Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A06
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: 115140250
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2234201 characters in sequence are not A, C, G, or T
File 20 of 345
Found at i:5842337 original size:15 final size:16
Alignment explanation
Indices: 5842302--5842345 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
5842292 TTGTTTCGTT
*
5842302 TTTATTTATTTTATGC
1 TTTATTTATTTTATAC
*
5842318 TTTATTTCTTTT-TAC
1 TTTATTTATTTTATAC
*
5842333 TTTATTTAATTTA
1 TTTATTTATTTTA
5842346 ATTCATGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.70
Consensus pattern (16 bp):
TTTATTTATTTTATAC
Found at i:5848760 original size:51 final size:50
Alignment explanation
Indices: 5848688--5848815 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 50
5848678 CCTAAACAGT
* * * * * *
5848688 AATCAGTAACGGTAGCAGTAACAGTAACAGTATTCAACACATAAAGTGTTG
1 AATCGGTAACAGTAACAGTAAC-GTAACAGTATTCAACACACAAAGTATCG
* * *
5848739 AATCTGTAACAGTAAC-G----GTAACAATATTCGACACACAAAGTATCG
1 AATCGGTAACAGTAACAGTAACGTAACAGTATTCAACACACAAAGTATCG
5848784 AATCGGTAACAGTAACAGTAACGGTAACAGTA
1 AATCGGTAACAGTAACAGTAAC-GTAACAGTA
5848816 ACAGTAGTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
45 38 0.62
46 1 0.02
50 1 0.02
51 21 0.34
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (50 bp):
AATCGGTAACAGTAACAGTAACGTAACAGTATTCAACACACAAAGTATCG
Found at i:5848767 original size:45 final size:45
Alignment explanation
Indices: 5848697--5848805 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
5848687 TAATCAGTAA
* * * * *
5848697 CGGTAGCAGTAACAGTAACAGTATTCAACACATAAAGTGTTGAAT
1 CGGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
* * *
5848742 CTGTAACAGTAACGGTAACAATATTCGACACACAAAGTATCGAAT
1 CGGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
5848787 CGGTAACAGTAACAGTAAC
1 CGGTAACAGTAACAGTAAC
5848806 GGTAACAGTA
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.41, C:0.18, G:0.18, T:0.22
Consensus pattern (45 bp):
CGGTAACAGTAACAGTAACAATATTCAACACACAAAGTATCGAAT
Found at i:5848800 original size:6 final size:6
Alignment explanation
Indices: 5848789--5848821 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
5848779 TATCGAATCG
*
5848789 GTAACA GTAACA GTAACG GTAACA GTAACA GTA
1 GTAACA GTAACA GTAACA GTAACA GTAACA GTA
5848822 GTTGGCACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.45, C:0.15, G:0.21, T:0.18
Consensus pattern (6 bp):
GTAACA
Found at i:5848810 original size:18 final size:18
Alignment explanation
Indices: 5848787--5848821 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5848777 AGTATCGAAT
5848787 CGGTAACAGTAACAGTAA
1 CGGTAACAGTAACAGTAA
5848805 CGGTAACAGTAACAGTA
1 CGGTAACAGTAACAGTA
5848822 GTTGGCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.23, T:0.17
Consensus pattern (18 bp):
CGGTAACAGTAACAGTAA
Found at i:5849067 original size:40 final size:40
Alignment explanation
Indices: 5849021--5849107 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
5849011 AATTCATTAC
* * * *
5849021 TTCAGTAATTTCACAGTTCAATGCAGTACACATAATAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
* **
5849061 TTCAGTAACTTCACAATTCAATTCAGTACTTAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
5849101 TTCAGTA
1 TTCAGTA
5849108 TTCCATAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.40, C:0.18, G:0.08, T:0.33
Consensus pattern (40 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAACAATA
Found at i:5849715 original size:33 final size:33
Alignment explanation
Indices: 5849646--5849708 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
5849636 ATTATTTAAT
*
5849646 TAATAAATATATCTTAATTTTAATAATAATAAA
1 TAATAAATATATCTTAATTTAAATAATAATAAA
*
5849679 TAATAAATATCTAC-TAATTTAAATAA-AATA
1 TAATAAATATAT-CTTAATTTAAATAATAATA
5849709 TTATAATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 4 0.15
33 22 0.81
34 1 0.04
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (33 bp):
TAATAAATATATCTTAATTTAAATAATAATAAA
Found at i:5857689 original size:19 final size:19
Alignment explanation
Indices: 5857645--5857689 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
5857635 TATTTTTTTC
*
5857645 TATTGTTGTTTTGTTGTTT
1 TATTGTTGTTTTGTTATTT
**
5857664 TGCTGTTGTTTTGTTATTT
1 TATTGTTGTTTTGTTATTT
5857683 TATTGTT
1 TATTGTT
5857690 ATTGTTTGCA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.71
Consensus pattern (19 bp):
TATTGTTGTTTTGTTATTT
Found at i:5861428 original size:27 final size:27
Alignment explanation
Indices: 5861347--5861430 Score: 116
Period size: 27 Copynumber: 3.1 Consensus size: 27
5861337 TATAGGGGTA
*
5861347 GGTTGAGCCTATCT-AGTAGGCGCGACT
1 GGTTGAGCCTATCTGA-CAGGCGCGACT
* * *
5861374 CGTTGTGCCTATCTGACAGGTGCGACT
1 GGTTGAGCCTATCTGACAGGCGCGACT
5861401 GGTTGAGCCTATCTGACAGGCGCGACT
1 GGTTGAGCCTATCTGACAGGCGCGACT
5861428 GGT
1 GGT
5861431 GGGTCCTACA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.17, C:0.24, G:0.33, T:0.26
Consensus pattern (27 bp):
GGTTGAGCCTATCTGACAGGCGCGACT
Found at i:5861438 original size:27 final size:27
Alignment explanation
Indices: 5861364--5861438 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 27
5861354 CCTATCTAGT
* *
5861364 AGGCGCGACTCGT-TGTGCCTATCTGAC
1 AGGCGCGACTGGTGAGT-CCTATCTGAC
*
5861391 AGGTGCGACTGGTTGAG-CCTATCTGAC
1 AGGCGCGACTGG-TGAGTCCTATCTGAC
*
5861418 AGGCGCGACTGGTGGGTCCTA
1 AGGCGCGACTGGTGAGTCCTA
5861439 CAGGAGCATC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 3 0.08
27 35 0.88
28 1 0.03
29 1 0.03
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (27 bp):
AGGCGCGACTGGTGAGTCCTATCTGAC
Found at i:5861522 original size:24 final size:24
Alignment explanation
Indices: 5861494--5861543 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
5861484 AAAATCAAAT
5861494 GAGCAACAGACACAAAATTTAGCA
1 GAGCAACAGACACAAAATTTAGCA
5861518 GAGCAACAGACACAAAATTTAGCA
1 GAGCAACAGACACAAAATTTAGCA
5861542 GA
1 GA
5861544 ACGGAAGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (24 bp):
GAGCAACAGACACAAAATTTAGCA
Found at i:5864222 original size:38 final size:38
Alignment explanation
Indices: 5864055--5864494 Score: 292
Period size: 39 Copynumber: 11.4 Consensus size: 38
5864045 AAAAGTAGAA
* * * * **
5864055 TACTGATTCTACTAAAAGTTTGCTCAAGCGAGTGAATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAGCAAATC
* * ** * *
5864093 TACTGTTTATACTGAATGCTTGTTCAAAAAGAACGAATC
1 TACTGATTATACTGAATGCTTGCTC-AAGCGAGCAAATC
* * * * * ** *
5864132 CACTGATTTTATTGAATACTTGTTCTAAAAGAGCGAATC
1 TACTGATTATACTGAATGCTTGCTC-AAGCGAGCAAATC
* * * *
5864171 CACTGATTTTACTGAATGATTGCTTAAGCGAGCAAATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAGCAAATC
* * * * *
5864209 TACCGATTATACTGGATGCTTGTTCAAAACGAGCGAATC
1 TACTGATTATACTGAATGCTTGCTC-AAGCGAGCAAATC
* * * * *
5864248 CACT-AGTTTTACCGAATGGTTGCTCAAGCGAGCGAATC
1 TACTGA-TTATACTGAATGCTTGCTCAAGCGAGCAAATC
* * * *
5864286 TACTGATTATATTGAATGCTTGTTCAAAACAAGCAAATC
1 TACTGATTATACTGAATGCTTGCTC-AAGCGAGCAAATC
* **
5864325 TACTGATTTTACTGAATGCTTGCTCAAGCGAGTGAATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAGCAAATC
* * * * **
5864363 TACTAATTATCCTGAATGCTTGTTCAAAGCAAGGGAATC
1 TACTGATTATACTGAATGCTTGCTC-AAGCGAGCAAATC
* * *
5864402 CACTGATTTTACTGAATG-TTGCTCAA-CGAGCCATATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAG-CAAATC
* * * *
5864439 TACTGATTATATTGAATGTTTGCTCAAACGAGCATTATC
1 TACTGATTATACTGAATGCTTGCTCAAGCGAGCA-AATC
*
5864478 CACTGATTATACTGAAT
1 TACTGATTATACTGAAT
5864495 AAGATTTTCT
Statistics
Matches: 314, Mismatches: 78, Indels: 19
0.76 0.19 0.05
Matches are distributed among these distances:
36 3 0.01
37 20 0.06
38 122 0.39
39 169 0.54
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (38 bp):
TACTGATTATACTGAATGCTTGCTCAAGCGAGCAAATC
Found at i:5864245 original size:77 final size:76
Alignment explanation
Indices: 5864128--5864494 Score: 402
Period size: 77 Copynumber: 4.8 Consensus size: 76
5864118 AAAAAGAACG
* * * *
5864128 AATCCACTGATTTTATTGAATACTTGTTCTAAAA-GAGCGAATCCACTGATTTTACTGAATGATT
1 AATCTACTGATTATACTGAATGCTTGTTC-AAAACGAGCGAATCCACTGATTTTACTGAATG-TT
*
5864192 GCTTAAGCGAGCA
64 GCTCAAGCGAGCA
* * *
5864205 AATCTACCGATTATACTGGATGCTTGTTCAAAACGAGCGAATCCACT-AGTTTTACCGAATGGTT
1 AATCTACTGATTATACTGAATGCTTGTTCAAAACGAGCGAATCCACTGA-TTTTACTGAAT-GTT
*
5864269 GCTCAAGCGAGCG
64 GCTCAAGCGAGCA
* * * *
5864282 AATCTACTGATTATATTGAATGCTTGTTCAAAACAAGCAAATCTACTGATTTTACTGAATGCTTG
1 AATCTACTGATTATACTGAATGCTTGTTCAAAACGAGCGAATCCACTGATTTTACTGAATG-TTG
**
5864347 CTCAAGCGAGTG
65 CTCAAGCGAGCA
* * * * *
5864359 AATCTACTAATTATCCTGAATGCTTGTTCAAAGCAAGGGAATCCACTGATTTTACTGAATGTTGC
1 AATCTACTGATTATACTGAATGCTTGTTCAAAACGAGCGAATCCACTGATTTTACTGAATGTTGC
5864424 TCAA-CGAGCCA
66 TCAAGCGAG-CA
* * * * *
5864435 TATCTACTGATTATATTGAATGTTTGCTC-AAACGAGC-ATTATCCACTGATTATACTGAAT
1 AATCTACTGATTATACTGAATGCTTGTTCAAAACGAGCGA--ATCCACTGATTTTACTGAAT
5864495 AAGATTTTCT
Statistics
Matches: 246, Mismatches: 36, Indels: 17
0.82 0.12 0.06
Matches are distributed among these distances:
74 1 0.00
75 9 0.04
76 56 0.23
77 178 0.72
78 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (76 bp):
AATCTACTGATTATACTGAATGCTTGTTCAAAACGAGCGAATCCACTGATTTTACTGAATGTTGC
TCAAGCGAGCA
Found at i:5864321 original size:116 final size:116
Alignment explanation
Indices: 5864089--5864351 Score: 298
Period size: 116 Copynumber: 2.3 Consensus size: 116
5864079 CAAGCGAGTG
* **
5864089 AATCTACTGTTTATACTGAATGCTTGTTCAAAAAGAACGAATCCACTGATTTTATTGAATACTTG
1 AATCTACTGATTATACTGAATGCTTGTTCAAAAAGAACGAATCCACTGATTTTACCGAATACTTG
* * * *
5864154 TTCTAAAAGAGCGAATCCACTGATTTTACTGAATGATTGCTTAAGCGAGCA
66 CTCTAAAAGAGCGAATCCACTGATTATACTGAATGATTGCTTAAACAAGCA
* * * * **
5864205 AATCTACCGATTATACTGGATGCTTGTTCAAAACGAGCGAATCCACT-AGTTTTACCGAATGGTT
1 AATCTACTGATTATACTGAATGCTTGTTCAAAAAGAACGAATCCACTGA-TTTTACCGAATACTT
** * * *
5864269 GCTC-AAGCGAGCGAATCTACTGATTATATTGAATGCTTG-TTCAAAACAAGCA
65 GCTCTAAAAGAGCGAATCCACTGATTATACTGAATGATTGCTT--AAACAAGCA
* *
5864321 AATCTACTGATTTTACTGAATGCTTGCTCAA
1 AATCTACTGATTATACTGAATGCTTGTTCAA
5864352 GCGAGTGAAT
Statistics
Matches: 122, Mismatches: 22, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
114 2 0.02
115 30 0.25
116 90 0.74
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Consensus pattern (116 bp):
AATCTACTGATTATACTGAATGCTTGTTCAAAAAGAACGAATCCACTGATTTTACCGAATACTTG
CTCTAAAAGAGCGAATCCACTGATTATACTGAATGATTGCTTAAACAAGCA
Found at i:5864412 original size:154 final size:152
Alignment explanation
Indices: 5864126--5864494 Score: 456
Period size: 154 Copynumber: 2.4 Consensus size: 152
5864116 TCAAAAAGAA
* * * *
