Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 179 of 207
Found at i:54990615 original size:7 final size:7
Alignment explanation
Indices: 54990605--54990653 Score: 64
Period size: 7 Copynumber: 6.9 Consensus size: 7
54990595 TAATGTTTAG
54990605 GGATTAT
1 GGATTAT
*
54990612 GGATTTAG
1 GGA-TTAT
54990620 GGATTAT
1 GGATTAT
54990627 GGATTA-
1 GGATTAT
54990633 GTGATTAT
1 G-GATTAT
54990641 GGATTAT
1 GGATTAT
54990648 GGATTA
1 GGATTA
54990654 GGGGTTGGGA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
6 1 0.03
7 29 0.78
8 7 0.19
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.41
Consensus pattern (7 bp):
GGATTAT
Found at i:54990620 original size:15 final size:15
Alignment explanation
Indices: 54990600--54990645 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
54990590 TATTTTAATG
54990600 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
54990615 TTTAGGGATTATGGA
1 TTTAGGGATTATGGA
*
54990630 -TTAGTGATTATGGA
1 TTTAGGGATTATGGA
54990644 TT
1 TT
54990646 ATGGATTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 13 0.45
15 16 0.55
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.43
Consensus pattern (15 bp):
TTTAGGGATTATGGA
Found at i:54990638 original size:14 final size:14
Alignment explanation
Indices: 54990601--54990653 Score: 79
Period size: 14 Copynumber: 3.7 Consensus size: 14
54990591 ATTTTAATGT
54990601 TTAGGGATTATGGA
1 TTAGGGATTATGGA
54990615 TTTAGGGATTATGGA
1 -TTAGGGATTATGGA
*
54990630 TTAGTGATTATGGA
1 TTAGGGATTATGGA
*
54990644 TTATGGATTA
1 TTAGGGATTA
54990654 GGGGTTGGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
14 21 0.60
15 14 0.40
ACGTcount: A:0.28, C:0.00, G:0.30, T:0.42
Consensus pattern (14 bp):
TTAGGGATTATGGA
Found at i:54990692 original size:15 final size:15
Alignment explanation
Indices: 54990655--54990705 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
54990645 TATGGATTAG
*
54990655 GGGTT-GGGATTTAA
1 GGGTTAGGGGTTTAA
*
54990669 GGTTTAGGGG-TTAGA
1 GGGTTAGGGGTTTA-A
54990684 GGGTTAGGGGTTTAA
1 GGGTTAGGGGTTTAA
54990699 GGGTTAG
1 GGGTTAG
54990706 ATGTGCTAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
14 7 0.23
15 21 0.68
16 3 0.10
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
GGGTTAGGGGTTTAA
Found at i:54990923 original size:14 final size:15
Alignment explanation
Indices: 54990885--54990926 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
54990875 TATTTTAAGG
*
54990885 TTTAGGGAGTATGAA
1 TTTAGGGATTATGAA
*
54990900 TTTAGAGATTATGAA
1 TTTAGGGATTATGAA
54990915 -TTAGGGATTATG
1 TTTAGGGATTATG
54990927 GTTTAAGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.33, C:0.00, G:0.29, T:0.38
Consensus pattern (15 bp):
TTTAGGGATTATGAA
Found at i:54990975 original size:14 final size:14
Alignment explanation
Indices: 54990956--54990990 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
54990946 AAGTTGAGGG
54990956 GTTAGGGGTT-AGA
1 GTTAGGGGTTAAGA
54990969 TGTTAGGGGTTAAGA
1 -GTTAGGGGTTAAGA
54990984 GTTAGGG
1 GTTAGGG
54990991 ATTTAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 17 0.85
15 3 0.15
ACGTcount: A:0.23, C:0.00, G:0.46, T:0.31
Consensus pattern (14 bp):
GTTAGGGGTTAAGA
Found at i:54992382 original size:152 final size:148
Alignment explanation
Indices: 54992072--54992352 Score: 359
Period size: 152 Copynumber: 1.9 Consensus size: 148
54992062 GCGTTTTTAT
*
54992072 TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAGCA
1 TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAACA
* * * * *
54992137 AAACGGCGTCATTTTGTTCAAAATAAAAACTTTTTTGTGGCATTTTTATTAAAGACGCCGCAAAA
66 AAACGGCGTCATTTTGTTCAAAATAAAAA----TTAGCGGCATTTTTATAAAAAACGCAGCAAAA
* ** *** * *
54992202 GATAAGCAATAGCAGCGTTTTA
127 AATAAGCAATAAAAAAATATAA
*
54992224 TTAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAACA
1 TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAACA
* *
54992289 AAACGGCGTCATTTTGTTCAAAAT-GAAA-TAGCGGCGTTTTTATAAAAAACGCAGCAAAAAATA
66 AAACGGCGTCATTTTGTTCAAAATAAAAATTAGCGGCATTTTTATAAAAAACGCAGCAAAAAATA
54992352 A
131 A
54992353 ATCAATTTAT
Statistics
Matches: 119, Mismatches: 10, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
146 29 0.24
151 3 0.03
152 87 0.73
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.27
Consensus pattern (148 bp):
TAAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAATAAAATAAAAAATTTTTAGCATAACA
AAACGGCGTCATTTTGTTCAAAATAAAAATTAGCGGCATTTTTATAAAAAACGCAGCAAAAAATA
AGCAATAAAAAAATATAA
Found at i:54992407 original size:108 final size:109
Alignment explanation
Indices: 54992209--54992482 Score: 394
Period size: 108 Copynumber: 2.5 Consensus size: 109
54992199 AAAGATAAGC
*
54992209 AATAGCAGCG-TTTTATTAAAAACGCCGCAAAAAATAAATCAATTTAT-AAAAAAATAAAATAAA
1 AATAGCGGCGTTTTTA-TAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAATAAA
54992272 AAATTTTTAGCATAACAAAACGGCGTCATTTTGTTCAAAATG-A-
65 AAATTTTTAGCATAACAAAACGGCGTCATTTTGTTCAAAATGAAT
* *
54992315 AATAGCGGCGTTTTTATAAAAAACGCAGCAAAAAATAAATCAATTTATAAAAAAAATATAATAAA
1 AATAGCGGCGTTTTTAT-AAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAATAAA
*
54992380 AAATTTTTAGCATAGCAAAACGGCGTCATTTTGTTCAAAATGAAAT
65 AAATTTTTAGCATAACAAAACGGCGTCATTTTGTTCAAAATG-AAT
* *
54992426 AATATTTTGCGGCGTTTTTCATAAAAACGCCGCAAATAATAAATCAATTAATAAAAA
1 AATA----GCGGCGTTTTT-ATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAA
54992483 CCAAAATAGC
Statistics
Matches: 150, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
106 10 0.07
107 34 0.23
108 56 0.37
110 1 0.01
111 4 0.03
115 43 0.29
116 2 0.01
ACGTcount: A:0.49, C:0.12, G:0.11, T:0.28
Consensus pattern (109 bp):
AATAGCGGCGTTTTTATAAAAACGCCGCAAAAAATAAATCAATTTATAAAAAAAATAAAATAAAA
AATTTTTAGCATAACAAAACGGCGTCATTTTGTTCAAAATGAAT
Found at i:54992579 original size:97 final size:97
Alignment explanation
Indices: 54992391--54992578 Score: 308
Period size: 96 Copynumber: 1.9 Consensus size: 97
54992381 AATTTTTAGC
*
54992391 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAATATTTTGCGGCGTTTTTCATAAAAACGC
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAAAATTTTGCGGCGTTTTTCATAAAAACGC
*
54992456 CGCAAATAATAAATCAATTAATAAAAACCAAA
66 CGCAAAAAATAAATCAATTAATAAAAACCAAA
* *
54992488 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAA-AAAATTTTGTGGCGTTTTT-ATAAAAAATG
1 ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAAAATTTTGCGGCGTTTTTCAT-AAAAACG
*
54992551 CCGCAAAAAATAAATCAATTTATAAAAA
65 CCGCAAAAAATAAATCAATTAATAAAAA
54992579 AATAAAATAA
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
95 2 0.02
96 49 0.58
97 34 0.40
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (97 bp):
ATAGCAAAACGGCGTCATTTTGTTCAAAATGAAATAAAATTTTGCGGCGTTTTTCATAAAAACGC
CGCAAAAAATAAATCAATTAATAAAAACCAAA
Found at i:54994592 original size:95 final size:94
Alignment explanation
Indices: 54994408--54994592 Score: 271
Period size: 95 Copynumber: 2.0 Consensus size: 94
54994398 TTAGCCTGAG
54994408 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
** *
54994473 CCATTCTTGCAGTAGGTACCTTTTTCTCA
66 CCATTCTTGCAACACGTACCTTTTTCTCA
* ** * **
54994502 TGCTTCCTCTTTCATTGCCTTTGTGCGCTTCCCTTTTTTGTTTTTGAAGTTCTAGAGTTGGTGAT
1 TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCC-TTTTTGTTTTTGAAGTTCTAGAGCTGGCAAT
*
54994567 ACCATTCTTGCAACACGTACTTTTTT
65 ACCATTCTTGCAACACGTACCTTTTT
54994593 TTCTCAATTA
Statistics
Matches: 80, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
94 30 0.38
95 50 0.62
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.45
Consensus pattern (94 bp):
TGCTTCCTCTTTCATTGCCTCTACGCGCTTCCCTTTTTGTTTTTGAAGTTCTAGAGCTGGCAATA
CCATTCTTGCAACACGTACCTTTTTCTCA
Found at i:54996055 original size:43 final size:43
Alignment explanation
Indices: 54995979--54996184 Score: 272
Period size: 43 Copynumber: 4.8 Consensus size: 43
54995969 TTTTTTCGAG
* * *
54995979 AAGCGTCGCTAAAGG-CTTGTTCTATAGCGGCGTTTGTGGAAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * *
54996021 AATCGCCGCTAAAGGTCTTGAGCTATAGCAGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* * * *
54996064 AGGCGCTGCTAAAGGCCTTGATCTATAGCGGCGTTTGT-GCAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* *
54996106 AAGCGTCGCTAAAGGTCCTGATCTATAGCGGCGTTTGTGGGAA
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
* *
54996149 AAGCGCCGCTAAATGTCATGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTT
54996185 ATTTTTAAAA
Statistics
Matches: 140, Mismatches: 22, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
42 49 0.35
43 91 0.65
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (43 bp):
AAGCGCCGCTAAAGGTCTTGATCTATAGCGGCGTTTGTGGGAA
Found at i:54996116 original size:85 final size:85
Alignment explanation
Indices: 54995979--54996184 Score: 279
Period size: 85 Copynumber: 2.4 Consensus size: 85
54995969 TTTTTTCGAG
* * * *
54995979 AAGCGTCGCTAAAGGCTTGTTCTATAGCGGCGTTTGTGGAAAAATCGCCGCTAAAGGTCTTGAGC
1 AAGCGCCGCTAAAGGCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGAGC
54996044 TATAGCAGCGTTTGTGGGAA
66 TATAGCAGCGTTTGTGGGAA
* * * * *
54996064 AGGCGCTGCTAAAGGCCTTGATCTATAGCGGCGTTTGT-GCAAAAGCGTCGCTAAAGGTCCTGAT
1 AAGCGCCGCTAAAGG-CTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGAG
*
54996128 CTATAGCGGCGTTTGTGGGAA
65 CTATAGCAGCGTTTGTGGGAA
* *
54996149 AAGCGCCGCTAAATGTCATGATCTATAGCGGCGTTT
1 AAGCGCCGCTAAA-GGCTTGATCTATAGCGGCGTTT
54996185 ATTTTTAAAA
Statistics
Matches: 105, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
85 83 0.79
86 22 0.21
ACGTcount: A:0.24, C:0.19, G:0.30, T:0.27
Consensus pattern (85 bp):
AAGCGCCGCTAAAGGCTTGATCTATAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGAGC
TATAGCAGCGTTTGTGGGAA
Found at i:54998102 original size:42 final size:42
Alignment explanation
Indices: 54998043--54998150 Score: 162
Period size: 42 Copynumber: 2.6 Consensus size: 42
54998033 CAACAAAAAA
* *
54998043 CGCCGCTAAAGATCATGTTCTTTAGCAGCGTTTTTCCATAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCAGCATTTTTCCATAAG
* * *
54998085 CGCCGCTGAAGAACATGTTCTTTAGCGGCATTTTTCTATAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCAGCATTTTTCCATAAG
*
54998127 CACCGCTAAAGAACATGTTCTTTA
1 CGCCGCTAAAGAACATGTTCTTTA
54998151 ACGACGCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGTTCTTTAGCAGCATTTTTCCATAAG
Found at i:54998192 original size:43 final size:43
Alignment explanation
Indices: 54998145--54998260 Score: 126
Period size: 43 Copynumber: 2.7 Consensus size: 43
54998135 AAGAACATGT
* * *
54998145 TCTTTAACGACGCTTTGTATAAAAACGCCGCTAGAG-ATCATAA
1 TCTTTAGCGGCGCTTTGTATAAAAACGCCGCTACAGAAT-ATAA
* * * **
