Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 137 of 318
Found at i:41924787 original size:22 final size:22
Alignment explanation
Indices: 41924735--41924799 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
41924725 TTAAAGCCTT
* *
41924735 CTGATTATGGCTTTGTGTCAAC
1 CTGATTATGGCTCTGTGCCAAC
*
41924757 CT-ACATATGGCTCTGTGCCAAC
1 CTGA-TTATGGCTCTGTGCCAAC
* *
41924779 CTGATTATGGCTGTGTACCAA
1 CTGATTATGGCTCTGTGCCAA
41924800 ACGTATTTGC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 33 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (22 bp):
CTGATTATGGCTCTGTGCCAAC
Found at i:41924988 original size:27 final size:27
Alignment explanation
Indices: 41924958--41925059 Score: 116
Period size: 27 Copynumber: 3.8 Consensus size: 27
41924948 ATTCTGTTAA
* *
41924958 GTGGCTTTGCCACATTATCTGTTTTTG
1 GTGGCTCTGCCACAATATCTGTTTTTG
* *
41924985 GTGGCTATGCCACAAATATCTG-TTCTG
1 GTGGCTCTGCCAC-AATATCTGTTTTTG
* *
41925012 ATGGCTCTGCCACAATATCTGTATTTG
1 GTGGCTCTGCCACAATATCTGTTTTTG
* *
41925039 GTGACTCTGTCACAATATCTG
1 GTGGCTCTGCCACAATATCTG
41925060 ATAACTGAGC
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
26 8 0.13
27 48 0.76
28 7 0.11
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.38
Consensus pattern (27 bp):
GTGGCTCTGCCACAATATCTGTTTTTG
Found at i:41925205 original size:6 final size:6
Alignment explanation
Indices: 41925196--41925376 Score: 158
Period size: 6 Copynumber: 29.8 Consensus size: 6
41925186 TTGCATTCAC
* * * * *
41925196 ATTCTG ATTCTG ATTCT- ATCACCTA ATTCTG ATTTTG -TTACTA ATACTG
1 ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATT-CTG ATTCTG
* *
41925245 ATTCTG ATTCTG ATTCTG -TTACTG ATTCTG ATTCTG ATTCTG -TCACCTA
1 ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG AT--TCTG
* * *
41925294 ATTCTG ATTCTG ATTCTG ATTCTG -TTACTA ATACTG ATTTTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG
41925342 ATTCTG -TTACTG ATTCTG ATTCTG ATTCTG ATTCT
1 ATTCTG ATT-CTG ATTCTG ATTCTG ATTCTG ATTCT
41925377 CATTTTGGTT
Statistics
Matches: 142, Mismatches: 19, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
5 11 0.08
6 118 0.83
7 10 0.07
8 3 0.02
ACGTcount: A:0.20, C:0.18, G:0.13, T:0.49
Consensus pattern (6 bp):
ATTCTG
Found at i:41925257 original size:30 final size:30
Alignment explanation
Indices: 41925221--41925376 Score: 207
Period size: 30 Copynumber: 5.4 Consensus size: 30
41925211 CTATCACCTA
*
41925221 ATTCTGATTTTGTTACTAATACTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
41925251 ATTCTGATTCTG----T--TACTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
* *
41925275 ATTCTGATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGATTCTGTTA-CTAATACTGATTCTG
*
41925306 ATTCTGATTCTGTTACTAATACTGATTTTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
* *
41925336 ATTCTGATTCTGTTACTGATTCTGATTCTG
1 ATTCTGATTCTGTTACTAATACTGATTCTG
41925366 ATTCTGATTCT
1 ATTCTGATTCT
41925377 CATTTTGGTT
Statistics
Matches: 111, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
24 23 0.21
26 1 0.01
29 1 0.01
30 62 0.56
31 24 0.22
ACGTcount: A:0.20, C:0.17, G:0.14, T:0.49
Consensus pattern (30 bp):
ATTCTGATTCTGTTACTAATACTGATTCTG
Found at i:41925331 original size:73 final size:73
Alignment explanation
Indices: 41925196--41925359 Score: 201
Period size: 73 Copynumber: 2.2 Consensus size: 73
41925186 TTGCATTCAC
* * * *
41925196 ATTCTGATTCTGATTCTATCACCTAATTCTGATTTTGTTACTAATACTGATTCTGATTCTGATTC
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGTTACTAATACTGATTCTAATACTGATTC
41925261 TG-TTACTG
66 TGATT-CTG
* *
41925269 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGATT-CTGATTCTG-TTACTAATACTGAT
1 ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTG-TTACTAATACTGATT-CTAATACTGAT
*
41925332 TTTGATTCTG
64 TCTGATTCTG
41925342 ATTCTG-TTACTGATTCTG
1 ATTCTGATT-CTGATTCTG
41925360 ATTCTGATTC
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
72 4 0.05
73 72 0.90
74 4 0.05
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (73 bp):
ATTCTGATTCTGATTCTGTCACCTAATTCTGATTCTGTTACTAATACTGATTCTAATACTGATTC
TGATTCTG
Found at i:41932871 original size:30 final size:30
Alignment explanation
Indices: 41932837--41932919 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
41932827 TAAACTAAAA
41932837 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
41932867 TGAGCTGAGGC-TAAACTCTTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
*
41932897 TGAGCTAAGGTTTAGCTCGTGAG
1 TGAGCTAAGCTTTAGCTCGTGAG
41932920 TTGAAAGTGA
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
29 2 0.05
30 34 0.87
31 3 0.08
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:41934116 original size:31 final size:30
Alignment explanation
Indices: 41934081--41934142 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
41934071 TCCTTAACTC
41934081 AAACTTTGGCAAAAATTACAATTTTGCCCCT
1 AAACTTTGGC-AAAATTACAATTTTGCCCCT
* * * *
41934112 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGCAAAATTACAATTTTGCCCCT
41934142 A
1 A
41934143 GGCTCAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.31, C:0.24, G:0.08, T:0.37
Consensus pattern (30 bp):
AAACTTTGGCAAAATTACAATTTTGCCCCT
Found at i:41936557 original size:24 final size:24
Alignment explanation
Indices: 41936502--41936630 Score: 108
Period size: 24 Copynumber: 5.5 Consensus size: 24
41936492 AAGTCATGGT
*
41936502 CGGTAAGCTCCACTTGAGCTGATAAA
1 CGGTAAGCTCTA-TTGAGCTGA-AAA
* *
41936528 CAGTAAGCTCTATTAAGCTGAAAA
1 CGGTAAGCTCTATTGAGCTGAAAA
41936552 CGGTAAGCTCTATTGAGCTGAACAA
1 CGGTAAGCTCTATTGAGCTGAA-AA
* *
41936577 ---TAAGCTCTTTTGAGCTGAATTA
1 CGGTAAGCTCTATTGAGCTGAA-AA
* *
41936599 --GTAAGCTCCAATGAGCTG-AAA
1 CGGTAAGCTCTATTGAGCTGAAAA
*
41936620 CAGTAAGCTCT
1 CGGTAAGCTCT
41936631 TACGAGCTCT
Statistics
Matches: 86, Mismatches: 13, Indels: 11
0.78 0.12 0.10
Matches are distributed among these distances:
21 1 0.01
22 20 0.23
23 22 0.26
24 23 0.27
25 10 0.12
26 10 0.12
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (24 bp):
CGGTAAGCTCTATTGAGCTGAAAA
Found at i:41936593 original size:46 final size:48
Alignment explanation
Indices: 41936502--41936631 Score: 151
Period size: 46 Copynumber: 2.7 Consensus size: 48
41936492 AAGTCATGGT
*
41936502 CGGTAAGCTCCACTTGAGCTGATAAACAGTAAGCTCTATTAAGCTGAA-AA
1 CGGTAAGCTCCA-TTGAGCTG--AAACAGTAAGCTCTTTTAAGCTGAATAA
* * * *
41936552 CGGTAAGCTCTATTGAGCTG-AACAATAAGCTCTTTTGAGCTGAATTA
1 CGGTAAGCTCCATTGAGCTGAAACAGTAAGCTCTTTTAAGCTGAATAA
*
41936599 --GTAAGCTCCAATGAGCTGAAACAGTAAGCTCTT
1 CGGTAAGCTCCATTGAGCTGAAACAGTAAGCTCTT
41936632 ACGAGCTCTG
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
45 16 0.23
46 34 0.49
47 1 0.01
49 8 0.11
50 11 0.16
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (48 bp):
CGGTAAGCTCCATTGAGCTGAAACAGTAAGCTCTTTTAAGCTGAATAA
Found at i:41936637 original size:23 final size:23
Alignment explanation
Indices: 41936516--41936638 Score: 99
Period size: 23 Copynumber: 5.3 Consensus size: 23
41936506 AAGCTCCACT
41936516 TGAGCTGATAAACAGTAAGCTC-TA
1 TGAGCTG--AAACAGTAAGCTCTTA
* *
41936540 TTAAGCTGAAAACGGTAAGCTC-TA
1 -TGAGCTG-AAACAGTAAGCTCTTA
* *
41936564 TTGAGCTG-AACAATAAGCTCTTT
1 -TGAGCTGAAACAGTAAGCTCTTA
** **
41936587 TGAGCTGAATTAGTAAGCTCCAA
1 TGAGCTGAAACAGTAAGCTCTTA
41936610 TGAGCTGAAACAGTAAGCTCTTA
1 TGAGCTGAAACAGTAAGCTCTTA
*
41936633 CGAGCT
1 TGAGCT
41936639 CTGGTGAGTC
Statistics
Matches: 78, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 17 0.22
23 34 0.44
24 21 0.27
25 6 0.08
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTTA
Found at i:41938895 original size:66 final size:68
Alignment explanation
Indices: 41938819--41939005 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
41938809 TAGTACCACT
*
41938819 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
41938881 CACG
65 CACG
41938885 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
41938950 ATCACG
63 ATCACG
41938956 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
41939006 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:41938930 original size:71 final size:71
Alignment explanation
Indices: 41938842--41939005 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41938832 CGATTTGTCT
41938842 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41938907 CTTTCA
66 CTTTCA
41938913 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41938978 CTTTCA
66 CTTTCA
41938984 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41939006 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:41939043 original size:71 final size:70
Alignment explanation
Indices: 41938842--41939039 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
41938832 CGATTTGTCT
* * *
41938842 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
41938907 CTTTCA
65 CTTTCA
* * *
41938913 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
41938978 CTTTCA
65 CTTTCA
* *
41938984 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
41939040 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41946462 original size:66 final size:68
Alignment explanation
Indices: 41946386--41946572 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
41946376 TAGTACCACT
*
41946386 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
41946448 CACG
65 CACG
41946452 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
41946517 ATCACG
63 ATCACG
41946523 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
41946573 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:41946497 original size:71 final size:71
Alignment explanation
Indices: 41946409--41946572 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
41946399 CGATTTGTCT
41946409 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41946474 CTTTCA
66 CTTTCA
41946480 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
41946545 CTTTCA
66 CTTTCA
41946551 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
41946573 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:41946610 original size:71 final size:70
Alignment explanation
Indices: 41946409--41946606 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
41946399 CGATTTGTCT
* * *
41946409 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
41946474 CTTTCA
65 CTTTCA
* * *
41946480 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
41946545 CTTTCA
65 CTTTCA
* *
41946551 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
41946607 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:41953201 original size:19 final size:19
Alignment explanation
Indices: 41953177--41953215 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41953167 GAATAAATTG
41953177 ATAAACATATAAAAATTTC
1 ATAAACATATAAAAATTTC
* *
41953196 ATAAACTTATAGAAATTTC
1 ATAAACATATAAAAATTTC
41953215 A
1 A
41953216 ACATTTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAACATATAAAAATTTC
Found at i:41954576 original size:24 final size:25
Alignment explanation
Indices: 41954534--41954592 Score: 75
Period size: 24 Copynumber: 2.4 Consensus size: 25
41954524 TATGCTCCTC
*
41954534 TTGAGCTGATAAACAGTAAGCTCTA
1 TTGAGCTGAAAAACAGTAAGCTCTA
* *
41954559 TTGAGCT-AAAAACGGTAAGCTTTA
1 TTGAGCTGAAAAACAGTAAGCTCTA
*
41954583 CTGAGCTGAA
1 TTGAGCTGAA
41954593 TAATAAGAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (25 bp):
TTGAGCTGAAAAACAGTAAGCTCTA
Found at i:41954625 original size:23 final size:23
Alignment explanation
Indices: 41954599--41954650 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
41954589 TGAATAATAA
*
41954599 GAGCTGAATCACTAAGCTCCAAT
1 GAGCTGAAACACTAAGCTCCAAT
* * **
41954622 GAGCTAAAACAGTAAGCTCTTAT
1 GAGCTGAAACACTAAGCTCCAAT
41954645 GAGCTG
1 GAGCTG
41954651 TGGTGAGTCC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (23 bp):
GAGCTGAAACACTAAGCTCCAAT
Found at i:41957533 original size:30 final size:30
Alignment explanation
Indices: 41957499--41957559 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
41957489 TTCCCGAGCC
41957499 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
41957529 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
41957559 T
1 T
41957560 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:41959361 original size:27 final size:27
Alignment explanation
Indices: 41959315--41959481 Score: 90
Period size: 27 Copynumber: 6.2 Consensus size: 27
41959305 ATTACTGAAA