5864126 CGAATCCACTGATTTTATTGAATACTTGTTCTAAAA-GAGCGAATCCACTGATTTTACTGAATGA
1 CGAATCTACTGATTATATTGAATGCTTGTTC-AAAACGAGCAAATCCACTGATTTTACTGAATGA
* * * *
5864190 TTGCTTAAGCGAGCAAATCTACCGATTATACTGGATGCTTGTTCAAAACGAGCGAATCCACTAGT
65 TTGCTCAAGCGAGCAAATCTACCAATTATACTGAATGCTTGTTCAAAACAAGCGAATCCACTAGT
5864255 TTTACCGAATGGTTGCTCAAGCGAG
130 TTTACCGAAT-GTTGCTCAA-CGAG
* * *
5864280 CGAATCTACTGATTATATTGAATGCTTGTTCAAAACAAGCAAATCTACTGATTTTACTGAATGCT
1 CGAATCTACTGATTATATTGAATGCTTGTTCAAAACGAGCAAATCCACTGATTTTACTGAATGAT
** * * * *
5864345 TGCTCAAGCGAGTGAATCTACTAATTATCCTGAATGCTTGTTCAAAGCAAGGGAATCCACT-GAT
66 TGCTCAAGCGAGCAAATCTACCAATTATACTGAATGCTTGTTCAAAACAAGCGAATCCACTAG-T
*
5864409 TTTACTGAATGTTGCTCAACGAG
130 TTTACCGAATGTTGCTCAACGAG
* * * * *
5864432 CCATATCTACTGATTATATTGAATGTTTGCTC-AAACGAGCATTATCCACTGATTATACTGAAT
1 CGA-ATCTACTGATTATATTGAATGCTTGTTCAAAACGAGCA-AATCCACTGATTTTACTGAAT
5864495 AAGATTTTCT
Statistics
Matches: 186, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
152 14 0.08
153 58 0.31
154 114 0.61
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Consensus pattern (152 bp):
CGAATCTACTGATTATATTGAATGCTTGTTCAAAACGAGCAAATCCACTGATTTTACTGAATGAT
TGCTCAAGCGAGCAAATCTACCAATTATACTGAATGCTTGTTCAAAACAAGCGAATCCACTAGTT
TTACCGAATGTTGCTCAACGAG
Found at i:5869781 original size:42 final size:42
Alignment explanation
Indices: 5869691--5869803 Score: 149
Period size: 42 Copynumber: 2.7 Consensus size: 42
5869681 AGTGCTAAAT
* ** **
5869691 AGAAACCCATAAGGGTTGAACGGAAGCTC-GTAGAGCTGAAC
1 AGAAACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAAC
*
5869732 GGAAACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAAC
1 AGAAACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAAC
5869774 AGAAACCCATAAGGGTTAAACAGAAA-CTCA
1 AGAAACCCATAAGGGTTAAACA-AAAGCTCA
5869804 TGAGTTAACA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
41 25 0.40
42 35 0.56
43 3 0.05
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (42 bp):
AGAAACCCATAAGGGTTAAACAAAAGCTCAAAAGAGCTGAAC
Found at i:5869797 original size:21 final size:21
Alignment explanation
Indices: 5869733--5869800 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
5869723 GAGCTGAACG
5869733 GAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGGGTTAAACA
* * * * *
5869754 -AAAGCTCAAAAGAGCTGAACA
1 GAAA-CCCATAAGGGTTAAACA
5869775 GAAACCCATAAGGGTTAAACA
1 GAAACCCATAAGGGTTAAACA
5869796 GAAAC
1 GAAAC
5869801 TCATGAGTTA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
20 3 0.09
21 29 0.83
22 3 0.09
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (21 bp):
GAAACCCATAAGGGTTAAACA
Found at i:5871012 original size:18 final size:19
Alignment explanation
Indices: 5870962--5871014 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 19
5870952 TTACCTAATT
* *
5870962 AATTCTTTTAAAATCACAA
1 AATTCTTCTAAATTCACAA
*
5870981 AATTC-ACT-AATTCA-AA
1 AATTCTTCTAAATTCACAA
5870997 AATTCTTCTAAATTCACA
1 AATTCTTCTAAATTCACA
5871015 CTTGACCAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 7 0.26
17 7 0.26
18 7 0.26
19 6 0.22
ACGTcount: A:0.45, C:0.19, G:0.00, T:0.36
Consensus pattern (19 bp):
AATTCTTCTAAATTCACAA
Found at i:5876098 original size:43 final size:44
Alignment explanation
Indices: 5876073--5876157 Score: 125
Period size: 45 Copynumber: 1.9 Consensus size: 44
5876063 CGATATCAGT
5876073 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGTATC
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAG-ATC
** * *
5876118 TCACCGGCATTATAGTTTGCTAAGCTCAAAGGCCCGAATA
1 TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATA
5876158 ATCAAGTCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (44 bp):
TCACCGGCATTATAGCCTGCTAGGCTCGAAGGCCCGAATAGATC
Found at i:5876535 original size:43 final size:43
Alignment explanation
Indices: 5876487--5876610 Score: 189
Period size: 43 Copynumber: 2.9 Consensus size: 43
5876477 CCGGCATTAC
*
5876487 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGTACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
*
5876530 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
* * *
5876573 GCCTACTAGGCACGAGGGCCCGAATATA-AT-ACCAGCAC
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCAC
5876611 TAGGCCTGTG
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
41 7 0.09
42 2 0.03
43 66 0.88
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCAGCACGAA
Found at i:5876647 original size:38 final size:38
Alignment explanation
Indices: 5876591--5876754 Score: 229
Period size: 38 Copynumber: 4.3 Consensus size: 38
5876581 GGCACGAGGG
* * * * *
5876591 CCCGAATATAATACCAGCACTAGGCCTGTGGGATTTAT
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
5876629 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
** *
5876667 CCCGGATATTTTACCAGCACGAAGCCTGCGGGTCTTTAA
1 CCCGGATATAATACCAGCACGAAGCCTGCGGG-ATTTAA
*
5876706 GCCCGGATATAATACCAGCACGAAGCCTGTGGGATTTAA
1 -CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
5876745 CCCGGATATA
1 CCCGGATATA
5876755 CATCGAATAT
Statistics
Matches: 112, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
38 73 0.65
39 10 0.09
40 29 0.26
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.23
Consensus pattern (38 bp):
CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAA
Found at i:5890033 original size:99 final size:97
Alignment explanation
Indices: 5889782--5890047 Score: 268
Period size: 99 Copynumber: 2.7 Consensus size: 97
5889772 CATTGAGATT
*
5889782 ATTTGTTTGAACTGAGTTAACCCTATTCTCCGAGTAAATTGGTTGAGTCGTATAAA-TTCCATCT
1 ATTTGCTTGAACTGAGTTAACCCTATTCT--GAGTAAATTGGTTGAGTCGTATAAACTT-CATCT
* * * *
5889846 TCTGGCAGGCTATTTCTAATATGATTATTGAACTT
63 TCTGGCAGGCTACTTCCAATATGATTATTAAACTG
* * * ** * *
5889881 ATTTTCTTGAA-TCGAGTTAACCCTACATTCCGAGCAAACCGATTGAGCCGTATAAACTTCATCT
1 ATTTGCTTGAACT-GAGTTAACCCT--ATTCTGAGTAAATTGGTTGAGTCGTATAAACTTCATCT
* **
5889945 TCTGGTATTCTACTTCCAATATGATTATTAAACTG
63 TCTGGCAGGCTACTTCCAATATGATTATTAAACTG
* * *
5889980 GTTTGCTTGAACTGAGTTAACCCTAGGTTCTGAGTAAATTGGTTGATTTGTATAAAC-TCGATCT
1 ATTTGCTTGAACTGAGTTAACCCTA--TTCTGAGTAAATTGGTTGAGTCGTATAAACTTC-ATCT
5890044 TCTG
63 TCTG
5890048 AGAGCCTTTC
Statistics
Matches: 134, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
97 1 0.01
98 3 0.02
99 123 0.92
100 3 0.02
101 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (97 bp):
ATTTGCTTGAACTGAGTTAACCCTATTCTGAGTAAATTGGTTGAGTCGTATAAACTTCATCTTCT
GGCAGGCTACTTCCAATATGATTATTAAACTG
Found at i:5895969 original size:9 final size:9
Alignment explanation
Indices: 5895955--5895985 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
5895945 AAAGTCAAAA
5895955 TCATTGAAG
1 TCATTGAAG
5895964 TCATTGAAG
1 TCATTGAAG
5895973 TCATTGAAG
1 TCATTGAAG
5895982 TCAT
1 TCAT
5895986 ATAATGGGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (9 bp):
TCATTGAAG
Found at i:5896301 original size:28 final size:31
Alignment explanation
Indices: 5896241--5896302 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
5896231 AATATTTTAT
**
5896241 TATTATTATTATTATTAGTTATTTTGGTTAAA
1 TATTATTATTATTATTAGTTATTTT-GAAAAA
5896273 TATT-TTATTATTATTAGTTA-TTT-AAAAA
1 TATTATTATTATTATTAGTTATTTTGAAAAA
5896301 TA
1 TA
5896303 AAATTAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 5 0.18
30 3 0.11
31 16 0.57
32 4 0.14
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.58
Consensus pattern (31 bp):
TATTATTATTATTATTAGTTATTTTGAAAAA
Found at i:5900970 original size:11 final size:10
Alignment explanation
Indices: 5900957--5900995 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
5900947 CTGATATTCA
5900957 TTCTTCTCTC
1 TTCTTCTCTC
*
5900967 ATTCTTCTATC
1 -TTCTTCTCTC
5900978 TTCTTCT-TC
1 TTCTTCTCTC
5900987 TTCTTCTCT
1 TTCTTCTCT
5900996 GGTTCATTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
9 9 0.35
10 8 0.31
11 9 0.35
ACGTcount: A:0.05, C:0.33, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCTTCTCTC
Found at i:5900989 original size:16 final size:18
Alignment explanation
Indices: 5900958--5900990 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
5900948 TGATATTCAT
5900958 TCTTCTCTCATTCTTCTA
1 TCTTCTCTCATTCTTCTA
5900976 TCTTCT-TC-TTCTTCT
1 TCTTCTCTCATTCTTCT
5900991 TCTCTGGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 2 0.13
18 6 0.40
ACGTcount: A:0.06, C:0.33, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTCTCTCATTCTTCTA
Found at i:5904036 original size:129 final size:127
Alignment explanation
Indices: 5903764--5904094 Score: 407
Period size: 129 Copynumber: 2.6 Consensus size: 127
5903754 TATTTAGTCC
* * * * * **
5903764 AACGGAAAACCGAAACCCAGCACGATAGAGCACTATTC-CACGAACTTCCAAGCATTGAACATTG
1 AACGGGAAATCGAAACCCAGCACGATAGGGCACGATTCTC-CGAATTTCCAAGCATCAAACATTG
* * * * * *
5903828 CCTTGTTTTAGAATTTAAAGAATACGAATGGAATTCTAAAGGAATATTTGATTATTTTGAACA
65 CCTTGTTTTAGAATTTAAAAAATACAAATGAAATTCTAAAGGAAGATTCGATTATCTTGAACA
*
5903891 AA-GGAGAAATCGAAACCCAACACGATAGGGCACGATTCTCCGAATTTCCAAGCATCAAACATTG
1 AACGG-GAAATCGAAACCCAGCACGATAGGGCACGATTCTCCGAATTTCCAAGCATCAAACATTG
* *
5903955 TCTTGTTTTAGAATTTAGAAAAAATACAAATGAAATTCTAAAGGAAGGTTCGATTATCTTGAACA
65 CCTTGTTTTAGAATTT--AAAAAATACAAATGAAATTCTAAAGGAAGATTCGATTATCTTGAACA
* * * *
5904020 AACGGGAAATCGAAACCCAGCACGGTAGGGCACGATT-TCCCGGATTTCCAAACATCAAACATTA
1 AACGGGAAATCGAAACCCAGCACGATAGGGCACGATTCT-CCGAATTTCCAAGCATCAAACATTG
5904084 CCTTCGTTTTA
65 CCTT-GTTTTA
5904095 AGGAATTTTT
Statistics
Matches: 175, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
126 2 0.01
127 66 0.38
128 2 0.01
129 97 0.55
130 8 0.05
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.25
Consensus pattern (127 bp):
AACGGGAAATCGAAACCCAGCACGATAGGGCACGATTCTCCGAATTTCCAAGCATCAAACATTGC
CTTGTTTTAGAATTTAAAAAATACAAATGAAATTCTAAAGGAAGATTCGATTATCTTGAACA
Found at i:5905200 original size:29 final size:29
Alignment explanation
Indices: 5905149--5905211 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
5905139 AGGAAACACT
* *
5905149 TATACATATAATAGATTTAAAAACATATA
1 TATACATATAATAAATTTAAAAAAATATA
5905178 TATACATA-AATAAATTTAGAAAAAATATA
1 TATACATATAATAAATTTA-AAAAAATATA
5905207 TATAC
1 TATAC
5905212 GAGAATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 9 0.29
29 22 0.71
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.33
Consensus pattern (29 bp):
TATACATATAATAAATTTAAAAAAATATA
Found at i:5907852 original size:27 final size:27
Alignment explanation
Indices: 5907822--5907873 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5907812 CTTTAATTTT
* * *
5907822 ATGATTCAGTTAATTTGATATTTTGAC
1 ATGATTCAATTAATCTGATAATTTGAC
5907849 ATGATTCAATTAATCTGATAATTTG
1 ATGATTCAATTAATCTGATAATTTG
