Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D09
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: 51526817
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 216316 characters in sequence are not A, C, G, or T
File 61 of 172
Found at i:16842508 original size:29 final size:28
Alignment explanation
Indices: 16842476--16842551 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
16842466 TATACTTACC
16842476 ATTCCTTCAGAGTTCGCCATATATATACT
1 ATTCCTTCAGAGTTCGCCA-ATATATACT
* *
16842505 ATTCCTTCAGAGTTCGGC-ATGTATACT
1 ATTCCTTCAGAGTTCGCCAATATATACT
* *
16842532 ACTCCTTCATAGTTCGCCAA
1 ATTCCTTCAGAGTTCGCCAA
16842552 GAATACCACT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 23 0.56
28 1 0.02
29 17 0.41
ACGTcount: A:0.25, C:0.26, G:0.13, T:0.36
Consensus pattern (28 bp):
ATTCCTTCAGAGTTCGCCAATATATACT
Found at i:16842712 original size:27 final size:27
Alignment explanation
Indices: 16842665--16842731 Score: 80
Period size: 27 Copynumber: 2.4 Consensus size: 27
16842655 TTCACCATAG
* * *
16842665 AGGCTTCTATTATAATAGATTTCCACAA
1 AGGCTTCCATT-TAATAGATTGCCAAAA
*
16842693 AGGCTTCCATTTCATAGATTGCCAAAA
1 AGGCTTCCATTTAATAGATTGCCAAAA
*
16842720 AGGTTTCCATTT
1 AGGCTTCCATTT
16842732 TCTAGTGTGC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 24 0.71
28 10 0.29
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.36
Consensus pattern (27 bp):
AGGCTTCCATTTAATAGATTGCCAAAA
Found at i:16844379 original size:13 final size:13
Alignment explanation
Indices: 16844343--16844494 Score: 96
Period size: 13 Copynumber: 11.5 Consensus size: 13
16844333 TGTAAATTTT
16844343 TTATATGAAATGG
1 TTATATGAAATGG
16844356 TTAT-TCGAAATGG
1 TTATAT-GAAATGG
* *
16844369 TTATATAAAATGA
1 TTATATGAAATGG
* *
16844382 ATATATGAATTGG
1 TTATATGAAATGG
*
16844395 TTATATGAATTGG
1 TTATATGAAATGG
**
16844408 TTATATTGAAATAT
1 TTATA-TGAAATGG
*
16844422 TTATACTG-AATGA
1 TTATA-TGAAATGG
*
16844435 TTATATG-AATCAG
1 TTATATGAAAT-GG
**
16844448 TTATATGGAAATAA
1 TTATAT-GAAATGG
*
16844462 TTATAT-AAAGTGT
1 TTATATGAAA-TGG
* *
16844475 TTATACGAAATGT
1 TTATATGAAATGG
16844488 TTATATG
1 TTATATG
16844495 GATAATTATG
Statistics
Matches: 111, Mismatches: 20, Indels: 16
0.76 0.14 0.11
Matches are distributed among these distances:
12 9 0.08
13 75 0.68
14 24 0.22
15 3 0.03
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.41
Consensus pattern (13 bp):
TTATATGAAATGG
Found at i:16844440 original size:53 final size:52
Alignment explanation
Indices: 16844343--16844459 Score: 128
Period size: 53 Copynumber: 2.2 Consensus size: 52
16844333 TGTAAATTTT
* **
16844343 TTATATGAAATGGTTATTCGAAATGGTTATATAAAATGAATATATGAATTGG
1 TTATATGAAATGGTTATTCGAAATAGTTATATAAAATGAATATATGAATCAG
* * * * *
16844395 TTATATGAATTGGTTATATTGAAATATTTATACT-GAATGATTATATGAATCAG
1 TTATATGAAATGGTTAT-TCGAAATAGTTATA-TAAAATGAATATATGAATCAG
16844448 TTATATGGAAAT
1 TTATAT-GAAAT
16844460 AATTATATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
52 16 0.30
53 32 0.60
54 5 0.09
ACGTcount: A:0.39, C:0.03, G:0.17, T:0.41
Consensus pattern (52 bp):
TTATATGAAATGGTTATTCGAAATAGTTATATAAAATGAATATATGAATCAG
Found at i:16844479 original size:40 final size:40
Alignment explanation
Indices: 16844395--16844479 Score: 100
Period size: 40 Copynumber: 2.1 Consensus size: 40
16844385 TATGAATTGG
** * * *
16844395 TTATATGAATTGGTTATATTGAAATATTTATACTGAATGA
1 TTATATGAATCAGTTATATGGAAATAATTATACTAAATGA
*
16844435 TTATATGAATCAGTTATATGGAAATAATTATA-TAAAGTGT
1 TTATATGAATCAGTTATATGGAAATAATTATACTAAA-TGA
16844475 TTATA
1 TTATA
16844480 CGAAATGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 3 0.08
40 35 0.92
ACGTcount: A:0.40, C:0.02, G:0.14, T:0.44
Consensus pattern (40 bp):
TTATATGAATCAGTTATATGGAAATAATTATACTAAATGA
Found at i:16844532 original size:13 final size:13
Alignment explanation
Indices: 16844514--16844551 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
16844504 GTAAAAAGGG
16844514 ACATTTGAAATGA
1 ACATTTGAAATGA
16844527 ACATTTGAAATGGA
1 ACATTTGAAAT-GA
*
16844541 A-ATGTGAAATG
1 ACATTTGAAATG
16844552 TTAAATGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 1 0.04
13 19 0.83
14 3 0.13
ACGTcount: A:0.45, C:0.05, G:0.21, T:0.29
Consensus pattern (13 bp):
ACATTTGAAATGA
Found at i:16849963 original size:26 final size:26
Alignment explanation
Indices: 16849931--16849996 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
16849921 CATCCCAACC
*
16849931 CACAGCTCGTGTGAGTATACCCATTT
1 CACAGCTCGTGTGAGTAGACCCATTT
* *
16849957 CATAGCTCGTGTGAGTAGGCCCATTT
1 CACAGCTCGTGTGAGTAGACCCATTT
*
16849983 CACAGATCGTGTGA
1 CACAGCTCGTGTGA
16849997 AATGTATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (26 bp):
CACAGCTCGTGTGAGTAGACCCATTT
Found at i:16853681 original size:23 final size:23
Alignment explanation
Indices: 16853655--16853705 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
16853645 TACGCATAAG
16853655 AATGAAATGCATGGAATTCCTCA
1 AATGAAATGCATGGAATTCCTCA
16853678 AATGAAATGCATGGAATTCCTCA
1 AATGAAATGCATGGAATTCCTCA
16853701 AATGA
1 AATGA
16853706 TCTACAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (23 bp):
AATGAAATGCATGGAATTCCTCA
Found at i:16857822 original size:18 final size:19
Alignment explanation
Indices: 16857798--16857865 Score: 70
Period size: 18 Copynumber: 3.6 Consensus size: 19
16857788 CCTCCATAAC
16857798 AAACAGAAGCTTGAAAGCT
1 AAACAGAAGCTTGAAAGCT
16857817 -AACAGAAGCTCGTGAGAA-CT
1 AAACAGAAGCT--TGA-AAGCT
* *
16857837 GAA-AGAAGCTCGAAAGCT
1 AAACAGAAGCTTGAAAGCT
16857855 AAACAGAAGCT
1 AAACAGAAGCT
16857866 CGTAAGAGCT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
17 2 0.05
18 16 0.39
19 7 0.17
20 12 0.29
21 4 0.10
ACGTcount: A:0.46, C:0.18, G:0.24, T:0.13
Consensus pattern (19 bp):
AAACAGAAGCTTGAAAGCT
Found at i:16869892 original size:126 final size:127
Alignment explanation
Indices: 16869744--16869999 Score: 460
Period size: 126 Copynumber: 2.0 Consensus size: 127
16869734 GAAAAACCTC
*
16869744 TTGTTCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
1 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
* *
16869809 TTTGACAAACAAGTTG-CCCCGAAATTAAAAGATCCTGGGAGCTTTACCATCCCATGTTCAA
66 TTTGACAAACAAGTTGCCCCCAAAATTAAAAGATCCTAGGAGCTTTACCATCCCATGTTCAA
* *
16869870 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGTTTT
1 TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
16869935 TTTGACAAACAAGTTGCCCCCAAAATTAAAAGATCCTAGGAGCTTTACCATCCCATGTTCAA
66 TTTGACAAACAAGTTGCCCCCAAAATTAAAAGATCCTAGGAGCTTTACCATCCCATGTTCAA
16869997 TTG
1 TTG
16870000 ACAATCATTA
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
126 78 0.63
127 46 0.37
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (127 bp):
TTGTCCATGAAGAAGAAGCTTACTGATATTGAAACTATTGCACTCACAGAAGGCTGTAGTGCTGT
TTTGACAAACAAGTTGCCCCCAAAATTAAAAGATCCTAGGAGCTTTACCATCCCATGTTCAA
Found at i:16892390 original size:67 final size:68
Alignment explanation
Indices: 16892313--16892452 Score: 246
Period size: 68 Copynumber: 2.1 Consensus size: 68
16892303 TGTGTGTTCT
16892313 ATTTTTCTTTC-TTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGA
1 ATTTTTCTTTCTTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGA
16892377 CAA
66 CAA
* * *
16892380 ATTTTTCTTTCTTTTTCTTTGTGATATATTGTCATTATCATCCTTCTATTTTTAACAATTATTGA
1 ATTTTTCTTTCTTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGA
16892445 CAA
66 CAA
16892448 ATTTT
1 ATTTT
16892453 GTTTTACTTC
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
67 11 0.16
68 58 0.84
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.56
Consensus pattern (68 bp):
ATTTTTCTTTCTTTTTCTTTGTGATATATTATCATTATCAACATTCTATTTTTAACAATTATTGA
CAA
Found at i:16892846 original size:28 final size:28
Alignment explanation
Indices: 16892806--16892863 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
16892796 TCACAAATTA
16892806 ATTGATATTCCAAACTTAAACACGTTTT
1 ATTGATATTCCAAACTTAAACACGTTTT
16892834 ATTGATATTCCAAACTTAAACACGTTTT
1 ATTGATATTCCAAACTTAAACACGTTTT
16892862 AT
1 AT
16892864 CCCTCTAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (28 bp):
ATTGATATTCCAAACTTAAACACGTTTT
Found at i:16896100 original size:16 final size:16
Alignment explanation
Indices: 16896081--16896111 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16896071 GTTAAAAATA
16896081 ATATAAAATTTATAAT
1 ATATAAAATTTATAAT
*
16896097 ATATAACATTTATAA
1 ATATAAAATTTATAA
16896112 AAAAAGTATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATAAAATTTATAAT
Found at i:16897377 original size:11 final size:11
Alignment explanation
Indices: 16897351--16897408 Score: 62
Period size: 11 Copynumber: 5.2 Consensus size: 11
16897341 AACTAATCCT
*
16897351 CTCTCAAATTTT
1 CTCTC-AATTTC
16897363 CTCTCAATTTC
1 CTCTCAATTTC
*
16897374 CTCTCAGTTTC
1 CTCTCAATTTC
* *
16897385 CTCTCAAATTG
1 CTCTCAATTTC
*
16897396 CTCTCAAATTC
1 CTCTCAATTTC
16897407 CT
1 CT
16897409 TCCAAATTTC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
11 35 0.88
12 5 0.12
ACGTcount: A:0.21, C:0.33, G:0.03, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:16897407 original size:22 final size:22
Alignment explanation
Indices: 16897351--16897426 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
16897341 AACTAATCCT
* *
16897351 CTCTCAAATTTTCTCTCAATTTC
1 CTCTCAAA-TTCCTCTCAAATTC
** *
16897374 CTCTCAGTTTCCTCTCAAATTG
1 CTCTCAAATTCCTCTCAAATTC
*
16897396 CTCTCAAATTCCT-TCCAAATTT
1 CTCTCAAATTCCTCT-CAAATTC
*
16897418 CACTCAAAT
1 CTCTCAAAT
16897427 CCATATTTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 3
0.78 0.16 0.05
Matches are distributed among these distances:
21 1 0.02
22 36 0.84
23 6 0.14
ACGTcount: A:0.25, C:0.32, G:0.03, T:0.41
Consensus pattern (22 bp):
CTCTCAAATTCCTCTCAAATTC
Found at i:16897451 original size:51 final size:51
Alignment explanation
Indices: 16897386--16897485 Score: 121
Period size: 51 Copynumber: 2.0 Consensus size: 51
16897376 CTCAGTTTCC
*
16897386 TCTCAAATTGCTCTCAAATTCCT-TCCAAATTTCACTCAAATCCATATTTAA
1 TCTCAAATTACTCTCAAATTCCTCT-CAAATTTCACTCAAATCCATATTTAA
* * * * * *
16897437 TCTCAATTTACTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTACTCTCAAATTCCTCTCAAATTTCACTCAAATCCATATTT
16897486 TTAAATATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
51 40 0.98
52 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (51 bp):
