Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 87 of 193
Found at i:28635706 original size:23 final size:23
Alignment explanation
Indices: 28635662--28635706 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28635652 AGTGAAAAGA
* *
28635662 ACAAAATGAAAATGAGTGGAAAT
1 ACAAAAAGAAAATGAGTAGAAAT
28635685 ACAAAAAGAAAA-GAGTAAGAAA
1 ACAAAAAGAAAATGAGT-AGAAA
28635707 AAGTGTAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.64, C:0.04, G:0.20, T:0.11
Consensus pattern (23 bp):
ACAAAAAGAAAATGAGTAGAAAT
Found at i:28637568 original size:13 final size:13
Alignment explanation
Indices: 28637550--28637576 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28637540 CATTATTTGC
28637550 AAGGATTCTATTT
1 AAGGATTCTATTT
28637563 AAGGATTCTATTT
1 AAGGATTCTATTT
28637576 A
1 A
28637577 CTATCGCCTT
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:0.33, C:0.07, G:0.15, T:0.44
Consensus pattern (13 bp):
AAGGATTCTATTT
Found at i:28644229 original size:21 final size:21
Alignment explanation
Indices: 28644180--28644259 Score: 65
Period size: 22 Copynumber: 3.7 Consensus size: 21
28644170 AAGTTTAGGG
* *
28644180 TTTTAAATTAAGG-TTT-ATA
1 TTTTAAATTAGGGTTTTGGTA
28644199 TTATTAAAATTAGGGTTTTGGTA
1 TT-TT-AAATTAGGGTTTTGGTA
* **
28644222 TTTTAAATAAGGGTGTAGGGTA
1 TTTTAAATTAGGGT-TTTGGTA
28644244 TTTTAAATTAAGGGTT
1 TTTTAAATT-AGGGTT
28644260 ATGGAAAATT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
19 2 0.04
20 2 0.04
21 17 0.35
22 19 0.39
23 9 0.18
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (21 bp):
TTTTAAATTAGGGTTTTGGTA
Found at i:28646554 original size:52 final size:52
Alignment explanation
Indices: 28646473--28646712 Score: 259
Period size: 52 Copynumber: 4.6 Consensus size: 52
28646463 GTAAATGAAA
* * * *
28646473 AAGGTCCT-ATGACTGTGTATCATCCTGAGTATATGAATCCTTTACAAATTAT
1 AAGGT-CTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
*
28646525 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGAATTAT
1 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
** * * * ** *
28646577 GTGGTCTGGTGACTATGTGTCATTGTGAGTATAAGAATTTTTTACGGATTAT
1 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
* * * * *
28646629 AAGGTCCGATGACTATATGTCATCTTGAGTATATGATTCCTTTACGGATTA-
1 AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
** *
28646680 AGAGGTCCAATGACTTTGTGTCATCGTGAGTAT
1 A-AGGTCTGATGACTATGTGTCATCGTGAGTAT
28646713 TAAATGAAAT
Statistics
Matches: 157, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
51 3 0.02
52 154 0.98
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (52 bp):
AAGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTAT
Found at i:28653850 original size:52 final size:52
Alignment explanation
Indices: 28653765--28654003 Score: 347
Period size: 52 Copynumber: 4.6 Consensus size: 52
28653755 TAAATGAAAA
* * *
28653765 AGGTCCGATGACTACGTGTCATCGTGAGTATATGAATCCTTTACAGATTATG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
28653817 A-GTTCCAATGACTACGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTT-CGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
28653869 AGG-TCTGATGACTATGTGTCATCGTGAGTATAAGAATCTTTTACGGATTATG
1 AGGTTC-GATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * *
28653921 AGGTTCGATGATTATGTGTCATCGTGAGTATATGATTCCTTTACGGATTAAG
1 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
*
28653973 AGGTTCGATGACTATGTGTAATCGTGAGTAT
1 AGGTTCGATGACTATGTGTCATCGTGAGTAT
28654004 TAAATGAAAT
Statistics
Matches: 169, Mismatches: 14, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
51 3 0.02
52 163 0.96
53 3 0.02
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:28689468 original size:19 final size:19
Alignment explanation
Indices: 28689423--28689469 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
28689413 ATAGTTTTCA
*
28689423 TGCATTTATATTTTATCAT
1 TGCATTTTTATTTTATCAT
* *
28689442 TGCATTTTTATTTTGTTAT
1 TGCATTTTTATTTTATCAT
28689461 TGCATTTTT
1 TGCATTTTT
28689470 GTTAAGTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.64
Consensus pattern (19 bp):
TGCATTTTTATTTTATCAT
Found at i:28689478 original size:19 final size:19
Alignment explanation
Indices: 28689440--28689486 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
28689430 ATATTTTATC
**
28689440 ATTGCATTTTTATTTTGTT
1 ATTGCATTTTTATTAAGTT
*
28689459 ATTGCATTTTTGTTAAGTT
1 ATTGCATTTTTATTAAGTT
28689478 AGTTGCATT
1 A-TTGCATT
28689487 GTCATCGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.60
Consensus pattern (19 bp):
ATTGCATTTTTATTAAGTT
Found at i:28707656 original size:15 final size:16
Alignment explanation
Indices: 28707636--28707668 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
28707626 GTTTGCATAC
28707636 TTAGG-ATAATTTGCA
1 TTAGGAATAATTTGCA
*
28707651 TTAGGAATCATTTGCA
1 TTAGGAATAATTTGCA
28707667 TT
1 TT
28707669 TAGTTTTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.42
Consensus pattern (16 bp):
TTAGGAATAATTTGCA
Found at i:28708541 original size:16 final size:16
Alignment explanation
Indices: 28708520--28708552 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
28708510 TGATGATTTT
*
28708520 AATGTTAAAGGACTAA
1 AATGTTAAAGGAATAA
28708536 AATGTTAAAGGAATAA
1 AATGTTAAAGGAATAA
28708552 A
1 A
28708553 TTTGTTAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (16 bp):
AATGTTAAAGGAATAA
Found at i:28708987 original size:18 final size:16
Alignment explanation
Indices: 28708964--28708999 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
28708954 CTTAGTAAAT
28708964 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
28708982 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
28708998 AT
1 AT
28709000 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:28709618 original size:52 final size:52
Alignment explanation
Indices: 28709540--28709684 Score: 281
Period size: 52 Copynumber: 2.8 Consensus size: 52
28709530 GAAATGCAAA
28709540 AGGTCTGATGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATG
28709592 AGGTCTGATGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATG
1 AGGTCTGATGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATG
*
28709644 AGGTCTGATGACTATGTGTCATCGTGAGTATATGAATCCTT
1 AGGTCTGATGACTATGTGTCATCGGGAGTATATGAATCCTT
28709685 GACTATGTGT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 92 1.00
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (52 bp):
AGGTCTGATGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATG
Found at i:28709688 original size:32 final size:32
Alignment explanation
Indices: 28709652--28709716 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
28709642 TGAGGTCTGA
*
28709652 TGACTATGTGTCATCGTGAGTATATGAATCCT
1 TGACTATGTGTCATCGTGAGCATATGAATCCT
28709684 TGACTATGTGTCATCGTGAGCATATGAATCCT
1 TGACTATGTGTCATCGTGAGCATATGAATCCT
28709716 T
1 T
28709717 TACGGATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.37
Consensus pattern (32 bp):
TGACTATGTGTCATCGTGAGCATATGAATCCT
Found at i:28709741 original size:84 final size:84
Alignment explanation
Indices: 28709600--28709768 Score: 293
Period size: 84 Copynumber: 2.0 Consensus size: 84
28709590 TGAGGTCTGA
* * *
28709600 TGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTATGTGTCA
1 TGACTATGTGTCATCGGGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
*
28709665 TCGTGAGTATATGAATCCT
66 TCGTAAGTATATGAATCCT
*
28709684 TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
1 TGACTATGTGTCATCGGGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
28709749 TCGTAAGTATATGAATCCT
66 TCGTAAGTATATGAATCCT
28709768 T
1 T
28709769 TACAGATTAT
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (84 bp):
TGACTATGTGTCATCGGGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
TCGTAAGTATATGAATCCT
Found at i:28709762 original size:52 final size:52
Alignment explanation
Indices: 28709684--28709859 Score: 289
Period size: 52 Copynumber: 3.4 Consensus size: 52
28709674 TATGAATCCT
28709684 TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGA
1 TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGA
* * * *
28709736 TGACTATGTGTCATCGTAAGTATATGAATCCTTTACAGATTATGAGGTCCGA
1 TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGA
* *
28709788 TGACTATGTGTCATTGTGAGCATATGAATCCTTTTCGGATTATAAGGTCCGA
1 TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGA
*
28709840 TGACTATGTGTCATTGTGAG
1 TGACTATGTGTCATCGTGAG
28709860 TATCAAATGA
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 114 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.35
Consensus pattern (52 bp):
TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGA
Found at i:28709792 original size:136 final size:136
Alignment explanation
Indices: 28709548--28709820 Score: 456
Period size: 136 Copynumber: 2.0 Consensus size: 136
28709538 AAAGGTCTGA
* * *
28709548 TGACTATGTGTCATCGGGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTATGTGTCA
1 TGACTATGTGTCATCGGGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
* * * *
28709613 TCGGGAGTATATGAATCCTTTACGGATTATGAGGTCTGATGACTATGTGTCATCGTGAGTATATG
66 TCGGAAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTGTCATCGTGAGCATATG
28709678 AATCCT
131 AATCCT
*
28709684 TGACTATGTGTCATCGTGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
1 TGACTATGTGTCATCGGGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
* *
28709749 TCGTAAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTGTCATTGTGAGCATATG
66 TCGGAAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTGTCATCGTGAGCATATG
28709814 AATCCT
131 AATCCT
28709820 T
1 T
28709821 TTCGGATTAT
Statistics
Matches: 127, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 127 1.00
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (136 bp):
TGACTATGTGTCATCGGGAGCATATGAATCCTTTACGGATTATAAGGTCCGATGACTATGTGTCA
TCGGAAGTATATGAATCCTTTACAGATTATGAGGTCCGATGACTATGTGTCATCGTGAGCATATG
AATCCT
Found at i:28709913 original size:62 final size:63
Alignment explanation
Indices: 28709811--28709940 Score: 165
Period size: 62 Copynumber: 2.1 Consensus size: 63
28709801 TTGTGAGCAT
* * * * *
28709811 ATGAATCCTTTTCGGATTATAAGGTCCGATGACTATGTGTCATTGTGAG-TATCAAATGAGAA
1 ATGAATCCTTTACGGATTATAAGGTCCAATGACTACGTGTCATCGTGAGTTACCAAATGAGAA
* *
28709873 ATGAATCCTATTACGGATTA-AAGGTCCAATGACTCCGTGTCATCGTGAGTTACCAAATGCGAA
1 ATGAATCCT-TTACGGATTATAAGGTCCAATGACTACGTGTCATCGTGAGTTACCAAATGAGAA
*
28709936 TTGAA
1 ATGAA
28709941 ACCAACCTCG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
62 34 0.59
63 24 0.41
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (63 bp):
ATGAATCCTTTACGGATTATAAGGTCCAATGACTACGTGTCATCGTGAGTTACCAAATGAGAA
Found at i:28714357 original size:18 final size:16
Alignment explanation
Indices: 28714334--28714369 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
28714324 CTTAGTAAAT
28714334 ATTAAATTGAGGAATGAA
1 ATTAAATTGA--AATGAA
28714352 ATTAAATTGAAATGAA
1 ATTAAATTGAAATGAA
28714368 AT
1 AT
28714370 GGTATTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.53, C:0.00, G:0.17, T:0.31
Consensus pattern (16 bp):
ATTAAATTGAAATGAA
Found at i:28714989 original size:52 final size:52
Alignment explanation
Indices: 28714908--28715095 Score: 313
Period size: 52 Copynumber: 3.6 Consensus size: 52
28714898 ATAAATGCAA
* * *
28714908 AAGGTTCGATGACTATGTGTCATCATGAGTATATGAATCCTTTATGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
28714960 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
28715012 AAGGTCCGATGACTATGTGTCATCGTGAGCATATGAATCCTTTACGAATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
* *
28715064 GAGGTCTGATGACTATGTGTCATCGTGAGTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTAT
28715096 CAAATGAGAA
Statistics
Matches: 128, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 128 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTAT
Found at i:28730540 original size:23 final size:23
Alignment explanation
Indices: 28730497--28730542 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
28730487 TCCATAATAA
*
28730497 TAATCACACCGAAATGTCAGTAT
1 TAATCACACCGAAATGCCAGTAT
*
28730520 TAATCACA-CTAAAGTGCCAGTAT
1 TAATCACACCGAAA-TGCCAGTAT
28730543 GCTCCTACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.22, G:0.13, T:0.26
Consensus pattern (23 bp):
TAATCACACCGAAATGCCAGTAT
Found at i:28749687 original size:12 final size:12
Alignment explanation
Indices: 28749670--28749714 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
28749660 GTGCAAAGAT
28749670 AAGAAGAAGCAC
1 AAGAAGAAGCAC
28749682 AAGAAGAAGCAC
1 AAGAAGAAGCAC
* * * *
28749694 CACAAGAAGAAG
1 AAGAAGAAGCAC
28749706 AAGAAGAAG
1 AAGAAGAAG
28749715 ACCAAAGCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.60, C:0.13, G:0.27, T:0.00
Consensus pattern (12 bp):
AAGAAGAAGCAC
Found at i:28749690 original size:15 final size:15
Alignment explanation
Indices: 28749670--28749708 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
28749660 GTGCAAAGAT
28749670 AAGAAGAAGCACAAG
1 AAGAAGAAGCACAAG
* *
28749685 AAGAAGCACCACAAG
1 AAGAAGAAGCACAAG
28749700 AAGAAGAAG
1 AAGAAGAAG
28749709 AAGAAGACCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.26, T:0.00
Consensus pattern (15 bp):
AAGAAGAAGCACAAG
Found at i:28772544 original size:13 final size:13
Alignment explanation
Indices: 28772534--28772569 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
28772524 TGATTTAATC
28772534 AATTAATTTAACT
1 AATTAATTTAACT
*
28772547 AATTAAATTAACT
1 AATTAATTTAACT
28772560 ACATTAATTT
1 A-ATTAATTT
28772570 CTCAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
AATTAATTTAACT
Found at i:28773714 original size:19 final size:19
Alignment explanation
Indices: 28773687--28773724 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28773677 CAATTAGACA
*
28773687 AAGGACATATTTTGATTAT
1 AAGGACATATTTAGATTAT
*
28773706 AAGGTCATATTTAGATTAT
1 AAGGACATATTTAGATTAT
28773725 CTACTAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (19 bp):
AAGGACATATTTAGATTAT
Found at i:28777911 original size:10 final size:10
Alignment explanation
Indices: 28777896--28777920 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28777886 TCAAGCGAAC
28777896 GCTTTCATCG
1 GCTTTCATCG
28777906 GCTTTCATCG
1 GCTTTCATCG
28777916 GCTTT
1 GCTTT
28777921 AATCCACTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.08, C:0.28, G:0.20, T:0.44
Consensus pattern (10 bp):
GCTTTCATCG
Found at i:28786664 original size:21 final size:21
Alignment explanation
Indices: 28786639--28786682 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
28786629 TTGGCAAATA
28786639 TGAGAACT-AATCTTAGAAGAT
1 TGAGAA-TAAATCTTAGAAGAT
*
28786660 TGAGAATAAAATCTTATAAGAT
1 TGAGAAT-AAATCTTAGAAGAT
28786682 T
1 T
28786683 AGATTTGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 1 0.05
21 6 0.30
22 13 0.65
ACGTcount: A:0.45, C:0.07, G:0.16, T:0.32
Consensus pattern (21 bp):
TGAGAATAAATCTTAGAAGAT
Found at i:28791258 original size:21 final size:22
Alignment explanation
Indices: 28791233--28791277 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
28791223 TTGACAAATA
28791233 TGAGAA-CAAATCTTAAAAGAT
1 TGAGAATCAAATCTTAAAAGAT
* *
28791254 TGAGAATCACATCTTATAAGAT
1 TGAGAATCAAATCTTAAAAGAT
28791276 TG
1 TG
28791278 GATTTGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (22 bp):
TGAGAATCAAATCTTAAAAGAT
Found at i:28804446 original size:17 final size:18
Alignment explanation
Indices: 28804420--28804463 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
28804410 GACGAGGAAG
28804420 GATT-AGCATACTGGCTC
1 GATTGAGCATACTGGCTC
28804437 -ATTGAGCATACTGGCTC
1 GATTGAGCATACTGGCTC
*
28804454 GTTTGAGCAT
1 GATTGAGCAT
28804464 TACTAGATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 13 0.54
18 8 0.33
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (18 bp):
GATTGAGCATACTGGCTC
Found at i:28829264 original size:17 final size:17
Alignment explanation
Indices: 28829228--28829266 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
28829218 ATTGTCATCA
*
28829228 CATTTTAATTGTCCATG
1 CATTTTAATTGTCCACG
* *
28829245 CATTTTATTTGTCGACG
1 CATTTTAATTGTCCACG
28829262 CATTT
1 CATTT
28829267 GCATTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.49
Consensus pattern (17 bp):
CATTTTAATTGTCCACG
Found at i:28830874 original size:14 final size:14
Alignment explanation
Indices: 28830855--28830883 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
28830845 AGGGTAGGAA
28830855 TAGAATGCTTCAAC
1 TAGAATGCTTCAAC
28830869 TAGAATGCTTCAAC
1 TAGAATGCTTCAAC
28830883 T
1 T
28830884 TATTCTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (14 bp):
TAGAATGCTTCAAC
Found at i:28834559 original size:29 final size:29
Alignment explanation
Indices: 28834517--28834578 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
28834507 TTTCACCATT
*
28834517 GATGAGTATGCTTATTCTTGAAAGATTAA
1 GATGAATATGCTTATTCTTGAAAGATTAA
28834546 GATGAATATGCTTATTCTTGAAAGATTAA
1 GATGAATATGCTTATTCTTGAAAGATTAA
28834575 GATG
1 GATG
28834579 GATTTATATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.37
Consensus pattern (29 bp):
GATGAATATGCTTATTCTTGAAAGATTAA
Found at i:28835129 original size:18 final size:18
Alignment explanation
Indices: 28835079--28835143 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
28835069 CGGAAGAATA
* *
28835079 AGCATACTGGCACGTTTA
1 AGCATACTGGCTCGTTTG
*
28835097 AGCATACTGGTTCGTTTG
1 AGCATACTGGCTCGTTTG
* *
28835115 AGCATACTAGCTCGTTAG
1 AGCATACTGGCTCGTTTG
28835133 AGCATTACTGG
1 AGCA-TACTGG
28835144 ATCACAAGAG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
18 34 0.87
19 5 0.13
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (18 bp):
AGCATACTGGCTCGTTTG
Found at i:28835856 original size:21 final size:21
Alignment explanation
Indices: 28835832--28835878 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28835822 TTGTTTTGGC
*
28835832 AAAAGAGTCACTTGTATCTGT
1 AAAAGAGTCACTTGTATCGGT
** *
28835853 AAAACTGTCATTTGTATCGGT
1 AAAAGAGTCACTTGTATCGGT
28835874 AAAAG
1 AAAAG
28835879 TCTGCATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (21 bp):
AAAAGAGTCACTTGTATCGGT
Found at i:28838764 original size:18 final size:17
Alignment explanation
Indices: 28838741--28838781 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
28838731 TTTTGAGAGC
28838741 ATAAAATAAAAAGATAAA
1 ATAAAATAAAAAG-TAAA
*
28838759 ATAAAATAGAAAGTAAA
1 ATAAAATAAAAAGTAAA
*
28838776 AGAAAA
1 ATAAAA
28838782 AGTTGATATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.76, C:0.00, G:0.10, T:0.15
Consensus pattern (17 bp):
ATAAAATAAAAAGTAAA
Found at i:28856719 original size:17 final size:17
Alignment explanation
Indices: 28856697--28856768 Score: 72
Period size: 17 Copynumber: 4.2 Consensus size: 17
28856687 TGTTAATAAG
*
28856697 CATTGTCATCACATTCC
1 CATTGTCATCACATTTC
* *
28856714 CATTGTCATTACATTTT
1 CATTGTCATCACATTTC
* * *
28856731 AATTGTCATCGCATTTG
1 CATTGTCATCACATTTC
**
28856748 CATTGTCATTGCATTTC
1 CATTGTCATCACATTTC
28856765 CATT
1 CATT
28856769 TGTCCTTATA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 45 1.00
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (17 bp):
CATTGTCATCACATTTC
Found at i:28856752 original size:34 final size:34
Alignment explanation
Indices: 28856698--28856763 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
28856688 GTTAATAAGC
28856698 ATTGTCATCACATTCCCATTGTCATTACATTTTA
1 ATTGTCATCACATTCCCATTGTCATTACATTTTA
* ** *
28856732 ATTGTCATCGCATTTGCATTGTCATTGCATTT
1 ATTGTCATCACATTCCCATTGTCATTACATTT
28856764 CCATTTGTCC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (34 bp):
ATTGTCATCACATTCCCATTGTCATTACATTTTA
Found at i:28860561 original size:24 final size:24
Alignment explanation
Indices: 28860545--28860619 Score: 141
Period size: 24 Copynumber: 3.1 Consensus size: 24
28860535 AGTTTGACTC
28860545 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
28860569 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
28860593 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
28860617 AAA
1 AAA
28860620 GATTATTTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.56, C:0.07, G:0.12, T:0.25
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:28862608 original size:24 final size:24
Alignment explanation
Indices: 28862547--28862609 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
28862537 TAGAGTAATA
* *
28862547 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
*
28862571 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTGAAACAAATAAAC
28862595 AGAGTTTAACTGAAA
1 AGAGTTTAACTGAAA
28862610 GATTATTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.51, C:0.11, G:0.14, T:0.24
Consensus pattern (24 bp):
AGAGTTTAACTGAAACAAATAAAC
Found at i:28871176 original size:21 final size:21
Alignment explanation
Indices: 28871150--28871203 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
28871140 TTGACGTTTG
28871150 TTTGAATCGATTATTTG-TTGT
1 TTTGAATCGATTATTTGCTT-T
*
28871171 TTTGAATCGATTCTTTGCTTT
1 TTTGAATCGATTATTTGCTTT
*
28871192 TTTGAATTGATT
1 TTTGAATCGATT
28871204 GTTTTTCATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.19, C:0.07, G:0.17, T:0.57
Consensus pattern (21 bp):
TTTGAATCGATTATTTGCTTT
Found at i:28876057 original size:18 final size:16
Alignment explanation
Indices: 28876036--28876075 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
28876026 AAAATATTTA
28876036 TTTTAATGTTATTAGTAT
1 TTTTAATG-TATTA-TAT
*
28876054 TTTTGATGTATTATAT
1 TTTTAATGTATTATAT
28876070 TTTTAA
1 TTTTAA
28876076 AATTTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 8 0.40
17 5 0.25
18 7 0.35
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (16 bp):
TTTTAATGTATTATAT
Found at i:28881987 original size:15 final size:15
Alignment explanation
Indices: 28881967--28881996 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
28881957 ATAAAACTAT
28881967 CATTTATATATCTGA
1 CATTTATATATCTGA
28881982 CATTTATATATCTGA
1 CATTTATATATCTGA
28881997 ATTCATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (15 bp):
CATTTATATATCTGA
Found at i:28882092 original size:17 final size:16
Alignment explanation
Indices: 28882065--28882099 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
28882055 CTTTTAATTA
*
28882065 TTAACTAAATCAATAT
1 TTAACTAAATCAACAT
28882081 TTAACATAAATCAACAT
1 TTAAC-TAAATCAACAT
28882098 TT
1 TT
28882100 TCATTTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAACTAAATCAACAT
Found at i:28894772 original size:20 final size:19
Alignment explanation
Indices: 28894725--28894772 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
28894715 ATTTTTAAAT
* *
28894725 TTTTTTATAATATATATTA
1 TTTTATATAATATATATAA
*
28894744 TTTTAATATAATATTTAATAA
1 TTTT-ATATAATATAT-ATAA
28894765 TTTTATAT
1 TTTTATAT
28894773 TCTTTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 4 0.17
20 13 0.54
21 7 0.29
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATATAATATATATAA
Found at i:28897673 original size:15 final size:15
Alignment explanation
Indices: 28897653--28897685 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28897643 CAATAAACCA
28897653 AGTGGTTTAATTCTT
1 AGTGGTTTAATTCTT
28897668 AGTGGTTTAATTCTT
1 AGTGGTTTAATTCTT
28897683 AGT
1 AGT
28897686 AATGACATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.21, C:0.06, G:0.21, T:0.52
Consensus pattern (15 bp):
AGTGGTTTAATTCTT