5907874 TCATCTTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.33, C:0.08, G:0.13, T:0.46
Consensus pattern (27 bp):
ATGATTCAATTAATCTGATAATTTGAC
Found at i:5912143 original size:54 final size:54
Alignment explanation
Indices: 5912061--5912204 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
5912051 TGGAGGAAGC
5912061 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
*
5912115 GTCCTAGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
* *
5912169 GTTCTGGTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTCCTGGTGGCTATGCCACAATTATCTG-ATCTGGTG
5912205 ACTTCGTCAC
Statistics
Matches: 85, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
53 6 0.07
54 79 0.93
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (54 bp):
GTCCTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCT
Found at i:5912215 original size:27 final size:27
Alignment explanation
Indices: 5912064--5912222 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
5912054 AGGAAGCGTC
*
5912064 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
*
5912091 CTGGTGGCTCTGCCACATATATCTGT-C
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
* *
5912118 CTAGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
5912145 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
5912172 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
5912199 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
5912223 GCAGCCTCGC
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 103 0.90
28 2 0.02
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:5912216 original size:81 final size:80
Alignment explanation
Indices: 5912064--5912222 Score: 207
Period size: 81 Copynumber: 2.0 Consensus size: 80
5912054 AGGAAGCGTC
*
5912064 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGGCTAT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTAT
5912129 GCCACAATTATCTGAT
66 GCCACAA-TATCTGAT
* * * *
5912145 CTGGTGGCTCTGCCAC-ATATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT
1 CTGGTGGCTATGCCACAAT-TATCTGATCTGGTGGCTCTGCCACATATATCTGT-CCTAGTGACT
*
5912208 -TCGTCACAATATCTG
64 AT-GCCACAATATCTG
5912223 GCAGCCTCGC
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
80 17 0.25
81 52 0.75
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (80 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTAT
GCCACAATATCTGAT
Found at i:5917084 original size:129 final size:127
Alignment explanation
Indices: 5916823--5917141 Score: 413
Period size: 129 Copynumber: 2.5 Consensus size: 127
5916813 CGGAAAACTG
* * * * **
5916823 AAACCCAGCACGATAGAGCACTATTCCACGAACTTCCAAGCATTGAACATTGCCTTGTTTTAGAA
1 AAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACATTGCCTTGTTTTAGAA
* * * * * * **
5916888 TTTAAAGAATACGAATGGAATTCTAAAGGAATATTTGATTATTTTGAACAAACGAGAAATTG
66 TTTAAAAAATACAAATGAAATTCTAAAGGAAGATTCGATTATCTTGAACAAACGAGAAATCA
* *
5916950 AAACCCAACACGATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACATTGTCTTGTTTTAGAA
1 AAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACATTGCCTTGTTTTAGAA
* *
5917015 TTTAGAAAAAATACAAATGAAATTCTAAAGGAAGGTTCGATTATCTTGAACAAACGGGAAATCA
66 TTT--AAAAAATACAAATGAAATTCTAAAGGAAGATTCGATTATCTTGAACAAACGAGAAATCA
* * * *
5917079 AAACCCAGCACGGTAGGGCACGATTTCCCGAATTTCCAAACATCAAACATTACCTTCGTTTTA
1 AAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACATTGCCTT-GTTTTA
5917142 AGGAATTTTT
Statistics
Matches: 165, Mismatches: 24, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
127 60 0.36
129 99 0.60
130 6 0.04
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (127 bp):
AAACCCAGCACGATAGGGCACGATTCCCCGAATTTCCAAGCATCAAACATTGCCTTGTTTTAGAA
TTTAAAAAATACAAATGAAATTCTAAAGGAAGATTCGATTATCTTGAACAAACGAGAAATCA
Found at i:5918251 original size:27 final size:28
Alignment explanation
Indices: 5918194--5918252 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
5918184 AGGAAACACT
* * *
5918194 TATACATATAATAGATTTAAAACATATA
1 TATACATATAATAAATTTAAAACAAAAA
5918222 TATACATA-AATAAATTTAGAAA-AAAAA
1 TATACATATAATAAATTTA-AAACAAAAA
5918249 TATA
1 TATA
5918253 TACGAGAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (28 bp):
TATACATATAATAAATTTAAAACAAAAA
Found at i:5920426 original size:92 final size:92
Alignment explanation
Indices: 5920319--5920624 Score: 499
Period size: 92 Copynumber: 3.3 Consensus size: 92
5920309 TTCAGTTTGC
*
5920319 TCCACTGCAACTTCA-GGAAGATAAGACTTGTTTCGACCTGCTCTACTGCAACTTCAGAGAGATA
1 TCCACTGCAACTTCAGGGAA-ATAAGATTTGTTTCGACCTGCTCTACTGCAACTTCAGAGAGATA
*
5920383 GGATCTGTAGTTTATGGCTTCAATCTGT
65 GGATCTGTAGTTTATAGCTTCAATCTGT
* *
5920411 TCCACCGTAACTTCAGGGAAATAAGATTTGTTTTC-ACCTGCTCTACTGCAACTTCAGAGAGATA
1 TCCACTGCAACTTCAGGGAAATAAGATTTG-TTTCGACCTGCTCTACTGCAACTTCAGAGAGATA
5920475 GGATCTGTAGTTTATAGCTTCAATCTGT
65 GGATCTGTAGTTTATAGCTTCAATCTGT
* * * * *
5920503 TCCACTGCAACTTCAGGGAAATATGATTTGTTTTGATCTGCTCTACTACAACTTCAGAGAGACAG
1 TCCACTGCAACTTCAGGGAAATAAGATTTGTTTCGACCTGCTCTACTGCAACTTCAGAGAGATAG
5920568 GATCTGTAGTTTATAGCTTCAATCTGT
66 GATCTGTAGTTTATAGCTTCAATCTGT
5920595 TCCACTGCAACTTCAGGGAAATAAGATTTG
1 TCCACTGCAACTTCAGGGAAATAAGATTTG
5920625 CTATTTTTAG
Statistics
Matches: 199, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
91 3 0.02
92 188 0.94
93 8 0.04
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (92 bp):
TCCACTGCAACTTCAGGGAAATAAGATTTGTTTCGACCTGCTCTACTGCAACTTCAGAGAGATAG
GATCTGTAGTTTATAGCTTCAATCTGT
Found at i:5920557 original size:184 final size:186
Alignment explanation
Indices: 5920319--5920662 Score: 523
Period size: 184 Copynumber: 1.8 Consensus size: 186
5920309 TTCAGTTTGC
* *
5920319 TCCACTGCAACTTCAGGAAGATAAGACTTGTTTCGACCTGCTCTACTGCAACTTCAGAGAGATAG
1 TCCACTGCAACTTCAGGAAGATAAGACTTGTTTCGACCTGCTCTACTACAACTTCAGAGAGACAG
* *
5920384 GATCTGTAGTTTATGGCTTCAATCTGTTCCACCGTAACTTCAGGGAAATAAGATTTG-TTTTCA-
66 GATCTGTAGTTTATAGCTTCAATCTGTTCCACCGCAACTTCAGGGAAATAAGATTTGATTTTCAG
*
5920447 CCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAGTTTATAGCTTCAATCTGT
131 CCTGCTCTACTACAACTTCAGAGAGATAGGATCTGTAGTTTATAGCTTCAATCTGT
* * * *
5920503 TCCACTGCAACTTCAGGGAA-ATATGATTTGTTTTGATCTGCTCTACTACAACTTCAGAGAGACA
1 TCCACTGCAACTTCA-GGAAGATAAGACTTGTTTCGACCTGCTCTACTACAACTTCAGAGAGACA
*
5920567 GGATCTGTAGTTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATTTT
65 GGATCTGTAGTTTATAGCTTCAATCTGTTCCACCGCAACTTCAGGGAAATAAGATTTG--ATTTT
* * *
5920632 TAGTCTGCTCTACTACAACTTCAGGGAGATA
128 CAGCCTGCTCTACTACAACTTCAGAGAGATA
5920663 AGACTTGTAA
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
184 108 0.76
185 4 0.03
187 5 0.04
188 25 0.18
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (186 bp):
TCCACTGCAACTTCAGGAAGATAAGACTTGTTTCGACCTGCTCTACTACAACTTCAGAGAGACAG
GATCTGTAGTTTATAGCTTCAATCTGTTCCACCGCAACTTCAGGGAAATAAGATTTGATTTTCAG
CCTGCTCTACTACAACTTCAGAGAGATAGGATCTGTAGTTTATAGCTTCAATCTGT
Found at i:5920738 original size:184 final size:183
Alignment explanation
Indices: 5920318--5920748 Score: 455
Period size: 184 Copynumber: 2.3 Consensus size: 183
5920308 CTTCAGTTTG
* * * * * * * *
5920318 CTCCACTGCAACTTCA-GGAAGATAAGACTTGTTTCGACCTGCTCTACTGCAACTTCAGAGAGAT
1 CTCCACTACAACTTCAGGGAA-ATAAGATTTGCTGCGATCTACTCTACTACAACTTCAGAGAGAC
* *
5920382 AGGATCTGTAGTTTATGGCTTCAATCTGTTCCACCGTAACTTCAGGGAAATAAGATTTGTTTTCA
65 AGGATCTGTAGTTTATAGCTTCAATCTGTTCCACCGCAACTTCAGGGAAATAAGATTTGTTTTCA
* * * *
5920447 CCTGCTCTACTGCAACTTCAGAGAGATAGGATCTGTAGTTTATAGCTTCAATCTG
130 CCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTAG-TTATAGCTTCAACCTA
* * * * ** *
5920502 TTCCACTGCAACTTCAGGGAAATATGATTTGTTTTGATCTGCTCTACTACAACTTCAGAGAGACA
1 CTCCACTACAACTTCAGGGAAATAAGATTTGCTGCGATCTACTCTACTACAACTTCAGAGAGACA
*
5920567 GGATCTGTAGTTTATAGCTTCAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGCTATTTT
66 GGATCTGTAGTTTATAGCTTCAATCTGTTCCACCGCAACTTCAGGGAAATAAGATTTG---TTTT
* * *
5920632 TAGTCTGCTCTACTACAACTTCAGGGAGATAAGA-CT-T-G-TA-A-CTTCAACCTA
128 CA-CCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTAGTTATAGCTTCAACCTA
* * * *
5920683 CTGCACTACAACTTCAGGGAGATAAGGTTAATGGCTGCGATCTACTCCT-CTACAACTTCAGGGA
1 CTCCACTACAACTTCAGGGAAATAAGATT--T-GCTGCGATCTACT-CTACTACAACTTCAGAGA
5920747 GA
62 GA
5920749 TAAGATTCAC
Statistics
Matches: 210, Mismatches: 28, Indels: 18
0.82 0.11 0.07
Matches are distributed among these distances:
181 31 0.15
182 1 0.00
183 3 0.01
184 133 0.63
185 7 0.03
186 1 0.00
187 7 0.03
188 27 0.13
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (183 bp):
CTCCACTACAACTTCAGGGAAATAAGATTTGCTGCGATCTACTCTACTACAACTTCAGAGAGACA
GGATCTGTAGTTTATAGCTTCAATCTGTTCCACCGCAACTTCAGGGAAATAAGATTTGTTTTCAC
CTGCTCTACTACAACTTCAGAGAGATAAGATCTGTAGTTATAGCTTCAACCTA
Found at i:5936911 original size:18 final size:19
Alignment explanation
Indices: 5936878--5936914 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
5936868 TGGACCCAGA
5936878 AATAAATCTAAAAAAAAAT
1 AATAAATCTAAAAAAAAAT
5936897 AATAAA-CTCAAAAAAAAA
1 AATAAATCT-AAAAAAAAA
5936915 AAGAAATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (19 bp):
AATAAATCTAAAAAAAAAT
Found at i:5936912 original size:20 final size:19
Alignment explanation
Indices: 5936878--5936915 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
5936868 TGGACCCAGA
*
5936878 AATAAATCTAAAAAAAAAT
1 AATAAATCAAAAAAAAAAT
5936897 AATAAACTCAAAAAAAAAA
1 AATAAA-TCAAAAAAAAAA
5936916 AGAAATCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (19 bp):
AATAAATCAAAAAAAAAAT
Found at i:5937058 original size:19 final size:19
Alignment explanation
Indices: 5937034--5937141 Score: 163
Period size: 19 Copynumber: 5.9 Consensus size: 19
5937024 ATAATCTTCA
5937034 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5937053 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5937072 ATGATA--CAATATTAGAT
1 ATGATATGCAATCTTAGAT
*
5937089 ATGAT-TGCAATATTAGAT
1 ATGATATGCAATCTTAGAT
5937107 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5937126 ATGATA--CAATCTTAGA
1 ATGATATGCAATCTTAGA
5937142 AGATATGATT
Statistics
Matches: 84, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
17 25 0.30
18 16 0.19
19 43 0.51
ACGTcount: A:0.40, C:0.09, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5937099 original size:54 final size:55
Alignment explanation
Indices: 5937034--5937148 Score: 191
Period size: 54 Copynumber: 2.1 Consensus size: 55
5937024 ATAATCTTCA
*
5937034 ATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATATTAGAT
1 ATGATATGCAATATTAGATATGATATGCAATCTTAGATATGATACAATATTAGAT
*
5937089 ATGAT-TGCAATATTAGATATGATATGCAATCTTAGATATGATACAATCTTAGA-
1 ATGATATGCAATATTAGATATGATATGCAATCTTAGATATGATACAATATTAGAT
5937142 A-GATATG
1 ATGATATG
5937149 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