TCTCAAATTACTCTCAAATTCCTCTCAAATTTCACTCAAATCCATATTTAA
Found at i:16900927 original size:127 final size:124
Alignment explanation
Indices: 16900652--16901090 Score: 533
Period size: 126 Copynumber: 3.5 Consensus size: 124
16900642 AACATGCTAT
* * *
16900652 TGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCTTGCTAGA
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTC-CAAATTCTTCTCATAAAGCATCCTGCTTGA
* * * * *
16900717 AGCGATTTT-ATACTGTTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGGATCTAC
65 AGCGTTTTTAATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTAC
16900776 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCGCAAATTCTTCTCA-AATAGCATCCTGCTTG
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTC-CAAATTCTTCTCATAA-AGCATCCTGCTTG
* * *
16900840 CAGCGTTGTTTAATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCAAC
64 AAGCGTT-TTTAATACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCTAC
* * *
16900903 TGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCATAAAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCCAAA-TTCTTCTCATAAAGCATCCTGCTTGA
* * * * *
16900968 AGCATTTTTTAA-ACTATTTGCTTAAAAATGTCAACTCGAAATTATTTTTCTAGGACCTAC
65 AGC-GTTTTTAATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTAC
* * * * *** * *
16901028 TGTAGCAAAAGTGCGTACACGTGGGCGCGACTTAAAAAATTCTTCTGATAAATCATCCTGCTT
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGA-TTTCCAAATTCTTCTCATAAAGCATCCTGCTT
16901091 TGATTTTATC
Statistics
Matches: 278, Mismatches: 29, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
123 2 0.01
124 62 0.22
125 64 0.23
126 73 0.26
127 73 0.26
128 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (124 bp):
TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCCAAATTCTTCTCATAAAGCATCCTGCTTGAA
GCGTTTTTAATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTAC
Found at i:16901071 original size:125 final size:125
Alignment explanation
Indices: 16900652--16901090 Score: 542
Period size: 127 Copynumber: 3.5 Consensus size: 125
16900642 AACATGCTAT
* * * *
16900652 TGTAGCAAAAGCGCATCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCTTGCTAGA
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGCTTGA
* * * * *
16900717 AGCGA--TTTTATACTGTTTGCTCAGAAACGTCAAGTCAAAATTATTTTTCCAGGATCTAC
66 AGC-ATTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTAC
**
16900776 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCGCAAATTCTTCTCA-AATAGCATCCTGCTTG
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAA-AGCATCCTGCTTG
* * * * *
16900840 CAGCGTTGTTTAATACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCAAC
65 AAGCATTTTTTAA-ACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGACCTAC
* * *
16900903 TGTAGCAAAAGTGCGTCCACGAGGGCGCGATTTCAAAATTTCTTCTCATAAAGCATCCTGCTTGA
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGCTTGA
* * * *
16900968 AGCATTTTTTAAACTATTTGCTTAAAAATGTCAACTCGAAATTATTTTTCTAGGACCTAC
66 AGCATTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTAC
* * * * * * * *
16901028 TGTAGCAAAAGTGCGTACACGTGGGCGCGACTTAAAAAATTCTTCTGATAAATCATCCTGCTT
1 TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGCTT
16901091 TGATTTTATC
Statistics
Matches: 274, Mismatches: 35, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
123 2 0.01
124 60 0.22
125 71 0.26
126 62 0.23
127 77 0.28
128 2 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (125 bp):
TGTAGCAAAAGCGCATCCACGAGGGCGCGATTTCAAAAATTCTTCTCATAAAGCATCCTGCTTGA
AGCATTTTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTAC
Found at i:16901905 original size:21 final size:21
Alignment explanation
Indices: 16901881--16901923 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
16901871 AAAAAAAATA
* *
16901881 TTATTAAGTAAATGGAATTTT
1 TTATGAAGTAAATGGAAATTT
*
16901902 TTATGAATTAAATGGAAATTT
1 TTATGAAGTAAATGGAAATTT
16901923 T
1 T
16901924 AAATGTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.14, T:0.47
Consensus pattern (21 bp):
TTATGAAGTAAATGGAAATTT
Found at i:16905766 original size:6 final size:6
Alignment explanation
Indices: 16905755--16905790 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
16905745 TAGGTTTCTA
* *
16905755 GAAATG GAAATG GAAATG AAAATG AAAATG GAAATG
1 GAAATG GAAATG GAAATG GAAATG GAAATG GAAATG
16905791 AAAACTTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
GAAATG
Found at i:16905783 original size:18 final size:18
Alignment explanation
Indices: 16905756--16905794 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
16905746 AGGTTTCTAG
*
16905756 AAATGGAAATGGAAATGA
1 AAATGAAAATGGAAATGA
16905774 AAATGAAAATGGAAATGA
1 AAATGAAAATGGAAATGA
16905792 AAA
1 AAA
16905795 CTTGCAATCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (18 bp):
AAATGAAAATGGAAATGA
Found at i:16905791 original size:12 final size:12
Alignment explanation
Indices: 16905756--16905794 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
16905746 AGGTTTCTAG
*
16905756 AAATGGAAATGG
1 AAATGGAAATGA
*
16905768 AAATGAAAATGA
1 AAATGGAAATGA
16905780 AAATGGAAATGA
1 AAATGGAAATGA
16905792 AAA
1 AAA
16905795 CTTGCAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (12 bp):
AAATGGAAATGA
Found at i:16906732 original size:38 final size:39
Alignment explanation
Indices: 16906657--16906734 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 39
16906647 CCGCTATGTA
* *
16906657 AGAAAATCATTTTCAAACAAAGTTTTTTTTCAACAATTGG
1 AGAAAATAATTTTCAAACAAAG-ATTTTTTCAACAATTGG
16906697 AGAAAATAATTTTCAAACAAA-ATTTTTTCAACAATTGG
1 AGAAAATAATTTTCAAACAAAGATTTTTTCAACAATTGG
16906735 TATAAGAGCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 16 0.44
40 20 0.56
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (39 bp):
AGAAAATAATTTTCAAACAAAGATTTTTTCAACAATTGG
Found at i:16912464 original size:41 final size:41
Alignment explanation
Indices: 16912407--16912556 Score: 203
Period size: 41 Copynumber: 3.7 Consensus size: 41
16912397 TTTAACATAT
*
16912407 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* *
16912448 TCACCGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
* * * * *
16912489 TCACCAGCACTTAGCCTGTTAGG-TCCATAACCTGGTTTAGA
1 TCACCGGCACTTAGCCTGCTAGGCT-TATAACCTGATTCAGA
*
16912530 TCACCGGCACTTAGCCTGCTAGACTTA
1 TCACCGGCACTTAGCCTGCTAGGCTTA
16912557 AAGTCTGAAT
Statistics
Matches: 94, Mismatches: 13, Indels: 4
0.85 0.12 0.04
Matches are distributed among these distances:
40 1 0.01
41 92 0.98
42 1 0.01
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATTCAGA
Found at i:16912575 original size:82 final size:83
Alignment explanation
Indices: 16912405--16912581 Score: 202
Period size: 82 Copynumber: 2.2 Consensus size: 83
16912395 AATTTAACAT
* *
16912405 ATTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCGGCACGTAGCCTGCTAG
1 ATTCACCGGCACTTAGCCTGCTAGGCTCATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
**
16912470 GTTTATAACCTGATTCAG
66 ACTTATAACCTGATTCAG
* * * * *
16912488 A-TCACCAGCACTTAGCCTGTTAGG-TCCATAACCTGGTTTAGATCACCGGCACTTAGCCTGCTA
1 ATTCACCGGCACTTAGCCTGCTAGGCT-CATAACCTGATTCAGATCACCGGCACGTAGCCTGCTA
*
16912551 GACTTA-AAGTCTGAATT-A-
65 GACTTATAA-CCTG-ATTCAG
16912569 ATTCACCGGCACT
1 ATTCACCGGCACT
16912582 ACATCTGCTA
Statistics
Matches: 79, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
81 4 0.05
82 71 0.90
83 4 0.05
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.28
Consensus pattern (83 bp):
ATTCACCGGCACTTAGCCTGCTAGGCTCATAACCTGATTCAGATCACCGGCACGTAGCCTGCTAG
ACTTATAACCTGATTCAG
Found at i:16914622 original size:13 final size:13
Alignment explanation
Indices: 16914604--16914628 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16914594 CAATCAAATG
16914604 CACACAAAATAAA
1 CACACAAAATAAA
16914617 CACACAAAATAA
1 CACACAAAATAA
16914629 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:16922183 original size:19 final size:20
Alignment explanation
Indices: 16922159--16922197 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
16922149 TTTGTGTACG
16922159 CTATTT-TTCTGTGG-TTTTT
1 CTATTTGTTC-GTGGCTTTTT
16922178 CTATTTGTTCGTGGCTTTTT
1 CTATTTGTTCGTGGCTTTTT
16922198 TTTTCTAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.05, C:0.13, G:0.18, T:0.64
Consensus pattern (20 bp):
CTATTTGTTCGTGGCTTTTT
Found at i:16929102 original size:36 final size:36
Alignment explanation
Indices: 16929059--16929130 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
16929049 AGCTGAGAGA
16929059 ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
1 ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
* *
16929095 ATGAATAAAACCTTTCTTGACATGGTTTGTTCAATG
1 ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
16929131 TTAAGTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (36 bp):
ATGAATAAAACCTTACTTGACATGGTTCGTTCAATG
Found at i:16931876 original size:41 final size:41
Alignment explanation
Indices: 16931812--16931918 Score: 180
Period size: 41 Copynumber: 2.6 Consensus size: 41
16931802 TTTAAACAGA
* *
16931812 TTCACTGGCACTTCA-CCTACTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTT-AGCCTGCTAGGCTTATAGCCTGATTCAG
16931853 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
16931894 TTCACCGGCACTTAGCCTGCTAGGC
1 TTCACCGGCACTTAGCCTGCTAGGC
16931919 ACTTAGCCTG
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 1 0.02
41 62 0.98
ACGTcount: A:0.20, C:0.31, G:0.21, T:0.29
Consensus pattern (41 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
Found at i:16931921 original size:16 final size:16
Alignment explanation
Indices: 16931900--16931944 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
16931890 TCAGTTCACC
16931900 GGCACTTAGCCTGCTA
1 GGCACTTAGCCTGCTA
16931916 GGCACTTAGCCTGCTA
1 GGCACTTAGCCTGCTA
**
16931932 GGCTTTTAGCCTG
1 GGCACTTAGCCTG
16931945 ATTCAGTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.29
Consensus pattern (16 bp):
GGCACTTAGCCTGCTA
Found at i:16931961 original size:41 final size:41
Alignment explanation
Indices: 16931916--16932014 Score: 180
Period size: 41 Copynumber: 2.4 Consensus size: 41
16931906 TAGCCTGCTA
* *
16931916 GGCACTTAGCCTGCTAGGCTTTTAGCCTGATTCAGTTCACC
1 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACC
16931957 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACC
1 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACC
16931998 GGCACTTAGCCTGCTAG
1 GGCACTTAGCCTGCTAG
16932015 ACGTAAAGTC
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 56 1.00
ACGTcount: A:0.19, C:0.29, G:0.23, T:0.28
Consensus pattern (41 bp):
GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACC
Found at i:16931985 original size:57 final size:57
Alignment explanation
Indices: 16931859--16931975 Score: 225
Period size: 57 Copynumber: 2.1 Consensus size: 57
16931849 TCAGTTCACC
16931859 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
*
16931916 GGCACTTAGCCTGCTAGGCTTTTAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
16931973 GGC
1 GGC
16931976 TTATAGCCTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.18, C:0.30, G:0.24, T:0.28
Consensus pattern (57 bp):
GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
Found at i:16931987 original size:98 final size:98
Alignment explanation
Indices: 16931818--16932014 Score: 351
Period size: 98 Copynumber: 2.0 Consensus size: 98
16931808 CAGATTCACT
16931818 GGCACTTCACCTACTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATA
1 GGCACTTCACCTACTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATA
*
16931883 GCCTGATTCAGTTCACCGGCACTTAGCCTGCTA
66 GCCTGATTCAGATCACCGGCACTTAGCCTGCTA
* *
16931916 GGCACTT-AGCCTGCTAGGCTTTTAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTAT
1 GGCACTTCA-CCTACTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTAT
16931980 AGCCTGATTCAGATCACCGGCACTTAGCCTGCTA
65 AGCCTGATTCAGATCACCGGCACTTAGCCTGCTA
16932014 G
1 G
16932015 ACGTAAAGTC
Statistics
Matches: 95, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 1 0.01
98 94 0.99
ACGTcount: A:0.20, C:0.30, G:0.22, T:0.28
Consensus pattern (98 bp):
GGCACTTCACCTACTAGGCTTATAGCCTGATTCAGTTCACCGGCACTTAGCCTGCTAGGCTTATA
GCCTGATTCAGATCACCGGCACTTAGCCTGCTA
Found at i:16932038 original size:41 final size:41
Alignment explanation
Indices: 16931916--16932040 Score: 117
Period size: 41 Copynumber: 3.0 Consensus size: 41
16931906 TAGCCTGCTA
* * ** **
16931916 GGCACTTAGCCTGCTAGGCTTTTAGCCTGATTCAGTTCACC
1 GGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACC
* * * ** *
16931957 GGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACC
1 GGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACC
*
16931998 GGCACTTAGCCTGCTAGACGTAAAGTCC-GAAACATTTCACC
1 GGCACTTAGCCTGCTAGACGTAAAG-CCTGAAACAGTTCACC
16932039 GG
1 GG
16932041 AAATTTATCT
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
41 72 0.97
42 2 0.03
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.26
Consensus pattern (41 bp):
GGCACTTAGCCTGCTAGACGTAAAGCCTGAAACAGTTCACC
Found at i:16933741 original size:28 final size:31
Alignment explanation
Indices: 16933709--16933767 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
16933699 TGTTTTGTTT
16933709 TTATTATAATAA-CATTAT-AAT-ATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
* *
16933737 TTATTATTATAACCTTTATAAATAATATAAA
1 TTATTATAATAACCATTATAAATAATATAAA
16933768 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 11 0.42
29 5 0.19
30 3 0.12
31 7 0.27
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (31 bp):
TTATTATAATAACCATTATAAATAATATAAA
Found at i:16942340 original size:73 final size:71
Alignment explanation
Indices: 16942222--16942503 Score: 291
Period size: 73 Copynumber: 3.9 Consensus size: 71
16942212 AGGCCGACAT
* * * * *
16942222 TTAAAAAAGGTTGGGATAAACC-TGTCTGAAGAAATCTTAAAAAGGTTAGGATAGACCTATCTAA
1 TTAAAAAA-GTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGACCTGTCTAA
16942286 GACAACC
65 GACAACC
* * *
16942293 TTAAAAAATTTGGAATAGACCTTGTCTAAAGCAACCTTTAAAAAAGGTTAGGATAGACCCGTCTA
1 TTAAAAAAGTTGGGATAGACCTTGTCTAAAGCAACC-TT-AAAAAGGTTAGGATAGACCTGTCTA
* *
16942358 AAATAACC
64 AGACAACC
* * * * *
16942366 TTAGAAAGGTTGGGATAGACCTTGTCTAAAGCAACCATAAAAAGGTTGGGATAGACATTGTCTAA
1 TTAAAAAAGTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGAC-CTGTCTAA
* *
16942431 GGCAATCT
65 GACAA-CC
* * * *
16942439 TTAAAAAAAGTTGGGATAGACC-TATCT-AAGACAACCTTAAAAAGGTTGGGATAGACATGTTTA
1 TT-AAAAAAGTTGGGATAGACCTTGTCTAAAG-CAACCTTAAAAAGGTTAGGATAGACCTGTCTA
16942502 AG
64 AG
16942504 GCCATTTTTT
Statistics
Matches: 176, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
70 10 0.06
71 36 0.20
72 21 0.12
73 92 0.52
74 17 0.10
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (71 bp):
TTAAAAAAGTTGGGATAGACCTTGTCTAAAGCAACCTTAAAAAGGTTAGGATAGACCTGTCTAAG
ACAACC
Found at i:16942441 original size:109 final size:107
Alignment explanation
Indices: 16942221--16942494 Score: 343
Period size: 109 Copynumber: 2.5 Consensus size: 107
16942211 AAGGCCGACA
* * *
16942221 TTTAAAAAAGGTTGGGATAAACCTGTCTGAAGAAATCTTAAAAAGGTTAGGATAGACCTATCTAA
1 TTTAAAAAAGGTTGGGATAGACCTGTCT-AAGAAACCTTAAAAAGGTTGGGATAGACCTATCTAA
* * *
16942286 GACAACCTTAAAAAATTTGGAATAGACCTTGTCTAAAGCAACC
65 GACAACCATAAAAAAGTTGGAATAGACATTGTCTAAAGCAACC
* * * * *
16942329 TTTAAAAAAGGTTAGGATAGACCCGTCTAAAATAACCTTAGAAAGGTTGGGATAGACCTTGTCTA
1 TTTAAAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTTAAAAAGGTTGGGATAGACC-TATCTA
* * * *
16942394 A-AGCAACCATAAAAAGGTTGGGATAGACATTGTCTAAGGCAATC
64 AGA-CAACCATAAAAAAGTTGGAATAGACATTGTCTAAAGCAACC
* *
16942438 TTTAAAAAAAGTTGGGATAGACCTATCTAAGACAACCTTAAAAAGGTTGGGATAGAC
1 TTTAAAAAAGGTTGGGATAGACCTGTCTAAGA-AACCTTAAAAAGGTTGGGATAGAC
16942495 ATGTTTAAGG
Statistics
Matches: 141, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
107 3 0.02
108 48 0.34
109 90 0.64
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (107 bp):
TTTAAAAAAGGTTGGGATAGACCTGTCTAAGAAACCTTAAAAAGGTTGGGATAGACCTATCTAAG
ACAACCATAAAAAAGTTGGAATAGACATTGTCTAAAGCAACC
Found at i:16942492 original size:35 final size:35
Alignment explanation
Indices: 16942225--16942503 Score: 267
Period size: 35 Copynumber: 7.8 Consensus size: 35
16942215 CCGACATTTA
* *
16942225 AAAAAGGTTGGGATAAACCTGTCTGAAGA-AATCTT
1 AAAAAGGTTGGGATAGACCTGTCT-AAGACAACCTT
* *
16942260 AAAAAGGTTAGGATAGACCTATCTAAGACAACCTT
1 AAAAAGGTTGGGATAGACCTGTCTAAGACAACCTT
** *
16942295 AAAAAATTTGGAATAGACCTTGTCTAA-AGCAACCTTT
1 AAAAAGGTTGGGATAGACC-TGTCTAAGA-CAACC-TT
* * * *
16942332 AAAAAAGGTTAGGATAGACCCGTCTAAAATAACCTT
1 -AAAAAGGTTGGGATAGACCTGTCTAAGACAACCTT
* *
16942368 AGAAAGGTTGGGATAGACCTTGTCTAA-AGCAACCAT
1 AAAAAGGTTGGGATAGACC-TGTCTAAGA-CAACCTT
* * *
16942404 AAAAAGGTTGGGATAGACATTGTCTAAGGCAATCTTT
1 AAAAAGGTTGGGATAGAC-CTGTCTAAGACAA-CCTT
* *
16942441 AAAAAAAGTTGGGATAGACCTATCTAAGACAACCTT
1 -AAAAAGGTTGGGATAGACCTGTCTAAGACAACCTT
* *
16942477 AAAAAGGTTGGGATAGACATGTTTAAG
1 AAAAAGGTTGGGATAGACCTGTCTAAG
16942504 GCCATTTTTT
Statistics
Matches: 198, Mismatches: 34, Indels: 24
0.77 0.13 0.09
Matches are distributed among these distances:
34 4 0.02
35 83 0.42
36 54 0.27
37 24 0.12
38 33 0.17
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (35 bp):
AAAAAGGTTGGGATAGACCTGTCTAAGACAACCTT
Found at i:16944723 original size:29 final size:31
Alignment explanation
Indices: 16944691--16944761 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 31
16944681 AATATATGTC
16944691 ATTAAAAA-G-AACATAATATAATATTTTTA
1 ATTAAAAATGAAACATAATATAATATTTTTA
16944720 ATTAAAAAATGCATAACATAATATAATATTTTTA
1 ATT-AAAAATG-A-AACATAATATAATATTTTTA
16944754 ATTAAAAA
1 ATTAAAAA
16944762 ATGCATAGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
29 3 0.08
30 5 0.14
31 1 0.03
33 5 0.14
34 23 0.62
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (31 bp):
ATTAAAAATGAAACATAATATAATATTTTTA
Found at i:16944739 original size:34 final size:34
Alignment explanation
Indices: 16944700--16944768 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
16944690 CATTAAAAAG
16944700 AACATAATATAATATTTTTAATTAAAAAATGCAT
1 AACATAATATAATATTTTTAATTAAAAAATGCAT
16944734 AACATAATATAATATTTTTAATTAAAAAATGCAT
1 AACATAATATAATATTTTTAATTAAAAAATGCAT
16944768 A
1 A
16944769 GTTTTTAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.38
Consensus pattern (34 bp):
AACATAATATAATATTTTTAATTAAAAAATGCAT
Found at i:16945207 original size:139 final size:140
Alignment explanation
Indices: 16944957--16945214 Score: 360
Period size: 139 Copynumber: 1.9 Consensus size: 140
16944947 GGACAAAGTC
* *
16944957 GACTCTTATTTAAGAGTTATCTTAGGCATGCATATCCCAACCCTTATACAAAGAGTTGGCCAAAG
1 GACTCTTATTTAAGAGTTACCTTAGGCATGCATATCCCAAACCTTATACAAAGAGTTGGCCAAAG
* * * * *
16945022 CGCATGTTGGCAGGTCTATCCCAACACTTAGGAAAGTGTCGGCCCAAAAGTGTCAACATAATGTT
66 CGCATGCTGACAAGTCAATCCCAACACTTAGAAAAGTGTCGGCCCAAAAGTGTCAACATAATGTT
16945087 GGATACAACT
131 GGATACAACT
* * *
16945097 GACTCTTATTTAAGTA-TTGCCTTAGGCATGTATATCCCAAATCTTAT-CAAAGAGTTGGCCAAA
1 GACTCTTATTTAAG-AGTTACCTTAGGCATGCATATCCCAAACCTTATACAAAGAGTTGGCCAAA
* * *
16945160 GCATC-TGCTGACAAGTCAATCCCGACACTTAGAAAAGTGTTGGCCCAAAAGTGTC
65 GC-GCATGCTGACAAGTCAATCCCAACACTTAGAAAAGTGTCGGCCCAAAAGTGTC
16945215 GTATTAGGCC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
139 61 0.59
140 41 0.40
141 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.27
Consensus pattern (140 bp):
GACTCTTATTTAAGAGTTACCTTAGGCATGCATATCCCAAACCTTATACAAAGAGTTGGCCAAAG
CGCATGCTGACAAGTCAATCCCAACACTTAGAAAAGTGTCGGCCCAAAAGTGTCAACATAATGTT
GGATACAACT
Found at i:16946489 original size:27 final size:27
Alignment explanation
Indices: 16946410--16946513 Score: 102
Period size: 27 Copynumber: 3.9 Consensus size: 27
16946400 TATACAGGTA
* * *
16946410 AACCCCAGCTCTCCTAACCAACTGGTG
1 AACCCCAGTTCGCCAAACCAACTGGTG
* * * ** *
16946437 AACTCGAGTTTGCCAAATTAATTGGTG
1 AACCCCAGTTCGCCAAACCAACTGGTG
*
16946464 AACCCCA-TCTCGCTAAACCAACTGGTG
1 AACCCCAGT-TCGCCAAACCAACTGGTG
16946491 AACCCCAGTTCGCCAAACCAACT
1 AACCCCAGTTCGCCAAACCAACT
16946514 AGCGAGCACT
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
26 1 0.02
27 56 0.97
28 1 0.02
ACGTcount: A:0.30, C:0.34, G:0.15, T:0.21
Consensus pattern (27 bp):
AACCCCAGTTCGCCAAACCAACTGGTG
Found at i:16951700 original size:27 final size:26
Alignment explanation
Indices: 16951659--16951723 Score: 94
Period size: 27 Copynumber: 2.5 Consensus size: 26
16951649 TTTTATCAAG
* *
16951659 TTTATTAGTTAATCGATAAATAAATA
1 TTTATTAATTTATCGATAAATAAATA
*
16951685 TTTTATTAATTTATCGATAAATTAATA
1 -TTTATTAATTTATCGATAAATAAATA
16951712 TTTATTAATTTA
1 TTTATTAATTTA
16951724 GAGAATATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 12 0.34
27 23 0.66
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (26 bp):