Found at i:28898306 original size:18 final size:17
Alignment explanation
Indices: 28898285--28898384 Score: 110
Period size: 18 Copynumber: 5.6 Consensus size: 17
28898275 TTAAACTCAT
*
28898285 TTTAAGATTTATTTTAAG
1 TTTAA-ATTTATTTTAAA
* *
28898303 TTTAAATTGATTTTTGAA
1 TTTAAATTTA-TTTTAAA
28898321 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
28898338 TTTAAATTTTATTTGAAAA
1 TTTAAA-TTTATTT-TAAA
*
28898357 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
*
28898374 TTTAAACTTAT
1 TTTAAATTTAT
28898385 ATATGAATTT
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
17 28 0.41
18 32 0.46
19 9 0.13
ACGTcount: A:0.39, C:0.01, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:28898359 original size:36 final size:34
Alignment explanation
Indices: 28898285--28898397 Score: 129
Period size: 36 Copynumber: 3.2 Consensus size: 34
28898275 TTAAACTCAT
*
28898285 TTTAAGATTTATTTTAAGTTTAAATTGATTTTTGAA
1 TTTAA-ATTTATTTTAAATTTAAATT-ATTTTTGAA
28898321 TTTAAATTTATTTTAAATTTAAATT-TTATTTGAAAA
1 TTTAAATTTATTTTAAATTTAAATTATT-TTTG--AA
* * *
28898357 TTTAAATTTAATTTAAATTTAAACTTATATATGAA
1 TTTAAATTTATTTTAAATTTAAA-TTATTTTTGAA
28898392 TTTAAA
1 TTTAAA
28898398 ACTTATTATA
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
33 2 0.03
34 4 0.06
35 27 0.40
36 29 0.43
37 5 0.07
38 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTATTTTTGAA
Found at i:28898369 original size:5 final size:6
Alignment explanation
Indices: 28898319--28898379 Score: 65
Period size: 6 Copynumber: 10.3 Consensus size: 6
28898309 TTGATTTTTG
* *
28898319 AATTTA AATTT- ATTTTA AATTTA AATTT- TATTTGAA AATTTA AATTT-
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTT--A AATTTA AATTTA
28898366 AATTTA AATTTA AA
1 AATTTA AATTTA AA
28898380 CTTATATATG
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
5 13 0.28
6 29 0.63
8 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (6 bp):
AATTTA
Found at i:28898378 original size:11 final size:11
Alignment explanation
Indices: 28898319--28898378 Score: 59
Period size: 11 Copynumber: 5.2 Consensus size: 11
28898309 TTGATTTTTG
28898319 AATTTAAATTT
1 AATTTAAATTT
*
28898330 ATTTTAAATTT
1 AATTTAAATTT
*
28898341 AAATTT-TATTT
1 -AATTTAAATTT
28898352 GAAAATTTAAATTT
1 ---AATTTAAATTT
28898366 AATTTAAATTT
1 AATTTAAATTT
28898377 AA
1 AA
28898379 ACTTATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 27 0.66
12 4 0.10
13 6 0.15
14 4 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (11 bp):
AATTTAAATTT
Found at i:28899148 original size:21 final size:23
Alignment explanation
Indices: 28899122--28899172 Score: 65
Period size: 21 Copynumber: 2.4 Consensus size: 23
28899112 ATATTCAATA
*
28899122 AATAATAAAT-TTTA-TATTATT
1 AATAATAAATATTTATTAATATT
28899143 AATAAT-AATATTTATTAATATT
1 AATAATAAATATTTATTAATATT
28899165 AA-AATAAA
1 AATAATAAA
28899173 AAAAAGGAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 13 0.50
22 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AATAATAAATATTTATTAATATT
Found at i:28899506 original size:15 final size:15
Alignment explanation
Indices: 28899486--28899515 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
28899476 CTTTAAACTC
28899486 CCAGATCTGGATTTT
1 CCAGATCTGGATTTT
*
28899501 CCAGATCTGGGTTTT
1 CCAGATCTGGATTTT
28899516 GATTTAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (15 bp):
CCAGATCTGGATTTT
Found at i:28900273 original size:30 final size:30
Alignment explanation
Indices: 28900233--28900425 Score: 214
Period size: 30 Copynumber: 6.4 Consensus size: 30
28900223 AGAAGTCCGT
* *
28900233 AAACTATCTAAAAATTATATTTTGACCCCA
1 AAACTTTCTAAAAATTATATTTTAACCCCA
* *
28900263 AAACTTTCTAAAAATTACATTTTGACCTCC-
1 AAACTTTCTAAAAATTATATTTTAACC-CCA
**
28900293 AAACTTTTCT-AAAATTATATTTTAACCTTA
1 AAAC-TTTCTAAAAATTATATTTTAACCCCA
*
28900323 AAACTTTCTAAAAATTACATTTTAACCCTC-
1 AAACTTTCTAAAAATTATATTTTAACCC-CA
* * *
28900353 GAACTTCTCT-AAAATTATATTTTAAACCAA
1 AAACTT-TCTAAAAATTATATTTTAACCCCA
* *
28900383 AAACTTTCTAAAAATTATATTTTTACCCCT
1 AAACTTTCTAAAAATTATATTTTAACCCCA
28900413 AAACTTTCTAAAA
1 AAACTTTCTAAAA
28900426 TTCCATTTTT
Statistics
Matches: 137, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
29 8 0.06
30 119 0.87
31 10 0.07
ACGTcount: A:0.41, C:0.19, G:0.02, T:0.38
Consensus pattern (30 bp):
AAACTTTCTAAAAATTATATTTTAACCCCA
Found at i:28900326 original size:60 final size:58
Alignment explanation
Indices: 28900243--28900427 Score: 237
Period size: 60 Copynumber: 3.1 Consensus size: 58
28900233 AAACTATCTA
* * *
28900243 AAAATTATATTTTGACCCCAAAACTTTCTAAAAATTACATTTTGACCTCCAAACTTTTCT
1 AAAATTATATTTT-AACCAAAAACTTTCTAAAAATTACATTTTAACC-CCAAACTTTTCT
* * *
28900303 AAAATTATATTTTAACCTTAAAACTTTCTAAAAATTACATTTTAACCCTCGAACTTCTCT
1 AAAATTATATTTTAACC-AAAAACTTTCTAAAAATTACATTTTAACCC-CAAACTTTTCT
* *
28900363 AAAATTATATTTTAAACCAAAAACTTTCTAAAAATTATATTTTTACCCCTAAAC-TTTCT
1 AAAATTATATTTT-AACCAAAAACTTTCTAAAAATTACATTTTAACCCC-AAACTTTTCT
28900422 AAAATT
1 AAAATT
28900428 CCATTTTTGC
Statistics
Matches: 111, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
59 15 0.14
60 92 0.83
61 4 0.04
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (58 bp):
AAAATTATATTTTAACCAAAAACTTTCTAAAAATTACATTTTAACCCCAAACTTTTCT
Found at i:28900464 original size:30 final size:29
Alignment explanation
Indices: 28900422--28900526 Score: 101
Period size: 29 Copynumber: 3.6 Consensus size: 29
28900412 TAAACTTTCT
* *
28900422 AAAATTCCATTTTTGCCCTCGATTTCACC
1 AAAATACCATTTTTACCCTCGATTTCACC
**
28900451 AAAATCACCA-TTTTACCCCTAAACTTT--CC
1 AAAAT-ACCATTTTTA-CCCTCGA-TTTCACC
*
28900480 AAAATTCCATTTTTACCCTCGATTTCACC
1 AAAATACCATTTTTACCCTCGATTTCACC
28900509 AAAATTACCA-TTTTACCC
1 AAAA-TACCATTTTTACCC
28900527 CCAAACTCTC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
27 3 0.05
28 8 0.13
29 35 0.57
30 12 0.20
31 3 0.05
ACGTcount: A:0.30, C:0.31, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATACCATTTTTACCCTCGATTTCACC
Found at i:28900474 original size:58 final size:58
Alignment explanation
Indices: 28900403--28900586 Score: 269
Period size: 58 Copynumber: 3.1 Consensus size: 58
28900393 AAAATTATAT
* *
28900403 TTTTACCCCTAAACTTTCTAAAATTCCATTTTTGCCCTCGATTTCACCAAAATCACCA
1 TTTTACCCCTAAACTTTCTAAAATTCCATTTTTACCCTCGATTTCACCAAAATTACCA
*
28900461 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTACCCTCGATTTCACCAAAATTACCA
1 TTTTACCCCTAAACTTTCTAAAATTCCATTTTTACCCTCGATTTCACCAAAATTACCA
* * * * * *
28900519 TTTTACCCCCAAACTCTCTAAAATTTCATTTTTTAACCTCGATTTTACCAAAAATTACTA
1 TTTTACCCCTAAACTTTCTAAAATTCCA-TTTTTACCCTCGATTTCACC-AAAATTACCA
28900579 TTTTACCC
1 TTTTACCC
28900587 TCGAGTATCT
Statistics
Matches: 114, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
58 79 0.69
59 18 0.16
60 17 0.15
ACGTcount: A:0.30, C:0.29, G:0.02, T:0.38
Consensus pattern (58 bp):
TTTTACCCCTAAACTTTCTAAAATTCCATTTTTACCCTCGATTTCACCAAAATTACCA
Found at i:28900612 original size:59 final size:59
Alignment explanation
Indices: 28900403--28900613 Score: 171
Period size: 58 Copynumber: 3.6 Consensus size: 59
28900393 AAAATTATAT
* * * ** *
28900403 TTTTACCCCTAAACTTTCTAAAAT-TC-CATTTTTGCCCTCGATTTCACCAAAATCACCA
1 TTTTACCCCCAAACTATCTAAAATGTCAC-GTTTTAACCTCGATTTCACCAAAATTACCA
* * * * *
28900461 TTTTACCCCTAAACTTTCCAAAAT-TC-CATTTTTACCCTCGATTTCACCAAAATTACCA
1 TTTTACCCCCAAACTATCTAAAATGTCAC-GTTTTAACCTCGATTTCACCAAAATTACCA
* * ** * *
28900519 TTTTACCCCCAAACTCTCTAAAATTTCATTTTTTAACCTCGATTTTACCAAAAATTACTA
1 TTTTACCCCCAAACTATCTAAAATGTCACGTTTTAACCTCGATTTCACC-AAAATTACCA
* * * *
28900579 TTTTACCCTC-GAGTATCTAAAATGTCCCGTTTTAA
1 TTTTACCCCCAAACTATCTAAAATGTCACGTTTTAA
28900614 ATTCCCATTG
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
58 76 0.58
59 38 0.29
60 18 0.14
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (59 bp):
TTTTACCCCCAAACTATCTAAAATGTCACGTTTTAACCTCGATTTCACCAAAATTACCA
Found at i:28900986 original size:6 final size:6
Alignment explanation
Indices: 28900971--28901070 Score: 78
Period size: 6 Copynumber: 16.2 Consensus size: 6
28900961 TTTAAAATTT
* * *
28900971 ATTTAA ATTTAG ATTT-A TTTTAA ATTTTAAA ATTTAA ATTT-A ATTTGA
1 ATTTAA ATTTAA ATTTAA ATTTAA A-TTT-AA ATTTAA ATTTAA ATTTAA
** * *
28901019 ATTTAA ATTTAA ATAAAA ATTAAA ATATTAA ATTTAA TATTAAAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA -ATT-TAA ATTTAA
28901070 A
1 A
28901071 GCCCAATGTC
Statistics
Matches: 76, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
5 8 0.11
6 46 0.61
7 17 0.22
8 5 0.07
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:28901003 original size:25 final size:23
Alignment explanation
Indices: 28900971--28901055 Score: 80
Period size: 25 Copynumber: 3.5 Consensus size: 23
28900961 TTTAAAATTT
* *
28900971 ATTTAAATTTAGATTTATTTTAA
1 ATTTAAATTTAAATTTAATTTAA
*
28900994 ATTTTAAAATTTAAATTTAATTTGA
1 A-TTT-AAATTTAAATTTAATTTAA
** *
28901019 ATTTAAATTTAAATAAAAATTAAA
1 ATTTAAATTTAAAT-TTAATTTAA
28901043 ATATTAAATTTAA
1 AT-TTAAATTTAA
28901056 TATTAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
23 11 0.22
24 13 0.25
25 27 0.53
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAATTTAA
Found at i:28901022 original size:42 final size:42
Alignment explanation
Indices: 28900965--28901062 Score: 110
Period size: 42 Copynumber: 2.3 Consensus size: 42
28900955 TAGTTTTTTA
* ** **
28900965 AAATTT-ATTTAAATTTAGATTTATTTTAAATTTTAAAAT-TT
1 AAATTTAATTTAAATTTAAATTTA-AATAAAAATTAAAATATT
*
28901006 AAATTTAATTTGAATTTAAATTTAAATAAAAATTAAAATATT
1 AAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATATT
28901048 AAATTTAATATTAAA
1 AAATTTAAT-TTAAA
28901063 AATTTAAAGC
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 17 0.36
42 26 0.55
43 4 0.09
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (42 bp):
AAATTTAATTTAAATTTAAATTTAAATAAAAATTAAAATATT
Found at i:28901041 original size:17 final size:17
Alignment explanation
Indices: 28900998--28901042 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
28900988 TTTTAAATTT
*
28900998 TAAAATTTAAATTTAAT
1 TAAAATTTAAATTTAAA
**
28901015 TTGAATTTAAATTTAAA
1 TAAAATTTAAATTTAAA
*
28901032 TAAAAATTAAA
1 TAAAATTTAAA
28901043 ATATTAAATT
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
TAAAATTTAAATTTAAA
Found at i:28901281 original size:16 final size:16
Alignment explanation
Indices: 28901260--28901290 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28901250 ATCAGCTCTG
*
28901260 CCACCACCAGTTCCAT
1 CCACCACCAGCTCCAT
28901276 CCACCACCAGCTCCA
1 CCACCACCAGCTCCA
28901291 CCATGCCCTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.55, G:0.06, T:0.13
Consensus pattern (16 bp):
CCACCACCAGCTCCAT
Found at i:28901826 original size:22 final size:23
Alignment explanation
Indices: 28901801--28901854 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 23
28901791 ATAAATGTTT
28901801 TTAATTAGTG-TTAATGAAATTA
1 TTAATTAGTGATTAATGAAATTA
*
28901823 TTAATGATGGTGATTAATGAAATTA
1 TTAAT--TAGTGATTAATGAAATTA
28901848 TTAATTA
1 TTAATTA
28901855 ACAATTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 5 0.19
23 1 0.04
24 4 0.15
25 17 0.63
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (23 bp):
TTAATTAGTGATTAATGAAATTA
Found at i:28902786 original size:161 final size:162
Alignment explanation
Indices: 28902609--28902921 Score: 445
Period size: 162 Copynumber: 1.9 Consensus size: 162
28902599 CTTTTCAATT
* *
28902609 TAGTCCTTTGACTGTTTGACTGTACCATAGGCTGCCACATGTCA-CTTTTTGGATTATTTCTGCA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCATCTTTTTGGATTATTTCTGCA
* *
28902673 TTAAGTCC-TTTTTATTTTTTATTTGTTTTAATTTAATCC-CAAATCAAC-TTTATTTTAATTAC
66 TTAAGTCCTTTTTTA-TTTTAATTTGTTATAA-TTAATCCTCAAATCAACTTTTA-TTTAATTAC