52 3 0.05
53 3 0.05
54 46 0.81
55 5 0.09
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (55 bp):
ATGATATGCAATATTAGATATGATATGCAATCTTAGATATGATACAATATTAGAT
Found at i:5937456 original size:18 final size:17
Alignment explanation
Indices: 5937433--5937466 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5937423 TTTCCCTGAT
*
5937433 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
5937451 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
5937467 GTATCATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:5945549 original size:44 final size:44
Alignment explanation
Indices: 5945493--5945630 Score: 161
Period size: 44 Copynumber: 3.1 Consensus size: 44
5945483 GATCTAAGAT
* *
5945493 GATTTGGCGTCTCTGTATTGTCAGGGAGCAGATC-AAAGATAGCA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAA-ATAACA
5945537 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAAATAACA
1 GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAAATAACA
* ** * * *
5945581 GATTTGGCATCTCCATATTCGACGGAAAGCAGATCGAAGACATAACA
1 GATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCGAA-A-ATAACA
5945628 GAT
1 GAT
5945631 CTAACCTTCG
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
44 54 0.66
45 18 0.22
46 1 0.01
47 9 0.11
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.25
Consensus pattern (44 bp):
GATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCGAAAATAACA
Found at i:5945909 original size:78 final size:78
Alignment explanation
Indices: 5945801--5946093 Score: 426
Period size: 78 Copynumber: 3.8 Consensus size: 78
5945791 CGAAGAAACA
* * * * * *
5945801 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGTAAATCTGACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTAACCTTCATTGAA
*
5945866 ACAGATCCAAGAT
66 GCAGATCCAAGAT
* * *
5945879 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATATAACCTTCATTGAA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTAACCTTCATTGAA
5945944 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * * *
5945957 GATTTGGCATCTTTATATTAGACGGGGAGCAGATCAAAGACATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCT-AACCTTCATTGA
5946021 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* *
5946035 GATTTGACATCTCTGTATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTAACCTTC
1 GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTAACCTTC
5946094 GAATGTCTTC
Statistics
Matches: 191, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
77 1 0.01
78 189 0.99
79 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (78 bp):
GATTTGGCATCTCTATATTAGACGGGGAGCAGATCGAAGACATAGCAGATCTAACCTTCATTGAA
GCAGATCCAAGAT
Found at i:5946385 original size:78 final size:78
Alignment explanation
Indices: 5946255--5946441 Score: 293
Period size: 78 Copynumber: 2.4 Consensus size: 78
5946245 CGAAGAAACA
** * * * *
5946255 GATTTGGCATCTCCATATTCGACGGAGAGCAGATCGAAGACATAGCATATCTGACCTTCATTAAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTAAA
5946320 GCAGATCCAAGAT
66 GCAGATCCAAGAT
* * *
5946333 GATTTGGCATCTTTGTATTAGACGGGGAGCAGATCGAAGACACAGTAGATCTGACCTTCATTGAA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTAAA
5946398 GCAGATCCAAGAT
66 GCAGATCCAAGAT
5946411 GATTTGGCATCTCTGTATTAGACGGGGAGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCA
5946442 AATAAGAGAT
Statistics
Matches: 99, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
78 99 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATCGAAGACACAGCAGATCTGACCTTCATTAAA
GCAGATCCAAGAT
Found at i:5946517 original size:44 final size:45
Alignment explanation
Indices: 5946411--5946578 Score: 259
Period size: 45 Copynumber: 3.8 Consensus size: 45
5946401 GATCCAAGAT
* *
5946411 GATTTGGCATCTCTGTATTAGACGGGGAGCA-AATAAGAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGA-AGATAACA
* *
5946456 GATTTGGCATCTCTGTATTAGACGGGGAGTAGATTGAAGA-AGCA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGATAACA
*
5946500 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATTGAAGATAACA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGATAACA
*
5946545 GATTTGGCTTCTCTGTATTAGACGGGGAGCAGAT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAGAT
5946579 CAAAAATAGT
Statistics
Matches: 113, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
44 41 0.36
45 69 0.61
46 3 0.03
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAGATTGAAGATAACA
Found at i:5946562 original size:89 final size:89
Alignment explanation
Indices: 5946411--5946578 Score: 275
Period size: 89 Copynumber: 1.9 Consensus size: 89
5946401 GATCCAAGAT
5946411 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATAAGAGATAACAGATTTGGCATCTCTGTATTA
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATAAGAGATAACAGATTTGGCATCTCTGTATTA
*
5946476 GACGGGGAGTAGATTGAAGAAGCA
66 GACGGGGAGCAGATTGAAGAAGCA
* * * *
5946500 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGAT-TGAAGATAACAGATTTGGCTTCTCTGTATT
1 GATTTGGCATCTCTGTATTAGACGGGGAGCAAATAAG-AGATAACAGATTTGGCATCTCTGTATT
5946564 AGACGGGGAGCAGAT
65 AGACGGGGAGCAGAT
5946579 CAAAAATAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
88 1 0.01
89 72 0.99
ACGTcount: A:0.29, C:0.13, G:0.30, T:0.27
Consensus pattern (89 bp):
GATTTGGCATCTCTGTATTAGACGGGGAGCAAATAAGAGATAACAGATTTGGCATCTCTGTATTA
GACGGGGAGCAGATTGAAGAAGCA
Found at i:5946967 original size:19 final size:19
Alignment explanation
Indices: 5946943--5947032 Score: 143
Period size: 19 Copynumber: 4.9 Consensus size: 19
5946933 ATAATCTTCA
5946943 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
5946962 ATGATA--CAATATTAGAT
1 ATGATATGCAATCTTAGAT
5946979 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5946998 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
5947017 ATGATA--CAATCTTAGA
1 ATGATATGCAATCTTAGA
5947033 AGATATGATT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
17 26 0.39
19 41 0.61
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:5946983 original size:36 final size:37
Alignment explanation
Indices: 5946943--5947032 Score: 141
Period size: 36 Copynumber: 2.5 Consensus size: 37
5946933 ATAATCTTCA
5946943 ATGATATGCAATCTTAGATATGATA-CAATATTAGAT
1 ATGATATGCAATCTTAGATATGATAGCAATATTAGAT
*
5946979 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGATATGATA-GCAATATTAGAT
5947017 ATGATA--CAATCTTAGA
1 ATGATATGCAATCTTAGA
5947033 AGATATGATT
Statistics
Matches: 51, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
36 35 0.69
38 16 0.31
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (37 bp):
ATGATATGCAATCTTAGATATGATAGCAATATTAGAT
Found at i:5947074 original size:16 final size:14
Alignment explanation
Indices: 5947042--5947069 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5947032 AAGATATGAT
5947042 TTTGTAATCTTAGA
1 TTTGTAATCTTAGA
5947056 TTTGTAATCTTAGA
1 TTTGTAATCTTAGA
5947070 GATTTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
TTTGTAATCTTAGA
Found at i:5948967 original size:313 final size:311
Alignment explanation
Indices: 5948419--5949317 Score: 1193
Period size: 313 Copynumber: 2.9 Consensus size: 311
5948409 TTCACAAGTC
* * ** * * * * * *
5948419 CATCATTTCACCTTCAATTATAATATTTTTCTCATTTCCATAATCTAGGTTTGTGAATGCCTTCC
1 CATCATTTCGCCTTCAATTATACTATTTTTCTCATTTTGATAATCCAAGTTTATGACTGCCCTAC
* * * * *
5948484 CAACAATTTTGTCTCCAACATTCATACCTCCCTTAAATCGATAAATAACTAAATGAAATGCAACT
66 CAACAATGTTGTCTCCAACATTCGTACCTCCCCTAAATCGATAAATGACTAAATGAAATGTAACT
* * * *
5948549 TTAAATATCAAAGTGG-C-TAAA--AA-A-ATTTAGAAAACAGTATAATTTAGCTTAATCATTAG
131 TTAGATATCAAAGTGGTCAAAAATTAACACAATAAGAAAACAGTATAATTTAGCTTAATCATTAG
*
5948608 TAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCAAAAATAACATCCAGAA
196 TAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACTAAAAATAACATCCAGAA
** * * *
5948673 TGTCACATTATAAGTTCGAAATTCAAATTTTACAAGTCCATGGATAACATT
261 CATCACATGATAAGTTCAAAATTCAAATTTCACAAGTCCATGGATAACATT
* *
5948724 CATCATTTCGCCTTCAATTCTACTATTTTTCTCATTTTTGATAATCCATGTTTATGACTGCCCTA
1 CATCATTTCGCCTTCAATTATACTATTTTTCTCA-TTTTGATAATCCAAGTTTATGACTGCCCTA
**
5948789 CCAACAATGCCGTCTCCAACATTCGTACCTCCCCTAAATCGATAAATGACTAAATGAAATGTAAC
65 CCAACAATGTTGTCTCCAACATTCGTACCTCCCCTAAATCGATAAATGACTAAATGAAATGTAAC
* *
5948854 TTTAGATATAAAAGTGGTCAAGAAATTAACACAATAAGAAAACAGTAAAATTTAGCTTAATCATT
130 TTTAGATATCAAAGTGGTCAA-AAATTAACACAATAAGAAAACAGTATAATTTAGCTTAATCATT
* * * *
5948919 AGAAAAAGATTAATTACATTATAGAAGAAAACTAAACCTCCAACTATACTAAAAATAACATCCAT
194 AGTAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACTAAAAATAACATCCAG
*
5948984 ACCATCACATGATAAGTTCAAAATTCAAATTTCACAAGTCCATGGATAACATT
259 AACATCACATGATAAGTTCAAAATTCAAATTTCACAAGTCCATGGATAACATT
* * * * *
5949037 CATCATTTTGCCTTCAATTATACT-TTTATTCTCATTTTGATAATCCAAATTTATAACTACTCTA
1 CATCATTTCGCCTTCAATTATACTATTT-TTCTCATTTTGATAATCCAAGTTTATGACTGCCCTA
* *
5949101 CCAACAATGTTGTCTCCAACATTCGTACCTCCCCTAAACCGATAAATGACT-AATGAAAAGTAAC
65 CCAACAATGTTGTCTCCAACATTCGTACCTCCCCTAAATCGATAAATGACTAAATGAAATGTAAC
* * * *
5949165 TTTAGATATCAAAGTGGTTTTAAAAATTAACACAATAAGAAAAAACAATTTAATTTAACTTAATC
130 TTTAGATATCAAAGTGG--TCAAAAATTAACACAATAAG--AAAACAGTATAATTTAGCTTAATC
* * * *
5949230 ATTAGTAAAAGTTTAATTATATTATAAAAGAAAATTAAACTTCCAACTATACTAAAAAAAACATC
191 ATTAGTAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACTAAAAATAACATC
* * *
5949295 CACAACATCACATAATAATTTCA
256 CAGAACATCACATGATAAGTTCA
5949318 TTTTTAAAGT
Statistics
Matches: 518, Mismatches: 63, Indels: 17
0.87 0.11 0.03
Matches are distributed among these distances:
305 31 0.06
306 95 0.18
307 1 0.00
309 3 0.01
311 30 0.06
312 93 0.18
313 168 0.32
314 97 0.19
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.32
Consensus pattern (311 bp):
CATCATTTCGCCTTCAATTATACTATTTTTCTCATTTTGATAATCCAAGTTTATGACTGCCCTAC
CAACAATGTTGTCTCCAACATTCGTACCTCCCCTAAATCGATAAATGACTAAATGAAATGTAACT
TTAGATATCAAAGTGGTCAAAAATTAACACAATAAGAAAACAGTATAATTTAGCTTAATCATTAG
TAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACTAAAAATAACATCCAGAA
CATCACATGATAAGTTCAAAATTCAAATTTCACAAGTCCATGGATAACATT
Found at i:5952267 original size:99 final size:98
Alignment explanation
Indices: 5952164--5952383 Score: 253
Period size: 99 Copynumber: 2.2 Consensus size: 98
5952154 AAACCAATTT
* * * *
5952164 AGTTGTATAAACTCCATCTTTTGAGAGGTTACTTCCAATATGACTATTGAGATTATTAGCTTT-A
1 AGTTGTATAAACTCCATCTTTTGA-AGGCTACTTCCAACATGACTATTAAGATGATT-GCTTTGA
* * * *
5952228 ATTGAGTTAACCCTACGTTCTGAGTAAACCGGTTG
64 ACTAAGTTAACCCTACGCTCTGAGTAAACAGGTTG
* * *
5952263 AGTTGTATAAACTCCATCTTCTCGAAGGCTACTTCCAACATGACTATTAAGCTGATTGGTTTGAA
1 AGTTGTATAAACTCCATCTT-TTGAAGGCTACTTCCAACATGACTATTAAGATGATTGCTTTGAA
** *
5952328 CTAAGTTAACCCTGTGCTCTGAGTAAATAGGTTG