TTTATTAATTTATCGATAAATAAATA
Found at i:16954560 original size:37 final size:36
Alignment explanation
Indices: 16954511--16954581 Score: 90
Period size: 37 Copynumber: 1.9 Consensus size: 36
16954501 CATAGATATT
* * *
16954511 CCACCTGAAACACGCCA-ACTGCTCGTAAGAGCTAAA
1 CCACCCGAAACACGCCAGA-TGCTCATAAAAGCTAAA
16954547 CCACCCGATAACACGCCAGATGCTCATAAAAGCTA
1 CCACCCGA-AACACGCCAGATGCTCATAAAAGCTA
16954582 GTCTATCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 7 0.23
37 22 0.73
38 1 0.03
ACGTcount: A:0.37, C:0.34, G:0.15, T:0.14
Consensus pattern (36 bp):
CCACCCGAAACACGCCAGATGCTCATAAAAGCTAAA
Found at i:16957097 original size:7 final size:8
Alignment explanation
Indices: 16957080--16957104 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
16957070 TTGGAATATT
16957080 AAAATTAA
1 AAAATTAA
16957088 AAAATTAA
1 AAAATTAA
16957096 AAAATTAA
1 AAAATTAA
16957104 A
1 A
16957105 TAGAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:16957544 original size:28 final size:27
Alignment explanation
Indices: 16957500--16957554 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
16957490 TAAATTACAT
**
16957500 TAACATGTTTAGTATTAACAAAAATAGC
1 TAACATGTTTACCATTAA-AAAAATAGC
*
16957528 TAACATGTTTACCATTAAAAATATAGC
1 TAACATGTTTACCATTAAAAAAATAGC
16957555 CGATGCCTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 8 0.33
28 16 0.67
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (27 bp):
TAACATGTTTACCATTAAAAAAATAGC
Found at i:16957586 original size:3 final size:3
Alignment explanation
Indices: 16957578--16957639 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
16957568 CGTTAACATG
16957578 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
16957626 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
16957640 AATGATTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16969142 original size:16 final size:17
Alignment explanation
Indices: 16969112--16969147 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
16969102 AAATATTGAG
*
16969112 TTTTTTAAGTGTTTCTA
1 TTTTTTAAGTGTTTCGA
16969129 TTTTTTAAGT-TTTCGA
1 TTTTTTAAGTGTTTCGA
16969145 TTT
1 TTT
16969148 AGTCCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTTTTAAGTGTTTCGA
Found at i:16976973 original size:101 final size:102
Alignment explanation
Indices: 16976854--16977038 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
16976844 AAAGTGATGG
* *
16976854 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTA-C-CAAAATGATAGGTCGCATGTGTAGT
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGCAAAATGAT-GGTCACATGTGTAGT
16976917 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 ACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
* * *
16976955 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGCAAAATGATGGTCACATGTGTAGTA
*
16977020 CTATGTGCATGCTACTATG
66 CTATGTGCAGGCTACTATG
16977039 TGAACCGATA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 36 0.47
102 34 0.45
103 6 0.08
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (102 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGCAAAATGATGGTCACATGTGTAGTA
CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
Found at i:16976974 original size:51 final size:50
Alignment explanation
Indices: 16976854--16977038 Score: 178
Period size: 51 Copynumber: 3.7 Consensus size: 50
16976844 AAAGTGATGG
* * * * * * *
16976854 TCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACC--AAAATGATAGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-AT-GA
*
16976904 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * *
16976955 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
*
16977006 TCACATGTGTAGTACTATGTGCATGCTACTATG
1 TCACATGTGTAGTACTATGTGCAGGCTACTATG
16977039 TGAACCGATA
Statistics
Matches: 112, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
50 35 0.31
51 73 0.65
52 3 0.03
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:16977040 original size:26 final size:26
Alignment explanation
Indices: 16976960--16977040 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
16976950 TTCGATCACG
*
16976960 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
* * *
16976986 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCATGCT-ACTA
16977011 TGTGTAGTACTATGTGCATGCTACTA
1 TGTGTAGTACTATGTGCATGCTACTA
16977037 TGTG
1 TGTG
16977041 AACCGATATC
Statistics
Matches: 41, Mismatches: 7, Indels: 14
0.66 0.11 0.23
Matches are distributed among these distances:
24 1 0.02
25 17 0.41
26 22 0.54
27 1 0.02
ACGTcount: A:0.22, C:0.15, G:0.28, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCATGCTACTA
Found at i:16977133 original size:46 final size:44
Alignment explanation
Indices: 16977045--16977134 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 44
16977035 TATGTGAACC
* *
16977045 GATATCATTAATTATAAGGTGGTTGCTATGTGCTGATCCCACCG
1 GATATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCCACCG
* *
16977089 GATATCATTGATTACAAAGGGTGGTTGCTGTGTGCTAAAT-CCACCG
1 GATATCATTAATTA-AAA-GGTGGTTGCTATGTGCT-AATCCCACCG
16977135 TGTATCTGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 13 0.33
45 2 0.05
46 22 0.56
47 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (44 bp):
GATATCATTAATTAAAAGGTGGTTGCTATGTGCTAATCCCACCG
Found at i:16986657 original size:17 final size:17
Alignment explanation
Indices: 16986631--16986664 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16986621 ATATTTTAGA
16986631 TTTATTATTTA-AAACT
1 TTTATTATTTAGAAACT
16986647 TTTAGTTATTTAGAAACT
1 TTTA-TTATTTAGAAACT
16986665 ATGATGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTATTATTTAGAAACT
Found at i:16989273 original size:91 final size:91
Alignment explanation
Indices: 16989118--16989291 Score: 222
Period size: 91 Copynumber: 1.9 Consensus size: 91
16989108 TCATCCACAT
* * * **
16989118 ATTATCTAGCAGCTTTTATCTAAAATTAAGTTGTGTATTTACAACCATCTGGCGGCGTATTAACC
1 ATTATCTAGCAGCTTTTATCTAAAATTAAGTTGTGTACTCACAACCATCTAGCAACGTATTAACC
* *
16989183 TACAACTTTTGGTTGTTCGCCCACCC
66 TACAACATTTGGTGGTTCGCCCACCC
* * ** * *
16989209 ATTATCTGGTAGCTTTTATCTGCAATTATGTTGTGTACTCACAATCATCTAGCAACGTATTAACC
1 ATTATCTAGCAGCTTTTATCTAAAATTAAGTTGTGTACTCACAACCATCTAGCAACGTATTAACC
*
16989274 TGCAACATTTGGTGGTTC
66 TACAACATTTGGTGGTTC
16989292 ATCCACAACC
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
91 69 1.00
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.37
Consensus pattern (91 bp):
ATTATCTAGCAGCTTTTATCTAAAATTAAGTTGTGTACTCACAACCATCTAGCAACGTATTAACC
TACAACATTTGGTGGTTCGCCCACCC
Found at i:16991874 original size:18 final size:19
Alignment explanation
Indices: 16991822--16991876 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
16991812 TTACAAAAAG
*
16991822 AAATTCAAAATAGTTT-TTA
1 AAATTCAAAATA-TTTATAA
16991841 AAATTCAAAATATTTATAA
1 AAATTCAAAATATTTATAA
*
16991860 AAATTCTAAAT-TTTATA
1 AAATTCAAAATATTTATA
16991877 TTTTTAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
18 9 0.27
19 24 0.73
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATTCAAAATATTTATAA
Found at i:16991933 original size:30 final size:28
Alignment explanation
Indices: 16991881--16991948 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 28
16991871 TTTATATTTT
16991881 TAAAAAATATATAAAATATTAAAAATTC
1 TAAAAAATATATAAAATATTAAAAATTC
* *
16991909 TAAAGAATATATTAAAAATTTTAAAAATTC
1 TAAAAAATATA-T-AAAATATTAAAAATTC
16991939 TAAAATAATA
1 TAAAA-AATA
16991949 ATTGTTGGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 10 0.29
29 1 0.03
30 19 0.56
31 4 0.12
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.34
Consensus pattern (28 bp):
TAAAAAATATATAAAATATTAAAAATTC
Found at i:16991937 original size:9 final size:9
Alignment explanation
Indices: 16991878--16991943 Score: 51
Period size: 9 Copynumber: 6.9 Consensus size: 9
16991868 AATTTTATAT
16991878 TTTTAAAAA
1 TTTTAAAAA
* *
16991887 ATATATAAAA
1 TTTTA-AAAA
*
16991897 TATTAAAAA
1 TTTTAAAAA
*
16991906 TTCTAAAGAA
1 TTTTAAA-AA
16991916 TATATTAAAAA
1 T-T-TTAAAAA
16991927 TTTTAAAAA
1 TTTTAAAAA
*
16991936 TTCTAAAA
1 TTTTAAAA
16991944 TAATAATTGT
Statistics
Matches: 44, Mismatches: 9, Indels: 8
0.72 0.15 0.13
Matches are distributed among these distances:
9 26 0.59
10 10 0.23
11 4 0.09
12 4 0.09
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:16994510 original size:24 final size:24
Alignment explanation
Indices: 16994464--16994510 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
16994454 AAAACGGAAG
*
16994464 AGAAAAGAAAAGGGAGAAAAGAGA
1 AGAAAAGAAAAGAGAGAAAAGAGA
*
16994488 AGAAAAGAAGAAGAG-GAAGAGAG
1 AGAAAAGAA-AAGAGAGAAAAGAG
16994511 GGAAGCATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (24 bp):
AGAAAAGAAAAGAGAGAAAAGAGA
Found at i:16999221 original size:29 final size:30
Alignment explanation
Indices: 16999188--16999253 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
16999178 TAAAAAATTT
*
16999188 ATGTATAAAATTGCACA-AAATCAAAGTTC
1 ATGTATAAAATTGCACATAAACCAAAGTTC
* **
16999217 ATGTATATAATTGCACATAAACCCTAGTTC
1 ATGTATAAAATTGCACATAAACCAAAGTTC
16999247 ATGTATA
1 ATGTATA
16999254 GTTTTGAGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (30 bp):
ATGTATAAAATTGCACATAAACCAAAGTTC
Found at i:17001627 original size:125 final size:126
Alignment explanation
Indices: 17001254--17001670 Score: 739
Period size: 126 Copynumber: 3.3 Consensus size: 126
17001244 TAATTTAAAT
* *
17001254 AAGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCCTGAAAAAATAAATTTGAGTTGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGACGTTT
*
17001319 CTGAGCAAATAGTGTCAAAAACACTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
* *
17001380 AAGCTCCCACGTGGATGCGCTTTTGCTATAGTAGCTCCTGAAAAAATAATTTTGAGTTGACGTTT
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGACGTTT
17001445 CTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
66 CTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
17001506 ATA-CTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG-AAAAATAATTTTGAGTTGACGTT
1 A-AGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGACGTT
* *
17001569 TCTGAGCAAATAGTGTCAAAAACGCTTTAAGTATGATGCTTTGTCAGCAAAAGTACTGAAAG
65 TCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
*
17001631 AAGCTCCCACGTGGACGCGTTTTTGCTACAGTAGCTCCTG
1 AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