* *
28902735 GAAATTGGCCCAATAATTTTTCAAGGTTTATAAAC
128 AAAATTGGCCCAAAAATTTTTCAAGGTTTATAAAC
* * * *
28902770 TAGTCCTTTGACTGTTTGACTGCACCAGAGGTTGCCACGTGTCATCTTTTTGGATTTTTTCTGTA
1 TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCATCTTTTTGGATTATTTCTGCA
* * *
28902835 TTTAGTCCTTTTTTATTTTAATTTGTTATAATTAATCCTTAAATCGACTTTTATTTAATTACAAA
66 TTAAGTCCTTTTTTATTTTAATTTGTTATAATTAATCCTCAAATCAACTTTTATTTAATTACAAA
*
28902900 ATTGGTCCAAAAATTTTTCAAG
131 ATTGGCCCAAAAATTTTTCAAG
28902922 ATTTTCAAAT
Statistics
Matches: 134, Mismatches: 14, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
161 47 0.35
162 77 0.57
163 10 0.07
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (162 bp):
TAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACATGTCATCTTTTTGGATTATTTCTGCA
TTAAGTCCTTTTTTATTTTAATTTGTTATAATTAATCCTCAAATCAACTTTTATTTAATTACAAA
ATTGGCCCAAAAATTTTTCAAGGTTTATAAAC
Found at i:28903053 original size:30 final size:30
Alignment explanation
Indices: 28903019--28903120 Score: 150
Period size: 30 Copynumber: 3.4 Consensus size: 30
28903009 AATTGTCCAG
* *
28903019 AAATTACATTTTGACCCTAAAACTTTCCCA
1 AAATTACATTTTGACCCCAAAACTTTACCA
* *
28903049 AAATTACATTTTAACCCCGAAACTTTACCA
1 AAATTACATTTTGACCCCAAAACTTTACCA
* *
28903079 AAATTACTTTTTGACCCCAAAACTTTTCCA
1 AAATTACATTTTGACCCCAAAACTTTACCA
28903109 AAATTACATTTT
1 AAATTACATTTT
28903121 TAACCCCGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 63 1.00
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (30 bp):
AAATTACATTTTGACCCCAAAACTTTACCA
Found at i:28903250 original size:59 final size:59
Alignment explanation
Indices: 28903108--28903562 Score: 573
Period size: 59 Copynumber: 7.7 Consensus size: 59
28903098 AAACTTTTCC
* * *
28903108 AAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTA-CCCTCGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTC-AAGCTTCT
* ** *
28903167 AAAATTCTA-TTTTAACCCTAATTTCATCGAAAATTACCATTTTACCCCTCAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTCAAGCTTCT
*
28903225 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCC-CGAAGCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTC-AAGCTTCT
* *
28903284 AAAATTCCATTTTTAACCCCGATTTCACAGAAAATTACCATTTTTACCACC-GAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCA-TTTTACC-CCTCAAGCTTCT
** * * *
28903344 AAAATTCCA-TTTTAACCTTGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTCAAGCTTCT
* * * *
28903402 AAAATTCTATTTTTAACCCCGATTTTACTGAAAATTACCATTTTACCCCTGAAGCTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTCAAGCTTCT
* * * * * *
28903461 AAGATTCCGTTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCC-CGAATCTTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTC-AAGCTTCT
* *
28903520 AAAATTCCATTTTTAATCCCGATTACACC-AAAATTACCATTTT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTT
28903563 GCCCTCGAGT
Statistics
Matches: 344, Mismatches: 44, Indels: 17
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.01
58 82 0.24
59 235 0.68
60 23 0.07
61 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCTCAAGCTTCT
Found at i:28903377 original size:177 final size:174
Alignment explanation
Indices: 28903108--28903562 Score: 635
Period size: 177 Copynumber: 2.6 Consensus size: 174
28903098 AAACTTTTCC
* *
28903108 AAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACAGAAAATTACCATTTTACCC-CGAATCTTTTAAAATT
* * * *
28903173 CTATTTTAACCCTAATTTCATCGAAAATTACCATTTTACCCCTCAAGCTTCTAAAATTCCATTTT
65 CCATTTTAA-CCTGATTTCACCGAAAATTACCATTTTACCCCTAAAGCTTCTAAAATTCCATTTT
*
28903238 TAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTT
129 TAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCT
* *
28903284 AAAATTCCATTTTTAACCCCGATTTCACAGAAAATTACCATTTTTACCACCGAAGCTTCTAAAAT
1 AAAATTCCATTTTTAACCCCGATTTCACAGAAAATTACCA-TTTTACC-CCGAATCTTTTAAAAT
* * *
28903349 TCCATTTTAACCTTGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATTCTATTT
64 TCCATTTTAACC-TGATTTCACCGAAAATTACCATTTTACCCCTAAAGCTTCTAAAATTCCATTT
* * *
28903414 TTAACCCCGATTTTACTGAAAATTACCATTTTACCCCTGAAGCTTCT
128 TTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCT
* * *
28903461 AAGATTCCGTTTTTAACCTCGATTTCACCA-AAAATTACCATTTTACCCCCGAATCTTTTAAAAT
1 AAAATTCCATTTTTAACCCCGATTTCA-CAGAAAATTACCATTTTA-CCCCGAATCTTTTAAAAT
* *
28903525 TCCATTTTTAATCCCGATTACACC-AAAATTACCATTTT
64 TCCA-TTTTAA-CCTGATTTCACCGAAAATTACCATTTT
28903563 GCCCTCGAGT
Statistics
Matches: 250, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
176 77 0.31
177 168 0.67
178 5 0.02
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (174 bp):
AAAATTCCATTTTTAACCCCGATTTCACAGAAAATTACCATTTTACCCCGAATCTTTTAAAATTC
CATTTTAACCTGATTTCACCGAAAATTACCATTTTACCCCTAAAGCTTCTAAAATTCCATTTTTA
ACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTCT
Found at i:28903382 original size:118 final size:117
Alignment explanation
Indices: 28903108--28903562 Score: 664
Period size: 118 Copynumber: 3.9 Consensus size: 117
28903098 AAACTTTTCC
* *
28903108 AAAATTACATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCTCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
* ** *
28903173 CTA-TTTTAACCCTAATTTCATCGAAAATTACCATTTTACCCCTCAAGCTTCT
66 CCATTTTTAACCCCGATTTCA-CGAAAATTACCATTTTACCCCTGAAGCTTCT
*
28903225 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAAGCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
28903290 CCATTTTTAACCCCGATTTCACAGAAAATTACCATTTTTACCACC-GAAGCTTCT
66 CCATTTTTAACCCCGATTTCAC-GAAAATTACCA-TTTTACC-CCTGAAGCTTCT
** **
28903344 AAAATTCCA-TTTTAACCTTGATTTCACCGAAAATTACCATTTTACCCCTAAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
* *
28903408 CTATTTTTAACCCCGATTTTACTGAAAATTACCATTTTACCCCTGAAGCTTCT
66 CCATTTTTAACCCCGATTTCAC-GAAAATTACCATTTTACCCCTGAAGCTTCT
* * * *
28903461 AAGATTCCGTTTTTAACCTCGATTTCACCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
1 AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
* * *
28903526 CCATTTTTAATCCCGATTACACCAAAATTACCATTTT
66 CCATTTTTAACCCCGATTTCACGAAAATTACCATTTT
28903563 GCCCTCGAGT
Statistics
Matches: 306, Mismatches: 26, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
116 2 0.01
117 102 0.33
118 176 0.58
119 24 0.08
120 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.05, T:0.37
Consensus pattern (117 bp):
AAAATTCCATTTTTAACCCCGATTTCACCGAAAATTACCATTTTACCCCCGAATCTTTTAAAATT
CCATTTTTAACCCCGATTTCACGAAAATTACCATTTTACCCCTGAAGCTTCT
Found at i:28903436 original size:30 final size:30
Alignment explanation
Indices: 28903108--28903543 Score: 133
Period size: 29 Copynumber: 14.8 Consensus size: 30
28903098 AAACTTTTCC
* * *
28903108 AAAATTACATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTTACTG
28903138 AAAATTACCA-TTTT-ACCCTCGAATCTTT--T-
1 AAAATT-CCATTTTTAACCC-CG-AT-TTTACTG
* ** *
28903167 AAAATTCTA-TTTTAACCCTAATTTCA-TCG
1 AAAATTCCATTTTTAACCCCGATTTTACT-G
* * **
28903196 AAAATTACCA-TTTTACCCCTCAAGCTT-CT-
1 AAAATT-CCATTTTTAACCC-CGATTTTACTG
* *
28903225 AAAATTCCATTTTTAACCCCGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTTACTG
* *
28903255 AAAATTACCA-TTTTACCCCCGAAGCTTT--T-
1 AAAATT-CCATTTTTAACCCCG-A-TTTTACTG
* *
28903284 AAAATTCCATTTTTAACCCCGATTTCACAG
1 AAAATTCCATTTTTAACCCCGATTTTACTG
**
28903314 AAAATTACCATTTTT-ACCACCGAAGCTT-CT-
1 AAAATT-CCATTTTTAACC-CCG-ATTTTACTG
** * *
28903344 AAAATTCCA-TTTTAACCTTGATTTCACCG
1 AAAATTCCATTTTTAACCCCGATTTTACTG
*
28903373 AAAATTACCA-TTTT-ACCCCTAAATCTTT--T-
1 AAAATT-CCATTTTTAACCCC--GAT-TTTACTG
*
28903402 AAAATTCTATTTTTAACCCCGATTTTACTG
1 AAAATTCCATTTTTAACCCCGATTTTACTG
**
28903432 AAAATTACCA-TTTT-ACCCCTGAAGCTT-CT-
1 AAAATT-CCATTTTTAACCCC-G-ATTTTACTG
* * * * **
28903461 AAGATTCCGTTTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTTAACCCCGATTTTACTG
*
28903491 AAAATTACCA-TTTTACCCCCGAATCTTT--T-
1 AAAATT-CCATTTTTAACCCCG-AT-TTTACTG
*
28903520 AAAATTCCATTTTTAATCCCGATT
1 AAAATTCCATTTTTAACCCCGATT
28903544 ACACCAAAAT
Statistics
Matches: 297, Mismatches: 62, Indels: 97
0.65 0.14 0.21
Matches are distributed among these distances:
26 2 0.01
27 11 0.04
28 35 0.12
29 108 0.36
30 96 0.32
31 35 0.12
32 10 0.03
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.37
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCCCGATTTTACTG
Found at i:28915068 original size:9 final size:9
Alignment explanation
Indices: 28915054--28915079 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28915044 TCTCGATTGA
28915054 AAAAAAAAC
1 AAAAAAAAC
28915063 AAAAAAAAC
1 AAAAAAAAC
28915072 AAAAAAAA
1 AAAAAAAA
28915080 AGGTTCACGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:28916262 original size:201 final size:200
Alignment explanation
Indices: 28915906--28916431 Score: 836
Period size: 201 Copynumber: 2.6 Consensus size: 200
28915896 TTAGTTCAAC
* *
28915906 AAAACAAGCGAGACAGTCATCTTCCTGATGAGATATAGAGAAGAATACCAACTCAAATGCTCAAT
1 AAAACAAGCGAGACGGTCATCTT-CTGATGAGATACAGAGAAGAATACCAACTCAAATGCTCAAT
* * *
28915971 ACGAGTAAATCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
65 GCGAGCAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
*
28916036 GTTAGCTTCTTGATGAGACACAGAGAAGTAGACCAAATTCGTCTTCCCGAGGAGATCCAGAGAAG
130 GTTAGCTTCTTGATGAGACACAGAGAAGTAGACCAAATTCGTCTTCCCGAGGAGATCCAGAAAAG
*
28916101 CGGATT
195 CGAATT
* *
28916107 AAAATAAGCGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGAATACCAACTCAAATGCTCAAT
1 AAAACAAGCGAGACGGTCATCTTC-TGATGAGATACAGAGAAGAATACCAACTCAAATGCTCAAT
28916172 GCGAGCAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
65 GCGAGCAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
* * *
28916237 GTTAGCTTCTTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAAAAG
130 GTTAGCTTCTTGATGAGACACAGAGAAGTAGACCAAATTCGTCTTCCCGAGGAGATCCAGAAAAG
*
28916302 TGAATT
195 CGAATT
* * * *
28916308 AAAACAATCGAGACGGTCATCTTACTGATGAGATACTGAGAAGAAGACCAAATCAAACCAATGCT
1 AAAACAAGCGAGACGGTCATCTT-CTGATGAGATACAGAGAAGAATACCAACTC--A--AATGCT
28916373 CAATGCGAGCAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
61 CAATGCGAGCAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAG
28916432 TCAACGAAAC
Statistics
Matches: 300, Mismatches: 19, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
200 1 0.00
201 232 0.77
202 1 0.00
203 1 0.00
205 65 0.22
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (200 bp):
AAAACAAGCGAGACGGTCATCTTCTGATGAGATACAGAGAAGAATACCAACTCAAATGCTCAATG
CGAGCAAATCTTCGAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGG
TTAGCTTCTTGATGAGACACAGAGAAGTAGACCAAATTCGTCTTCCCGAGGAGATCCAGAAAAGC
GAATT
Found at i:28916808 original size:18 final size:17
Alignment explanation
Indices: 28916787--28916843 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
28916777 TTAAACCCAT
28916787 TTTAAGATTTATTTTAAA
1 TTTAA-ATTTATTTTAAA
* *
28916805 TTTAAATTGATTTTTGAA
1 TTTAAATTTA-TTTTAAA
*
28916823 TTTAAATTTAATTTAAA
1 TTTAAATTTATTTTAAA
28916840 TTTA
1 TTTA
28916844 GACTTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
17 13 0.39
18 20 0.61
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:28916837 original size:11 final size:11
Alignment explanation
Indices: 28916787--28916843 Score: 51
Period size: 12 Copynumber: 4.9 Consensus size: 11
28916777 TTAAACCCAT
*
28916787 TTTAAGATTTAT
1 TTTAA-ATTTAA
28916799 TTTAAATTTAAA
1 TTTAAATTT-AA
* **
28916811 TTGATTTTTGAA
1 TTTAAATTT-AA
28916823 TTTAAATTTAA
1 TTTAAATTTAA
28916834 TTTAAATTTA
1 TTTAAATTTA
28916844 GACTTATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
11 16 0.44
12 20 0.56
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:28917629 original size:25 final size:22
Alignment explanation
Indices: 28917587--28917638 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 22
