Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 22 of 208
Found at i:6392659 original size:33 final size:33
Alignment explanation
Indices: 6392609--6392733 Score: 97
Period size: 33 Copynumber: 3.5 Consensus size: 33
6392599 TCCCCCAAGG
* *
6392609 GGTTACTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
* * * *
6392642 GGTTGCTAAGTGTTGATTCCACTGTATTTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CTG-A--AT-CAT-T---GGT
* *
6392684 GGTTGCTAAGTGTTGATTCCCTGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
6392717 GGTTGCTAAGTGCTGAT
1 GGTTGCTAAGTGCTGAT
6392734 CCCACCGTAT
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
33 36 0.49
34 2 0.03
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 1 0.01
40 1 0.01
41 3 0.04
42 22 0.30
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.37
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCTGAATCATTGGT
Found at i:6392749 original size:75 final size:73
Alignment explanation
Indices: 6392605--6392815 Score: 287
Period size: 75 Copynumber: 2.8 Consensus size: 73
6392595 TGATTCCCCC
* * * *
6392605 AAGGGGTTACTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGTTGATTCCACTGTATT
1 AAGGGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGA-TCCACCGTATC
6392670 TTAAATGTGA
64 TTAAATGTGA
* * *
6392680 AGGGGGTTGCTAAGTGTTGATTCCCTGACTCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCC-GAATCATTGGTGGTTGCTAAGTGCTGAT-CCACCGTATC
6392745 TTAAATGTGA
64 TTAAATGTGA
* *
6392755 AAAGGGTTGCTAAGTGCTGATTCTCCGAATCACTGGTGGTTGCTAAGTGCTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTC-CCGAATCATTGGTGGTTGCTAAGTGCTG-ATCCACCG
6392816 ATAACAGACA
Statistics
Matches: 120, Mismatches: 12, Indels: 8
0.86 0.09 0.06
Matches are distributed among these distances:
74 4 0.03
75 112 0.93
76 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.33
Consensus pattern (73 bp):
AAGGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCACCGTATCTT
AAATGTGA
Found at i:6394891 original size:19 final size:19
Alignment explanation
Indices: 6394867--6394904 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6394857 GAAGTTAATT
6394867 ACAAATTTAATTAGGGTGG
1 ACAAATTTAATTAGGGTGG
* *
6394886 ACAAATTTGATTATGGTGG
1 ACAAATTTAATTAGGGTGG
6394905 GTGACAGTGA
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:0.34, C:0.05, G:0.26, T:0.34
Consensus pattern (19 bp):
ACAAATTTAATTAGGGTGG
Found at i:6397037 original size:10 final size:10
Alignment explanation
Indices: 6397014--6397054 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
6397004 AAGTTACAAT
6397014 TTTTTTATAA
1 TTTTTTATAA
6397024 -TTTTTATAA
1 TTTTTTATAA
*
6397033 TTTTTTACAA
1 TTTTTTATAA
*
6397043 TTTTTTGTAA
1 TTTTTTATAA
6397053 TT
1 TT
6397055 ATTAATTTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 9 0.33
10 18 0.67
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:6398370 original size:2 final size:2
Alignment explanation
Indices: 6398363--6398397 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
6398353 CTATTATTAC
*
6398363 AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6398398 AAAAGAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6402338 original size:25 final size:25
Alignment explanation
Indices: 6402310--6402392 Score: 130
Period size: 25 Copynumber: 3.3 Consensus size: 25
6402300 ACTTTAGCGC
6402310 GCTCTCTGATTATTAGCACGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
*
6402335 GCTCTCTGATTATTAGCATGTTGGT
1 GCTCTCTGATTATTAGCACGTTGGT
* **
6402360 GCTCTCTGATTACTAGCACGTCAGT
1 GCTCTCTGATTATTAGCACGTTGGT
6402385 GCTCTCTG
1 GCTCTCTG
6402393 TTTAGCACAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAGCACGTTGGT
Found at i:6402408 original size:22 final size:22
Alignment explanation
Indices: 6402381--6402438 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
6402371 ACTAGCACGT
*
6402381 CAGTGCTCTCTGTTTAGCACAC
1 CAGTGCTCTCTGTTTAACACAC
* * * **
6402403 CTGTGCTCTATGTATAACACTT
1 CAGTGCTCTCTGTTTAACACAC
6402425 CAGTGCTCTCTGTT
1 CAGTGCTCTCTGTT
6402439 CATTAGTGCA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (22 bp):
CAGTGCTCTCTGTTTAACACAC
Found at i:6403392 original size:28 final size:27
Alignment explanation
Indices: 6403361--6403414 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
6403351 ATTTGAGAAA
6403361 TTAAGAGC-TAAATTGTGAAAATAAATTT
1 TTAAGAGCTTAAA-TGTG-AAATAAATTT
*
6403389 TTAAGGGCTTTAAATGTGAAATAAAT
1 TTAAGAGC-TTAAATGTGAAATAAAT
6403415 GAAATGTGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 15 0.65
29 4 0.17
30 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (27 bp):
TTAAGAGCTTAAATGTGAAATAAATTT
Found at i:6406843 original size:41 final size:41
Alignment explanation
Indices: 6406786--6406903 Score: 200
Period size: 41 Copynumber: 2.9 Consensus size: 41
6406776 AGTAAGATGA
* * *
6406786 TTCAGACTTTACGTCTAGCAGGCTTGATGCCGGTGTAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
6406827 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
*
6406868 TTCAGACTTTACGTCTAGCAGGCTAAATGCCGGTGA
1 TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGA
6406904 TCTGAATCAA
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTAATGCCGGTGAAATAT
Found at i:6407144 original size:41 final size:41
Alignment explanation
Indices: 6407082--6407257 Score: 226
Period size: 41 Copynumber: 4.3 Consensus size: 41
6407072 GTTTGGAATT
* * * * *
6407082 GGTGATTTAAATCAGGTTATAAACTTAGCAGGCTAAGTGTC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
**
6407123 GGTGATCTGAATCAGGCTATAAGTCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
6407164 GGTGATCTGAAACAGGCTATAAGCCTAGTAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
* * *
6407205 GGTGATATGAATCAAGTTATAAACCTAGCAGGCTAAGTGCC
1 GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
*
6407246 GGGGATCTGAAT
1 GGTGATCTGAAT
6407258 ATGTTTAATT
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 117 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (41 bp):
GGTGATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCC
Found at i:6410375 original size:173 final size:173
Alignment explanation
Indices: 6410086--6410432 Score: 694
Period size: 173 Copynumber: 2.0 Consensus size: 173
6410076 TGAAAAAGGT
6410086 TAGATTAAAAACCCTGATAGCAAAATTAGAAAGGTCACTGCATCAATATCGTAGTTGCAACTCCG
1 TAGATTAAAAACCCTGATAGCAAAATTAGAAAGGTCACTGCATCAATATCGTAGTTGCAACTCCG
6410151 CAATTGAGTTGAAAACAGGCCTAAATAAGATTAAAGAGTTGAAGAGAAAGATAGAAGAGTTTGAG
66 CAATTGAGTTGAAAACAGGCCTAAATAAGATTAAAGAGTTGAAGAGAAAGATAGAAGAGTTTGAG
6410216 ACCGCATTGCAAAATTGTGAACTTTGAGTTGAACTTCTAGAAA
131 ACCGCATTGCAAAATTGTGAACTTTGAGTTGAACTTCTAGAAA
6410259 TAGATTAAAAACCCTGATAGCAAAATTAGAAAGGTCACTGCATCAATATCGTAGTTGCAACTCCG
1 TAGATTAAAAACCCTGATAGCAAAATTAGAAAGGTCACTGCATCAATATCGTAGTTGCAACTCCG
6410324 CAATTGAGTTGAAAACAGGCCTAAATAAGATTAAAGAGTTGAAGAGAAAGATAGAAGAGTTTGAG
66 CAATTGAGTTGAAAACAGGCCTAAATAAGATTAAAGAGTTGAAGAGAAAGATAGAAGAGTTTGAG
6410389 ACCGCATTGCAAAATTGTGAACTTTGAGTTGAACTTCTAGAAA
131 ACCGCATTGCAAAATTGTGAACTTTGAGTTGAACTTCTAGAAA
6410432 T
1 T
6410433 GAACAATGAA
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (173 bp):
TAGATTAAAAACCCTGATAGCAAAATTAGAAAGGTCACTGCATCAATATCGTAGTTGCAACTCCG
CAATTGAGTTGAAAACAGGCCTAAATAAGATTAAAGAGTTGAAGAGAAAGATAGAAGAGTTTGAG
ACCGCATTGCAAAATTGTGAACTTTGAGTTGAACTTCTAGAAA
Found at i:6417422 original size:44 final size:44
Alignment explanation
Indices: 6417359--6417913 Score: 591
Period size: 44 Copynumber: 12.6 Consensus size: 44
6417349 TCGTGGCGAG
* *
6417359 TCTTATCTC-CTTGAAGTTGCAGTGGAGCAGATTAAAGTTATAAA
1 TCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * *
6417403 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAACCTACAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* *
6417447 TCTTATCT-TCCTGAAGTTGTAGTGGAGCAGATTAAAGCCACAAA
1 TCTTATCTCT-CTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * *
6417491 TCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTCAAGATAGCAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAA
* *
6417536 TCTTATCTCTCAGAAGTTGCAGTAGAGCAGATTAAAGCTACAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * * *
6417580 T-TTGTTGTCCCTG-AGTTGCAGTGAAGCAGATTGAAGATAGCAAA
1 TCTT-ATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAA
* * * *
6417624 TCTTATCACTCTGAAGTTGTAGTAGAGCAGATTAAAGCTATAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * *
6417668 TTTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGCAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAA
* * *
6417713 TCTTATCACTCTGAAGTTGTAGTAGAGCAGATTAAAGCTACAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
*
6417757 TCTTATCTCTCTAAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * * *
6417801 TCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGATACAAA
1 TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
* * * *
6417845 TCTTATTTC-CTTGAAGTTGCAGTGGAGTAGATTGAAA-TTACAAT
1 TCTTATCTCTC-TGAAGTTGCAGTGGAGCAGATT-AAAGCTACAAA
* * * *
6417889 TCCTATATCCCTGAAGTTGTAGTGG
1 TCTTATCTCTCTGAAGTTGCAGTGG
6417914 GTTAGACTGA
Statistics
Matches: 430, Mismatches: 69, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
43 26 0.06
44 302 0.70
45 102 0.24
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (44 bp):
TCTTATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAA
Found at i:6417879 original size:177 final size:176
Alignment explanation
Indices: 6417370--6417880 Score: 673
Period size: 177 Copynumber: 2.9 Consensus size: 176
6417360 CTTATCTCCT
* * * * *
6417370 TGAAGTTGCAGTGGAGCAGATTAAAGTTATAAATCTTATCTCTCTGAAGTTGCAGTAGAGTAGAT
1 TGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT-AAGTTGCAGTGGAGCAGAT
* * *
6417435 TAAACCTACAAATCTTATCTTCCTGAAGTTGTAGTGGAGCAGATTAAAGCCACAAATCTTATCTC
65 TAAAGCTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAATCTTATCTC
* * *
6417500 CCTAAAGTTGCAGTGGAGCAGATTCAAGATAGCAAATCTTATCTCTC
130 CCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCACTC
* * * * * *
6417547 AGAAGTTGCAGTAGAGCAGATTAAAGCTACAAAT-TTGTTGTCCCTGAGTTGCAGTGAAGCAGAT
1 TGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTT-ATCTCTCTAAGTTGCAGTGGAGCAGAT
* * * * * * *
6417611 TGAAGATAGCAAATCTTATCACTCTGAAGTTGTAGTAGAGCAGATTAAAGCTATAAATTTTATCT
65 TAAAGCTA-CAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAATCTTATCT
*
6417676 CCCTGAAGTTGTAGTGGAGCAGATTGAAGATAGCAAATCTTATCACTC
129 CCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCACTC
*
6417724 TGAAGTTGTAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCTAAAGTTGCAGTGGAGCAGAT
1 TGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCT-AAGTTGCAGTGGAGCAGAT
* * * * * *
6417789 TAAAGCTACAAATCTTATCTCCCTAAAGTTGCAGTGGAGTAGATTGAAGATACAAATCTTATTTC
65 TAAAGCTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAATCTTATCTC
* *
6417854 CTTGAAGTTGCAGTGGAGTAGATTGAA
130 CCTGAAGTTGCAGTGGAGCAGATTGAA
6417881 ATTACAATTC
Statistics
Matches: 282, Mismatches: 48, Indels: 8
0.83 0.14 0.02
Matches are distributed among these distances:
176 22 0.08
177 235 0.83
178 25 0.09
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.30
Consensus pattern (176 bp):
TGAAGTTGCAGTAGAGCAGATTAAAGCTACAAATCTTATCTCTCTAAGTTGCAGTGGAGCAGATT
AAAGCTACAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCTACAAATCTTATCTCC
CTGAAGTTGCAGTGGAGCAGATTGAAGATAGCAAATCTTATCACTC
Found at i:6420531 original size:28 final size:26
Alignment explanation