54998188 TCTTTAGCGGCGCTTTTTTTACAAACGCCGCTACAGAATATGT
1 TCTTTAGCGGCGCTTTGTATAAAAACGCCGCTACAGAATATAA
*
54998231 TCTTTAGCGGCGCTTTTGTACAAAAACGCC
1 TCTTTAGCGGCGC-TTTGTATAAAAACGCC
54998261 ACTATTTTTG
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
43 45 0.76
44 14 0.24
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (43 bp):
TCTTTAGCGGCGCTTTGTATAAAAACGCCGCTACAGAATATAA
Found at i:54998233 original size:86 final size:86
Alignment explanation
Indices: 54998103--54998260 Score: 210
Period size: 86 Copynumber: 1.8 Consensus size: 86
54998093 AAGAACATGT
* * *
54998103 TCTTTAGCGGCATTTTTCTATAAGCACCGCTAAAGAACATGTTCTTTAACGACGC-TTTGTATAA
1 TCTTTAGCGGCATTTTTCTACAAACACCGCTAAAGAACATGTTCTTTAACGACGCTTTTGTACAA
54998167 AAACGCCGCTAGAGATCATAA
66 AAACGCCGCTAGAGATCATAA
* * * * * * *
54998188 TCTTTAGCGGCGCTTTTTTTACAAACGCCGCTACAGAATATGTTCTTTAGCGGCGCTTTTGTACA
1 TCTTTAGCGGC-ATTTTTCTACAAACACCGCTAAAGAACATGTTCTTTAACGACGCTTTTGTACA
54998253 AAAACGCC
65 AAAACGCC
54998261 ACTATTTTTG
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 11 0.18
86 35 0.57
87 15 0.25
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (86 bp):
TCTTTAGCGGCATTTTTCTACAAACACCGCTAAAGAACATGTTCTTTAACGACGCTTTTGTACAA
AAACGCCGCTAGAGATCATAA
Found at i:54998653 original size:21 final size:21
Alignment explanation
Indices: 54998629--54998679 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
54998619 TTCTTTTGAA
*
54998629 CCTCTGCTTCTCTCGCTGCAG
1 CCTCTGCTTCCCTCGCTGCAG
*
54998650 CCTCTGCTTCCCTCGCTGCCG
1 CCTCTGCTTCCCTCGCTGCAG
*
54998671 CGTCTGCTT
1 CCTCTGCTT
54998680 TAAGTTGTAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.02, C:0.45, G:0.20, T:0.33
Consensus pattern (21 bp):
CCTCTGCTTCCCTCGCTGCAG
Found at i:55003020 original size:9 final size:9
Alignment explanation
Indices: 55003006--55003089 Score: 88
Period size: 9 Copynumber: 9.8 Consensus size: 9
55002996 TTTTTATGTA
55003006 TTATGTAAG
1 TTATGTAAG
55003015 TTATGTAAG
1 TTATGTAAG
55003024 TTATGT-A-
1 TTATGTAAG
55003031 TTATGTAAG
1 TTATGTAAG
55003040 -TACTGTAAG
1 TTA-TGTAAG
*
55003049 TAATGTAAG
1 TTATGTAAG
*
55003058 TCATGTAAG
1 TTATGTAAG
*
55003067 TCATGT-A-
1 TTATGTAAG
55003074 TTATGTAAG
1 TTATGTAAG
*
55003083 TTGTGTA
1 TTATGTA
55003090 TAACTTGTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
7 11 0.17
8 6 0.09
9 47 0.72
10 1 0.02
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55003033 original size:25 final size:25
Alignment explanation
Indices: 55002999--55003080 Score: 89
Period size: 25 Copynumber: 3.3 Consensus size: 25
55002989 TGATATATTT
55002999 TTATGTATTATGTAAGTTATGTAAG
1 TTATGTATTATGTAAGTTATGTAAG
55003024 TTATGTATTATGTAAG-TACTGTAAG
1 TTATGTATTATGTAAGTTA-TGTAAG
* * *
55003049 TAATGTAAGTCATGTAAGTCATGT-A-
1 TTATGT-A-TTATGTAAGTTATGTAAG
55003074 TTATGTA
1 TTATGTA
55003081 AGTTGTGTAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
24 3 0.06
25 32 0.65
26 2 0.04
27 11 0.22
28 1 0.02
ACGTcount: A:0.33, C:0.04, G:0.20, T:0.44
Consensus pattern (25 bp):
TTATGTATTATGTAAGTTATGTAAG
Found at i:55006087 original size:21 final size:20
Alignment explanation
Indices: 55006047--55006101 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
55006037 CGCTGAAATG
* * *
55006047 TAAACTCTAAACCTTAAACC
1 TAAACTCCAAGCCCTAAACC
*
55006067 TCAATCTCCAAGCCCTAAACC
1 T-AAACTCCAAGCCCTAAACC
*
55006088 TAAACTCTAAGCCC
1 TAAACTCCAAGCCC
55006102 AGATCACAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.22
Consensus pattern (20 bp):
TAAACTCCAAGCCCTAAACC
Found at i:55006902 original size:133 final size:134
Alignment explanation
Indices: 55006453--55006880 Score: 478
Period size: 133 Copynumber: 3.2 Consensus size: 134
55006443 CCATTTCCGA
* * * * *
55006453 CGTTTTTTAACATTTCGCCACTAAAG-CATAAAAAGGAAACAACAAAACAGTACCGTTTTGCTCA
1 CGTTTTTTAA-AATGCGCCACTAAAGAAAT-AAAATGAAACAACAAAACGGTA-CGTTTTGCTCA
* * * * *
55006517 AAATTTTTCCTCAAATTAGATATCTTTACTGGCGTTTCTCCA-ATAACGCCACTATATCCCAA-T
63 AATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCT-CAGAAAACGCCGCTATATTCCAATT
*
55006580 ATTTGCGG
127 TTTTGCGG
* * * *
55006588 CGTTTTTTACAATGCGCCACTAAGGAAATAAAATGAAGCAATAAAACGGTAGCGTTTTG-TCCAA
1 CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTA-CGTTTTGCT-CAA
* * *
55006652 ATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCCCTGAAAACGCCGCTA-A-TGC-ATTCT
64 ATTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATT-T
55006714 TTT-CTGG
128 TTTGC-GG
*
55006721 CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACTGTTTTGCTCAGA
1 CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTAC-GTTTTGCTCAAA
* * * *
55006786 TTTTTTTCTCAAATTCGTTATCGTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTTT
65 TTTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTTT
55006851 TGCGG
130 TGCGG
**
55006856 CGTTTTTGTGGAA-GCGCCACTAAAG
1 CGTTTTT-TAAAATGCGCCACTAAAG
55006881 TCATAAAGTA
Statistics
Matches: 247, Mismatches: 33, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
131 1 0.00
132 4 0.02
133 110 0.45
134 87 0.35
135 38 0.15
136 7 0.03
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (134 bp):
CGTTTTTTAAAATGCGCCACTAAAGAAATAAAATGAAACAACAAAACGGTACGTTTTGCTCAAAT
TTTTTCCTCAAATTAGATATCTTTACCGGCGTTTCTCAGAAAACGCCGCTATATTCCAATTTTTT
GCGG
Found at i:55012034 original size:69 final size:69
Alignment explanation
Indices: 55011923--55012056 Score: 268
Period size: 69 Copynumber: 1.9 Consensus size: 69
55011913 TCAAGGTAGA
55011923 ATAGTAGAAAACATTAGTTGATATCACAAAATCATTATTTGGGTATGTAATCTTTTAGTGGAAAT
1 ATAGTAGAAAACATTAGTTGATATCACAAAATCATTATTTGGGTATGTAATCTTTTAGTGGAAAT
55011988 TTTC
66 TTTC
55011992 ATAGTAGAAAACATTAGTTGATATCACAAAATCATTATTTGGGTATGTAATCTTTTAGTGGAAAT
1 ATAGTAGAAAACATTAGTTGATATCACAAAATCATTATTTGGGTATGTAATCTTTTAGTGGAAAT
55012057 GTTGAAAATT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.37, C:0.08, G:0.16, T:0.38
Consensus pattern (69 bp):
ATAGTAGAAAACATTAGTTGATATCACAAAATCATTATTTGGGTATGTAATCTTTTAGTGGAAAT
TTTC
Found at i:55013469 original size:11 final size:12
Alignment explanation
Indices: 55013439--55013481 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
55013429 GACGTGGGTA
*
55013439 AAAATAATTATGT
1 AAAA-AATTATAT
55013452 AATAAAATTAT-T
1 AA-AAAATTATAT
55013464 AAAAAATTATAT
1 AAAAAATTATAT
55013476 AAAAAA
1 AAAAAA
55013482 ACAAATGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 8 0.29
12 10 0.36
13 8 0.29
14 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (12 bp):
AAAAAATTATAT
Found at i:55027213 original size:23 final size:23
Alignment explanation
Indices: 55027183--55027231 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
55027173 ACTGTAATTG
* *
55027183 TAATATCTCGAAAATTATTACTA
1 TAATATCTCGAAAATTACTACAA
*
55027206 TAATATCTTGAAAATTACTACAA
1 TAATATCTCGAAAATTACTACAA
55027229 TAA
1 TAA
55027232 GAAAGTAGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.47, C:0.12, G:0.04, T:0.37
Consensus pattern (23 bp):
TAATATCTCGAAAATTACTACAA
Found at i:55033681 original size:21 final size:20
Alignment explanation
Indices: 55033655--55033693 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
55033645 AATTTTTTCC
55033655 CCAAATTTTGGATAACTTTTT
1 CCAAATTTTGGAT-ACTTTTT
55033676 CCAAATTTTGGATACTTT
1 CCAAATTTTGGATACTTT
55033694 ACATATTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (20 bp):
CCAAATTTTGGATACTTTTT
Found at i:55040962 original size:20 final size:20
Alignment explanation
Indices: 55040939--55040978 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55040929 TATTCAAACT
* *
55040939 ATATTACTTGAATAGTTATA
1 ATATTACATGAATAATTATA
*
55040959 ATATTAGATGAATAATTATA
1 ATATTACATGAATAATTATA
55040979 TGTCTTTGTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
ATATTACATGAATAATTATA
Found at i:55042545 original size:27 final size:27
Alignment explanation
Indices: 55042507--55042561 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
55042497 CTTCCGGAAA
*
55042507 AGGTTTTAACCTTGAATGACGTATATT
1 AGGTTTTAACCTTGAATGACGCATATT
*
55042534 AGGTTTTAACCTTGAATGATGCATATT
1 AGGTTTTAACCTTGAATGACGCATATT
55042561 A
1 A
55042562 TGTATCAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (27 bp):
AGGTTTTAACCTTGAATGACGCATATT
Found at i:55044126 original size:24 final size:25
Alignment explanation
Indices: 55044064--55044127 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
55044054 TCTTGGTACT
* * *
55044064 TAATTAGAAATA-TGTTAAAATCAT
1 TAATTAAAAATATTTTTAAAATCAC
55044088 TAATTAAAAAATATTTTTAAAAT-AC
1 TAATT-AAAAATATTTTTAAAATCAC
*
55044113 TAATTACAAATATTT
1 TAATTAAAAATATTT
55044128 AATGGTTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
24 14 0.41
25 12 0.35
26 8 0.24
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (25 bp):
TAATTAAAAATATTTTTAAAATCAC
Found at i:55046397 original size:50 final size:51
Alignment explanation
Indices: 55046342--55046478 Score: 156
Period size: 50 Copynumber: 2.7 Consensus size: 51
55046332 AATTTGAAAA
*
55046342 AAAAAATTTGAGGGTTTGGAGGGAAGTAAAGTTTTGGGAGAAAGCAAAAGG
1 AAAAAATTTGAGGGTTTGGAGGGAAGTAAATTTTTGGGAGAAAGCAAAAGG
** * *
55046393 AAAAAA-AAG-GGGTTTAGA-GGAAGTAACATTTTTTGGGAGAAAGTAAAAGG
1 AAAAAATTTGAGGGTTTGGAGGGAAGTAA-A-TTTTTGGGAGAAAGCAAAAGG
*
55046443 AAAAAACTTTTGAGGGTTTGGGGGGAAG-AAATTTTT
1 AAAAAA--TTTGAGGGTTTGGAGGGAAGTAAATTTTT
55046479 TTAGGGGAAG
Statistics
Matches: 70, Mismatches: 9, Indels: 13
0.76 0.10 0.14
Matches are distributed among these distances:
48 8 0.11
49 9 0.13
50 26 0.37
51 6 0.09
52 5 0.07
53 2 0.03
54 9 0.13
55 5 0.07
ACGTcount: A:0.41, C:0.02, G:0.32, T:0.25
Consensus pattern (51 bp):
AAAAAATTTGAGGGTTTGGAGGGAAGTAAATTTTTGGGAGAAAGCAAAAGG
Found at i:55047418 original size:9 final size:8
Alignment explanation
Indices: 55047406--55047500 Score: 64
Period size: 9 Copynumber: 10.5 Consensus size: 8
55047396 AAATAAAAAA
55047406 AATTCAGGT
1 AATTC-GGT
55047415 AATTCTGGT
1 AATTC-GGT
*
55047424 ATTTTTCGGT
1 A-AT-TCGGT
*
55047434 AATTCAGTT
1 AATTC-GGT
*
55047443 AATTCGATT
1 AATTCG-GT
55047452 AATTCGAGT
1 AATTCG-GT
55047461 AATTCGAGT
1 AATTCG-GT
55047470 AATTCGGGT
1 AATTC-GGT
55047479 AATTCGGGT
1 AATTC-GGT
55047488 AATTCGGGT
1 AATTC-GGT
55047497 AATT
1 AATT
55047501 TTTAACCAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
8 3 0.04
9 65 0.86
10 6 0.08
11 2 0.03
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (8 bp):
AATTCGGT
Found at i:55047472 original size:27 final size:26
Alignment explanation
Indices: 55047428--55047500 Score: 85
Period size: 27 Copynumber: 2.7 Consensus size: 26
55047418 TCTGGTATTT
*
