Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 180 of 202
Found at i:55643897 original size:91 final size:91
Alignment explanation
Indices: 55643737--55643913 Score: 230
Period size: 91 Copynumber: 1.9 Consensus size: 91
55643727 TATTGGTGGC
* * * * *
55643737 TTATCCACAAATTTACTGGCAGTTTTTATCTGCAACTATGTTGTGCATTCACAACCCACTAGTAG
1 TTATCCACAAATTTACTGGCAGCTTTTATATGCAAATATGTTGTGCATCCACAACCCACTAGCAG
*
55643802 TGTATTAACCTGTAAACACTGATGGT
66 TGTATTAACCTGCAAACACTGATGGT
* * * * *
55643828 TTATCCATAAATTTACTGGCAGCTTTTGTATGCAAATATGTTGTGCATCCACAACCTATTGGCCA
1 TTATCCACAAATTTACTGGCAGCTTTTATATGCAAATATGTTGTGCATCCACAACCCACTAG-CA
*
55643893 -TGTATTAACTTGCAAACACTG
65 GTGTATTAACCTGCAAACACTG
55643914 GGAACTCTTA
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
91 72 0.99
92 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (91 bp):
TTATCCACAAATTTACTGGCAGCTTTTATATGCAAATATGTTGTGCATCCACAACCCACTAGCAG
TGTATTAACCTGCAAACACTGATGGT
Found at i:55649969 original size:37 final size:37
Alignment explanation
Indices: 55649908--55650053 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55649898 TACATATGAT
* *
55649908 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55649943 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55649980 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55650017 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55650054 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 9 0.09
36 3 0.03
37 92 0.88
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:55650070 original size:46 final size:46
Alignment explanation
Indices: 55650017--55650429 Score: 529
Period size: 46 Copynumber: 8.6 Consensus size: 46
55650007 TAAGTGTAGC
* * **
55650017 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
55650063 CACTTATCACTTTGTCTCTTGATCAGATAAGCATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
55650109 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* **
55650161 CACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGTTGAAGCTAT
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
55650213 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
55650259 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
55650305 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
55650351 TACTTATCACTTCCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC-T-----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
55650403 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55650430 AGTACTCAAA
Statistics
Matches: 336, Mismatches: 18, Indels: 26
0.88 0.05 0.07
Matches are distributed among these distances:
46 201 0.60
47 1 0.00
49 1 0.00
50 1 0.00
51 4 0.01
52 128 0.38
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:55655585 original size:46 final size:46
Alignment explanation
Indices: 55655535--55655626 Score: 157
Period size: 46 Copynumber: 2.0 Consensus size: 46
55655525 CTACATAGGC
*
55655535 TCTTCCACTCACACCAATGTATCCCTTTCCCCATTTTGGAGTTTCT
1 TCTTCCACTCACACCAATGTATCCCCTTCCCCATTTTGGAGTTTCT
* *
55655581 TCTTCCACTCGCACCAATGTATCCCCTTCCCCGTTTTGGAGTTTCT
1 TCTTCCACTCACACCAATGTATCCCCTTCCCCATTTTGGAGTTTCT
55655627 CCACAAAAAC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.15, C:0.36, G:0.11, T:0.38
Consensus pattern (46 bp):
TCTTCCACTCACACCAATGTATCCCCTTCCCCATTTTGGAGTTTCT
Found at i:55671137 original size:44 final size:44
Alignment explanation
Indices: 55671074--55671162 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
55671064 TGGGAGAAAG
55671074 ATGGTTCAAATTTTGCATCCAGTGGATTGAACTTAGAGGTTTAC
1 ATGGTTCAAATTTTGCATCCAGTGGATTGAACTTAGAGGTTTAC
* *
55671118 ATGGTTTAAATTTTGCATCCAGTGGATTGAACTTGGAGGTTTAC
1 ATGGTTCAAATTTTGCATCCAGTGGATTGAACTTAGAGGTTTAC
55671162 A
1 A
55671163 GTAGGGGCAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.12, G:0.24, T:0.37
Consensus pattern (44 bp):
ATGGTTCAAATTTTGCATCCAGTGGATTGAACTTAGAGGTTTAC
Found at i:55671735 original size:91 final size:93
Alignment explanation
Indices: 55671514--55671749 Score: 262
Period size: 91 Copynumber: 2.5 Consensus size: 93
55671504 TTCCAAGCAA
*
55671514 TGTAGCGGAACAGATTGAAGCTACAATGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGAT
1 TGTAGTGGAACAGATTGAAGCTACAATGGCGAATCTCACTT-CCC--CATTGCAA-TT--AAGAT
* * * *
55671579 CGAAGCCATAACGATGAATCTTACCTTCTGGCAT
60 CGAAGCCACAACGACGAATCTCACCTTCTGGCAG
* * *
55671613 TGCAGTGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAA-T-AGATCGAAGC
1 TGTAGTGGAACAGATTGAAGCTACAATGGCGAATCTCACTTCCCCATTGCAATTAAGATCGAAGC
* * * *
55671676 CACAACGGCGAATCTCA-TTTCCTTGCGG
66 CACAACGACGAATCTCACCTT-CTGGCAG
* *
55671704 TGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCA
1 TGTAGTGGAACAGATTGAAGCTACAATGGCGAATCTCACTTCCCCA
55671750 ACATTGCAGT
Statistics
Matches: 119, Mismatches: 17, Indels: 10
0.82 0.12 0.07
Matches are distributed among these distances:
90 2 0.02
91 68 0.57
94 1 0.01
96 8 0.07
98 3 0.03
99 37 0.31
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (93 bp):
TGTAGTGGAACAGATTGAAGCTACAATGGCGAATCTCACTTCCCCATTGCAATTAAGATCGAAGC
CACAACGACGAATCTCACCTTCTGGCAG
Found at i:55671773 original size:50 final size:50
Alignment explanation
Indices: 55671711--55672078 Score: 244
Period size: 50 Copynumber: 7.6 Consensus size: 50
55671701 CGGTGTAGTG
* *
55671711 GAACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGTA
1 GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAGTA
* * * *
55671761 GAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCAACATTGCAATT
1 GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAGTA
* * * * *** *
55671811 TAAAAGATCGAAGCCACAACGGCGAATCTTAC-CTT--CTGGCATTGCAGTG
1 GAACAGATTGAAGCTACAACGGCGAATC-T-CGCTTCCCCAACATTGCAGTA
* * *
55671860 GAACAGATTGAAGTTACAACGGCGAGTCTCACTT-CCC--CATTGC----
1 GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAGTA
* * * * * *** ** * *
55671903 -AATAGATCGAAGCCACAACGGCGAATCTC-ATTTCCTTGCGGTGTAGTG
1 GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAGTA
* *
55671951 GAACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGTCA
1 GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAGT-A
* * * * * *
55672002 -AACAGATTGAAGCTACAAGGGCGAACCTTGTTTTCCCGACATTGCAGCTA
1 GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAG-TA
**
55672052 -AA-AGATTGAAGCCGCAACGGCGAATCT
1 GAACAGATTGAAGCTACAACGGCGAATCT
55672079 TATTTCCTCA
Statistics
Matches: 245, Mismatches: 58, Indels: 31
0.73 0.17 0.09
Matches are distributed among these distances:
41 2 0.01
42 26 0.11
44 3 0.01
47 7 0.03
48 4 0.02
49 77 0.31
50 120 0.49
51 5 0.02
52 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (50 bp):
GAACAGATTGAAGCTACAACGGCGAATCTCGCTTCCCCAACATTGCAGTA
Found at i:55671854 original size:99 final size:94
Alignment explanation
Indices: 55671751--55671997 Score: 295
Period size: 91 Copynumber: 2.6 Consensus size: 94
55671741 GCTTCCCCAA
* *
55671751 CATTGCAGTAGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCAACATTGCAATTTAAAA
1 CATTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACATTGCAA--T---A
*
55671816 GATCGAAGCCACAACGGCGAATCTTACCTT-CTGG
61 GATCGAAGCCACAACGGCGAATCTCA-CTTCCTGG
* *
55671850 CATTGCAGTGGAACAGATTGAAGTTACAACGGCGAGTCTCACTT-CCC--CATTGCAATAGATCG
1 CATTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACATTGCAATAGATCG
* *
55671912 AAGCCACAACGGCGAATCTCATTTCCTTG
66 AAGCCACAACGGCGAATCTCACTTCCTGG
** * * * *
55671941 CGGTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCA
1 CATTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACATTGCA
55671998 GTCAAACAGA
Statistics
Matches: 129, Mismatches: 15, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
90 2 0.02
91 65 0.50
92 3 0.02
94 8 0.06
96 8 0.06
98 3 0.02
99 40 0.31
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (94 bp):
CATTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCAACATTGCAATAGATCG
AAGCCACAACGGCGAATCTCACTTCCTGG
Found at i:55671872 original size:149 final size:141
Alignment explanation
Indices: 55671610--55671898 Score: 364
Period size: 149 Copynumber: 2.0 Consensus size: 141
55671600 TACCTTCTGG
* * *
55671610 CATTGCAGTGGAACAGATTGAAGCTACAACGGCGAGTCTCACTTCCCCATTGCAATAGATCGAAG
1 CATTGCAGTAGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCATTGCAATAGATCGAAG
* * * * * *
55671675 CCACAACGGCGAATCTCATTTCCTTGCGGTGTAGTGGAACAGATTGAAGCTACGATGGCGAATCT
66 CCACAACGGCGAATCTCACTTCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCT
*
55671740 CGCTTCCCCAA
131 CACTTCCCCAA
55671751 CATTGCAGTAGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCAACATTGCAATTTAAAA
1 CATTGCAGTAGAACAGATTGAAGCTACAACAGCGAATCTCACTT-CCC--CATTGCAA--T---A
* * *
55671816 GATCGAAGCCACAACGGCGAATCTTACCTT-CTGGCATTGCAGTGGAACAGATTGAAGTTACAAC
58 GATCGAAGCCACAACGGCGAATCTCA-CTTCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAAC
*
55671880 GGCGAGTCTCACTTCCCCA
122 GGCGAATCTCACTTCCCCA
55671899 TTGCAATAGA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
141 41 0.33
142 3 0.02
144 8 0.06
146 1 0.01
149 70 0.56