28917577 ATATTCAATA
28917587 AATAATAAATTTTTATATTATT
1 AATAATAAATTTTTATATTATT
28917609 AATAATAATATTTATTA-A-TATT
1 AATAATAA-ATTT-TTATATTATT
28917631 AA-AATAAA
1 AATAATAAA
28917639 AAGGAAGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 5 0.18
22 14 0.50
23 5 0.18
24 3 0.11
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AATAATAAATTTTTATATTATT
Found at i:28918812 original size:29 final size:29
Alignment explanation
Indices: 28918714--28918893 Score: 161
Period size: 30 Copynumber: 6.1 Consensus size: 29
28918704 TAGAAGTCCG
* * *
28918714 TAAACTATCCAAAAATTATATTTTGA-CCC
1 TAAACTTTCTAAAAATTACATTTT-ACCCC
* *
28918743 TCGAACTTCTCT-AAAATTATATTTTAACCCC
1 T-AAACTT-TCTAAAAATTACATTTT-ACCCC
* *
28918774 AAAACATTCTAAAAATTACATTTTGACCCC
1 TAAACTTTCTAAAAATTACATTTT-ACCCC
* *
28918804 TAAA-TTTCTTTAAAATTATATTTTACCCC
1 TAAACTTTC-TAAAAATTACATTTTACCCC
*
28918833 AAAACTTTCTAAAAATTACATTTTACCCC
1 TAAACTTTCTAAAAATTACATTTTACCCC
* *
28918862 TAAACTTTC-CAAAATTCCATTTTTACCCC
1 TAAACTTTCTAAAAATTACA-TTTTACCCC
28918891 TAA
1 TAA
28918894 TTTCACCAAA
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
28 8 0.06
29 53 0.42
30 59 0.47
31 5 0.04
ACGTcount: A:0.38, C:0.23, G:0.02, T:0.37
Consensus pattern (29 bp):
TAAACTTTCTAAAAATTACATTTTACCCC
Found at i:28918818 original size:60 final size:59
Alignment explanation
Indices: 28918724--28918890 Score: 209
Period size: 60 Copynumber: 2.8 Consensus size: 59
28918714 TAAACTATCC
* * *
28918724 AAAAATTATATTTTGA-CCCTCGAACTTCTCTAAAATTATATTTTAACCCCAAAACATTCT
1 AAAAATTACATTTTGACCCCT-AAATTTCTCTAAAATTATATTTT-ACCCCAAAACATTCT
* *
28918784 AAAAATTACATTTTGACCCCTAAATTTCTTTAAAATTATATTTTACCCCAAAACTTTCT
1 AAAAATTACATTTTGACCCCTAAATTTCTCTAAAATTATATTTTACCCCAAAACATTCT
28918843 AAAAATTACATTTT-ACCCCTAAACTTTC-C-AAAATTCCAT-TTTTACCCC
1 AAAAATTACATTTTGACCCCTAAA-TTTCTCTAAAATT--ATATTTTACCCC
28918891 TAATTTCACC
Statistics
Matches: 97, Mismatches: 6, Indels: 10
0.86 0.05 0.09
Matches are distributed among these distances:
57 6 0.06
58 18 0.19
59 34 0.35
60 35 0.36
61 4 0.04
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (59 bp):
AAAAATTACATTTTGACCCCTAAATTTCTCTAAAATTATATTTTACCCCAAAACATTCT
Found at i:28918902 original size:29 final size:28
Alignment explanation
Indices: 28918785--28918999 Score: 134
Period size: 29 Copynumber: 7.5 Consensus size: 28
28918775 AAACATTCTA
* *
28918785 AAAATTACATTTTGACCCCTAAA-TTTCTTT
1 AAAATTCCATTTT-ACCCCTAAACTTTC--C
** * *
28918815 AAAATTATATTTTACCCCAAAACTTTCTA
1 AAAATTCCATTTTACCCCTAAACTTTC-C
*
28918844 AAAATTACATTTTACCCCTAAACTTTCC
1 AAAATTCCATTTTACCCCTAAACTTTCC
28918872 AAAATTCCATTTTTACCCCT-AA-TTTCACC
1 AAAATTCCA-TTTTACCCCTAAACTTT--CC
* *
28918901 AAAATCACCATTTTA-CCCTGAACTTTCC
1 AAAAT-TCCATTTTACCCCTAAACTTTCC
** * **
28918929 AAAATTCCATTTTTGCTCTCGA-TTTCACC
1 AAAATTCCATTTTACCCCTAAACTTT--CC
* * *
28918958 AAAATTGCCATTTTACCCCCAAACTCTCT
1 AAAATT-CCATTTTACCCCTAAACTTTCC
*
28918987 AAAATTTCATTTT
1 AAAATTCCATTTT
28919000 TTGACCCCGA
Statistics
Matches: 151, Mismatches: 22, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
27 13 0.09
28 31 0.21
29 73 0.48
30 32 0.21
31 2 0.01
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (28 bp):
AAAATTCCATTTTACCCCTAAACTTTCC
Found at i:28918925 original size:57 final size:58
Alignment explanation
Indices: 28918844--28919034 Score: 219
Period size: 57 Copynumber: 3.3 Consensus size: 58
28918834 AAACTTTCTA
*
28918844 AAAATTA-CATTTTACCCCTAAACTTTCCAAAATTCCATTTTTACCCCTAATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTACCCCTGATTTCACC
* * * *
28918901 AAAATCACCATTTTA-CCCTGAACTTTCCAAAATTCCATTTTT-GCTCTCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTACCCCT-GATTTCACC
* * * * * *
28918958 AAAATTGCCATTTTACCCCCAAACTCTCTAAAATTTCATTTTTTGACCCC-GATTTTACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCA-TTTTT-ACCCCTGATTTCACC
*
28919017 AAAATTACTATTTTACCC
1 AAAATTACCATTTTACCC
28919035 TCGGGTATCC
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
56 3 0.03
57 53 0.48
58 24 0.22
59 29 0.26
61 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.03, T:0.37
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTACCCCTGATTTCACC
Found at i:28922290 original size:16 final size:15
Alignment explanation
Indices: 28922243--28922297 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
28922233 AAAATAAAAT
28922243 TTAAAAAATTATTATA
1 TTAAAAAATT-TTATA
*
28922259 -TAATAAATTTTA-A
1 TTAAAAAATTTTATA
28922272 TTAAAATAATTTTATA
1 TTAAAA-AATTTTATA
*
28922288 TTAATAAATT
1 TTAAAAAATT
28922298 AAAAATCCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 1 0.03
14 7 0.21
15 19 0.58
16 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTAAAAAATTTTATA
Found at i:28925163 original size:43 final size:42
Alignment explanation
Indices: 28925099--28925259 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 42
28925089 GGTAAAAATC
* * *
28925099 GCGGCGTTTTTCCGCAAAAACGCCGCTATAAAACGTGGTCTTTA
1 GCGGCGCTTTTCC-CACAAACGCCGCTA-AAAACATGGTCTTTA
* *
28925143 GCGGTGCTTTTCTCACAAACGCCGCTAACAAACATGGTCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAA-AAACATGGTCTTTA
* * * *
28925186 ACGACGCTTCTCCCACAAACGCCGCTAAAGAACATTGTCTTTA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAA-AACATGGTCTTTA
* *
28925229 GCGGCACTTTTCCCACAAACGTCGCTAAAAA
1 GCGGCGCTTTTCCCACAAACGCCGCTAAAAA
28925260 ACTTCACCGC
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
42 4 0.04
43 85 0.86
44 10 0.10
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (42 bp):
GCGGCGCTTTTCCCACAAACGCCGCTAAAAACATGGTCTTTA
Found at i:28928770 original size:40 final size:41
Alignment explanation
Indices: 28928719--28929019 Score: 197
Period size: 41 Copynumber: 7.4 Consensus size: 41
28928709 AACCTTTATA
*
28928719 CTCTGAACTTTAGCGGTGCTTTTTCATAAGTGTCGCTAAT-
1 CTCTGATCTTTAGCGGTGCTTTTTCATAAGTGTCGCTAATG
* * **** * *
28928759 ATTTGATCTTTAGCGAAAATTTTTCATAACTGTCGTTAATG
1 CTCTGATCTTTAGCGGTGCTTTTTCATAAGTGTCGCTAATG
* * * *
28928800 CTCTGATTTTTAACGGTGCTTTTTTAT-AGATGCCGCTAATG
1 CTCTGATCTTTAGCGGTGCTTTTTCATAAG-TGTCGCTAATG
* * * *
28928841 CTCTGACCTTTAGCGGCT-CTTTCTCATAAGCGGCGCTAATG
1 CTCTGATCTTTAGCGG-TGCTTTTTCATAAGTGTCGCTAATG
** * **
28928882 CTCTGA-CTTTTAGCGACG-TTTTCTCATAGGCATCGCTAATG
1 CTCTGATC-TTTAGCGGTGCTTTT-TCATAAGTGTCGCTAATG
* * *
28928923 CTCTGACCTTTAGCGG-GACTTTCTCGT-A-TGTACTGCTAATG
1 CTCTGATCTTTAGCGGTG-CTTTTTCATAAGTGT-C-GCTAATG
* * * * * *
28928964 CTTTGACCTTTAGCGGCGCTTTCTCATAAGCGCCGCTAATG
1 CTCTGATCTTTAGCGGTGCTTTTTCATAAGTGTCGCTAATG
28929005 CTCTGA-CTTTAGCGG
1 CTCTGATCTTTAGCGG
28929020 CACTTTCACA
Statistics
Matches: 201, Mismatches: 45, Indels: 30
0.73 0.16 0.11
Matches are distributed among these distances:
39 1 0.00
40 47 0.23
41 142 0.71
42 10 0.05
43 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (41 bp):
CTCTGATCTTTAGCGGTGCTTTTTCATAAGTGTCGCTAATG
Found at i:28928878 original size:41 final size:41
Alignment explanation
Indices: 28928833--28929032 Score: 226
Period size: 41 Copynumber: 4.9 Consensus size: 41
28928823 TTATAGATGC
* *
28928833 CGCTAATGCTCTGACCTTTAGCGGCTCTTTCTCATAAGCGG
1 CGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAGCGA
* * ** *
28928874 CGCTAATGCTCTGACTTTTAGCGACGTTTTCTCATAGGC-A
1 CGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAGCGA
* * * *
28928914 TCGCTAATGCTCTGACCTTTAGCGGGACTTTCTCGTATG-TA
1 -CGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAGCGA
* * *
28928955 CTGCTAATGCTTTGACCTTTAGCGGCGCTTTCTCATAAGCGC
1 C-GCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAGCGA
*
28928997 CGCTAATGCTCTGA-CTTTAGCGGCACTTTCACATAA
1 CGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAA
28929033 ACGTCTCTAT
Statistics
Matches: 132, Mismatches: 23, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
40 21 0.16
41 110 0.83
42 1 0.01
ACGTcount: A:0.19, C:0.27, G:0.20, T:0.34
Consensus pattern (41 bp):
CGCTAATGCTCTGACCTTTAGCGGCACTTTCTCATAAGCGA
Found at i:28928881 original size:82 final size:81
Alignment explanation
Indices: 28928795--28929032 Score: 250
Period size: 82 Copynumber: 2.9 Consensus size: 81
28928785 TAACTGTCGT
* * * * *
28928795 TAATGCTCTGATTTTTAACGGTGCTTTTTTATAGATGCCGCTAATGCTCTGACCTTTAGCGGCTC
1 TAATGCTCTGACTTTTAGCGGCGCTTTTTCATAGA-GCCGCTAATGCTCTGACCTTTAGCGGCAC
*
28928860 TTTCTCATAAGCGGC-GC
65 TTTCTCATAAG-GACTGC
* *
28928877 TAATGCTCTGACTTTTAGCGACG-TTTTCTCATAG-GCATCGCTAATGCTCTGACCTTTAGCGGG
1 TAATGCTCTGACTTTTAGCGGCGCTTTT-TCATAGAGC--CGCTAATGCTCTGACCTTTAGCGGC
* * *
28928940 ACTTTCTCGTATGTACTGC
63 ACTTTCTCATAAGGACTGC
* * * *
28928959 TAATGCTTTGACCTTTAGCGGCGCTTTCTCATAAGCGCCGCTAATGCTCTGA-CTTTAGCGGCAC
1 TAATGCTCTGACTTTTAGCGGCGCTTTTTCAT-AGAGCCGCTAATGCTCTGACCTTTAGCGGCAC
*
28929023 TTTCACATAA
65 TTTCTCATAA
28929033 ACGTCTCTAT
Statistics
Matches: 130, Mismatches: 19, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
80 2 0.02
81 23 0.18
82 98 0.75
83 5 0.04
84 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (81 bp):
TAATGCTCTGACTTTTAGCGGCGCTTTTTCATAGAGCCGCTAATGCTCTGACCTTTAGCGGCACT
TTCTCATAAGGACTGC
Found at i:28930865 original size:29 final size:29
Alignment explanation
Indices: 28930778--28930868 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 29
28930768 AAATTTCCCG
*
28930778 CTTTTATTCTG-TTTTTTTAAATTAAATC
1 CTTTTATTCTGTTTTTTTTAAATTTAATC
*
28930806 CTTTTATT-T-TTATGCTTTTTAAAATCT--TC
1 CTTTTATTCTGTT-T--TTTTT-AAATTTAATC
28930835 CTTTTATTCTGTTTTTTTTAAATTTAATC
1 CTTTTATTCTGTTTTTTTTAAATTTAATC
28930864 CTTTT
1 CTTTT
28930869 TCTATTATAT
Statistics
Matches: 51, Mismatches: 3, Indels: 17
0.72 0.04 0.24
Matches are distributed among these distances:
27 7 0.14
28 14 0.27
29 17 0.33
30 7 0.14
31 6 0.12
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (29 bp):
CTTTTATTCTGTTTTTTTTAAATTTAATC
Found at i:28935255 original size:34 final size:34
Alignment explanation
Indices: 28935216--28935328 Score: 120
Period size: 34 Copynumber: 3.3 Consensus size: 34
28935206 TTAACCATCC
28935216 AACACACCAAATGCTCGTAAGAGCTAGTCTAATC-
1 AACACACCAAATGCTCGTAAGAGCTAGTC-AATCT
* * * * **
28935250 GACACACCATATGCTTGTAAGAGCTAATCCCTCT
1 AACACACCAAATGCTCGTAAGAGCTAGTCAATCT
* * * *
28935284 AACACCCCAAATGCTCGTAAGAGATAGTCCATCC
1 AACACACCAAATGCTCGTAAGAGCTAGTCAATCT
28935318 AACACACCAAA
1 AACACACCAAA
28935329 ACACTATAAC
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
33 2 0.03
34 61 0.97
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.19
Consensus pattern (34 bp):
AACACACCAAATGCTCGTAAGAGCTAGTCAATCT
Found at i:28937709 original size:29 final size:29
Alignment explanation
Indices: 28937675--28937737 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
28937665 CACTGTTGGG
28937675 CTGTCCATCATATTTGTTCGATGTTTGAA
1 CTGTCCATCATATTTGTTCGATGTTTGAA
28937704 CTGTCCATCATATTTGTTCGATGTTTGAA
1 CTGTCCATCATATTTGTTCGATGTTTGAA
28937733 CTGTC
1 CTGTC
28937738 TGCCACATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.44
Consensus pattern (29 bp):
CTGTCCATCATATTTGTTCGATGTTTGAA
Found at i:28937750 original size:29 final size:29
Alignment explanation
Indices: 28937675--28937757 Score: 85
Period size: 29 Copynumber: 2.9 Consensus size: 29
28937665 CACTGTTGGG
* * *
28937675 CTGTCCATCATATTTGTTCGATGTTTGAA
1 CTGTCCACCACATGTGTTCGATGTTTGAA
* * *
28937704 CTGTCCATCATATTTGTTCGATGTTTGAA
1 CTGTCCACCACATGTGTTCGATGTTTGAA
** *
28937733 CTGTCTGCCACATGTGTTCGCTGTT
1 CTGTCCACCACATGTGTTCGATGTT
28937758 GCATGGTTGG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (29 bp):
CTGTCCACCACATGTGTTCGATGTTTGAA
Found at i:28943969 original size:494 final size:492
Alignment explanation
Indices: 28942905--28943826 Score: 1368