55047428 TTCGGTAATTC-AGTTAATTCGATTAA
1 TTCGGTAATTCGAG-TAATTCGAGTAA
*
55047454 TTCGAGTAATTCGAGTAATTCGGGTAA
1 TTCG-GTAATTCGAGTAATTCGAGTAA
*
55047481 TTCGGGTAATTCGGGTAATT
1 TTC-GGTAATTCGAGTAATT
55047501 TTTAACCAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.10
27 34 0.83
28 3 0.07
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.38
Consensus pattern (26 bp):
TTCGGTAATTCGAGTAATTCGAGTAA
Found at i:55047493 original size:18 final size:18
Alignment explanation
Indices: 55047428--55047500 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 18
55047418 TCTGGTATTT
* *
55047428 TTCG-GTAATTCAGTTAA
1 TTCGAGTAATTCGGGTAA
* *
55047445 TTCGATTAATTCGAGTAA
1 TTCGAGTAATTCGGGTAA
55047463 TTCGAGTAATTCGGGTAA
1 TTCGAGTAATTCGGGTAA
*
55047481 TTCGGGTAATTCGGGTAA
1 TTCGAGTAATTCGGGTAA
55047499 TT
1 TT
55047501 TTTAACCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
17 4 0.08
18 44 0.92
ACGTcount: A:0.27, C:0.11, G:0.23, T:0.38
Consensus pattern (18 bp):
TTCGAGTAATTCGGGTAA
Found at i:55048342 original size:28 final size:28
Alignment explanation
Indices: 55048302--55048371 Score: 113
Period size: 28 Copynumber: 2.5 Consensus size: 28
55048292 TACATGGACG
*
55048302 GATTATTTAACTAGTAGATAAAGTGCAA
1 GATTATTTAACTACTAGATAAAGTGCAA
* *
55048330 GATTATTTAACTACTAGATGAAGTGTAA
1 GATTATTTAACTACTAGATAAAGTGCAA
55048358 GATTATTTAACTAC
1 GATTATTTAACTAC
55048372 ATAAACAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (28 bp):
GATTATTTAACTACTAGATAAAGTGCAA
Found at i:55052890 original size:18 final size:18
Alignment explanation
Indices: 55052855--55052889 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
55052845 CAAAATATAC
55052855 CAAAAAAAAACTAAAAAA
1 CAAAAAAAAACTAAAAAA
55052873 CAAAAAAAAA-TAAAAAA
1 CAAAAAAAAACTAAAAAA
55052890 AAACTGGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.06
Consensus pattern (18 bp):
CAAAAAAAAACTAAAAAA
Found at i:55053062 original size:14 final size:14
Alignment explanation
Indices: 55053031--55053130 Score: 57
Period size: 14 Copynumber: 7.1 Consensus size: 14
55053021 GTTGGTGGGG
* **
55053031 GGAAGAAGGAGAGG
1 GGAAGAAGAAGAAA
55053045 GGAAGAAGAAGAAA
1 GGAAGAAGAAGAAA
55053059 GGAAG--GAAGAAA
1 GGAAGAAGAAGAAA
*
55053071 -GAAAAAGAAGGAAAA
1 GGAAGAAGAA-G-AAA
*
55053086 GGAAAGAAGAGGAAA
1 GG-AAGAAGAAGAAA
* *
55053101 GAAAGAAAAAG-AA
1 GGAAGAAGAAGAAA
55053114 GGAAAGAA-AAGGAAA
1 GG-AAGAAGAA-GAAA
55053129 GG
1 GG
55053131 GGAGGAAAGA
Statistics
Matches: 67, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.04
12 7 0.10
13 8 0.12
14 30 0.45
15 11 0.16
16 2 0.03
17 6 0.09
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (14 bp):
GGAAGAAGAAGAAA
Found at i:55053123 original size:38 final size:38
Alignment explanation
Indices: 55053047--55053224 Score: 169
Period size: 38 Copynumber: 4.8 Consensus size: 38
55053037 AGGAGAGGGG
55053047 AAGAAGAA-GAAAGGA-AGG-AAGAAAGAAAAAGAA-G-
1 AAGAA-AAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
*
55053081 --GAAAAGGAAAGAAGAGGAAAGAAAGAAAAAGAAGGA
1 AAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
* *
55053117 AAGAAAAGGAAAGGGGAGGAAAGAAAGAAAAATAAGGA
1 AAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
* *
55053155 AAGAAAAGGAAAGGAGAAGAGAA-AAA-AAAAAGAAAGAA
1 AAGAAAAGGAAAGGAGAGGA-AAGAAAGAAAAAG-AAGGA
* * *
55053193 GAAGAAGAGGGAAGGA-AGGAAAAAAAAGAAAA
1 -AAGAAAAGGAAAGGAGAGG-AAAGAAAGAAAA
55053225 TAAAGTAATT
Statistics
Matches: 120, Mismatches: 11, Indels: 20
0.79 0.07 0.13
Matches are distributed among these distances:
31 2 0.02
32 9 0.08
33 3 0.03
34 15 0.12
35 1 0.01
37 5 0.04
38 62 0.52
39 19 0.16
40 4 0.03
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (38 bp):
AAGAAAAGGAAAGGAGAGGAAAGAAAGAAAAAGAAGGA
Found at i:55053221 original size:34 final size:32
Alignment explanation
Indices: 55053056--55053223 Score: 103
Period size: 34 Copynumber: 4.9 Consensus size: 32
55053046 GAAGAAGAAG
* * *
55053056 AAAGG-AA-GGAAGAAAGAAAAAGAAGGAAAAGG
1 AAAGGAAAGGGAAGGAAGAAAAA-AAAG-AAAGA
* * *
55053088 AAA-GAAGAGGAAAGAAAGAAAAAGAAGGAAAGA
1 AAAGGAA-AGGGAAGGAAGAAAAA-AAAGAAAGA
*
55053121 AAAGGAAAGGGGAGGAAAGAAAGAAAAATAAGGAAAGA
1 AAAGGAAAGGGAAGG-AAG--A-AAAAA-AA-GAAAGA
55053159 AAAGGAAAGGAGAAGAGAA-AAAAAAAAGAAAGA
1 AAAGGAAAGG-GAAG-GAAGAAAAAAAAGAAAGA
55053192 AGAA-GAAGAGGGAAGGAAGGAAAAAAAAGAAA
1 A-AAGGAA-AGGGAAGGAA-GAAAAAAAAGAAA
55053224 ATAAAGTAAT
Statistics
Matches: 113, Mismatches: 7, Indels: 30
0.75 0.05 0.20
Matches are distributed among these distances:
31 1 0.01
32 7 0.06
33 27 0.24
34 43 0.38
35 5 0.04
36 3 0.03
37 5 0.04
38 16 0.14
39 5 0.04
40 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (32 bp):
AAAGGAAAGGGAAGGAAGAAAAAAAAGAAAGA
Found at i:55053946 original size:19 final size:18
Alignment explanation
Indices: 55053906--55053956 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
55053896 AAAATATACA
**
55053906 TAATATTTTGGTATTTTT
1 TAATATTTTATTATTTTT
55053924 TAATATTTTATTATTTTT
1 TAATATTTTATTATTTTT
*
55053942 GTAATGTTTTATTAT
1 -TAATATTTTATTAT
55053957 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TAATATTTTATTATTTTT
Found at i:55054069 original size:28 final size:27
Alignment explanation
Indices: 55053992--55054222 Score: 230
Period size: 28 Copynumber: 8.7 Consensus size: 27
55053982 AAATAAAAAA
**
55053992 TTACCAAAATAT-TATAATTTTTTTTAT
1 TTACCAAAATATATA-AAAATTTTTTAT
*
55054019 TTACCGAAATATAT----ATTTTTTAT
1 TTACCAAAATATATAAAAATTTTTTAT
55054042 TTACCAAAATATTATAAAAATTTTTTAT
1 TTACCAAAATA-TATAAAAATTTTTTAT
* *
55054070 TTACCGAAATATAT--ATATTTTTTAT
1 TTACCAAAATATATAAAAATTTTTTAT
55054095 TTACCAAAATATTATAAAAATTTTTTAT
1 TTACCAAAATA-TATAAAAATTTTTTAT
* *
55054123 TTACCGAAATATAT---ATTTTTTTAT
1 TTACCAAAATATATAAAAATTTTTTAT
**
55054147 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATA-AAAATTTTTTAT
* **
55054175 TTACCAAAATATATATAGTTTTGTTTAT
1 TTACCAAAATATATAAAAATTT-TTTAT
55054203 TTACCAAAATATATCAAAAA
1 TTACCAAAATATAT-AAAAA
55054223 AAACTAAAAA
Statistics
Matches: 173, Mismatches: 16, Indels: 28
0.80 0.07 0.13
Matches are distributed among these distances:
23 18 0.10
24 25 0.14
25 20 0.12
26 3 0.02
27 22 0.13
28 83 0.48
29 2 0.01
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (27 bp):
TTACCAAAATATATAAAAATTTTTTAT
Found at i:55054087 original size:53 final size:53
Alignment explanation
Indices: 55053992--55054222 Score: 330
Period size: 53 Copynumber: 4.4 Consensus size: 53
55053982 AAATAAAAAA
**
55053992 TTACCAAAATATTAT-AATTTTTTTTATTTACCG-AA-ATATATATTTTTTAT
1 TTACCAAAATATTATAAAAATTTTTTATTTACCGAAATATATATATTTTTTAT
55054042 TTACCAAAATATTATAAAAATTTTTTATTTACCGAAATATATATATTTTTTAT
1 TTACCAAAATATTATAAAAATTTTTTATTTACCGAAATATATATATTTTTTAT
55054095 TTACCAAAATATTATAAAAATTTTTTATTTACCGAAATATATAT-TTTTTTAT
1 TTACCAAAATATTATAAAAATTTTTTATTTACCGAAATATATATATTTTTTAT
** *
55054147 TTACCAAAATA-TATATAATTTTTTTTATTTACCAAAATATATATAGTTTTGTTTAT
1 TTACCAAAATATTATA-AAAATTTTTTATTTACCGAAATATATATA--TTT-TTTAT
55054203 TTACCAAAATA-TATCAAAAA
1 TTACCAAAATATTAT-AAAAA
55054223 AAACTAAAAA
Statistics
Matches: 165, Mismatches: 7, Indels: 12
0.90 0.04 0.07
Matches are distributed among these distances:
50 15 0.09
51 20 0.12
52 46 0.28
53 59 0.36
55 3 0.02
56 21 0.13
57 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.02, T:0.49
Consensus pattern (53 bp):
TTACCAAAATATTATAAAAATTTTTTATTTACCGAAATATATATATTTTTTAT
Found at i:55057497 original size:16 final size:15
Alignment explanation
Indices: 55057473--55057506 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
55057463 ATCGGTCCAG
55057473 TTTTTTTTTCTATTT
1 TTTTTTTTTCTATTT
*
55057488 TTTTTGTTTTTTATTT
1 TTTTT-TTTTCTATTT
55057504 TTT
1 TTT
55057507 GGTATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.06, C:0.03, G:0.03, T:0.88
Consensus pattern (15 bp):
TTTTTTTTTCTATTT
Found at i:55057540 original size:28 final size:29
Alignment explanation
Indices: 55057509--55057565 Score: 107
Period size: 28 Copynumber: 2.0 Consensus size: 29
55057499 TATTTTTTGG
55057509 TATATTTTGGTAAAT-AAAAAAATTTATA
1 TATATTTTGGTAAATAAAAAAAATTTATA
55057537 TATATTTTGGTAAATAAAAAAAATTTATA
1 TATATTTTGGTAAATAAAAAAAATTTATA
55057566 GCATTTTGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (29 bp):
TATATTTTGGTAAATAAAAAAAATTTATA
Found at i:55057571 original size:28 final size:28
Alignment explanation
Indices: 55057512--55057577 Score: 98
Period size: 28 Copynumber: 2.4 Consensus size: 28
55057502 TTTTTGGTAT
*
55057512 ATTTTGGTAAATAAAAAAATTTATATAT
1 ATTTTGGTAAATAAAAAAATTTATATAC
*
55057540 ATTTTGGTAAATAAAAAAAATTTATA-GC
1 ATTTTGGTAAAT-AAAAAAATTTATATAC
55057568 ATTTTGGTAA
1 ATTTTGGTAA
55057578 TTTTTTATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
28 22 0.63
29 13 0.37
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.41
Consensus pattern (28 bp):
ATTTTGGTAAATAAAAAAATTTATATAC
Found at i:55067271 original size:22 final size:23
Alignment explanation
Indices: 55067243--55067290 Score: 80
Period size: 22 Copynumber: 2.1 Consensus size: 23
55067233 AAGTGTGTGT
*
55067243 AGGTTACTTGACTGTT-GGAGGC
1 AGGTTACTTGACTGTTAAGAGGC
55067265 AGGTTACTTGACTGTTAAGAGGC
1 AGGTTACTTGACTGTTAAGAGGC
55067288 AGG
1 AGG
55067291 AGATGTGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.29
Consensus pattern (23 bp):
AGGTTACTTGACTGTTAAGAGGC
Found at i:55081247 original size:14 final size:14
Alignment explanation
Indices: 55081203--55081248 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
55081193 TCTATGTCAA
*
55081203 TTTAGGATTAAGGG
1 TTTAGGGTTAAGGG
* * *
55081217 TTAAGGGTTTAGTG
1 TTTAGGGTTAAGGG
55081231 TTTAGGGTTAAGGG
1 TTTAGGGTTAAGGG
55081245 TTTA
1 TTTA
55081249 AAGTACTCTA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (14 bp):
TTTAGGGTTAAGGG
Found at i:55082426 original size:11 final size:11
Alignment explanation
Indices: 55082410--55082442 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55082400 TTCTTATTCA
55082410 TTTTATTTTTC
1 TTTTATTTTTC
55082421 TTTTATTTTT-
1 TTTTATTTTTC
*
55082431 GTTTATTTTTC
1 TTTTATTTTTC
55082442 T
1 T
55082443 GCAATCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:55083221 original size:3 final size:3
Alignment explanation
Indices: 55083213--55083259 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
55083203 GAATTAGTCC
* * *
55083213 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
55083260 CCTATTTATT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:55096229 original size:44 final size:43
Alignment explanation
Indices: 55096162--55096317 Score: 154
Period size: 44 Copynumber: 3.6 Consensus size: 43