41959315 TACCCTCGACTTGTA-A-AATTACCAAAG
1 TACCCTCGA-TT-TACAGAATTACCAAAG
****
41959342 TACTCC-CGATTTACAGAATTACCGTTT
1 TAC-CCTCGATTTACAGAATTACCAAAG
***
41959369 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCAAAG
* * * *
41959396 TACCTTCGATTTAAAAAATTACCAAAA
1 TACCCTCGATTTACAGAATTACCAAAG
* * * * *
41959423 TACCCTTGGTTTGCAAAATTACCAAAA
1 TACCCTCGATTTACAGAATTACCAAAG
* * * *
41959450 TATCCCT-GGTTTGCAAAATTACCAAAA
1 TA-CCCTCGATTTACAGAATTACCAAAG
41959477 TACCC
1 TACCC
41959482 CTGGTTTGTA
Statistics
Matches: 119, Mismatches: 16, Indels: 11
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.02
26 8 0.07
27 103 0.87
28 6 0.05
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCAAAG
Found at i:41959483 original size:27 final size:27
Alignment explanation
Indices: 41959410--41959565 Score: 206
Period size: 27 Copynumber: 5.8 Consensus size: 27
41959400 TTCGATTTAA
*
41959410 AAAATTACCAAAATACCCTTGGTTTGC
1 AAAATTACCAAAATACCCCTGGTTTGC
*
41959437 AAAATTACCAAAATATCCCTGGTTTGC
1 AAAATTACCAAAATACCCCTGGTTTGC
*
41959464 AAAATTACCAAAATACCCCTGGTTTGT
1 AAAATTACCAAAATACCCCTGGTTTGC
* *
41959491 AAAACTACCAAAATACCCATGGTTTGC
1 AAAATTACCAAAATACCCCTGGTTTGC
* ** *
41959518 AAAATTACTAAAATACCCCT-GTAGGGT
1 AAAATTACCAAAATACCCCTGGT-TTGC
*
41959545 AAAATTACCGAAATACCCCTG
1 AAAATTACCAAAATACCCCTG
41959566 TAAGGTAGAA
Statistics
Matches: 112, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
26 2 0.02
27 110 0.98
ACGTcount: A:0.39, C:0.23, G:0.12, T:0.26
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTGGTTTGC
Found at i:41965830 original size:68 final size:66
Alignment explanation
Indices: 41965758--41965929 Score: 170
Period size: 67 Copynumber: 2.6 Consensus size: 66
41965748 CATCATGTGT
* * * *
41965758 ACAAGAGAGCTACAAGACATTATGATGTAGCTAGGTCGCATGGGTGATACTA-TG-TGTACACCA
1 ACAAGAGAGCTAC--GACA-TAT-ATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCA
41965821 TGTAG
62 TGTAG
** * *
41965826 ACAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGT
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCA-GTGAAGGACACCATGT
41965891 AG
65 AG
* * * *
41965893 ACAAGAGAGCTACGAGATAAAT-TGGCTAGGTCACATG
1 ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATG
41965930 GGTGGTACTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
64 24 0.27
65 3 0.03
66 17 0.19
67 32 0.36
68 13 0.15
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (66 bp):
ACAAGAGAGCTACGACATATATGTAGCTAGGTCGCATGCGTGATACCAGTGAAGGACACCATGTA
G
Found at i:41965863 original size:64 final size:64
Alignment explanation
Indices: 41965782--41965965 Score: 203
Period size: 67 Copynumber: 2.8 Consensus size: 64
41965772 AGACATTATG
* * *
41965782 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * *
41965846 ATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGTGGTACTA--TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
41965911 AA
63 AA
* * *
41965913 AT-TGGCTAGGTCACATGGGTGGTACTGA-GTGTTCACCATGT-GTACAAGAGAGC
1 ATGTAGCTAGGTCGCATGGGTGGTACT-ATGTGTACACCATGTAG-ACAAGAGAGC
41965966 CGAACTATAT
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.19
64 25 0.25
66 21 0.21
67 33 0.33
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGGTACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:41971457 original size:27 final size:28
Alignment explanation
Indices: 41971427--41971516 Score: 105
Period size: 27 Copynumber: 3.3 Consensus size: 28
41971417 TTTAGTTTAC
41971427 TAAAATTACCGAAATACCCTTAG-TTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
41971454 TAAAAATACTGAAATACCC-TCGATTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
* * *
41971481 TAAATTTACCGAAATA-CCTTCGACTTG
1 TAAAATTACCGAAATACCCTTAGATTTG
41971508 TAAAATTAC
1 TAAAATTAC
41971517 TAAAGTACCC
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 4 0.08
27 49 0.92
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (28 bp):
TAAAATTACCGAAATACCCTTAGATTTG
Found at i:41971525 original size:27 final size:26
Alignment explanation
Indices: 41971451--41971526 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
41971441 TACCCTTAGT
* *
41971451 TTGTAAAAATACTGAAATACCCTCGAT
1 TTGTAAAATTACT-AAATACCCTCGAC
* * *
41971478 TTGTAAATTTACCGAAATACCTTCGAC
1 TTGTAAAATTA-CTAAATACCCTCGAC
41971505 TTGTAAAATTACTAAAGTACCC
1 TTGTAAAATTACTAAA-TACCC
41971527 CGATTTACAG
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
26 4 0.10
27 34 0.87
28 1 0.03
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.32
Consensus pattern (26 bp):
TTGTAAAATTACTAAATACCCTCGAC
Found at i:41971532 original size:53 final size:54
Alignment explanation
Indices: 41971427--41971532 Score: 137
Period size: 54 Copynumber: 2.0 Consensus size: 54
41971417 TTTAGTTTAC
*
41971427 TAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTGAAATACCCTCGATTTG
* * *
41971481 TAAATTTACCGAAATA-CCTTCGACTTGTAAAATTACT-AAAGTACCC-CGATTT
1 TAAAATTACCGAAATACCCTTAG-CTTGTAAAAATACTGAAA-TACCCTCGATTT
41971533 ACAGAATTAC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
53 14 0.30
54 32 0.70
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.32
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTAGCTTGTAAAAATACTGAAATACCCTCGATTTG
Found at i:41971543 original size:53 final size:53
Alignment explanation
Indices: 41971429--41971544 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 53
41971419 TAGTTTACTA
* **
41971429 AAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTGT
1 AAATTACCGAAATACCCTTAGCTTGTAAAAATACTGAAATACCCTCGATTTAC
* *
41971482 AAATTTACCGAAATA-CCTTCGACTTGTAAAATTACT-AAAGTACCC-CGATTTAC
1 AAA-TTACCGAAATACCCTTAG-CTTGTAAAAATACTGAAA-TACCCTCGATTTAC
41971535 AGAATTACCG
1 A-AATTACCG
41971545 TTTTACCCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
53 24 0.44
54 30 0.56
ACGTcount: A:0.38, C:0.21, G:0.11, T:0.30
Consensus pattern (53 bp):
AAATTACCGAAATACCCTTAGCTTGTAAAAATACTGAAATACCCTCGATTTAC
Found at i:41971567 original size:27 final size:27
Alignment explanation
Indices: 41971522--41971811 Score: 374
Period size: 27 Copynumber: 10.8 Consensus size: 27
41971512 ATTACTAAAG
*
41971522 TACCCC-GATTTACAGAATTACCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
* *
41971548 TACCCCTAATTTACATAATTATCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
41971575 TACCCCTGATTTACATAATTATCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
* *
41971602 TA-CCCTCGACTTACAGAATTACCGTTT
1 TACCCCT-GATTTACATAATTACCGTTT
*
41971629 TACCCCTAATTTACATAATTACCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
41971656 TACCCCTGATTTACATAATTATCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
* *
41971683 TA-CCCTCGACTTACAGAATTACCGTTT
1 TACCCCT-GATTTACATAATTACCGTTT
*
41971710 TACCCCTAATTTACATAATTACCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
41971737 TACCCCTGATTTACATAATTATCGTTT
1 TACCCCTGATTTACATAATTACCGTTT
* * *
41971764 TA-CCTTGATTTACAGAATTACTGTTT
1 TACCCCTGATTTACATAATTACCGTTT
*
41971790 TA-CCCTCGATTTACAAAATTAC
1 TACCCCT-GATTTACATAATTAC
41971812 TAAAATACCC
Statistics
Matches: 232, Mismatches: 26, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
26 39 0.17
27 185 0.80
28 8 0.03
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCCTGATTTACATAATTACCGTTT
Found at i:41971626 original size:81 final size:81
Alignment explanation
Indices: 41971522--41971811 Score: 487
Period size: 81 Copynumber: 3.6 Consensus size: 81
41971512 ATTACTAAAG
* *
41971522 TACCC-CGATTTACAGAATTACCGTTTTACCCCTAATTTACATAATTATCGTTTTACCCCTGATT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
41971586 TACATAATTATCGTTT
66 TACATAATTATCGTTT
41971602 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
41971667 TACATAATTATCGTTT
66 TACATAATTATCGTTT
41971683 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
41971748 TACATAATTATCGTTT
66 TACATAATTATCGTTT
* * * * *
41971764 TA-CCTTGATTTACAGAATTACTGTTTTA-CCCTCGATTTACAAAATTAC
1 TACCCTCGACTTACAGAATTACCGTTTTACCCCT-AATTTACATAATTAC
41971812 TAAAATACCC
Statistics
Matches: 201, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
79 4 0.02
80 41 0.20
81 156 0.78
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (81 bp):
TACCCTCGACTTACAGAATTACCGTTTTACCCCTAATTTACATAATTACCGTTTTACCCCTGATT
TACATAATTATCGTTT
Found at i:41971930 original size:27 final size:27
Alignment explanation
Indices: 41971882--41971946 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
41971872 ACCCCTATTA
41971882 GGTAAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAGTGACCGTAAAGCCCCTGTAG
* *
41971909 GGTAAAGTGACCGTGATA-CCCCTGTAT
1 GGTAAAGTGACCGT-AAAGCCCCTGTAG
*
41971936 GGTAAAATGAC
1 GGTAAAGTGAC
41971947 GAATATGCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.94
28 2 0.06
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.22
Consensus pattern (27 bp):
GGTAAAGTGACCGTAAAGCCCCTGTAG
Found at i:41973134 original size:24 final size:25
Alignment explanation
Indices: 41973103--41973149 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
41973093 TTATAATATG
* *
41973103 AAAATGACC-TTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
41973127 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
41973150 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:41973233 original size:11 final size:11
Alignment explanation
Indices: 41973197--41973252 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
41973187 TATGGTATGT
41973197 ATGATATGCAC
1 ATGATATGCAC
* *
41973208 ATGAAATG--T
1 ATGATATGCAC
41973217 ATGATATGCAC
1 ATGATATGCAC
*
41973228 ATGATATG--T
1 ATGATATGCAC
41973237 ATGATATGCAC
1 ATGATATGCAC
41973248 ATGAT
1 ATGAT
41973253 GTAATCATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:41973252 original size:20 final size:20
Alignment explanation
Indices: 41973192--41973252 Score: 113
Period size: 20 Copynumber: 3.0 Consensus size: 20
41973182 ATAAATATGG
41973192 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
*
41973212 AATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
41973232 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
41973252 T
1 T
41973253 GTAATCATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.20, T:0.34
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:41973329 original size:24 final size:24
Alignment explanation
Indices: 41973302--41973454 Score: 254
Period size: 24 Copynumber: 6.4 Consensus size: 24
41973292 GAGGAAGTGA
41973302 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
41973326 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
41973350 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
41973374 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
41973397 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
41973421 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
41973445 AAAAGAGGCT
1 AAAAG-GGCT
41973455 AGGCCTCTAG
Statistics
Matches: 124, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
23 23 0.19
24 97 0.78
25 4 0.03
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:41973695 original size:31 final size:31
Alignment explanation
Indices: 41973660--41973754 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
41973650 CGTTTACAGT
41973660 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41973691 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
41973722 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
41973753 AA
1 AA
41973755 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:41976108 original size:30 final size:30
Alignment explanation
Indices: 41976074--41976134 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
41976064 TTCCCGAGCC
41976074 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
* * * *
41976104 TAGGGGCAAAATTGTAATTTTTCAAAAGTT
1 TAGGGGCAAAAGTGTAAATATGCAAAAGTT
41976134 T
1 T
41976135 GAGTTAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.31
Consensus pattern (30 bp):
TAGGGGCAAAAGTGTAAATATGCAAAAGTT
Found at i:41978241 original size:939 final size:937
Alignment explanation
Indices: 41976844--41978712 Score: 3299
Period size: 939 Copynumber: 2.0 Consensus size: 937
41976834 ATGTGTACAA
*
41976844 GAGAGCTACAAGACATTATGATGTAGCTAGGTAACATGGGTGATACTATGTGTACACCATGTAGA
1 GAGAGCTACAAGACATTATGATGTAGCAAGGTAACATGGGTGATACTATGTGTACACCATGTAGA
* *
41976909 CAAGAGAGCTATGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACACCATGTA
66 CAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACAACATGTA
41976974 GACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTCGTACTGAGTGTTCACCATGTGTA
131 GACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTCGTACTGAGTGTTCACCATGTGTA
** * *
41977039 CAAGGGAGTCGAACTATATGATGGGTGGAGCTATGTGCTGAAACCACCAAGTATCGAGGATTGAT
196 CAAGAAAGCCGAAATATATGATGGGTGGAGCTATGTGCTGAAACCACCAAGTATCGAGGATTGAT
*
41977104 CCGAAGTGTTCAACTGGAGACTCTCAATGTATTGCTTTGTGAGTTTTGTGATGAATAAGTGTAGG
261 CCGAAGTGTTCAACTGGAGACTCTCAATGTATTGCTTTGTGAGTTTTGTGATGAATAAGTGCAGG
*
41977169 AACTTGGTTATGTGAATGATATGTTCATTAAATGACCAGGATGTGGGAAGGTTATAAACAAGTAA
326 AACTTGGTTATGTGAATGATATGTTCATTAAATGACCAAGATGTGGGAAGGTTATAAACAAGTAA
*
41977234 GTTATAAATGAGGGTGATTTTATGGTGACCTTGTGATCATGGGCCTATACTTGCGATGTATGAAA
391 GTTATAAATGAGGGTGATTCTATGGTGACCTTGTGATCATGGGCCTATACTTGCGATGTATGAAA
41977299 TGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGGTTAATACAAAGAAAGTGTGAAAGAG
456 TGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGGTTAATACAAAGAAAGTGTG--AGAG
*
41977364 TGAATTAGCAATAAAACTGTTTTGGACAGTAGCAGTGACGTGATTTTGAAAAATCACCAAAAATA
519 TGAATTAGCAATAAAACTATTTTGGACAGTAGCAGTGACGTGATTTTGAAAAATCACCAAAAATA
* *
41977429 GTAGAAATTGAATCAGAGACTTAATAAGATATCAAATTAAATCTTAATGAGTCTATTTTCATATA
584 GTAGAAATTGAATCAGAGACTGAATAAGATATAAAATTAAATCTTAATGAGTCTATTTTCATATA
41977494 AAAGAAACAGATAAAGAAAAGAAGTTCTATATTTTGAGATATTTATGTTTTTGTGAGACTGGTTC
649 AAAGAAACAGATAAAGAAAAGAAGTTCTATATTTTGAGATATTTATGTTTTTGTGAGACTGGTTC
41977559 AGAATGATTACGTGATCCCCTGTTCTGACTTTAGAAAATCACAAAAATTTGGATAAACATAATTA
714 AGAATGATTACGTGATCCCCTGTTCTGACTTTAGAAAATCACAAAAATTTGGATAAACATAATTA
* * * *
41977624 GAGGCTTAAACTTATATTTTTAAAATCCCTAATGAGTTTATTTTCAAGATAAATCAACCAA-AAC
779 GAGGCTTAAACTTATATATTTAAAATCCATAATGAGTCTATTTTCAAGATAAATCAA-CAAGAAA
* * *
41977688 ATTATTCGAGTTCTGTACTGTGAGATAATTAATTTTTAGTGAAGAGAAGTCAGAACTGTCAGAAT
843 ATTATCCGAGGTCTGTACTGTGAGATAATTAATTTTTAGTGAAGAGAAGTCAGAACTATCAGAAT
41977753 GTGAAACAGGAGAAATTTTAATGTGTAATG
908 GTGAAACAGGAGAAATTTTAATGTGTAATG
* **
41977783 GAGAGCTAGAAGACATTATGATGTAGCAAGGTCGCATGGGTGATACTATGTGTACACCATGTAGA
1 GAGAGCTACAAGACATTATGATGTAGCAAGGTAACATGGGTGATACTATGTGTACACCATGTAGA
* *
41977848 CAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGTGTGGTTCCAGGTGAAGGACAAGATGTA
66 CAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACAACATGTA
* *
41977913 GACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTGGTATTGAGTGTTCACCATGTGTA
131 GACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTCGTACTGAGTGTTCACCATGTGTA
41977978 CAAGAAAGCCGAAATATATGATGGGTGGAGCTATGTGCTGAAACCACCAAGTATCGAGGATTGAT
196 CAAGAAAGCCGAAATATATGATGGGTGGAGCTATGTGCTGAAACCACCAAGTATCGAGGATTGAT
*
41978043 CCGAAGTGTTCAACTGGAGACTCTCAATGTCTTGCTTTGTGAGTTTTGTGATGAATAAGTGCAGG
261 CCGAAGTGTTCAACTGGAGACTCTCAATGTATTGCTTTGTGAGTTTTGTGATGAATAAGTGCAGG
* *
41978108 AACTTGGTTATGTGAATGATATGTTCATTAAGTGACCAAGATGTGGTAAGGTTATAAACAAGTAA
326 AACTTGGTTATGTGAATGATATGTTCATTAAATGACCAAGATGTGGGAAGGTTATAAACAAGTAA
* *
41978173 GTTATAAATGAGGGTGATTCTATGGTGACCTTGTGATCATGGGTCTATACTTGTGATGTATGAAA
391 GTTATAAATGAGGGTGATTCTATGGTGACCTTGTGATCATGGGCCTATACTTGCGATGTATGAAA
41978238 TGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGGTTAATACAAAGAAAGTGTGAGAGTG
456 TGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGGTTAATACAAAGAAAGTGTGAGAGTG
* *
41978303 AATTAGCAATAAAACTATTTTGGACAGTAGGAGTGATGTGATTTTGAAAAATCACCAAAAATAGT
521 AATTAGCAATAAAACTATTTTGGACAGTAGCAGTGACGTGATTTTGAAAAATCACCAAAAATAGT
* * *
41978368 AGAAATTTAATTAGAGACTGAATGAGATATAAAATTAAATCTTAATGAGTCTATTTTCATATAAA
586 AGAAATTGAATCAGAGACTGAATAAGATATAAAATTAAATCTTAATGAGTCTATTTTCATATAAA
* * *
41978433 AGAAACAGATGAAGAAAATAAGTTCTGTATTTTGAGATATTTATGTTTTTGTGAGACTGGTTCAG
651 AGAAACAGATAAAGAAAAGAAGTTCTATATTTTGAGATATTTATGTTTTTGTGAGACTGGTTCAG
* *
41978498 AATGATTACGTGATCCCTTGTTCTGACTTTGGAAAATCACAAAAATTTGGATAAACATAATTAGA
716 AATGATTACGTGATCCCCTGTTCTGACTTTAGAAAATCACAAAAATTTGGATAAACATAATTAGA
*
41978563 GGCTTAAACTTATATATTTAAAATCTATAATGAGTCTATTTTCAAGATAAATCAACAAGAAAATT
781 GGCTTAAACTTATATATTTAAAATCCATAATGAGTCTATTTTCAAGATAAATCAACAAGAAAATT
* *
41978628 ATCCGAGGTCTGTACTGTGAGATAATTAATTTTTAGTGAAGAGAGGTTAGAACTATCAGAATGTG
846 ATCCGAGGTCTGTACTGTGAGATAATTAATTTTTAGTGAAGAGAAGTCAGAACTATCAGAATGTG
41978693 AAACAGGAGAAATTTTAATG
911 AAACAGGAGAAATTTTAATG
41978713 AATAAACTGT
Statistics
Matches: 884, Mismatches: 45, Indels: 4
0.95 0.05 0.00
Matches are distributed among these distances:
936 3 0.00
937 389 0.44
939 492 0.56
ACGTcount: A:0.35, C:0.11, G:0.23, T:0.31
Consensus pattern (937 bp):
GAGAGCTACAAGACATTATGATGTAGCAAGGTAACATGGGTGATACTATGTGTACACCATGTAGA
CAAGAGAGCTACGGGATATATGTAGCTAGGTCGCATGCGTGGTTCCAGGTGAAGGACAACATGTA
GACAAGAGAGCTACGAGATAAATTGGCTAGGTCACATGGGTCGTACTGAGTGTTCACCATGTGTA
CAAGAAAGCCGAAATATATGATGGGTGGAGCTATGTGCTGAAACCACCAAGTATCGAGGATTGAT
CCGAAGTGTTCAACTGGAGACTCTCAATGTATTGCTTTGTGAGTTTTGTGATGAATAAGTGCAGG
AACTTGGTTATGTGAATGATATGTTCATTAAATGACCAAGATGTGGGAAGGTTATAAACAAGTAA
GTTATAAATGAGGGTGATTCTATGGTGACCTTGTGATCATGGGCCTATACTTGCGATGTATGAAA
TGTGGTGAAAATGATTTGTGATATGTATGTTAAAATGAGGTTAATACAAAGAAAGTGTGAGAGTG
AATTAGCAATAAAACTATTTTGGACAGTAGCAGTGACGTGATTTTGAAAAATCACCAAAAATAGT
AGAAATTGAATCAGAGACTGAATAAGATATAAAATTAAATCTTAATGAGTCTATTTTCATATAAA
AGAAACAGATAAAGAAAAGAAGTTCTATATTTTGAGATATTTATGTTTTTGTGAGACTGGTTCAG
AATGATTACGTGATCCCCTGTTCTGACTTTAGAAAATCACAAAAATTTGGATAAACATAATTAGA
GGCTTAAACTTATATATTTAAAATCCATAATGAGTCTATTTTCAAGATAAATCAACAAGAAAATT
ATCCGAGGTCTGTACTGTGAGATAATTAATTTTTAGTGAAGAGAAGTCAGAACTATCAGAATGTG
AAACAGGAGAAATTTTAATGTGTAATG
Found at i:41980491 original size:29 final size:29
Alignment explanation
Indices: 41980458--41980618 Score: 178
Period size: 29 Copynumber: 5.6 Consensus size: 29
41980448 GTGACGAGAT
*
41980458 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
41980487 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
41980516 TGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
41980545 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* ** * * ***
41980574 CGGCACTGGGTGTGCGAGCTCGAAGGGTA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
41980603 TGGCACTATGTGTGCG
1 TGGCACTAAGTGTGCG
41980619 GGCTTAAATT
Statistics
Matches: 115, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 115 1.00
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:41987810 original size:40 final size:40
Alignment explanation
Indices: 41987702--41987871 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
41987692 CGGGATTTAA
* * * * *
41987702 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
41987742 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
41987782 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
41987822 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
41987862 CCGGATATAT
1 CCGGATATAT
41987872 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:41995905 original size:40 final size:40
Alignment explanation
Indices: 41995797--41995966 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
41995787 CGGGATTTAA
* * * * *
41995797 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
41995837 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
41995877 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
41995917 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
41995957 CCGGATATAT
1 CCGGATATAT
41995967 TTCCAATGTT
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
39 1 0.01
40 112 0.99
ACGTcount: A:0.22, C:0.28, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:41998662 original size:15 final size:15
Alignment explanation
Indices: 41998642--41998670 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41998632 TTGGATGGTT
41998642 TTAATAATTTTGAGG
1 TTAATAATTTTGAGG
41998657 TTAATAATTTTGAG
1 TTAATAATTTTGAG
41998671 ACATGTTTGA
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:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (15 bp):
TTAATAATTTTGAGG
Found at i:41999285 original size:18 final size:18
Alignment explanation
Indices: 41999262--41999300 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
41999252 TTTTTCAACT
41999262 GGTATTCTAATTTGTTTA
1 GGTATTCTAATTTGTTTA
41999280 GGTATTCTAATTTGTTTA
1 GGTATTCTAATTTGTTTA
41999298 GGT
1 GGT
41999301 TACATTTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.54
Consensus pattern (18 bp):
GGTATTCTAATTTGTTTA
Found at i:42007920 original size:28 final size:28
Alignment explanation
Indices: 42007838--42007976 Score: 197
Period size: 28 Copynumber: 4.9 Consensus size: 28
42007828 CGCATACTCG
* *
42007838 ATGTCTTGCACACTAAGTGCCACAATCA
1 ATGTCTCGCACACTAAGTGCCATAATCA
* *
42007866 ACGTCTTGCACTTTACTAAGTGCCATAATCA
1 ATGTCTCGCAC---ACTAAGTGCCATAATCA
42007897 ATGTCTCGCACACTAAGTGCCATAATCA
1 ATGTCTCGCACACTAAGTGCCATAATCA
*
42007925 ATGTCTCGCACACTAAGTGGCATAATCA
1 ATGTCTCGCACACTAAGTGCCATAATCA
*
42007953 ATGTCTCGCACACTAAGTGTCATA
1 ATGTCTCGCACACTAAGTGCCATA
42007977 CATAGTCGAA
Statistics
Matches: 102, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
28 77 0.75
31 25 0.25
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (28 bp):
ATGTCTCGCACACTAAGTGCCATAATCA
Found at i:42007961 original size:56 final size:57
Alignment explanation
Indices: 42007829--42007976 Score: 199
Period size: 59 Copynumber: 2.6 Consensus size: 57
42007819 GAATGTCGTC
* * * * *
42007829 GCATACTCGATGTCTTGCACACTAAGTGCCACAATCAACGTCTTGCACTTTACTAAGTG
1 GCATAATCAATGTCTCGCACACTAAGTGCCATAATCAACGTCTCGCAC--TACTAAGTG
* *
42007888 CCATAATCAATGTCTCGCACACTAAGTGCCATAATCAATGTCTCGCAC-ACTAAGTG
1 GCATAATCAATGTCTCGCACACTAAGTGCCATAATCAACGTCTCGCACTACTAAGTG
*
42007944 GCATAATCAATGTCTCGCACACTAAGTGTCATA
1 GCATAATCAATGTCTCGCACACTAAGTGCCATA
42007977 CATAGTCGAA
Statistics
Matches: 80, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
56 39 0.49
59 41 0.51
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (57 bp):
GCATAATCAATGTCTCGCACACTAAGTGCCATAATCAACGTCTCGCACTACTAAGTG
Found at i:42008817 original size:14 final size:14
Alignment explanation
Indices: 42008798--42008860 Score: 67
Period size: 14 Copynumber: 4.6 Consensus size: 14
42008788 AATTATTGAT
42008798 TTACTAATTTAACC
1 TTACTAATTTAACC
*
42008812 TTACTAATTTAAAC
1 TTACTAATTTAACC
* * * *
42008826 TTAATTA-TTGA-T
1 TTACTAATTTAACC
42008838 TTACTAATTTAACC
1 TTACTAATTTAACC
42008852 TTACTAATT
1 TTACTAATT
42008861 AAACTTAAAA
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
12 5 0.13
13 6 0.16
14 27 0.71
ACGTcount: A:0.37, C:0.14, G:0.02, T:0.48
Consensus pattern (14 bp):
TTACTAATTTAACC
Found at i:42008838 original size:40 final size:39
Alignment explanation
Indices: 42008783--42008868 Score: 163
Period size: 40 Copynumber: 2.2 Consensus size: 39
42008773 TATTTTACTT
42008783 AACTTAATTATTGATTTACTAATTTAACCTTACTAATTTA
1 AACTTAATTATTGATTTACTAATTTAACCTTACTAA-TTA
42008823 AACTTAATTATTGATTTACTAATTTAACCTTACTAATTA
1 AACTTAATTATTGATTTACTAATTTAACCTTACTAATTA
42008862 AACTTAA
1 AACTTAA
42008869 AAATCACTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 10 0.22
40 36 0.78
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (39 bp):
AACTTAATTATTGATTTACTAATTTAACCTTACTAATTA
Found at i:42012367 original size:40 final size:40
Alignment explanation
Indices: 42012297--42012474 Score: 245
Period size: 40 Copynumber: 4.5 Consensus size: 40
42012287 AAACCAAGTA
* *
42012297 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
42012336 CCTTTGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42012376 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
42012416 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATT
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
42012456 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42012475 TTATCATCCG
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
39 14 0.11
40 111 0.89
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42014278 original size:46 final size:46
Alignment explanation
Indices: 42014223--42014403 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
42014213 TAGGATGGTT
42014223 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
42014269 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
42014315 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** * *
42014362 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42014404 GCGGGTTACA
Statistics