65 CTAAGTTAACCCTACGCTCTGAGTAAACAGGTTG
** *
5952362 AGCCGCATAAACTCCATCTTTT
1 AGTTGTATAAACTCCATCTTTT
5952384 AGGAGCATTT
Statistics
Matches: 101, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
98 5 0.05
99 93 0.92
100 3 0.03
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (98 bp):
AGTTGTATAAACTCCATCTTTTGAAGGCTACTTCCAACATGACTATTAAGATGATTGCTTTGAAC
TAAGTTAACCCTACGCTCTGAGTAAACAGGTTG
Found at i:5958252 original size:311 final size:311
Alignment explanation
Indices: 5957689--5958340 Score: 884
Period size: 311 Copynumber: 2.1 Consensus size: 311
5957679 CTAATGTATC
* * * *
5957689 AAAATAACATCCATAACGTCACATGATAAGTTCGAAATTCAAATTTTACAAGTCCATGGATAACA
1 AAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAAATTCACAAGTCCATGGATAACA
* * ** *
5957754 TTCATCATTTCGCCTTCAAATATACTAATTTTCTCATTTTGATAATCTAGGTTTCTAACTGTCCT
66 TTCATCATTTCGCCTTCAAATATACTAATTTTCTCACTTTGATAATCCAAATTTATAAC-GTCCT
* * * *
5957819 ACGAGCAATGTCATCTTCAACATTCATACCTCCCCTAAATTGATAAATGACTAAATGAAATGTAA
130 ACCAACAATGTCATCTTCAACATTCATACCTCCCCTAAATCGATAAATGACTAAATGAAAAGTAA
5957884 CTTTAGATATAAAAGTGGCTAAAAAATTAACACAAAAAGAAAACAGTATAATTTAGCTTAATAAT
195 CTTTAGATATAAAAGTGGCTAAAAAATTAACACAAAAAGAAAACAGTATAATTTAGCTTAATAAT
*
5957949 TAG-AAAA-TCTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATAGCA
260 TAGTAAAAGT-TTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCA
* *
5958000 AAAATAACATCCATAACATCACATGATATGTTCAAAATTCAAAATTCACAAGTCCGTGGATAACA
1 AAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAAATTCACAAGTCCATGGATAACA
* * * *
5958065 TTCATCATTTTGCCTTCAATTATACTTTTATTTTCTCACTTTGATAATCCAAATTTATGAC-T-C
66 TTCATCATTTCGCCTTCAAATATAC--TAATTTTCTCACTTTGATAATCCAAATTTATAACGTCC
* ** * *
5958128 TACCAACAATTTTGTC-TCTGACATTCGTACCTCCCCTAAATCGATAAATGACTAAATGAAAAGT
129 TACCAACAATGTCATCTTC-AACATTCATACCTCCCCTAAATCGATAAATGACTAAATGAAAAGT
* * * * * * *
5958192 GACTTTAGGTATCAAAGTGGTTAAAAAAATTACCACAACCAA-AAAACAGTGTAATTTAGCTTAA
193 AACTTTAGATATAAAAGTGGCT-AAAAAATTAACACAA-AAAGAAAACAGTATAATTTAGCTTAA
* *
5958256 TCATTAGTAAAAGTTTAATTACATTATAAAAGAAAACTAAACTTCCAACTATACCA
256 TAATTAGTAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCA
*
5958312 AAAATAACATCCATAACATCACATAATAA
1 AAAATAACATCCATAACATCACATGATAA
5958341 TGTCATTTGT
Statistics
Matches: 298, Mismatches: 36, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
309 2 0.01
310 71 0.24
311 124 0.42
312 73 0.24
313 28 0.09
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.31
Consensus pattern (311 bp):
AAAATAACATCCATAACATCACATGATAAGTTCAAAATTCAAAATTCACAAGTCCATGGATAACA
TTCATCATTTCGCCTTCAAATATACTAATTTTCTCACTTTGATAATCCAAATTTATAACGTCCTA
CCAACAATGTCATCTTCAACATTCATACCTCCCCTAAATCGATAAATGACTAAATGAAAAGTAAC
TTTAGATATAAAAGTGGCTAAAAAATTAACACAAAAAGAAAACAGTATAATTTAGCTTAATAATT
AGTAAAAGTTTAATTACATTATAAAAGAAAACTAAACCTCCAACTATACCA
Found at i:5961730 original size:46 final size:45
Alignment explanation
Indices: 5961677--5961852 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
5961667 TATTTGGGCA
5961677 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
** * *
5961723 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATAT-AACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC---ACTTATGGA-T-GCGAAG
* *
5961770 TCTGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
5961816 CCCGAGCTCGTTGAGTTGAGTCCGATTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
5961853 GCAAGTTACA
Statistics
Matches: 108, Mismatches: 13, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
43 1 0.01
44 7 0.06
45 1 0.01
46 63 0.58
47 27 0.25
48 1 0.01
49 7 0.06
50 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:5970032 original size:29 final size:32
Alignment explanation
Indices: 5969977--5970037 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 32
5969967 GGGGGCTGGG
*
5969977 GTGGGATGGGAAGTAAAAGTTTTAGGGGGAAA
1 GTGGGATGGGAAGTAAAAGATTTAGGGGGAAA
5970009 GTGGGA-GGG-AGTAAAA-ATTTAGGGGGAAA
1 GTGGGATGGGAAGTAAAAGATTTAGGGGGAAA
5970038 ATAAAAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.43
30 7 0.25
31 3 0.11
32 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (32 bp):
GTGGGATGGGAAGTAAAAGATTTAGGGGGAAA
Found at i:5972577 original size:20 final size:20
Alignment explanation
Indices: 5972554--5972612 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
5972544 TGAAATTCTA
*
5972554 AAAGATAAATAAAAATAATT
1 AAAGATAAATAAAAATAAAT
* *
5972574 AAAGATAATTAAAGATAAAT
1 AAAGATAAATAAAAATAAAT
* *
5972594 ACAGA-AAATGAAAATAAAT
1 AAAGATAAATAAAAATAAAT
5972613 CCTAAAATTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (20 bp):
AAAGATAAATAAAAATAAAT
Found at i:5974273 original size:18 final size:18
Alignment explanation
Indices: 5974250--5974287 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
5974240 AATATCTGAA
5974250 AATAAGA-AATAATAAAAT
1 AATAAGATAA-AATAAAAT
*
5974268 AATAAGATAAAATTAAAT
1 AATAAGATAAAATAAAAT
5974286 AA
1 AA
5974288 AAATTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (18 bp):
AATAAGATAAAATAAAAT
Found at i:5977061 original size:12 final size:12
Alignment explanation
Indices: 5977044--5977076 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
5977034 TTACTTGCAA
*
5977044 AATAGTAAAATT
1 AATAGTAAAAAT
5977056 AATAGTAAAAAT
1 AATAGTAAAAAT
5977068 AATAGTAAA
1 AATAGTAAA
5977077 GGAGAAGTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.09, T:0.27
Consensus pattern (12 bp):
AATAGTAAAAAT
Found at i:5978016 original size:10 final size:10
Alignment explanation
Indices: 5977989--5978038 Score: 66
Period size: 10 Copynumber: 5.0 Consensus size: 10
5977979 TGAAATCCTA
5977989 AAAGATAAAT
1 AAAGATAAAT
*
5977999 ACAA-ATAATT
1 A-AAGATAAAT
*
5978009 AAAGATAATT
1 AAAGATAAAT
5978019 AAAGATAAAT
1 AAAGATAAAT
5978029 AAAGATAAAT
1 AAAGATAAAT
5978039 GAAAAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 2 0.06
10 32 0.89
11 2 0.06
ACGTcount: A:0.66, C:0.02, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:5978048 original size:20 final size:19
Alignment explanation
Indices: 5977989--5978048 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
5977979 TGAAATCCTA
*
5977989 AAAGATAAATACAAATAATT
1 AAAGATAAATA-AAATAAAT
*
5978009 AAAGATAATTAAAGATAAAT
1 AAAGATAAATAAA-ATAAAT
*
5978029 AAAGATAAATGAAAAAAAAT
1 AAAGATAAAT-AAAATAAAT
5978049 CCTAAAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 29 0.85
21 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (19 bp):
AAAGATAAATAAAATAAAT
Found at i:5978434 original size:25 final size:25
Alignment explanation
Indices: 5978395--5978451 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 25
5978385 AACTGAGTTT
*
5978395 TGTAACCTTGCTCTGATACCACTAAA
1 TGTAA-CTCGCTCTGATACCACTAAA
5978421 TGTAACTCGCTCTGATACCACTAAA
1 TGTAACTCGCTCTGATACCACTAAA
5978446 TGTAAC
1 TGTAAC
5978452 ACCCCAAACC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 25 0.83
26 5 0.17
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (25 bp):
TGTAACTCGCTCTGATACCACTAAA
Found at i:5985159 original size:99 final size:98
Alignment explanation
Indices: 5984951--5985201 Score: 252
Period size: 99 Copynumber: 2.5 Consensus size: 98
5984941 TTTCTTGAAG
* * * *
5984951 TGAGTTAACCTTACACTCCAAGTAAACTGATTTAGCTGTATAAACTCCATCTTTTAGAAGGCTAC
1 TGAGTTAACCCTACACTCCAAGTAAACTG-TTGAGTTGTATAAACTCCATCTTCTAGAAGGCTAC
** *
5985016 TTCCAATATGACCATTGAGGTTATTGGATTTAAC
65 TTCCAATATGACCATTGAAATTATTGGATTCAAC
* * * * * * *
5985050 TAAGTGAACCCTACATTTCAAGTAAACTAGTTGAGTTGTATATACTCCATCTTCTGGGAGGCTAC
1 TGAGTTAACCCTACACTCCAAGTAAACT-GTTGAGTTGTATAAACTCCATCTTCTAGAAGGCTAC
** * *
5985115 TTCCAATATGACTGTT-AAATTGATTTGCTTCAAC
65 TTCCAATATGACCATTGAAATT-ATTGGATTCAAC
* * ** *
5985149 TGAGTTAACCCTGCACTCCGAGTAAACTGGTTGAGTCATATAAACTCTATCTT
1 TGAGTTAACCCTACACTCCAAGTAAACT-GTTGAGTTGTATAAACTCCATCTT
5985202 TTGGTAGCAT
Statistics
Matches: 121, Mismatches: 29, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
98 3 0.02
99 117 0.97
100 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (98 bp):
TGAGTTAACCCTACACTCCAAGTAAACTGTTGAGTTGTATAAACTCCATCTTCTAGAAGGCTACT
TCCAATATGACCATTGAAATTATTGGATTCAAC
Found at i:5988828 original size:16 final size:16
Alignment explanation
Indices: 5988803--5988833 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5988793 ACTTTGGTTA
*
5988803 ACAATTTTCTTAGGGG
1 ACAATGTTCTTAGGGG
5988819 ACAATGTTCTTAGGG
1 ACAATGTTCTTAGGG
5988834 AGTTTAGTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (16 bp):
ACAATGTTCTTAGGGG
Found at i:5992651 original size:30 final size:30
Alignment explanation
Indices: 5992617--5992675 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
5992607 ATTTTCGAGC
* *
5992617 CTAGGGGTAAAATGGTCATTTTATCAAAGT
1 CTAGGGGCAAAATGGTCATTTTACCAAAGT
5992647 CTAGGGGCAAAATGGTCATTTTACCAAAG
1 CTAGGGGCAAAATGGTCATTTTACCAAAG
5992676 ATATGAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (30 bp):
CTAGGGGCAAAATGGTCATTTTACCAAAGT
Found at i:5993180 original size:46 final size:46
Alignment explanation
Indices: 5993014--5993181 Score: 162
Period size: 46 Copynumber: 3.6 Consensus size: 46
5993004 TCACTTGTGT
* * * * *
5993014 GAGCTAGTGTAAAACATGTCTGGGACATGCATCGGCCAC-ATTATGA
1 GAGCCAGTGTAAGACATGTCTGGGACATACATCGGCCTCGA-GATGA
* * *
5993060 GAGCCAGTGTAAGACCATGTCTGGAACATAACATCGGCATTGAGATGA
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-ACATCGGCCTCGAGATGA
* *
5993108 GTGCTAGTGTAAGACATG-CATGGGACATACATCGGCCTCGAGATGTA
1 GAGCCAGTGTAAGACATGTC-TGGGACATACATCGGCCTCGAGATG-A
* *
5993155 -AGCCAATGTAAGACATGTCTAGGACAT
1 GAGCCAGTGTAAGACATGTCTGGGACAT
5993182 GTATCAGCTA
Statistics
Matches: 99, Mismatches: 17, Indels: 12
0.77 0.13 0.09
Matches are distributed among these distances:
46 49 0.49
47 26 0.26
48 23 0.23
49 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.27, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATACATCGGCCTCGAGATGA
Found at i:5996289 original size:56 final size:56
Alignment explanation
Indices: 5996173--5996290 Score: 139
Period size: 56 Copynumber: 2.1 Consensus size: 56
5996163 TTCCTCATAT
* * **** **
5996173 ATATATATATAAGTATTAAAAGGATAAAAGTGTAAGAATGTATTATACGTGTGTGT
1 ATATATATATAAGTATTAAAAAGATAAAAGTGTAAAAATGTATTATACGAAAATCC
*
5996229 ATATATATATAAGTATTAAAAAGATAAAAGTGTAAAAATGTATTAT-TGAAAAATCC
1 ATATATATATAAGTATTAAAAAGATAAAAGTGTAAAAATGTATTATACG-AAAATCC
5996285 ATATAT
1 ATATAT
5996291 TTTTATGTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
55 1 0.02
56 51 0.98
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (56 bp):
ATATATATATAAGTATTAAAAAGATAAAAGTGTAAAAATGTATTATACGAAAATCC
Found at i:5999368 original size:3 final size:3
Alignment explanation
Indices: 5999360--5999427 Score: 93