150 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.22
Consensus pattern (141 bp):
CATTGCAGTAGAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCATTGCAATAGATCGAAG
CCACAACGGCGAATCTCACTTCCTGGCAGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCT
CACTTCCCCAA
Found at i:55671944 original size:240 final size:241
Alignment explanation
Indices: 55671521--55672080 Score: 946
Period size: 240 Copynumber: 2.3 Consensus size: 241
55671511 CAATGTAGCG
*
55671521 GAACAGATTGAAGCTACAATGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCC
1 GAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCC
* **
55671586 ATAACGATGAATCTTACCTTCTGGCATTGCAGTGGAACAGATTGAAGCTACAACGGCGAGTCTCA
66 ACAACGGCGAATCTTACCTTCTGGCATTGCAGTGGAACAGATTGAAGCTACAACGGCGAGTCTCA
55671651 CTTCCCCATTGCAATAGATCGAAGCCACAACGGCGAATCTCATTTCCTTGCGGTGTAGTGGAACA
131 CTTCCCCATTGCAATAGATCGAAGCCACAACGGCGAATCTCATTTCCTTGCGGTGTAGTGGAACA
55671716 GATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGT-A
196 GATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGTCA
* *
55671761 GAACAGATTGAAGCTACAACAGCGAATCTCACTTCCCCAACATTGCAATTTAAAAGATCGAAGCC
1 GAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCC
*
55671826 ACAACGGCGAATCTTACCTTCTGGCATTGCAGTGGAACAGATTGAAGTTACAACGGCGAGTCTCA
66 ACAACGGCGAATCTTACCTTCTGGCATTGCAGTGGAACAGATTGAAGCTACAACGGCGAGTCTCA
55671891 CTTCCCCATTGCAATAGATCGAAGCCACAACGGCGAATCTCATTTCCTTGCGGTGTAGTGGAACA
131 CTTCCCCATTGCAATAGATCGAAGCCACAACGGCGAATCTCATTTCCTTGCGGTGTAGTGGAACA
55671956 GATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGTCA
196 GATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGTCA
* * *** * ** *
55672002 -AACAGATTGAAGCTACAAGGGCGAACCTTGTTTTCCCGACATTGC-AGCTAAAAGATTGAAGCC
1 GAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCC
*
55672065 GCAACGGCGAATCTTA
66 ACAACGGCGAATCTTA
55672081 TTTCCTCAAC
Statistics
Matches: 300, Mismatches: 19, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
239 30 0.10
240 269 0.90
241 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (241 bp):
GAACAGATTGAAGCTACAACGGCGAATCTCACTTCCCCGACATTGCAATTTAAAAGATCGAAGCC
ACAACGGCGAATCTTACCTTCTGGCATTGCAGTGGAACAGATTGAAGCTACAACGGCGAGTCTCA
CTTCCCCATTGCAATAGATCGAAGCCACAACGGCGAATCTCATTTCCTTGCGGTGTAGTGGAACA
GATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATTGCAGTCA
Found at i:55673284 original size:3 final size:3
Alignment explanation
Indices: 55673276--55673310 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
55673266 TCCTGTCATT
55673276 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55673311 GCATTTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55677006 original size:7 final size:7
Alignment explanation
Indices: 55676994--55677037 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
55676984 AAGTCAAGCT
55676994 TGGATAA
1 TGGATAA
55677001 TGGATAA
1 TGGATAA
55677008 TGGATAA
1 TGGATAA
55677015 TGGATAA
1 TGGATAA
55677022 TGGATAA
1 TGGATAA
55677029 TGGATAA
1 TGGATAA
55677036 TG
1 TG
55677038 AATATTCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.41, C:0.00, G:0.30, T:0.30
Consensus pattern (7 bp):
TGGATAA
Found at i:55678373 original size:21 final size:21
Alignment explanation
Indices: 55678347--55678387 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
55678337 AACCAAAGGC
*
55678347 GAATCTAGGTGGTTGGCAGGT
1 GAATCTAGGGGGTTGGCAGGT
55678368 GAATCTAGGGGGTTGGCAGG
1 GAATCTAGGGGGTTGGCAGG
55678388 CGCCCCAGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.10, G:0.46, T:0.24
Consensus pattern (21 bp):
GAATCTAGGGGGTTGGCAGGT
Found at i:55679712 original size:16 final size:16
Alignment explanation
Indices: 55679693--55679726 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55679683 AGTTGATTTG
* *
55679693 ATTTTAAATTTTAATA
1 ATTTTAAACTTAAATA
55679709 ATTTTAAACTTAAATA
1 ATTTTAAACTTAAATA
55679725 AT
1 AT
55679727 CTAAATTCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (16 bp):
ATTTTAAACTTAAATA
Found at i:55682727 original size:25 final size:25
Alignment explanation
Indices: 55682699--55682748 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
55682689 TTCTTAAATT
55682699 TATTTAT-TTAA-ATATAATTATAAAA
1 TATTTATATTAATAT-TAA-TATAAAA
55682724 TATTTATATTAATATTAATATAAAA
1 TATTTATATTAATATTAATATAAAA
55682749 ATTATAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 14 0.61
26 7 0.30
27 2 0.09
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTTATATTAATATTAATATAAAA
Found at i:55698313 original size:18 final size:17
Alignment explanation
Indices: 55698267--55698328 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
55698257 TGCAAAGCTA
* *
55698267 GAATCCAACTCTATACTT
1 GAATCTAACTCTATGC-T
*
55698285 GAATCTGACTCTATGCT
1 GAATCTAACTCTATGCT
*
55698302 GAAGTCTAACTCTAAGCT
1 GAA-TCTAACTCTATGCT
55698320 GAAATCTAA
1 G-AATCTAA
55698329 TTATAAGATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 4 0.11
18 31 0.84
19 2 0.05
ACGTcount: A:0.34, C:0.23, G:0.13, T:0.31
Consensus pattern (17 bp):
GAATCTAACTCTATGCT
Found at i:55699023 original size:8 final size:8
Alignment explanation
Indices: 55699008--55699054 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 8
55698998 CAAAATATAT
55699008 CAAAAAAA
1 CAAAAAAA
55699016 CCAAAAAAA
1 -CAAAAAAA
55699025 CAAAAAAA
1 CAAAAAAA
*
55699033 AATAAAAAA
1 CA-AAAAAA
55699042 CAGAAAAAA
1 CA-AAAAAA
55699051 -AAAA
1 CAAAA
55699055 CCTGGACCGA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 3 0.09
8 10 0.29
9 21 0.62
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.02
Consensus pattern (8 bp):
CAAAAAAA
Found at i:55699030 original size:17 final size:17
Alignment explanation
Indices: 55699019--55699052 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
55699009 AAAAAAACCA
55699019 AAAAAACAAAAAAAAAT
1 AAAAAACAAAAAAAAAT
55699036 AAAAAACAGAAAAAAAA
1 AAAAAACA-AAAAAAAA
55699053 AACCTGGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (17 bp):
AAAAAACAAAAAAAAAT
Found at i:55699158 original size:28 final size:27
Alignment explanation
Indices: 55699093--55699188 Score: 149
Period size: 27 Copynumber: 3.6 Consensus size: 27
55699083 CAAGGGAACA
* **
55699093 CTGTTGGCGGCACCAAAGAAGGGAACC
1 CTGTTGGCGGCACCAAACAAGGGTTCC
55699120 CTGTTGGCGGCACCAAACAAGGGTTTCC
1 CTGTTGGCGGCACCAAACAAGGG-TTCC
55699148 CTGTTGGCGGCACCAAACAAGGGTTCC
1 CTGTTGGCGGCACCAAACAAGGGTTCC
55699175 CTGTT-GCGGCACCA
1 CTGTTGGCGGCACCA
55699189 CTCGTGTTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.14
27 31 0.48
28 25 0.38
ACGTcount: A:0.23, C:0.29, G:0.30, T:0.18
Consensus pattern (27 bp):
CTGTTGGCGGCACCAAACAAGGGTTCC
Found at i:55699952 original size:18 final size:18
Alignment explanation
Indices: 55699924--55699968 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
55699914 TTGATATGGT
*
55699924 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
*
55699942 TGGTTGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
55699960 TGGTGGCGA
1 TGGTGGCGA
55699969 TCATTGGGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.04, G:0.49, T:0.18
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:55703188 original size:17 final size:17
Alignment explanation
Indices: 55703168--55703201 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55703158 TTTTTTTCCT
55703168 TTTTTTA-TTCTTTTTTG
1 TTTTTTACTT-TTTTTTG
55703185 TTTTTTACTTTTTTTTG
1 TTTTTTACTTTTTTTTG
55703202 AAATATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTTTACTTTTTTTTG
Found at i:55703267 original size:28 final size:27
Alignment explanation
Indices: 55703203--55703271 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
55703193 TTTTTTTTGA
55703203 AATATTTTGGTAAATAATAAAAATTAT
1 AATATTTTGGTAAATAATAAAAATTAT
* *
55703230 ATATTTTTTGGTCAATAA-AAAAGAGTTAT
1 A-ATATTTTGGTAAATAATAAAA-A-TTAT
55703259 AATATTTTGGTAA
1 AATATTTTGGTAA
55703272 TTTTTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 5 0.14
28 25 0.71
29 5 0.14
ACGTcount: A:0.45, C:0.01, G:0.12, T:0.42
Consensus pattern (27 bp):
AATATTTTGGTAAATAATAAAAATTAT
Found at i:55704090 original size:38 final size:40
Alignment explanation
Indices: 55704042--55704185 Score: 120
Period size: 41 Copynumber: 3.6 Consensus size: 40
55704032 ATTACCTTAT
55704042 TTTCTT-TTT-TTTCCT-TCCTTCTTTCCCTCTTCTTCTTC
1 TTTCTTCTTTCTTTCCTCTCCTTCTTT-CCTCTTCTTCTTC
* * * *
55704080 TTTCTT-TTTTTTTCCTCTTCTCCTTTCCTTTTCTTTCCTTC
1 TTTCTTCTTTCTTTCCTCTCCTTCTTTCCTCTTC-TT-CTTC
* *
55704121 TTT-TTCTTTCTTTCCTCTCCTTTCCTTTTC-CTTCTTTTTC
1 TTTCTTCTTTCTTTCCTCTCC-TT-CTTTCCTCTTCTTCTTC
* *
55704161 TTTCTTCCTTTCTTTCTTCTTCTTC
1 TTTCTT-CTTTCTTTCCTCTCCTTC
55704186 CCCTCTCCTT
Statistics
Matches: 86, Mismatches: 11, Indels: 16
0.76 0.10 0.14
Matches are distributed among these distances:
38 9 0.10
39 12 0.14
40 18 0.21
41 25 0.29
42 17 0.20
43 5 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (40 bp):
TTTCTTCTTTCTTTCCTCTCCTTCTTTCCTCTTCTTCTTC
Found at i:55704105 original size:23 final size:24
Alignment explanation
Indices: 55704070--55704198 Score: 97