Indices: 6420500--6420552 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
6420490 TTTAAAAATT
*
6420500 AAAATTTAACCCTATACTTTTATTTTTA
1 AAAATTTAACCC-AT-CTGTTATTTTTA
*
6420528 AAAATTTAATCCATCTGTTATTTTT
1 AAAATTTAACCCATCTGTTATTTTT
6420553 CTTATGTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
27 2 0.09
28 11 0.48
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (26 bp):
AAAATTTAACCCATCTGTTATTTTTA
Found at i:6424609 original size:6 final size:6
Alignment explanation
Indices: 6424598--6424623 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6424588 TATGTCATGC
6424598 TTTCAT TTTCAT TTTCAT TTTCAT TT
1 TTTCAT TTTCAT TTTCAT TTTCAT TT
6424624 GACTCTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTCAT
Found at i:6426393 original size:17 final size:16
Alignment explanation
Indices: 6426356--6426392 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
6426346 AAAACCAAGA
6426356 TTTTTACAACATGCAT
1 TTTTTACAACATGCAT
* *
6426372 TTTTTACAATATTCAT
1 TTTTTACAACATGCAT
6426388 TTTTT
1 TTTTT
6426393 TTTCATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTTTACAACATGCAT
Found at i:6430180 original size:46 final size:46
Alignment explanation
Indices: 6430118--6430210 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
6430108 TTAAAAACAC
*
6430118 AAAAATTACAAGAAAAGAGCAAGAATTGAACTCACATGATGCAAAA
1 AAAAAATACAAGAAAAGAGCAAGAATTGAACTCACATGATGCAAAA
6430164 AAAAAATACAAGAAAAGAGCAAGAATTGAACTCACATGATGCAAAA
1 AAAAAATACAAGAAAAGAGCAAGAATTGAACTCACATGATGCAAAA
6430210 A
1 A
6430211 TATGAAAAAC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.58, C:0.13, G:0.15, T:0.14
Consensus pattern (46 bp):
AAAAAATACAAGAAAAGAGCAAGAATTGAACTCACATGATGCAAAA
Found at i:6445007 original size:18 final size:18
Alignment explanation
Indices: 6444974--6445023 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
6444964 TATTATGCTC
*
6444974 ATTTTGAAAATAATATCAT
1 ATTTT-AAATTAATATCAT
*
6444993 ATTTTAAATTAATATTAT
1 ATTTTAAATTAATATCAT
*
6445011 ATTATTTAATTAA
1 ATT-TTAAATTAA
6445024 ATCCCTTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 14 0.52
19 13 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTTAAATTAATATCAT
Found at i:6445655 original size:61 final size:60
Alignment explanation
Indices: 6445531--6445663 Score: 167
Period size: 61 Copynumber: 2.2 Consensus size: 60
6445521 TTTTCTAAAC
* * ** * *
6445531 TTTTAGAATTAAAACTAAATTGACAAACTTTGTAAATGTTGAGGGCTAAATTTATTGATTT
1 TTTTAGAATTAGAACTAAAATGACAAACTTTGTAAACATTGAGGGCTAAATTTATAGA-AT
** *
6445592 TTTTAGAATTAGAACTAAAATGACAATTTTTGTAAACATTGAGGGCTAAATTTGTAGAAT
1 TTTTAGAATTAGAACTAAAATGACAAACTTTGTAAACATTGAGGGCTAAATTTATAGAAT
*
6445652 TTTTAGATTTAG
1 TTTTAGAATTAG
6445664 GATCAAATTG
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
60 12 0.19
61 50 0.81
ACGTcount: A:0.38, C:0.06, G:0.16, T:0.41
Consensus pattern (60 bp):
TTTTAGAATTAGAACTAAAATGACAAACTTTGTAAACATTGAGGGCTAAATTTATAGAAT
Found at i:6446894 original size:14 final size:14
Alignment explanation
Indices: 6446877--6446905 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
6446867 AAAAATATTT
6446877 TAAAAATAAAAATA
1 TAAAAATAAAAATA
6446891 TAAAAATAAAAATA
1 TAAAAATAAAAATA
6446905 T
1 T
6446906 TTTTAAAGTA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAAATAAAAATA
Found at i:6446945 original size:43 final size:42
Alignment explanation
Indices: 6446872--6446953 Score: 121
Period size: 42 Copynumber: 1.9 Consensus size: 42
6446862 CACAAAAAAA
*
6446872 TATTTTAAAAATAAAAATATAAAAATAAAAATATTTTTAAAG
1 TATTTTAAAAATAAAAATATAAAAATAAAAATATATTTAAAG
*
6446914 TATTTTAAAATTAAAAA-ATAAAAATAAAAAAATATATTTA
1 TATTTTAAAAATAAAAATATAAAAAT--AAAAATATATTTA
6446954 TTATATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 8 0.22
42 16 0.44
43 12 0.33
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (42 bp):
TATTTTAAAAATAAAAATATAAAAATAAAAATATATTTAAAG
Found at i:6446963 original size:41 final size:41
Alignment explanation
Indices: 6446876--6446965 Score: 103
Period size: 41 Copynumber: 2.2 Consensus size: 41
6446866 AAAAAATATT
* *
6446876 TTAAAAATAAAAATATAAAAATAAAAATATTTTTAAAGTATT
1 TTAAAAATAAAAATATAAAAATAAAAATATATTT-AAGTATA
* *
6446918 TTAAAATTAAAAA-ATAAAAATAAAAAAATATATTT-ATTATA
1 TTAAAAATAAAAATATAAAAAT--AAAAATATATTTAAGTATA
6446959 TTAAAAA
1 TTAAAAA
6446966 GTTGAGCCCG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
41 18 0.44
42 12 0.29
43 11 0.27
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (41 bp):
TTAAAAATAAAAATATAAAAATAAAAATATATTTAAGTATA
Found at i:6447706 original size:19 final size:20
Alignment explanation
Indices: 6447681--6447729 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
6447671 TTCATTCTTC
*
6447681 ATCTATTTTTTTTATATTTT
1 ATCTATTTTTTATATATTTT
*
6447701 -TCTATTATTTATATATTTT
1 ATCTATTTTTTATATATTTT
*
6447720 ATATATTTTT
1 ATCTATTTTT
6447730 AATTTCAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
ATCTATTTTTTATATATTTT
Found at i:6468760 original size:28 final size:27
Alignment explanation
Indices: 6468718--6468771 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
6468708 AAAATTTTCC
6468718 AAAAAAATTCATTTC-CCCTTTGTTTTA
1 AAAAAAATTCATTTCTCCCTTT-TTTTA
*
6468745 AAAAAAATCTCTTTTCTCCCTTTTTTT
1 AAAAAAAT-TCATTTCTCCCTTTTTTT
6468772 CCTCTAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 8 0.33
28 10 0.42
29 6 0.25
ACGTcount: A:0.30, C:0.20, G:0.02, T:0.48
Consensus pattern (27 bp):
AAAAAAATTCATTTCTCCCTTTTTTTA
Found at i:6479054 original size:77 final size:77
Alignment explanation
Indices: 6478923--6479069 Score: 179
Period size: 77 Copynumber: 1.9 Consensus size: 77
6478913 TCGTACCGAT
* * ** * * *
6478923 TCATGGGTTAATCAATTTTTTACCTCTCACTGAACCGATACCCTAGCTGTTTCTT-ATTCCAACC
1 TCATGGGTCAATCAATTTTCTACCTCTCACCAAACCAATACCCCAGCTGGTTCTTGA-TCCAACC
6478987 AGTCTATATCGGA
65 AGTCTATATCGGA
* * * *
6479000 TCATGGGTCAATCAGTTTTCTCCCTCTCACCAAACTAATACCCCAGCTGGTTCTTGATCCAATCA
1 TCATGGGTCAATCAATTTTCTACCTCTCACCAAACCAATACCCCAGCTGGTTCTTGATCCAACCA
6479065 GTCTA
66 GTCTA
6479070 GTTCAAATTA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
77 57 0.98
78 1 0.02
ACGTcount: A:0.24, C:0.29, G:0.13, T:0.34
Consensus pattern (77 bp):
TCATGGGTCAATCAATTTTCTACCTCTCACCAAACCAATACCCCAGCTGGTTCTTGATCCAACCA
GTCTATATCGGA
Found at i:6479102 original size:8 final size:8
Alignment explanation
Indices: 6479089--6479113 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6479079 AGATAACATT
6479089 GAATTTTG
1 GAATTTTG
6479097 GAATTTTG
1 GAATTTTG
6479105 GAATTTTG
1 GAATTTTG
6479113 G
1 G
6479114 TTTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (8 bp):
GAATTTTG
Found at i:6479177 original size:11 final size:12
Alignment explanation
Indices: 6479148--6479181 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
6479138 TTTTAAAGAG
6479148 TTTTTTTCTATAA
1 TTTTTTT-TATAA
6479161 TTTTTTTT-TAA
1 TTTTTTTTATAA
6479172 TTTTTTTTAT
1 TTTTTTTTAT
6479182 TTTTTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 2 0.10
13 7 0.35
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTTATAA
Found at i:6480071 original size:30 final size:29
Alignment explanation
Indices: 6480026--6480086 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
6480016 ATTATTTTAT
* * *
6480026 TTCTTAAAATTTATTTTTAAATTCTTGGA
1 TTCTCAAAATTTATTTTAAAATTCTTAGA
6480055 TTCTCAAAATTTTATTTTAAAATTCTTAGA
1 TTCTCAAAA-TTTATTTTAAAATTCTTAGA
6480085 TT
1 TT
6480087 GTCACGAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (29 bp):
TTCTCAAAATTTATTTTAAAATTCTTAGA
Found at i:6480072 original size:29 final size:30
Alignment explanation
Indices: 6480026--6480086 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
6480016 ATTATTTTAT
* *
6480026 TTCTTAAAATTTATTTTT-AAATTCTTGGA
1 TTCTCAAAATTTATTTTTAAAATTCTTAGA
6480055 TTCTCAAAATTT-TATTTTAAAATTCTTAGA
1 TTCTCAAAATTTAT-TTTTAAAATTCTTAGA
6480085 TT
1 TT
6480087 GTCACGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.04
29 15 0.54
30 12 0.43
ACGTcount: A:0.33, C:0.08, G:0.05, T:0.54
Consensus pattern (30 bp):
TTCTCAAAATTTATTTTTAAAATTCTTAGA
Found at i:6483172 original size:318 final size:318
Alignment explanation
Indices: 6482595--6483230 Score: 1254
Period size: 318 Copynumber: 2.0 Consensus size: 318
6482585 ATTTTAAGCT
*
6482595 ATTTTTTAAGTCGGACCCAGATCTAAAAAATATATCTAAATTTTTTCAGAAACCCGATCTGTCCC
1 ATTTTTTAAGTCGGACCCAGATCTAAAAAATATATCTAAATTTTTGCAGAAACCCGATCTGTCCC
6482660 TACTTATGATCATATCTACTTCTACCCACCACTCTTGTAGCCACTGCTGTAGGGCAGAAGAGTGT
66 TACTTATGATCATATCTACTTCTACCCACCACTCTTGTAGCCACTGCTGTAGGGCAGAAGAGTGT
6482725 TTTTAAGTTTCACCTTAGATTGGTCTCGACTCATATAAGATGGGGTTTTATATGATGAATGTGGA
131 TTTTAAGTTTCACCTTAGATTGGTCTCGACTCATATAAGATGGGGTTTTATATGATGAATGTGGA
6482790 GTCTAATGGTAGTCCACAACACGAGAATCCCATTGCGTAGGCTCTGGCGTATAACAACGGATGTA
196 GTCTAATGGTAGTCCACAACACGAGAATCCCATTGCGTAGGCTCTGGCGTATAACAACGGATGTA
6482855 ACTAGCCATAGCTGAGCTTAATGGGTTAGTTATGATGGTTTTTTGTTCAAGCAACCCC
261 ACTAGCCATAGCTGAGCTTAATGGGTTAGTTATGATGGTTTTTTGTTCAAGCAACCCC
6482913 ATTTTTTAAGTCGGACCCAGATCTAAAAAATATATCTAAATTTTTGCAGAAACCCGATCTGTCCC
1 ATTTTTTAAGTCGGACCCAGATCTAAAAAATATATCTAAATTTTTGCAGAAACCCGATCTGTCCC
6482978 TACTTATGATCATATCTACTTCTACCCACCACTCTTGTAGCCACTGCTGTAGGGCAGAAGAGTGT
66 TACTTATGATCATATCTACTTCTACCCACCACTCTTGTAGCCACTGCTGTAGGGCAGAAGAGTGT
6483043 TTTTAAGTTTCACCTTAGATTGGTCTCGACTCATATAAGATGGGGTTTTATATGATGAATGTGGA
131 TTTTAAGTTTCACCTTAGATTGGTCTCGACTCATATAAGATGGGGTTTTATATGATGAATGTGGA
6483108 GTCTAATGGTAGTCCACAACACGAGAATCCCATTGCGTAGGCTCTGGCGTATAACAACGGATGTA
196 GTCTAATGGTAGTCCACAACACGAGAATCCCATTGCGTAGGCTCTGGCGTATAACAACGGATGTA
*
6483173 ACTAGCCATAGCTGAGCTTAATGGGTTAGTTATGATGGTTTTTTGTTCAAGCGACCCC
261 ACTAGCCATAGCTGAGCTTAATGGGTTAGTTATGATGGTTTTTTGTTCAAGCAACCCC
6483231 CATCTTAGGC
Statistics
Matches: 316, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
318 316 1.00
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (318 bp):
ATTTTTTAAGTCGGACCCAGATCTAAAAAATATATCTAAATTTTTGCAGAAACCCGATCTGTCCC
TACTTATGATCATATCTACTTCTACCCACCACTCTTGTAGCCACTGCTGTAGGGCAGAAGAGTGT
TTTTAAGTTTCACCTTAGATTGGTCTCGACTCATATAAGATGGGGTTTTATATGATGAATGTGGA
GTCTAATGGTAGTCCACAACACGAGAATCCCATTGCGTAGGCTCTGGCGTATAACAACGGATGTA
ACTAGCCATAGCTGAGCTTAATGGGTTAGTTATGATGGTTTTTTGTTCAAGCAACCCC
Found at i:6483556 original size:28 final size:27
Alignment explanation
Indices: 6483518--6483591 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
6483508 AAAAATAAAA
*
6483518 ATTTATCAAAATATTATAAATTTTTTT
1 ATTTACCAAAATATTATAAATTTTTTT
* *
6483545 ATTTACCAAAAAATATATAATTTTTTTT
1 ATTTACCAAAATAT-TATAAATTTTTTT
6483573 ATTTACCAAAATA-TATAAA
1 ATTTACCAAAATATTATAAA
6483592 AAAATCTGCA
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.12
27 12 0.29
28 24 0.59
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.47
Consensus pattern (27 bp):
ATTTACCAAAATATTATAAATTTTTTT
Found at i:6483677 original size:27 final size:27
Alignment explanation
Indices: 6483647--6483723 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
6483637 ACGCCAATGG
6483647 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
* **
6483674 CATTGGCGGCACCAAAAGTGCCAATGC
1 CATTGGCGGCACCAAAGGTGCCAAAAC
*
6483701 CATTGGCGGCACCAATGGTGCCA
1 CATTGGCGGCACCAAAGGTGCCA
6483724 TATTGATTGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (27 bp):
CATTGGCGGCACCAAAGGTGCCAAAAC
Found at i:6483732 original size:27 final size:25
Alignment explanation