55096152 GGAGAATTTC
* *
55096162 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA
1 AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA
* *
55096205 GAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
1 -AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA
** * * * *
55096249 CTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT-AAAATAA
1 AGATCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGA-CA
* *
55096292 AGGATCTTATCTCTCTGAGGTTACAG
1 A-GATCTTATCTCCCTGAGATTACAG
55096318 CAGAGTAGAT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
42 4 0.04
43 29 0.32
44 58 0.64
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.26
Consensus pattern (43 bp):
AGATCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGACA
Found at i:55096275 original size:87 final size:87
Alignment explanation
Indices: 55096168--55096329 Score: 218
Period size: 87 Copynumber: 1.9 Consensus size: 87
55096158 TTTCAGATCT
* * * *
55096168 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGC-CAGAGATCTTATCTCCCTGAGATTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAG-GATCTTATCTCCCTGAGATTACAGC
*
55096232 GGAGCAGATCGAAGACACTATCC
65 AGAGCAGATCGAAGACACTATCC
* * * *
55096255 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTCTGAGGTTACAGCA
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
*
55096320 GAGTAGATCG
66 GAGCAGATCG
55096330 CATCAAGTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
87 62 0.97
88 2 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAAGGATCTTATCTCCCTGAGATTACAGCA
GAGCAGATCGAAGACACTATCC
Found at i:55096280 original size:211 final size:214
Alignment explanation
Indices: 55095904--55096368 Score: 645
Period size: 211 Copynumber: 2.2 Consensus size: 214
55095894 GTTTATTATA
* * *
55095904 CAGGTCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAATAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
55095969 GTTACAGCGGAACAGATTGAAGCCAGAGGATCTTTCTCCCTGAGATTACAGCGGGCAGATCAAAG
66 GTTACAGCGGAACAGATTGAAGCCAGAGGATCTTTCTCCCTGAGATTACAGCGGGCAGATCAAAG
* * *
55096034 ATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGA-T-TAAAGGATCTTATCTCTCTGAAGT
131 ACACTAATCCTATCTCCCTGAGATTACAATGGAGCGGATTATAAAGGATCTTATCTCTCTGAAGT
*
55096097 TACAGTAGAGAAGAT-CAT
196 TACAGCAGAGAAGATCCAT
* **
55096115 CAGGTCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGATCTTATCTCCCTGAG
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAATAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
* * *
55096180 GTTACAGTGGAGCAGATTGAAGCCAGA-GATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGA
66 GTTACAGCGGAACAGATTGAAGCCAGAGGATCTT-TCTCCCTGAGATTACAGCGG-GCAGATCAA
*
55096244 AGACACT-ATCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAAGGATCTTATCTCTC
129 AGACACTAATCCTATCTCCCTGAGA-TTACAATGGAGCGGATT---ATAAAGGATCTTATCTCTC
* *
55096307 TGAGGTTACAGCAGAGTAGATCGCAT
190 TGAAGTTACAGCAGAGAAGATC-CAT
* * * *
55096333 CAAGTCTTATTTCCCTGAAGATGCAGTGGAATAGAC
1 CAGGTCTTATTTCCCTGAGGTTACAGTGGAATAGAC
55096369 TGAAAACAAC
Statistics
Matches: 223, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
210 7 0.03
211 132 0.59
212 14 0.06
216 36 0.16
218 34 0.15
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (214 bp):
CAGGTCTTATTTCCCTGAGGTTACAGTGGAATAGACCAAAGAATTTCAGATCTTATCTCCCTGAG
GTTACAGCGGAACAGATTGAAGCCAGAGGATCTTTCTCCCTGAGATTACAGCGGGCAGATCAAAG
ACACTAATCCTATCTCCCTGAGATTACAATGGAGCGGATTATAAAGGATCTTATCTCTCTGAAGT
TACAGCAGAGAAGATCCAT
Found at i:55097274 original size:11 final size:11
Alignment explanation
Indices: 55097258--55097290 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
55097248 TTCTTATTCA
55097258 TTTTATTTTTC
1 TTTTATTTTTC
55097269 TTTTATTTTT-
1 TTTTATTTTTC
*
55097279 GTTTATTTTTC
1 TTTTATTTTTC
55097290 T
1 T
55097291 GCAATCGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.09, C:0.06, G:0.03, T:0.82
Consensus pattern (11 bp):
TTTTATTTTTC
Found at i:55098071 original size:3 final size:3
Alignment explanation
Indices: 55098063--55098115 Score: 70
Period size: 3 Copynumber: 17.7 Consensus size: 3
55098053 GAATTAGTCC
* * * *
55098063 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55098111 TAT TA
1 TAT TA
55098116 CCTATTTATT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:55101516 original size:18 final size:18
Alignment explanation
Indices: 55101493--55101537 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
55101483 AAACAATTTT
55101493 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
55101511 TAAATTATATAACTTACA
1 TAAATTATATAACTTACA
*
55101529 TAACTTATA
1 TAAATTATA
55101538 AATATTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
TAAATTATATAACTTACA
Found at i:55101522 original size:9 final size:9
Alignment explanation
Indices: 55101497--55101537 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
55101487 AATTTTTAAA
55101497 TTATATAAC
1 TTATATAAC
* *
55101506 TTACATAAA
1 TTATATAAC
55101515 TTATATAAC
1 TTATATAAC
*
55101524 TTACATAAC
1 TTATATAAC
55101533 TTATA
1 TTATA
55101538 AATATTTATA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.41
Consensus pattern (9 bp):
TTATATAAC
Found at i:55101690 original size:23 final size:27
Alignment explanation
Indices: 55101636--55101705 Score: 85
Period size: 28 Copynumber: 2.7 Consensus size: 27
55101626 TCAATCATAT
55101636 CATAACTTATATATAAACATACATAATA
1 CATAACTTATATATAAACATACA-AATA
55101664 CATAACTTA-A-AT-AACATAC-AATA
1 CATAACTTATATATAAACATACAAATA
*
55101687 CATAAACTTACATATAAAC
1 CAT-AACTTATATATAAAC
55101706 TTGCATAACT
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
23 7 0.18
24 6 0.16
25 8 0.21
26 4 0.11
27 4 0.11
28 9 0.24
ACGTcount: A:0.54, C:0.17, G:0.00, T:0.29
Consensus pattern (27 bp):
CATAACTTATATATAAACATACAAATA
Found at i:55101722 original size:9 final size:9
Alignment explanation
Indices: 55101703--55101762 Score: 75
Period size: 9 Copynumber: 6.7 Consensus size: 9
55101693 CTTACATATA
*
55101703 AACTTGCAT
1 AACTTACAT
*
55101712 AACTTATAT
1 AACTTACAT
*
55101721 AAATTACAT
1 AACTTACAT
55101730 AACTTACAT
1 AACTTACAT
* *
55101739 AAATTATAT
1 AACTTACAT
55101748 AACTTACAT
1 AACTTACAT
55101757 AACTTA
1 AACTTA
55101763 TAAATATTTA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 42 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (9 bp):
AACTTACAT
Found at i:55101732 original size:18 final size:18
Alignment explanation
Indices: 55101685--55101758 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
55101675 TAACATACAA
55101685 TACATAAACTTACATATAAACT
1 TACAT-AACTTAC--ATAAA-T
* *
55101707 TGCATAACTTATATAAAT
1 TACATAACTTACATAAAT
55101725 TACATAACTTACATAAAT
1 TACATAACTTACATAAAT
*
55101743 TATATAACTTACATAA
1 TACATAACTTACATAA
55101759 CTTATAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 32 0.68
19 5 0.11
21 6 0.13
22 4 0.09
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.35
Consensus pattern (18 bp):
TACATAACTTACATAAAT
Found at i:55101739 original size:27 final size:27
Alignment explanation
Indices: 55101703--55101762 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
55101693 CTTACATATA
* *
55101703 AACTTGCATAACTTATATAAATTACAT
1 AACTTACATAAATTATATAAATTACAT
*
55101730 AACTTACATAAATTATATAACTTACAT
1 AACTTACATAAATTATATAAATTACAT
55101757 AACTTA
1 AACTTA
55101763 TAAATATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (27 bp):
AACTTACATAAATTATATAAATTACAT
Found at i:55101763 original size:18 final size:18
Alignment explanation
Indices: 55101710--55101764 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
55101700 ATAAACTTGC
* *
55101710 ATAACTTATATAAATTAC
1 ATAACTTACATAAATTAT
55101728 ATAACTTACATAAATTAT
1 ATAACTTACATAAATTAT
*
55101746 ATAACTTACATAACTTAT
1 ATAACTTACATAAATTAT
55101764 A
1 A
55101765 AATATTTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAACTTACATAAATTAT
Found at i:55101806 original size:17 final size:18
Alignment explanation
Indices: 55101786--55101819 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55101776 ACATTTTTAA
55101786 TATATATTTTT-AAAATC
1 TATATATTTTTCAAAATC
*
55101803 TATATTTTTTTCAAAAT
1 TATATATTTTTCAAAAT
55101820 TTATCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATTTTTCAAAATC
Found at i:55101892 original size:231 final size:229
Alignment explanation
Indices: 55101493--55101916 Score: 762
Period size: 231 Copynumber: 1.8 Consensus size: 229
55101483 AAACAATTTT
*
55101493 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
55101558 TATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCAAAT
66 TATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCAAAT
*
55101623 TTATCAATCATATCATAACTTATATATAAACATACAT-AA-TACATAACTTAAATAACATACAAT
131 TTATCAATCATATCATAACTTATATATAAACATACATAAATTAAATAACTTAAATAACATACAAT
55101686 ACATAAACTTACATATAAACTTGCATAACTTATA
196 ACATAAACTTACATATAAACTTGCATAACTTATA
55101720 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACA-TTTT-
55101785 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
64 -TATATA-TTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
* *
55101850 AAATTTATCAATCATATCATAACTTATATATAAACTTACATAAATTAAATAACTTAAATAACTTA
127 AAATTTATCAATCATATCATAACTTATATATAAACATACATAAATTAAATAACTTAAATAACATA
55101915 CA
192 CA
55101917 TAACTTAAAT
Statistics
Matches: 187, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
227 58 0.31
228 4 0.02
230 6 0.03
231 97 0.52
232 2 0.01
233 20 0.11
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (229 bp):
TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
TATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCAAAT
TTATCAATCATATCATAACTTATATATAAACATACATAAATTAAATAACTTAAATAACATACAAT
ACATAAACTTACATATAAACTTGCATAACTTATA
Found at i:55101906 original size:9 final size:9
Alignment explanation
Indices: 55101882--55102138 Score: 224
Period size: 9 Copynumber: 28.3 Consensus size: 9
55101872 CTTATATATA
55101882 AACTTACAT
1 AACTTACAT
* *
55101891 AAATTAAAT
1 AACTTACAT
*
55101900 AACTTAAAT
1 AACTTACAT
55101909 AACTTACAT
1 AACTTACAT
*
55101918 AACTTAAAT
1 AACTTACAT
55101927 AACTTACAT
1 AACTTACAT
55101936 AA--TACAT
1 AACTTACAT
*
55101943 AACCTT-CCT
1 AA-CTTACAT
*
55101952 AACTTAAAT
1 AACTTACAT
* *
55101961 TATTTACAT
1 AACTTACAT
55101970 AA--TACAT
1 AACTTACAT
55101977 AACTTAGTACAT
1 AAC-T--TACAT
55101989 AACTTACAT
1 AACTTACAT
* *
55101998 AATTTTTTC-T
1 AA--CTTACAT
55102008 AAATTGCTTACAT
1 -AA---CTTACAT
* *
55102021 AAATTATAT
1 AACTTACAT
55102030 AACTTACAT
1 AACTTACAT
55102039 AACTTACAT
1 AACTTACAT
55102048 AACTTACAT
1 AACTTACAT
* *
55102057 AAATTAAAT