Period size: 23 Copynumber: 5.5 Consensus size: 24
55704060 TTCTTTCCCT
*
55704070 CTTCTTCTTCTTTCTTTTTTTTTC
1 CTTCTTCTTCTTTCTTTTTCTTTC
* *
55704094 C-TCTTCTCCTTTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTCTTTC
* * *
55704117 CTTCTTTTTCTTTC-TTTCCTCTC
1 CTTCTTCTTCTTTCTTTTTCTTTC
*
55704140 CTTTCCTT-TTCCTTCTTTTTCTTT-
1 C-TT-CTTCTTCTTTCTTTTTCTTTC
* * *
55704164 CTTCCT-TTCTTTCTTCTTCTTCC
1 CTTCTTCTTCTTTCTTTTTCTTTC
* *
55704187 CCTCTCCTTCTT
1 CTTCTTCTTCTT
55704199 CCCCCCACCA
Statistics
Matches: 82, Mismatches: 17, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
22 15 0.18
23 33 0.40
24 25 0.30
25 9 0.11
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (24 bp):
CTTCTTCTTCTTTCTTTTTCTTTC
Found at i:55704117 original size:10 final size:10
Alignment explanation
Indices: 55704077--55704164 Score: 65
Period size: 10 Copynumber: 8.7 Consensus size: 10
55704067 CCTCTTCTTC
*
55704077 TTCTTTCTTT
1 TTCTTTCCTT
*
55704087 TTTTTTCCTCT
1 TTCTTTCCT-T
55704098 TCTCCTTTCCTT
1 T-T-CTTTCCTT
55704110 TTCTTTCCTT
1 TTCTTTCCTT
55704120 CTT-TTT-C-T
1 -TTCTTTCCTT
*
55704128 TTCTTTCCTC
1 TTCTTTCCTT
*
55704138 TCCTTTCCTT
1 TTCTTTCCTT
* *
55704148 TTCCTTCTTT
1 TTCTTTCCTT
55704158 TTCTTTC
1 TTCTTTC
55704165 TTCCTTTCTT
Statistics
Matches: 61, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
7 2 0.03
8 4 0.07
9 2 0.03
10 39 0.64
11 5 0.08
12 3 0.05
13 6 0.10
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTTCCTT
Found at i:55704125 original size:33 final size:33
Alignment explanation
Indices: 55704077--55704181 Score: 99
Period size: 33 Copynumber: 3.2 Consensus size: 33
55704067 CCTCTTCTTC
* *
55704077 TTCTTTCTTTTTTTTTCCTCTTCTCCTTTCCTT
1 TTCTTTCCTTCTTTTTCCTCTTCTCCTTTCCTT
* *
55704110 TTCTTTCCTTCTTTTTCTTTCTT-TCCTCTCCTT
1 TTCTTTCCTTCTTTTTC-CTCTTCTCCTTTCCTT
* *
55704143 TCCTTTTCCTTCTTTTT-CT-TTCTTCCTTTCTTT
1 TTC-TTTCCTTCTTTTTCCTCTTC-TCCTTTCCTT
55704176 CTTCTT
1 -TTCTT
55704182 CTTCCCCTCT
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
31 2 0.03
32 1 0.02
33 36 0.62
34 19 0.33
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (33 bp):
TTCTTTCCTTCTTTTTCCTCTTCTCCTTTCCTT
Found at i:55704151 original size:34 final size:34
Alignment explanation
Indices: 55704095--55704167 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 34
55704085 TTTTTTTTCC
* *
55704095 TCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTT
1 TCTTCTCCTCTCCTTTCCTTTCCTTCTTTTTCTT
55704129 TCTT-TCCTCTCCTTTCCTTTTCCTTCTTTTTCTT
1 TCTTCTCCTCTCCTTTCC-TTTCCTTCTTTTTCTT
55704163 TCTTC
1 TCTTC
55704168 CTTTCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
33 11 0.31
34 24 0.69
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (34 bp):
TCTTCTCCTCTCCTTTCCTTTCCTTCTTTTTCTT
Found at i:55704165 original size:10 final size:10
Alignment explanation
Indices: 55704071--55704184 Score: 54
Period size: 10 Copynumber: 11.1 Consensus size: 10
55704061 TCTTTCCCTC
*
55704071 TTCTTCTTCT
1 TTCTTTTTCT
*
55704081 TTCTTTTTTT
1 TTCTTTTTCT
*
55704091 TTCCTCTTCTCCT
1 TT-CT-TT-TTCT
*
55704104 TTCCTTTTCT
1 TTCTTTTTCT
*
55704114 TTC--CTTCT
1 TTCTTTTTCT
55704122 TT-TTCTTTCT
1 TTCTT-TTTCT
* * *
55704132 TTCCTCTCCT
1 TTCTTTTTCT
* *
55704142 TTCCTTTTCC
1 TTCTTTTTCT
55704152 TTCTTTTTCT
1 TTCTTTTTCT
55704162 TTCTTCCTTTCT
1 TTCTT--TTTCT
*
55704174 TTCTTCTTCT
1 TTCTTTTTCT
55704184 T
1 T
55704185 CCCCTCTCCT
Statistics
Matches: 78, Mismatches: 17, Indels: 18
0.69 0.15 0.16
Matches are distributed among these distances:
8 6 0.08
10 50 0.64
11 5 0.06
12 13 0.17
13 4 0.05
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:55704182 original size:28 final size:30
Alignment explanation
Indices: 55704095--55704185 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 30
55704085 TTTTTTTTCC
*
55704095 TCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTT
1 TCTT-TCC-TTCC-TTTCTTT-CTTCTTCTTCTT
*
55704129 TCTTTCCTCTCCTTTCCTTT-TCCTTCTT-TT
1 TCTTTCCT-TCCTTT-CTTTCTTCTTCTTCTT
55704159 TCTTT-CTTCCTTTCTTTCTTCTTCTTC
1 TCTTTCCTTCCTTTCTTTCTTCTTCTTC
55704186 CCCTCTCCTT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
27 4 0.08
28 13 0.26
29 2 0.04
30 7 0.14
31 6 0.12
32 4 0.08
33 10 0.20
34 4 0.08
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (30 bp):
TCTTTCCTTCCTTTCTTTCTTCTTCTTCTT
Found at i:55704195 original size:42 final size:40
Alignment explanation
Indices: 55704041--55704198 Score: 107
Period size: 42 Copynumber: 4.0 Consensus size: 40
55704031 AATTACCTTA
* * *
55704041 TTTTCTTTTT-TTTCCTTCCT-T-CTTTCCCTCTTCTTCT
1 TTTTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCT
* * * *
55704078 TCTTTCTTTTTTTTTC-CTCTTCTCCTT-TCCT-T--TTCT
1 T-TTTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCT
* * *
55704114 TTCCTTCTTTTTCTTTCTTTCCTCTCCTTTCCTTTTCCTTCT
1 TT--TTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCT
* *
55704156 TTTTCTTTCTTCCTTTCTTTCTTCTTCTTCCCCTCTCCTTCT
1 TTTTCTTT-TT-CTTTCTTTCCTCTCCTTCCCCTCTCCTTCT
55704198 T
1 T
55704199 CCCCCCACCA
Statistics
Matches: 95, Mismatches: 13, Indels: 21
0.74 0.10 0.16
Matches are distributed among these distances:
35 1 0.01
36 5 0.05
37 13 0.14
38 22 0.23
39 10 0.11
40 10 0.11
41 2 0.02
42 32 0.34
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (40 bp):
TTTTCTTTTTCTTTCTTTCCTCTCCTTCCCCTCTCCTTCT
Found at i:55704271 original size:27 final size:27
Alignment explanation
Indices: 55704233--55704300 Score: 118
Period size: 27 Copynumber: 2.5 Consensus size: 27
55704223 ATATTTAAGG
55704233 TGGTGCCGCCAACAAGGAATCCTTGTT
1 TGGTGCCGCCAACAAGGAATCCTTGTT
**
55704260 TGGTGCCGCCAACAAGGTTTCCTTGTT
1 TGGTGCCGCCAACAAGGAATCCTTGTT
55704287 TGGTGCCGCCAACA
1 TGGTGCCGCCAACA
55704301 GTGTTCCCTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.19, C:0.28, G:0.26, T:0.26
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGAATCCTTGTT
Found at i:55704310 original size:27 final size:27
Alignment explanation
Indices: 55704233--55704311 Score: 108
Period size: 27 Copynumber: 2.9 Consensus size: 27
55704223 ATATTTAAGG
*
55704233 TGGTGCCGCCAACAAGGAAT-CCTTGTT
1 TGGTGCCGCCAACAAGG-TTCCCTTGTT
*
55704260 TGGTGCCGCCAACAAGGTTTCCTTGTT
1 TGGTGCCGCCAACAAGGTTCCCTTGTT
55704287 TGGTGCCGCCAAC-AGTGTTCCCTTG
1 TGGTGCCGCCAACAAG-GTTCCCTTG
55704312 ACCAAGGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
26 3 0.06
27 45 0.94
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.29
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGTTCCCTTGTT
Found at i:55704402 original size:28 final size:29
Alignment explanation
Indices: 55704363--55704433 Score: 110
Period size: 28 Copynumber: 2.5 Consensus size: 29
55704353 GTTTTTTTTT
*
55704363 TATATATATTGGTAAATAAAAAAAAT-TA
1 TATATATTTTGGTAAATAAAAAAAATGTA
55704391 TATATATTTTGGTAAATAAAAAAAATGTA
1 TATATATTTTGGTAAATAAAAAAAATGTA
*
55704420 TA-ACATTTTGGTAA
1 TATATATTTTGGTAA
55704434 TTTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
28 36 0.90
29 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.10, T:0.38
Consensus pattern (29 bp):
TATATATTTTGGTAAATAAAAAAAATGTA
Found at i:55704716 original size:16 final size:16
Alignment explanation
Indices: 55704695--55704731 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
55704685 TCCAAACCCA
55704695 GCCCGAACCCGGCTTG
1 GCCCGAACCCGGCTTG
55704711 GCCCGAACCCGGCTTG
1 GCCCGAACCCGGCTTG
55704727 GCCCG
1 GCCCG
55704732 GCCCATGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.11, C:0.46, G:0.32, T:0.11
Consensus pattern (16 bp):
GCCCGAACCCGGCTTG
Found at i:55705170 original size:13 final size:13
Alignment explanation
Indices: 55705152--55705187 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
55705142 TTTTGCCCAA
55705152 GCCCATATTTCGG
1 GCCCATATTTCGG
55705165 GCCCATATTTCGG
1 GCCCATATTTCGG
*
55705178 GCCTATATTT
1 GCCCATATTT
55705188 TTACCCGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (13 bp):
GCCCATATTTCGG
Found at i:55705816 original size:18 final size:18
Alignment explanation
Indices: 55705772--55705823 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
55705762 ATTTAGGTCC
*
55705772 AAAAATTAT-TATTCTATA
1 AAAAATTATATATT-TTTA
* *
55705790 GAAATTTATATATTTTTA
1 AAAAATTATATATTTTTA
*
55705808 AAAAATTATAAATTTT
1 AAAAATTATATATTTT
55705824 GAAATTTTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
AAAAATTATATATTTTTA
Found at i:55705850 original size:18 final size:19
Alignment explanation
Indices: 55705819--55705868 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
55705809 AAAATTATAA
*
55705819 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AA-TTTTAAAAATT
55705839 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTAAAAATT
55705858 ATTTTG-ATTTT
1 ATTTTGAATTTT
55705869 TTTTTTTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 13 0.46
19 9 0.32
20 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTAAAAATT
Found at i:55705850 original size:19 final size:20
Alignment explanation
Indices: 55705819--55705869 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