Matches: 115, Mismatches: 13, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 70 0.61
47 33 0.29
48 2 0.02
50 4 0.03
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:42014384 original size:93 final size:93
Alignment explanation
Indices: 42014225--42014396 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42014215 GGATGGTTGA
* *
42014225 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42014290 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42014318 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42014383 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42014397 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42017337 original size:15 final size:15
Alignment explanation
Indices: 42017317--42017385 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
42017307 GTATCTTGGG
42017317 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
42017332 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
42017347 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
42017362 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
42017377 TTTCTTTAT
1 TTTCTTTAT
42017386 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:42017386 original size:30 final size:30
Alignment explanation
Indices: 42017308--42017395 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
42017298 CATAGTATCG
* * * *
42017308 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
42017338 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
42017368 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
42017396 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:42019814 original size:46 final size:46
Alignment explanation
Indices: 42019764--42019939 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
42019754 ATGGTTGGCA
42019764 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
42019810 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
42019857 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
42019903 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42019940 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:42019919 original size:93 final size:93
Alignment explanation
Indices: 42019760--42019931 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42019750 TAGGATGGTT
* *
42019760 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42019825 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
42019853 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42019918 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
42019932 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:42028834 original size:40 final size:40
Alignment explanation
Indices: 42028757--42028933 Score: 261
Period size: 40 Copynumber: 4.5 Consensus size: 40
42028747 AAACCAAGTA
* *
42028757 CCTTCGGGATTTAG-CCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
42028796 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42028836 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
42028876 CCTTCGGGGCTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
42028916 CCTTCGGGACTTAGCCCG
1 CCTTCGGGACTTAGCCCG
42028934 ATTATCATCC
Statistics
Matches: 127, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 15 0.12
40 112 0.88
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42031093 original size:93 final size:93
Alignment explanation
Indices: 42030981--42031152 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42030971 GCCCATAAGT
* *
42030981 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42031046 CGAGCTCGGATGCCTAGTTACATCTCTC
66 CGAGCTCGGATGCCTAGTTACATCTCTC
*
42031074 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
42031139 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
42031153 CAAATATCCT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTCTC
Found at i:42031148 original size:46 final size:46
Alignment explanation
Indices: 42030973--42031148 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
42030963 TGTAACCCGC
* *
42030973 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
42031019 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
42031065 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
42031112 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
42031149 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
46 70 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:42033565 original size:29 final size:29
Alignment explanation
Indices: 42033526--42033613 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
42033516 CAAAGATAAC
*
42033526 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
42033555 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
42033584 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
42033614 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:42033584 original size:15 final size:15
Alignment explanation
Indices: 42033526--42033604 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
42033516 CAAAGATAAC
*
42033526 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
42033540 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
42033555 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
42033569 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
42033584 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
42033599 AAGAAA
1 AAGAAA
42033605 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:42033613 original size:15 final size:15
Alignment explanation
Indices: 42033537--42033613 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
42033527 AGAAAACCGA
42033537 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
42033552 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
42033566 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
42033580 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
42033596 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42033611 ATA
1 ATA
42033614 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42036540 original size:46 final size:45
Alignment explanation
Indices: 42036473--42036645 Score: 204
Period size: 46 Copynumber: 3.8 Consensus size: 45
42036463 TGTAACCCGC
*
42036473 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
* * *
42036519 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--GCTTCGCAT
* *** *
42036565 ACATCTCTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGTTCGGGC-TTCGCAT
*
42036612 CCATAAGTGAACTCGGACTCAGCTCAACGAGTTC
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTC
42036646 TGTGACAGCC
Statistics
Matches: 105, Mismatches: 17, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
45 1 0.01
46 67 0.64
47 35 0.33
48 2 0.02
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCTTCGCAT
Found at i:42038552 original size:40 final size:39
Alignment explanation
Indices: 42038329--42038554 Score: 215
Period size: 39 Copynumber: 5.7 Consensus size: 39
42038319 TTCGAACGAT
* * *
42038329 ATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAGTGACTA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA
* * *
42038369 TATCCGGACTAAGAT-CTGAAGGCCTTTGTGCGAGTTACTA
1 -ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA
* * *
42038409 ATTCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGTTACTA
1 ATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTA
** *
42038448 ATCCCGGGCTAAG-CCCGAAGGCATGGGTACGAGTTACTAA
1 AT-CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT-A
* * *
42038488 ATCCGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTGCTA
1 ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
* *
42038527 TAACCGGGCTATGTCCCGAAGGCATTTG
1 -ATCCGGGCTAAGTCCCGAAGGCATTTG
42038555 AACGAGTAGC
Statistics
Matches: 157, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
39 68 0.43
40 63 0.40
41 25 0.16
42 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
ATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA
Found at i:42038561 original size:40 final size:40
Alignment explanation
Indices: 42038331--42038573 Score: 149
Period size: 40 Copynumber: 6.1 Consensus size: 40
42038321 CGAACGATAT
* * * *
42038331 CCGGGCTAAGTCCCGAAGGCTTTTGTGCTAAG-TGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTAC-GAGTTG-CTATAA
* * * * * *
42038372 CCGGACTAAGAT-CTGAAGGCCTTTGTGCGAGTTACTA-AT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTGCTATAA
* * * * * *
42038411 TCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGTTACTA-ATC
1 CCGGGCTAAG-TCCCGAAGGCATTTGTACGAGTTGCTATA-A
** *
42038451 CCGGGCTAAG-CCCGAAGGCATGGGTACGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTGCTATAA
* * *
42038489 TCCGGGTTAGGTCCCGAAGGCATTTGTGCGAGTTGCTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTGCTATAA
* * * *
42038530 CCGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTGCTATAA
42038570 CCGG
1 CCGG
42038574 TTAAACTCCG
Statistics
Matches: 168, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
39 68 0.40
40 73 0.43
41 26 0.15
42 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTACGAGTTGCTATAA
Found at i:42038585 original size:79 final size:78
Alignment explanation
Indices: 42038422--42038587 Score: 176
Period size: 79 Copynumber: 2.1 Consensus size: 78
42038412 CGGACTAAGA
* * *
42038422 TCCGAAGGCCTTTGTGCGAGTTACTAATCCCGGGCTAAGCCCGAAGGCATGGGTACGAGTTACTA
1 TCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATGGGAACGAGTTACTA
**
42038487 AATCCGGGTTAGG
66 AATCCGGGTTAAC
* * **
42038500 TCCCGAAGGCATTTGTGCGAGTTGCT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TA
1 T-CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATGGGAACGAGTTA
*
42038563 GCTATATCC-GGTTAAAC
63 -CTAAATCCGGGTT-AAC
42038580 TCCGAAGG
1 TCCGAAGG
42038588 TACGTGATTC
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
78 3 0.04
79 44 0.60
80 26 0.36
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.24
Consensus pattern (78 bp):
TCCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATGGGAACGAGTTACTA
AATCCGGGTTAAC
Found at i:42042360 original size:30 final size:30
Alignment explanation
Indices: 42042316--42042404 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
42042306 CAAAGATAAC
*
42042316 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAACCCGGAATAAAGAAATCCAAGATA
*
42042345 GAGAAACCCGGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGGAATAAAGAAATCCAAG-ATA
* * *
42042375 AAGAGATCCAGG-ATAAAGAAACCCAAGATA
1 AAGA-AACCCGGAATAAAGAAATCCAAGATA
42042405 CGATACTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
29 9 0.18
30 34 0.68
31 7 0.14
ACGTcount: A:0.56, C:0.16, G:0.18, T:0.10
Consensus pattern (30 bp):
AAGAAACCCGGAATAAAGAAATCCAAGATA
Found at i:42042364 original size:15 final size:14
Alignment explanation
Indices: 42042316--42042398 Score: 58
Period size: 15 Copynumber: 5.6 Consensus size: 14
42042306 CAAAGATAAC
*
42042316 AAGAAAACCGAATA
1 AAGAAACCCGAATA
* *
42042330 AAGAAATCCAAGATA
1 AAGAAACCCGA-ATA
*
42042345 GAGAAACCCGGAATA
1 AAGAAACCC-GAATA
*
42042360 AAGAAATCCAGAATA
1 AAGAAA-CCCGAATA
* * *
42042375 AAGAGATCCAGGATA
1 AAGA-AACCCGAATA
42042390 AAGAAACCC
1 AAGAAACCC
42042399 AAGATACGAT
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
14 12 0.22
15 38 0.70
16 4 0.07
ACGTcount: A:0.55, C:0.17, G:0.18, T:0.10
Consensus pattern (14 bp):
AAGAAACCCGAATA
Found at i:42042404 original size:15 final size:15
Alignment explanation
Indices: 42042327--42042404 Score: 70
Period size: 15 Copynumber: 5.2 Consensus size: 15
42042317 AGAAAACCGA
42042327 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* **
42042342 ATAGAGAAA-CCCGG
1 ATAAAGAAATCCAAG
42042356 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
42042371 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
42042387 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42042402 ATA
1 ATA
42042405 CGATACTATG
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
14 3 0.06
15 44 0.88
16 3 0.06
ACGTcount: A:0.55, C:0.15, G:0.18, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42045436 original size:46 final size:46
Alignment explanation
Indices: 42045263--42045436 Score: 198
Period size: 46 Copynumber: 3.8 Consensus size: 46
42045253 TGTAACCCGC
* *
42045263 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
42045309 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA---C-A-TTCGCAT