17001671 TTAGGCCTGA
Statistics
Matches: 279, Mismatches: 10, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
124 1 0.00
125 120 0.43
126 157 0.56
127 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (126 bp):
AAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTTGAGTTGACGTTT
CTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACTGAAAG
Found at i:17002785 original size:7 final size:7
Alignment explanation
Indices: 17002773--17002797 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17002763 TTAGTTATAT
17002773 ATACTAA
1 ATACTAA
17002780 ATACTAA
1 ATACTAA
17002787 ATACTAA
1 ATACTAA
17002794 ATAC
1 ATAC
17002798 CAATTGACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.28
Consensus pattern (7 bp):
ATACTAA
Found at i:17003957 original size:29 final size:29
Alignment explanation
Indices: 17003919--17003975 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
17003909 TCAAAAAAAT
*
17003919 AAAATTTAAAACTTTTTTAAAAATAATTA
1 AAAAATTAAAACTTTTTTAAAAATAATTA
*
17003948 AAAAATTAAAGCTTTTTTAAAAATAATT
1 AAAAATTAAAACTTTTTTAAAAATAATT
17003976 TGAGAGGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (29 bp):
AAAAATTAAAACTTTTTTAAAAATAATTA
Found at i:17004027 original size:12 final size:10
Alignment explanation
Indices: 17003972--17004038 Score: 89
Period size: 11 Copynumber: 6.2 Consensus size: 10
17003962 TTTTAAAAAT
17003972 AATTTGAGAGG
1 AATTTGAGA-G
17003983 AATTTGAGAGG
1 AATTTGAGA-G
17003994 AATTTGAGAAG
1 AATTTGAG-AG
17004005 AATTTGAGAG
1 AATTTGAGAG
17004015 AATATTAGAGAG
1 AAT-TT-GAGAG
17004027 AATTTGAGAG
1 AATTTGAGAG
17004037 AA
1 AA
17004039 AGGATTAAGT
Statistics
Matches: 53, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
10 12 0.23
11 32 0.60
12 9 0.17
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (10 bp):
AATTTGAGAG
Found at i:17005025 original size:21 final size:21
Alignment explanation
Indices: 17005001--17005068 Score: 52
Period size: 21 Copynumber: 3.3 Consensus size: 21
17004991 TTAAAAAAAA
17005001 TTAAAATATATTTATATTATT
1 TTAAAATATATTTATATTATT
** *
17005022 TTAATTTAATATTTA-ATAATT
1 TTAAAAT-ATATTTATATTATT
* * *
17005043 TT-AAATATTTTTTTATT-TA
1 TTAAAATATATTTATATTATT
17005062 TTAAAAT
1 TTAAAAT
17005069 TTTATATATA
Statistics
Matches: 35, Mismatches: 9, Indels: 7
0.69 0.18 0.14
Matches are distributed among these distances:
19 8 0.23
20 8 0.23
21 12 0.34
22 7 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAAATATATTTATATTATT
Found at i:17013200 original size:69 final size:69
Alignment explanation
Indices: 17013085--17013308 Score: 268
Period size: 69 Copynumber: 3.2 Consensus size: 69
17013075 ATATCACCTG
* * * ***
17013085 TAAAATTAAGGTTCGCAAGCGAAGAGCATTAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTA
1 TAAAATTAAGGTTCGTAGGCGAACAGCCGCAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTA
17013150 GCTA
66 GCTA
* * * * * * *
17013154 TAAAATTCAGGTTCGTAGGTGAATAGCTGCAACCTCCAATATAGTTAGTGAGAGCAAAGCTCCTA
1 TAAAATTAAGGTTCGTAGGCGAACAGCCGCAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTA
17013219 GCTA
66 GCTA
** * *
17013223 TAAAATTAAGGTTCACAGGCGAACAGCCGCAACCTCCAACACGGTTAGCGAGAGCAAAGCTCCCA
1 TAAAATTAAGGTTCGTAGGCGAACAGCCGCAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTA
* *
17013288 ACTG
66 GCTA
*
17013292 TAAAACTAAGGTTCGTA
1 TAAAATTAAGGTTCGTA
17013309 TGTAAAAATT
Statistics
Matches: 128, Mismatches: 27, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
69 128 1.00
ACGTcount: A:0.36, C:0.23, G:0.21, T:0.21
Consensus pattern (69 bp):
TAAAATTAAGGTTCGTAGGCGAACAGCCGCAACCTCCAACACAGTTAGCGAGAGCAAAGCTCCTA
GCTA
Found at i:17016102 original size:40 final size:40
Alignment explanation
Indices: 17016018--17016241 Score: 296
Period size: 40 Copynumber: 5.7 Consensus size: 40
17016008 TTGAATGATG
* * * *
17016018 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
17016058 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
17016098 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
17016136 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
17016176 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
17016217 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
17016242 AACGAGGAGC
Statistics
Matches: 165, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
38 25 0.15
39 19 0.12
40 111 0.67
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:17016236 original size:80 final size:80
Alignment explanation
Indices: 17016018--17016241 Score: 296
Period size: 78 Copynumber: 2.8 Consensus size: 80
17016008 TTGAATGATG
* * * * *
17016018 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTAAG-TCCCGAAGGCAT
*
17016081 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
*
17016098 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCGGGCTAAGTCCCGAAGGCATT
*
17016160 TGTGCGAGTTACTAAA
65 TGTGCGAGATACTAAA
* *
17016176 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
17016241 G
66 G
17016242 AACGAGGAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
77 2 0.02
78 49 0.39
79 25 0.20
80 49 0.39
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:17024121 original size:39 final size:40
Alignment explanation
Indices: 17024024--17024244 Score: 297
Period size: 40 Copynumber: 5.5 Consensus size: 40
17024014 AATGATGTCC
* * * *
17024024 GGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCG
* * *
17024064 GACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAATTCCG
1 GGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
17024104 GGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
17024143 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
*
17024183 GGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CCG
1 GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCG
*
17024223 GGCTATGTCCCGAAGGCATTTG
1 GGCTAAGTCCCGAAGGCATTTG
17024245 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 15, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
39 35 0.22
40 116 0.72
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
GGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCG
Found at i:17029297 original size:23 final size:22
Alignment explanation
Indices: 17029266--17029317 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
17029256 TTTTGTTATA
17029266 TATATATATACATGCATACATTTT
1 TATA-ATATACATGCATA-ATTTT
* * *
17029290 TATAATATACGTTCATATTTTT
1 TATAATATACATGCATAATTTT
17029312 TATAAT
1 TATAAT
17029318 TTATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 10 0.40
23 11 0.44
24 4 0.16
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
TATAATATACATGCATAATTTT
Found at i:17029378 original size:35 final size:36
Alignment explanation
Indices: 17029304--17029378 Score: 98
Period size: 36 Copynumber: 2.1 Consensus size: 36
17029294 ATATACGTTC
*
17029304 ATATTTTTTATAATTTATATATATAAATACTTATAT
1 ATATTTTTTATAATTTATATATATAAATACATATAT
* * * *
17029340 ATATTTTTTATATTTTATA-ATTTATATACATATCT
1 ATATTTTTTATAATTTATATATATAAATACATATAT
17029375 ATAT
1 ATAT
17029379 ATATCTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 16 0.47
36 18 0.53
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (36 bp):
ATATTTTTTATAATTTATATATATAAATACATATAT
Found at i:17029420 original size:42 final size:43
Alignment explanation
Indices: 17029349--17029480 Score: 121
Period size: 42 Copynumber: 3.1 Consensus size: 43
17029339 TATATTTTTT
* * *
17029349 ATATTTTATAATTTAT-ATACATATCTATATATATCTATATAC
1 ATATTTTTTAATTTATCATAAATATATATATATATCTATATAC
*
17029391 ATATTTTTTAATTT-TCATAAATATATATATACATACTGATAT--
1 ATATTTTTTAATTTATCATAAATATATATATATAT-CT-ATATAC
* * * *
17029433 ATATTTTTT-ATTATATCTTATAATTTATATATATATGTACATAC
1 ATATTTTTTAATT-TATCATA-AATATATATATATATCTATATAC
17029477 ATAT
1 ATAT
17029481 ATCTTTCTAC
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
41 4 0.05
42 41 0.56
43 7 0.10
44 21 0.29
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.52
Consensus pattern (43 bp):
ATATTTTTTAATTTATCATAAATATATATATATATCTATATAC
Found at i:17036087 original size:9 final size:9
Alignment explanation
Indices: 17036073--17036109 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
17036063 ACATTAATCA
17036073 AAAGAAAAG
1 AAAGAAAAG
*
17036082 AAAGAAAAT
1 AAAGAAAAG
17036091 AAAG-AAAG
1 AAAGAAAAG
17036099 AAAGAAAAG
1 AAAGAAAAG
17036108 AA
1 AA
17036110 GTTTAACGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.28
9 18 0.72
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:17036107 original size:13 final size:13
Alignment explanation
Indices: 17036073--17036109 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
17036063 ACATTAATCA
17036073 AAAGAAAAGAAAG
1 AAAGAAAAGAAAG
17036086 AAA-ATAAAGAAAG
1 AAAGA-AAAGAAAG
17036099 AAAGAAAAGAA
1 AAAGAAAAGAA
17036110 GTTTAACGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 1 0.05
13 20 0.91
14 1 0.05
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAGAAAAGAAAG
Found at i:17041602 original size:33 final size:33
Alignment explanation
Indices: 17041551--17041711 Score: 109
Period size: 33 Copynumber: 4.7 Consensus size: 33
17041541 TTATCTGTTA
*
17041551 TCGGTGGATTCAGCACTTAGCAACCACCAGTGAT
1 TCGG-GGAATCAGCACTTAGCAACCACCAGTGAT
17041585 TCGGGGAATCAGCACTTAGCAAACCCTTTCACATTCAGTGAT
1 TCGGGGAATCAGCACTTAGC-AA--C---CAC---CAGTGAT
* * * *
17041627 ACGGTGGAATCAGCACTTAGCAACTACCAATGAA
1 TCGG-GGAATCAGCACTTAGCAACCACCAGTGAT
* *
17041661 TCAGGGAATTAGCACTTAGCAACC-CC-----T
1 TCGGGGAATCAGCACTTAGCAACCACCAGTGAT
*
17041688 TGGGGGAATCAGCACTTAGCAACC
1 TCGGGGAATCAGCACTTAGCAACC
17041712 CCCTTCACAT
Statistics
Matches: 104, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
27 21 0.20
32 2 0.02
33 33 0.32
34 13 0.12
36 1 0.01
37 2 0.02
39 3 0.03
40 1 0.01
42 12 0.12
43 16 0.15
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (33 bp):
TCGGGGAATCAGCACTTAGCAACCACCAGTGAT
Found at i:17041754 original size:42 final size:42
Alignment explanation
Indices: 17041692--17041795 Score: 172
Period size: 42 Copynumber: 2.5 Consensus size: 42
17041682 ACCCCTTGGG
* *
17041692 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATACGAT
* *
17041734 TGAATCAGCACTTAGTAACCCCCTTCACATTCAAAATACGAT
1 GGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATACGAT
17041776 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