55705809 AAAATTATAA
*
55705819 ATTTTGAAATTTTTATAAA-T
1 ATTTTG-AATTTTTAAAAATT
55705839 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
55705858 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
55705870 TTTTTTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 9 0.32
19 13 0.46
20 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:55706317 original size:28 final size:27
Alignment explanation
Indices: 55706286--55706342 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 27
55706276 AAAATTATGA
55706286 TTATTTGAA-TAGAATTAAATTTTATTTT
1 TTATTT-AATTAGAATT-AATTTTATTTT
*
55706314 TTATTTAATTTATAATTAATTTTATTTT
1 TTATTTAA-TTAGAATTAATTTTATTTT
55706342 T
1 T
55706343 ATGATAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 2 0.08
28 18 0.69
29 6 0.23
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (27 bp):
TTATTTAATTAGAATTAATTTTATTTT
Found at i:55707435 original size:14 final size:14
Alignment explanation
Indices: 55707416--55707451 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
55707406 AAATTTACAC
55707416 ATTTTATCAATCTA
1 ATTTTATCAATCTA
55707430 ATTTTA--AATCTA
1 ATTTTATCAATCTA
55707442 ATTTTATCAA
1 ATTTTATCAA
55707452 ATGTATTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTTATCAATCTA
Found at i:55711789 original size:221 final size:217
Alignment explanation
Indices: 55711403--55711819 Score: 726
Period size: 221 Copynumber: 1.9 Consensus size: 217
55711393 AAGTGTCCAC
* * * *
55711403 AAAGATTAAGAACTATTTAATGAAATGAAAGAACCCCATCAAAGCAATAGCTTAAGTTAATGGAA
1 AAAGATAAAGAACTATTGAATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTTAATGGAA
55711468 AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
66 AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
* *
55711533 ACCTAAAGTTAACGGAAACCTTTCAAGATAACAAGAAAAAGAGAAGGCAATGGCATGGAATGAGA
131 ACCTAAAGTTAACGGAAACCGTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAATGAGA
55711598 ACCCCCCCCCCAAAAAAAAAAA
196 ACCCCCCCCCCAAAAAAAAAAA
*
55711620 AAAGATAAAGAACTATTGCATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTAGGTTAAT
1 AAAGATAAAGAACTATTGAATGAAATGAAAGAACCCAATCAAAACAATAGCTT-A--A-GTTAAT
55711685 GGAAAACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAA
62 GGAAAACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAA
*
55711750 CAATACCTAAAGTTAACGGAAACCGTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAAT
127 CAACACCTAAAGTTAACGGAAACCGTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAAT
55711815 GAGAA
192 GAGAA
55711820 AACCCCCCAT
Statistics
Matches: 188, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
217 48 0.26
218 1 0.01
220 1 0.01
221 138 0.73
ACGTcount: A:0.50, C:0.16, G:0.18, T:0.16
Consensus pattern (217 bp):
AAAGATAAAGAACTATTGAATGAAATGAAAGAACCCAATCAAAACAATAGCTTAAGTTAATGGAA
AACCTTTCAAGATAACAAGTGAAAAGAAAGATGGCATGAAATGGAAAGAACCCCATCAAAACAAC
ACCTAAAGTTAACGGAAACCGTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGGAATGAGA
ACCCCCCCCCCAAAAAAAAAAA
Found at i:55711931 original size:89 final size:88
Alignment explanation
Indices: 55711831--55712149 Score: 398
Period size: 89 Copynumber: 3.6 Consensus size: 88
55711821 ACCCCCCATT
55711831 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGGAAACAAGAAAGGAACAAAAAGAAACCATTG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAA-GAAACAAGAAAGGAACAAAAAGAAACCATTG
* *
55711896 CATGAAATAAAAAATATCCAACTG
65 CATGAAATGAAAAATATCCAACTA
* * * * * * *
55711920 AAAACAGTACCTGAAGTAAATGAAACCTTTCAAGATAACAAGAAA--AA-GAGAAGAGA--ATGG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGA-AACAAGAAAGGAACAAAAAGAAACCATTG
* * *** * *
55711980 CATGGAATGAGAAACCCCCCA-TT
65 CATGAAATGAAAAATATCCAACTA
55712003 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAGGAACAAAAAGAAACCATTG
1 AAAACATTACCTGAAGTAAAAGAAACCTTCC-AAGAAACAAGAAAGGAACAAAAAGAAACCATTG
55712068 CATGAAATGAAAAATATCCAACTA
65 CATGAAATGAAAAATATCCAACTA
* *
55712092 AAAACATTACCTAAAGTAAATGAAACCTTCCAAGAAAGCAAGAAAGGAACAAAAAGAA
1 AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGAAA-CAAGAAAGGAACAAAAAGAA
55712150 CGATTGAATG
Statistics
Matches: 190, Mismatches: 31, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
83 38 0.20
84 21 0.11
85 2 0.01
86 12 0.06
87 2 0.01
88 26 0.14
89 89 0.47
ACGTcount: A:0.54, C:0.17, G:0.15, T:0.14
Consensus pattern (88 bp):
AAAACATTACCTGAAGTAAAAGAAACCTTCCAAGAAACAAGAAAGGAACAAAAAGAAACCATTGC
ATGAAATGAAAAATATCCAACTA
Found at i:55712029 original size:172 final size:173
Alignment explanation
Indices: 55711746--55712136 Score: 651
Period size: 172 Copynumber: 2.3 Consensus size: 173
55711736 GAACCCCATC
* ** *
55711746 AAAACAATACCTAAAGTTAACGGAAACCGTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATG
1 AAAACAGTACCTAAAG-TAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATG
*
55711811 GAATGAGAAAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAGGAAACAAGAAA
65 GAATGAGAAAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAA
*
55711876 GGAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTG
130 GGAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
* *
55711920 AAAACAGTACCTGAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGAGAATGGCATGG
1 AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGG
55711985 AATGAG-AAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAG
66 AATGAGAAAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAG
*
55712049 GAACAAAAAGAAACCATTGCATGAAATGAAAAATATCCAACTA
131 GAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
* *
55712092 AAAACATTACCTAAAGTAAATGAAACCTTCCAAGA-AAGCAAGAAA
1 AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAA-CAAGAAA
55712137 GGAACAAAAA
Statistics
Matches: 204, Mismatches: 12, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
171 2 0.01
172 137 0.67
173 51 0.25
174 14 0.07
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (173 bp):
AAAACAGTACCTAAAGTAAATGAAACCTTTCAAGATAACAAGAAAAAGAGAAGACAATGGCATGG
AATGAGAAAACCCCCCATTAAAACATTACCTGAAGTAAAAGAAACCTTCCAAAGAAACAAGAAAG
GAACAAAAAGAAACCATTGCATGAAATAAAAAATATCCAACTA
Found at i:55723326 original size:12 final size:13
Alignment explanation
Indices: 55723302--55723330 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
55723292 GGGCTATAAC
55723302 TATTGCATTTATT
1 TATTGCATTTATT
55723315 TATTGC-TTTATT
1 TATTGCATTTATT
55723327 TATT
1 TATT
55723331 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:55732566 original size:15 final size:15
Alignment explanation
Indices: 55732546--55732577 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
55732536 ATTAAGATAG
55732546 TTGAATCAACTGTCA
1 TTGAATCAACTGTCA
55732561 TTGAATCAACTGTCA
1 TTGAATCAACTGTCA
55732576 TT
1 TT
55732578 AACAGTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (15 bp):
TTGAATCAACTGTCA
Found at i:55736248 original size:14 final size:15
Alignment explanation
Indices: 55736229--55736266 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
55736219 AGAATGGGTT
55736229 TTTAATTAAAT-AAA
1 TTTAATTAAATGAAA
*
55736243 TTTAATTAATTGAAA
1 TTTAATTAAATGAAA
*
55736258 TTAAATTAA
1 TTTAATTAA
55736267 TTATACCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
TTTAATTAAATGAAA
Found at i:55747767 original size:25 final size:25
Alignment explanation
Indices: 55747729--55747779 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
55747719 ATAAATACGA
*
55747729 AAAAAATTGCAATAAAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
* *
55747754 AAAAAATCGTAATACAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
55747779 A
1 A
55747780 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAATCGCAATAAAAAATTAATT
Found at i:55750285 original size:18 final size:17
Alignment explanation
Indices: 55750236--55750297 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
55750226 AAAAAAAAAT
*
55750236 TAAA-TTTATAAATTTT
1 TAAATTTTATAAATTTA
** *
55750252 TATTTTTTATATATTTA
1 TAAATTTTATAAATTTA
*
55750269 TACATTTATATAAATTTA
1 TAAATTT-TATAAATTTA
55750287 TAAATTTTATA
1 TAAATTTTATA
55750298 TTTTATATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
16 2 0.06
17 19 0.53
18 15 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TAAATTTTATAAATTTA
Found at i:55750302 original size:7 final size:7
Alignment explanation
Indices: 55750249--55750315 Score: 53
Period size: 7 Copynumber: 8.6 Consensus size: 7
55750239 ATTTATAAAT
*
55750249 TTTTATT
1 TTTTATA
55750256 TTTTATA
1 TTTTATA
55750263 TATTTATACA
1 T-TTTAT--A
55750273 TTTATATAAA
1 TTT-TAT--A
*
55750283 TTTATAAA
1 TTT-TATA
55750291 TTTTATA
1 TTTTATA
55750298 TTTTATA
1 TTTTATA
55750305 TTTTATA
1 TTTTATA
55750312 TTTT
1 TTTT
55750316 TCAAAATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
7 28 0.54
8 9 0.17
9 2 0.04
10 13 0.25
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (7 bp):
TTTTATA
Found at i:55750310 original size:33 final size:35
Alignment explanation
Indices: 55750242--55750312 Score: 92
Period size: 35 Copynumber: 2.1 Consensus size: 35