* * *
42045359 -C-TCA-CGAACT--GACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
42045400 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
42045437 TGCCCAAACA
Statistics
Matches: 108, Mismatches: 9, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
40 2 0.02
41 4 0.04
42 2 0.02
43 2 0.02
44 5 0.05
45 21 0.19
46 58 0.54
47 5 0.05
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:42045455 original size:46 final size:45
Alignment explanation
Indices: 42045268--42045455 Score: 143
Period size: 46 Copynumber: 4.1 Consensus size: 45
42045258 CCCGCCCATA
* * * * * *
42045268 AGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCAT-A
1 AGTGAACTCGGACTCAACTCAACGAGTTC-GG-ATGCCCATACATCC
* *
42045314 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTTACATCTC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA--TACATC-C
* * * * *
42045362 A-CGAACT--GACTCAACTCAACGAGTTCGGACATTCGCATCCAT-A
1 AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATACATCC
*
42045405 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAACATCCC
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACAT-CC
42045451 AGTGA
1 AGTGA
42045456 CATGTCACTT
Statistics
Matches: 112, Mismatches: 19, Indels: 22
0.73 0.12 0.14
Matches are distributed among these distances:
43 1 0.01
44 16 0.14
45 26 0.23
46 59 0.53
47 9 0.08
48 1 0.01
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATACATCC
Found at i:42049792 original size:48 final size:48
Alignment explanation
Indices: 42049732--42050544 Score: 1224
Period size: 48 Copynumber: 17.0 Consensus size: 48
42049722 AGATAAATAT
*
42049732 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
42049780 ATACATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * * *
42049828 ATATGTATGAGA-ATGTATATATGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
42049875 ATAAATGTGTGATATGTATATGAGGTAAAGACGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42049923 A-ATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
42049970 TATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 -ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42050019 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
42050067 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
42050115 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
** *
42050163 ATATATGCATGATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42050211 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA
* * *
42050260 TATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 -ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42050309 ATATATGTGTGATATGTA-ATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
42050356 ATATATGTGTGATATGTATATGTGGTAAAGCTGAATGGCTAATGCGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
42050404 ATATA---GAGATATGTATATGTGGTAAAGCCGACTAGCTAATGTAAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42050449 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * * *
42050497 GTAAATATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42050545 TGTTGTAACA
Statistics
Matches: 694, Mismatches: 62, Indels: 18
0.90 0.08 0.02
Matches are distributed among these distances:
45 39 0.06
47 130 0.19
48 435 0.63
49 47 0.07
50 43 0.06
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:42050648 original size:37 final size:37
Alignment explanation
Indices: 42050592--42050732 Score: 212
Period size: 37 Copynumber: 3.8 Consensus size: 37
42050582 AATATATTTT
*
42050592 GGGTGAGACCCGATAACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
** *
42050629 GGGTAAGACCCGAGGACTACGTATGGAGATTATGTCC
1 GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
* *
42050666 GGGTAAGACCCGATGACTACGTGTGGAGAGTATGTCC
1 GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
*
42050703 GGGTAAGA-CCGATAACTTCGTGTGGAGATT
1 GGGTAAGACCCGATAACTACGTGTGGAGATT
42050733 TCGTCCGAGC
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
36 19 0.20
37 75 0.80
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (37 bp):
GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
Found at i:42052114 original size:39 final size:39
Alignment explanation
Indices: 42051959--42052226 Score: 439
Period size: 40 Copynumber: 6.8 Consensus size: 39
42051949 GAGAATTGAG
* * *
42051959 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGT-CCGAAGAGCATTCGTGCT
42051999 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAG-TCCGAAGAGCATTCGTGCT
42052039 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAG-TCCGAAGAGCATTCGTGCT
42052079 AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCT
42052118 AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCT
*
42052157 AGTGATGTATCCGGACTAAGTCCCGAAGAGTATTCGTGCT
1 AGTGATGTATCCGGACTAAGT-CCGAAGAGCATTCGTGCT
* *
42052197 -GTGATGTATCCGGGCTAGGTCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTCCGAAGAGCA
42052227 ATCATGCTGG
Statistics
Matches: 219, Mismatches: 7, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
38 9 0.04
39 97 0.44
40 112 0.51
41 1 0.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCT
Found at i:42052177 original size:78 final size:78
Alignment explanation
Indices: 42051959--42052226 Score: 439
Period size: 78 Copynumber: 3.4 Consensus size: 78
42051949 GAGAATTGAG
* * *
42051959 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTTCCG
1 AGTGATGTATCCGGACTAAGT-CCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAG-TCCG
42052024 AAGAGCATTCGTGCT
64 AAGAGCATTCGTGCT
42052039 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCGA
1 AGTGATGTATCCGGACTAAG-TCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCGA
42052104 AGAGCATTCGTGCT
65 AGAGCATTCGTGCT
42052118 AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCCGA
1 AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGT-CCGA
*
42052183 AGAGTATTCGTGCT
65 AGAGCATTCGTGCT
* *
42052197 -GTGATGTATCCGGGCTAGGTCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTCCGAAGAGCA
42052227 ATCATGCTGG
Statistics
Matches: 180, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
78 68 0.38
79 56 0.31
80 55 0.31
81 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (78 bp):
AGTGATGTATCCGGACTAAGTCCGAAGAGCATTCGTGCTAGTGATGTATCCGGACTAAGTCCGAA
GAGCATTCGTGCT
Found at i:42055602 original size:46 final size:45
Alignment explanation
Indices: 42055535--42055705 Score: 145
Period size: 46 Copynumber: 3.8 Consensus size: 45
42055525 TGTAACCCGC
* *
42055535 CCATAAGCGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGTAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGTAT
* *
42055581 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGT-T
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--GCTTCGTAT
* *** * * * *
42055627 ACATCTCTCGAA--C-GACTCAACTCAACCAGTTCGGACATTCGCA-
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGGC-TTCGTAT
*
42055670 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
42055706 ATGCCCAAAC
Statistics
Matches: 98, Mismatches: 19, Indels: 17
0.73 0.14 0.13
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 20 0.20
45 21 0.21
46 39 0.40
47 6 0.06
48 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.20
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCTTCGTAT
Found at i:42060125 original size:48 final size:48
Alignment explanation
Indices: 42059991--42060800 Score: 1158
Period size: 48 Copynumber: 17.0 Consensus size: 48
42059981 TGTACAAGAT
* *
42059991 AAATATATATGTGTGTAT-TATATGTGGTAAAGCCGAATGGATAATGTG
1 AAATATATATGTG-ATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
42060039 AAATACATGTGTGATATG--TATGTGGTAAAGCCGAATGGCGAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * * * *
42060085 AAATATGTATGAGACATGTATATATGGTAAAGCCGAATGGCGAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
42060133 ----ATATATGTGATATGTATATGAGGT-AAGACGAATGGCGAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
42060176 AAA-ATATGTGTTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATATATG-TGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
42060224 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
42060272 AAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
42060320 AAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
42060368 AAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*** *
42060416 AAATATATGCATGATATGTATATGTGGTAAAGCTGAATGGCTAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
42060464 AAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
42060512 AAATATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTG
1 -AA-ATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
42060562 AAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
42060610 AAATATATGTGTGATATGTATATGTGGTAAAG-CGAATGGCTAATGCG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* * *
42060657 AAATATATATGAGATATGTATATGTGGTAAAGCCGAATAGCTAATGTA
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
*
42060705 AAATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
* *
42060753 AAATA-ATATGAGATATGAATATGTGGTAAAG-CGAATGGCTAATGTG
1 AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
42060799 AA
1 AA
42060801 TGTTGTAACA
Statistics
Matches: 690, Mismatches: 60, Indels: 26
0.89 0.08 0.03
Matches are distributed among these distances:
43 18 0.03
44 19 0.03
46 62 0.09
47 86 0.12
48 452 0.66
49 10 0.01
50 43 0.06
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
AAATATATATGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG
Found at i:42060901 original size:36 final size:36
Alignment explanation
Indices: 42060846--42060984 Score: 183
Period size: 36 Copynumber: 3.8 Consensus size: 36
42060836 GAAATATATT
* *
42060846 GGGTGAGACCCGATAACTACGTGTGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGAGATTATGTCC
*
42060882 GGGTAAGACCCGAGGACTACGTGTGAGATTATGTCC
1 GGGTAAGACCCGATGACTACGTGTGAGATTATGTCC
*
42060918 GGGTGAAGA-CCGATGACTACGTGTGGAGAGTATGTCC
1 GGGT-AAGACCCGATGACTACGTGT-GAGATTATGTCC
* *
42060955 GGGTAAGA-CCGATAACTTCGTGTGGAGATT
1 GGGTAAGACCCGATGACTACGTGT-GAGATT
42060985 TCGTCGAGCT
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
36 74 0.80
37 19 0.20
ACGTcount: A:0.25, C:0.17, G:0.34, T:0.24
Consensus pattern (36 bp):
GGGTAAGACCCGATGACTACGTGTGAGATTATGTCC
Found at i:42062810 original size:14 final size:14
Alignment explanation
Indices: 42062791--42062868 Score: 68
Period size: 15 Copynumber: 5.4 Consensus size: 14
42062781 CAAAGATAAC
*
42062791 AAGAAAACCGAATA
1 AAGAAATCCGAATA
*
42062805 AAGAAATCCAAGATA
1 AAGAAATCCGA-ATA
* *
42062820 GAGAAACCCGAATA
1 AAGAAATCCGAATA
42062834 AA-AAATCCAGAATA
1 AAGAAATCC-GAATA
* *
42062848 AAGAGATCCAGGATA
1 AAGAAATCC-GAATA
42062863 AAGAAA
1 AAGAAA
42062869 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
13 5 0.10
14 20 0.39
15 26 0.51
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (14 bp):
AAGAAATCCGAATA
Found at i:42062830 original size:29 final size:29
Alignment explanation
Indices: 42062791--42062877 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
42062781 CAAAGATAAC
*
42062791 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
42062820 GAGAAACCCGAATAAA-AAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
42062848 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
42062878 CGATACTATG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
27 2 0.04
28 12 0.26
29 23 0.49
30 8 0.17
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:42062858 original size:15 final size:15
Alignment explanation
Indices: 42062791--42062868 Score: 74
Period size: 14 Copynumber: 5.4 Consensus size: 15
42062781 CAAAGATAAC
*
42062791 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
42062805 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
42062820 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
42062834 AA-AAATCCAGAATA
1 AAGAAATCCAGAATA
* *
42062848 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
42062863 AAGAAA
1 AAGAAA
42062869 CCCAAGATAC
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 3 0.06
14 24 0.47
15 24 0.47
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:42062877 original size:15 final size:15
Alignment explanation
Indices: 42062802--42062877 Score: 68
Period size: 15 Copynumber: 5.2 Consensus size: 15
42062792 AGAAAACCGA