1 AACTTACAT
55102066 AACTTACAT
1 AACTTACAT
55102075 AACTTACAT
1 AACTTACAT
*
55102084 AACTTAAAT
1 AACTTACAT
*
55102093 AGCTTACAT
1 AACTTACAT
55102102 AACTTACAT
1 AACTTACAT
55102111 AACTTACAT
1 AACTTACAT
55102120 AACTTACAT
1 AACTTACAT
55102129 AA--TACAT
1 AACTTACAT
55102136 AAC
1 AAC
55102139 CTTCCTTACA
Statistics
Matches: 203, Mismatches: 30, Indels: 31
0.77 0.11 0.12
Matches are distributed among these distances:
7 21 0.10
8 3 0.01
9 156 0.77
10 2 0.01
11 6 0.03
12 14 0.07
13 1 0.00
ACGTcount: A:0.46, C:0.17, G:0.01, T:0.35
Consensus pattern (9 bp):
AACTTACAT
Found at i:55101970 original size:231 final size:226
Alignment explanation
Indices: 55101493--55101971 Score: 705
Period size: 231 Copynumber: 2.1 Consensus size: 226
55101483 AAACAATTTT
*
55101493 TAAATTATATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTAAATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
55101558 TATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCAAAT
66 TATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCAAAT
*
55101623 TTATCAATCATATCATAACTTATATATAAACATACATAATACATAACTTAAATAACATACAATAC
131 TTATCAATCATATCATAACTTATATATAAACATACATAATAAATAACTTAAATAACATACAATAC
* * * *
55101688 ATAAACTTACATATAAACTTGCATAACTTATA
196 ATAAACTAACATACAAAC-TACATAACTTACA
*
55101720 TAAATTACATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
1 TAAATTAAATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACA-TTTT-
55101785 ATATATATTTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
64 -TATATA-TTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTC
* *
55101850 AAATTTATCAATCATATCATAACTTATATATAAACTTACATAAATTAAATAACTTAAATAACTTA
127 AAATTTATCAATCATATCATAACTTATATATAAACATACAT-AA-TAAATAACTTAAATAACATA
* * *
55101915 C-ATAACTTAAA-TAACTTACATAA-TACATAACCTT-CC
190 CAAT-ACATAAACTAACATACA-AACTACATAA-CTTACA
* * *
55101951 TAACTTAAATTATTTACATAA
1 TAAATTAAATAACTTACATAA
55101972 TACATAACTT
Statistics
Matches: 228, Mismatches: 15, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
227 58 0.25
228 4 0.02
230 6 0.03
231 120 0.53
232 13 0.06
233 27 0.12
ACGTcount: A:0.46, C:0.14, G:0.01, T:0.40
Consensus pattern (226 bp):
TAAATTAAATAACTTACATAAATTATATAACTTACATAACTTATAAATATTTATATACATTTTTA
TATATTTTAAAATCTATATTTTTTTCAAAATTTATCAATCATAGCATAACTTACATAACTCAAAT
TTATCAATCATATCATAACTTATATATAAACATACATAATAAATAACTTAAATAACATACAATAC
ATAAACTAACATACAAACTACATAACTTACA
Found at i:55103106 original size:21 final size:21
Alignment explanation
Indices: 55103081--55103146 Score: 89
Period size: 21 Copynumber: 3.1 Consensus size: 21
55103071 CAACTTAAAA
*
55103081 CAGAGGCAGCAGCGAGGGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
55103102 CAGAGGCTGCAGCGAGAGAAG
1 CAGAGGCAGCAGCGAGAGAAG
*
55103123 CAGAGACCA-CAGCGAGAGAAG
1 CAGAG-GCAGCAGCGAGAGAAG
55103144 CAG
1 CAG
55103147 CGAGAGAAGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 39 0.98
22 1 0.03
ACGTcount: A:0.36, C:0.21, G:0.41, T:0.02
Consensus pattern (21 bp):
CAGAGGCAGCAGCGAGAGAAG
Found at i:55103149 original size:12 final size:12
Alignment explanation
Indices: 55103110--55103158 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
55103100 AGCAGAGGCT
55103110 GCAGCGAGAGAA
1 GCAGCGAGAGAA
**
55103122 GCA--GAGACCA
1 GCAGCGAGAGAA
55103132 -CAGCGAGAGAA
1 GCAGCGAGAGAA
55103143 GCAGCGAGAGAA
1 GCAGCGAGAGAA
55103155 GCAG
1 GCAG
55103159 AGGTTCAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
9 2 0.07
10 5 0.17
11 5 0.17
12 18 0.60
ACGTcount: A:0.41, C:0.20, G:0.39, T:0.00
Consensus pattern (12 bp):
GCAGCGAGAGAA
Found at i:55103631 original size:43 final size:43
Alignment explanation
Indices: 55103584--55103667 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
55103574 TATAGTGGCG
55103584 TTTGTGAAAT-AAGCGCCGCGAAAGAACACTACTTTTAGCGGTA
1 TTTGT-AAATGAAGCGCCGCGAAAGAACACTACTTTTAGCGGTA
* * *
55103627 TTTGTAGATGAAGCGCCGCTAAAGAACATTACTTTTAGCGG
1 TTTGTAAATGAAGCGCCGCGAAAGAACACTACTTTTAGCGG
55103668 CGTTTTCTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 3 0.08
43 34 0.92
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (43 bp):
TTTGTAAATGAAGCGCCGCGAAAGAACACTACTTTTAGCGGTA
Found at i:55103739 original size:43 final size:43
Alignment explanation
Indices: 55103637--55103760 Score: 189
Period size: 43 Copynumber: 2.9 Consensus size: 43
55103627 TTTGTAGATG
* * *
55103637 AAGCGCCGCTAAAGAACATTA-CTTTTAGCGGCG-TTTTCTCCC
1 AAGCGCCGCTAAAGAACATGATC-ATTAGCGGCGTTTTTTTCCC
*
55103679 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCC
55103722 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTT
1 AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTT
55103761 GTGGCGTTTC
Statistics
Matches: 76, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
42 29 0.38
43 47 0.62
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (43 bp):
AAGCGCCGCTAAAGAACATGATCATTAGCGGCGTTTTTTTCCC
Found at i:55103833 original size:22 final size:22
Alignment explanation
Indices: 55103802--55103845 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55103792 TAGTGGCGTT
* *
55103802 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAACGCCGCTAAAAACCTA
55103824 AAAAAACGCCGCTAAAAACCTA
1 AAAAAACGCCGCTAAAAACCTA
55103846 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.27, G:0.14, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAAACCTA
Found at i:55105650 original size:3 final size:3
Alignment explanation
Indices: 55105636--55105671 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
55105626 GAGAGAAAGG
*
55105636 AGA AGG AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
55105672 AGAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:55105660 original size:14 final size:14
Alignment explanation
Indices: 55105636--55105675 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
55105626 GAGAGAAAGG
55105636 AGAAGGAGAAGAAGA
1 AGAA-GAGAAGAAGA
55105651 AGAAGAGAAGAAGA
1 AGAAGAGAAGAAGA
55105665 AGAAGA-AAGAA
1 AGAAGAGAAGAA
55105676 AAAAAAAGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 5 0.20
14 16 0.64
15 4 0.16
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (14 bp):
AGAAGAGAAGAAGA
Found at i:55105911 original size:19 final size:19
Alignment explanation
Indices: 55105864--55105920 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
55105854 TTTAACTTTT
* *
55105864 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
55105884 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
*
55105903 TTGTATGAATACTGTAAT
1 TTGTATGAATATTGTAAT
55105921 TATTTTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:55105926 original size:83 final size:84
Alignment explanation
Indices: 55105874--55106034 Score: 190
Period size: 83 Copynumber: 2.0 Consensus size: 84
55105864 TTGTATGAAT
* * * *
55105874 ATTA-TAATTTTTT-TATGAATATTGTAATGTTGTATGAATACTGT-AATTATTTTATAATTAA-
1 ATTAGTAATTTTTTGTATGAATATTATAATGTTGTATGAATACTATAAATTATTTTGT-ATGAAT
*
55105935 ATTTGTATTTATAGTTTTGG
65 ATTTGTATTTATAGTTATGG
* *
55105955 ATTAGTAATTTTTTGTATGAATATTATAATTTTGTATGAATATTATAAATT-TTTTGTATGAATA
1 ATTAGTAATTTTTTGTATGAATATTATAATGTTGTATGAATACTATAAATTATTTTGTATGAATA
55106019 -TTGTAATATTATAGTT
66 TTTGT-AT-TTATAGTT
55106035 TTGTATGAAT
Statistics
Matches: 68, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
81 4 0.06
82 17 0.25
83 35 0.51
84 12 0.18
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.54
Consensus pattern (84 bp):
ATTAGTAATTTTTTGTATGAATATTATAATGTTGTATGAATACTATAAATTATTTTGTATGAATA
TTTGTATTTATAGTTATGG
Found at i:55105989 original size:19 final size:19
Alignment explanation
Indices: 55105965--55106025 Score: 86
Period size: 19 Copynumber: 3.1 Consensus size: 19
55105955 ATTAGTAATT
55105965 TTTTGTATGAATATTATAA
1 TTTTGTATGAATATTATAA
55105984 TTTTGTATGAATATTATAAA
1 TTTTGTATGAATATTAT-AA
*
55106004 TTTTTTGTATGAATATTGTAA
1 --TTTTGTATGAATATTATAA
55106025 T
1 T
55106026 ATTATAGTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 18 0.47
20 2 0.05
21 2 0.05
22 16 0.42
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (19 bp):
TTTTGTATGAATATTATAA
Found at i:55106027 original size:49 final size:50
Alignment explanation
Indices: 55105984--55106233 Score: 288
Period size: 49 Copynumber: 5.0 Consensus size: 50
55105974 AATATTATAA
*
55105984 TTTTGTATGAATATTATAA-A-T-T-TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGTAATATTGTATTTTGTATGAATATTGTAATATT-T
*
55106031 AGTTTTGTATGAATATTGTAATTTTGTAATTTTGTATGAATA-T-T-ATATTT
1 --TTTTGTATGAATATTGTAATATTGT-ATTTTGTATGAATATTGTAATATTT
* *
55106081 TTTTGTATGAATATTGTAATATTATAATTTTGTATGAATATTG-CA-ATTT
1 TTTTGTATGAATATTGTAATATTGT-ATTTTGTATGAATATTGTAATATTT
55106130 TTTTGTATGAATATTGTAATATTGTAATTTTGTATGAATATTGT-A-ATTT
1 TTTTGTATGAATATTGTAATATTGT-ATTTTGTATGAATATTGTAATATTT
*
55106179 TTTTGTATGAATATTGTAATATTGTAATTTTTTGTATGAATATTATAATTATTT
1 TTTTGTATGAATATTGTAATATTGT-A--TTTTGTATGAATATTGTAA-TATTT
55106233 T
1 T
55106234 ATAATTAATT
Statistics
Matches: 181, Mismatches: 6, Indels: 23
0.86 0.03 0.11
Matches are distributed among these distances:
48 38 0.21
49 97 0.54
50 2 0.01
51 22 0.12
52 3 0.02
53 1 0.01
54 18 0.10
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (50 bp):
TTTTGTATGAATATTGTAATATTGTATTTTGTATGAATATTGTAATATTT
Found at i:55106041 original size:27 final size:25
Alignment explanation
Indices: 55105974--55106232 Score: 256
Period size: 27 Copynumber: 10.3 Consensus size: 25
55105964 TTTTTGTATG
*
55105974 AATATTATAATTTTGTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
55106001 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
55106023 AATATTATAGTTTTGTATGAATATTGT
1 AATATT-TA-TTTTGTATGAATATTGT
*
55106050 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
55106075 -ATATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
55106098 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
55106124 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
55106147 AATATTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
55106174 -A-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
55106196 AATATTGTAATTTTTTGTATGAATATTAT
1 AATATT-T-A--TTTTGTATGAATATTGT
55106225 AATTATTT
1 AA-TATTT
55106233 TATAATTAAT
Statistics
Matches: 200, Mismatches: 7, Indels: 48
0.78 0.03 0.19
Matches are distributed among these distances:
21 13 0.06
22 52 0.26
23 5 0.03
24 19 0.09
25 12 0.06
26 4 0.02
27 71 0.35
28 1 0.00
29 19 0.09
30 4 0.02
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:55106122 original size:19 final size:19
Alignment explanation
Indices: 55106098--55106155 Score: 53
