTTGGCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:535600 original size:155 final size:155
Alignment explanation
Indices: 535351--535680 Score: 416
Period size: 155 Copynumber: 2.1 Consensus size: 155
535341 AAAAGACCCG
*
535351 ATATGATAT-AACATGACAAACCTATCCCTAAAGCAATACCTTCAACATGAAAGTATCTTGATGA
1 ATATGATATGAA-ATGACAAACCTATCCCTAAAGCAATACCTTCAACATGAAAGTATCTCGATGA
** * * *
535415 TCCTAAAAGACTTGGCTTTGGGGTGAAATTATTAAAATGCTTCTAAGGTATACTTTTAATATGAA
65 TCCTAAAAGACTTGGCTTTAAGGTAAAATTATTAAAATGC-CCTAAGGTATACCTTTAATATGAA
535480 AGTATC-CTAGTAACCATAATAGACTCA
129 AGTATCTC-AGTAACCATAATAGACTCA
* * * *
535507 ATATGATATGAAATGACAAACTTATCCTTAAA-CTATACCTTCGACATGAAAGTATCTCGATGAT
1 ATATGATATGAAATGACAAACCTATCCCTAAAGCAATACCTTCAACATGAAAGTATCTCGATGAT
* * * * *
535571 CTTAAAGGGCTTGGCTTTAATGTAAAATTATTAAAATGCCCTAAGGTATACCTTTGATATGAAAG
66 CCTAAAAGACTTGGCTTTAAGGTAAAATTATTAAAATGCCCTAAGGTATACCTTTAATATGAAAG
* * *
535636 TATCTCCGTAACCTTAATAGACTTA
131 TATCTCAGTAACCATAATAGACTCA
*
535661 ATAAT-ATCATGTAATGACAA
1 AT-ATGAT-ATGAAATGACAA
535681 TCATATTTTA
Statistics
Matches: 151, Mismatches: 19, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
154 47 0.31
155 75 0.50
156 27 0.18
157 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (155 bp):
ATATGATATGAAATGACAAACCTATCCCTAAAGCAATACCTTCAACATGAAAGTATCTCGATGAT
CCTAAAAGACTTGGCTTTAAGGTAAAATTATTAAAATGCCCTAAGGTATACCTTTAATATGAAAG
TATCTCAGTAACCATAATAGACTCA
Found at i:536810 original size:13 final size:13
Alignment explanation
Indices: 536792--536817 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
536782 ATTTTTTTGG
536792 TGTATCGATACAT
1 TGTATCGATACAT
536805 TGTATCGATACAT
1 TGTATCGATACAT
536818 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:539375 original size:12 final size:12
Alignment explanation
Indices: 539346--539380 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
539336 TTCATAATCC
539346 TGTATCGATACA
1 TGTATCGATACA
*
539358 -GTATCGCTACA
1 TGTATCGATACA
539369 TGTATCGATACA
1 TGTATCGATACA
539381 AAGAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.31
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:549598 original size:13 final size:13
Alignment explanation
Indices: 549580--549618 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
549570 ATAATCCCCC
*
549580 TGTATCGATACAG
1 TGTATCGATACAA
549593 TGTATCGATACAA
1 TGTATCGATACAA
549606 TGTATCGATACAA
1 TGTATCGATACAA
549619 AGAAAGATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:549634 original size:46 final size:46
Alignment explanation
Indices: 549580--549681 Score: 125
Period size: 46 Copynumber: 2.2 Consensus size: 46
549570 ATAATCCCCC
* *
549580 TGTATCGATACAGTGTATCGATACA-ATGTATCGATACAAAGAAAGA
1 TGTATCGATACAGTGAAT-GATACAGATGTATCGATACAAAGAAACA
* ** * *
549626 TGTATCGATACATTGAATTTTCCAGATGTATCGATACACAGAAACA
1 TGTATCGATACAGTGAATGATACAGATGTATCGATACAAAGAAACA
549672 TGTATCGATA
1 TGTATCGATA
549682 AATTTTGGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
45 3 0.06
46 45 0.94
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (46 bp):
TGTATCGATACAGTGAATGATACAGATGTATCGATACAAAGAAACA
Found at i:557729 original size:217 final size:217
Alignment explanation
Indices: 557354--558008 Score: 1256
Period size: 217 Copynumber: 3.0 Consensus size: 217
557344 TGGAAAGATG
557354 GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACAGGATATTCCGTGTCAAGCA
1 GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACAGGATATTCCGTGTCAAGCA
*
557419 CTGGAGAGATACCGACACGGAACATTGCCTTATAGTTTTTGTAAACCAATTTTAAAACATGTATG
66 CTGGAGAGATACCGACACGGAACATTGCCTTATGGTTTTTGTAAACCAATTTTAAAACATGTATG
557484 CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
131 CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
* *
557549 ATAAATAAATTATGCTGAACAA
196 ATAAATTAATTATGCCGAACAA
*
557571 GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACATGATATTCCGTGTCAAGCA
1 GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACAGGATATTCCGTGTCAAGCA
557636 CTGGAGAGATACCGACACGGAACATTGCCTTATGGTTTTTGTAAACCAATTTTAAAACATGTATG
66 CTGGAGAGATACCGACACGGAACATTGCCTTATGGTTTTTGTAAACCAATTTTAAAACATGTATG
557701 CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
131 CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
557766 ATAAATTAATTATGCCGAACAA
196 ATAAATTAATTATGCCGAACAA
557788 GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACAGGATATTCCGTGTCAAGCA
1 GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACAGGATATTCCGTGTCAAGCA
* *
557853 CTGGAGAGATACCTACACGAAACATTGCCTTATGGTTTTTGTAAACCAATTTTAAAACATGTATG
66 CTGGAGAGATACCGACACGGAACATTGCCTTATGGTTTTTGTAAACCAATTTTAAAACATGTATG
557918 CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
131 CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
557983 ATAAATTAATTATGCCGAACAA
196 ATAAATTAATTATGCCGAACAA
558005 GGAA
1 GGAA
558009 GAAGAAAGAA
Statistics
Matches: 431, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
217 431 1.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (217 bp):
GGAAACATAGAGATATAAAAGCTCTCTGGATTTTACTTTGAAAACAGGATATTCCGTGTCAAGCA
CTGGAGAGATACCGACACGGAACATTGCCTTATGGTTTTTGTAAACCAATTTTAAAACATGTATG
CCATCAAGATTAATTAGGAGGAAGCGTGCTGACAAAGCAATAGAGGCATATGATATTTCATGCAA
ATAAATTAATTATGCCGAACAA
Found at i:560400 original size:32 final size:32
Alignment explanation
Indices: 560359--560434 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
560349 CATTTAATAG
*
560359 TGTATCGATACATCTGGGCAAATTTGCCTGCA
1 TGTATCGATACATCTGGGCAAATTTACCTGCA
*
560391 TGTATCGATACATCTGGGCAAATTTACCTGTA
1 TGTATCGATACATCTGGGCAAATTTACCTGCA
560423 TGTATCGATACA
1 TGTATCGATACA
560435 AAGATCAGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATCTGGGCAAATTTACCTGCA
Found at i:560461 original size:13 final size:13
Alignment explanation
Indices: 560443--560467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
560433 CAAAGATCAG
560443 TGTATCGATACAA
1 TGTATCGATACAA
560456 TGTATCGATACA
1 TGTATCGATACA
560468 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:562968 original size:21 final size:22
Alignment explanation
Indices: 562935--562976 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
562925 ATTCTAATTT
562935 ATTAATTTATAGTTGTTTTTAG
1 ATTAATTTATAGTTGTTTTTAG
* *
562957 ATTAGTTT-TAGTTTTTTTTA
1 ATTAATTTATAGTTGTTTTTA
562977 AAAAAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (22 bp):
ATTAATTTATAGTTGTTTTTAG
Found at i:565579 original size:29 final size:29
Alignment explanation
Indices: 565517--565584 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
565507 ATAATGCTAG
* *
565517 AATGCATGAAATTAAATAATTGTATTTAA
1 AATGCATGGAATTAAATAATTGTATTAAA
*
565546 GATGCATGGAATATAGAATAATT-T-TTAAA
1 AATGCATGGAAT-TA-AATAATTGTATTAAA
565575 AATGCATGGA
1 AATGCATGGA
565585 GTGACATAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 23 0.70