42062802 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
42062817 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
42062831 ATAAA-AAATCC-AG
1 ATAAAGAAATCCAAG
* *
42062844 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
42062860 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42062875 ATA
1 ATA
42062878 CGATACTATG
Statistics
Matches: 47, Mismatches: 10, Indels: 8
0.72 0.15 0.12
Matches are distributed among these distances:
12 1 0.02
13 5 0.11
14 9 0.19
15 31 0.66
16 1 0.02
ACGTcount: A:0.57, C:0.16, G:0.16, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42065878 original size:46 final size:44
Alignment explanation
Indices: 42065738--42065903 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 44
42065728 CCGCCCATAA
* *
42065738 GAACTCGGACTCAACTCAACGAGCTCGGGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATTCGCATCCATAAGT
* * ***
42065782 GAACTCGGACTCAACTCAACGAG-TCGGATGC-CTAGTTACATCTCT
1 GAACTCGGACTCAACTCAACGAGTTCGGATTCGC-A--TCCATAAGT
42065827 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 -GAACTCGGACTCAACTCAACGAGTTCGG--ATTCGCATCCATAAGT
42065874 GAACTCGGACTCAACTCAACGAGTTCGGAT
1 GAACTCGGACTCAACTCAACGAGTTCGGAT
42065904 GCCCAACATC
Statistics
Matches: 103, Mismatches: 11, Indels: 16
0.79 0.08 0.12
Matches are distributed among these distances:
42 1 0.01
43 7 0.07
44 25 0.24
45 5 0.05
46 51 0.50
47 9 0.09
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATTCGCATCCATAAGT
Found at i:42065893 original size:92 final size:91
Alignment explanation
Indices: 42065738--42065906 Score: 295
Period size: 92 Copynumber: 1.8 Consensus size: 91
42065728 CCGCCCATAA
*
42065738 GAACTCGGACTCAACTCAACGAGCTCGGGTTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTCGGATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
42065803 AG-TCGGATGCCTAGTTACATCTCTC
66 AGTTCGGATGCCTAGTTACATCTCTC
*
42065828 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG--ATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42065893 CGAGTTCGGATGCC
64 CGAGTTCGGATGCC
42065907 CAACATCCTA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
90 27 0.36
92 38 0.51
93 9 0.12
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGATTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCTC
Found at i:42070266 original size:48 final size:48
Alignment explanation
Indices: 42070206--42071023 Score: 1253
Period size: 48 Copynumber: 17.0 Consensus size: 48
42070196 AGATAAATAT
*
42070206 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
42070254 ATACATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * * * *
42070302 ATATGTATGAGACATGTATATATGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
42070350 ATATATGTGTGATATGTATATGAGGTAAAGACGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42070398 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA
* * *
42070447 TATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 -ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42070496 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
42070544 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
42070592 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
** *
42070640 ATATATGCATGATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42070688 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA
* * *
42070737 TATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 -ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42070786 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
42070834 ATATATGTGTGATATGTATATGTGGTAAAGCTGAATGGCTAATGCGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
42070882 ATATATATGAGATATGTATATGTGGTAAAGCCGACTAGCTAATGT-AA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42070929 A-ATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * * *
42070976 GTAAATATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42071024 TGTTGTAACA
Statistics
Matches: 702, Mismatches: 62, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
46 39 0.06
47 5 0.01
48 564 0.80
49 8 0.01
50 86 0.12
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (48 bp):
ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:42070726 original size:290 final size:289
Alignment explanation
Indices: 42070206--42071023 Score: 1370
Period size: 290 Copynumber: 2.8 Consensus size: 289
42070196 AGATAAATAT
* *
42070206 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGATAATGTGAAATACATGTGTGATATGT
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGT
* * *
42070271 ATATGTGGTAAAGCCGAATGGCGAATGTGAAATATGTATGAGACATGTATATATGGTAAAGCCGA
66 ATATGTGGTAAAGCCGAATGGCGAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
* *
42070336 ATGGCGAATGTGAAATATATGTGTGATATGTATATGAGGTAAAGACGAATGGCGAATGTGAAATA
131 ATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAG-CGAATGGCTAATGTGAAATA
42070401 TATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTA
195 TATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTA
42070466 TATGTGGTAAAGCCGAATGGCGAATGTGAA
260 TATGTGGTAAAGCCGAATGGCGAATGTGAA
* * *
42070496 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAGATATGT
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGT
* *
42070561 ATATGTGGTAAAGCCGAATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCCGA
66 ATATGTGGTAAAGCCGAATGGCGAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
**
42070626 ATGGCGAATGTGAAATATATGCATGATATGTATATGTGGTAAAGCTGAATGGCTAATGTGAAATA
131 ATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGC-GAATGGCTAATGTGAAATA
42070691 TATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTA
195 TATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTA
42070756 TATGTGGTAAAGCCGAATGGCGAATGTGAA
260 TATGTGGTAAAGCCGAATGGCGAATGTGAA
42070786 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGT
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGT
* * *
42070851 ATATGTGGTAAAGCTGAATGGCTAATGCGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
66 ATATGTGGTAAAGCCGAATGGCGAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
* * * *
42070916 CTAGCTAATGT-AAA-ATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAGTA
131 ATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAG-CGAATGGCTAATGTGAAATA
* * * *
42070979 AATATGAGATATGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
195 TATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42071024 TGTTGTAACA
Statistics
Matches: 494, Mismatches: 32, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
288 85 0.17
289 5 0.01
290 404 0.82
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.31
Consensus pattern (289 bp):
ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATGTGTGATATGT
ATATGTGGTAAAGCCGAATGGCGAATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGA
ATGGCGAATGTGAAATATATGTGTGATATGTATATGTGGTAAAGCGAATGGCTAATGTGAAATAT
ATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATATATATGAGATATGTAT
ATGTGGTAAAGCCGAATGGCGAATGTGAA
Found at i:42071126 original size:37 final size:37
Alignment explanation
Indices: 42071070--42071210 Score: 212
Period size: 37 Copynumber: 3.8 Consensus size: 37
42071060 AAATATATTT
*
42071070 GGGTGAGACCCGATAACTACGTGTGGAGATTATGTCC
1 GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
** *
42071107 GGGTAAGACCCGAGGACTACGTATGGAGATTATGTCC
1 GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
* *
42071144 GGGTAAGACCCGATGACTACGTGTGGAGAGTATGTCC
1 GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
*
42071181 GGGTAAGA-CCGATAACTTCGTGTGGAGATT
1 GGGTAAGACCCGATAACTACGTGTGGAGATT
42071211 TCGTCCGAGC
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
36 19 0.20
37 75 0.80
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.23
Consensus pattern (37 bp):
GGGTAAGACCCGATAACTACGTGTGGAGATTATGTCC
Found at i:42072509 original size:40 final size:40
Alignment explanation
Indices: 42072443--42072714 Score: 472
Period size: 40 Copynumber: 6.8 Consensus size: 40
42072433 GAGAATTGAG
* * *
42072443 AGTGATATATCCGGGCTAAATCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
42072483 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
42072523 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
42072563 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
42072603 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
42072643 AGTGATGTATCCGGACTAAGTCCCGAAGAGTATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
42072683 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCA
42072715 ATCATGCTGG
Statistics
Matches: 223, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 223 1.00
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
Found at i:42076267 original size:48 final size:48
Alignment explanation
Indices: 42076198--42077011 Score: 1393
Period size: 48 Copynumber: 17.0 Consensus size: 48
42076188 AGATAAATAT
*
42076198 ATATATGTGTGATATGTATATGTGGTAAAGTCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
42076246 ATATATGTGTGATATGTATATGTGGTAAAGCCAAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * * *
42076294 ATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
42076342 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076390 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
42076438 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076486 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
42076534 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
*
42076582 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076630 ATATATGTGTGATATGTAT-TGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076677 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTG-AA
* * *
42076726 TATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCGAATGTGAA
1 -ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076775 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076823 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* *
42076871 ATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTAATGT-AA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42076918 A-ATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
* * *
42076965 ATATATATGAG-TATGAATATGTGGTAAAGCCGAATGGCTAATGTGAA
1 ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
42077012 TGTTGTAACA
Statistics
Matches: 729, Mismatches: 32, Indels: 11
0.94 0.04 0.01
Matches are distributed among these distances:
46 41 0.06
47 87 0.12
48 554 0.76
49 4 0.01
50 43 0.06
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.32
Consensus pattern (48 bp):
ATATATGTGTGATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAA
Found at i:42077112 original size:37 final size:37
Alignment explanation
Indices: 42077055--42077198 Score: 218
Period size: 37 Copynumber: 3.9 Consensus size: 37
42077045 GGAAATATAT
*
42077055 TCCGGGTGAGA-CCGATGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
42077091 TCCCGGTAAGACCCGAGGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
42077128 TCCGGGTAAGACCCGATGACTACGTGTGGAGAGTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* * *
42077165 TCCGGGTAAGACCCGATAACTTCATGTGGAGATT
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATT
42077199 TCGTCGAGCT
Statistics
Matches: 97, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
36 9 0.09
37 88 0.91
ACGTcount: A:0.24, C:0.19, G:0.33, T:0.24
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:42078475 original size:40 final size:40
Alignment explanation
Indices: 42078406--42078637 Score: 365
Period size: 40 Copynumber: 5.8 Consensus size: 40
42078396 GAGAATTGAG
* * * *
42078406 AGTGATATATCCGGGCTAAATCCCAAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
42078446 AATGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
42078486 AGTGATGTATCCAGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
*
42078526 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
42078566 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
* *
42078606 AGTGATGTATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGACTAAGTCCCGAAGAGCA
42078638 ATCATGCTGG
Statistics
Matches: 180, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 180 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (40 bp):
AGTGATGTATCCGGACTAAGTCCCGAAGAGCATTCGTGCT
Found at i:42081520 original size:38 final size:38