Period size: 3 Copynumber: 22.7 Consensus size: 3
5999350 ATACAGATGT
* * *
5999360 AGA AGA AGA AGA AGA AGA AG- CGA AGGA TGT AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA AGA AGA
5999405 AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AG
5999428 CAAAGGAAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
2 1 0.02
3 54 0.95
4 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.35, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:6000595 original size:16 final size:16
Alignment explanation
Indices: 6000571--6000617 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
6000561 TGTATAACGA
* *
6000571 TTAATTAAATTAATTT
1 TTAAATAAATAAATTT
6000587 TTAAATAAATAAATTT
1 TTAAATAAATAAATTT
6000603 TTAATATAAA-AAATT
1 TTAA-ATAAATAAATT
6000618 CATAATACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATAAATAAATTT
Found at i:6002769 original size:78 final size:78
Alignment explanation
Indices: 6002677--6002846 Score: 250
Period size: 78 Copynumber: 2.2 Consensus size: 78
6002667 TTACGTCATA
* * * * *
6002677 ATCCTCATATAATTGGGATATTCCATTTACACACAATTCAATATGACTGACCAATTAAAATAGTT
1 ATCCTTATATAATTGGGATACTCCATTTACACACAATTCAATAGGACTGACCAATTAAAATAATC
6002742 ACTCAAATATGTC
66 ACTCAAATATGTC
* * * * *
6002755 ATCTTTATGTAATTGGGATGCTCCATTTACACACAATTCAATGGGATTGACCAATTAAAATAATC
1 ATCCTTATATAATTGGGATACTCCATTTACACACAATTCAATAGGACTGACCAATTAAAATAATC
6002820 ACTCAAATATGTC
66 ACTCAAATATGTC
6002833 ATCCTTATATAATT
1 ATCCTTATATAATT
6002847 ATAAACAATT
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (78 bp):
ATCCTTATATAATTGGGATACTCCATTTACACACAATTCAATAGGACTGACCAATTAAAATAATC
ACTCAAATATGTC
Found at i:6007130 original size:23 final size:23
Alignment explanation
Indices: 6007102--6007147 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
6007092 ATTAAATGTG
*
6007102 TAAGACCATGGTTGAAAGATACC
1 TAAGACCATGGTCGAAAGATACC
6007125 TAAGACCATGGTCGAAAGATACC
1 TAAGACCATGGTCGAAAGATACC
6007148 ATGGCAACAT
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:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (23 bp):
TAAGACCATGGTCGAAAGATACC
Found at i:6007303 original size:13 final size:12
Alignment explanation
Indices: 6007259--6007305 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
6007249 TTGAACAACT
*
6007259 AATGGTTATA-C
1 AATGGTTATATG
6007270 AGATGGTTATATG
1 A-ATGGTTATATG
6007283 AATGGTTATATG
1 AATGGTTATATG
6007295 AATTGGTTATA
1 AA-TGGTTATA
6007306 CAAAATGGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
11 1 0.03
12 22 0.69
13 9 0.28
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.40
Consensus pattern (12 bp):
AATGGTTATATG
Found at i:6007314 original size:13 final size:12
Alignment explanation
Indices: 6007259--6007315 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
6007249 TTGAACAACT
6007259 AATGGTTATACA
1 AATGGTTATACA
* **
6007271 GATGGTTATATG
1 AATGGTTATACA
*
6007283 AATGGTTATATGA
1 AATGGTTATA-CA
*
6007296 ATTGGTTATACAA
1 AATGGTTATAC-A
6007309 AATGGTT
1 AATGGTT
6007316 GTGTGAAATG
Statistics
Matches: 34, Mismatches: 9, Indels: 3
0.74 0.20 0.07
Matches are distributed among these distances:
12 18 0.53
13 16 0.47
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.39
Consensus pattern (12 bp):
AATGGTTATACA
Found at i:6008187 original size:16 final size:16
Alignment explanation
Indices: 6008151--6008204 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
6008141 GAAAATTTAT
* *
6008151 ATTTTTCATCCTTATA
1 ATTTTCCATCCTTCTA
*
6008167 GTTTTCCAATCCTTC-A
1 ATTTTCC-ATCCTTCTA
*
6008183 ATTTTCCATCTTTCTA
1 ATTTTCCATCCTTCTA
6008199 ATTTTC
1 ATTTTC
6008205 TTTCCTTTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
15 6 0.19
16 19 0.61
17 6 0.19
ACGTcount: A:0.20, C:0.24, G:0.02, T:0.54
Consensus pattern (16 bp):
ATTTTCCATCCTTCTA
Found at i:6013461 original size:13 final size:13
Alignment explanation
Indices: 6013443--6013469 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6013433 CGGTTTATTG
6013443 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
6013456 ATTTTTAAAAAAT
1 ATTTTTAAAAAAT
6013469 A
1 A
6013470 GTTATTGGTA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATTTTTAAAAAAT
Found at i:6016050 original size:25 final size:25
Alignment explanation
Indices: 6016019--6016066 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
6016009 TATGTTAAAA
6016019 ATTTAATTTCATACATGTTAATATT
1 ATTTAATTTCATACATGTTAATATT
*
6016044 ATTTAATTTCATGCATGTTAATA
1 ATTTAATTTCATACATGTTAATA
6016067 ATATATTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (25 bp):
ATTTAATTTCATACATGTTAATATT
Found at i:6021565 original size:18 final size:18
Alignment explanation
Indices: 6021522--6021574 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
6021512 ATTTATTTAG
* *
6021522 TAATAGTCAATTATTCGGA
1 TAATAATCAATTATTC-AA
*
6021541 -AACAATCAATTATTCAA
1 TAATAATCAATTATTCAA
*
6021558 TAATAATCAGTTATTCA
1 TAATAATCAATTATTCA
6021575 GTATCAATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 1 0.04
18 27 0.96
ACGTcount: A:0.43, C:0.13, G:0.08, T:0.36
Consensus pattern (18 bp):
TAATAATCAATTATTCAA
Found at i:6021583 original size:18 final size:19
Alignment explanation
Indices: 6021543--6021585 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
6021533 TATTCGGAAA
6021543 CAATCAATTATTCAATAAT
1 CAATCAATTATTCAATAAT
* *
6021562 -AATCAGTTATTCAGT-AT
1 CAATCAATTATTCAATAAT
6021579 CAATCAA
1 CAATCAA
6021586 CTGATCGGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (19 bp):
CAATCAATTATTCAATAAT
Found at i:6021620 original size:18 final size:18
Alignment explanation
Indices: 6021594--6021667 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
6021584 AACTGATCGG
*
6021594 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
* * *
6021612 TTATTCAGTAAAAATTAGA
1 TTATTCAGTAACAGTCA-A
* * *
6021631 -TATACAGTAACAATTAAA
1 TTATTCAGTAAC-AGTCAA
6021649 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
6021667 T
1 T
6021668 CTTTCCAGTT
Statistics
Matches: 42, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
18 28 0.67
19 14 0.33
ACGTcount: A:0.45, C:0.14, G:0.09, T:0.32
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:6021659 original size:19 final size:19
Alignment explanation
Indices: 6021610--6021661 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
6021600 AGTAACAGTC
*
6021610 AATTATTCAGTAAAAATTA
1 AATTATTCAGTAACAATTA
* *
6021629 GA-TATACAGTAACAATTA
1 AATTATTCAGTAACAATTA
6021647 AATTATTCAGTAACA
1 AATTATTCAGTAACA
6021662 GTCAATCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 15 0.56
19 12 0.44
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.33
Consensus pattern (19 bp):
AATTATTCAGTAACAATTA
Found at i:6021859 original size:53 final size:53
Alignment explanation
Indices: 6021783--6022016 Score: 288
Period size: 53 Copynumber: 4.2 Consensus size: 53
6021773 CCGGAACAGT
* * * *
6021783 AACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATTGGAACAAATTCGA
1 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
6021836 AACAATAATAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAAACAAATCCGA
1 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATC-G---------G--AACAAATCCGA
*
6021901 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGA
1 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
6021954 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACGAATCCGA
1 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
*
6022007 AACAGTAACA
1 AACAATAACA
6022017 ATATCCGAAT
Statistics
Matches: 159, Mismatches: 10, Indels: 24
0.82 0.05 0.12
Matches are distributed among these distances:
53 107 0.67
54 1 0.01
63 1 0.01
64 1 0.01
65 49 0.31
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (53 bp):
AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGA
Found at i:6021896 original size:65 final size:64
Alignment explanation
Indices: 6021825--6022008 Score: 246
Period size: 65 Copynumber: 3.0 Consensus size: 64
6021815 ACCTCATTGG
6021825 AACAAATTCGAAACAATAATAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAA
1 AACAAATTCGAAACAATAA-AGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAA
* *
6021890 AACAAATCCGAAACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCG-A
1 AACAAATTCGAAACAATAA-AGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAA
*
6021954 AAC-AA-T---AAC-----AGTAACAGTACGGTACACAGAGTACCTCATCGGAACGAATCCGAA
1 AACAAATTCGAAACAATAAAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAA
6022008 A
1 A
6022009 CAGTAACAAT
Statistics
Matches: 112, Mismatches: 6, Indels: 13
0.85 0.05 0.10
Matches are distributed among these distances:
53 41 0.37
54 2 0.02
59 3 0.03
63 2 0.02
64 4 0.04
65 60 0.54
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15
Consensus pattern (64 bp):
AACAAATTCGAAACAATAAAGTAACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAA
Found at i:6021905 original size:11 final size:12
Alignment explanation
Indices: 6021878--6021902 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6021868 ACCTCATCGG
6021878 AACAAATCCGAA
1 AACAAATCCGAA
6021890 AACAAATCCGAA
1 AACAAATCCGAA
6021902 A
1 A
6021903 CAATAACAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (12 bp):
AACAAATCCGAA
Found at i:6021949 original size:118 final size:118
Alignment explanation
Indices: 6021783--6022008 Score: 389
Period size: 118 Copynumber: 1.9 Consensus size: 118
6021773 CCGGAACAGT
* * * * * *
6021783 AACAGTAACAGTAGCAGTACGGTACACAGAGTACCTCATTGGAACAAATTCGAAACAATAATAGT
1 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAATAACAGT
6021848 AACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAAACAAATCCGA
66 AACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAAACAAATCCGA
6021901 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAATAACAGT
1 AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAATAACAGT
*
6021966 AACAGTACGGTACACAGAGTACCTCATCGGAACGAATCCGAAA
66 AACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAA
6022009 CAGTAACAAT
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 101 1.00
ACGTcount: A:0.44, C:0.23, G:0.17, T:0.16
Consensus pattern (118 bp):
AACAATAACAGTAACAGTACGGTACACAGAGTACCTCATCGAAACAAATCCGAAACAATAACAGT
AACAGTACGGTACACAGAGTACCTCATCGGAACAAATCCGAAAACAAATCCGA
Found at i:6022025 original size:24 final size:24
Alignment explanation
Indices: 6021998--6022048 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
6021988 CTCATCGGAA
6021998 CGAATCCGAAACAGTAACAATATC
1 CGAATCCGAAACAGTAACAATATC
6022022 CGAATCCGAAACAGTAACAATATC
1 CGAATCCGAAACAGTAACAATATC
6022046 CGA
1 CGA