17041796 ACCAATGAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.35, C:0.29, G:0.13, T:0.23
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTCAAAATACGAT
Found at i:17041812 original size:144 final size:145
Alignment explanation
Indices: 17041590--17041857 Score: 448
Period size: 144 Copynumber: 1.9 Consensus size: 145
17041580 GTGATTCGGG
* ** * *
17041590 GAATCAGCACTTAGCAAACCCTTTCACATTCAGTGATACGGTGGAATCAGCACTTAGCAACTACC
1 GAATCAGCACTTAGCAAACCCCTTCACATTCAGAAATACGATGGAATCAGCACTTAGCAACCACC
*
17041655 AATGAATCAGGGAATTAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCAC
66 AATGAATCAGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCAC
17041720 ATTTAAAATACGGTT
131 ATTTAAAATACGGTT
* *
17041735 GAATCAGCACTTAGTAACCCCCTTCACATTCA-AAATACGATGGAATCAGCACTTAGCAACCACC
1 GAATCAGCACTTAGCAAACCCCTTCACATTCAGAAATACGATGGAATCAGCACTTAGCAACCACC
*
17041799 AATGAATCGGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCC
66 AATGAATCAGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCC
17041858 ATTTATATTC
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
144 85 0.75
145 29 0.25
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (145 bp):
GAATCAGCACTTAGCAAACCCCTTCACATTCAGAAATACGATGGAATCAGCACTTAGCAACCACC
AATGAATCAGGGAATCAGCACTTAGCAACCCCTTGGGGGAATCAGCACTTAGCAACCCCCTTCAC
ATTTAAAATACGGTT
Found at i:17041818 original size:33 final size:27
Alignment explanation
Indices: 17041776--17041857 Score: 101
Period size: 27 Copynumber: 2.8 Consensus size: 27
17041766 AAAATACGAT
17041776 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACC-CC--T---TCGG
*
17041809 GGAATCAGCACTTAGCAACCCCTTGGG
1 GGAATCAGCACTTAGCAACCCCTTCGG
17041836 GGAATCAGCACTTAGCAACCCC
1 GGAATCAGCACTTAGCAACCCC
17041858 ATTTATATTC
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
27 25 0.52
30 1 0.02
32 2 0.04
33 20 0.42
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.16
Consensus pattern (27 bp):
GGAATCAGCACTTAGCAACCCCTTCGG
Found at i:17041961 original size:51 final size:51
Alignment explanation
Indices: 17041875--17042075 Score: 214
Period size: 51 Copynumber: 4.0 Consensus size: 51
17041865 TTCAAAGATA
* * * *
17041875 CCGGTTCACATAGTAGCCTGCACATGGTACTACACATGTGACCATCACTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
* *
17041926 CCGATACACGTAGTAGCCTGCACATAGTACTACACACGT-A--ATTGAAGCTAT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCA-T-CA-CTAT
* * * * **
17041977 CCGGTACGCATAGTAGCCTACACATAGTACTACACATGCCACCTATCA-T-T
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTAT
*
17042027 CTGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
17042076 TTCACTTTTA
Statistics
Matches: 122, Mismatches: 20, Indels: 17
0.77 0.13 0.11
Matches are distributed among these distances:
48 1 0.01
49 5 0.04
50 40 0.33
51 72 0.59
52 1 0.01
53 1 0.01
54 1 0.01
55 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (51 bp):
CCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATCACTAT
Found at i:17042063 original size:101 final size:102
Alignment explanation
Indices: 17041883--17042065 Score: 289
Period size: 101 Copynumber: 1.8 Consensus size: 102
17041873 TACCGGTTCA
* * **
17041883 CATAGTAGCCTGCACATGGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCCACCATCACTATCCGATACACGTAGTAGCCTGCA
17041948 CATAGTACTACACACGTAATTGAAGCTATCCGGTACG
66 CATAGTACTACACACGTAATTGAAGCTATCCGGTACG
* *
17041985 CATAGTAGCCTACACATAGTACTACACATGCCACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTACACATAGTACTACACATGCCACC-ATCACTATCCGATACACGTAGTAGCCTGC
17042048 ACATAGTACTACACACGT
65 ACATAGTACTACACACGT
17042066 GACCATCACT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.51
102 32 0.43
103 4 0.05
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTACACATAGTACTACACATGCCACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTAATTGAAGCTATCCGGTACG
Found at i:17054654 original size:23 final size:23
Alignment explanation
Indices: 17054624--17054669 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
17054614 TATCTTTAGG
*
17054624 ATTTACAATAATTACCTTGATAA
1 ATTTACAATAATTACCCTGATAA
17054647 ATTTACAATAATTACCCTGATAA
1 ATTTACAATAATTACCCTGATAA
17054670 CTCTAGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.15, G:0.04, T:0.37
Consensus pattern (23 bp):
ATTTACAATAATTACCCTGATAA
Found at i:17057539 original size:25 final size:26
Alignment explanation
Indices: 17057465--17057546 Score: 98
Period size: 26 Copynumber: 3.3 Consensus size: 26
17057455 GTCCTGTTAT
* *
17057465 ATGGCTCTTTGTGAGCTTCTCGGTTA
1 ATGGCTCTTTGTGAGCTTCTTGATTA
* *
17057491 AAGGCTCTTTGTGAGCTTCCTGATTA
1 ATGGCTCTTTGTGAGCTTCTTGATTA
*
17057517 ATGGCTCTCTG-GAGCTTCTTGA-T-
1 ATGGCTCTTTGTGAGCTTCTTGATTA
17057540 ATGGCTC
1 ATGGCTC
17057547 GCTTAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 7 0.14
24 1 0.02
25 10 0.20
26 31 0.63
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.39
Consensus pattern (26 bp):
ATGGCTCTTTGTGAGCTTCTTGATTA
Found at i:17060750 original size:46 final size:46
Alignment explanation
Indices: 17060668--17060775 Score: 139
Period size: 46 Copynumber: 2.4 Consensus size: 46
17060658 GTCTTTGACT
** * * *
17060668 TATGGTCTTACTC-AATTTTATCCTGATGTCATAGCATCTTTCAAC
1 TATGGTCTTACTCTTTTTTTATCCTAATGCCATAGCATCCTTCAAC
*
17060713 TATGGTCTTACTCTTTTTTTATCCTAATGCCATAGCATCCTTCAGC
1 TATGGTCTTACTCTTTTTTTATCCTAATGCCATAGCATCCTTCAAC
*
17060759 TATGGTCTCACT-TTTTT
1 TATGGTCTTACTCTTTTT
17060776 CTTTTTTTGC
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 18 0.33
46 37 0.67
ACGTcount: A:0.20, C:0.23, G:0.11, T:0.45
Consensus pattern (46 bp):
TATGGTCTTACTCTTTTTTTATCCTAATGCCATAGCATCCTTCAAC
Found at i:17062086 original size:25 final size:24
Alignment explanation
Indices: 17062058--17062122 Score: 58
Period size: 25 Copynumber: 2.7 Consensus size: 24
17062048 CGATACTCAG
*
17062058 CTCGTATGAGCTTACAATTTTTCAA
1 CTCGTATGAGCTTACAATTTAT-AA
* * * * *
17062083 CTCGGAGGAGTTTACCATTTATAG
1 CTCGTATGAGCTTACAATTTATAA
*
17062107 CTCGTATGAGCATACA
1 CTCGTATGAGCTTACA
17062123 TGAATAAGAA
Statistics
Matches: 29, Mismatches: 11, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
24 12 0.41
25 17 0.59
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (24 bp):
CTCGTATGAGCTTACAATTTATAA
Found at i:17063821 original size:21 final size:21
Alignment explanation
Indices: 17063795--17063834 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
17063785 ACTGTATGGT
17063795 GATATCTGATAGAAAGTCTGC
1 GATATCTGATAGAAAGTCTGC
17063816 GATATCTGATAGAAAGTCT
1 GATATCTGATAGAAAGTCT
17063835 CGTTTCCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.23, T:0.30
Consensus pattern (21 bp):
GATATCTGATAGAAAGTCTGC
Found at i:17064219 original size:76 final size:76
Alignment explanation
Indices: 17064133--17064286 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 76
17064123 GTAAATCTCT
17064133 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTCAAAATGGTTTTGGAAACTCTTAACTTTG
1 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTCAAAATGGTTTTGGAAACTCTTAACTTTG
17064198 TTTTCTGAATC
66 TTTTCTGAATC
*
17064209 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTTAAAATGGTTTTGGAAACTCTTAACTTTG
1 TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTCAAAATGGTTTTGGAAACTCTTAACTTTG
17064274 TTTTCTGAATC
66 TTTTCTGAATC
17064285 TT
1 TT
17064287 ACATACACCA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.40
Consensus pattern (76 bp):
TTTTAAACTTAGTTTTCCAGGAACATGCAGAACCCTCAAAATGGTTTTGGAAACTCTTAACTTTG
TTTTCTGAATC
Found at i:17066496 original size:15 final size:16
Alignment explanation
Indices: 17066476--17066508 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17066466 TGATACTGAT
17066476 TTGAGACAGGC-CATA
1 TTGAGACAGGCGCATA
*
17066491 TTGAGAGAGGCGCATA
1 TTGAGACAGGCGCATA
17066507 TT
1 TT
17066509 ATCCCTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.24
Consensus pattern (16 bp):
TTGAGACAGGCGCATA
Found at i:17070801 original size:13 final size:13
Alignment explanation
Indices: 17070768--17070801 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
17070758 CTTTACATTC
17070768 TCAAAAAGGTGAA
1 TCAAAAAGGTGAA
*
17070781 TCAGAAAGGTGAA
1 TCAAAAAGGTGAA
*
17070794 TTAAAAAG
1 TCAAAAAG
17070802 ATGAGTTGGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.24, T:0.18
Consensus pattern (13 bp):
TCAAAAAGGTGAA
Found at i:17078310 original size:43 final size:44
Alignment explanation
Indices: 17078153--17078317 Score: 228
Period size: 43 Copynumber: 3.8 Consensus size: 44
17078143 TTATGAGGCA
* * * *
17078153 AAACGCCGCTAAAGATCATGTTCTTTAGTGGCAC-TTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCCAC
** * *
17078196 AAATACCGCTAAAGAACATGATCTTTAGTGGCG-TCTTACCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCCAC
*
17078239 AAATGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTA-CCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCCAC
17078282 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTT
17078318 GTGTTTAAAG
Statistics
Matches: 110, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
43 106 0.96
44 4 0.04
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.25
Consensus pattern (44 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGCTTTTACCCAC
Found at i:17083114 original size:47 final size:48
Alignment explanation
Indices: 17083056--17083154 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 48
17083046 CATAGTTTTG
*
17083056 TTTAAGTAATATTTATAAAAATTAGATAAAATTATAAATTTTAGT-TT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
*
17083103 TTTAAGTAATATTTATAATAATTAGATAAAATTAAAAATTTTAGTGTT
1 TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
17083151 TTTA
1 TTTA
17083155 TTTCATTTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
47 43 0.88
48 6 0.12
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (48 bp):
TTTAAGTAATATTTATAAAAATTAGATAAAATTAAAAATTTTAGTGTT
Found at i:17083168 original size:25 final size:26
Alignment explanation
Indices: 17083140--17083192 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 26
17083130 AAAATTAAAA
* *
17083140 ATTTTAGTGTTTTTATTTCATTT-TT
1 ATTTTAGTATTTTAATTTCATTTCTT
* *
17083165 ATTTTTGTATTTTAATTTTATTTCTT
1 ATTTTAGTATTTTAATTTCATTTCTT
17083191 AT
1 AT
17083193 AATTTGGTCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.19, C:0.04, G:0.06, T:0.72