55750232 AAATTAAATT
* **
55750242 TATAAATTTTTATTTTTTATATATTTATACATTTA
1 TATAAATTTATAAATTTTATATATTTATACATTTA
*
55750277 TATAAATTTATAAATTTTATAT-TTTATA-TTTTA
1 TATAAATTTATAAATTTTATATATTTATACATTTA
55750310 TAT
1 TAT
55750313 TTTTCAAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 7 0.22
34 6 0.19
35 19 0.59
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (35 bp):
TATAAATTTATAAATTTTATATATTTATACATTTA
Found at i:55750381 original size:26 final size:26
Alignment explanation
Indices: 55750331--55750381 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
55750321 ATATTGTAGG
* * *
55750331 ATTTTTATATATTTTTAATTGTATAC
1 ATTTTTATAAATTTATAATTATATAC
*
55750357 ATTTTTATAAATTTATATTTATATA
1 ATTTTTATAAATTTATAATTATATA
55750382 TTTCAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTTTATAAATTTATAATTATATAC
Found at i:55750933 original size:19 final size:19
Alignment explanation
Indices: 55750875--55750933 Score: 50
Period size: 19 Copynumber: 3.2 Consensus size: 19
55750865 GAAAAGGAAA
55750875 AATATGTATAATTTAAATG
1 AATATGTATAATTTAAATG
* * ** **
55750894 AACA--AATTTTTTAAAAA
1 AATATGTATAATTTAAATG
55750911 AATATGTATAATTTAAATG
1 AATATGTATAATTTAAATG
55750930 AATA
1 AATA
55750934 ATAATTCAAA
Statistics
Matches: 26, Mismatches: 12, Indels: 4
0.62 0.29 0.10
Matches are distributed among these distances:
17 11 0.42
19 15 0.58
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (19 bp):
AATATGTATAATTTAAATG
Found at i:55761152 original size:25 final size:25
Alignment explanation
Indices: 55761114--55761164 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
55761104 GTAAATACGA
55761114 AAAAAATCGCAATAAAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
* * *
55761139 AAAAAATTGTAATACAAAATTAATT
1 AAAAAATCGCAATAAAAAATTAATT
55761164 A
1 A
55761165 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.63, C:0.06, G:0.04, T:0.27
Consensus pattern (25 bp):
AAAAAATCGCAATAAAAAATTAATT
Found at i:55763637 original size:8 final size:8
Alignment explanation
Indices: 55763624--55763688 Score: 51
Period size: 8 Copynumber: 7.9 Consensus size: 8
55763614 AAAAAAAAAT
55763624 TAAATTTA
1 TAAATTTA
*
55763632 TAAATTTT
1 TAAATTTA
**
55763640 TATTTTTTA
1 TA-AATTTA
*
55763649 TATATTTA
1 TAAATTTA
*
55763657 TACATTTATA
1 TA-AATT-TA
55763667 TAAATTTA
1 TAAATTTA
55763675 TAAA-TTA
1 TAAATTTA
55763682 TAAATTT
1 TAAATTT
55763689 TATATTTTAT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
7 7 0.16
8 24 0.53
9 10 0.22
10 4 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (8 bp):
TAAATTTA
Found at i:55763769 original size:26 final size:26
Alignment explanation
Indices: 55763719--55763769 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
55763709 ATATTGTAGG
* * *
55763719 ATTTTTATATATTTTTAATTGTATAC
1 ATTTTTATAAATTTATAATTATATAC
*
55763745 ATTTTTATAAATTTATATTTATATA
1 ATTTTTATAAATTTATAATTATATA
55763770 TTTCAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTTTATAAATTTATAATTATATAC
Found at i:55772279 original size:221 final size:223
Alignment explanation
Indices: 55771882--55772340 Score: 688
Period size: 221 Copynumber: 2.1 Consensus size: 223
55771872 AATTTTGTTA
* * * *
55771882 TTGGTCTCATGATATATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATTTAAATTTCAATT
1 TTGGT-TCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATCTAAATTTCAATC
* * ** * * *
55771947 CTAATTGAAACGATAGTTGTTAAATCTATTTGTGACATGTTTATGGGTATTATGTGAAAATAACA
65 CCAATTCAAACGATAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTATGTGAAAATAACA
*
55772012 AATTGACATGATATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATA
130 AATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATA
* *
55772077 TAAC-T-TAATGAATGTAATGTCTACAAT
195 TAACTTATAATAAATGTAACGTCTACAAT
*
55772104 TTGGTTCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAATATCTAAATTTCAATCC
1 TTGGTTCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATCTAAATTTCAATCC
* * * * *
55772169 CGATTCAAAGGGTAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTGTGTGAAAATAATAA
66 CAATTCAAACGATAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTATGTGAAAATAACAA
55772234 ATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATAT
131 ATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATAT
* *
55772299 AACTTAATAATAAATGTAACGTTTACCAT
196 AACTT-ATAATAAATGTAACGTCTACAAT
55772328 TTGGTTCGTGATT
1 TTGGTTCGTGATT
55772341 GAAATTTAAA
Statistics
Matches: 212, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
221 175 0.83
222 6 0.03
224 31 0.15
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (223 bp):
TTGGTTCGTGATTTATGTAAGTTATAGGTTTAATCTATACTTTTTGAAAATCTAAATTTCAATCC
CAATTCAAACGATAGTCATTAAATCCATTTGTGACATGTTTACGAGTATTATGTGAAAATAACAA
ATTGACATGACATTATACTTGTGATAATCTATTTGTCACATACAATTTTAGAAATAGCAAAATAT
AACTTATAATAAATGTAACGTCTACAAT
Found at i:55791324 original size:13 final size:13
Alignment explanation
Indices: 55791306--55791333 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
55791296 AAAAGAAAAC
55791306 TGTTTCATTTCAT
1 TGTTTCATTTCAT
55791319 TGTTTCATTTCAT
1 TGTTTCATTTCAT
55791332 TG
1 TG
55791334 ATGTCATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.11, T:0.61
Consensus pattern (13 bp):
TGTTTCATTTCAT
Found at i:55807941 original size:25 final size:25
Alignment explanation
Indices: 55807908--55807958 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
55807898 GTAAATACGA
55807908 AAAAAATTGCAATAAAAAATTAATT
1 AAAAAATTGCAATAAAAAATTAATT
* *
55807933 AAAAAATTGTAATACAAAATTAATT
1 AAAAAATTGCAATAAAAAATTAATT
55807958 A
1 A
55807959 GGCTAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.29
Consensus pattern (25 bp):
AAAAAATTGCAATAAAAAATTAATT
Found at i:55833670 original size:41 final size:41
Alignment explanation
Indices: 55833625--55833800 Score: 298
Period size: 41 Copynumber: 4.3 Consensus size: 41
55833615 AATTTAACAT
* *
55833625 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
* * *
55833666 ATTCATATCACCGGCATTTAGCCTACTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
*
55833707 ATTCAGACCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
55833748 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
55833789 ATTCAGATCACC
1 ATTCAGATCACC
55833801 AATTCCAAAC
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 125 1.00
ACGTcount: A:0.24, C:0.29, G:0.19, T:0.28
Consensus pattern (41 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTG
Found at i:55836255 original size:26 final size:26
Alignment explanation
Indices: 55836226--55836287 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
55836216 TACCCTCAAC
*
55836226 AAAATTTTGACGAGTTTAC-CATTGGT
1 AAAATTTTGACGAGTTTACTC-CTGGT
* * *
55836252 AAAACTTTGACGATTTTGCTCCTGGT
1 AAAATTTTGACGAGTTTACTCCTGGT
55836278 AAAATTTTGA
1 AAAATTTTGA
55836288 AAAAATATGT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.39
Consensus pattern (26 bp):
AAAATTTTGACGAGTTTACTCCTGGT
Found at i:55839231 original size:24 final size:24
Alignment explanation
Indices: 55839204--55839252 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
55839194 TAAATACGAA
55839204 AAAAATTGCAATAAAAAATTAATT
1 AAAAATTGCAATAAAAAATTAATT
* *
55839228 AAAAATTGTAATACAAAATTAATT
1 AAAAATTGCAATAAAAAATTAATT
55839252 A
1 A
55839253 GGCTAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.31
Consensus pattern (24 bp):
AAAAATTGCAATAAAAAATTAATT
Found at i:55863402 original size:284 final size:284
Alignment explanation
Indices: 55862892--55863460 Score: 1129
Period size: 284 Copynumber: 2.0 Consensus size: 284
55862882 CCAACAATGG
55862892 TTCGATGTCTTTCAATTACTTCCTATTTGCAAAAATCATTAAACTCTGATGAATAAGACTCAAGA
1 TTCGATGTCTTTCAATTACTTCCTATTTGCAAAAATCATTAAACTCTGATGAATAAGACTCAAGA
*
55862957 CCATTATTCATTCTCAATCGCTTCATAGGTTTTCCAGTTTTTTTCTAACAGTGTCTTCCGCTATT
66 CCATTATTCATTCTCAATCACTTCATAGGTTTTCCAGTTTTTTTCTAACAGTGTCTTCCGCTATT
55863022 TAAAGATTTTGAAGACTTTGCTTTTATATTTCAAGAAATAAATCCAACCTTTTCTGGAGTGATCA
131 TAAAGATTTTGAAGACTTTGCTTTTATATTTCAAGAAATAAATCCAACCTTTTCTGGAGTGATCA
55863087 TCAATAAAAGTTTTGTTATGCCCGTTGTTGAATCAAAACTGACTCAGGTTTGTTTCCCGAAAATG
196 TCAATAAAAGTTTTGTTATGCCCGTTGTTGAATCAAAACTGACTCAGGTTTGTTTCCCGAAAATG
55863152 CATAAATCGGTTTGAAGATTATAT
261 CATAAATCGGTTTGAAGATTATAT
55863176 TTCGATGTCTTTCAATTACTTCCTATTTGCAAAAATCATTAAACTCTGATGAATAAGACTCAAGA
1 TTCGATGTCTTTCAATTACTTCCTATTTGCAAAAATCATTAAACTCTGATGAATAAGACTCAAGA
55863241 CCATTATTCATTCTCAATCACTTCATAGGTTTTCCAGTTTTTTTCTAACAGTGTCTTCCGCTATT
66 CCATTATTCATTCTCAATCACTTCATAGGTTTTCCAGTTTTTTTCTAACAGTGTCTTCCGCTATT
55863306 TAAAGATTTTGAAGACTTTGCTTTTATATTTCAAGAAATAAATCCAACCTTTTCTGGAGTGATCA
131 TAAAGATTTTGAAGACTTTGCTTTTATATTTCAAGAAATAAATCCAACCTTTTCTGGAGTGATCA
55863371 TCAATAAAAGTTTTGTTATGCCCGTTGTTGAATCAAAACTGACTCAGGTTTGTTTCCCGAAAATG
196 TCAATAAAAGTTTTGTTATGCCCGTTGTTGAATCAAAACTGACTCAGGTTTGTTTCCCGAAAATG
55863436 CATAAATCGGTTTGAAGATTATAT
261 CATAAATCGGTTTGAAGATTATAT
55863460 T
1 T
55863461 CAAAGTTTTG
Statistics
Matches: 284, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