Indices: 6483639--6483739 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 25
6483629 CCTTGGTCAC
6483639 GCCAATGGCATTGGCGGCACCAAAGGT
1 GCCAAT-G-ATTGGCGGCACCAAAGGT
** *
6483666 GCCAAAACCATTGGCGGCACCAAAAGT
1 GCC--AATGATTGGCGGCACCAAAGGT
*
6483693 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATG--ATTGGCGGCACCAAAGGT
6483720 GCCATATTGATTGGCGGCAC
1 GCCA-A-TGATTGGCGGCAC
6483740 TATTCGTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
25 2 0.03
27 54 0.89
28 1 0.02
29 4 0.07
ACGTcount: A:0.27, C:0.28, G:0.29, T:0.17
Consensus pattern (25 bp):
GCCAATGATTGGCGGCACCAAAGGT
Found at i:6483911 original size:19 final size:21
Alignment explanation
Indices: 6483873--6483911 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
6483863 AAAATTTGAT
*
6483873 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
6483894 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
6483912 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:6483984 original size:3 final size:3
Alignment explanation
Indices: 6483978--6484003 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6483968 ATTATTATTA
6483978 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
6484004 AGTATTAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:6489665 original size:16 final size:15
Alignment explanation
Indices: 6489644--6489673 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
6489634 AATAAAACTA
6489644 TATTATTTTCATATTT
1 TATTATTTT-ATATTT
6489660 TATTATTTTATATT
1 TATTATTTTATATT
6489674 GTTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTATTTTATATTT
Found at i:6505875 original size:86 final size:85
Alignment explanation
Indices: 6505719--6505878 Score: 209
Period size: 86 Copynumber: 1.9 Consensus size: 85
6505709 ATCTCTTACA
* * *
6505719 ATGCCAATGTCCCAGACATGGTCTTACATGTAATCAAATATCGATGTCACTGTTCCAGACAGGGT
1 ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
6505784 CTTACACGAAATCGTATATG
66 CTTACACGAAATCGTATATG
* * *
6505804 ATGCCGATGTTCCAGACATGGTCTTACACGTAAATCTCAA-ATCGATGCCAAC-GTCCCAGAC-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGT-AATC-AAATATCGATGCC-ACTGTCCCAGACAG
6505866 TGGTCTTACACGA
63 -GGTCTTACACGA
6505879 TAACTCATAT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
85 29 0.45
86 32 0.49
87 4 0.06
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.26
Consensus pattern (85 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGTAATCAAATATCGATGCCACTGTCCCAGACAGGGT
CTTACACGAAATCGTATATG
Found at i:6506555 original size:16 final size:14
Alignment explanation
Indices: 6506520--6506547 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
6506510 CACAAACGAT
6506520 AAAATTTTCACACA
1 AAAATTTTCACACA
6506534 AAAATTTTCACACA
1 AAAATTTTCACACA
6506548 TATAAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATTTTCACACA
Found at i:6508244 original size:2 final size:2
Alignment explanation
Indices: 6508237--6508272 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6508227 GGAAAATTAA
6508237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6508273 ACAATATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6519364 original size:26 final size:25
Alignment explanation
Indices: 6519329--6519392 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
6519319 AATGAAAAAT
*
6519329 AAAGAAAAAATAGTTAAAATAACATA
1 AAAGAAAAAATAATT-AAATAACATA
* * *
6519355 AAAGAAAAAAAAATTAAATTACTTA
1 AAAGAAAAAATAATTAAATAACATA
6519380 AAATGAAAAAATA
1 AAA-GAAAAAATA
6519393 TAGGGACAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
25 11 0.34
26 21 0.66
ACGTcount: A:0.70, C:0.03, G:0.06, T:0.20
Consensus pattern (25 bp):
AAAGAAAAAATAATTAAATAACATA
Found at i:6520025 original size:7 final size:8
Alignment explanation
Indices: 6520009--6520033 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6519999 ATAAATAGAA
6520009 TTTTATTT
1 TTTTATTT
6520017 TTTTATTT
1 TTTTATTT
6520025 TTTTATTT
1 TTTTATTT
6520033 T
1 T
6520034 GTTGTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTATTT
Found at i:6520772 original size:24 final size:24
Alignment explanation
Indices: 6520739--6520790 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
6520729 TTTGTAGGTC
* *
6520739 AAATAAATTATGTTAAGAAATGTT
1 AAATAAATTATATTAAGAAATATT
* *
6520763 AAATATATTATATTAATAAATATT
1 AAATAAATTATATTAAGAAATATT
6520787 AAAT
1 AAAT
6520791 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (24 bp):
AAATAAATTATATTAAGAAATATT
Found at i:6521337 original size:178 final size:177
Alignment explanation
Indices: 6521033--6521376 Score: 530
Period size: 178 Copynumber: 1.9 Consensus size: 177
6521023 AGAGTATTCA
* * * ** * *
6521033 ATATGATAGAGATATTTGATCAGTTCTAAAATTTATATGTATGACAAATACAATTATATTGATAA
1 ATATAATAGAGATATTTGACCAGTTCAAAAATTTATATACATGACAAATACAATTATACTAATAA
*
6521098 ATTCAATTAGTTTATACGTTATGTAAGTGGAGCCCTCCTATGGACTTATACATAATTATTTATTA
66 ATTCAATTAGTTTATACATTATGTAAGTGGAGCCCTCCTATGGACTTATACATAATTATTTATTA
6521163 CACCAAGTAATTTTTTTTCTCAAATATGAAACTTTCATGTTTAGATAG
131 CACCAAGT-ATTTTTTTTCTCAAATATGAAACTTTCATGTTTAGATAG
*
6521211 ATATAATAGAGATATTTGACCAGTTCAAAAATTTATATACATGACAAATACAATTTTACTAATAA
1 ATATAATAGAGATATTTGACCAGTTCAAAAATTTATATACATGACAAATACAATTATACTAATAA
*
6521276 ATTCAATTAGTTTTTACATTATGTAAGTGG-GCCC-CTCTAATGGACTTATACATAATTATTTAT
66 ATTCAATTAGTTTATACATTATGTAAGTGGAGCCCTC-CT-ATGGACTTATACATAATTATTTAT
* **
6521339 TACCCCTTGTATTTTTTTTCTCAAATATGAAACTTTCA
129 TACACCAAGTATTTTTTTTCTCAAATATGAAACTTTCA
6521377 CATCCCAACT
Statistics
Matches: 151, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
176 1 0.01
177 34 0.23
178 116 0.77
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (177 bp):
ATATAATAGAGATATTTGACCAGTTCAAAAATTTATATACATGACAAATACAATTATACTAATAA
ATTCAATTAGTTTATACATTATGTAAGTGGAGCCCTCCTATGGACTTATACATAATTATTTATTA
CACCAAGTATTTTTTTTCTCAAATATGAAACTTTCATGTTTAGATAG
Found at i:6522051 original size:42 final size:42
Alignment explanation
Indices: 6522001--6522096 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
6521991 CAAACAAAAA
* *
6522001 CGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTTCCTAAG
1 CGCCGCTAAAGATAATGTTCTTTAACAGCGTTTTTTCCTAAG
*
6522043 CGCCGCTAAAGATAATGTTCTTTAACAGCGTTTTTTTCTAAG
1 CGCCGCTAAAGATAATGTTCTTTAACAGCGTTTTTTCCTAAG
6522085 CGCCGCTAAAGA
1 CGCCGCTAAAGA
6522097 ACGCCGCTAA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (42 bp):
CGCCGCTAAAGATAATGTTCTTTAACAGCGTTTTTTCCTAAG
Found at i:6522103 original size:13 final size:13
Alignment explanation
Indices: 6522085--6522111 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6522075 TTTTTCTAAG
6522085 CGCCGCTAAAGAA
1 CGCCGCTAAAGAA
6522098 CGCCGCTAAAGAA
1 CGCCGCTAAAGAA
6522111 C
1 C
6522112 ATGATCTTTA
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:0.37, C:0.33, G:0.22, T:0.07
Consensus pattern (13 bp):
CGCCGCTAAAGAA
Found at i:6522129 original size:55 final size:55
Alignment explanation
Indices: 6522043--6522150 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
6522033 TTTTCCTAAG
* * * *
6522043 CGCCGCTAAAGATAATGTTCTTTAACAGCGTTTTTTTCTAAGCGCCGCTAAAGAA
1 CGCCGCTAAAGATAATGATCTTTAACAGCGTTTTCTACAAAGCGCCGCTAAAGAA
* *
6522098 CGCCGCTAAAGA-ACATGATCTTTAGCGGCGTTTTCTACAAAGCGCCGCTAAAG
1 CGCCGCTAAAGATA-ATGATCTTTAACAGCGTTTTCTACAAAGCGCCGCTAAAG
6522151 GACATGATCT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 1 0.02
55 45 0.98
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (55 bp):
CGCCGCTAAAGATAATGATCTTTAACAGCGTTTTCTACAAAGCGCCGCTAAAGAA
Found at i:6522189 original size:97 final size:97
Alignment explanation
Indices: 6521999--6522195 Score: 216
Period size: 97 Copynumber: 2.0 Consensus size: 97
6521989 TACAAACAAA
* * * * * *
6521999 AACGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTTCCTAAGCGCCGCTAAAGATAATGTTCT
1 AACGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTCTACAAAGCGCCGCTAAAGATAATGATCT
** ***
6522064 TTAACAGCGTTTTTTTCTAAGCGCCGCTAAAG
66 TTAACAGCGTTAGTGAATAAGCGCCGCTAAAG
* *
6522096 AACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCTACAAAGCGCCGCTAAAGGA-CATGATC
1 AACGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTCTACAAAGCGCCGCTAAA-GATAATGATC
*** * *
6522160 TTTAGTGGCGTTAGTGAATATGCGTCGCTAAAG
65 TTTAACAGCGTTAGTGAATAAGCGCCGCTAAAG
6522193 AAC
1 AAC
6522196 ATGTTCTTTA
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
97 79 0.98
98 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (97 bp):
AACGCCGCTAAAGAACATGATCTTTAGCAGCGTTTTCTACAAAGCGCCGCTAAAGATAATGATCT
TTAACAGCGTTAGTGAATAAGCGCCGCTAAAG
Found at i:6522277 original size:43 final size:42
Alignment explanation
Indices: 6522096--6522308 Score: 164
Period size: 42 Copynumber: 5.0 Consensus size: 42
6522086 GCCGCTAAAG
*
6522096 AACGCCGCTAAAGAACATGA-TCTTTAGCGGCG-TTTTCTACA
1 AACGCCGCTAAAGAACAT-ATTCTTTAGCGGCGTTTTTGTACA
* * ** * *
6522137 AAGCGCCGCTAAAGGACATGA-TCTTTAGTGGCGTTAGTGAATA
1 AA-CGCCGCTAAAGAACAT-ATTCTTTAGCGGCGTTTTTGTACA
** * * * * *
6522180 TGCGTCGCTAAAGAACATGTTCTTTAACGGCG-CTTTGTAGAA
1 AACGCCGCTAAAGAACATATTCTTTAGCGGCGTTTTTGTA-CA
* * * * * * *
6522222 AACACTGCTAAAGATCATGTTTTTTAGCGCGCTTTTTTTTACA
1 AACGCCGCTAAAGAACATATTCTTTAGCG-GCGTTTTTGTACA
6522265 AACGCCGCTAAAGAACATATTCTTTAGCGGCGTTTTTGTACA
1 AACGCCGCTAAAGAACATATTCTTTAGCGGCGTTTTTGTACA
6522307 AA
1 AA
6522309 AACGCCACTA
Statistics
Matches: 128, Mismatches: 38, Indels: 11
0.72 0.21 0.06
Matches are distributed among these distances:
41 5 0.04
42 87 0.68
43 31 0.24
44 5 0.04
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
AACGCCGCTAAAGAACATATTCTTTAGCGGCGTTTTTGTACA
Found at i:6522733 original size:21 final size:21
Alignment explanation
Indices: 6522685--6522733 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
6522675 CTTTTGAACA
*
6522685 TCTGCTTCTCTCGCTGCAGCC
1 TCTGCTTCCCTCGCTGCAGCC
*
6522706 TCCGCTTCCCTCGCTGCCA-CC
1 TCTGCTTCCCTCGCTG-CAGCC
6522727 TCTGCTT
1 TCTGCTT
6522734 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.04, C:0.47, G:0.16, T:0.33
Consensus pattern (21 bp):
TCTGCTTCCCTCGCTGCAGCC
Found at i:6525082 original size:9 final size:9
Alignment explanation
Indices: 6525070--6525422 Score: 231
Period size: 9 Copynumber: 38.3 Consensus size: 9
6525060 CGTCGTTTAC
*
6525070 GTTATTTAA
1 GTTATGTAA
6525079 GTTATGTAA
1 GTTATGTAA
*
6525088 GTTATTTAA
1 GTTATGTAA
*
6525097 TTTATGTAA
1 GTTATGTAA
6525106 GTTATGTAA
1 GTTATGTAA
*
6525115 GTTATTTAA
1 GTTATGTAA
*
6525124 TTTATGTAA
1 GTTATGTAA
* *
6525133 GCTATTTAGAAAAA
1 G-T-TAT-G--TAA
*
6525147 ATTATGTAA
1 GTTATGTAA
6525156 GTTATGTACTAA
1 GTTATG---TAA
6525168 GTTATGT-A
1 GTTATGTAA
6525176 -TTATGTAA
1 GTTATGTAA
* *
6525184 ATAATGTAA
1 GTTATGTAA
*
6525193 GTTA-GGAA
1 GTTATGTAA
6525201 GGTTATGT-A
1 -GTTATGTAA
*
6525210 -TTATATAA
1 GTTATGTAA
*
6525218 GTTATTTAA
1 GTTATGTAA
6525227 GTTATGTAA
1 GTTATGTAA
*
6525236 GTTATGCAA
1 GTTATGTAA
*
6525245 GTTA-GGAA
1 GTTATGTAA
6525253 GGTTATGT-A
1 -GTTATGTAA
6525262 -TTATGTAA
1 GTTATGTAA
*
6525270 GTTATTTAA
1 GTTATGTAA
6525279 GTTATGTAA
1 GTTATGTAA
*
6525288 GTTATTTAA
1 GTTATGTAA
*
6525297 GTTATTTAA
1 GTTATGTAA
*
6525306 TTTATGTAA
1 GTTATGTAA
6525315 GTTATGTAA
1 GTTATGTAA
*
6525324 GTTATTTAA
1 GTTATGTAA
*
6525333 TTTATGTAA
1 GTTATGTAA
* *
6525342 GCTATTTAGAAAAA
1 G-T-TAT-G--TAA
*
6525356 ATTATGTAA
1 GTTATGTAA
6525365 GTTATGTACTAA
1 GTTATG---TAA
6525377 GTTATGT-A
1 GTTATGTAA
6525385 -TTATGTAA
1 GTTATGTAA
6525393 GTTATGTAA
1 GTTATGTAA
* *
6525402 TTTATATAA
1 GTTATGTAA