Period size: 494 Copynumber: 1.9 Consensus size: 492
28942895 AAATAGAATC
** ** * *
28942905 CATATAGAACTACAGTTATTCTATTTGACATTGATTAGAATAAT-GTTTTTCAACCTTTAAATAG
1 CATATAGAACTACAGTTATTCTATTT-ACAAAGAAAAGAATAATAG-TTTTCAACATTGAAATAG
* *
28942969 ATGTAGTTAAAACTCTTATTGTATCATTCAAATTCGATATTAGTGAATTTTTTCTTTTTTACCCG
64 AAGTAGTTAAAACTCCTATTGTATCATTCAAATTCGATATTAGTGAATTTTTTCTTTTTTACCCG
* * *
28943034 TGTTTTTTCCCGAAAATATTTTTCACGTAAAATTCATGTTTTTTTTCTTTTCTTATTGTTTCGCG
129 TGTTTTTTCCCAAAAAGATTTTTCACGTAAAATTCATGTTTTTTTTCCTTTCTTATTGTTTCGCG
28943099 ATCGTTTCTATTGTCATTATCGACGTTAATTCAACACTTTTTGTCACCTTCTTTTTATTATTTTT
194 ATCGTTTCTATTGTCATTATCGACGTTAATTCAACACTTTTTGTCACCTTCTTTTTATTATTTTT
*
28943164 GGACCACTTTCACTCTCAACCTTAAATTTCTAATCAAATTATTTTTTTGGCCTGTTAAAATATTA
259 GGACCACTTTCACTCTCAACCTTAAATTTCTAATCAAATTATTTTTCTGGCCTGTTAAAATATTA
* *
28943229 AGTAGAGTAATGTGAAAACCCACTAGTCAATCTCTCTATATATTATAGAAATTTAAATTTATAAA
324 AGTACAGTAATGTGAAAACCCACTAATCAATCTCTCTATATATTATAGAAATTTAAATTTATAAA
*** * * **
28943294 TAAAAATAATAAAAGTACATAAAATTAAAAAAAATAATTAGGGGAGCTGTGTAGGGCTTACGGTC
389 TAAAAATAATAAAAGTACATAAAATTAAAAAAAATAATTACAAGAGCTATGAAGAAC-TACGGTC
* * **
28943359 GAAGGTCCTTGCAGTACAGTATATGTTGCACAAGTAAAATT
453 GAAGAT-CTTGCAGTACAGCATATAATGCACAAGTAAAATT
** ** ** * *
28943400 CATATAGAACTACAGTTATTCTATTTGACATTGATTAGAATAATTTTTTTCAACCTTTAAATAGA
1 CATATAGAACTACAGTTATTCTATTT-ACAAAGAAAAGAATAATAGTTTTCAACATTGAAATAGA
* **
28943465 TGTAGTTAAAACTCCTATTGTATCATTCAAATTCGATATTAGTGAATTTTTTTCTTTTTTGTCCG
65 AGTAGTTAAAACTCCTATTGTATCATTCAAATTCGATATTAGTGAA-TTTTTTCTTTTTTACCCG
* * *
28943530 TGGTTTTTT-CCAAAAAGGTTTTTCACGTAAAGTTTATGTTTTTTTTCCTTTCTTATTGTTTCGC
129 T-GTTTTTTCCCAAAAAGATTTTTCACGTAAAATTCATGTTTTTTTTCCTTTCTTATTGTTTCGC
*
28943594 GATCGTTTCTATTGTCATTATCGGCGTTAATTCAACACTTTTTGTCACCTTC-TTTTATTA-TTT
193 GATCGTTTCTATTGTCATTATCGACGTTAATTCAACACTTTTTGTCACCTTCTTTTTATTATTTT
*
28943657 TGGACCACTTTCACTCTCAACCTTAAATTTCTAATCAAATTATTTTTCTGGCCTGTTAAAATTTT
258 TGGACCACTTTCACTCTCAACCTTAAATTTCTAATCAAATTATTTTTCTGGCCTGTTAAAATATT
28943722 AAGTACAGTAATGTGAAAACCCACTAATCAATCTCTCTATATATTATAGAAATTTAAATTTATAA
323 AAGTACAGTAATGTGAAAACCCACTAATCAATCTCTCTATATATTATAGAAATTTAAATTTATAA
*
28943787 ATAAAAATAATAAAAGTTCATAAAATT-AAAAAAATAATTA
388 ATAAAAATAATAAAAGTACATAAAATTAAAAAAAATAATTA
28943827 TCAATATCAA
Statistics
Matches: 408, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
493 13 0.03
494 155 0.38
495 116 0.28
496 117 0.29
497 7 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (492 bp):
CATATAGAACTACAGTTATTCTATTTACAAAGAAAAGAATAATAGTTTTCAACATTGAAATAGAA
GTAGTTAAAACTCCTATTGTATCATTCAAATTCGATATTAGTGAATTTTTTCTTTTTTACCCGTG
TTTTTTCCCAAAAAGATTTTTCACGTAAAATTCATGTTTTTTTTCCTTTCTTATTGTTTCGCGAT
CGTTTCTATTGTCATTATCGACGTTAATTCAACACTTTTTGTCACCTTCTTTTTATTATTTTTGG
ACCACTTTCACTCTCAACCTTAAATTTCTAATCAAATTATTTTTCTGGCCTGTTAAAATATTAAG
TACAGTAATGTGAAAACCCACTAATCAATCTCTCTATATATTATAGAAATTTAAATTTATAAATA
AAAATAATAAAAGTACATAAAATTAAAAAAAATAATTACAAGAGCTATGAAGAACTACGGTCGAA
GATCTTGCAGTACAGCATATAATGCACAAGTAAAATT
Found at i:28947216 original size:20 final size:20
Alignment explanation
Indices: 28947186--28947224 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
28947176 TTTTAATTTT
28947186 TTTAGTAAAAAAAAACTTGGA
1 TTTAGTAAAAAAAAA-TTGGA
28947207 TTTA-TAAAAAAAAATTGG
1 TTTAGTAAAAAAAAATTGG
28947225 TTAATACATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (20 bp):
TTTAGTAAAAAAAAATTGGA
Found at i:28948689 original size:30 final size:30
Alignment explanation
Indices: 28948649--28948706 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
28948639 AGAAATAAAA
28948649 ATTTTAATTTTAGGCATTGGCGTTAAAACC
1 ATTTTAATTTTAGGCATTGGCGTTAAAACC
* * **
28948679 ATTTTCATTTTAGTCATTGTTGTTAAAA
1 ATTTTAATTTTAGGCATTGGCGTTAAAA
28948707 AATGTTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.14, T:0.47
Consensus pattern (30 bp):
ATTTTAATTTTAGGCATTGGCGTTAAAACC
Found at i:28955557 original size:59 final size:58
Alignment explanation
Indices: 28955480--28955735 Score: 313
Period size: 59 Copynumber: 4.4 Consensus size: 58
28955470 TTGACTTTCG
** **
28955480 GGGGTAAAAAT-GTAATTTTTGGTGAAATTAGGGTCGAAAATGAGATTTTAGGAAATTTAA
1 GGGGT-AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTT-GGAAATTT-A
* *
28955540 GGGGTAAAATGGT-A-TTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAA-TTTA
*
28955597 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-AGGATTTTGGGAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGA-GATTTT-GGAAATTTA
* * * **
28955656 TGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAA-TTTA
28955715 GGGGTAAAATGGTAATTTTTG
1 GGGGTAAAATGGTAATTTTTG
28955736 AACAGTCCGG
Statistics
Matches: 172, Mismatches: 16, Indels: 17
0.84 0.08 0.08
Matches are distributed among these distances:
57 18 0.10
58 36 0.21
59 107 0.62
60 11 0.06
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.34
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAATTTA
Found at i:28955718 original size:118 final size:117
Alignment explanation
Indices: 28955476--28955735 Score: 382
Period size: 118 Copynumber: 2.2 Consensus size: 117
28955466 AATTTTGACT
* *
28955476 TTCGGGGGTAAAAAT-GTAATTTTTGGTGAAATTAGGGTCGAAAATGAGATTTTAGGAAATTTAA
1 TTCGGGGGT-AAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGAGATTTTAGGAAATTTAA
*
28955540 GGGGTAAAATGGTATTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAG
65 GGGGTAAAATGGTATTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
* * * * *
28955593 TTTGGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAAT-AGGATTTTGGGAAGTTT-A
1 TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGA-GATTTTAGGAAATTTAA
*
28955656 TGGGTAAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
65 GGGGTAAAATGGT-A-TTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
28955711 TTCGGGGGTAAAATGGTAATTTTTG
1 TTCGGGGGTAAAATGGTAATTTTTG
28955736 AACAGTCCGG
Statistics
Matches: 129, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
116 19 0.15
117 48 0.37
118 62 0.48
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.34
Consensus pattern (117 bp):
TTCGGGGGTAAAATGGTAATTTTTGGTGAAATCAGGGTCAAAAATGAGATTTTAGGAAATTTAAG
GGGTAAAATGGTATTTTGGTGAAATCGAGGTTAAAAATGGGATTTTGGAAAG
Found at i:28955732 original size:29 final size:29
Alignment explanation
Indices: 28955452--28955733 Score: 137
Period size: 29 Copynumber: 9.7 Consensus size: 29
28955442 TAGATGCCCG
**
28955452 GGGGGTAAAATGGTAATTTT--GACTTTC
1 GGGGGTAAAATGGTAATTTTGGGAAATTC
*
28955479 GGGGGTAAAAAT-GTAATTTTTGGTGAAATTA
1 GGGGGT-AAAATGGTAA-TTTTGG-GAAATTC
* * *
28955510 GGGTCG-AAAAT-G-AGATTTTAGGAAATTTA
1 GGG-GGTAAAATGGTA-ATTTTGGGAAA-TTC
*
28955539 AGGGGTAAAATGGT-ATTTTGGTGAAA-TC
1 GGGGGTAAAATGGTAATTTTGG-GAAATTC
* * *
28955567 GGGGTTAAAAATGG-GATTTT-GGAAAGTTT
1 GGGGGT-AAAATGGTAATTTTGGGAAA-TTC
28955596 GGGGGTAAAATGGTAATTTTTGGTGAAA-TC
1 GGGGGTAAAATGGTAA-TTTTGG-GAAATTC
* * *
28955626 GGGGTTAAAAATAGG--ATTTTGGGAAGTTT
1 GGGGGT-AAAAT-GGTAATTTTGGGAAATTC
**
28955655 ATGGGTAAAATGGTAATTTTTGGTGAAA-TC
1 GGGGGTAAAATGGTAA-TTTTGG-GAAATTC
* * *
28955685 GAGGTTAAAAATGG-GATTTT-GGAAAGTTC
1 GGGGGT-AAAATGGTAATTTTGGGAAA-TTC
28955714 GGGGGTAAAATGGTAATTTT
1 GGGGGTAAAATGGTAATTTT
28955734 TGAACAGTCC
Statistics
Matches: 194, Mismatches: 30, Indels: 60
0.68 0.11 0.21
Matches are distributed among these distances:
27 20 0.10
28 43 0.22
29 67 0.35
30 34 0.18
31 23 0.12
32 7 0.04
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.34
Consensus pattern (29 bp):
GGGGGTAAAATGGTAATTTTGGGAAATTC
Found at i:28956837 original size:9 final size:9
Alignment explanation
Indices: 28956823--28956848 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
28956813 TTTTTTGAAT
28956823 TTATTAATA
1 TTATTAATA
28956832 TTATTAATA
1 TTATTAATA
28956841 TTATTAAT
1 TTATTAAT
28956849 GGCTATTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTATTAATA
Found at i:28961860 original size:29 final size:31
Alignment explanation
Indices: 28961809--28961872 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
28961799 GTTCGGGTGT
* *
28961809 AAAATGGTAATTTTAGATGAATTT-GGGGTC
1 AAAATGGTAATTTTAGATAAATTTAGGAGTC
28961839 AAAAT-GTAATTTTGAGA-AAATTTAGGAGTC
1 AAAATGGTAATTTT-AGATAAATTTAGGAGTC
28961869 AAAA
1 AAAA
28961873 ACATAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (31 bp):
AAAATGGTAATTTTAGATAAATTTAGGAGTC
Found at i:28961976 original size:29 final size:29
Alignment explanation
Indices: 28961804--28962049 Score: 110
Period size: 29 Copynumber: 8.4 Consensus size: 29
28961794 TGGATGTTCG
28961804 GGTGT-AAAATGGTAATTTTAGATGAA-TTT-
1 GGTGTCAAAAT-GTAATTTTAGA--AAGTTTA
* *
28961833 GGGGTCAAAATGTAATTTTGAGAAAATTTA
1 GGTGTCAAAATGTAATTTT-AGAAAGTTTA
* ** * * *
28961863 GGAGTCAAAAACATAATTTTTGGAAGTTCA
1 GGTGTC-AAAATGTAATTTTAGAAAGTTTA
** * * * * **
28961893 ACT-TTAAAATGTGATTTTTGCGAAGTACA
1 GGTGTCAAAATGTAATTTTAG-AAAGTTTA
* *
28961922 GAG-GTCAAAATATAATTTT-GTGAAGTTTA
1 G-GTGTCAAAATGTAATTTTAG-AAAGTTTA
*
28961951 GGTGTCAAAATGTAATTTTAGAAAGTTTG
1 GGTGTCAAAATGTAATTTTAGAAAGTTTA
* * * *
28961980 GGGGTTAAAATGTAATTTTGGGAAGTTTGA
1 GGTGTCAAAATGTAATTTTAGAAAGTTT-A
* * *
28962010 GG-GTTAAAATGTAATTTTTGGAAAGTTCA
1 GGTGTCAAAATGTAA-TTTTAGAAAGTTTA
*
28962039 GGAGTCAAAAT
1 GGTGTCAAAAT
28962050 TTGATTTTTG
Statistics
Matches: 169, Mismatches: 35, Indels: 25
0.74 0.15 0.11
Matches are distributed among these distances:
28 15 0.09
29 91 0.54
30 52 0.31
31 11 0.07
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (29 bp):
GGTGTCAAAATGTAATTTTAGAAAGTTTA
Found at i:28962036 original size:30 final size:29
Alignment explanation
Indices: 28961928--28962036 Score: 132
Period size: 29 Copynumber: 3.7 Consensus size: 29
28961918 TACAGAGGTC
* *
28961928 AAAATATAATTTTGTG-AAGTTT-AGGTGTC
1 AAAATGTAATTTTG-GAAAGTTTGAGG-GTT
* *
28961957 AAAATGTAATTTTAGAAAGTTTGGGGGTT
1 AAAATGTAATTTTGGAAAGTTTGAGGGTT
*
28961986 AAAATGTAATTTTGGGAAGTTTGAGGGTT
1 AAAATGTAATTTTGGAAAGTTTGAGGGTT
28962015 AAAATGTAATTTTTGGAAAGTT
1 AAAATGTAA-TTTTGGAAAGTT
28962037 CAGGAGTCAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
28 1 0.01
29 55 0.80
30 13 0.19
ACGTcount: A:0.35, C:0.01, G:0.25, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTGGAAAGTTTGAGGGTT
Found at i:28964428 original size:39 final size:39
Alignment explanation
Indices: 28964385--28964490 Score: 133
Period size: 39 Copynumber: 2.7 Consensus size: 39
28964375 TGGTTGCAAT
* * *
28964385 CTGCCCCTGGCTC-GGGATAAGAGATTGGCTGATGGTGAC
1 CTGCCCCAGGCTCAAGG-TAAGAGATCGGCTGATGGTGAC
28964424 CTGCCCCAGGCTCAAGGTAAGAGATCGGCTGATGGTGAC
1 CTGCCCCAGGCTCAAGGTAAGAGATCGGCTGATGGTGAC
* * * *
28964463 CTACCTCAGACTGAAGGTAAGAGATCGG
1 CTGCCCCAGGCTCAAGGTAAGAGATCGG
28964491 ATGGCTGCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
39 57 0.97
40 2 0.03
ACGTcount: A:0.24, C:0.24, G:0.33, T:0.20
Consensus pattern (39 bp):
CTGCCCCAGGCTCAAGGTAAGAGATCGGCTGATGGTGAC
Found at i:28964506 original size:78 final size:78
Alignment explanation
Indices: 28964424--28964850 Score: 380
Period size: 78 Copynumber: 5.4 Consensus size: 78
28964414 TGATGGTGAC
* * * * * *
28964424 CTGCCCCAGGCTCAAGGTAAGAGATCGGCTGATGGTGACCTACCTCAGACT-GAAGGTAAGAGAT
1 CTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGACTCG-GGGTAAGAGAT
28964488 CGGATGGCTGCAAT
65 CGGATGGCTGCAAT
* * * * *
28964502 CTGCC-CTAGGCTCTGGGTAAGAGATTGGCTGATAGTGATTTACCCCAGGCTCGGGGTAAAAGAT
1 CTGCCTC-AGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGACTCGGGGTAAGAGAT
* * *
28964566 TGGATAGCTGTAAT
65 CGGATGGCTGCAAT
* * *
28964580 TTGCCTCAGGCTC-GGGTTAAGAGATTGACTGATGGTGATCTACCTCAG-CTCGGGGTAAGAGAT
1 CTGCCTCAGGCTCAGGG-TAAGAGATTGGCTGATGGTGATCTACCCCAGACTCGGGGTAAGAGAT
*
28964643 CGGATGGCTGTAAT