284 284 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (284 bp):
TTCGATGTCTTTCAATTACTTCCTATTTGCAAAAATCATTAAACTCTGATGAATAAGACTCAAGA
CCATTATTCATTCTCAATCACTTCATAGGTTTTCCAGTTTTTTTCTAACAGTGTCTTCCGCTATT
TAAAGATTTTGAAGACTTTGCTTTTATATTTCAAGAAATAAATCCAACCTTTTCTGGAGTGATCA
TCAATAAAAGTTTTGTTATGCCCGTTGTTGAATCAAAACTGACTCAGGTTTGTTTCCCGAAAATG
CATAAATCGGTTTGAAGATTATAT
Found at i:55869983 original size:27 final size:27
Alignment explanation
Indices: 55869953--55870008 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
55869943 AGTTCGAGAG
* *
55869953 CAATGAAGCGTCAACGAAGTGGACCAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
**
55869980 CAATGATTCGTCAACGAAGCGGAACAT
1 CAATGAAGCGTCAACGAAGCGGAACAT
55870007 CA
1 CA
55870009 TCGAAACACG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (27 bp):
CAATGAAGCGTCAACGAAGCGGAACAT
Found at i:55879589 original size:44 final size:44
Alignment explanation
Indices: 55879539--55879623 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
55879529 GCCCAATCGG
* * *
55879539 CCCAAAACAGTTCCTAGTCCAACATTACAAAATTAAACAGACGA
1 CCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGACGA
* * * *
55879583 CCCAAAACGGTCCCTGGCCCAACACTACAAAGTTAAGCAGA
1 CCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGA
55879624 AAAACCCTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.41, C:0.31, G:0.13, T:0.15
Consensus pattern (44 bp):
CCCAAAACAGTCCCTAGCCCAACACTACAAAATTAAACAGACGA
Found at i:55882496 original size:16 final size:16
Alignment explanation
Indices: 55882475--55882518 Score: 88
Period size: 16 Copynumber: 2.8 Consensus size: 16
55882465 TTTTGTTTTG
55882475 ATTGCATGACATCATA
1 ATTGCATGACATCATA
55882491 ATTGCATGACATCATA
1 ATTGCATGACATCATA
55882507 ATTGCATGACAT
1 ATTGCATGACAT
55882519 TTCATTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (16 bp):
ATTGCATGACATCATA
Found at i:55893012 original size:89 final size:89
Alignment explanation
Indices: 55892912--55893107 Score: 261
Period size: 89 Copynumber: 2.2 Consensus size: 89
55892902 ATGTACCGAC
* ** * *
55892912 GTGAAACAGATCAAAGATAGTAGGTCCTGTCCTCCTATATCTG-TAGCGAAGTGGATCGAATATA
1 GTGAAGCAGATCAAAGATAACAGGTCCTGTCCTCCTATATC-GATAGCGAAATGGATCAAATATA
*
55892976 CAGATTTTATCTTCCCGTACTGATG
65 CAGATTTTATCTTCCCATACTGATG
*
55893001 GTGAAGCAGATCAAATG-TAACAGGTCCTGTCTTCCTATATCGATAGCGAAATGGATCAAATATA
1 GTGAAGCAGATCAAA-GATAACAGGTCCTGTCCTCCTATATCGATAGCGAAATGGATCAAATATA
*
55893065 CAGATTTTATCTTCCCATACTGGTG
65 CAGATTTTATCTTCCCATACTGATG
* * *
55893090 GCGAAGTAGATCGAAGAT
1 GTGAAGCAGATCAAAGAT
55893108 TACGGATCTT
Statistics
Matches: 93, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
88 2 0.02
89 90 0.97
90 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (89 bp):
GTGAAGCAGATCAAAGATAACAGGTCCTGTCCTCCTATATCGATAGCGAAATGGATCAAATATAC
AGATTTTATCTTCCCATACTGATG
Found at i:55893094 original size:44 final size:44
Alignment explanation
Indices: 55892957--55893101 Score: 130
Period size: 44 Copynumber: 3.3 Consensus size: 44
55892947 TATATCTGTA
* *
55892957 GCGAAGTGGATCGAATATACAGATTTTATCTTCCCGTACTGATG
1 GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
* ** * * ** * * *
55893001 GTGAAGCAGATCAAATGTAACAGGTCCTGTCTTCCTATA-TCGATA
1 GCGAAGTGGATCAAATAT-ACAGATTTTATCTTCCCATACT-GATG
* *
55893046 GCGAAATGGATCAAATATACAGATTTTATCTTCCCATACTGGTG
1 GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
*
55893090 GCGAAGTAGATC
1 GCGAAGTGGATC
55893102 GAAGATTACG
Statistics
Matches: 72, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
44 41 0.57
45 31 0.43
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
GCGAAGTGGATCAAATATACAGATTTTATCTTCCCATACTGATG
Found at i:55895051 original size:15 final size:15
Alignment explanation
Indices: 55895031--55895068 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
55895021 TTATTCTATC
55895031 TTTTAT-CCTTTATAT
1 TTTTATACC-TTATAT
55895046 TTTTATACCTTATAT
1 TTTTATACCTTATAT
55895061 TTTATATA
1 TTT-TATA
55895069 TATGTGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTATACCTTATAT
Found at i:55897114 original size:25 final size:25
Alignment explanation
Indices: 55897085--55897132 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
55897075 TTTGCTATTC
*
55897085 ATATACACGCATATTTTTATATACA
1 ATATACACGCATATTTTAATATACA
***
55897110 ATATATGTGCATATTTTAATATA
1 ATATACACGCATATTTTAATATA
55897133 TACTTTTAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.10, G:0.06, T:0.44
Consensus pattern (25 bp):
ATATACACGCATATTTTAATATACA
Found at i:55904960 original size:32 final size:32
Alignment explanation
Indices: 55904890--55904966 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
55904880 TTCAATAAAT
* *
55904890 AAAAAAT-ATATAAAATTTTATTAAATATTAA
1 AAAAAATCATATAAAATTTTATAAAAAATTAA
55904921 AATAAAATCATATAAATATTTT-TAAAAAAATT-A
1 AA-AAAATCATATAAA-ATTTTAT-AAAAAATTAA
55904954 AAAAAATCATATA
1 AAAAAATCATATA
55904967 GGTGAGCCTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
31 2 0.05
32 16 0.40
33 11 0.28
34 11 0.28
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (32 bp):
AAAAAATCATATAAAATTTTATAAAAAATTAA
Found at i:55913008 original size:22 final size:22
Alignment explanation
Indices: 55912985--55913029 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
55912975 TATTTTATTT
55912985 AAATAATTAAAAATTATTAATTA
1 AAAT-ATTAAAAATTATTAATTA
**
55913008 AAATATTATTAATTATTAATTA
1 AAATATTAAAAATTATTAATTA
55913030 TTAACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATATTAAAAATTATTAATTA
Found at i:55913017 original size:15 final size:14
Alignment explanation
Indices: 55912988--55913033 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
55912978 TTTATTTAAA
55912988 TAATTAAAAATTAT
1 TAATTAAAAATTAT
55913002 TAATTAAAATATTAT
1 TAATTAAAA-ATTAT
**
55913017 TAATTATTAATTAT
1 TAATTAAAAATTAT
55913031 TAA
1 TAA
55913034 CAAAAATTGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 17 0.59
15 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TAATTAAAAATTAT
Found at i:55917112 original size:30 final size:30
Alignment explanation
Indices: 55917047--55917117 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 30
55917037 ACCAATGCAC
*
55917047 TATTTTTTAATCAATTTAGCCCTTGTACTT
1 TATTTTTTAATCAATTTAGCCCTTATACTT
* *
55917077 TATTTTTT-ATCAGTTTAGCTCC-TATCCTT
1 TATTTTTTAATCAATTTAGC-CCTTATACTT
*
55917106 TCATTTTGTAAT
1 T-ATTTTTTAAT
55917118 TCTTGTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
29 16 0.47
30 16 0.47
31 2 0.06
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (30 bp):
TATTTTTTAATCAATTTAGCCCTTATACTT
Found at i:55923399 original size:13 final size:13
Alignment explanation
Indices: 55923381--55923406 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55923371 GTCTTTTACA
55923381 AATATAGACAAAT
1 AATATAGACAAAT
55923394 AATATAGACAAAT
1 AATATAGACAAAT
55923407 TTAAACAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
AATATAGACAAAT
Found at i:55931460 original size:12 final size:12
Alignment explanation
Indices: 55931443--55931467 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55931433 ATGATAAACG
55931443 ATGAAAATTTAA
1 ATGAAAATTTAA
55931455 ATGAAAATTTAA
1 ATGAAAATTTAA
55931467 A
1 A
55931468 AACATGTAAA
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:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAAAATTTAA
Found at i:55939418 original size:46 final size:46
Alignment explanation
Indices: 55939351--55939641 Score: 426
Period size: 46 Copynumber: 6.6 Consensus size: 46
55939341 TTTGAATACT
*
55939351 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
55939397 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
55939443 TCTGATCAAGTGACAAAGTGAT-A-----AG---TA-CTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
55939479 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
55939525 TCTGATCAAGTGACAAAGTGATAATTGTTAGCTTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* * *
55939571 TTTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
55939617 TCTGATCAAG-GAC-AAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
55939642 ATCATACGTA
Statistics
Matches: 224, Mismatches: 11, Indels: 22
0.87 0.04 0.09
Matches are distributed among these distances:
36 30 0.13
37 3 0.01
40 2 0.01
42 2 0.01
44 12 0.05
45 6 0.03
46 169 0.75
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.30
Consensus pattern (46 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:55939475 original size:36 final size:36
Alignment explanation
Indices: 55939434--55939504 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
55939424 GTAGCTTTAG
*
55939434 CTACACTTATCTGATCAAGTGACAAAGTGATAAGTA
1 CTACACTTATCTGATCAAGAGACAAAGTGATAAGTA
55939470 CTACACTTATCTGATCAAGAGACAAAGTGATAAGT
1 CTACACTTATCTGATCAAGAGACAAAGTGATAAGT
55939505 GGTAGCTTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (36 bp):
CTACACTTATCTGATCAAGAGACAAAGTGATAAGTA
Found at i:55939481 original size:82 final size:83
Alignment explanation
Indices: 55939385--55939640 Score: 383