*
6525411 GTTATGCAA
1 GTTATGTAA
6525420 GTT
1 GTT
6525423 TATATATAAG
Statistics
Matches: 269, Mismatches: 47, Indels: 56
0.72 0.13 0.15
Matches are distributed among these distances:
7 23 0.09
8 12 0.04
9 194 0.72
10 4 0.01
11 6 0.02
12 24 0.09
13 2 0.01
14 4 0.01
ACGTcount: A:0.36, C:0.02, G:0.17, T:0.46
Consensus pattern (9 bp):
GTTATGTAA
Found at i:6525218 original size:25 final size:25
Alignment explanation
Indices: 6525187--6525273 Score: 104
Period size: 25 Copynumber: 3.4 Consensus size: 25
6525177 TATGTAAATA
6525187 ATGTAAGTTAGGAAGGTTATGTATT
1 ATGTAAGTTAGGAAGGTTATGTATT
* **
6525212 ATATAAGTTATTTAA-GTTATGTAAGTT
1 ATGTAAGTTA-GGAAGGTTATGT-A-TT
*
6525239 ATGCAAGTTAGGAAGGTTATGTATT
1 ATGTAAGTTAGGAAGGTTATGTATT
6525264 ATGTAAGTTA
1 ATGTAAGTTA
6525274 TTTAAGTTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
25 27 0.54
26 6 0.12
27 17 0.34
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.41
Consensus pattern (25 bp):
ATGTAAGTTAGGAAGGTTATGTATT
Found at i:6525235 original size:52 final size:52
Alignment explanation
Indices: 6525176--6525342 Score: 219
Period size: 52 Copynumber: 3.2 Consensus size: 52
6525166 AAGTTATGTA
* * *
6525176 TTATGTAAATAATGTAAGTTAGGAAGGTTATGTATTATATAAGTTATTTAAG
1 TTATGTAAGTTATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAAG
*
6525228 TTATGTAAGTTATGCAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAAG
1 TTATGTAAGTTATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAAG
* ** * *
6525280 TTATGTAAGTTATTTAAGTTATTTAA-TTTATGTAAGTTATGTAAGTTATTTAAT
1 TTATGTAAGTTATGTAAGTTA-GGAAGGTTATGT-A-TTATGTAAGTTATTTAAG
6525334 TTATGTAAG
1 TTATGTAAG
6525343 CTATTTAGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
52 73 0.72
53 3 0.03
54 26 0.25
ACGTcount: A:0.35, C:0.01, G:0.19, T:0.46
Consensus pattern (52 bp):
TTATGTAAGTTATGTAAGTTAGGAAGGTTATGTATTATGTAAGTTATTTAAG
Found at i:6525395 original size:16 final size:18
Alignment explanation
Indices: 6525374--6525428 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
6525364 AGTTATGTAC
*
6525374 TAAGTTATGT-A-TTATG
1 TAAGTTATGTAATTTATA
6525390 TAAGTTATGTAATTTATA
1 TAAGTTATGTAATTTATA
*
6525408 TAAGTTATGCAAGTTTATA
1 TAAGTTATGTAA-TTTATA
6525427 TA
1 TA
6525429 TAAGTTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
16 10 0.29
17 1 0.03
18 15 0.44
19 8 0.24
ACGTcount: A:0.36, C:0.02, G:0.15, T:0.47
Consensus pattern (18 bp):
TAAGTTATGTAATTTATA
Found at i:6525558 original size:18 final size:17
Alignment explanation
Indices: 6525532--6525570 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6525522 TGCTATGATT
6525532 TATAAATTTTGAAAAAAA
1 TATAAATTTT-AAAAAAA
* *
6525550 TATAGATTTTAAAAATA
1 TATAAATTTTAAAAAAA
6525567 TATA
1 TATA
6525571 TTAAAAATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.38
Consensus pattern (17 bp):
TATAAATTTTAAAAAAA
Found at i:6528300 original size:14 final size:14
Alignment explanation
Indices: 6528279--6528324 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
6528269 CCTTAGACAT
*
6528279 TAAACCCTAAACCC
1 TAAACCCTTAACCC
* *
6528293 TTAACCCTTAACAC
1 TAAACCCTTAACCC
*
6528307 TAAACCATTAACCC
1 TAAACCCTTAACCC
6528321 TAAA
1 TAAA
6528325 TTGACCTAGA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTTAACCC
Found at i:6528530 original size:21 final size:22
Alignment explanation
Indices: 6528506--6528554 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
6528496 AACTATAAAC
* *
6528506 CCCTAAACCCCTAACCCTTA-A
1 CCCTAAACACCTAAACCTTAGA
*
6528527 CCCTAAACACTTAAACCTTAGA
1 CCCTAAACACCTAAACCTTAGA
6528549 CCCTAA
1 CCCTAA
6528555 CCATTGCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 17 0.71
22 7 0.29
ACGTcount: A:0.37, C:0.41, G:0.02, T:0.20
Consensus pattern (22 bp):
CCCTAAACACCTAAACCTTAGA
Found at i:6528643 original size:14 final size:14
Alignment explanation
Indices: 6528623--6528655 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6528613 TAGAACATAT
6528623 ATAAACCCTAAATC
1 ATAAACCCTAAATC
*
6528637 CTAAACCCTAAATC
1 ATAAACCCTAAATC
6528651 ATAAA
1 ATAAA
6528656 ACATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAACCCTAAATC
Found at i:6528681 original size:39 final size:40
Alignment explanation
Indices: 6528595--6528687 Score: 127
Period size: 39 Copynumber: 2.4 Consensus size: 40
6528585 TCAGCCATAT
* * *
6528595 TCCTTAAACCTTGAATCATAGAACATATATAAACCCTAAA
1 TCCTTAAACCTTAAATCATAAAACATATATAAACCATAAA
* *
6528635 TCC-TAAACCCTAAATCATAAAACATATATAAACTATAAA
1 TCCTTAAACCTTAAATCATAAAACATATATAAACCATAAA
6528674 -CCTTAAACCTTAAA
1 TCCTTAAACCTTAAA
6528688 CCTCAACCCT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
38 2 0.04
39 41 0.89
40 3 0.07
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (40 bp):
TCCTTAAACCTTAAATCATAAAACATATATAAACCATAAA
Found at i:6530062 original size:3 final size:3
Alignment explanation
Indices: 6530054--6530115 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
6530044 TAATGATGTA
6530054 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6530102 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
6530116 AGAAGTCATG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6530523 original size:21 final size:21
Alignment explanation
Indices: 6530498--6530539 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6530488 AAATTTTAAT
** *
6530498 TACATAACTAAATAATTAAAA
1 TACATAAAAAAATAAGTAAAA
6530519 TACATAAAAAAATAAGTAAAA
1 TACATAAAAAAATAAGTAAAA
6530540 ATTAAATTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
TACATAAAAAAATAAGTAAAA
Found at i:6535583 original size:8 final size:8
Alignment explanation
Indices: 6535570--6535595 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
6535560 GGAAAAAAAA
6535570 ATATGTAT
1 ATATGTAT
6535578 ATATGTAT
1 ATATGTAT
6535586 ATATGTAT
1 ATATGTAT
6535594 AT
1 AT
6535596 GAAGATTGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:6535847 original size:26 final size:27
Alignment explanation
Indices: 6535780--6535848 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
6535770 AAATATTTAT
*
6535780 AAAA-ATGTATATATATATATTATAAA
1 AAAACATGTATATATATAGATTATAAA
*
6535806 AAAACATGCA-AGTATACTAGA-TA-AAA
1 AAAACATGTATA-TATA-TAGATTATAAA
6535832 AAAACATGTATATATAT
1 AAAACATGTATATATAT
6535849 GTATTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 1 0.03
26 21 0.58
27 11 0.31
28 3 0.08
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAACATGTATATATATAGATTATAAA
Found at i:6535856 original size:26 final size:26
Alignment explanation
Indices: 6535780--6535861 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
6535770 AAATATTTAT
*
6535780 AAAA-ATGTATATATATATATTATAAA
1 AAAACATGTATATATATGTATTA-AAA
*
6535806 AAAACATGCA-AGTATACTAG-A-TAAAA
1 AAAACATGTATA-TATA-T-GTATTAAAA
*
6535832 AAAACATGTATATATATGTATTAAAT
1 AAAACATGTATATATATGTATTAAAA
6535858 AAAA
1 AAAA
6535862 GAACGACGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
26 29 0.64
27 11 0.24
28 2 0.04
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAACATGTATATATATGTATTAAAA
Found at i:6535890 original size:3 final size:3
Alignment explanation
Indices: 6535882--6535929 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
6535872 TGTATGAATA
6535882 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6535930 TGAACTTAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6541081 original size:3 final size:3
Alignment explanation
Indices: 6541073--6541125 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
6541063 AACCCAATTT
6541073 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
6541121 TTA TT
1 TTA TT
6541126 TTTCTTTACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:6541148 original size:12 final size:12
Alignment explanation
Indices: 6541131--6541164 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
6541121 TTATTTTTCT
6541131 TTACTTTATTTA
1 TTACTTTATTTA
6541143 TTACTTTATTTTA
1 TTACTTTA-TTTA
6541156 TTA-TTTATT
1 TTACTTTATT
6541165 ACCTATTTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 2 0.10
12 12 0.57
13 7 0.33
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (12 bp):
TTACTTTATTTA
Found at i:6542269 original size:10 final size:10
Alignment explanation
Indices: 6542254--6542291 Score: 58
Period size: 10 Copynumber: 3.7 Consensus size: 10
6542244 AAAGCATAAC
6542254 AAAAAAAACAA
1 AAAAAAAAC-A
6542265 AAAAAAAACA
1 AAAAAAAACA
*
6542275 AAAAAAAAGA
1 AAAAAAAACA
6542285 AAAAAAA
1 AAAAAAA
6542292 TAATTTGGGG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.92, C:0.05, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:6542270 original size:11 final size:11
Alignment explanation
Indices: 6542254--6542291 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
6542244 AAAGCATAAC
6542254 AAAAAAAACAA
1 AAAAAAAACAA
6542265 AAAAAAAACAA
1 AAAAAAAACAA
6542276 AAAAAAAGA-AA
1 AAAAAAA-ACAA
6542287 AAAAA
1 AAAAA
6542292 TAATTTGGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 25 0.96
12 1 0.04
ACGTcount: A:0.92, C:0.05, G:0.03, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:6542276 original size:20 final size:20
Alignment explanation
Indices: 6542251--6542291 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
6542241 CCTAAAGCAT
6542251 AACAAAAAAAACA-AAAAAAA
1 AACAAAAAAAA-AGAAAAAAA
6542271 AACAAAAAAAAAGAAAAAAA
1 AACAAAAAAAAAGAAAAAAA
6542291 A
1 A
6542292 TAATTTGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 1 0.05
20 19 0.95
ACGTcount: A:0.90, C:0.07, G:0.02, T:0.00
Consensus pattern (20 bp):
AACAAAAAAAAAGAAAAAAA
Found at i:6544378 original size:44 final size:44
Alignment explanation
Indices: 6544264--6544513 Score: 178
Period size: 44 Copynumber: 5.8 Consensus size: 44
6544254 GCTATCTTTA
*
6544264 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTA-TAGCTTC-
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTAGTGGCTTCT
* * *** * * * * *
6544307 AACTTGTTCTGGTACAAATTCAAGGAGATAGGATTAGTTTG-TTCT
1 ATC-TGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TGGCTTCT
* * *
6544352 GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGAT-G---CG
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAG-TGGCTTCT
* * * *
6544393 ATCTGC-CCTCTGCAACTTCAGAGAGATAAGATCT-GTGGTTTCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TAGTGGCTTCT
* * *
6544436 ATCTGTTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTT-T
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTCT
*
6544479 AACCTGCTCCACTGCAACTTCAGGGAGATAAGATT
1 -ATCTGCTCCACTGCAACTTCAGGGAGATAAGATT
6544514 TGCCATCTTC
Statistics
Matches: 157, Mismatches: 38, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
39 1 0.01
40 25 0.16
41 7 0.04
43 13 0.08
44 108 0.69
45 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATTAGTGGCTTCT
Found at i:6544443 original size:128 final size:129
Alignment explanation
Indices: 6544264--6544511 Score: 299
Period size: 128 Copynumber: 1.9 Consensus size: 129
6544254 GCTATCTTTA
* ***
6544264 ATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATAGCTTCAACTTGTTCTGGTACAAATTCA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTATAGCTTCAACTTGTTCCACTACAAATTCA
* **
6544329 AGGAGATAGGATTAGTTTG-TTCT-GTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC
66 AGGAGATAGGATTA-TTGGCTT-TAACCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC
6544392 G
129 G
* * * * * *
6544393 ATCTGC-CCTCTGCAACTTCAGAGAGATAAGA-TCTGTGGTTTCAA-TCTGTTCCACTGCAACTT