Period size: 22 Copynumber: 2.9 Consensus size: 19
55106088 TGAATATTGT
55106098 AATATTATAATTTTGTATG
1 AATATTATAATTTTGTATG
**
55106117 AATATTGCAATTTTTTTGTATG
1 AATATT---ATAATTTTGTATG
* *
55106139 AATATTGTAATATTGTA
1 AATATTATAATTTTGTA
55106156 ATTTTGTATG
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
19 13 0.43
22 17 0.57
ACGTcount: A:0.34, C:0.02, G:0.12, T:0.52
Consensus pattern (19 bp):
AATATTATAATTTTGTATG
Found at i:55106152 original size:8 final size:8
Alignment explanation
Indices: 55106139--55106206 Score: 50
Period size: 8 Copynumber: 8.4 Consensus size: 8
55106129 TTTTTGTATG
55106139 AATATTGT
1 AATATTGT
55106147 AATATTGT
1 AATATTGT
*
55106155 AATTTTGTAT
1 AATATTG--T
55106165 GAATATTGT
1 -AATATTGT
* *
55106174 AATTTTTT
1 AATATTGT
**
55106182 TGTA-TG-
1 AATATTGT
55106188 AATATTGT
1 AATATTGT
55106196 AATATTGT
1 AATATTGT
55106204 AAT
1 AAT
55106207 TTTTTGTATG
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
6 2 0.04
7 3 0.07
8 32 0.71
9 1 0.02
10 1 0.02
11 6 0.13
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (8 bp):
AATATTGT
Found at i:55106302 original size:60 final size:60
Alignment explanation
Indices: 55106224--55106342 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
55106214 ATGAATATTA
* * * * * *
55106224 TAATTATTTTATAATTAATTTGTTAGCAATTTGGGATTATGTTATAAATTTTTGTGTTTG
1 TAATTATTTTAAAATTAATTTATTAGCAATTTAGGATTAAGCTATAAATTGTTGTGTTTG
* *
55106284 TAATTA-TTTAAAATTTAATTTATTAGTAATTTAGGATTAAGCTATAAGTTGTTGTGTTT
1 TAATTATTTTAAAA-TTAATTTATTAGCAATTTAGGATTAAGCTATAAATTGTTGTGTTT
55106343 AGTTTAGTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
59 6 0.12
60 44 0.88
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.53
Consensus pattern (60 bp):
TAATTATTTTAAAATTAATTTATTAGCAATTTAGGATTAAGCTATAAATTGTTGTGTTTG
Found at i:55106421 original size:38 final size:38
Alignment explanation
Indices: 55106376--55106456 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 38
55106366 CATATAAAGT
55106376 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
*
55106414 TTAT-AAAAAATTAAAAATCATTTTATTAAAAGTTTAA
1 TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
55106451 TTATAA
1 TTATAA
55106457 CTGACTTTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
37 36 0.88
38 5 0.12
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (38 bp):
TTATAAAAAAATTAAAAATCATTTCATTAAAAGTTTAA
Found at i:55106534 original size:15 final size:15
Alignment explanation
Indices: 55106493--55106534 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
55106483 GTTAAATCAT
*
55106493 TTAATTTTTATATAA
1 TTAAATTTTATATAA
*
55106508 TGTAACTTTTATATAA
1 T-TAAATTTTATATAA
55106524 TTAAATTTTAT
1 TTAAATTTTAT
55106535 TTGATTTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (15 bp):
TTAAATTTTATATAA
Found at i:55111456 original size:27 final size:27
Alignment explanation
Indices: 55111418--55111493 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
55111408 AAAATAACAG
*
55111418 CATTGGCGCCTCTCAGA-ATGGCACCAC
1 CATTGGCGCCTCCCAGATA-GGCACCAC
*
55111445 CATTGGCGCCTCCCAGGTAGGCACCAC
1 CATTGGCGCCTCCCAGATAGGCACCAC
*
55111472 CATTGGCGCTTCCCAGATAGGC
1 CATTGGCGCCTCCCAGATAGGC
55111494 GCCAATACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 43 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.25, T:0.18
Consensus pattern (27 bp):
CATTGGCGCCTCCCAGATAGGCACCAC
Found at i:55112466 original size:90 final size:90
Alignment explanation
Indices: 55112311--55112487 Score: 248
Period size: 90 Copynumber: 2.0 Consensus size: 90
55112301 TCTTAGTTGT
* * * * * *
55112311 TTATAATTGAGGAGACTTGTATAGTTGATGCATTGATTCGTGAGCACTTATTTTGTTCATTGAGG
1 TTATAATTAAGGACACTTGTATAGTTGATGCACTGATTCGTGAACACTTATTTTATTCATCGAGG
*
55112376 AGCATTTCTTTGGAGTGCATTGTGC
66 AACATTTCTTTGGAGTGCATTGTGC
*
55112401 TTATAATTAAGGACACTTGTATAGTTGATGCACTGA-TCTTCGAACACTTATTTTATTCATCGAG
1 TTATAATTAAGGACACTTGTATAGTTGATGCACTGATTCGT-GAACACTTATTTTATTCATCGAG
* *
55112465 GAACATTTTTTTGGATTGCATTG
65 GAACATTTCTTTGGAGTGCATTG
55112488 AATGTAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
89 3 0.04
90 73 0.96
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.41
Consensus pattern (90 bp):
TTATAATTAAGGACACTTGTATAGTTGATGCACTGATTCGTGAACACTTATTTTATTCATCGAGG
AACATTTCTTTGGAGTGCATTGTGC
Found at i:55121170 original size:103 final size:104
Alignment explanation
Indices: 55121002--55121362 Score: 530
Period size: 104 Copynumber: 3.5 Consensus size: 104
55120992 GGTGGATTCC
* * *
55121002 GCACTTAGCAACCACTAATGAATCGGGGAATCAGCACACAGCAACCCCTTGGGGGAATCAGCACT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCAGCACT
*
55121067 TAGCAACCCCCTTT-ACATTTAGAAATACGGTGGGATCA
66 TAGCAACCCCCTTTCACATTTAAAAATACGGTGGGATCA
* * **
55121105 GCAGTTAGCAACCACCAAT-AAGTAGGGGAATCAACACTTAGCAACCCCTCGGGGGAATCAGCAC
1 GCACTTAGCAACCACCAATGAA-TAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCAGCAC
* * *
55121169 TTAGCAACCCCCTTTCACATTTAAAAATAGGGTGGAATTA
65 TTAGCAACCCCCTTTCACATTTAAAAATACGGTGGGATCA
* **
55121209 GCACTTAGCAACCACC-ATTAAGTAGGGGAATCAGCACTTAGCAACCCCTCGGGGGAATCAGCAC
1 GCACTTAGCAACCACCAATGAA-TAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCAGCAC
55121273 TTAGCAACCCCCTTTCACATTTAAAAAATACGGTGGGATCA
65 TTAGCAACCCCCTTTCACATTT-AAAAATACGGTGGGATCA
* *
55121314 GCACTTAGCAACCACCGATGAATCGGGGAATCAGCACACAGCAACCCCT
1 GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCT
55121363 TTATATGCAA
Statistics
Matches: 233, Mismatches: 20, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
102 2 0.01
103 71 0.30
104 101 0.43
105 55 0.24
106 4 0.02
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (104 bp):
GCACTTAGCAACCACCAATGAATAGGGGAATCAGCACACAGCAACCCCTCGGGGGAATCAGCACT
TAGCAACCCCCTTTCACATTTAAAAATACGGTGGGATCA
Found at i:55121245 original size:33 final size:27
Alignment explanation
Indices: 55121196--55121283 Score: 95
Period size: 27 Copynumber: 3.0 Consensus size: 27
55121186 CATTTAAAAA
*
55121196 TAGGGTGGAATTAGCACTTAGCAACCACC
1 TAGGG-GGAATCAGCACTTAGCAACC-CC
55121225 ATTAAGTAGGGGAATCAGCACTTAGCAACCCC
1 --T-AG--GGGGAATCAGCACTTAGCAACCCC
*
55121257 TCGGGGGAATCAGCACTTAGCAACCCC
1 TAGGGGGAATCAGCACTTAGCAACCCC
55121284 CTTTCACATT
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
27 24 0.46
29 1 0.02
30 1 0.02
31 1 0.02
32 4 0.08
33 19 0.37
34 2 0.04
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (27 bp):
TAGGGGGAATCAGCACTTAGCAACCCC
Found at i:55128716 original size:33 final size:33
Alignment explanation
Indices: 55128674--55128756 Score: 139
Period size: 33 Copynumber: 2.5 Consensus size: 33
55128664 ATATGGTGGG
* *
55128674 ATCAGCACTTAGCAACCACCAATAAGTAGGGGA
1 ATCAGCACTTAGCAACCACCAATAAGTAAGGAA
*
55128707 ATCAGCACTTAGCAACCACCATTAAGTAAGGAA
1 ATCAGCACTTAGCAACCACCAATAAGTAAGGAA
55128740 ATCAGCACTTAGCAACC
1 ATCAGCACTTAGCAACC
55128757 CCCTTTCACA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.40, C:0.27, G:0.17, T:0.17
Consensus pattern (33 bp):
ATCAGCACTTAGCAACCACCAATAAGTAAGGAA
Found at i:55128791 original size:111 final size:104
Alignment explanation
Indices: 55128575--55128836 Score: 357
Period size: 111 Copynumber: 2.5 Consensus size: 104
55128565 GGTGGATTCC
* *
55128575 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAA-CCCATTGGGGGAATCAGCAC
1 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCATTGAGGAAATCAGCAC
* *
55128639 TTAGAAACCCCCTTTACATTTAGAAATATGGTGGGATCA
66 TTAGAAACCCCCTTTACATTTAAAAATACGGTGGGATCA
* **
55128678 GCACTTAGCAACCACCAAT-AAGTAGGGGAATCAGCACTTAGCAACCACCATTAAGTAAGGAAAT
1 GCACTTAGCAACCACCAATGAA-TCGGGGAATCAGCACACAGCAACC-CCATT--G--AGGAAAT
*
55128742 CAGCACTTAGCAACCCCCTTTCACATTTAAAAAATACGGTGGGATCA
60 CAGCACTTAGAAACCCCCTTT-ACATTT-AAAAATACGGTGGGATCA
*
55128789 GCACTTAGCAACCACCGATGAATCGGGGAATCAGCACACAGCAACCCC
1 GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCC
55128837 TTTATATGCA
Statistics
Matches: 137, Mismatches: 12, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
102 2 0.01
103 38 0.28
104 1 0.01
105 5 0.04
107 1 0.01
109 25 0.18
110 8 0.06
111 55 0.40
112 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.18
Consensus pattern (104 bp):
GCACTTAGCAACCACCAATGAATCGGGGAATCAGCACACAGCAACCCCATTGAGGAAATCAGCAC
TTAGAAACCCCCTTTACATTTAAAAATACGGTGGGATCA
Found at i:55130764 original size:34 final size:34
Alignment explanation
Indices: 55130726--55130791 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
55130716 CACAAATTAA
55130726 ATAAAAATTGT-TCTATTTATATTTCAT-TATATAT
1 ATAAAAATT-TATCTATTTATATTT-ATCTATATAT
* *
55130760 ATAAATATTTATTTATTTATATTTATCTATAT
1 ATAAAAATTTATCTATTTATATTTATCTATAT
55130792 TATTTTGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 3 0.11
34 25 0.89
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (34 bp):
ATAAAAATTTATCTATTTATATTTATCTATATAT
Found at i:55131658 original size:45 final size:45
Alignment explanation
Indices: 55131585--55131678 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
55131575 AAGAGTCCTA
* *
55131585 GTAAACGAGGATTGCATTGGTGTGATTGGGAATCTCTATGTGGAT
1 GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
55131630 GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
1 GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
55131675 -TAAA
1 GTAAA
55131679 GGAAAATGGT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 4 0.09
45 43 0.91
ACGTcount: A:0.29, C:0.09, G:0.30, T:0.33
Consensus pattern (45 bp):
GTAAACGAGGATTGCATTGATGTAATTGGGAATCTCTATGTGGAT
Found at i:55135106 original size:42 final size:42
Alignment explanation
Indices: 55135021--55135112 Score: 112
Period size: 42 Copynumber: 2.2 Consensus size: 42
55135011 GTTTTTCAAA
* * ** * * **
55135021 AGTTACACGGCCTATCACATGGGCGTGTGAGGCCATTTCGAG
1 AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
55135063 AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
1 AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
55135105 AGTTACAC
1 AGTTACAC
55135113 AGGCATGGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (42 bp):
AGTTACACGGCCTAGCACACGGGCGTGTGACACAAGTGAGAG
Found at i:55141298 original size:22 final size:21
Alignment explanation
Indices: 55141238--55141298 Score: 52
Period size: 26 Copynumber: 2.6 Consensus size: 21
55141228 TCTAAAGAAA
55141238 AAAATCAAAATAAATCTTGATT
1 AAAAT-AAAATAAATCTTGATT
55141260 AAAATAAATAGGTTAAAT-TATGGATT
1 AAAATAAA-A---TAAATCT-T-GATT
55141286 AAAATAAAATAAA
1 AAAATAAAATAAA
55141299 AACGGAATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
21 3 0.09
22 10 0.30
24 1 0.03
25 7 0.21
26 12 0.36