Alignment explanation
Indices: 42081478--42081553 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
42081468 GAATTATAGG
42081478 CTGAATAAAATATGTAATCAAAGCTTAGTTGGTCTAGT
1 CTGAATAAAATATGTAATCAAAGCTTAGTTGGTCTAGT
42081516 CTGAATAAAATATGTAATCAAAGCTTAGTTGGTCTAGT
1 CTGAATAAAATATGTAATCAAAGCTTAGTTGGTCTAGT
42081554 TTCTTATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (38 bp):
CTGAATAAAATATGTAATCAAAGCTTAGTTGGTCTAGT
Found at i:42087227 original size:29 final size:29
Alignment explanation
Indices: 42087193--42087353 Score: 186
Period size: 29 Copynumber: 5.6 Consensus size: 29
42087183 TAATCGATCA
*
42087193 CGCACACTTAGTGCCAT-GTGATTT-AAGCT
1 CGCACACTTAGTGCCATACT--TTTCAAGCT
* * **
42087222 CGCACACATAGTGCCGTATA-ATTT-AAATT
1 CGCACACTTAGTGCC--ATACTTTTCAAGCT
42087251 CGCACACTTAGTGCCATACTTTTCAAGCT
1 CGCACACTTAGTGCCATACTTTTCAAGCT
*
42087280 TGCACACTTAGTGCCATACTTTTCAAGCT
1 CGCACACTTAGTGCCATACTTTTCAAGCT
*
42087309 TGCACACTTAGTGCCATACTTTTCAAGCT
1 CGCACACTTAGTGCCATACTTTTCAAGCT
*
42087338 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
42087354 ATCTTGTCAC
Statistics
Matches: 118, Mismatches: 9, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.03
28 3 0.03
29 110 0.93
31 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (29 bp):
CGCACACTTAGTGCCATACTTTTCAAGCT
Found at i:42096305 original size:40 final size:40
Alignment explanation
Indices: 42096250--42096602 Score: 364
Period size: 40 Copynumber: 8.8 Consensus size: 40
42096240 TGATTATTGA
* * *
42096250 TGATTGCACATACGTGCCCTTATTTGTACTTTGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
** * *
42096290 TGATTGCACATACGTGCATCTGTTTGTGCTTCGATACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
*
42096330 TGATTGAACATACGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * * *
42096370 TGATTTCATATACTTGCCCCTATTTGTACTTCGGCACCAC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* ** * * ***
42096410 TGATTTCACATATATGCCCCTGTTTTTACTTTGGTACTGT
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
42096450 TGATTGCACATACATGCCCTTCTTTGTACTTCGGTACCAC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
42096490 TAATTGCACATACATGCCCCTGTTTGTACTTCGGTACCCC
1 TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * **
42096530 TGATTGCACATATGTGCCCCTATTTTGTATTTTAGTACCCCC
1 TGATTGCACATACGTGCCCCT-GTTTGTACTTCGGTA-CCCC
* * *
42096572 TGGTTGCACATAAGTGCCCTTGTTTGTACTT
1 TGATTGCACATACGTGCCCCTGTTTGTACTT
42096603 TGATACCTTT
Statistics
Matches: 257, Mismatches: 54, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
40 216 0.84
41 19 0.07
42 22 0.09
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (40 bp):
TGATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:42096369 original size:20 final size:20
Alignment explanation
Indices: 42096309--42096371 Score: 56
Period size: 20 Copynumber: 3.1 Consensus size: 20
42096299 ATACGTGCAT
* *
42096309 CTGTTTGTGCTTCGATACCC
1 CTGTTTGTACTTCGGTACCC
* * * *
42096329 CTGATTGAACATAC-GTGCCC
1 CTGTTTGTAC-TTCGGTACCC
42096349 CTGTTTGTACTTCGGTACCC
1 CTGTTTGTACTTCGGTACCC
42096369 CTG
1 CTG
42096372 ATTTCATATA
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (20 bp):
CTGTTTGTACTTCGGTACCC
Found at i:42103394 original size:31 final size:29
Alignment explanation
Indices: 42103352--42103454 Score: 82
Period size: 29 Copynumber: 3.5 Consensus size: 29
42103342 GGCCCAATCT
* *
42103352 CATTTATATGGCCCGTCAAGCCC-AATTCA
1 CATTCATATGGCCCATCAAGCCCAAATT-A
* *
42103381 CATATTCATATGGCCTATCAGGCCCAAATTA
1 C--ATTCATATGGCCCATCAAGCCCAAATTA
* * * *
42103412 CATTCATATGGCCTATTAGGCCCAAATAA
1 CATTCATATGGCCCATCAAGCCCAAATTA
* *
42103441 CCTTTATATGGCCC
1 CATTCATATGGCCC
42103455 GTTAGGCCCA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
29 38 0.61
31 20 0.32
32 4 0.06
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CATTCATATGGCCCATCAAGCCCAAATTA
Found at i:42103426 original size:29 final size:29
Alignment explanation
Indices: 42103384--42103467 Score: 114
Period size: 29 Copynumber: 2.9 Consensus size: 29
42103374 CAATTCACAT
* *
42103384 ATTCATATGGCCTATCAGGCCCAAATTAC
1 ATTCATATGGCCTATTAGGCCCAAATAAC
42103413 ATTCATATGGCCTATTAGGCCCAAATAAC
1 ATTCATATGGCCTATTAGGCCCAAATAAC
* * **
42103442 CTTTATATGGCCCGTTAGGCCCAAAT
1 ATTCATATGGCCTATTAGGCCCAAAT
42103468 CATCTTATAT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (29 bp):
ATTCATATGGCCTATTAGGCCCAAATAAC
Found at i:42108525 original size:29 final size:27
Alignment explanation
Indices: 42108491--42108593 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
42108481 TACTCAATCA
*
42108491 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
42108520 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
42108549 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
42108578 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42108594 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:42116321 original size:29 final size:27
Alignment explanation
Indices: 42116287--42116389 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
42116277 TACTCAATCA
*
42116287 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
42116316 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
42116345 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
42116374 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
42116390 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:42135493 original size:77 final size:80
Alignment explanation
Indices: 42135351--42135573 Score: 271
Period size: 77 Copynumber: 2.8 Consensus size: 80
42135341 GCTACTCGTT
*
42135351 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
42135416 A-TTAGTAACTCGCA
66 ATTTAGTAACTCGCA
* **
42135430 CAAATGCCTTCGGG-CTTAG-CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGTCC
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
42135491 GGATTTAGTAACTCGCA
64 GGATTTAGTAACTCGCA
* * * * * *
42135508 CAAATGCCTTC-AGATCTTAGTCCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CATAGCCCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCC
42135571 GGA
64 GGA
42135574 CATCATTCGA
Statistics
Matches: 127, Mismatches: 8, Indels: 17
0.84 0.05 0.11
Matches are distributed among these distances:
76 4 0.03
77 37 0.29
78 28 0.22
79 19 0.15
80 27 0.21
81 12 0.09
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Found at i:42135573 original size:40 final size:40
Alignment explanation
Indices: 42135332--42135573 Score: 284
Period size: 40 Copynumber: 6.1 Consensus size: 40
42135322 CGGAATTTAA
** *
42135332 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
42135372 CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
42135412 CCGGAT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAG-
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
42135449 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
42135489 CCGGATTTAGTAACTCGCACAAATGCCTTC-AGATCTTAGT
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* *
42135529 CCGGATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
42135569 CCGGA
1 CCGGA
42135574 CATCATTCGA
Statistics
Matches: 179, Mismatches: 14, Indels: 18
0.85 0.07 0.09
Matches are distributed among these distances:
37 7 0.04
38 27 0.15
39 32 0.18
40 103 0.58
41 10 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:42143546 original size:79 final size:78
Alignment explanation
Indices: 42143435--42143601 Score: 241
Period size: 79 Copynumber: 2.1 Consensus size: 78
42143425 GCTACTCGTT
*
42143435 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCG
1 CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTT--GGATCTTAACCCG
42143499 GATTTAGTAACTCGCA
64 GA-TTAGTAACTCGCA
* **
42143515 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTAACTCGCACAAATGCCTTGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTGGATCTTAACCCGG
42143578 ATTAGTAACTCGCA
65 ATTAGTAACTCGCA
42143592 CAAATGCCTT
1 CAAATGCCTT
42143602 AGATCTTAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 7
0.88 0.04 0.08
Matches are distributed among these distances:
77 26 0.32
78 10 0.12
79 31 0.38
80 14 0.17
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (78 bp):
CAAATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTGGATCTTAACCCGGA
TTAGTAACTCGCA
Found at i:42143549 original size:39 final size:39
Alignment explanation
Indices: 42143435--42143654 Score: 249
Period size: 40 Copynumber: 5.7 Consensus size: 39
42143425 GCTACTCGTT
* *
42143435 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGAT-TAGTAACTCGCA
*
42143475 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGA-TTAGTAACTCGCA
42143515 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-ATTAGTAACTCGCA
*
42143554 CAAATGCCTT--GGATCTTAGTCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTAGTAACTCGCA
* * * *
42143592 CAAATGCCTT--AGATCTTAG-TCGGA-TATGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTA-GTAAC-TCGCA
42143630 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42143655 CATCATTCGA
Statistics
Matches: 160, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
36 2 0.01
37 15 0.09
38 45 0.28
39 47 0.29
40 50 0.31
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTAGTAACTCGCA
Found at i:42143591 original size:38 final size:39
Alignment explanation
Indices: 42143435--42143654 Score: 224
Period size: 39 Copynumber: 5.7 Consensus size: 39
42143425 GCTACTCGTT
* *
42143435 CAAATGCCTTCGGGA-CATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGAT-TAGTAACTCGCA
*
42143475 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTC-GGATCTTAGCCCGGA-TTAGTAACTCGCA
*
42143515 CAAATGCCTTCGG-GCTTAGCCCGGAATTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGG-ATTAGTAACTCGCA
*
42143554 CAAATGCCTT-GGATCTTAGTCCGGATTAGTAACTCGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTAGTAACTCGCA
* * * *
42143592 CAAATGCCTT-AGATCTTAG-TCGGA-TATGTCACTTAGCA
1 CAAATGCCTTCGGATCTTAGCCCGGATTA-GTAAC-TCGCA
42143630 CAAA-GCCTTCGGGA-CTTAGCCCGGA
1 CAAATGCCTTC-GGATCTTAGCCCGGA
42143655 CATCATTCGA
Statistics
Matches: 159, Mismatches: 12, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
36 2 0.01
37 13 0.08
38 47 0.30
39 49 0.31
40 47 0.30
41 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (39 bp):
CAAATGCCTTCGGATCTTAGCCCGGATTAGTAACTCGCA
Found at i:42143638 original size:37 final size:38
Alignment explanation
Indices: 42143463--42143638 Score: 153
Period size: 38 Copynumber: 4.6 Consensus size: 38
42143453 AGCCCGGTTA
* * **
42143463 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATT
1 TAGTAACTAGCACAAATGCCTT--AGATCTTAGTCCGGA-T
* * ** *
42143503 TAGTAACTCGCACAAATGCCTTCGGGCTTAGCCCGGAAT
1 TAGTAACTAGCACAAATGCCTTAGATCTTAGTCCGG-AT
* *
42143542 TAGTAACTCGCACAAATGCCTTGGATCTTAGTCCGGAT
1 TAGTAACTAGCACAAATGCCTTAGATCTTAGTCCGGAT
*
42143580 TAGTAACTCGCACAAATGCCTTAGATCTTAGT-CGGA-
1 TAGTAACTAGCACAAATGCCTTAGATCTTAGTCCGGAT
*
42143616 TATGTCACTTAGCACAAA-GCCTT
1 TA-GTAAC-TAGCACAAATGCCTT
42143639 CGGGACTTAG
Statistics
Matches: 122, Mismatches: 10, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
36 2 0.02
37 13 0.11
38 42 0.34
39 42 0.34
40 23 0.19
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.27
Consensus pattern (38 bp):
TAGTAACTAGCACAAATGCCTTAGATCTTAGTCCGGAT
Found at i:42148395 original size:29 final size:29
Alignment explanation
Indices: 42148360--42148416 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
42148350 CCCAATCTCA
42148360 TTTATATCGCCCATCAGGCCCAAATCACT
1 TTTATATCGCCCATCAGGCCCAAATCACT
* ** *
42148389 TTTATATGGCCTGTTAGGCCCAAATCAC
1 TTTATATCGCCCATCAGGCCCAAATCAC
42148417 CTTATATACA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.30
Consensus pattern (29 bp):
TTTATATCGCCCATCAGGCCCAAATCACT
Found at i:42150408 original size:38 final size:38
Alignment explanation
Indices: 42150357--42150434 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
42150347 TAATTATATA
42150357 TAGATCATTCTTAGCACATACAATTCTCATCATTTTAC
1 TAGATCATTCTTAGCACATACAATTCTCATCATTTTAC
*
42150395 TAGATCATTCTTAGCATATACAATTCTCATCATTTTAC
1 TAGATCATTCTTAGCACATACAATTCTCATCATTTTAC
42150433 TA
1 TA
42150435 TCTCAAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (38 bp):
TAGATCATTCTTAGCACATACAATTCTCATCATTTTAC
Found at i:42150704 original size:40 final size:39
Alignment explanation