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGACT-TATAGCTTCAACT-TGTTCCACTACAAATT
*
6544455 CAGGGAGATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
64 CAAGGAGATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGA
6544512 TTTGCCATCT
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
127 6 0.06
128 89 0.88
129 6 0.06
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.29
Consensus pattern (129 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTATAGCTTCAACTTGTTCCACTACAAATTCA
AGGAGATAGGATTATTGGCTTTAACCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCG
Found at i:6544612 original size:44 final size:44
Alignment explanation
Indices: 6544555--6544746 Score: 158
Period size: 44 Copynumber: 4.4 Consensus size: 44
6544545 GATCTACTTC
* *
6544555 GCTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACT
1 GCTGCCCAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT
* * * *
6544599 GTTGCCCAGGGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACT
1 GCTGCCCAGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACT
* * * ** *
6544642 G-TAACCTCAGGGAGGTAAAATCTGCCATCTTCGATCTACTCCACT
1 GCT-GCC-CAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT
* * * * *
6544687 ACTGTCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCTACT
1 GCTGCCCAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT
*
6544731 GCTGCCCAGGTAGATA
1 GCTGCCCAGGGAGATA
6544747 GAATTACTGG
Statistics
Matches: 110, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 21 0.19
44 63 0.57
45 18 0.16
46 2 0.02
47 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (44 bp):
GCTGCCCAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT
Found at i:6544640 original size:43 final size:44
Alignment explanation
Indices: 6544582--6544775 Score: 128
Period size: 44 Copynumber: 4.4 Consensus size: 44
6544572 GATCTGTAAT
*
6544582 CTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACTGG
* ** * * * ***
6544625 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGTTGCC-CAGGGAGATAGAATCTACTGG
* ** * * *
6544670 CTTCGATCTACTCCACTACTGTCTAGGGAGATA-AGATCTGTAAT--
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGA-ATC--TACTGG
* * * *
6544714 CTTCAATCTATTCTACTGCTGCCCAGGTAGATAGAAT-TACTGG
1 CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACTGG
*
6544757 CTTCAATGTACTCCACTGT
1 CTTCAATCTACTCCACTGT
6544776 AACCTCAGGG
Statistics
Matches: 109, Mismatches: 34, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
41 3 0.03
43 35 0.32
44 51 0.47
45 19 0.17
46 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTTGCCCAGGGAGATAGAATCTACTGG
Found at i:6544686 original size:150 final size:150
Alignment explanation
Indices: 6544415--6544686 Score: 332
Period size: 150 Copynumber: 1.8 Consensus size: 150
6544405 CAACTTCAGA
** * * * * *
6544415 GAGATAAGATCTGTGGTTTCAATCTGTTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTA
1 GAGATAAGATCTGTAATTTCAATCTATTCCACTGCAACTCCAGGGAGATAGAATTACTGGCTTCA
* * * * *
6544480 ACCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTTCAGTCTGCCCCACTGCAACTTT
66 ACCTACTCCACTGCAACCTCAGGGAGATAAAATCTGCCATCTTCAGTCTACCCCACTGCAACTTT
6544545 GATCTACTTCGCTGCCTAGG
131 GATCTACTTCGCTGCCTAGG
***
6544565 GAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGC-CCAGGGAGATAGAATTACTGGCTTC
1 GAGATAAGATCTGTAAT-TTCAATCTATTCCACTGCAACTCCAGGGAGATAGAATTACTGGCTTC
** * * *
6544629 AATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTC-GATCTACTCCACT
65 AACCTACTCCACTGCAACCTCAGGGAGATAAAATCTGCCATCTTCAG-TCTACCCCACT
6544687 ACTGTCTAGG
Statistics
Matches: 100, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
149 1 0.01
150 82 0.82
151 17 0.17
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (150 bp):
GAGATAAGATCTGTAATTTCAATCTATTCCACTGCAACTCCAGGGAGATAGAATTACTGGCTTCA
ACCTACTCCACTGCAACCTCAGGGAGATAAAATCTGCCATCTTCAGTCTACCCCACTGCAACTTT
GATCTACTTCGCTGCCTAGG
Found at i:6544711 original size:132 final size:131
Alignment explanation
Indices: 6544560--6544855 Score: 486
Period size: 132 Copynumber: 2.2 Consensus size: 131
6544550 ACTTCGCTGC
*
6544560 CTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGGGAGATAGAATTACTGG
1 CTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGG
* * *
6544625 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCTGCCAT-CTTCGATCTACTCCACTAC
66 CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTT-GACCCACTCCACTAC
6544689 TG
130 TG
* *
6544691 TCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCTACTGCTGCCCAGGTAGATAGAATTACTG
1 -CTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTG
*
6544756 GCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGACCCGCTCCACTAC
65 GCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGACCCACTCCACTAC
6544821 TG
130 TG
*
6544823 CTTAGGGAGATAAGATCTGTAATCTTCGATCTA
1 C-TAGGGAGATAAGATCTGTAATCTTCAATCTA
6544856 CTTCACGCCA
Statistics
Matches: 154, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
131 1 0.01
132 150 0.97
133 3 0.02
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (131 bp):
CTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTACTGG
CTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCCTTGACCCACTCCACTACT
G
Found at i:6544897 original size:44 final size:44
Alignment explanation
Indices: 6544845--6545158 Score: 439
Period size: 44 Copynumber: 7.1 Consensus size: 44
6544835 AGATCTGTAA
*
6544845 TCTTCGATCTACTTCACGCCAATCCATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * *** *
6544889 TCTTCGATCTACTTCGCCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
*
6544934 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* *
6544978 TCTTAGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
* * * * * *
6545022 TCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTT
* *
6545067 TCTTCGATCTACTTCACGCAAATACATAAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
6545111 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
1 TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
6545155 TCTT
1 TCTT
6545159 TTTAACCTGC
Statistics
Matches: 231, Mismatches: 37, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
44 158 0.68
45 73 0.32
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (44 bp):
TCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTT
Found at i:6544987 original size:89 final size:86
Alignment explanation
Indices: 6544834--6545158 Score: 418
Period size: 89 Copynumber: 3.7 Consensus size: 86
6544824 TTAGGGAGAT
*
6544834 AAGATCTG-TAATCTTCGATCTACTTCACGCCAATCCATGAAGACAAGATCTGCTTTCTTCGATC
1 AAGATCTGCT-ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATC
***
6544898 TACTTCGCCACCAGTATGGGAAGAC
65 TACTTCGCCA--A-TACATGAAGAC
* *
6544923 AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGTTTTCTTAGATCT
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
6544988 ACTTCATGCCAATACATGAAGAC
66 ACTTC--GCCAATACATGAAGAC
* * * * * * *
6545011 AAGATCTGCTTTCTTCGATCTACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTCGATC
1 AAGATCTGCTATCTTCGATCTACTTC-ACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATC
* *
6545076 TACTTCACGCAAATACATAAAGAC
65 TACTT--CGCCAATACATGAAGAC
*
6545100 AAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
6545159 TTTAACCTGC
Statistics
Matches: 207, Mismatches: 23, Indels: 13
0.85 0.09 0.05
Matches are distributed among these distances:
88 60 0.29
89 141 0.68
90 1 0.00
91 5 0.02
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (86 bp):
AAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
ACTTCGCCAATACATGAAGAC
Found at i:6545072 original size:133 final size:133
Alignment explanation
Indices: 6544834--6545158 Score: 569
Period size: 133 Copynumber: 2.4 Consensus size: 133
6544824 TTAGGGAGAT
** *
6544834 AAGATCTGTAATCTTCGATCTACTTCACGCCAATCCATGAAGACAAGATCTGCTTTCTTCGATCT
1 AAGATCTGTTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
* * *
6544899 ACTTCGCCACCAGTATGGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAA
66 ACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCAAATACATAAA
6544964 GAC
131 GAC
* *
6544967 AAGATCTGTTTTCTTAGATCTACTTCATGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
1 AAGATCTGTTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
6545032 ACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCAAATACATAAA
66 ACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCAAATACATAAA
6545097 GAC
131 GAC
*
6545100 AAGATCTGCTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 AAGATCTGTTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
6545159 TTTAACCTGC
Statistics
Matches: 181, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
133 181 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (133 bp):
AAGATCTGTTTTCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCT
ACTTCGCCACCAGTATAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACGCAAATACATAAA
GAC
Found at i:6546341 original size:7 final size:7
Alignment explanation
Indices: 6546320--6546371 Score: 54
Period size: 8 Copynumber: 7.3 Consensus size: 7
6546310 TCTCATTTTC
6546320 TTTTC-T
1 TTTTCAT
6546326 TTTTCCAT
1 TTTT-CAT
6546334 TTTTCAT
1 TTTTCAT
*
6546341 TTCTCA-
1 TTTTCAT
6546347 TTTTCATT
1 TTTTCA-T
6546355 TTTTCATT
1 TTTTCA-T
6546363 TTTTCAT
1 TTTTCAT
6546370 TT
1 TT
6546372 CATTATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 9 0.22
7 12 0.30
8 19 0.47
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
TTTTCAT
Found at i:6546357 original size:21 final size:21
Alignment explanation
Indices: 6546333--6546380 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 21
6546323 TCTTTTTCCA
6546333 TTTTTCA-TTTCTCATTTTCAT
1 TTTTTCATTTTCTCA-TTTCAT
*
6546354 TTTTTCATTTTTTCATTTCAT
1 TTTTTCATTTTCTCATTTCAT
6546375 TATTTT
1 T-TTTT
6546381 TACGACTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTTTCATTTTCTCATTTCAT
Found at i:6547291 original size:18 final size:17
Alignment explanation
Indices: 6547268--6547306 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
6547258 TGGTTTGGCA
6547268 GAAAAAATCCAAAAGAAT
1 GAAAAAA-CCAAAAGAAT
**
6547286 GAAAAAACGTAAAGAAT
1 GAAAAAACCAAAAGAAT
6547303 GAAA
1 GAAA
6547307 GAACATTCGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.67, C:0.08, G:0.15, T:0.10
Consensus pattern (17 bp):
GAAAAAACCAAAAGAAT
Found at i:6549273 original size:13 final size:13
Alignment explanation
Indices: 6549255--6549280 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6549245 TGTTTAATTT
6549255 TTTACTAGAAAAC
1 TTTACTAGAAAAC
6549268 TTTACTAGAAAAC
1 TTTACTAGAAAAC
6549281 AAATCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:6551391 original size:26 final size:27
Alignment explanation
Indices: 6551324--6551392 Score: 74
Period size: 26 Copynumber: 2.6 Consensus size: 27
6551314 AAATATTTAT
*
6551324 AAAA-ATGTATATATATATATTATAAA
1 AAAACATGTATATATATAGATTATAAA
*
6551350 AAAACATGCA-AGTATACTAGA-TA-AAA
1 AAAACATGTATA-TATA-TAGATTATAAA
6551376 AAAACATGTATATATAT
1 AAAACATGTATATATAT
6551393 GTATTAAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
25 1 0.03
26 21 0.58
27 11 0.31
28 3 0.08
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (27 bp):
AAAACATGTATATATATAGATTATAAA
Found at i:6551400 original size:26 final size:26
Alignment explanation
Indices: 6551324--6551405 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
6551314 AAATATTTAT