6022049 CACACAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.25, G:0.14, T:0.16
Consensus pattern (24 bp):
CGAATCCGAAACAGTAACAATATC
Found at i:6022730 original size:12 final size:11
Alignment explanation
Indices: 6022705--6022741 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
6022695 TAATTAATAC
6022705 AATTTCTATTT
1 AATTTCTATTT
6022716 AATTTCTACTTT
1 AATTTCTA-TTT
*
6022728 AATTTCAATTT
1 AATTTCTATTT
6022739 AAT
1 AAT
6022742 CTTAACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (11 bp):
AATTTCTATTT
Found at i:6023160 original size:19 final size:18
Alignment explanation
Indices: 6023119--6023165 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
6023109 AAACCTTCAA
6023119 TTTTCCCTTTCTTCTTTC
1 TTTTCCCTTTCTTCTTTC
6023137 TTTTCTCCTTTCTTTCTTTC
1 TTTTC-CCTTTC-TTCTTTC
6023157 -TTTCCCTTT
1 TTTTCCCTTT
6023166 TGCCTATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 10 0.37
19 10 0.37
20 7 0.26
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCCCTTTCTTCTTTC
Found at i:6023740 original size:15 final size:16
Alignment explanation
Indices: 6023721--6023757 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
6023711 CAATTATTCT
*
6023721 TAATTAAATTAAATTC
1 TAATTAAATTAAACTC
6023737 -AATT-AATTAAACTC
1 TAATTAAATTAAACTC
6023751 TAATTAA
1 TAATTAA
6023758 CCACTCATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
14 9 0.50
15 8 0.44
16 1 0.06
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATTAAATTAAACTC
Found at i:6026246 original size:36 final size:35
Alignment explanation
Indices: 6026199--6026271 Score: 128
Period size: 36 Copynumber: 2.1 Consensus size: 35
6026189 TGGTTTTGAC
6026199 TCAAACCTAGCTTAACAAGAGAATACAAATTTCCTA
1 TCAAACCTAGCTTAACAAGAGAATACAAATTT-CTA
*
6026235 TCAAACCTAGCTTAACAAGAGAATACAAGTTTCTA
1 TCAAACCTAGCTTAACAAGAGAATACAAATTTCTA
6026270 TC
1 TC
6026272 TCCTTATTAG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
35 5 0.14
36 31 0.86
ACGTcount: A:0.42, C:0.22, G:0.10, T:0.26
Consensus pattern (35 bp):
TCAAACCTAGCTTAACAAGAGAATACAAATTTCTA
Found at i:6026398 original size:21 final size:21
Alignment explanation
Indices: 6026373--6026425 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
6026363 AACTAATTAG
*
6026373 TAACTAACTATAACTAGAATAC
1 TAACTAACTATAAC-AAAATAC
*
6026395 -AACTGACTATAACAAAATAC
1 TAACTAACTATAACAAAATAC
6026415 TAACTAA-TATA
1 TAACTAACTATA
6026426 GTTACTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.53, C:0.17, G:0.04, T:0.26
Consensus pattern (21 bp):
TAACTAACTATAACAAAATAC
Found at i:6028879 original size:25 final size:23
Alignment explanation
Indices: 6028851--6028972 Score: 109
Period size: 25 Copynumber: 5.0 Consensus size: 23
6028841 GCTTTATCAT
**
6028851 ATAACTAGAGGCCTAGCCTCTTTTA
1 ATAACTAG-GGCAAAGCC-CTTTTA
6028876 ATAACTAGGGCAAAGCCCTTTTA
1 ATAACTAGGGCAAAGCCCTTTTA
* *
6028899 ATAACTGGGGCATAAGCCCTTTATC
1 ATAACTAGGGCA-AAGCCCTTT-TA
* * *
6028924 ATAACTGGGGCATAAGCCCCTTATC
1 ATAACTAGGGCA-AAG-CCCTTTTA
*
6028949 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTAGGGCA-AAGCCCTTTTA
6028973 CACTTCCTCC
Statistics
Matches: 87, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
23 17 0.20
24 22 0.25
25 43 0.49
26 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (23 bp):
ATAACTAGGGCAAAGCCCTTTTA
Found at i:6028915 original size:24 final size:24
Alignment explanation
Indices: 6028865--6028972 Score: 146
Period size: 25 Copynumber: 4.4 Consensus size: 24
6028855 CTAGAGGCCT
*
6028865 AGCCTCTTTTAATAACTAGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
6028889 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
6028913 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
* *
6028938 AGCCCCTTATCATAACTGGGGCATA
1 AG-CCCTTTTAATAACTGGGGCATA
6028963 AGCCCTTTTA
1 AGCCCTTTTA
6028973 CACTTCCTCC
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
23 17 0.22
24 19 0.25
25 35 0.46
26 5 0.07
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:6029046 original size:20 final size:20
Alignment explanation
Indices: 6029021--6029087 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
6029011 TTATGAATAC
6029021 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
6029041 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
6029061 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
6029081 ACCATGT
1 ATCATGT
6029088 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:6029052 original size:11 final size:11
Alignment explanation
Indices: 6029021--6029076 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
6029011 TTATGAATAC
6029021 ATCATGTGCAT
1 ATCATGTGCAT
*
6029032 ATCA--TACAT
1 ATCATGTGCAT
6029041 ATCATGTGCAT
1 ATCATGTGCAT
*
6029052 ATCA--TACAT
1 ATCATGTGCAT
*
6029061 GTCATGTGCAT
1 ATCATGTGCAT
6029072 ATCAT
1 ATCAT
6029077 ACATACCATG
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:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:6031144 original size:15 final size:15
Alignment explanation
Indices: 6031126--6031157 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
6031116 CCAAAGAAGA
6031126 ATCCACAAGACTAGT
1 ATCCACAAGACTAGT
*
6031141 ATCCACACGACTAGT
1 ATCCACAAGACTAGT
6031156 AT
1 AT
6031158 TACTAGCTAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (15 bp):
ATCCACAAGACTAGT
Found at i:6036238 original size:31 final size:30
Alignment explanation
Indices: 6036200--6036260 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
6036190 CGAATTCAAT
* *
6036200 TTTTTTTTTAAAAATATTGAACTCTTAATTA
1 TTTTTTTTT-AAAATATCGAACTCCTAATTA
6036231 TTTTTTTTTAAAATATCGAACTCCTAATTA
1 TTTTTTTTTAAAATATCGAACTCCTAATTA
6036261 CCCAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 19 0.68
31 9 0.32
ACGTcount: A:0.34, C:0.10, G:0.03, T:0.52
Consensus pattern (30 bp):
TTTTTTTTTAAAATATCGAACTCCTAATTA
Found at i:6054852 original size:21 final size:21
Alignment explanation
Indices: 6054810--6054857 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
6054800 ATGTGGCCCA
**
6054810 CACGTGATAGACCCTTACAAG
1 CACGTGATAGACCCCAACAAG
* *
6054831 CACGTGATAGGCCCCAAGAAG
1 CACGTGATAGACCCCAACAAG
6054852 CACGTG
1 CACGTG
6054858 CACCCCAAAG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.25, T:0.15
Consensus pattern (21 bp):
CACGTGATAGACCCCAACAAG
Found at i:6058356 original size:26 final size:26
Alignment explanation
Indices: 6058327--6058436 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
6058317 TGATACAAAT
6058327 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
6058353 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
6058379 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
6058405 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
6058431 TGATAA
1 TGATAA
6058437 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:6060098 original size:27 final size:27
Alignment explanation
Indices: 6060057--6060169 Score: 129
Period size: 27 Copynumber: 4.2 Consensus size: 27
6060047 GAGGAAGCGT
*
6060057 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
6060084 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
6060111 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
6060139 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
6060165 TCTGG
1 TCTGG
6060170 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
26 5 0.07
27 55 0.73
28 15 0.20
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:6060162 original size:54 final size:54
Alignment explanation
Indices: 6060055--6060169 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
6060045 TGGAGGAAGC
*
6060055 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * * *
6060109 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTATGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
6060163 GTTCTGG
1 GTTCTGG
6060170 CAGCCATGCT
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTATGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:6062368 original size:21 final size:20
Alignment explanation
Indices: 6062334--6062372 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
6062324 ATTTTAGGAT
6062334 TTATTTTCATTTATCTTTAA
1 TTATTTTCATTTATCTTTAA
*
6062354 TTATTTATTATTTATCTTT
1 TTATTT-TCATTTATCTTT
6062373 TAGAATTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (20 bp):
TTATTTTCATTTATCTTTAA
Found at i:6062380 original size:21 final size:22
Alignment explanation
Indices: 6062342--6062385 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
6062332 ATTTATTTTC
**
6062342 ATTTATCTTTAATTATTT-ATT
1 ATTTATCTTTAAGAATTTCATT
*
6062363 ATTTATCTTTTAGAATTTCATT
1 ATTTATCTTTAAGAATTTCATT
6062385 A
1 A
6062386 GGAATAGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (22 bp):
ATTTATCTTTAAGAATTTCATT
Found at i:6066121 original size:20 final size:20
Alignment explanation
Indices: 6066098--6066157 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
6066088 AAGACTACAT
6066098 AAATATGTACATATATATTA
1 AAATATGTACATATATATTA
** *
6066118 AAATAAATACATAATGATAGTA
1 AAATATGTACAT-AT-ATATTA
6066140 AAAGTATGTACATA-ATAT
1 AAA-TATGTACATATATAT
6066158 AGCGTTGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
20 13 0.42
21 2 0.06
22 9 0.29
23 7 0.23
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.33
Consensus pattern (20 bp):
AAATATGTACATATATATTA
Found at i:6066152 original size:23 final size:21
Alignment explanation
Indices: 6066098--6066159 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
6066088 AAGACTACAT
*
6066098 AAATATGTACAT-ATATATTA
1 AAATATGTACATAATATAGTA
**
6066118 AAATAAATACATAATGATAGTA
1 AAATATGTACATAAT-ATAGTA
6066140 AAAGTATGTACATAATATAG
1 AAA-TATGTACATAATATAG
6066160 CGTTGAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.29
21 2 0.06
22 12 0.35
23 10 0.29
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (21 bp):
AAATATGTACATAATATAGTA
Found at i:6066297 original size:24 final size:25
Alignment explanation
Indices: 6066266--6066328 Score: 80
Period size: 24 Copynumber: 2.6 Consensus size: 25
6066256 CATATATAAA
6066266 AATATAATATTAAAAA-G-ATATAT
1 AATATAATATTAAAAATGCATATAT
6066289 -ATACGTAATA-TAAAAATGCATATAT
1 AATA--TAATATTAAAAATGCATATAT
6066314 AATATAATATTAAAA
1 AATATAATATTAAAA
6066329 TATTTACATA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
22 3 0.09
23 6 0.18
24 11 0.32
25 11 0.32
26 3 0.09
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (25 bp):
AATATAATATTAAAAATGCATATAT
Found at i:6066420 original size:23 final size:23
Alignment explanation
Indices: 6066394--6066459 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 23
6066384 CAATATTACA
*
6066394 TAAACATATACCTATATATAT-AT
1 TAAACATATA-CTACATATATAAT
*