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (21 bp):
AAAATAAAATAAATCTTGATT
Found at i:55142926 original size:131 final size:131
Alignment explanation
Indices: 55142686--55143138 Score: 672
Period size: 131 Copynumber: 3.5 Consensus size: 131
55142676 AGTTTTAGGG
* * * * ** * * *
55142686 AGATAAGATTCACCATATTCGATCCGCTCTGCTACTGCTTAGGGAGATAGGATCTACAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTACAATTTCCA
* * * * * * *
55142751 ACCTATTCCACTGCTGGTTAGAGATATAGGACTTGTGACCTAAATCTATTTCCCTACTCCCGGGG
66 ACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGG
55142816 A
131 A
* * * *
55142817 AGATAAGATTCGCCGTCTTCGATCTGCTCCATTATTGCTTAGGGAGATAAGATCTACATTTTCTA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTACAATTTCCA
*
55142882 ACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTAGGG
66 ACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGG
55142947 A
131 A
*
55142948 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTGCAATTTCCA
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTACAATTTCCA
*
55143013 ACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCTTGGGG
66 ACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGG
55143078 A
131 A
* * *
55143079 AGATAAGATTCGCCGTCTTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTGCAAT
1 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTACAAT
55143139 CTTTACTGAT
Statistics
Matches: 294, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
131 294 1.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (131 bp):
AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGGAGACAAGATCTACAATTTCCA
ACCTATTCCACTGCTGGTCAGGGACATAGGACTTGTGGCTTAAATCTGTTTCCCTACTCCTGGGG
A
Found at i:55156390 original size:14 final size:14
Alignment explanation
Indices: 55156371--55156403 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
55156361 TGGTGCTTTT
55156371 TGATTTTTGTATTC
1 TGATTTTTGTATTC
55156385 TGATTTTTGTATTC
1 TGATTTTTGTATTC
55156399 TGATT
1 TGATT
55156404 GCGTATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (14 bp):
TGATTTTTGTATTC
Found at i:55158619 original size:17 final size:17
Alignment explanation
Indices: 55158587--55158621 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55158577 AAGATATAAT
55158587 TCAACAACTTAATTAAC
1 TCAACAACTTAATTAAC
55158604 TCAA-AACTTAACTTAAC
1 TCAACAACTTAA-TTAAC
55158621 T
1 T
55158622 AACTCAAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (17 bp):
TCAACAACTTAATTAAC
Found at i:55159441 original size:3 final size:3
Alignment explanation
Indices: 55159433--55159494 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
55159423 AAAGCTTCTT
55159433 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
55159481 TTA TTA TTC TTA TT
1 TTA TTA TTA TTA TT
55159495 TTGCATTCTT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:55159886 original size:4 final size:4
Alignment explanation
Indices: 55159877--55159914 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
55159867 ACAAAACGGC
* *
55159877 TACA TACA TACA TACA TGCA TGCA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TA
55159915 TATATATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:55160698 original size:3 final size:3
Alignment explanation
Indices: 55160690--55160725 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
55160680 TTTGTCACAT
55160690 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
55160726 AATATGGTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55163246 original size:4 final size:4
Alignment explanation
Indices: 55163239--55163286 Score: 87
Period size: 4 Copynumber: 12.0 Consensus size: 4
55163229 ATATGCATGC
*
55163239 CTAT CTAT TTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
1 CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT CTAT
55163287 ATAGTAATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.25, C:0.23, G:0.00, T:0.52
Consensus pattern (4 bp):
CTAT
Found at i:55165692 original size:13 final size:13
Alignment explanation
Indices: 55165674--55165698 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55165664 TGATTATGAA
55165674 ACTAACAATAAAT
1 ACTAACAATAAAT
55165687 ACTAACAATAAA
1 ACTAACAATAAA
55165699 CATTTGGTAC
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:0.64, C:0.16, G:0.00, T:0.20
Consensus pattern (13 bp):
ACTAACAATAAAT
Found at i:55168815 original size:22 final size:21
Alignment explanation
Indices: 55168767--55168819 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
55168757 TTTTTTGTCA
* * *
55168767 AAAAAATATTTTTTTAAATGT
1 AAAAAATATTATTTCAAATCT
55168788 ATAAAAATATATATTTCAAATCT
1 A-AAAAATAT-TATTTCAAATCT
55168811 -AAAAATATT
1 AAAAAATATT
55168820 TTAAAAAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 1 0.04
21 9 0.33
22 8 0.30
23 9 0.33
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
AAAAAATATTATTTCAAATCT
Found at i:55173685 original size:9 final size:9
Alignment explanation
Indices: 55173673--55173697 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
55173663 ACTTAATGGA
55173673 TTTATTTTT
1 TTTATTTTT
55173682 TTTATTTTT
1 TTTATTTTT
55173691 TTTATTT
1 TTTATTT
55173698 GGTTTTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:55175324 original size:56 final size:55
Alignment explanation
Indices: 55175207--55175330 Score: 176
Period size: 56 Copynumber: 2.2 Consensus size: 55
55175197 TTGACTTTCG
* *
55175207 ACACTAAGTGTGCGAATTTAATTGTAAAGCACTAAGTGTGCGAGTTTAATTGTAA
1 ACACTAAGTGTGCGAATTTAATGGCAAAGCACTAAGTGTGCGAGTTTAATTGTAA
* * * *
55175262 AGCACTAAGTGTGCGAGTTTAATGGCAAAGCACTAAGTGTGCGAGTTTGATTATTGA
1 A-CACTAAGTGTGCGAATTTAATGGCAAAGCACTAAGTGTGCGAGTTTAATT-GTAA
55175319 ACACTAAGTGTG
1 ACACTAAGTGTG
55175331 AGAACTTATT
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
55 1 0.02
56 57 0.93
57 3 0.05
ACGTcount: A:0.32, C:0.12, G:0.25, T:0.31
Consensus pattern (55 bp):
ACACTAAGTGTGCGAATTTAATGGCAAAGCACTAAGTGTGCGAGTTTAATTGTAA
Found at i:55175330 original size:28 final size:28
Alignment explanation
Indices: 55175208--55175309 Score: 177
Period size: 28 Copynumber: 3.6 Consensus size: 28
55175198 TGACTTTCGA
*
55175208 CACTAAGTGTGCGAATTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
55175236 CACTAAGTGTGCGAGTTTAATTGTAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
* *
55175264 CACTAAGTGTGCGAGTTTAATGGCAAAG
1 CACTAAGTGTGCGAGTTTAATTGTAAAG
55175292 CACTAAGTGTGCGAGTTT
1 CACTAAGTGTGCGAGTTT
55175310 GATTATTGAA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 71 1.00
ACGTcount: A:0.31, C:0.13, G:0.25, T:0.30
Consensus pattern (28 bp):
CACTAAGTGTGCGAGTTTAATTGTAAAG
Found at i:55176095 original size:23 final size:23
Alignment explanation
Indices: 55176030--55176328 Score: 218
Period size: 23 Copynumber: 12.9 Consensus size: 23
55176020 TAAAATTGGA
* *
55176030 ATATATATGCTGCCCAATTTTGGT
1 ATATACATGCTGTCCAATTTT-GT
*
55176054 GA-ATAAATGCTGTCCAATTTTGT
1 -ATATACATGCTGTCCAATTTTGT
* *
55176077 ATATACATGCCGTCAAATTTTGT
1 ATATACATGCTGTCCAATTTTGT
* *
55176100 GTATA-AGTGCTGTCCAA-ATTGCT
1 ATATACA-TGCTGTCCAATTTTG-T
* * **
55176123 ACATATATGCTACCCAATTTTGGT
1 ATATACATGCTGTCCAATTTT-GT
* *
55176147 GA-ATAAATTCTGTCCAATTTTGT
1 -ATATACATGCTGTCCAATTTTGT
55176170 ATATACATGCTGTCCAATTTTGT
1 ATATACATGCTGTCCAATTTTGT
* * *
55176193 GTATA-AGTGCTGTCCAAATTGGT
1 ATATACA-TGCTGTCCAATTTTGT
* *
55176216 ATATATATGCTGCCCAATTTTGGT
1 ATATACATGCTGTCCAATTTT-GT
* *
55176240 GA-ATAAATGTTGTCCAATTTTGT
1 -ATATACATGCTGTCCAATTTTGT
*
55176263 ATATACATGCTGTCAAATTTTGT
1 ATATACATGCTGTCCAATTTTGT
* * *
55176286 GTATA-AGTGCTGTCCAAATTGGT
1 ATATACA-TGCTGTCCAATTTTGT
*
55176309 ATATACGTGCTG-CTCAATTT
1 ATATACATGCTGTC-CAATTT
55176329 CTGATGTATA
Statistics
Matches: 218, Mismatches: 40, Indels: 34
0.75 0.14 0.12
Matches are distributed among these distances:
22 10 0.05
23 149 0.68
24 55 0.25
25 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (23 bp):
ATATACATGCTGTCCAATTTTGT
Found at i:55176139 original size:93 final size:93
Alignment explanation
Indices: 55176032--55176350 Score: 487
Period size: 93 Copynumber: 3.4 Consensus size: 93
55176022 AAATTGGAAT
*
55176032 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCCGTCAAATTT
1 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
55176097 TGTGTATAAGTGCTGTCCAAATTGCTAC
66 TGTGTATAAGTGCTGTCCAAATTGCTAC
* * *
55176125 ATATATGCTACCCAATTTTGGTGAATAAATTCTGTCCAATTTTGTATATACATGCTGTCCAATTT
1 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
* *
55176190 TGTGTATAAGTGCTGTCCAAATTGGTAT
66 TGTGTATAAGTGCTGTCCAAATTGCTAC
*
55176218 ATATATGCTGCCCAATTTTGGTGAATAAATGTTGTCCAATTTTGTATATACATGCTGTCAAATTT
1 ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
* *
55176283 TGTGTATAAGTGCTGTCCAAATTGGTAT
66 TGTGTATAAGTGCTGTCCAAATTGCTAC
** * * *
55176311 ATACGTGCTGCTCAATTTCTGATGTATAAGA-GCTGTCCAA
1 ATATATGCTGCCCAATTT-TGGTGAATAA-ATGCTGTCCAA
55176351 ACAGGGTAGA
Statistics
Matches: 208, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
93 191 0.92
94 16 0.08
95 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.39
Consensus pattern (93 bp):
ATATATGCTGCCCAATTTTGGTGAATAAATGCTGTCCAATTTTGTATATACATGCTGTCAAATTT
TGTGTATAAGTGCTGTCCAAATTGCTAC
Found at i:55183758 original size:9 final size:9
Alignment explanation
Indices: 55183744--55183819 Score: 68
Period size: 9 Copynumber: 8.7 Consensus size: 9
55183734 AATTAAACCA
55183744 TTATGTAAG
1 TTATGTAAG
*
55183753 TTATGTAAT
1 TTATGTAAG
*
55183762 TTATGTAAT
1 TTATGTAAG
*
55183771 TTATGATATG
1 TTATG-TAAG
* * *
55183781 ATATAT-AT
1 TTATGTAAG
55183789 TTATGT-A-
1 TTATGTAAG
55183796 TTATGTAAG
1 TTATGTAAG
55183805 TTATGTAAG
1 TTATGTAAG
55183814 TTATGT
1 TTATGT
55183820 TCTAAAGTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 6
0.79 0.13 0.09
Matches are distributed among these distances:
7 6 0.11
8 6 0.11
9 38 0.69
10 5 0.09
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55186189 original size:22 final size:22
Alignment explanation
Indices: 55186146--55186189 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
55186136 ATATTTTGAT
*
55186146 TAAATTAATCAAAATTTACAAA
1 TAAATTAATCAAAAATTACAAA
*
55186168 TAAA-TAATCCAAAAATTGCAAA
1 TAAATTAAT-CAAAAATTACAAA
55186190 CAACAGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.59, C:0.11, G:0.02, T:0.27
Consensus pattern (22 bp):
TAAATTAATCAAAAATTACAAA
Found at i:55187822 original size:41 final size:41
Alignment explanation
Indices: 55187755--55188149 Score: 562
Period size: 41 Copynumber: 9.7 Consensus size: 41
55187745 CCATTCGGGG
* * *
55187755 CTTTAGTGGCGTTTTTTAGAAAAGCGCCGCTAATGCTCAGGGT