*
6551324 AAAA-ATGTATATATATATATTATAAA
1 AAAACATGTATATATATGTATTA-AAA
*
6551350 AAAACATGCA-AGTATACTAG-A-TAAAA
1 AAAACATGTATA-TATA-T-GTATTAAAA
*
6551376 AAAACATGTATATATATGTATTAAAT
1 AAAACATGTATATATATGTATTAAAA
6551402 AAAA
1 AAAA
6551406 GAACGACGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
24 1 0.02
25 2 0.04
26 29 0.64
27 11 0.24
28 2 0.04
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (26 bp):
AAAACATGTATATATATGTATTAAAA
Found at i:6551434 original size:3 final size:3
Alignment explanation
Indices: 6551426--6551480 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
6551416 TGTATGAATA
6551426 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6551474 AAT AAT A
1 AAT AAT A
6551481 GTAGTAGTAG
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6552067 original size:16 final size:15
Alignment explanation
Indices: 6552046--6552096 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 15
6552036 TTTTATATTT
6552046 TAAAAGAAATAAAAAA
1 TAAAAGAAA-AAAAAA
6552062 TAAAAGGAAAAAACAAA
1 TAAAA-GAAAAAA-AAA
*
6552079 -AATAAGAAAAAAGAA
1 TAA-AAGAAAAAAAAA
6552094 TAA
1 TAA
6552097 TTGTGAATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
15 2 0.07
16 19 0.63
17 9 0.30
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (15 bp):
TAAAAGAAAAAAAAA
Found at i:6553569 original size:21 final size:21
Alignment explanation
Indices: 6553544--6553586 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
6553534 GGATTACAAC
6553544 AATACTAATCGCCATCAAACA
1 AATACTAATCGCCATCAAACA
6553565 AATACTAATCGCCATCAAACA
1 AATACTAATCGCCATCAAACA
6553586 A
1 A
6553587 TGTATATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.28, G:0.05, T:0.19
Consensus pattern (21 bp):
AATACTAATCGCCATCAAACA
Found at i:6580489 original size:63 final size:62
Alignment explanation
Indices: 6580301--6580492 Score: 303
Period size: 63 Copynumber: 3.0 Consensus size: 62
6580291 TCACACGAAG
* * *
6580301 ATATTCTTATCACATCAGGAATGAAGCGCATCTTAATAGAGTTTGAATTATCAAATGTAAGTC
1 ATATTCTTATCACATCAGGAATGAGGCGCATCTTAATAGAGTTTGAATTA-CAAATTTAAGTT
*
6580364 ATATTCTTATCACATCAGGAATGAGGCGCATCTTAATAGAGTTTGAATTACCAAATTAAAGTT
1 ATATTCTTATCACATCAGGAATGAGGCGCATCTTAATAGAGTTTGAATTA-CAAATTTAAGTT
* *
6580427 ATATTCTTATCACATCAGGAATGGGGCACATCTTAATAGAGTTTGAATTACGAAATTTAAGTT
1 ATATTCTTATCACATCAGGAATGAGGCGCATCTTAATAGAGTTTGAATTAC-AAATTTAAGTT
6580490 ATA
1 ATA
6580493 AATCAGGTTG
Statistics
Matches: 120, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
62 1 0.01
63 119 0.99
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (62 bp):
ATATTCTTATCACATCAGGAATGAGGCGCATCTTAATAGAGTTTGAATTACAAATTTAAGTT
Found at i:6585520 original size:2 final size:2
Alignment explanation
Indices: 6585513--6585553 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
6585503 ATTAATTACC
6585513 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6585554 CCATATCAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:6585893 original size:22 final size:23
Alignment explanation
Indices: 6585867--6585917 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
6585857 ACTGTTAAAA
6585867 CCCTAAACACC-AAAT-CCCTAAC
1 CCCTAAAC-CCTAAATCCCCTAAC
6585889 CCCT-AACCCTAAATCCCCTAAC
1 CCCTAAACCCTAAATCCCCTAAC
*
6585911 CCATAAA
1 CCCTAAA
6585918 TCCCCCTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 7 0.28
22 14 0.56
23 2 0.08
ACGTcount: A:0.39, C:0.45, G:0.00, T:0.16
Consensus pattern (23 bp):
CCCTAAACCCTAAATCCCCTAAC
Found at i:6585919 original size:16 final size:16
Alignment explanation
Indices: 6585888--6585934 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
6585878 AAATCCCTAA
6585888 CCCCTAACCCTAAAT-
1 CCCCTAACCCTAAATC
6585903 CCCCTAACCCATAAATC
1 CCCCTAACCC-TAAATC
6585920 CCCCTAACCCCTAAA
1 CCCCTAA-CCCTAAA
6585935 GCATAACACT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 10 0.34
16 5 0.17
17 11 0.38
18 3 0.10
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (16 bp):
CCCCTAACCCTAAATC
Found at i:6586451 original size:118 final size:116
Alignment explanation
Indices: 6586191--6586586 Score: 564
Period size: 118 Copynumber: 3.4 Consensus size: 116
6586181 TAAATTATTT
* * *
6586191 TAAATCCCTAAGCATTAGCGGCGC-TTCTTAAAAACGTCGCTAAATCCCCGAAAGCTCAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
* *
6586255 GGCGCCGTTGGGCTTAG--TTTTTTATGCGGCGCTTTCCCAAAAACGACGC
66 GGCGCCGTTGGGCTTAGTTTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* * * *
6586304 TAAAGCCTTGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAATCCCTGAAAGCTCAGAAAAT
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
6586369 GGCGCCGTTGGGCTTAGTTTTTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
66 GGCGCCGTTGGGCTTAG--TTTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
* *
6586422 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCACTAAATCCCCGAAAGCTTAGAAAAC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
** * ** * *
6586487 AACGTCGTTGGGCTTAGGTTTTTTTTTTGCGGCATTTTTCTCAAAAACGCTGC
66 GGCGCCGTTGGGCTTA-GTTTTTTTTTTGCGGC-GCTTTCCCAAAAACGCCGC
*
6586540 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCAAAATC
1 TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATC
6586587 NNNNNNNNNN
Statistics
Matches: 252, Mismatches: 24, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
113 21 0.08
114 53 0.21
117 15 0.06
118 162 0.64
119 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.27
Consensus pattern (116 bp):
TAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAAC
GGCGCCGTTGGGCTTAGTTTTTTTTTTGCGGCGCTTTCCCAAAAACGCCGC
Found at i:6587080 original size:115 final size:115
Alignment explanation
Indices: 6586687--6587625 Score: 1260
Period size: 115 Copynumber: 8.1 Consensus size: 115
6586677 NNNNNNNNNN
* *
6586687 CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAGCGCCGCTAAATCCCCGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
6586752 AGCTCAGAAAACGGCGTCGTTGGGCTTAGG--TTTTTTGCGGCGGCTTTCT
66 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGC-GCTTTCT
* * * * * *
6586801 CAAAAACGCCGGTAAAGCCTTGAGTATTAGTGGTGCTTTTTTAAAAACGCCGCTAAATCCCCGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* *
6586866 AGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTTTTGCGGCACTTTCT
66 AGCTCAGAAAACGGCGTCGTTGGGCTTAGG--TTTTTTTTGCGGCGCTTTCT
* * * *
6586918 CAAAAACGTCGGTAAAGCCCTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* * *
6586983 AGCTCAGAAAATGGCATCGTTGGGCTTAGGTTTTTTTTGCGGCACTTTCT
66 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
* *
6587033 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCC-CGTAAATCCCCGA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC-TAAATCCCCGA
* *
6587097 AAGCTTAGAAAACTGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
65 AAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
* * * * ** * *
6587148 CAAACACGCTGCTAAAGCCCTGGGCATTAGCAGCAATTTCTCAAAAACACCGCTAAATCCCCGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* *
6587213 AGCTCAGAAAAAGGCGTCGTTGGGCTTAGGTTTTTTTTACGGCGCTTTCT
66 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
*
6587263 CAAAAAACGCCAG-TAAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCG
1 C-AAAAACGCC-GCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCG
* *
6587327 AAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTCGCGGCGCTTTCT
64 AAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
* * *
6587379 CAAAAATGCC-CTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAATCCCTGAA
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* * * * *
6587443 AGCTCAGAAAATGGCGCCGTTGGGCTTAGTTTTTTTTTTTTGCGGTGCTTTCC
66 AGCTCAGAAAACGGCGTCGTTGGGCTTAG---GTTTTTTTTGCGGCGCTTTCT
* * * * * * *
6587496 CAAAAACGCCGCTAAAACCCTGAGCGTTATCCGCACTTTCTTAAAAACGCCTCTAAATCCCCGAT
1 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* * * * * *
6587561 AGCTTAGAAAACGACGCCGTTGGGCTTA-GTTTTTTTTGTGGCGCTTCCC
66 AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
6587610 CAAAAACGCCGCTAAA
1 CAAAAACGCCGCTAAA
6587626 TCCCGAAAGC
Statistics
Matches: 731, Mismatches: 81, Indels: 26
0.87 0.10 0.03
Matches are distributed among these distances:
114 196 0.27
115 234 0.32
116 101 0.14
117 119 0.16
118 81 0.11
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (115 bp):
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
AGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
Found at i:6587134 original size:231 final size:229
Alignment explanation
Indices: 6586687--6587887 Score: 1293
Period size: 231 Copynumber: 5.1 Consensus size: 229
6586677 NNNNNNNNNN
* *
6586687 CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAGCGCCGCTAAATCCCCGAA
1 CAAAAACG-CGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* *
6586752 AGCTCAGAAAACGGCGTCGTTGGGCTTAGG--TTTTTTGCGGCGGCTTTCTCAAAAACGCCGGTA
65 AGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGC-GCTTTCTCAAAAACGCCGCTA
* * * ** *
6586815 AAGCCTTGAGTATTAGTGGTGCTTTTTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGA
129 AAGCCCTGAGCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGA
*
6586880 CGTCGTTGGGCTTAGGTTTTTTTTTTGCGGCACTTTCT
194 CGTCGTTGGGCTTAGG--TTTTTTTTGCGGCGCTTTCT
* * *
6586918 CAAAAACGTCGGTAAAGCCCTAAGCATTAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
1 CAAAAACG-CGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* *
6586983 AGCTCAGAAAATGGCATCGTTGGGCTTAGGTTTTTTTTGCGGCACTTTCTCAAAAACGCCGCTAA
65 AGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
* *
6587048 AGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCC-CGTAAATCCCCGAAAGCTTAGAAAACTG
130 AGCCCTGAGCATTAGCGGCACTTTCTTAAAAACGCCGC-TAAATCCCCGAAAGCTCAGAAAAC-G
6587112 -CGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
193 ACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
* * * ** * *
6587148 CAAACACGCTGCTAAAGCCCTGGGCATTAGCAGCAATTTCTCAAAAACACCGCTAAATCCCCGAA
1 CAAAAACGC-GCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* *
6587213 AGCTCAGAAAAAGGCGTCGTTGGGCTTAGGTTTTTTTTACGGCGCTTTCTCAAAAAACGCCAG-T
65 AGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTC-AAAAACGCC-GCT
* *
6587277 AAAGCCCTAAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACG
128 AAAGCCCTGAGCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACG
* * *
6587342 GCATCGTTGGGCTTAGGTTTTTTTCGCGGCGCTTTCT
193 ACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
* * * *
6587379 CAAAAATGCCCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAATCCCTGAAA
1 CAAAAACGCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAA
* * * *
6587444 GCTCAGAAAATGGCGCCGTTGGGCTTAGTTTTTTTTTTTTGCGGTGCTTTCCCAAAAACGCCGCT
66 GCTCAGAAAATGGCGTCGTTGGGCTTAG---GTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCT
* * * * * * *
6587509 AAAACCCTGAGCGTTATCCGCACTTTCTTAAAAACGCCTCTAAATCCCCGATAGCTTAGAAAACG
128 AAAGCCCTGAGCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACG
* * * *
6587574 ACGCCGTTGGGCTTA-GTTTTTTTTGTGGCGCTTCCC
193 ACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
* *
6587610 CAAAAACGCCGCTAAATCCCGAAAGCTCAGAAAACGGCGTCGTTGGTCTTAGGGTTTTTGCGGCG
1 CAAAAACG-CGC----T----AAAG--C------C--C-T-G--AG-C--A-----TTAGCGGCG
* * * * * *
6587675 CTTTCTCAAAAACGCCTCTAAATCCCCGAAAGCTTAGAAAACGGTGTCGTTTGGCTTAGG-TTTT
35 CTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTT
* * * * * * *
6587739 TTTGCGGCGCTTACCCAAAAACACCGCTAAGGCCCTGAAACATTAGCGGCGCTTTTCTAAAAAAC