30 3 0.09
31 7 0.21
ACGTcount: A:0.46, C:0.04, G:0.16, T:0.34
Consensus pattern (29 bp):
AATGCATGGAATTAAATAATTGTATTAAA
Found at i:565702 original size:29 final size:30
Alignment explanation
Indices: 565633--565702 Score: 69
Period size: 29 Copynumber: 2.4 Consensus size: 30
565623 AAGCTCATAG
*
565633 ATCATAGAAAATGACTTTAATATCTCTAAA
1 ATCATAGAAAATGACTATAATATCTCTAAA
565663 ATGCAT-G-AAATGA-TATAATAAT-T-TATAA
1 AT-CATAGAAAATGACTATAAT-ATCTCTA-AA
565691 ATCATAGAAAAT
1 ATCATAGAAAAT
565703 AACTTAAGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 11
0.74 0.02 0.24
Matches are distributed among these distances:
27 5 0.15
28 11 0.32
29 12 0.35
30 3 0.09
31 3 0.09
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.33
Consensus pattern (30 bp):
ATCATAGAAAATGACTATAATATCTCTAAA
Found at i:567038 original size:21 final size:20
Alignment explanation
Indices: 567012--567064 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
567002 AAAACTTGAT
567012 ATTGTATTGATACAAAGACAC
1 ATTGTATTGATACAAAG-CAC
* * *
567033 ATTGTATTAATACAATGCTC
1 ATTGTATTGATACAAAGCAC
567053 ATTGTATTGATA
1 ATTGTATTGATA
567065 TAATATGGCC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 13 0.46
21 15 0.54
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (20 bp):
ATTGTATTGATACAAAGCAC
Found at i:568631 original size:20 final size:20
Alignment explanation
Indices: 568580--568633 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
568570 TTCAGCAATT
568580 TGTATCGATACAATAAGGTAA
1 TGTATCGATAC-ATAAGGTAA
* **
568601 TATATTAATACATAA-GTATA
1 TGTATCGATACATAAGGTA-A
568621 TGTATCGATACAT
1 TGTATCGATACAT
568634 GTTTGAAATA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.12
20 15 0.58
21 8 0.31
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATAAGGTAA
Found at i:575584 original size:11 final size:11
Alignment explanation
Indices: 575568--575592 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
575558 TTTGTAATTT
575568 ATCTTGCTAAA
1 ATCTTGCTAAA
575579 ATCTTGCTAAA
1 ATCTTGCTAAA
575590 ATC
1 ATC
575593 AAGATAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (11 bp):
ATCTTGCTAAA
Found at i:576763 original size:82 final size:82
Alignment explanation
Indices: 576541--576782 Score: 297
Period size: 82 Copynumber: 3.0 Consensus size: 82
576531 AGGTTCTATC
* * * *
576541 TTAGTCTAAGTAAAAGATAGAGAGTTGTAAAAATTATACTTTATCTTTGAAAGATAACAATTAAA
1 TTAGCCTAAGTAAAAGATAGAGAGTTGTAAAAATTATACCTTATCTTTAAAAGATAATAATTAAA
* * *
576606 ATGAATAAATTGTGAAA
66 ATTAGTGAATTGTGAAA
* * ** * *
576623 CTAGCTTAAGTAAAAGATAGAGAGTTGTAAATGTTATATCTTATCTTTGAAAA-ATAATAATTTA
1 TTAGCCTAAGTAAAAGATAGAGAGTTGTAAAAATTATACCTTATCTTT-AAAAGATAATAATTAA
576687 AATTAGTGAATTGTGAAA
65 AATTAGTGAATTGTGAAA
* * * * *
576705 TTAGCCTAAGTAAAAGATAGAGAGTTATAAAACTTATACCTTATCATTAAAAGGTAATAATTCAA
1 TTAGCCTAAGTAAAAGATAGAGAGTTGTAAAAATTATACCTTATCTTTAAAAGATAATAATTAAA
*
576770 GTTAGTGAATTGT
66 ATTAGTGAATTGT
576783 AAAACTTTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
81 4 0.03
82 128 0.95
83 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.34
Consensus pattern (82 bp):
TTAGCCTAAGTAAAAGATAGAGAGTTGTAAAAATTATACCTTATCTTTAAAAGATAATAATTAAA
ATTAGTGAATTGTGAAA
Found at i:582030 original size:6 final size:6
Alignment explanation
Indices: 582015--582047 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
582005 AATTGTAGTG