65 CGGATGGCTGCAAT
** * * * * * * *
28964657 CTGCCTCATACTCAAGGTAAGAGATTAGTTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATC
1 CTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGACTCGGGGTAAGAGATC
* *
28964722 AGATGGTTGCAAT
66 GGATGGCTGCAAT
* * * * *
28964735 CTGCCTCAGGGGTCGGGGTAAGGGATTGGCTTATGGTGATCTACCCCA-AGCTCGAGGTAAAGAG
1 CTGCCTCA-GGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGA-CTCGGGGT-AAGA-
*
28964799 GTATCAGATGGCTGCAAT
62 G-ATCGGATGGCTGCAAT
* * *
28964817 CTGCCTCTCAAGCTCGGGGTAAGA-ATTTGCTGAT
1 CTG-C-CTCAGGCTCAGGGTAAGAGATTGGCTGAT
28964851 TGATTATGAT
Statistics
Matches: 281, Mismatches: 55, Indels: 22
0.78 0.15 0.06
Matches are distributed among these distances:
77 65 0.23
78 133 0.47
79 37 0.13
80 3 0.01
81 1 0.00
82 26 0.09
83 12 0.04
84 4 0.01
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (78 bp):
CTGCCTCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTACCCCAGACTCGGGGTAAGAGATC
GGATGGCTGCAAT
Found at i:28964521 original size:39 final size:39
Alignment explanation
Indices: 28964478--28964756 Score: 134
Period size: 39 Copynumber: 7.2 Consensus size: 39
28964468 TCAGACTGAA
* *
28964478 GGTAAGAGATCGGATGGCTGCAATCTGCCCTAGGCTCTG
1 GGTAAGAGATCGGATGGCTGTAATCTGCCCTAGGCTCGG
* * * * * * *
28964517 GGTAAGAGATTGGCT-GATAGTGATTTACCCCAGGCTCGG
1 GGTAAGAGATCGGATGGCT-GTAATCTGCCCTAGGCTCGG
* * * *
28964556 GGTAAAAGATTGGATAGCTGTAATTTG-CCTCAGGCTCGG
1 GGTAAGAGATCGGATGGCTGTAATCTGCCCT-AGGCTCGG
* * *
28964595 GTTAAGAGATTGACTGATGG-TG--ATCT-ACCTCA-GCTCGG
1 GGTAAGAGA-T--CGGATGGCTGTAATCTGCCCT-AGGCTCGG
**
28964633 GGTAAGAGATCGGATGGCTGTAATCTGCCTCATA--CTCAA
1 GGTAAGAGATCGGATGGCTGTAATCTGCC-C-TAGGCTCGG
*
28964672 GGTAAGAGATTAGTTGATGG-TG--ATCTGCCCTAGGCTCGG
1 GGTAAGAGA-TCG--GATGGCTGTAATCTGCCCTAGGCTCGG
* * * * *
28964711 GGTAAAAGATCAGATGGTTGCAATCTG-CCTCAGGGGTCGG
1 GGTAAGAGATCGGATGGCTGTAATCTGCCCT-A-GGCTCGG
28964751 GGTAAG
1 GGTAAG
28964757 GGATTGGCTT
Statistics
Matches: 183, Mismatches: 34, Indels: 45
0.70 0.13 0.17
Matches are distributed among these distances:
35 6 0.03
36 7 0.04
37 5 0.03
38 27 0.15
39 106 0.58
40 18 0.10
41 5 0.03
42 9 0.05
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (39 bp):
GGTAAGAGATCGGATGGCTGTAATCTGCCCTAGGCTCGG
Found at i:28964707 original size:155 final size:156
Alignment explanation
Indices: 28964439--28964942 Score: 448
Period size: 155 Copynumber: 3.1 Consensus size: 156
28964429 CCAGGCTCAA
* *
28964439 GGTAAGAGATCGGCTGATGGTGACCTACCTCAGACT-GAAGGTAAGAGATCGGATGGCTGCAATC
1 GGTAAGAGATTGGCTGATGGTGATCTACCTCAG-CTCG-AGGTAAGAGATCGGATGGCTGCAATC
** * * *
28964503 TGCC-CTAGGCTCTGGGTAAGAGATTGGCTGATAGTGATTTACCCCAGGCTCGGGGTAAAAGATT
64 TGCCTCTA-GCTCAAGGTAAGAGATTAGCTGATAGTGATCTACCCCAGGCTCGGGGTAAAAGATC
* * *
28964567 GGATAGCTGTAATTTGCCTCA-GGCTCGG
128 AGATAGCTGCAATCTGCCTCAGGGCTCGG
* * * *
28964595 GTTAAGAGATTGACTGATGGTGATCTACCTCAGCTCGGGGTAAGAGATCGGATGGCTGTAATCTG
1 GGTAAGAGATTGGCTGATGGTGATCTACCTCAGCTCGAGGTAAGAGATCGGATGGCTGCAATCTG
* * * *
28964660 CCTCATA-CTCAAGGTAAGAGATTAGTTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCAG
66 CCTC-TAGCTCAAGGTAAGAGATTAGCTGATAGTGATCTACCCCAGGCTCGGGGTAAAAGATCAG
* * *
28964724 ATGGTTGCAATCTGCCTCAGGGGTCGG
130 ATAGCTGCAATCTGCCTCAGGGCTCGG
* * * *
28964751 GGTAAGGGATTGGCTTATGGTGATCTACCCCAAGCTCGAGGTAAAGAGGTATCAGATGGCTGCAA
1 GGTAAGAGATTGGCTGATGGTGATCTACCTC-AGCTCGAGGT-AAGA-G-ATCGGATGGCTGCAA
** * * * *
28964816 TCTGCCTCTCAAGCTCGGGGTAAGA-ATTTGCTGATTGATTATGATCTGCCCC-GAGCTCGGGGC
62 TCTGCCTCT--AGCTCAAGGTAAGAGATTAGCTGA-T-A--GTGATCTACCCCAG-GCTCGGGGT
* * * *
28964879 AAAAGATCAAAT-GCCTGTAATCTGCCCCA-AGCTCGGGAG
120 AAAAGATCAGATAG-CTGCAATCTGCCTCAGGGCTC--G-G
28964918 AGGCTAAGAGATTGGCTGATGGTGA
1 -GG-TAAGAGATTGGCTGATGGTGA
28964943 CCTGCCCTAG
Statistics
Matches: 281, Mismatches: 45, Indels: 31
0.79 0.13 0.09
Matches are distributed among these distances:
155 92 0.33
156 63 0.22
157 11 0.04
158 4 0.01
159 2 0.01
160 21 0.07
161 8 0.03
162 11 0.04
164 5 0.02
165 41 0.15
166 1 0.00
167 1 0.00
168 2 0.01
169 19 0.07
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (156 bp):
GGTAAGAGATTGGCTGATGGTGATCTACCTCAGCTCGAGGTAAGAGATCGGATGGCTGCAATCTG
CCTCTAGCTCAAGGTAAGAGATTAGCTGATAGTGATCTACCCCAGGCTCGGGGTAAAAGATCAGA
TAGCTGCAATCTGCCTCAGGGCTCGG
Found at i:28965159 original size:39 final size:42
Alignment explanation
Indices: 28965063--28965177 Score: 148
Period size: 43 Copynumber: 2.8 Consensus size: 42
28965053 CTAATTGTAT
*
28965063 TCTGCCCTAAGCTCGGGGTAAAAGATCGGATGGATGGCTGCAA
1 TCTGCCCTAAGCTCGGGGTAAAAGATCAGATGGATGGCTG-AA
* *
28965106 TCTGCCCTAAGCTCGAGGTAAAAGATTAGAT-GATGG-TG-A
1 TCTGCCCTAAGCTCGGGGTAAAAGATCAGATGGATGGCTGAA
*
28965145 TCTGACCC-AAGCTCGGGGTAAAAGATCAAATGG
1 TCTG-CCCTAAGCTCGGGGTAAAAGATCAGATGG
28965178 CTGCAATCTA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
39 25 0.39
40 4 0.06
41 2 0.03
42 5 0.08
43 28 0.44
ACGTcount: A:0.30, C:0.19, G:0.30, T:0.22
Consensus pattern (42 bp):
TCTGCCCTAAGCTCGGGGTAAAAGATCAGATGGATGGCTGAA
Found at i:28971829 original size:29 final size:29
Alignment explanation
Indices: 28971795--28971852 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
28971785 AAATGAAAGG
28971795 ACTTTGCCTTACTGCCTAAAGCTTTGATC
1 ACTTTGCCTTACTGCCTAAAGCTTTGATC
*
28971824 ACTTTGTCTTACTGCCTAAAGCTTTGATC
1 ACTTTGCCTTACTGCCTAAAGCTTTGATC
28971853 TTCCAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.21, C:0.26, G:0.14, T:0.40
Consensus pattern (29 bp):
ACTTTGCCTTACTGCCTAAAGCTTTGATC
Found at i:28974569 original size:29 final size:29
Alignment explanation
Indices: 28974537--28974611 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
28974527 ATTTTTGAGG
*
28974537 AATTTGGGGTCAAAATTGAAATTTTAGAA
1 AATTTGGGGTCAAAATCGAAATTTTAGAA
* * * * *
28974566 AATTTGGGATTAGAATCGAACTTTTGGAA
1 AATTTGGGGTCAAAATCGAAATTTTAGAA
*
28974595 AATTTGAGGTCGAAAAT
1 AATTTGGGGTC-AAAAT
28974612 GTGACTTTTC
Statistics
Matches: 35, Mismatches: 10, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
29 31 0.89
30 4 0.11
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (29 bp):
AATTTGGGGTCAAAATCGAAATTTTAGAA
Found at i:28974765 original size:29 final size:29
Alignment explanation
Indices: 28974675--28974780 Score: 99
Period size: 29 Copynumber: 3.6 Consensus size: 29
28974665 AAAATGGTAA
* * *
28974675 TTTTGGATGAGTTTGGGGTCAAAATATGAT
1 TTTTGGA-AAGTTTAGGGTCAAAATATAAT
*
28974705 TTTTGTG-AAGTTTAGGGGTTAAAATATAA-
1 TTTTG-GAAAGTTTA-GGGTCAAAATATAAT
* *
28974734 TTTTGGAAAGTTTGAGGGTCAAAATGTTAT
1 TTTTGGAAAGTTT-AGGGTCAAAATATAAT
*
28974764 TTTTGCAAAGTTTAGGG
1 TTTTGGAAAGTTTAGGG
28974781 GCCTCCTAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
28 1 0.02
29 31 0.49
30 30 0.48
31 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.27, T:0.41
Consensus pattern (29 bp):
TTTTGGAAAGTTTAGGGTCAAAATATAAT
Found at i:28977381 original size:30 final size:30
Alignment explanation
Indices: 28977341--28977542 Score: 164
Period size: 30 Copynumber: 6.8 Consensus size: 30
28977331 AACCCTCGAG
*
28977341 CTTCCTAAAAATTTAGATTTGACCCCTAAA
1 CTTCCAAAAAATTTAGATTTGACCCCTAAA
** ** * *
28977371 CTTTTAAAAAATACAAATTTGACCCTTAAA
1 CTTCCAAAAAATTTAGATTTGACCCCTAAA
28977401 CTTCCAAAAAATTTAGATTTGACCCC-AAA
1 CTTCCAAAAAATTTAGATTTGACCCCTAAA
** * *
28977430 AATCCCAAAAATTGA-ATTTGACCCCTAAA
1 CTTCCAAAAAATTTAGATTTGACCCCTAAA
*
28977459 CTTTCC-AAAAATTTAGATTTGA-CCCTCGAA
1 C-TTCCAAAAAATTTAGATTTGACCCCT-AAA
* * *
28977489 CTTCCTAAAAATTT-GAATTGGCCCC-AAA
1 CTTCCAAAAAATTTAGATTTGACCCCTAAA
* * **
28977517 ATTCTCAAAAACTTTATTTTTGACCC
1 CTTC-CAAAAAATTTAGATTTGACCC
28977543 TTTTTTTTCT
Statistics
Matches: 133, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
28 15 0.11
29 46 0.35
30 72 0.54
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (30 bp):
CTTCCAAAAAATTTAGATTTGACCCCTAAA
Found at i:28977457 original size:88 final size:88
Alignment explanation
Indices: 28977347--28977527 Score: 229
Period size: 88 Copynumber: 2.1 Consensus size: 88
28977337 CGAGCTTCCT
* * *
28977347 AAAAATTTAGATTTGACCCCTAAACTTTTAAAAAATACAAATTTGACCCTTAAACTTCCAAAAAA
1 AAAAATTGAGATTTGACCCCTAAACTTTCAAAAAATACAAATTTGACCCTCAAACTTCCAAAAAA
*
28977412 TTTAGATTTGACCCCAAAAATCCC
66 TTT-GAATTGACCCCAAAAATCCC
* ** * * *
28977436 AAAAATTGA-ATTTGACCCCTAAACTTTCCAAAAATTTAGATTTGACCCTCGAACTTCCTAAAAA
1 AAAAATTGAGATTTGACCCCTAAACTTTCAAAAAATACAAATTTGACCCTCAAACTTCCAAAAAA
* * *
28977500 TTTGAATTGGCCCCAAAATTCTC
66 TTTGAATTGACCCCAAAAATCCC
28977523 AAAAA
1 AAAAA
28977528 CTTTATTTTT
Statistics
Matches: 79, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
87 21 0.27
88 50 0.63
89 8 0.10
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (88 bp):
AAAAATTGAGATTTGACCCCTAAACTTTCAAAAAATACAAATTTGACCCTCAAACTTCCAAAAAA
TTTGAATTGACCCCAAAAATCCC
Found at i:28979353 original size:21 final size:21
Alignment explanation
Indices: 28979325--28979386 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
28979315 ACTGAAAAAC
*
28979325 TAAA-TAACTGAGCTAGAAGA
1 TAAAGTAACGGAGCTAGAAGA
28979345 TAAAGTAACGGAGCTAGAAGA
1 TAAAGTAACGGAGCTAGAAGA
*
28979366 TAAAGTAACGGAGCTATAAGA
1 TAAAGTAACGGAGCTAGAAGA
28979387 GTCTTTAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
20 4 0.10
21 35 0.90
ACGTcount: A:0.48, C:0.10, G:0.24, T:0.18
Consensus pattern (21 bp):
TAAAGTAACGGAGCTAGAAGA
Found at i:28979647 original size:14 final size:14
Alignment explanation
Indices: 28979628--28979664 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
28979618 GGCAAAGCCA
28979628 TTTATGTAATTCGC
1 TTTATGTAATTCGC
28979642 TTTATGTAATTCGC
1 TTTATGTAATTCGC
28979656 TTTATGTAA
1 TTTATGTAA
28979665 AGAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.14, T:0.51
Consensus pattern (14 bp):
TTTATGTAATTCGC
Found at i:28982844 original size:12 final size:12
Alignment explanation
Indices: 28982829--28982889 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
28982819 AGCAAAAAGG
28982829 AAAAGAAAAGAA
1 AAAAGAAAAGAA
** *
28982841 AAAACTAAA-CA
1 AAAAGAAAAGAA
*
28982852 AAAAG-AGAGAA
1 AAAAGAAAAGAA
*
28982863 AAAAAAAAAGAA
1 AAAAGAAAAGAA
*
28982875 GAAAGAAAAGAA
1 AAAAGAAAAGAA
28982887 AAA
1 AAA
28982890 GGAGAGGTCA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
10 2 0.06
11 10 0.28
12 24 0.67
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAGAA
Found at i:28982872 original size:16 final size:16
Alignment explanation
Indices: 28982796--28982888 Score: 73
Period size: 16 Copynumber: 5.5 Consensus size: 16
28982786 CCCAAAAAAA
*
28982796 AAAAAAAATAAGAAAG
1 AAAAAAAAGAAGAAAG
*
28982812 AAAAAGAAGCAA-AAAGG
1 AAAAAAAAG-AAGAAA-G
* *
28982829 AAAAGAAAAGAAAAAACT
1 AAAA-AAAAGAAGAAA-G
28982847 AAACAAAAAGAGAGAAA-
1 AAA-AAAAAGA-AGAAAG
28982864 AAAAAAAAGAAGAAAG
1 AAAAAAAAGAAGAAAG
28982880 AAAAGAAAA
1 AAAA-AAAA
28982889 AGGAGAGGTC
Statistics
Matches: 63, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
15 5 0.08
16 21 0.33
17 16 0.25
18 16 0.25
19 5 0.08
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.02
Consensus pattern (16 bp):
AAAAAAAAGAAGAAAG
Found at i:28983911 original size:49 final size:49
Alignment explanation
Indices: 28983737--28983976 Score: 145
Period size: 49 Copynumber: 4.9 Consensus size: 49
28983727 GAGGTGGAAA
* * * * * * *
28983737 AGATTGAATCCGCAATGG-TGAATCTTGTACCATAAGAACGTGAAGGAAG
1 AGATTGAAGCCACAATGGACGAATCTTATACC-TTAGAATGTGAAGGGAG
* * * * * *
28983786 AGATTAAAGTCGCAAT-GACGAATCTTATAACTTAGAGATGTGATGGGAA
1 AGATTGAAGCCACAATGGACGAATCTTATACCTTAGA-ATGTGAAGGGAG
* * * * *
28983835 AGTTTGAAGCCATAA-CGACAAACCTTATACCTTAGCAATGTGAAGGGAG
1 AGATTGAAGCCACAATGGACGAATCTTATACCTTAG-AATGTGAAGGGAG
*
28983884 AGATTGAAGCCACAATGGA-GAATCTTATACCCTA-AA-GATGAAGAGG-G