1 CTTTAGCGGCG-TTTTTGGAAAAGCGCCGCTAATGCTC-TGGT
*
55187798 -TTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTTTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
**
55187838 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* * *
55187879 CTTTAGTGGCGTTTTTGGAAATGCGCCGTTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
** *
55187920 CTTTAGCGGCGTTTTTGGGGAAGCGCCGCTAATCCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
55187961 CTTTAGCGGCGTTTTTGGAAAAGCACCGCTAGTGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* **
55188002 CTTTAGTGGCGTTTTTGGGGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
* *
55188043 CTTTAGCGGCGTTTTTGG-GAAGCG-CGCTAATGCTCTAGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
55188082 CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGCTCTGGT
1 CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
*
55188123 CTTTAGCGGCGTTTTTGGGAAAGCGCC
1 CTTTAGCGGCGTTTTTGGAAAAGCGCC
55188150 ACAAAAACAT
Statistics
Matches: 316, Mismatches: 33, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
39 32 0.10
40 15 0.05
41 260 0.82
42 9 0.03
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGCTCTGGT
Found at i:55188544 original size:22 final size:23
Alignment explanation
Indices: 55188498--55188554 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 23
55188488 GATTTAGAGC
*
55188498 TTAAGGTTTA-GGAGTTACTATT
1 TTAAGGTTTATGGAGTTACTAGT
55188520 TTAAGGTTTATGGA-TTA-TGAGT
1 TTAAGGTTTATGGAGTTACT-AGT
* *
55188542 TTAGGGGTTATGG
1 TTAAGGTTTATGG
55188555 TTTACACTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 1 0.03
22 26 0.87
23 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.30, T:0.44
Consensus pattern (23 bp):
TTAAGGTTTATGGAGTTACTAGT
Found at i:55188586 original size:21 final size:21
Alignment explanation
Indices: 55188570--55188655 Score: 72
Period size: 21 Copynumber: 4.1 Consensus size: 21
55188560 ACTTTATGGT
55188570 TTAAGATTTAGGGTTTAAGGG
1 TTAAGATTTAGGGTTTAAGGG
* *
55188591 TTACGATTTATGGTTTAAGGG
1 TTAAGATTTAGGGTTTAAGGG
* *
55188612 -TATAGATTAAGGG-TT-GGGG
1 TTA-AGATTTAGGGTTTAAGGG
*
55188631 TTTAA-AGTTTAGGGGTTAAGGG
1 -TTAAGA-TTTAGGGTTTAAGGG
55188653 TTA
1 TTA
55188656 GGGGTTGAGG
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
19 4 0.08
20 11 0.22
21 33 0.65
22 3 0.06
ACGTcount: A:0.27, C:0.01, G:0.34, T:0.38
Consensus pattern (21 bp):
TTAAGATTTAGGGTTTAAGGG
Found at i:55188667 original size:21 final size:21
Alignment explanation
Indices: 55188643--55188682 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
55188633 TAAAGTTTAG
*
55188643 GGGTTAAGGGTTAGGGGTTGA
1 GGGTTAAGAGTTAGGGGTTGA
55188664 GGGTTAAGAGTTAGGGGTT
1 GGGTTAAGAGTTAGGGGTT
55188683 TAAAATTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.50, T:0.30
Consensus pattern (21 bp):
GGGTTAAGAGTTAGGGGTTGA
Found at i:55188681 original size:14 final size:14
Alignment explanation
Indices: 55188618--55188669 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
55188608 AGGGTATAGA
55188618 TTAAGGGTT-GGGG
1 TTAAGGGTTAGGGG
* *
55188631 TTTAAAGTTTAGGGG
1 -TTAAGGGTTAGGGG
55188646 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
55188660 TTGAGGGTTA
1 TTAAGGGTTA
55188670 AGAGTTAGGG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 28 0.88
15 4 0.12
ACGTcount: A:0.21, C:0.00, G:0.44, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:55195613 original size:43 final size:43
Alignment explanation
Indices: 55195535--55195784 Score: 173
Period size: 43 Copynumber: 5.8 Consensus size: 43
55195525 TTTTTGCAAG
55195535 AAGCGTCGCTAAAGGT-TTGT-TCTATAGCGGCGTTTGTGGTAA
1 AAGCGTCGCTAAAGGTCTT-TATCTATAGCGGCGTTTGTGGTAA
* * *
55195577 AAGCGTTGCTAAAGGTCTTTAGCTATAGCGGCGTTTGTGGGAA
1 AAGCGTCGCTAAAGGTCTTTATCTATAGCGGCGTTTGTGGTAA
* * * * * * *
55195620 AAGCGCCGCTAAAGATCCTGATCTATAGCAGCGTTTCTCGTAA
1 AAGCGTCGCTAAAGGTCTTTATCTATAGCGGCGTTTGTGGTAA
* * * ** * * *
55195663 AAGCGTCGTTAAAGGCCATGGTCTTTAGCGGCATTTGTTGG-AG
1 AAGCGTCGCTAAAGGTCTTTATCTATAGCGGCGTTTG-TGGTAA
* * *** * * * *
55195706 AAGCGCCGCTAAAGGTCATGGCCTTTAGCGGAGTTTTTGGGAA
1 AAGCGTCGCTAAAGGTCTTTATCTATAGCGGCGTTTGTGGTAA
* * ** *
55195749 AAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTT
1 AAGCGTCGCTAAAGGTCTTTATCTATAGCGGCGTTT
55195785 ATTTCTAAAA
Statistics
Matches: 169, Mismatches: 35, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
42 19 0.11
43 148 0.88
44 2 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (43 bp):
AAGCGTCGCTAAAGGTCTTTATCTATAGCGGCGTTTGTGGTAA
Found at i:55195692 original size:86 final size:86
Alignment explanation
Indices: 55195602--55195784 Score: 222
Period size: 86 Copynumber: 2.1 Consensus size: 86
55195592 TCTTTAGCTA
* * * *
55195602 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCCTGATCTATAGCAGCGTTTCTCGTAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGACCTATAGCAGAGTTTCTCGGAAAAGC
* *
55195667 GTCGTTAAAGGCCATGGTCTT
66 GCCGCTAAAGGCCATGGTCTT
* * * * * * * * *
55195688 TAGCGGCATTTGTTGGAGAAGCGCCGCTAAAGGTCATGGCCTTTAGCGGAGTTTTTGGGAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGACCTATAGCAGAGTTTCTCGGAAAAGC
*
55195753 GCCGCTAAAGGTCATGGTCTT
66 GCCGCTAAAGGCCATGGTCTT
55195774 TAGCGGCGTTT
1 TAGCGGCGTTT
55195785 ATTTCTAAAA
Statistics
Matches: 80, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
86 80 1.00
ACGTcount: A:0.22, C:0.20, G:0.31, T:0.27
Consensus pattern (86 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGATCATGACCTATAGCAGAGTTTCTCGGAAAAGC
GCCGCTAAAGGCCATGGTCTT
Found at i:55195874 original size:22 final size:22
Alignment explanation
Indices: 55195848--55195889 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
55195838 CGGCGCTTTG
*
55195848 AAAAGCGCCGCTAAAGGCCTAA
1 AAAAGCGCCGCTAAAAGCCTAA
55195870 AAAAGCGCCGCTAAAAGCCT
1 AAAAGCGCCGCTAAAAGCCT
55195890 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.29, G:0.21, T:0.10
Consensus pattern (22 bp):
AAAAGCGCCGCTAAAAGCCTAA
Found at i:55196768 original size:25 final size:25
Alignment explanation
Indices: 55196734--55196781 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
55196724 AGAGAGGATT
55196734 TTGTTAAATGAAATAATAAAAATAA
1 TTGTTAAATGAAATAATAAAAATAA
55196759 TTGTTAAATGAAATAATAAAAAT
1 TTGTTAAATGAAATAATAAAAAT
55196782 TGAGCTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.33
Consensus pattern (25 bp):
TTGTTAAATGAAATAATAAAAATAA
Found at i:55197007 original size:27 final size:27
Alignment explanation
Indices: 55196976--55197049 Score: 103
Period size: 27 Copynumber: 2.7 Consensus size: 27
55196966 GCAGAGGAGT
* *
55196976 GTCGACGGCGATGCAATAGAGGGGATA
1 GTCGACGGCGATGCAACAGAGGGGACA
*
55197003 GTCGACGGTGATGCAACAGAGGGGACA
1 GTCGACGGCGATGCAACAGAGGGGACA
* *
55197030 GTTGACGGCGATGCAGCAGA
1 GTCGACGGCGATGCAACAGA
55197050 TGGTCGGGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.28, C:0.18, G:0.41, T:0.14
Consensus pattern (27 bp):
GTCGACGGCGATGCAACAGAGGGGACA
Found at i:55197258 original size:40 final size:40
Alignment explanation
Indices: 55197203--55197339 Score: 123
Period size: 41 Copynumber: 3.4 Consensus size: 40
55197193 AAAATGATAC
* * * *
55197203 TTTGCGGTATTTTTCTTATAGCA-CCATTAATGCTTGACCT
1 TTTGCGGTGTTTTTCTCATA-AAGCCACTAATGCTTGACCT
* *
55197243 TTTGCGGCGTTTTTCTCATAAATGCCGCTAATGCTTGACCT
1 TTTGCGGTGTTTTTCTCATAAA-GCCACTAATGCTTGACCT
* * * *
55197284 TTTGCAGTGTTTTTCTCATAAACGCTACTACTGCTTTACCT
1 TTTGCGGTGTTTTTCTCATAAA-GCCACTAATGCTTGACCT
* * *
55197325 ATTGTGGCGTTTTTC
1 TTTGCGGTGTTTTTC
55197340 CGTTAGTGCC
Statistics
Matches: 78, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 1 0.01
40 17 0.22
41 60 0.77
ACGTcount: A:0.18, C:0.22, G:0.17, T:0.44
Consensus pattern (40 bp):
TTTGCGGTGTTTTTCTCATAAAGCCACTAATGCTTGACCT
Found at i:55197284 original size:41 final size:41
Alignment explanation
Indices: 55197230--55197339 Score: 139
Period size: 41 Copynumber: 2.7 Consensus size: 41
55197220 ATAGCACCAT
* *
55197230 TAATGCTTGACCTTTTGCGGCGTTTTTCTCATAAATGCCGC
1 TAATGCTTGACCTTTTGCGGCGTTTTTCTCATAAACGCCAC
* * *
55197271 TAATGCTTGACCTTTTGCAGTGTTTTTCTCATAAACGCTAC
1 TAATGCTTGACCTTTTGCGGCGTTTTTCTCATAAACGCCAC
* * * *
55197312 TACTGCTTTACCTATTGTGGCGTTTTTC
1 TAATGCTTGACCTTTTGCGGCGTTTTTC
55197340 CGTTAGTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.43
Consensus pattern (41 bp):
TAATGCTTGACCTTTTGCGGCGTTTTTCTCATAAACGCCAC
Found at i:55197400 original size:12 final size:12
Alignment explanation
Indices: 55197383--55197408 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
55197373 TTTTCCGTCC
55197383 AAACGCCACTAA
1 AAACGCCACTAA
55197395 AAACGCCACTAA
1 AAACGCCACTAA
55197407 AA
1 AA
55197409 CCTTACGTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.31, G:0.08, T:0.08
Consensus pattern (12 bp):
AAACGCCACTAA
Found at i:55198599 original size:158 final size:158
Alignment explanation
Indices: 55198311--55198627 Score: 634
Period size: 158 Copynumber: 2.0 Consensus size: 158
55198301 TGAGGTTCAA
55198311 ATCCCACACTTGGAAAAGAATTTTATTTTTGATCCAAGCTTTATCCCTATTGGGTGGGCTTATAT
1 ATCCCACACTTGGAAAAGAATTTTATTTTTGATCCAAGCTTTATCCCTATTGGGTGGGCTTATAT
55198376 AAGATTGTTTGTAAACTCATATCAGAATGAGCCTGCTGGTTCAAGTGGTAAGGTGTTAGTTTGTT
66 AAGATTGTTTGTAAACTCATATCAGAATGAGCCTGCTGGTTCAAGTGGTAAGGTGTTAGTTTGTT
55198441 TGAGGTCTTGTGTTTGATTCCTTGTGTG
131 TGAGGTCTTGTGTTTGATTCCTTGTGTG
55198469 ATCCCACACTTGGAAAAGAATTTTATTTTTGATCCAAGCTTTATCCCTATTGGGTGGGCTTATAT
1 ATCCCACACTTGGAAAAGAATTTTATTTTTGATCCAAGCTTTATCCCTATTGGGTGGGCTTATAT
55198534 AAGATTGTTTGTAAACTCATATCAGAATGAGCCTGCTGGTTCAAGTGGTAAGGTGTTAGTTTGTT
66 AAGATTGTTTGTAAACTCATATCAGAATGAGCCTGCTGGTTCAAGTGGTAAGGTGTTAGTTTGTT
55198599 TGAGGTCTTGTGTTTGATTCCTTGTGTG
131 TGAGGTCTTGTGTTTGATTCCTTGTGTG
55198627 A
1 A
55198628 GCGTGGGTGA
Statistics
Matches: 159, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
158 159 1.00
ACGTcount: A:0.23, C:0.14, G:0.23, T:0.40
Consensus pattern (158 bp):
ATCCCACACTTGGAAAAGAATTTTATTTTTGATCCAAGCTTTATCCCTATTGGGTGGGCTTATAT
AAGATTGTTTGTAAACTCATATCAGAATGAGCCTGCTGGTTCAAGTGGTAAGGTGTTAGTTTGTT
TGAGGTCTTGTGTTTGATTCCTTGTGTG
Found at i:55202361 original size:25 final size:26
Alignment explanation
Indices: 55202328--55202377 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
55202318 GCTAAATTCA
*
55202328 ATATATTT-AAAATTTTTTCAAAATTT
1 ATATATTTAAAAATTTTAT-AAAATTT
55202354 ATAT-TTTAAAAATTTTATAAAATT
1 ATATATTTAAAAATTTTATAAAATT
55202378 CTAAAAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 13 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATATTTAAAAATTTTATAAAATTT
Done.