582015 AAAGAGA AAAGAA AAA-AA AAAGAA AAAGAA AAA
1 AAAGA-A AAAGAA AAAGAA AAAGAA AAAGAA AAA
582048 AGATAGAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.20
6 15 0.60
7 5 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:582035 original size:11 final size:12
Alignment explanation
Indices: 582015--582047 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
582005 AATTGTAGTG
582015 AAAGAGAAAAGAA
1 AAAGA-AAAAGAA
582028 AAA-AAAAAGAA
1 AAAGAAAAAGAA
582039 AAAGAAAAA
1 AAAGAAAAA
582048 AGATAGAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.53
12 6 0.32
13 3 0.16
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAGAA
Found at i:582043 original size:17 final size:18
Alignment explanation
Indices: 582015--582048 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
582005 AATTGTAGTG
582015 AAAGAGAAAAGAAAAAAA
1 AAAGAGAAAAGAAAAAAA
582033 AAAGA-AAAAGAAAAAA
1 AAAGAGAAAAGAAAAAA
582049 GATAGAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAGAGAAAAGAAAAAAA
Found at i:585823 original size:10 final size:9
Alignment explanation
Indices: 585805--585857 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 9
585795 TCCTTTTAGA
585805 TTTTTTAAT
1 TTTTTTAAT
585814 TTTTTCTAAT
1 TTTTT-TAAT
* *
585824 ATTTTGAAT
1 TTTTTTAAT
585833 TTTTCTTAAT
1 TTTT-TTAAT
*
585843 TATTTTTTAT
1 T-TTTTTAAT
585853 TTTTT
1 TTTTT
585858 AATCACTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
9 15 0.42
10 18 0.50
11 3 0.08
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.74
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:585854 original size:20 final size:19
Alignment explanation
Indices: 585804--585857 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
585794 TTCCTTTTAG
585804 ATTTTTTAATTTTTTCTAAT
1 ATTTTTT-ATTTTTTCTAAT
* *
585824 A-TTTTGAATTTTTCTTAATT
1 ATTTTTTATTTTTTC-TAA-T
585844 ATTTTTTATTTTTT
1 ATTTTTTATTTTTT
585858 AATCACTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
18 7 0.26
19 7 0.26
20 3 0.11
21 10 0.37
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.72
Consensus pattern (19 bp):
ATTTTTTATTTTTTCTAAT
Found at i:591058 original size:13 final size:13
Alignment explanation
Indices: 591040--591123 Score: 51
Period size: 13 Copynumber: 5.5 Consensus size: 13
591030 AGCTTCGTAG
591040 CGATACATTGTAT
1 CGATACATTGTAT
591053 CGATACAAAACTTTTGTAT
1 CGATAC---A--TT-GTAT
591072 CGATACATTGTAT
1 CGATACATTGTAT
*
591085 TGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
591104 CGATACATTGTAT
1 CGATACATTGTAT
591117 CGATACA
1 CGATACA
591124 AATCTTTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 24
0.69 0.02 0.29
Matches are distributed among these distances:
13 25 0.44
14 3 0.05
16 8 0.14
18 3 0.05
19 18 0.32
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.36
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:591081 original size:32 final size:32
Alignment explanation
Indices: 591040--591130 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
591030 AGCTTCGTAG
591040 CGATACATTGTATCGATACAAAACTTTTGTAT
1 CGATACATTGTATCGATACAAAACTTTTGTAT
* * *
591072 CGATACATTGTATTGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTTTGTAT
*
591104 CGATACATTGTATCGATACAAATCTTT
1 CGATACATTGTATCGATACAAAACTTT
591131 GAAATTCAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.37
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTTTGTAT
Done.