1 AGATTGAAGCCACAATGGACGAATCTTATACCTTAGAATG-TGAAG-GGAG
* * * *
28983931 AAATGTGGAAGCCACAA-CGACGAACCTTATACCCTAGAGATGTGAA
1 AGAT-T-GAAGCCACAATGGACGAATCTTATACCTTAGA-ATGTGAA
28983977 AGAAAAGGTC
Statistics
Matches: 148, Mismatches: 30, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
46 1 0.01
47 11 0.07
48 10 0.07
49 116 0.78
50 4 0.03
51 5 0.03
52 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (49 bp):
AGATTGAAGCCACAATGGACGAATCTTATACCTTAGAATGTGAAGGGAG
Found at i:28983911 original size:98 final size:98
Alignment explanation
Indices: 28983776--28983976 Score: 230
Period size: 98 Copynumber: 2.1 Consensus size: 98
28983766 CCATAAGAAC
* * * * *
28983776 GTGAAGGAAGAGATTAAAGTCGCAATGACGAATCTTATAACTTAGAGATG-TGATGGGAAA-GTT
1 GTGAAGGAAGAGATTAAAGCCACAATGACGAATCTTATAACCTAAAGATGAAGA-GGGAAATG-T
* * *
28983839 TGAAGCCATAACGACAAACCTTATACCTTAGCA-AT
64 GGAAGCCACAACGACAAACCTTATACCCTAG-AGAT
* * *
28983874 GTGAAGGGAGAGATTGAAGCCACAATGGA-GAATCTTATACCCTAAAGATGAAGAGGGAAATGTG
1 GTGAAGGAAGAGATTAAAGCCACAAT-GACGAATCTTATAACCTAAAGATGAAGAGGGAAATGTG
*
28983938 GAAGCCACAACGACGAACCTTATACCCTAGAGAT
65 GAAGCCACAACGACAAACCTTATACCCTAGAGAT
28983972 GTGAA
1 GTGAA
28983977 AGAAAAGGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
97 1 0.01
98 81 0.93
99 5 0.06
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (98 bp):
GTGAAGGAAGAGATTAAAGCCACAATGACGAATCTTATAACCTAAAGATGAAGAGGGAAATGTGG
AAGCCACAACGACAAACCTTATACCCTAGAGAT
Found at i:28984426 original size:48 final size:48
Alignment explanation
Indices: 28984365--28984522 Score: 158
Period size: 48 Copynumber: 3.5 Consensus size: 48
28984355 AAACCCCATA
*
28984365 TTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATC
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATC
* * **
28984413 TTCCTGATGAGATACAAAGAAGT-GG----A-C---CAAAT--TCGCC
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATC
* **
28984450 TTCCTAATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATC
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATC
*
28984498 TTCCTGATGAGAAACAGAGAAGTGG
1 TTCCTGATGAGATACAGAGAAGTGG
28984523 ACCAAATCCG
Statistics
Matches: 85, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
37 24 0.28
38 2 0.02
39 4 0.05
42 2 0.02
43 2 0.02
46 2 0.02
47 2 0.02
48 47 0.55
ACGTcount: A:0.37, C:0.16, G:0.25, T:0.22
Consensus pattern (48 bp):
TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATC
Found at i:28984453 original size:37 final size:37
Alignment explanation
Indices: 28984412--28984560 Score: 127
Period size: 37 Copynumber: 3.7 Consensus size: 37
28984402 AAATGGTCAT
* *
28984412 CTTCCTGATGAGATACAAAGAAGTGGACCAAATTCGC
1 CTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGC
* * * *
28984449 CTTCCTAATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTC
1 CTTCCTGATGAGATACAGAGAAGT-GG----A-C--CAAATCCG-C
*
28984495 ATCTTCCTGATGAGAAACAGAGAAGTGGACCAAATCCGC
1 --CTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGC
*
28984534 CTTCCTGATGAGACACAGAGAAGTGGA
1 CTTCCTGATGAGATACAGAGAAGTGGA
28984561 TTAAATCAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
37 48 0.54
38 2 0.02
39 1 0.01
40 5 0.06
42 2 0.02
43 2 0.02
45 4 0.04
46 1 0.01
47 2 0.02
48 22 0.25
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.19
Consensus pattern (37 bp):
CTTCCTGATGAGATACAGAGAAGTGGACCAAATCCGC
Found at i:28984508 original size:85 final size:85
Alignment explanation
Indices: 28984365--28984615 Score: 367
Period size: 85 Copynumber: 3.0 Consensus size: 85
28984355 AAACCCCATA
* ** *
28984365 TTCCTGATAAGATACAGAGAAGTGGGTCAAAGCAATAAAATGGTCATCTTCCTGATGAGATACAA
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAG
*
28984430 AGAAGTGGACCAAATTCGCC
66 AGAAGTGGACCAAATCCGCC
* *
28984450 TTCCTAATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGAAACAG
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAG
28984515 AGAAGTGGACCAAATCCGCC
66 AGAAGTGGACCAAATCCGCC
* * * * * *
28984535 TTCCTGATGAGACACAGAGAAGTGGATTAAATCAATGAAGCGGTCATCTTCCTAATGAGATACAG
1 TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAG
* *
28984600 AGAAGTAGATCAAATC
66 AGAAGTGGACCAAATC
28984616 AATGAAGCGA
Statistics
Matches: 149, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
85 149 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (85 bp):
TTCCTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGATACAG
AGAAGTGGACCAAATCCGCC
Found at i:28984826 original size:48 final size:48
Alignment explanation
Indices: 28984744--28984835 Score: 132
Period size: 48 Copynumber: 1.9 Consensus size: 48
28984734 ACCAAATCTG
* **
28984744 TCTTCTTGATGAGATACAAAGAAGTGAATTAAATCAATGAAGCGGTCA
1 TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCAATGAAGCGGTCA
*
28984792 TCTTCCTGATGAGATACAAAGAAGT-AGACCAAATCGATGAAGCG
1 TCTTCCTGATGAGATACAAAGAAGTGA-ACCAAATCAATGAAGCG
28984836 AAGCTCAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
47 1 0.03
48 38 0.97
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (48 bp):
TCTTCCTGATGAGATACAAAGAAGTGAACCAAATCAATGAAGCGGTCA
Found at i:28984941 original size:211 final size:210
Alignment explanation
Indices: 28984449--28984949 Score: 731
Period size: 211 Copynumber: 2.4 Consensus size: 210
28984439 CCAAATTCGC
* * * *
28984449 CTTCCTAATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTGATGAGAAAC-
1 CTTCCTGATGAGATATAGAGAAGTGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGATACA
* *
28984513 AGAGAAGTGGACCAAATCCGCCTTCCTGATGAGACACAGAGAAGTGGATTAAATCAATGAAGCGG
66 AGAGAAGTGGACCAAATCCGCCTTCCTGATGAGACACAAAGAAGTGAATTAAATCAATGAAGCGG
* *
28984578 TCATCTTCCTAATGAGATACAGAGAAGTAGATCAAATCAATGAAGCGAAGCTCAATACGAATGAG
131 TCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAG
28984643 ACTTCAAACCTCCAT
196 ACTTCAAACCTCCAT
* * * *
28984658 CTTCTTGAAT-AGATATAGAGAAGTGGGTGTGAAAGCAATAAAACAGTCATCTTCCTGATGAGAT
1 CTTCCTG-ATGAGATATAGAGAAGTGGGT-CG-AAGCAATAAAGCGGTCATCTTCCTGATGAGAT
* * * *
28984722 AC-AGAGAAGTGGACCAAATCTGTCTTCTTGATGAGATACAAAGAAGTGAATTAAATCAATGAAG
63 ACAAGAGAAGTGGACCAAATCCGCCTTCCTGATGAGACACAAAGAAGTGAATTAAATCAATGAAG
* *
28984786 CGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCGATGAAGCGAAGCTCAATACGAAT
128 CGGTCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAAT
28984851 GAGACTTCAAACC-CCTAT
193 GAGACTTCAAACCTCC-AT
* * *
28984869 CTTCCTGATGAGATATAGAGAAATGGGTCGAAGTAATAAAGCGGTCATCTTCCTAATGAGATACA
1 CTTCCTGATGAGATATAGAGAAGTGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGATACA
*
28984934 GAGAGAAGTAGACCAA
66 -AGAGAAGTGGACCAA
28984950 GAAATGAAGC
Statistics
Matches: 259, Mismatches: 26, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
209 52 0.20
210 7 0.03
211 200 0.77
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (210 bp):
CTTCCTGATGAGATATAGAGAAGTGGGTCGAAGCAATAAAGCGGTCATCTTCCTGATGAGATACA
AGAGAAGTGGACCAAATCCGCCTTCCTGATGAGACACAAAGAAGTGAATTAAATCAATGAAGCGG
TCATCTTCCTAATGAGATACAAAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATACGAATGAG
ACTTCAAACCTCCAT
Found at i:28986618 original size:61 final size:60
Alignment explanation
Indices: 28986553--28986815 Score: 224
Period size: 61 Copynumber: 4.3 Consensus size: 60
28986543 CAAGCTTCCA
* * ** *
28986553 AAAAATTTAGATTTGACCCTCAAACTTTTTTAAAAATGCAAATTTGACCCTCAAACTTCTC
1 AAAAATTTAGATTTGACCCTCAAAC-TTCTAAAAAATTTAGATTTGACCCTCAAACTTCTC
* * ** *
28986614 AAAAATTTAGATTTGGCCCCTAAAACTTCCCAAAAATTTAGATTTGACCCCCAAACTT-TCC
1 AAAAATTTAGATTT-GACCCTCAAACTTCTAAAAAATTTAGATTTGACCCTCAAACTTCT-C
** * * * * * *
28986675 AAAAATGCAAATCTAACCCTCGAACTTCTAAAAAATTTAGATTTGACCTCTAAAACTTCCC
1 AAAAATTTAGATTTGACCCTCAAACTTCTAAAAAATTTAGATTTGACC-CTCAAACTTCTC
* ** * * *
28986736 AAAAATTTAGATTTGACCCCCAAACTTCCCAAAAATTTAAATTTGGCCC-CAAAATTCTC
1 AAAAATTTAGATTTGACCCTCAAACTTCTAAAAAATTTAGATTTGACCCTCAAACTTCTC
* **
28986795 ACAAACTTTATTTTTGACCCT
1 A-AAAATTTAGATTTGACCCT
28986816 TTTTTTTTCT
Statistics
Matches: 157, Mismatches: 40, Indels: 11
0.75 0.19 0.05
Matches are distributed among these distances:
59 8 0.05
60 45 0.29
61 95 0.61
62 9 0.06
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.31
Consensus pattern (60 bp):
AAAAATTTAGATTTGACCCTCAAACTTCTAAAAAATTTAGATTTGACCCTCAAACTTCTC
Found at i:28986640 original size:31 final size:31
Alignment explanation
Indices: 28986553--28986785 Score: 217
Period size: 31 Copynumber: 7.6 Consensus size: 31
28986543 CAAGCTTCCA
* *
28986553 AAAAATTTAGATTTGA-CCCTCAAACTTTTTT
1 AAAAATTTAGATTTGACCCCTCAAAC-TTCTC
** *
28986584 AAAAATGCAAATTTGA-CCCTCAAACTTCTC
1 AAAAATTTAGATTTGACCCCTCAAACTTCTC
* * *
28986614 AAAAATTTAGATTTGGCCCCTAAAACTTCCC
1 AAAAATTTAGATTTGACCCCTCAAACTTCTC
28986645 AAAAATTTAGATTTGACCCC-CAAACTT-TCC
1 AAAAATTTAGATTTGACCCCTCAAACTTCT-C
** * * * * *
28986675 AAAAATGCAAATCT-AACCCTCGAACTTCTA
1 AAAAATTTAGATTTGACCCCTCAAACTTCTC
* * *
28986705 AAAAATTTAGATTTGACCTCTAAAACTTCCC
1 AAAAATTTAGATTTGACCCCTCAAACTTCTC
*
28986736 AAAAATTTAGATTTGACCCC-CAAACTTCCC
1 AAAAATTTAGATTTGACCCCTCAAACTTCTC
* *
28986766 AAAAATTTAAATTTGGCCCC
1 AAAAATTTAGATTTGACCCC
28986786 AAAATTCTCA
Statistics
Matches: 162, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
29 4 0.02
30 75 0.46
31 83 0.51
ACGTcount: A:0.38, C:0.24, G:0.07, T:0.30
Consensus pattern (31 bp):
AAAAATTTAGATTTGACCCCTCAAACTTCTC
Found at i:28986811 original size:91 final size:91
Alignment explanation
Indices: 28986547--28986814 Score: 349
Period size: 91 Copynumber: 2.9 Consensus size: 91
28986537 AACCCCCAAG
* * **
28986547 CTTCCAAAAAATTTAGATTTGACCCTCAAACTTTTTTAAAAATGCAAATTTGACCCTCAAACTTC
1 CTTCCCAAAAATTTAGATTTGACCCCCAAAC-TTTCCAAAAATGCAAATTTGACCCTCAAACTTC
*
28986612 TCAAAAATTTAGATTTGGCCCCTAAAA
65 TCAAAAATTTAGATTTGACCCCTAAAA
* * *
28986639 CTTCCCAAAAATTTAGATTTGACCCCCAAACTTTCCAAAAATGCAAATCTAACCCTCGAACTTCT
1 CTTCCCAAAAATTTAGATTTGACCCCCAAACTTTCCAAAAATGCAAATTTGACCCTCAAACTTCT
* *
28986704 AAAAAATTTAGATTTGACCTCTAAAA
66 CAAAAATTTAGATTTGACCCCTAAAA
* ** * *
28986730 CTTCCCAAAAATTTAGATTTGACCCCCAAACTTCCCAAAAATTTAAATTTGGCCC-CAAAATTCT
1 CTTCCCAAAAATTTAGATTTGACCCCCAAACTTTCCAAAAATGCAAATTTGACCCTCAAACTTCT
* **
28986794 CACAAACTTTATTTTTGACCC
66 CA-AAAATTTAGATTTGACCC
28986815 TTTTTTTTTC
Statistics
Matches: 152, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
90 8 0.05
91 115 0.76
92 29 0.19
ACGTcount: A:0.37, C:0.25, G:0.07, T:0.31
Consensus pattern (91 bp):
CTTCCCAAAAATTTAGATTTGACCCCCAAACTTTCCAAAAATGCAAATTTGACCCTCAAACTTCT
CAAAAATTTAGATTTGACCCCTAAAA
Found at i:28988147 original size:18 final size:18
Alignment explanation
Indices: 28988106--28988182 Score: 95
Period size: 18 Copynumber: 4.4 Consensus size: 18
28988096 CCAAATCCAT
*
28988106 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAAAA
*
28988124 -TTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAAA
*
28988141 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTTAAAA
* *
28988159 TTTAAAATTATTAT-AAA
1 TTTAAATTTATTTTAAAA
28988176 TTTAAAT
1 TTTAAAT
28988183 GAATAAATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
17 24 0.47
18 27 0.53
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTAAATTTATTTTAAAA
Found at i:28988177 original size:35 final size:35
Alignment explanation
Indices: 28988106--28988182 Score: 95
Period size: 35 Copynumber: 2.2 Consensus size: 35
28988096 CCAAATCCAT
* * *
28988106 TTTAAATTTATTTTAAGATTAAATTTGTTTTAAAA
1 TTTAAATTTATTTTAAGATTAAAATTATTATAAAA
28988141 TTTAAATTTATTTTCAA-ATTTAAAATTATTAT-AAA
1 TTTAAATTTATTTT-AAGA-TTAAAATTATTATAAAA
28988176 TTTAAAT
1 TTTAAAT
28988183 GAATAAATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 25 0.68
36 12 0.32
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTAAATTTATTTTAAGATTAAAATTATTATAAAA
Done.