6066417 TAAAGATATA-TACATATATAAT
1 TAAACATATACTACATATATAAT
*
6066439 AAAACATATACTA-ATAT-TAAT
1 TAAACATATACTACATATATAAT
6066460 AATAATAAGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
21 12 0.32
22 14 0.38
23 11 0.30
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.36
Consensus pattern (23 bp):
TAAACATATACTACATATATAAT
Found at i:6066435 original size:21 final size:20
Alignment explanation
Indices: 6066409--6066458 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
6066399 ATATACCTAT
*
6066409 ATATATATTAAAGATATATAC
1 ATATATATTAAA-ACATATAC
*
6066430 ATATATAATAAAACATATAC
1 ATATATATTAAAACATATAC
6066450 -TA-ATATTAA
1 ATATATATTAA
6066459 TAATAATAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 6 0.23
19 2 0.08
20 7 0.27
21 11 0.42
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (20 bp):
ATATATATTAAAACATATAC
Found at i:6066461 original size:21 final size:23
Alignment explanation
Indices: 6066385--6066455 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 23
6066375 ACCTATTAAC
6066385 AATAT-TACAT-AAACATATACCT
1 AATATATACATAAAACATATA-CT
* * *
6066407 -ATATATATATTAAAGATATA-T
1 AATATATACATAAAACATATACT
6066428 ACATATATA-ATAAAACATATACT
1 A-ATATATACATAAAACATATACT
6066451 AATAT
1 AATAT
6066456 TAATAATAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
21 5 0.12
22 18 0.45
23 17 0.43
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.35
Consensus pattern (23 bp):
AATATATACATAAAACATATACT
Found at i:6066523 original size:23 final size:22
Alignment explanation
Indices: 6066470--6066516 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 22
6066460 AATAATAAGG
6066470 ATAATATATAAATATATATATAT
1 ATAATATATAAA-ATATATATAT
6066493 ATGAAATAGTATAAAATATATATA
1 AT--AATA-TATAAAATATATATA
6066517 ACTAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 2 0.10
25 13 0.62
26 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
ATAATATATAAAATATATATAT
Found at i:6066718 original size:3 final size:3
Alignment explanation
Indices: 6066710--6066738 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6066700 ATATATGTAT
6066710 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
6066739 GTTAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:6068834 original size:90 final size:90
Alignment explanation
Indices: 6068669--6068834 Score: 262
Period size: 90 Copynumber: 1.8 Consensus size: 90
6068659 AAGCAGATTT
*
6068669 TGAAAATACCTCGACATGTGACCCGATGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
1 TGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
* *
6068734 AAATATAAATTGAAAAAACAAAAAC
66 AAACAGAAATTGAAAAAACAAAAAC
*
6068759 TGAAAATACCTC-AGCATGTGATCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
1 TGAAAATACCTCGA-CATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGA
**
6068823 CGAACAGAAATT
65 AAAACAGAAATT
6068835 AACAATATCT
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
89 1 0.01
90 68 0.99
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (90 bp):
TGAAAATACCTCGACATGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTGAA
AAACAGAAATTGAAAAAACAAAAAC
Found at i:6068920 original size:14 final size:14
Alignment explanation
Indices: 6068903--6068929 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6068893 TTTTGACAAA
6068903 CAGAAATTGAAAAG
1 CAGAAATTGAAAAG
6068917 CAGAAATTGAAAA
1 CAGAAATTGAAAA
6068930 TACCTCAGCG
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:0.59, C:0.07, G:0.19, T:0.15
Consensus pattern (14 bp):
CAGAAATTGAAAAG
Found at i:6069040 original size:79 final size:79
Alignment explanation
Indices: 6068909--6069064 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
6068899 CAAACAGAAA
*
6068909 TTGAAAAGCAGAAATTGAAAATACCTCAGCGTGAGACCCGAAGCTCAACTCACCTCTCACAATAT
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGAGACCCGAAGCTCAACTCACCTCTCACAATAT
6068974 GAGTTAATTTTTTT
66 GAGTTAATTTTTTT
* * ** * * * *
6068988 TTGAAAAACAGGAATTGAGAATACCTTGGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAGTA
1 TTGAAAAACAGAAATTGAAAATACCTCAGCGTGAGACCCGAA-GCTCAACTCACCTCTCACAATA
*
6069052 TGAGTTGATTTTT
65 TGAGTTAATTTTT
6069065 GAAAAATAGA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
78 2 0.03
79 64 0.97
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (79 bp):
TTGAAAAACAGAAATTGAAAATACCTCAGCGTGAGACCCGAAGCTCAACTCACCTCTCACAATAT
GAGTTAATTTTTTT
Found at i:6069061 original size:169 final size:166
Alignment explanation
Indices: 6068539--6069228 Score: 682
Period size: 165 Copynumber: 4.1 Consensus size: 166
6068529 TCAATTCATT
* * * * *
6068539 TCTCGCAATATGAATTGACTCTTT-AAAAACAGACATT-AAAAACAGAAATTGAAAATAGCTCAG
1 TCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCAG
* * * * * * *
6068602 CACGTGAG-CCAAAGTTTAACTCACCTCTCGCAATATGAGTTGGTTTTTGAAACTT-AAAAGCAG
65 --CGTGAGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT----TTTGAAAAACAG
** * * * * * * *
6068665 ATTTTGAAAATACCTCGACATGTGACCCGATGCTCAACTCACC
124 AAATTAAAAATACCTTGGCGTGTGAGCCAAGGCTCAACTCACC
* * *
6068708 TCTCGCAATATGAGTTGATTTTTGAAAAATATAAATTGAAAAAACAAAAACTGAAAATACCTCAG
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTG-AAAAACAGAAATTGAAAATACCTCAG
* * **
6068773 CATGTGATCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA---TTTTTGACGAACAGAAATT
65 CGTGAGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATT
* * *
6068835 AACAATATCTTGGCGTGTGAGCCAAGGCTCAACTCACA
129 AAAAATACCTTGGCGTGTGAGCCAAGGCTCAACTCACC
* * * *
6068873 TCTCGCAATATGGGTTGATTTTTTGACAAACAGAAATTGAAAAGCAGAAATTGAAAATACCTCAG
1 TCTCGCAATATGAGTTGA-TTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCAG
* * * *
6068938 CGTGAGACCCGAAGCTCAACTCACCTCTCACAATATGAGTTAATTTTTTTTTGAAAAACAGGAAT
65 CGTGAGA-CCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-TTTTTTTTGAAAAACAGAAAT
* *
6069003 TGAGAATACCTTGGCGTGTGAGCCAAGGCTCAACTCACC
128 TAAAAATACCTTGGCGTGTGAGCCAAGGCTCAACTCACC
* * * * *
6069042 TCTCGCAGTATGAGTTGATTTTTGAAAAATAGAATTTGAAAAACGGAATTTGAAAATACATC-GA
1 TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCAG-
* *
6069106 TGTGAGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAGCAGAAATTA
65 CGTGAGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTA
*** ** *
6069171 AAAATACCTCAACGTGT---CTTGAGGTTCAACTCACC
130 AAAATACCTTGGCGTGTGAGC-CAAGGCTCAACTCACC
*
6069206 TCTTGCAATATGAGTTGATTTTT
1 TCTCGCAATATGAGTTGATTTTT
6069229 TGAATTCAGA
Statistics
Matches: 432, Mismatches: 76, Indels: 31
0.80 0.14 0.06
Matches are distributed among these distances:
163 1 0.00
164 36 0.08
165 113 0.26
166 50 0.12
167 33 0.08
168 49 0.11
169 97 0.22
171 53 0.12
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.28
Consensus pattern (166 bp):
TCTCGCAATATGAGTTGATTTTTGAAAAATAGAAATTGAAAAACAGAAATTGAAAATACCTCAGC
GTGAGACCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTGAAAAACAGAAATTAA
AAATACCTTGGCGTGTGAGCCAAGGCTCAACTCACC
Found at i:6069081 original size:14 final size:14
Alignment explanation
Indices: 6069062--6069097 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
6069052 TGAGTTGATT
*
6069062 TTTGAAAAATAGAA
1 TTTGAAAAACAGAA
*
6069076 TTTGAAAAACGGAA
1 TTTGAAAAACAGAA
6069090 TTTGAAAA
1 TTTGAAAA
6069098 TACATCGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.03, G:0.17, T:0.28
Consensus pattern (14 bp):
TTTGAAAAACAGAA
Found at i:6081310 original size:23 final size:24
Alignment explanation
Indices: 6081268--6081319 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
6081258 GAACATATAC
*
6081268 AATATATATTAGAAATACTA-AAA
1 AATATATATTAGAAACACTACAAA
*
6081291 AATATATATTA-ATAACACTACATA
1 AATATATATTAGA-AACACTACAAA
6081315 AATAT
1 AATAT
6081320 GTACATATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 1 0.04
23 17 0.68
24 7 0.28
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (24 bp):
AATATATATTAGAAACACTACAAA
Found at i:6081344 original size:20 final size:21
Alignment explanation
Indices: 6081321--6081374 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 21
6081311 CATAAATATG
6081321 TACATATATATTAAAA-TAAA
1 TACATATATATTAAAAGTAAA
* *
6081341 TACATAATGATAGTAAAAGTATA
1 TACAT-AT-ATATTAAAAGTAAA
6081364 TACATAATATA
1 TACAT-ATATA
6081375 GTGTTGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 5 0.17
21 2 0.07
22 11 0.38
23 11 0.38
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (21 bp):
TACATATATATTAAAAGTAAA
Found at i:6081409 original size:25 final size:24
Alignment explanation
Indices: 6081324--6081409 Score: 88
Period size: 25 Copynumber: 3.6 Consensus size: 24
6081314 AAATATGTAC
6081324 ATATA-TATTAAAATAAATACATA
1 ATATAGTATTAAAATAAATACATA
* *
6081347 ATGATAGTA--AAAGTATATACATA
1 AT-ATAGTATTAAAATAAATACATA
* *
6081370 ATATAGTGTTGAAAATACATACATA
1 ATATAGTATT-AAAATAAATACATA
6081395 ATATAGCTATTAAAA
1 ATATAG-TATTAAAA
6081410 ATATATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
22 5 0.10
23 16 0.31
24 3 0.06
25 24 0.47
26 3 0.06
ACGTcount: A:0.53, C:0.06, G:0.08, T:0.33
Consensus pattern (24 bp):
ATATAGTATTAAAATAAATACATA
Found at i:6081487 original size:36 final size:36
Alignment explanation
Indices: 6081447--6081520 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 36
6081437 TAAAAAATGT
* * *
6081447 AATATAGTATTAGAAATATATACATGACAT-ATATAA
1 AATATAATATTAAAAAGATATACAT-ACATAATATAA
*
6081483 AATATAATATTAAAAAGATATATATACATAATATAA
1 AATATAATATTAAAAAGATATACATACATAATATAA
6081519 AA
1 AA
6081521 AATGCATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.32
Consensus pattern (36 bp):
AATATAATATTAAAAAGATATACATACATAATATAA
Found at i:6081507 original size:20 final size:21
Alignment explanation
Indices: 6081484--6081537 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 21
6081474 CATATATAAA
6081484 ATATAATAT-TAAAAAGAT-AT
1 ATATAATATATAAAAA-ATCAT
6081504 ATATACATAATATAAAAAATGCAT
1 ATATA-AT-ATATAAAAAAT-CAT
6081528 ATATAATATA
1 ATATAATATA
6081538 ATATTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
20 5 0.17
21 2 0.07
22 7 0.24
23 8 0.28
24 7 0.24
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (21 bp):
ATATAATATATAAAAAATCAT
Found at i:6081521 original size:24 final size:25
Alignment explanation
Indices: 6081477--6081546 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
6081467 TACATGACAT
* *
6081477 ATATAAAATATAATATTAAAAA-G-
1 ATATATAACATAATATTAAAAATGC
*
6081500 ATATATATACATAATATAAAAAATGC
1 ATATATA-ACATAATATTAAAAATGC
*
6081526 ATATATAATATAATATTAAAA
1 ATATATAACATAATATTAAAA
6081547 TATTTACATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
23 6 0.15
24 13 0.33
25 13 0.33
26 7 0.18
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (25 bp):
ATATATAACATAATATTAAAAATGC
Done.