Consensus pattern (26 bp):
ATTTTAGTATTTTAATTTCATTTCTT
Found at i:17083175 original size:19 final size:18
Alignment explanation
Indices: 17083139--17083192 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 18
17083129 TAAAATTAAA
17083139 AATTTTAGTGTTTTTATTTC
1 AATTTTA-T-TTTTTATTTC
* *
17083159 ATTTTTATTTTTGTATTTT
1 AATTTTATTTTT-TATTTC
*
17083178 AATTTTATTTCTTAT
1 AATTTTATTTTTTAT
17083193 AATTTGGTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.70
Consensus pattern (18 bp):
AATTTTATTTTTTATTTC
Found at i:17083552 original size:21 final size:21
Alignment explanation
Indices: 17083511--17083564 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
17083501 TCCTTATGTC
* *
17083511 CTAACCCCTAAATCTCTAACT-
1 CTAACCCCT-AACCCCTAACTA
17083532 CTTAACCCCTAACCCCTAACTA
1 C-TAACCCCTAACCCCTAACTA
17083554 CTAACCCCTAA
1 CTAACCCCTAA
17083565 ACCTTAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 20 0.69
22 9 0.31
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (21 bp):
CTAACCCCTAACCCCTAACTA
Found at i:17083727 original size:20 final size:21
Alignment explanation
Indices: 17083702--17083741 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
17083692 CTAGTTAATC
17083702 TAAACCCTAAAC-CATAAACT
1 TAAACCCTAAACTCATAAACT
17083722 TAAACCCTAAACTCATAAAC
1 TAAACCCTAAACTCATAAAC
17083742 CCTTAACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.63
21 7 0.37
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.20
Consensus pattern (21 bp):
TAAACCCTAAACTCATAAACT
Found at i:17083826 original size:22 final size:21
Alignment explanation
Indices: 17083779--17083870 Score: 62
Period size: 22 Copynumber: 4.3 Consensus size: 21
17083769 ACCCCAGCCT
*
17083779 TTAAACCATAAACCATAACCC
1 TTAAACCATAAACCATAAACC
* *
17083800 CTAAACCCATAATCCATAAACC
1 TTAAA-CCATAAACCATAAACC
***
17083822 TTAAAATGGTAACACC-TAAACC
1 TT-AAACCATAA-ACCATAAACC
*
17083844 TTAAACTC-TAAACCATATACC
1 TTAAAC-CATAAACCATAAACC
*
17083865 CTAAAC
1 TTAAAC
17083871 TATAGTGATA
Statistics
Matches: 54, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
20 3 0.06
21 20 0.37
22 26 0.48
23 5 0.09
ACGTcount: A:0.46, C:0.30, G:0.02, T:0.22
Consensus pattern (21 bp):
TTAAACCATAAACCATAAACC
Found at i:17083870 original size:14 final size:14
Alignment explanation
Indices: 17083701--17083826 Score: 60
Period size: 15 Copynumber: 8.9 Consensus size: 14
17083691 ACTAGTTAAT
*
17083701 CTAAACCCTAAACC
1 CTAAACCATAAACC
* *
17083715 ATAAA-CTTAAACC
1 CTAAACCATAAACC
17083728 CTAAACTCATAAACC
1 CTAAAC-CATAAACC
*
17083743 CTTAACACAT-AACC
1 CTAAAC-CATAAACC
* *
17083757 TTTAAACCTTAAACC
1 -CTAAACCATAAACC
* * *
17083772 C-CAGCCTTTAAACC
1 CTAAACC-ATAAACC
* *
17083786 ATAAACCATAACCC
1 CTAAACCATAAACC
*
17083800 CTAAACCCATAATCC
1 CTAAA-CCATAAACC
* *
17083815 ATAAACCTTAAA
1 CTAAACCATAAA
17083827 ATGGTAACAC
Statistics
Matches: 83, Mismatches: 22, Indels: 14
0.70 0.18 0.12
Matches are distributed among these distances:
13 14 0.17
14 31 0.37
15 38 0.46
ACGTcount: A:0.44, C:0.33, G:0.01, T:0.21
Consensus pattern (14 bp):
CTAAACCATAAACC
Found at i:17084109 original size:41 final size:41
Alignment explanation
Indices: 17084052--17084130 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
17084042 TTTTAAATCC
*
17084052 CTGAGCATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGCA
1 CTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCA
* *
17084093 CTGAGCATTAGCGGCGCTTTATTAAAAACGTCGCTAAA
1 CTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAA
17084131 TCCCCGAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (41 bp):
CTGAGCATTAGCGGCGCTTTATCAAAAACGCCGCTAAAGCA
Found at i:17084262 original size:114 final size:114
Alignment explanation
Indices: 17084062--17084658 Score: 826
Period size: 114 Copynumber: 5.2 Consensus size: 114
17084052 CTGAGCATTA
*
17084062 GCGGCGCTTTCTCAAAAACGCCGCTAAAG-CACTGAGCATTAGCGGCGCTTTATTAAAAACGTCG
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCA-TGAGCATTAGCGGCGCTTTATTAAAAACGCCG
*
17084126 CTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGAGCTTAGGTTTTTTT
65 CTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* ** *
17084176 GCGGCGCTTTCCCAAAAACGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTCCTAAAAATGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
*
17084241 TAAATCCCCGAAAGCTCAGAAAACGGCGTCATTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * *
17084290 GCGGCGCTTTCCCAAAAATGCCGCTAAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAACGCCG
1 GCGGCGCTTTCTCAAAAACGCCGCT-AAAGCCATGAGCATTAGCGGCGCTTTATTAAAAACGCCG
* * * *
17084355 CTAAATCCCCAAAAGCTCAGAAAACGGTGTCGTTAGGCTTA-GATTTTTT
65 CTAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * *
17084404 GAGGCGCTTTCTAAAAAACGCCGCTAAAGCCCTGAACATTAGCGGCGCTTTATTAAAAAAGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
* * *
17084469 TAAATCCTCGGAAGCTCAGAAAACGACGTCGTTGGGCTTAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
* * * * * * *
17084518 ACGGCGCTTTCTCAAAAATGCTGCTAAAGCCTTAAACATTAGCGGCGCTTTATTAATAACGCCGC
1 GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
* * *
17084583 CAAATCCCCGAAAGCTCAGAAAACAGAGTCGTTGGGAC-TAGGTTTTTTT
66 TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGG-CTTAGGTTTTTTT
17084632 GCGGCGCTTTCTTC--AAACGCCGCTAAA
1 GCGGCGCTTTC-TCAAAAACGCCGCTAAA
17084659 TCCCCGAAAC
Statistics
Matches: 430, Mismatches: 48, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
113 82 0.19
114 270 0.63
115 78 0.18
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCTCAAAAACGCCGCTAAAGCCATGAGCATTAGCGGCGCTTTATTAAAAACGCCGC
TAAATCCCCGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGGTTTTTTT
Found at i:17084677 original size:72 final size:73
Alignment explanation
Indices: 17084559--17084701 Score: 193
Period size: 72 Copynumber: 2.0 Consensus size: 73
17084549 TTAAACATTA
*
17084559 GCGGCGCTTTATTAATAACGCCGCCAAATCCCCGAAAGCTCAGAAAACAGA-GTCGTTGGGAC-T
1 GCGGCGCTTTATTAATAACGCCGCCAAATCCCCGAAACCTCAGAAAAC-GACGTCGTTGGG-CTT
17084622 AGGTTTTTTT
64 AGGTTTTTTT
* * * **
17084632 GCGGCGCTTTCTTCA-AACGCCGCTAAATCCCCGAAACCTTGGAAAACGACGTCGTTGGGCTTAG
1 GCGGCGCTTTATTAATAACGCCGCCAAATCCCCGAAACCTCAGAAAACGACGTCGTTGGGCTTAG
17084696 GTTTTT
66 GTTTTT
17084702 AGTGGCGCTG
Statistics
Matches: 62, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
71 3 0.05
72 46 0.74
73 13 0.21
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.27
Consensus pattern (73 bp):
GCGGCGCTTTATTAATAACGCCGCCAAATCCCCGAAACCTCAGAAAACGACGTCGTTGGGCTTAG
GTTTTTTT
Found at i:17084726 original size:72 final size:72
Alignment explanation
Indices: 17084556--17084729 Score: 174
Period size: 72 Copynumber: 2.4 Consensus size: 72
17084546 GCCTTAAACA
* * * * *
17084556 TTAGCGGCGCTTTATTAATAACGCCGCCAAATCCCCGAAAGCTCAGAAAACAGAGTCGTTGGGAC
1 TTAGCGGCGCTGTCTGAA-AACGCCGCTAAATCCCCGAAACCTCAGAAAACAGAGTCGTTGGGAC
17084621 TAGGTTTT
65 TAGGTTTT
* * ** **
17084629 TTTGCGGCGCTTTCTTCAAACGCCGCTAAATCCCCGAAACCTTGGAAAAC-GACGTCGTTGGG-C
1 TTAGCGGCGCTGTCTGAAAACGCCGCTAAATCCCCGAAACCTCAGAAAACAGA-GTCGTTGGGAC
17084692 TTAGG-TTT
65 -TAGGTTTT
* *
17084700 TTAGTGGCGCTGTCTGGAAAATGCCGCTAA
1 TTAGCGGCGCTGTCT-GAAAACGCCGCTAA
17084730 TACTTATTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
71 18 0.21
72 52 0.61
73 15 0.18
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (72 bp):
TTAGCGGCGCTGTCTGAAAACGCCGCTAAATCCCCGAAACCTCAGAAAACAGAGTCGTTGGGACT
AGGTTTT
Found at i:17086529 original size:21 final size:21
Alignment explanation
Indices: 17086505--17086557 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
17086495 CATTGTTTCT
* *
17086505 AATCTCACCGTTACAATATCC
1 AATCTCACCGCTACAATAACC
* * *
17086526 AATCTCACAGCTACAGTAACT
1 AATCTCACCGCTACAATAACC
17086547 AATCTCACCGC
1 AATCTCACCGC
17086558 CACCGCTGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.34, C:0.34, G:0.08, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:17089964 original size:5 final size:5
Alignment explanation
Indices: 17089956--17089986 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
17089946 GAGATGAAAT
17089956 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA TCGAA T
17089987 ATGTTTGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:17090380 original size:17 final size:17
Alignment explanation
Indices: 17090352--17090410 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
17090342 TAAACAATTC
*
17090352 AATAATATAAATAATAT
1 AATAATGTAAATAATAT
*
17090369 AA-AATGTGAAATTTAATTT
1 AATAATGT-AAA--TAATAT
17090388 AATAATGTAAATAATAT
1 AATAATGTAAATAATAT
17090405 ATATAA
1 A-ATAA
17090411 ATAAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
16 4 0.12
17 11 0.32
18 4 0.12
19 10 0.29
20 5 0.15
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (17 bp):
AATAATGTAAATAATAT
Found at i:17090521 original size:18 final size:20
Alignment explanation
Indices: 17090490--17090528 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17090480 GGTGAGAAGT
17090490 AAAAGTTTAGGGGGAA-AAA
1 AAAAGTTTAGGGGGAATAAA
*
17090509 AAAAGTTT-TGGGGAATAAA
1 AAAAGTTTAGGGGGAATAAA
17090528 A
1 A
17090529 GTTTGAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (20 bp):
AAAAGTTTAGGGGGAATAAA
Found at i:17090660 original size:31 final size:30
Alignment explanation
Indices: 17090625--17090684 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
17090615 GGAGGTGGGA
*
17090625 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* *
17090656 TGGGAGGGAATAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
17090685 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:17093148 original size:100 final size:101
Alignment explanation
Indices: 17092969--17093150 Score: 285
Period size: 100 Copynumber: 1.8 Consensus size: 101
17092959 GATAATAACA
** * *
17092969 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTGGTGCCCATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATTGGTGCCAACGCCATGT
*
17093034 CCCAGACATGGTCTTACGAATGACCTCTCATCTCGG
66 CCCAAACATGGTCTTACGAATGACCTCTCATCTCGG
* * *
17093070 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGA-CCTCTCATCTTGGTGCCAACGCCATGT
1 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATTGGTGCCAACGCCATGT
17093134 CCCAAACATGGTCTTAC
66 CCCAAACATGGTCTTAC
17093151 ATGGGATTTC