Indices: 42150648--42150790 Score: 105
Period size: 40 Copynumber: 3.6 Consensus size: 39
42150638 AAAACCACAC
* *
42150648 CAGTTTGGCACGCAGTGCCTCATCGGATAATTCGAAGTAA
1 CAGTTTGACACCCAGTGCCTCATCGGAT-ATTCGAAGTAA
*
42150688 CAGTTTGACACCCAGTGTCTCATCGGCCATATT-GAAGT-A
1 CAGTTTGACACCCAGTGCCTCATCGG--ATATTCGAAGTAA
** * ** *
42150727 -A-TTTGGTACCTAGAACCTCATCGAATTTATTCGAAGTAA
1 CAGTTTGACACCCAGTGCCTCATCGGA--TATTCGAAGTAA
* * *
42150766 CAATTCGAAACCCAGTGCCTCATCG
1 CAGTTTGACACCCAGTGCCTCATCG
42150791 ACTCGAGGTC
Statistics
Matches: 79, Mismatches: 16, Indels: 15
0.72 0.15 0.14
Matches are distributed among these distances:
35 1 0.01
37 20 0.25
38 6 0.08
39 2 0.03
40 29 0.37
41 19 0.24
42 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (39 bp):
CAGTTTGACACCCAGTGCCTCATCGGATATTCGAAGTAA
Found at i:42151992 original size:23 final size:23
Alignment explanation
Indices: 42151966--42152014 Score: 98
Period size: 23 Copynumber: 2.1 Consensus size: 23
42151956 AAATATGAAA
42151966 GGCCAGCTCAAATCCTCTTCAAT
1 GGCCAGCTCAAATCCTCTTCAAT
42151989 GGCCAGCTCAAATCCTCTTCAAT
1 GGCCAGCTCAAATCCTCTTCAAT
42152012 GGC
1 GGC
42152015 TATTTTTGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.24
Consensus pattern (23 bp):
GGCCAGCTCAAATCCTCTTCAAT
Found at i:42155258 original size:22 final size:24
Alignment explanation
Indices: 42155228--42155276 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
42155218 CGACCCATGC
** *
42155228 AAACACAAAGCAAACCA-AGAAAT
1 AAACACAAAAAAAACCATAAAAAT
42155251 AAAC-CAAAAAAAACCATAAAAAT
1 AAACACAAAAAAAACCATAAAAAT
42155274 AAA
1 AAA
42155277 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.06
Consensus pattern (24 bp):
AAACACAAAAAAAACCATAAAAAT
Found at i:42157938 original size:131 final size:129
Alignment explanation
Indices: 42157761--42158057 Score: 310
Period size: 131 Copynumber: 2.3 Consensus size: 129
42157751 AGATTTGATA
* * * * * * *
42157761 TTTGGCAATTCGTGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCTCGTTTGCTCAAAATAAT
1 TTTGGCAATTCG-AGAATCATGCCCTATCGTGCTGGGTTGCAATTTCCCATTTGCTCAAAACAAT
* * *
42157826 CAAATATTCCTTCGA-AATTTCACTCAGGTTT-TCTAAAAATCTTTTAAAACGAAGGCAATACTC
65 CAAATATTCCTT-GAGAATTTCACTCAGGTTTAT-TAAAAACCTTTCAAAACAAAGG--ATACTC
*
42157889 GGTG
126 GATG
* **
42157893 TTTGTCAATTCGAGAATCATGCCCTATCGTGCTGGGTTGTGATTTCCCATTTGCTCAAAACAATC
1 TTTGGCAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCAATTTCCCATTTGCTCAAAACAATC
* * * ** * ** *
42157958 GAATATTTCTTTAGGTTTTCACTCATGTTTATTAAAAACCTTTCAAAACAAAGGATGTTTGATG
66 AAATATTCCTTGAGAATTTCACTCAGGTTTATTAAAAACCTTTCAAAACAAAGGATACTCGATG
* *
42158022 TTTGGCGATTTGAGAATCATGCCCTATCGTGCTGGG
1 TTTGGCAATTCGAGAATCATGCCCTATCGTGCTGGG
42158058 ATCCGCTTTT
Statistics
Matches: 137, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
129 39 0.28
130 1 0.01
131 85 0.62
132 12 0.09
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (129 bp):
TTTGGCAATTCGAGAATCATGCCCTATCGTGCTGGGTTGCAATTTCCCATTTGCTCAAAACAATC
AAATATTCCTTGAGAATTTCACTCAGGTTTATTAAAAACCTTTCAAAACAAAGGATACTCGATG
Found at i:42169605 original size:44 final size:44
Alignment explanation
Indices: 42169531--42170097 Score: 656
Period size: 44 Copynumber: 12.9 Consensus size: 44
42169521 GGCAAATCTT
* * * *
42169531 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * * *
42169575 TCAGGTTTGGCGGT-TCTGTATTGGTGGAGAGTAGATCAAAGATA
1 GCAGATTTGGC-GTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* ** * *
42169619 GCAGATTTGGCATCTCTGTATTGAAAGG-GAGTAGATCGAAGATG
1 GCAGATTTGGCGTCTCTGTATTG-GCGGAGAGCAGATCGAAGATA
* *
42169663 GTAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAAATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * *
42169707 GCAGATTTGGCATCTTTGTATTGGCAGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
42169751 GCAGATTTTGCGTCTCTGTATTGGCGGAGAGTAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
42169795 GTAGATTTGGCGTCTCTGTATTGGTGGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * *
42169839 GCAGATTTGGCATCTCTGTGTTGACAGAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
42169883 ACAGATTTGTGC--CTCTGTATTGGTGGAGAGCAGATCAAAGATA
1 GCAGATTTG-GCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * * * * * *
42169926 GTAGATTTGGCATTTCTGTGTTGACAGAGAGTAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
42169970 GTAGATTTGGCGTCTCTATATTGGCGTAGAGCAGATCGAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* *
42170014 GCAGATTTGGCGTCTCTGTATTGGCAGAGAGCAGATCAAAGATA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
* * *
42170058 GCAGATTTGGCATCTCTGTATTGGCAGAGAGCATATCGAA
1 GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAA
42170098 AATAACATAT
Statistics
Matches: 438, Mismatches: 78, Indels: 14
0.83 0.15 0.03
Matches are distributed among these distances:
42 2 0.00
43 36 0.08
44 395 0.90
45 5 0.01
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.28
Consensus pattern (44 bp):
GCAGATTTGGCGTCTCTGTATTGGCGGAGAGCAGATCGAAGATA
Found at i:42173423 original size:40 final size:39
Alignment explanation
Indices: 42173379--42173555 Score: 169
Period size: 40 Copynumber: 4.4 Consensus size: 39
42173369 GCTCGGTTGT
* *
42173379 CTTCGGGACATAGCCCGGTTATAGTAATTCGCACAATTGC
1 CTTCGGGACATAGCCCGGTT-TAGTAACTCGCACAAATGC
42173419 CTTCGGGA-ATTAGCCCGGATTTAGTAACTCGCACAAATGC
1 CTTCGGGACA-TAGCCCGG-TTTAGTAACTCGCACAAATGC
* * * *
42173459 TTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGC
1 CTTCGGGACATAGCCCGG-TTTAGTAACTCGCACAAATGC
* * * * *
42173499 CTTCGGG-GATTGACCCGGATTTAGTCACTTAGCACAAAAGC
1 CTTCGGGACATAG-CCCGG-TTTAGTAAC-TCGCACAAATGC
*
42173540 CTTCGGGACTTAGCCC
1 CTTCGGGACATAGCCC
42173556 AGATACCATT
Statistics
Matches: 111, Mismatches: 20, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.02
40 85 0.77
41 22 0.20
42 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (39 bp):
CTTCGGGACATAGCCCGGTTTAGTAACTCGCACAAATGC
Found at i:42173477 original size:80 final size:81
Alignment explanation
Indices: 42173379--42173551 Score: 224
Period size: 80 Copynumber: 2.1 Consensus size: 81
42173369 GCTCGGTTGT
* * * *
42173379 CTTCGGGACATAGCCCGGTTATAGTAATTCGCACAATTGCCTTCGGGAATT-AGCCCGGATTTAG
1 CTTCGGGACTTAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGA-CCCGGATTTAG
* *
42173443 TAAC-TCGCACAAATGC
65 TAACTTAGCACAAAAGC
* * * *
42173459 TTTCGGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTCGGGGATTGACCCGGATTTAGT
1 CTTCGGGACTTAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
*
42173524 CACTTAGCACAAAAGC
66 AACTTAGCACAAAAGC
42173540 CTTCGGGACTTA
1 CTTCGGGACTTA
42173552 GCCCAGATAC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
80 57 0.72
81 22 0.28
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.27
Consensus pattern (81 bp):
CTTCGGGACTTAACCCGGTTATAGTAACTCGCACAAATGCCTTCGGGAATTGACCCGGATTTAGT
AACTTAGCACAAAAGC
Found at i:42181437 original size:40 final size:40
Alignment explanation
Indices: 42181377--42181591 Score: 242
Period size: 40 Copynumber: 5.4 Consensus size: 40
42181367 GGTTGTCTTT
* * *
42181377 GGGACATAG-CCGG-TTATAGTAATTCGCACAATTGCCTTC
1 GGGACTTAGCCCGGATT-TAGTAACTCGCACAAATGCCTTC
*
42181416 GGGAATTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC
* * *
42181456 GGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTT-
1 GGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC
* * *
42181495 GGGACTTAACCCGGTTTTGGTAACTCGCACAAATGCCTTC
1 GGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC
* * *
42181535 GGGGA-TT-GACCCGGATTTAGTCACTTAGCACAAAAGCCTTC
1 -GGGACTTAG-CCCGGATTTAGTAAC-TCGCACAAATGCCTTC
42181576 GGGACTTAGCCCGGAT
1 GGGACTTAGCCCGGAT
42181592 ACCATTCGGA
Statistics
Matches: 154, Mismatches: 14, Indels: 14
0.85 0.08 0.08
Matches are distributed among these distances:
39 46 0.30
40 78 0.51
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (40 bp):
GGGACTTAGCCCGGATTTAGTAACTCGCACAAATGCCTTC
Found at i:42181508 original size:79 final size:80
Alignment explanation
Indices: 42181386--42181591 Score: 263
Period size: 79 Copynumber: 2.6 Consensus size: 80
42181376 TGGGACATAG
* * * *
42181386 CCGGTTATAGTAATTCGCACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTCGCACAAATG
1 CCGGTTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
42181451 CCTTC-GGGACTTAAC
66 CCTTCGGGGA-TTAAC
* * * *
42181466 CCGGTTTTGGTAACTCGCACAAATGCCTT-GGGACTTAACCCGGTTTTGGTAACTCGCACAAATG
1 CCGGTTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
*
42181530 CCTTCGGGGATTGAC
66 CCTTCGGGGATTAAC
* * * *
42181545 CCGGATTTAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 CCGGTTTTAGTAAC-TCGCACAAATGCCTTCGGGACTTAGCCCGGAT
42181592 ACCATTCGGA
Statistics
Matches: 107, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
79 51 0.48
80 42 0.39
81 14 0.13
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (80 bp):
CCGGTTTTAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAAATG
CCTTCGGGGATTAAC
Found at i:42185062 original size:25 final size:25
Alignment explanation
Indices: 42185034--42185098 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
42185024 CTTGGATTTT
*
42185034 AAGGAATGTTTCACTTTTAGGTTTC
1 AAGGAATGTTTCACTTATAGGTTTC
42185059 AAGGAATGTTTCACTTATAGGTTTC
1 AAGGAATGTTTCACTTATAGGTTTC
42185084 AAGGAATGTTTCACT
1 AAGGAATGTTTCACT
42185099 AACATTTAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (25 bp):
AAGGAATGTTTCACTTATAGGTTTC
Found at i:42187688 original size:7 final size:7
Alignment explanation
Indices: 42187676--42187706 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
42187666 TTTGATTGTA
42187676 ATTGGAC
1 ATTGGAC
42187683 ATTGGAC
1 ATTGGAC
42187690 ATTGGAC
1 ATTGGAC
42187697 ATTGGAC
1 ATTGGAC
42187704 ATT
1 ATT
42187707 TTATTTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (7 bp):
ATTGGAC
Found at i:42190359 original size:28 final size:28
Alignment explanation
Indices: 42190319--42190417 Score: 101
Period size: 28 Copynumber: 3.5 Consensus size: 28
42190309 GTAATAAGCC
*
42190319 CGCACACTTAGTGCTTAATAGTCGAACT
1 CGCACACTTAGTGCTTAATAATCGAACT
*
42190347 CGCACACTTAGTGC-TATATAATCAAACT
1 CGCACACTTAGTGCTTA-ATAATCGAACT
* ** * * *
42190375 TGCACACTTAGTGCTATACCATTTGAACC
1 CGCACACTTAGTGCT-TAATAATCGAACT
42190404 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42190418 CAATTTGTGA
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
27 2 0.03
28 36 0.62
29 18 0.31
30 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.28
Consensus pattern (28 bp):
CGCACACTTAGTGCTTAATAATCGAACT
Found at i:42196443 original size:28 final size:28
Alignment explanation
Indices: 42196378--42196478 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
42196368 ATAGTGAATC
*
42196378 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
42196407 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
42196435 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
42196465 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42196479 CATACCCTTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:42196527 original size:29 final size:29
Alignment explanation
Indices: 42196503--42196596 Score: 170
Period size: 29 Copynumber: 3.2 Consensus size: 29
42196493 TCGCACACCC
*
42196503 AGTGCCGTATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
42196532 AGTGCCATATATTTCCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
*
42196561 AGTGCCATATATTTTCAGCATGCACACTT
1 AGTGCCATATATTTCCAGCATGCACACTT
42196590 AGTGCCA
1 AGTGCCA
42196597 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.31
Consensus pattern (29 bp):
AGTGCCATATATTTCCAGCATGCACACTT
Found at i:42196528 original size:58 final size:58
Alignment explanation
Indices: 42196466--42196596 Score: 165
Period size: 58 Copynumber: 2.3 Consensus size: 58
42196456 TTTTAAACCC
* * * *
42196466 GCACACTTAGTGCCATACCCTTCGAG-TTCGCACACCCAGTGCCGTATATTTCCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCAT-GCACACCCAGTGCCATATATTTCCAGCAT
* * ** *
42196524 GCACACTTAGTGCCATATATTTCCAGCATGCACACTTAGTGCCATATATTTTCAGCAT
1 GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
42196582 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42196597 ATCTCGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 62 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.31, G:0.16, T:0.28
Consensus pattern (58 bp):
GCACACTTAGTGCCATACACTTCCAGCATGCACACCCAGTGCCATATATTTCCAGCAT
Done.