100 TTTGCGGCGCTTTCTCAAAAACGCCGCTAAAGCCCTG-AGCATTAGCGGCAC-TTTCTTAAAAAC
* *
6587804 GCCGCTAAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAGG-TTTTTTTGCGGCGCT
163 GCCGCT-AAAT-CCCCGAAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCT
6587868 TTCT
226 TTCT
6587872 CAAAAACGCCGCTAAA
1 CAAAAACG-CGCTAAA
6587888 TCCCCCGAAA
Statistics
Matches: 815, Mismatches: 106, Indels: 75
0.82 0.11 0.08
Matches are distributed among these distances:
229 1 0.00
230 193 0.24
231 222 0.27
232 170 0.21
233 30 0.04
236 1 0.00
240 4 0.00
242 1 0.00
248 1 0.00
250 1 0.00
251 1 0.00
252 1 0.00
254 4 0.00
255 1 0.00
257 1 0.00
258 37 0.05
259 9 0.01
260 16 0.02
261 4 0.00
262 116 0.14
263 1 0.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (229 bp):
CAAAAACGCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAA
GCTCAGAAAATGGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAA
GCCCTGAGCATTAGCGGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACG
TCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCT
Found at i:6587327 original size:346 final size:345
Alignment explanation
Indices: 6586687--6587887 Score: 1358
Period size: 346 Copynumber: 3.4 Consensus size: 345
6586677 NNNNNNNNNN
*
6586687 CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAGCGCCGCTAAATCCCCGAA
1 CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* *
6586752 AGCTCAGAAAACGGCGTCGTTGGGCTTAGG--TTTTTTGCGGCGGCTTTCTCAAAAACGCCGGTA
66 AGCTCAGAAAACTGCGTCGTTGGGCTTAGGTTTTTTTTGCGGC-GCTTTCTCAAAAACGCCGCTA
* * ** ** *
6586815 AAGCCTTGAGTATTAGTGGTGCTTTTTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGA
130 AAGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGA
* * *
6586880 CGTCGTTGGGCTTAGGTTTTTTTTTTGCGGCACTTTCTCAAAAACGTCGGTAAAGCCCTAAGCAT
195 CGTCGTTGGGCTTAGG--TTTTTTTTGCGGCGCTTTCTCAAAAACGCCAGTAAAGCCCTAAGCAT
* *
6586945 TAGTGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAATGGCATCGTTGGGCTT
258 TAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTT
*
6587010 AGGTTTTTTTTGCGGCACTTTCT
323 AGGTTTTTTTCGCGGCACTTTCT
* * *
6587033 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCC-CGTAAATCCCCGA
1 CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGC-TAAATCCCCGA
* * *
6587097 AAGCTTAGAAAACTGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAACACGCTGCTA
65 AAGCTCAGAAAACTGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTA
* * * * * *
6587162 AAGCCCTGGGCATTAGCAGCAATTTCTCAAAAACACCGCTAAATCCCCGAAAGCTCAGAAAAAGG
130 AAGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGA
*
6587227 CGTCGTTGGGCTTAGGTTTTTTTTACGGCGCTTTCTCAAAAAACGCCAGTAAAGCCCTAAGCATT
195 CGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTC-AAAAACGCCAGTAAAGCCCTAAGCATT
6587292 AGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTA
259 AGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTA
*
6587357 GGTTTTTTTCGCGGCGCTTTCT
324 GGTTTTTTTCGCGGCACTTTCT
* *
6587379 CAAAAATGCC-CTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCTGCTAAATCCCTGAA
1 CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
* * * *
6587443 AGCTCAGAAAA-TGGCGCCGTTGGGCTTAGTTTTTTTTTTTTGCGGTGCTTTCCCAAAAACGCCG
66 AGCTCAGAAAACT-GCGTCGTTGGGCTTAG---GTTTTTTTTGCGGCGCTTTCTCAAAAACGCCG
* * * * * * *
6587507 CTAAAACCCTGAGCGTTATCCGCACTTTCTTAAAAACGCCTCTAAATCCCCGATAGCTTAGAAAA
127 CTAAAGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAA
* * * * *
6587572 CGACGCCGTTGGGCTTA-GTTTTTTTTGTGGCGCTTCCCCAAAAACGCC-GCTAAATCCCGAAAG
192 CGACGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCAG-TAAA-GCC-----
* * *
6587635 CTCAGAAAACGGCGTCGTTGGTCTTAGGGTTTTTGCGGCGCTTTCTCAAAAACGCCTCTAAATCC
250 CT-----AA-----------G-C--A-----TTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCC
* ** * * * *
6587700 CCGAAAGCTTAGAAAACGGTGTCGTTTGGCTTAGGTTTTTTT-GCGGCGCTTACC
291 CCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGGTTTTTTTCGCGGCACTTTCT
** * * *
6587754 CAAAAACACCGCTAAGGCCCTGAAACATTAGCGGCGCTTTTCTAAAAAACGCCGCTAAAATCCCC
1 CAAAAATGCCGCTAAAGCCCTG-AGCATTAGCGGCGC-TTTCTTAAAAACGCCGCT-AAAT-CCC
* *
6587819 CGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAGG-TTTTTTTGCGGCGCTTTCTCAAAAACGCCG
62 CGAAAGCTCAGAAAACTGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCG
6587883 CTAAA
127 CTAAA
6587888 TCCCCCGAAA
Statistics
Matches: 726, Mismatches: 83, Indels: 62
0.83 0.10 0.07
Matches are distributed among these distances:
344 1 0.00
345 94 0.13
346 218 0.30
347 106 0.15
348 106 0.15
352 2 0.00
357 2 0.00
368 1 0.00
369 1 0.00
371 1 0.00
375 18 0.02
376 112 0.15
377 13 0.02
378 16 0.02
379 4 0.01
380 31 0.04
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (345 bp):
CAAAAATGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAA
AGCTCAGAAAACTGCGTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
AGCCCTGAGCATTAGCAGCACTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGAC
GTCGTTGGGCTTAGGTTTTTTTTGCGGCGCTTTCTCAAAAACGCCAGTAAAGCCCTAAGCATTAG
CGGCGCTTTCTTAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCATCGTTGGGCTTAGG
TTTTTTTCGCGGCACTTTCT
Found at i:6587625 original size:73 final size:72
Alignment explanation
Indices: 6587538--6587768 Score: 293
Period size: 72 Copynumber: 3.2 Consensus size: 72
6587528 GCACTTTCTT
* * * * *
6587538 AAAAACGCCTCTAAATCCCCGATAGCTTAGAAAACGACGCCGTTGGGCTTAGTTTTTTTTGTGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTTAG-TTTTTTTGCGGC
*
6587603 GCTTCCCC
65 GCTTACCC
* * **
6587611 AAAAACGCCGCTAAAT-CCCGAAAGCTCAGAAAACGGCGTCGTTGGTCTTAGGGTTTTTGCGGCG
1 AAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTTAGTTTTTTTGCGGCG
* *
6587675 CTTTCTC
66 CTTACCC
* * *
6587682 AAAAACGCCTCTAAATCCCCGAAAGCTTAGAAAACGGTGTCGTTTGGCTTAGGTTTTTTTGCGGC
1 AAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTTA-GTTTTTTTGCGGC
6587747 GCTTACCC
65 GCTTACCC
*
6587755 AAAAACACCGCTAA
1 AAAAACGCCGCTAA
6587769 GGCCCTGAAA
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
71 30 0.22
72 60 0.45
73 44 0.33
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (72 bp):
AAAAACGCCGCTAAATCCCCGAAAGCTTAGAAAACGGCGTCGTTGGGCTTAGTTTTTTTGCGGCG
CTTACCC
Found at i:6587846 original size:118 final size:115
Alignment explanation
Indices: 6587669--6587886 Score: 346
Period size: 118 Copynumber: 1.9 Consensus size: 115
6587659 TAGGGTTTTT
* * * *
6587669 GCGGCGCTTTCTCAAAAACGCCTCTAAATCCCCGAAAGCTTAGAAAACGGTGTCGTTTGGCTTAG
1 GCGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAG
6587734 GTTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAGGCCCTGAAACATTA
66 GTTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAGGCCCTGAAACATTA
6587784 GCGGCGCTTTTCTAAAAAACGCCGCTAAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCT
1 GCGGCGC-TTTCTAAAAAACGCCGCT-AAAT-CCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCT
* * *
6587849 TAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAA
63 TAGGTTTTTTTGCGGCGCTTACCCAAAAACACCGCTAA
6587887 ATCCCCCGAA
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
115 7 0.08
116 16 0.17
117 4 0.04
118 66 0.71
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (115 bp):
GCGGCGCTTTCTAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAG
GTTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAGGCCCTGAAACATTA
Found at i:6587878 original size:262 final size:260
Alignment explanation
Indices: 6587407--6588013 Score: 756
Period size: 262 Copynumber: 2.3 Consensus size: 260
6587397 CTGAGCATTA
* * * * *
6587407 GCGGCGCTTTCTTAAAAACG-CTGCTAAATCCCTGAAAGCTCAGAAAATGGCGCCGTTGGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCT-CTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTA
* * * * * * *
6587471 GTTTTTTTTTTTTGCGGTGCTTTCCCAAAAACGCCGCTAAAACCCTGAGCGTTATCCGCACTTTC
65 G----ATTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAAACCCTGAACATTAGCCGCACTTTC
* * * * * *
6587536 TTAAAAACGCCTCTAAATCCCCGATAGCTTAGAAAACGACGCCGTTGGGCTTAGTTTTTTTTGTG
126 TAAAAAACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTTTTTGCG
6587601 GCGCTTCCCCAAAAACGCCGCTAAAT-CCCG-AAAGCTCAGAAAACGGCGTCG-TTGGTCTTAGG
191 GCGCTTCCCCAAAAACGCCGCTAAATCCCCGAAAAGCTCA-AAAACGGCGTCGTTTGG-CTTAGG
6587663 -GTTTTT
254 TGTTTTT
* *
6587669 GCGGCGCTTTCTCAAAAACGCCTCTAAATCCCCGAAAGCTTAGAAAACGGTGTCGTTTGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCTCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAG
* ** * *
6587734 GTTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAGGCCCTGAAACATTAGCGGCGCTTTTCTAA
66 ATTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAAACCCTG-AACATTAGCCGCAC-TTTCTAA
* * *
6587799 AAAACGCCGCTAAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAGGTTTTTTTGCGG
129 AAAACGCCGCT-AAAT-CCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTTTTTGCGG
* * *
6587864 CGCTTTCTCAAAAACGCCGCTAAATCCCCCGAAAAGCTCAAAAACGGCGTCGTTTGGCTTAGGTT
192 CGCTTCCCCAAAAACGCCGCTAAAT-CCCCGAAAAGCTCAAAAACGGCGTCGTTTGGCTTAGGTG
6587929 TTTTT
256 TTTTT
* * * *
6587934 GCGGCGCTTTATCAAAAACGCCACTAAATCCCCGGAAGCTCAAAAAACGGCGTCGTTTGGCTTAG
1 GCGGCGCTTTCTCAAAAACGCCTCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAG
6587999 ATTTTTTTGCGGCGC
66 ATTTTTTTGCGGCGC
6588014 GTTCTTAAAA
Statistics
Matches: 298, Mismatches: 37, Indels: 17
0.85 0.11 0.05
Matches are distributed among these distances:
258 36 0.12
259 9 0.03
260 16 0.05
261 4 0.01
262 119 0.40
263 2 0.01
264 22 0.07
265 90 0.30
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (260 bp):
GCGGCGCTTTCTCAAAAACGCCTCTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCTTAG
ATTTTTTTGCGGCGCTTACCCAAAAACACCGCTAAAACCCTGAACATTAGCCGCACTTTCTAAAA
AACGCCGCTAAATCCCCGAAAGCTCAGAAAACGACGCCGTTGGGCTTAGGTTTTTTTGCGGCGCT
TCCCCAAAAACGCCGCTAAATCCCCGAAAAGCTCAAAAACGGCGTCGTTTGGCTTAGGTGTTTTT
Found at i:6587981 original size:147 final size:148
Alignment explanation
Indices: 6587784--6588089 Score: 422
Period size: 147 Copynumber: 2.1 Consensus size: 148
6587774 TGAAACATTA
* *
6587784 GCGGCGCTTTTCTAAAAAACGCCGCTAAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCT
1 GCGGCGCTTTTC-AAAAAACGCCACTAAAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCT
* *
6587849 TAGGTTTTTTTGCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCGAAAAGCTC-AAAAACGGCG
65 TAGATTTTTTTGCGGCGCGTTCTCAAAAACGCCGCTAAAT-CCCCG-AAAGCTCGAAAAACGGCG
* *
6587913 TCGTTTGGCTTAGGTTTTTTT
128 TCGGTGGGCTTAGGTTTTTTT
*
6587934 GCGGCGCTTTATC-AAAAACGCCACT-AAAT-CCCCGGAAGCTCAAAAAACGGCGTCGTTTGGCT
1 GCGGCGCTTT-TCAAAAAACGCCACTAAAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCT
* * * * ** *
6587996 TAGATTTTTTTGCGGCGCGTTCTTAAAAACGCTGCTAACTCTCCGAAAGCTCGGTAAATGGCGTC
65 TAGATTTTTTTGCGGCGCGTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCGAAAAACGGCGTC
6588061 GGTGGGCTTAGGTTTTTTT
130 GGTGGGCTTAGGTTTTTTT
6588080 GCGGCGCTTT
1 GCGGCGCTTT
6588090 CTGGAAAACG
Statistics
Matches: 140, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
145 7 0.05
146 40 0.29
147 66 0.47
148 4 0.03
149 11 0.08
150 10 0.07
151 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.28
Consensus pattern (148 bp):
GCGGCGCTTTTCAAAAAACGCCACTAAAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTT
AGATTTTTTTGCGGCGCGTTCTCAAAAACGCCGCTAAATCCCCGAAAGCTCGAAAAACGGCGTCG
GTGGGCTTAGGTTTTTTT
Found at i:6587989 original size:73 final size:74
Alignment explanation
Indices: 6587784--6588106 Score: 427
Period size: 73 Copynumber: 4.4 Consensus size: 74