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
100 38 0.52
101 35 0.48
ACGTcount: A:0.22, C:0.30, G:0.21, T:0.27
Consensus pattern (101 bp):
TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCCTCTCATATTGGTGCCAACGCCATGT
CCCAAACATGGTCTTACGAATGACCTCTCATCTCGG
Found at i:17093155 original size:50 final size:50
Alignment explanation
Indices: 17092969--17093156 Score: 254
Period size: 50 Copynumber: 3.7 Consensus size: 50
17092959 GATAATAACA
* ** *
17092969 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTTGG
* * *
17093020 TGCCCATGCCATGTCCCAGACATGGTCTTACGAAT--GACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC--ATGGGACCTCTCATCTTGG
*
17093070 TGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
*
17093120 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
17093157 TTTCTTTACC
Statistics
Matches: 121, Mismatches: 12, Indels: 9
0.85 0.08 0.06
Matches are distributed among these distances:
48 2 0.02
50 86 0.71
51 31 0.26
53 2 0.02
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTTGG
Found at i:17093279 original size:13 final size:13
Alignment explanation
Indices: 17093261--17093287 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17093251 AGTCAACATT
17093261 AAATAAATTCATA
1 AAATAAATTCATA
17093274 AAATAAATTCATA
1 AAATAAATTCATA
17093287 A
1 A
17093288 TTGCTGGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (13 bp):
AAATAAATTCATA
Found at i:17095678 original size:235 final size:235
Alignment explanation
Indices: 17095109--17095817 Score: 1161
Period size: 235 Copynumber: 3.0 Consensus size: 235
17095099 TCATTTGATA
* * * *
17095109 AAAAGTTTCCAAGTTTTGCAAGAAATCCTAAGAATGTAAGGTTTGGGCTTGCATCTGATGGCCTT
1 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
* *
17095174 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCTTGTTGTACTTGTT-TCTTACAATT
66 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCT-TTACAATT
* * *
17095238 TCCCTTCATGAATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAA
130 TGCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAA
* *
17095303 GGCCTAAAGAACAATATTGGCATTTATATGC-GTCGCTTAT
195 GGTCTAAAGAACGATATTGGCATTTATATGCAGTCGCTTAT
* *
17095343 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGTTTACATCTAATGGCCTT
1 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
* *
17095408 AATCCTTTTAAAATTATGAGTCCTTCATATAGTACTTAGCCTGTTGTGCTTGTTCTTTACAATTT
66 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
* *
17095473 GCCTCCATGGATTTGCATGAAACAATATTCTTTTATTTTATCTATGATAATCCTTGGGGAGAAGG
131 GCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAAG
17095538 GTCTAAAGAACGATATTGGCATTTATATGCAGTCGCTTAT
196 GTCTAAAGAACGATATTGGCATTTATATGCAGTCGCTTAT
* * *
17095578 AAAAGTTTCCAAGTTTTGCAAGCAATCTTAAGAATGTGAGGCTTGGGCCTATATCTGATGGCCTT
1 AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
* *
17095643 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCCTTACAACTT
66 AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
* * *
17095708 GCCTCCATGGATTTGCATGAAACAATGTTCTTTTATCTTATCTATGATAATCATTGGGGAGAAAA
131 GCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAAG
*
17095773 GTCAAAAGAACGATATTGGCATTTATATGCAGTCGCTTAT
196 GTCTAAAGAACGATATTGGCATTTATATGCAGTCGCTTAT
17095813 AAAAG
1 AAAAG
17095818 AGTTGAAGTA
Statistics
Matches: 441, Mismatches: 32, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
234 206 0.47
235 235 0.53
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (235 bp):
AAAAGTTTCCAAGTTTTGCAAGCAATCCTAAGAATGTGAGGCTTGGGCTTACATCTGATGGCCTT
AATCCTTTTAAAATCATGAGTCCTTCATATAGTACTTGGCCTGTTGTGCTTGTTCTTTACAATTT
GCCTCCATGGATTTGCATGAAACAATATTCTTTTATCTTATCTATGATAATCCTTGGGGAGAAAG
GTCTAAAGAACGATATTGGCATTTATATGCAGTCGCTTAT
Found at i:17105761 original size:41 final size:41
Alignment explanation
Indices: 17105699--17105889 Score: 319
Period size: 41 Copynumber: 4.6 Consensus size: 41
17105689 GACTATACGT
*
17105699 CTAGCAGGCTAAGTGCTGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
17105740 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
*
17105781 CTAGCAGGCTAAGTGCCGGTGATTTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * *
17105822 CTAGCAGGCTAAGTGCCGGTGATCTAAATTAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
17105863 CTAGCAGGCTAAGTGCCGGTGAATCTG
1 CTAGCAGGCTAAGTGCCGGTG-ATCTG
17105890 TTAAATTAAG
Statistics
Matches: 141, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
41 137 0.97
42 4 0.03
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:17107778 original size:50 final size:50
Alignment explanation
Indices: 17107676--17107966 Score: 375
Period size: 50 Copynumber: 5.7 Consensus size: 50
17107666 GGGAATGAGA
* * *
17107676 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCATCATTGATATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CG--A-GATGAGAGG
* * *
17107732 TCCCATGTAGGACCATGTTTGGGACATGGCATTGGTACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
17107782 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
17107832 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * **
17107882 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * *
17107932 TCTCATGTAAGACCATATCTGGGATATGGCATTGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGG
17107967 TAATACAGAA
Statistics
Matches: 213, Mismatches: 22, Indels: 6
0.88 0.09 0.02
Matches are distributed among these distances:
50 177 0.83
51 1 0.00
53 1 0.00
55 1 0.00
56 33 0.15
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:17108248 original size:16 final size:16
Alignment explanation
Indices: 17108227--17108262 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
17108217 TAGTAAGCAT
*
17108227 GTAAGTAAAAAAGTGA
1 GTAAGTAAAAAAGCGA
*
17108243 GTAAGTAAAGAAGCGA
1 GTAAGTAAAAAAGCGA
17108259 GTAA
1 GTAA
17108263 AGATTCTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.28, T:0.17
Consensus pattern (16 bp):
GTAAGTAAAAAAGCGA
Found at i:17114344 original size:17 final size:17
Alignment explanation
Indices: 17114322--17114354 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17114312 AGAAAGTCGA
17114322 CCCATGGTTGTTAACTC
1 CCCATGGTTGTTAACTC
17114339 CCCATGGTTGTTAACT
1 CCCATGGTTGTTAACT
17114355 TCTTCGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (17 bp):
CCCATGGTTGTTAACTC
Found at i:17116744 original size:42 final size:42
Alignment explanation
Indices: 17116650--17116744 Score: 147
Period size: 42 Copynumber: 2.3 Consensus size: 42
17116640 TCTTATTCTA
* * *
17116650 GGAA-TATTTTATTTTATGTTTTAGTAGTTTATTAGAATAAG
1 GGAATTATTTTCTCTTATATTTTAGTAGTTTATTAGAATAAG
*
17116691 GGAATTATTTTCTCTTATATTTTAGTAGTTTATTAGAGTAAG
1 GGAATTATTTTCTCTTATATTTTAGTAGTTTATTAGAATAAG
17116733 GGAATTATTTTC
1 GGAATTATTTTC
17116745 CCAACTAGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.29, C:0.03, G:0.17, T:0.51
Consensus pattern (42 bp):
GGAATTATTTTCTCTTATATTTTAGTAGTTTATTAGAATAAG
Found at i:17118357 original size:15 final size:15
Alignment explanation
Indices: 17118333--17118382 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
17118323 TTGGCAGTGC
17118333 TTTA-TCTGGTGAAA
1 TTTACTCTGGTGAAA
17118347 TTTACTCTGGTGAAA
1 TTTACTCTGGTGAAA
*
17118362 TTTACTCTGGTGGAA
1 TTTACTCTGGTGAAA
17118377 TTTACT
1 TTTACT
17118383 TTCGTGACGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 4 0.12
15 30 0.88
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.44
Consensus pattern (15 bp):
TTTACTCTGGTGAAA
Found at i:17121379 original size:19 final size:19
Alignment explanation
Indices: 17121331--17121371 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
17121321 GAATATATTT
17121331 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
17121350 TAAATCTTATTTAGGTAGA
1 TAAATCTTATTTAGGTAGA
17121369 TAA
1 TAA
17121372 GTTTTATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
TAAATCTTATTTAGGTAGA
Found at i:17121439 original size:42 final size:42
Alignment explanation
Indices: 17121393--17121482 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
17121383 ATTCTAGGAA
**
17121393 TATTTTATTTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
1 TATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
** * * * *
17121435 TATTTCCCCTTATGTTTTAGTAGTTTATTAGAGTAAGGGAAT
1 TATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
17121477 TATTTT
1 TATTTT
17121483 CCCAATTAGG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (42 bp):
TATTTTACCTTATCTTTTAGTAGTTTATTAAAATAAGGAAAT
Found at i:17122852 original size:13 final size:13
Alignment explanation
Indices: 17122836--17122865 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
17122826 AGACTGAAGA
*
17122836 GCAAAACTGCAAT
1 GCAAAACCGCAAT
17122849 GCAAAACCGCAAT
1 GCAAAACCGCAAT
17122862 GCAA
1 GCAA
17122866 TTTTCATTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.10
Consensus pattern (13 bp):
GCAAAACCGCAAT
Found at i:17131438 original size:50 final size:49
Alignment explanation
Indices: 17131361--17131458 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
17131351 AGTCCATGGC
* ** **
17131361 ACCATATCGTGTAAGACTGTAGTTGGTGGGTTAT-GACTTCATATAGAAAG
1 ACCATATCGTATAAGACCATAACTGGTGGGTTATAG-CTTCATAT-GAAAG
17131411 ACCATATCGTATAAGACCATAACTGGTGGGTTATAGCTTCATATGAAA
1 ACCATATCGTATAAGACCATAACTGGTGGGTTATAGCTTCATATGAAA
17131459 AAAAATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 4 0.10
50 37 0.88
51 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.22, T:0.31
Consensus pattern (49 bp):
ACCATATCGTATAAGACCATAACTGGTGGGTTATAGCTTCATATGAAAG
Found at i:17135991 original size:14 final size:14
Alignment explanation
Indices: 17135972--17135998 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17135962 GATTGTATTT
17135972 TCTTCGTTATCATC
1 TCTTCGTTATCATC
17135986 TCTTCGTTATCAT
1 TCTTCGTTATCAT
17135999 TTCCATGTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.26, G:0.07, T:0.52
Consensus pattern (14 bp):
TCTTCGTTATCATC
Found at i:17137326 original size:12 final size:12
Alignment explanation
Indices: 17137311--17137340 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
17137301 TCTCATCTTC
17137311 ATTTTCATTTTT
1 ATTTTCATTTTT
17137323 ATTTTCATTTTT
1 ATTTTCATTTTT
17137335 AGTTTT
1 A-TTTT
17137341 GAGAAACCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.73
Consensus pattern (12 bp):
ATTTTCATTTTT
Done.