6587774 TGAAACATTA
* *
6587784 GCGGCGCTTTTCTAAAAAACGCCGCTAAAATCCCCCGAAAGCTCAGAAAACGGCGTCGTTTGGCT
1 GCGGCGC-TTTCTCAAAAACGCCGCT-AAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCT
6587849 TAGGTTTTTTT
64 TAGGTTTTTTT
6587860 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCGAAAAGCTC-AAAAACGGCGTCGTTTGGCTT
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCG-AAAGCTCAAAAAACGGCGTCGTTTGGCTT
6587924 AGGTTTTTTT
65 AGGTTTTTTT
* * *
6587934 GCGGCGCTTTATCAAAAACGCCACTAAAT-CCCCGGAAGCTCAAAAAACGGCGTCGTTTGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTA
*
6587998 GATTTTTTT
66 GGTTTTTTT
* * * * * *** * * *
6588007 GCGGCGCGTTCTTAAAAACGCTGCTAACT-CTCCGAAAGCTCGGTAAATGGCGTCGGTGGGCTTA
1 GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTA
6588071 GGTTTTTTT
66 GGTTTTTTT
**
6588080 GCGGCGCTTTCTGGAAAACGCCGCTAA
1 GCGGCGCTTTCTCAAAAACGCCGCTAA
6588107 TGATCGATCT
Statistics
Matches: 220, Mismatches: 25, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
72 6 0.03
73 116 0.53
74 67 0.30
75 24 0.11
76 7 0.03
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (74 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAATCCCCCGAAAGCTCAAAAAACGGCGTCGTTTGGCTTA
GGTTTTTTT
Found at i:6588153 original size:12 final size:12
Alignment explanation
Indices: 6588136--6588161 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6588126 TTTTTTATCC
6588136 AAACGCCGCTAA
1 AAACGCCGCTAA
6588148 AAACGCCGCTAA
1 AAACGCCGCTAA
6588160 AA
1 AA
6588162 GTCTGTTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAACGCCGCTAA
Found at i:6588729 original size:14 final size:14
Alignment explanation
Indices: 6588706--6588735 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6588696 AACAACCTTG
*
6588706 AAAAATAGTATATA
1 AAAAAAAGTATATA
6588720 AAAAAAAGTATATA
1 AAAAAAAGTATATA
6588734 AA
1 AA
6588736 CATTTAGCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (14 bp):
AAAAAAAGTATATA
Found at i:6588928 original size:21 final size:21
Alignment explanation
Indices: 6588904--6589000 Score: 58
Period size: 23 Copynumber: 4.4 Consensus size: 21
6588894 AGATATTAAA
*
6588904 AAAATAATAT-ATGATAAATTT
1 AAAATAATATAATAAT-AATTT
*
6588925 AAAA-CATATCAATAATAATTT
1 AAAATAATAT-AATAATAATTT
*
6588946 AAAATAATAGT-ATATTACATTTT
1 AAAATAATA-TAATAATA-A-TTT
6588969 AAAACT-ATACTAATAATAAGTTT
1 AAAA-TAATA-TAATAATAA-TTT
6588992 AAAAGTAAT
1 AAAA-TAAT
6589001 GTCAAACTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
20 4 0.07
21 18 0.31
22 8 0.14
23 21 0.36
24 8 0.14
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAATAATATAATAATAATTT
Found at i:6588949 original size:45 final size:45
Alignment explanation
Indices: 6588889--6588995 Score: 112
Period size: 45 Copynumber: 2.3 Consensus size: 45
6588879 ATAAAAATAT
6588889 ATAATAGATATTAAAAAAATAATATATGATA-AATTTAAAAC-ATA-TCA
1 ATAATA-AT-TTAAAAAAATAATATAT--TACAATTTAAAACTATACT-A
* * *
6588936 ATAATAATTTAAAATAATAGTATATTACATTTTAAAACTATACTA
1 ATAATAATTTAAAAAAATAATATATTACAATTTAAAACTATACTA
6588981 ATAATAAGTTTAAAA
1 ATAATAA-TTTAAAA
6588996 GTAATGTCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
43 2 0.04
44 9 0.17
45 26 0.49
46 10 0.19
47 6 0.11
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (45 bp):
ATAATAATTTAAAAAAATAATATATTACAATTTAAAACTATACTA
Found at i:6588951 original size:42 final size:46
Alignment explanation
Indices: 6588904--6589000 Score: 116
Period size: 45 Copynumber: 2.2 Consensus size: 46
6588894 AGATATTAAA
6588904 AAAATAATA-TATGA-TA-AATTTAAAAC-ATA-TCAATAATAA-TTT
1 AAAATAATAGTAT-ATTACAATTTAAAACTATACT-AATAATAAGTTT
*
6588946 AAAATAATAGTATATTACATTTTAAAACTATACTAATAATAAGTTT
1 AAAATAATAGTATATTACAATTTAAAACTATACTAATAATAAGTTT
6588992 AAAAGTAAT
1 AAAA-TAAT
6589001 GTCAAACTAA
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
42 10 0.21
43 5 0.11
44 9 0.19
45 11 0.23
46 8 0.17
47 4 0.09
ACGTcount: A:0.55, C:0.05, G:0.04, T:0.36
Consensus pattern (46 bp):
AAAATAATAGTATATTACAATTTAAAACTATACTAATAATAAGTTT
Found at i:6588992 original size:23 final size:21
Alignment explanation
Indices: 6588920--6588995 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 21
6588910 ATATATGATA
6588920 AATTTAAAAC-ATATCAATAAT
1 AATTTAAAACTATAT-AATAAT
*
6588941 AATTTAAAA-TA-ATAGTATATT
1 AATTTAAAACTATATA--ATAAT
6588962 ACATTTTAAAACTATACTAATAAT
1 A-A-TTTAAAACTATA-TAATAAT
6588986 AAGTTTAAAA
1 AA-TTTAAAA
6588996 GTAATGTCAA
Statistics
Matches: 44, Mismatches: 3, Indels: 14
0.72 0.05 0.23
Matches are distributed among these distances:
19 1 0.02
20 2 0.05
21 15 0.34
22 1 0.02
23 15 0.34
24 7 0.16
25 1 0.02
26 2 0.05
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.37
Consensus pattern (21 bp):
AATTTAAAACTATATAATAAT
Found at i:6589128 original size:3 final size:3
Alignment explanation
Indices: 6589122--6589179 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
6589112 ATAAAGAAGA
6589122 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6589170 AAT AAT AAT A
1 AAT AAT AAT A
6589180 GGAATTAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:6589219 original size:7 final size:6
Alignment explanation
Indices: 6589205--6589230 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
6589195 ATTAGAATTC
6589205 AAATAA AAATAA AAATAA AAATAA AA
1 AAATAA AAATAA AAATAA AAATAA AA
6589231 CAACTAACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:6589226 original size:18 final size:18
Alignment explanation
Indices: 6589121--6589230 Score: 76
Period size: 18 Copynumber: 6.1 Consensus size: 18
6589111 TATAAAGAAG
*
6589121 AAATAATAATAATAATAA
1 AAATAATAATAAAAATAA
* *
6589139 TAATAATAATAATAATAA
1 AAATAATAATAAAAATAA
* *
6589157 TAATAATAATAATAATAA
1 AAATAATAATAAAAATAA
* ** * *
6589175 TAATAGGAATTAAAATAG
1 AAATAATAATAAAAATAA
* * * **
6589193 ATATTAGAATTCAAATAA
1 AAATAATAATAAAAATAA
*
6589211 AAATAAAAATAAAAATAA
1 AAATAATAATAAAAATAA
6589229 AA
1 AA
6589231 CAACTAACAA
Statistics
Matches: 75, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 75 1.00
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (18 bp):
AAATAATAATAAAAATAA
Found at i:6589417 original size:3 final size:3
Alignment explanation
Indices: 6589411--6589474 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
6589401 ACGTAATTTA
* *
6589411 AAT AAT AAG AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
6589459 AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT A
6589475 GGATTAAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:6589522 original size:7 final size:6
Alignment explanation
Indices: 6589498--6589545 Score: 51
Period size: 6 Copynumber: 7.5 Consensus size: 6
6589488 TTTGGAATTC
* *
6589498 AAATAA AAATAA AAATAA AACATAA AACACTAC AAATAG AAATAA AAA
1 AAATAA AAATAA AAATAA AA-ATAA AA-A-TAA AAATAA AAATAA AAA
6589546 AAGAAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
6 24 0.65
7 9 0.24
8 4 0.11
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:6590778 original size:18 final size:20
Alignment explanation
Indices: 6590755--6590792 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6590745 ACTTTTAATA
6590755 ATTTTTG-TT-TTTATTTAT
1 ATTTTTGTTTATTTATTTAT
6590773 ATTTTTGTTTATTTATTTAT
1 ATTTTTGTTTATTTATTTAT
6590793 TTCTGATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 2 0.11
20 9 0.50
ACGTcount: A:0.18, C:0.00, G:0.05, T:0.76
Consensus pattern (20 bp):
ATTTTTGTTTATTTATTTAT
Found at i:6591834 original size:25 final size:24
Alignment explanation
Indices: 6591790--6591836 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
6591780 ATTACTAAAA
*
6591790 ACTATATTTTAAAATTTTTAATAG
1 ACTATATTTTAAAATGTTTAATAG
6591814 ACTATATATTTAAACA-GTTTAAT
1 ACTATAT-TTTAAA-ATGTTTAAT
6591837 TATTACTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 12 0.60
26 1 0.05
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (24 bp):
ACTATATTTTAAAATGTTTAATAG
Found at i:6596056 original size:15 final size:15
Alignment explanation
Indices: 6596021--6596049 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
6596011 AAATAAAAGC
6596021 AATAATGATAATAAT
1 AATAATGATAATAAT
6596036 AATAATGATAATAA
1 AATAATGATAATAA
6596050 AACTAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (15 bp):
AATAATGATAATAAT
Found at i:6596119 original size:16 final size:16
Alignment explanation
Indices: 6596064--6596119 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 16
6596054 AATTAATTTT
6596064 TAAAAACAATAA-ATAAA
1 TAAAAACAA-AATA-AAA
*
6596081 TAAAAAGACAAATAATAA
1 TAAAAACA-AAATAA-AA
*
6596099 AAAAAACAAAATAAAA
1 TAAAAACAAAATAAAA
6596115 TAAAA
1 TAAAA
6596120 CGGGACTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 6 0.19
17 16 0.50
18 10 0.31
ACGTcount: A:0.79, C:0.05, G:0.02, T:0.14
Consensus pattern (16 bp):
TAAAAACAAAATAAAA
Found at i:6599275 original size:10 final size:9
Alignment explanation
Indices: 6599243--6599318 Score: 64
Period size: 10 Copynumber: 7.9 Consensus size: 9
6599233 GAATAACCCT
6599243 TAAATAATTA
1 TAAA-AATTA
6599253 TAAAAA-TA
1 TAAAAATTA
*
6599261 AAAAAATTTA
1 TAAAAA-TTA
6599271 TAAAAATTA
1 TAAAAATTA
*
6599280 TATAAGATTA
1 TA-AAAATTA
6599290 TAATAAATTA
1 TAA-AAATTA
*
6599300 TTAAAAGTTA
1 -TAAAAATTA
6599310 TAAATAATT
1 TAAA-AATT
6599319 GTCATCTAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
8 7 0.13
9 12 0.22
10 32 0.59
11 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (9 bp):
TAAAAATTA
Found at i:6599653 original size:10 final size:10
Alignment explanation
Indices: 6599638--6599681 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
6599628 CCATTTTGTT
6599638 TTATAAAAAA
1 TTATAAAAAA
6599648 TTAT-AAAAA
1 TTATAAAAAA
*
6599657 TTATAGAAAA
1 TTATAAAAAA
*
6599667 -TATGAAAAA
1 TTATAAAAAA
6599676 TTATAA
1 TTATAA
6599682 TTTTTGTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 16 0.57
10 12 0.43
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:6599666 original size:19 final size:19
Alignment explanation
Indices: 6599638--6599681 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
6599628 CCATTTTGTT
6599638 TTATAAAAAATTAT-AAAAA
1 TTATAAAAAA-TATGAAAAA
*
6599657 TTATAGAAAATATGAAAAA
1 TTATAAAAAATATGAAAAA
6599676 TTATAA
1 TTATAA
6599682 TTTTTGTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (19 bp):
TTATAAAAAATATGAAAAA
Found at i:6600340 original size:16 final size:16
Alignment explanation
Indices: 6600319--6600351 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
6600309 ACTTTTTTCC
6600319 TTTTACTTCCCAAAAT
1 TTTTACTTCCCAAAAT
*
6600335 TTTTACTTCCCCAAAT
1 TTTTACTTCCCAAAAT
6600351 T
1 T
6600352 CCCAAACTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.27, G:0.00, T:0.45
Consensus pattern (16 bp):
TTTTACTTCCCAAAAT
Found at i:6600376 original size:48 final size:50
Alignment explanation
Indices: 6600274--6600392 Score: 143
Period size: 48 Copynumber: 2.4 Consensus size: 50
6600264 CTTTTACTTT
* *
6600274 TTCCCAAAAAATTTACCTTCCCCAATACCTCCAAAACTTTTTTCCTTTTAC
1 TTCCCAAAAATTTTA-CTTCCCCAATACCTCCAAAACTTTTCTCCTTTTAC
* * * *
6600325 TTCCCAAAATTTTTACTTCCCCAA-A-TTCCCAAACTTTTCTCCTTTTGC
1 TTCCCAAAAATTTTACTTCCCCAATACCTCCAAAACTTTTCTCCTTTTAC
* *
6600373 TTCCCCAAACTTTTACTTCC
1 TTCCCAAAAATTTTACTTCC
6600393 TCCTAAACCC
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 37 0.62
49 1 0.02
50 9 0.15
51 13 0.22
ACGTcount: A:0.25, C:0.34, G:0.01, T:0.39
Consensus pattern (50 bp):
TTCCCAAAAATTTTACTTCCCCAATACCTCCAAAACTTTTCTCCTTTTAC
Done.