Period size: 82 Copynumber: 3.0 Consensus size: 83
55939375 GTGGTAGCTT
55939385 TAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 TAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
55939450 AAGTGACAAAGTGATAAG
66 AAGTGACAAAGTGATAAG
55939468 TA-CTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
1 TAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
55939532 AAGTGACAAAGTGATAATTGTTAG
66 AAGTGACAAAGTGAT-A-----AG
* * *
55939556 CTTTAGCTACACTTATTTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTG
1 ---TAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTG
55939621 ATCAAG-GAC-AAGTGATAAG
63 ATCAAGTGACAAAGTGATAAG
55939640 T
1 T
55939641 GATCATACGT
Statistics
Matches: 160, Mismatches: 3, Indels: 22
0.86 0.02 0.12
Matches are distributed among these distances:
81 1 0.01
82 77 0.48
83 3 0.02
84 2 0.01
88 2 0.01
89 1 0.01
90 7 0.04
91 5 0.03
92 62 0.39
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (83 bp):
TAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATC
AAGTGACAAAGTGATAAG
Found at i:55939579 original size:128 final size:128
Alignment explanation
Indices: 55939351--55939596 Score: 447
Period size: 128 Copynumber: 1.9 Consensus size: 128
55939341 TTTGAATACT
*
55939351 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
55939416 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTACTACACTTA
66 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTACTACACTTA
*
55939479 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
* * *
55939544 GATAATTGTTAGCTTTAGCTACACTTATTTGATCAAGTGACAAAGTGATAAGT
66 GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGT
55939597 GGTAGCCTTA
Statistics
Matches: 113, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
128 113 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.30
Consensus pattern (128 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
GATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTACTACACTTA
Found at i:55940402 original size:28 final size:28
Alignment explanation
Indices: 55940356--55940410 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
55940346 AATATTTTAG
*
55940356 AATTTTATATTTTTATATTTTTTATATC
1 AATTTTATAATTTTATATTTTTTATATC
55940384 AATTTTCATAATTTT-TATTTTTTATAT
1 AATTTT-ATAATTTTATATTTTTTATAT
55940411 TTAATATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 18 0.72
29 7 0.28
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (28 bp):
AATTTTATAATTTTATATTTTTTATATC
Found at i:55940429 original size:30 final size:29
Alignment explanation
Indices: 55940357--55940430 Score: 87
Period size: 29 Copynumber: 2.5 Consensus size: 29
55940347 ATATTTTAGA
*
55940357 ATTTTATATTTTTATATTTTTTATATCAAT
1 ATTTAATATTTTT-TATTTTTTATATCAAT
* * *
55940387 -TTTCATAATTTTTATTTTTTATATTTAAT
1 ATTTAATATTTTTTATTTTTTATA-TCAAT
55940416 ATTTAATATTTTTTA
1 ATTTAATATTTTTTA
55940431 ATTATTTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 11 0.30
29 14 0.38
30 12 0.32
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (29 bp):
ATTTAATATTTTTTATTTTTTATATCAAT
Found at i:55946767 original size:21 final size:21
Alignment explanation
Indices: 55946741--55946797 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
55946731 ACACGAGCTG
55946741 CTCACATGGGCGTGTGCGGCC
1 CTCACATGGGCGTGTGCGGCC
* * *
55946762 CTCACACGGGCATGTGTGGCC
1 CTCACATGGGCGTGTGCGGCC
*
55946783 TTCACATGGGCGTGT
1 CTCACATGGGCGTGT
55946798 AGACCCCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.12, C:0.30, G:0.35, T:0.23
Consensus pattern (21 bp):
CTCACATGGGCGTGTGCGGCC
Found at i:55947496 original size:21 final size:20
Alignment explanation
Indices: 55947460--55947501 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
55947450 CTGAATATAC
55947460 GTCTGTTTGTCAGAACATTTT
1 GTCTGTTTGTCAGAAC-TTTT
**
55947481 GTCTGTTTGTGTGAACTTTT
1 GTCTGTTTGTCAGAACTTTT
55947501 G
1 G
55947502 GTTATTGACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.24, T:0.50
Consensus pattern (20 bp):
GTCTGTTTGTCAGAACTTTT
Found at i:55948339 original size:32 final size:32
Alignment explanation
Indices: 55948298--55948362 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
55948288 CATTAGCAAA
55948298 GTTAGCAACTATTAACTTTTCCATCCATTTTG
1 GTTAGCAACTATTAACTTTTCCATCCATTTTG
55948330 GTTAGCAACTATTAACTTTTCCATCCATTTTG
1 GTTAGCAACTATTAACTTTTCCATCCATTTTG
55948362 G
1 G
55948363 GGTGATTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.25, C:0.22, G:0.11, T:0.43
Consensus pattern (32 bp):
GTTAGCAACTATTAACTTTTCCATCCATTTTG
Found at i:55952542 original size:18 final size:18
Alignment explanation
Indices: 55952519--55952570 Score: 56
Period size: 18 Copynumber: 3.0 Consensus size: 18
55952509 TTGGGTTATA
55952519 AAAAAATTATTATTTTTT
1 AAAAAATTATTATTTTTT
* *
55952537 AAAAAA-TACT-TTCTTT
1 AAAAAATTATTATTTTTT
55952553 AAAATAATT-TTATTTTTT
1 AAAA-AATTATTATTTTTT
55952571 CTCATTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
16 9 0.33
17 6 0.22
18 12 0.44
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (18 bp):
AAAAAATTATTATTTTTT
Found at i:55956329 original size:22 final size:22
Alignment explanation
Indices: 55956304--55956349 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
55956294 CAAACAGAAA
*
55956304 CAAACTCAAAACAAATCAAATC
1 CAAACACAAAACAAATCAAATC
*
55956326 CAAACACAAAATAAATCAAATC
1 CAAACACAAAACAAATCAAATC
55956348 CA
1 CA
55956350 TTAAGCCAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.26, G:0.00, T:0.13
Consensus pattern (22 bp):
CAAACACAAAACAAATCAAATC
Found at i:55957060 original size:25 final size:25
Alignment explanation
Indices: 55957012--55957060 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55957002 ACTGTTATTT
* * * *
55957012 TATTATATATTTCTATTATTTTTAG
1 TATTATAGATTGCTATCATATTTAG
55957037 TATTATAGATTGCTATCATATTTA
1 TATTATAGATTGCTATCATATTTA
55957061 TTTATATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (25 bp):
TATTATAGATTGCTATCATATTTAG
Found at i:55957171 original size:27 final size:27
Alignment explanation
Indices: 55957104--55957171 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 27
55957094 ATTTTACTAC
55957104 ATATTATTTTAAAATTACTTTTATATA
1 ATATTATTTTAAAATTACTTTTATATA
* * ** *
55957131 GTTTTA-TTCCAAATT-GTTTTATATA
1 ATATTATTTTAAAATTACTTTTATATA
55957156 ATAATTATTTTAAAAT
1 AT-ATTATTTTAAAAT
55957172 CATCCTATAC
Statistics
Matches: 30, Mismatches: 9, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
25 10 0.33
26 10 0.33
27 10 0.33
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (27 bp):
ATATTATTTTAAAATTACTTTTATATA
Found at i:55967562 original size:16 final size:16
Alignment explanation
Indices: 55967541--55967579 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
55967531 ACTTGTTCTG
55967541 GTCATTTCAGGTTAAA
1 GTCATTTCAGGTTAAA
** *
55967557 GTCATTTTGGGTTCAA
1 GTCATTTCAGGTTAAA
55967573 GTCATTT
1 GTCATTT
55967580 TAGATTTGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.23, C:0.13, G:0.21, T:0.44
Consensus pattern (16 bp):
GTCATTTCAGGTTAAA
Found at i:55967580 original size:16 final size:16
Alignment explanation
Indices: 55967550--55967580 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55967540 GGTCATTTCA
55967550 GGTTAAAGTCATTTTG
1 GGTTAAAGTCATTTTG
*
55967566 GGTTCAAGTCATTTT
1 GGTTAAAGTCATTTT
55967581 AGATTTGGGT
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:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (16 bp):
GGTTAAAGTCATTTTG
Found at i:55972314 original size:28 final size:31
Alignment explanation
Indices: 55972264--55972320 Score: 75
Period size: 28 Copynumber: 1.9 Consensus size: 31
55972254 CAAATTTAAA
*
55972264 TATTTAAATTAAATCTTATTTTTTATAATAT
1 TATTTAAATTAAATCTTAGTTTTTATAATAT
*
55972295 TATTTAAA-T-AAT-TTAGTTTTTTTAAT
1 TATTTAAATTAAATCTTAGTTTTTATAAT
55972321 GTTCAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 3 0.12
30 1 0.04
31 8 0.33
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (31 bp):
TATTTAAATTAAATCTTAGTTTTTATAATAT
Found at i:55973108 original size:13 final size:13
Alignment explanation
Indices: 55973090--55973114 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55973080 TAATTTATAT
55973090 GTGTGAAAATTTC
1 GTGTGAAAATTTC
55973103 GTGTGAAAATTT
1 GTGTGAAAATTT
55973115 TATCGTTTGT
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:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:55974303 original size:42 final size:42
Alignment explanation
Indices: 55974201--55974359 Score: 187
Period size: 43 Copynumber: 3.7 Consensus size: 42
55974191 TATGTGATAT
55974201 CGTGTAAGACCACGTCTGGGACATTGGCATCG-ATTTGGGATTAA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTT--GATT-A
* * *
55974245 CGTGTAAGACCATGTCTGAGACATTGGCATCGTATATGATTA
1 CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
* *
55974287 CGTGTAAGACC-CTGTCTGGGACAGTGGCATCGTTATTTGATTG
1 CGTGTAAGACCAC-GTCTGGGACATTGGCATCG-TATTTGATTA
* * *
55974330 CATATAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACATTGGCAT
55974360 TTGTATGAGT
Statistics
Matches: 99, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
42 29 0.29
43 36 0.36
44 31 0.31
45 3 0.03
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACATTGGCATCGTATTTGATTA
Found at i:55977277 original size:31 final size:32
Alignment explanation
Indices: 55977242--55977304 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 32
55977232 ACAAACTAAC
* **
55977242 CAAAGACTAAAATGTCCAAAA-AAAAAGTCCA
1 CAAAGACCAAAATGAACAAAATAAAAAGTCCA
* *
55977273 CAAAGTCCATAATGAACAAAATAAAAAGTCCA
1 CAAAGACCAAAATGAACAAAATAAAAAGTCCA
55977305 TAGCATATAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
31 16 0.62
32 10 0.38
ACGTcount: A:0.57, C:0.19, G:0.10, T:0.14
Consensus pattern (32 bp):
CAAAGACCAAAATGAACAAAATAAAAAGTCCA
Found at i:55977591 original size:25 final size:25
Alignment explanation
Indices: 55977563--55977610 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55977553 ATCAGATCAG
* *
55977563 ATCAGACCATAGCATATCATATCGA
1 ATCAAACCATAGCATAACATATCGA
*
55977588 ATCAAATCATAGCATAACATATC
1 ATCAAACCATAGCATAACATATC
55977611 ATATCCTACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.44, C:0.23, G:0.08, T:0.25
Consensus pattern (25 bp):
ATCAAACCATAGCATAACATATCGA
Found at i:55979881 original size:23 final size:23
Alignment explanation
Indices: 55979838--55979881 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
55979828 GATATATTGC
*
55979838 ATTATATAATATTAAGGTAAACT
1 ATTATATAATATTAAGCTAAACT
*
55979861 ATTA-ATACATATTGAGCTAAA
1 ATTATATA-ATATTAAGCTAAA
55979882 AATGCTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.48, C:0.07, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAATATTAAGCTAAACT
Found at i:55985636 original size:66 final size:66
Alignment explanation
Indices: 55985553--55985682 Score: 233
Period size: 66 Copynumber: 2.0 Consensus size: 66
55985543 GTAAGAAGAG
* *
55985553 GTTCTGAACTATGTAAGTAATTAGTGTGTTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTTT
1 GTTCTGAACTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTTT
55985618 A
66 A
*
55985619 GTTCTGAATTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTT
1 GTTCTGAACTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTT
55985683 GCAACTCTCG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (66 bp):
GTTCTGAACTATGTAAGTAATTAGTATGCTAATTGTTTTATTTTTTTAATTTTAGTTGTAGCTTT
A
Found at i:55986207 original size:27 final size:27
Alignment explanation
Indices: 55986169--55986245 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
55986159 TAGTATTGGC
55986169 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
55986196 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
55986223 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
55986246 GCCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:55986452 original size:19 final size:19
Alignment explanation
Indices: 55986430--55986467 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55986420 AATTTAATTT
*
55986430 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
55986449 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
55986468 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:55986622 original size:22 final size:26
Alignment explanation
Indices: 55986563--55986684 Score: 152
Period size: 22 Copynumber: 4.9 Consensus size: 26
55986553 ATATACCGAC
55986563 ATTACAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAA-TATAAT
55986590 ATTACAATATTCATAC-AAA-A-AA-
1 ATTACAATATTCATACAAAATATAAT
*
55986612 ATTGCAATATTCATACAAAATTATAAT
1 ATTACAATATTCATACAAAA-TATAAT
55986639 ATTACAATATTCATAC-AAA-A-AA-
1 ATTACAATATTCATACAAAATATAAT
*
55986661 ATTACAATATTCATACTAAATATA
1 ATTACAATATTCATACAAAATATA
55986685 GATAATTTAT
Statistics
Matches: 85, Mismatches: 2, Indels: 18
0.81 0.02 0.17
Matches are distributed among these distances:
22 31 0.36
23 10 0.12
24 3 0.04
25 2 0.02
26 8 0.09
27 31 0.36
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
ATTACAATATTCATACAAAATATAAT
Found at i:55986630 original size:49 final size:49
Alignment explanation
Indices: 55986510--55986681 Score: 235
Period size: 49 Copynumber: 3.6 Consensus size: 49
55986500 AATTAATTAT
* *
55986510 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATA-T-ATAC
1 AAAAAAATTACAATATTCATAC--AAAATTATAATATTACAATATTCATAC
** *
55986559 --CGACATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
*
55986606 AAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
*
55986655 AAAAAAATTACAATATTCATACTAAAT
1 AAAAAAATTACAATATTCATACAAAAT
55986682 ATAGATAATT
Statistics
Matches: 108, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
45 19 0.18
46 1 0.01
47 20 0.19
49 68 0.63
ACGTcount: A:0.53, C:0.13, G:0.01, T:0.32
Consensus pattern (49 bp):
AAAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATAC
Found at i:55986756 original size:27 final size:27
Alignment explanation
Indices: 55986724--55986795 Score: 117
Period size: 27 Copynumber: 2.7 Consensus size: 27
55986714 AAAATATTGC
* * *
55986724 AATTTTATATGAATATTGTAATTTTGT
1 AATTTTGTATGAATATTGTAATATTAT
55986751 AATTTTGTATGAATATTGTAATATTAT
1 AATTTTGTATGAATATTGTAATATTAT
55986778 AATTTTGTATGAATATTG
1 AATTTTGTATGAATATTG
55986796 AATGTCGGTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (27 bp):
AATTTTGTATGAATATTGTAATATTAT
Found at i:55986917 original size:19 final size:19
Alignment explanation
Indices: 55986895--55986932 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55986885 ATAAATTTAT
*
55986895 TAGTAACTTATTAGTAATA
1 TAGTAACTTATTACTAATA
*
55986914 TAGTAATTTATTACTAATA
1 TAGTAACTTATTACTAATA
55986933 AATTAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (19 bp):
TAGTAACTTATTACTAATA
Found at i:55987135 original size:20 final size:21
Alignment explanation
Indices: 55987093--55987136 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
55987083 TATATTTTTA
55987093 TTTTTTATTTTTAAAATACTT
1 TTTTTTATTTTTAAAATACTT
55987114 TTTTTTATTTTTAAAA-A-TT
1 TTTTTTATTTTTAAAATACTT
55987133 TTTT
1 TTTT
55987137 GGTGTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.26
20 1 0.04
21 16 0.70
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTTTATTTTTAAAATACTT
Found at i:55987370 original size:27 final size:27
Alignment explanation
Indices: 55987298--55987359 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
55987288 GGTCTAGTAA
*
55987298 TGGCGCCTCTCTATAAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
55987325 TGGCGCCTCTCTATGAGGCACCTTCAT
1 TGGCGCCTCTCTATGAGGCACCTTCAT
55987352 TGGCGCCT
1 TGGCGCCT
55987360 ACCTGATAGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.15, C:0.34, G:0.23, T:0.29
Consensus pattern (27 bp):
TGGCGCCTCTCTATGAGGCACCTTCAT
Found at i:55987435 original size:12 final size:12
Alignment explanation
Indices: 55987420--55987451 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
55987410 CCGTATTTTT
55987420 TTAAAAAAATTA
1 TTAAAAAAATTA
55987432 TTAAAAAAA-TA
1 TTAAAAAAATTA
55987443 -TAAAAAAAT
1 TTAAAAAAAT
55987452 ATTTTATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 8 0.42
11 2 0.11
12 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (12 bp):
TTAAAAAAATTA
Found at i:55996151 original size:19 final size:20
Alignment explanation
Indices: 55996122--55996159 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
55996112 ACCAAAAATT
55996122 TATTTTAAAAATTAAAAAAG
1 TATTTTAAAAATTAAAAAAG
55996142 TATTTT-AAAATTAAAAAA
1 TATTTTAAAAATTAAAAAA
55996160 TAATAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (20 bp):
TATTTTAAAAATTAAAAAAG
Found at i:55996197 original size:29 final size:29
Alignment explanation
Indices: 55996122--55996198 Score: 75
Period size: 29 Copynumber: 2.6 Consensus size: 29
55996112 ACCAAAAATT
*
55996122 TATTTTAAAAATTAAAAAAGTATTTTAAAAT
1 TATTTT-AAAATT-AAAAAGTATTTTAAAAA
*** *
55996153 TA-AAAAATAATAAAAAAGTATTTTAAAAA
1 TATTTTAA-AATTAAAAAGTATTTTAAAAA
55996182 TATTTTAAAATTAAAAA
1 TATTTTAAAATTAAAAA
55996199 ATTAAAATAA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
29 28 0.80
30 5 0.14
31 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (29 bp):
TATTTTAAAATTAAAAAGTATTTTAAAAA
Found at i:55998858 original size:20 final size:19
Alignment explanation
Indices: 55998829--55998872 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
55998819 AAAATTATAA
*
55998829 AAAAAATCAAAATAATTTTT
1 AAAAAATCAAAAT-ATTTAT
*
55998849 AAAAAGTCAAAATATTTAT
1 AAAAAATCAAAATATTTAT
55998868 AAAAA
1 AAAAA
55998873 CTCCAAAGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAAATCAAAATATTTAT
Found at i:55998879 original size:20 final size:20
Alignment explanation
Indices: 55998829--55998875 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
55998819 AAAATTATAA
* *
55998829 AAAAAATCAAAATAATTTTT
1 AAAAACTCAAAATAATTTAT
*
55998849 AAAAAGTCAAAAT-ATTTAT
1 AAAAACTCAAAATAATTTAT
55998868 AAAAACTC
1 AAAAACTC
55998876 CAAAGTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.60, C:0.09, G:0.02, T:0.30
Consensus pattern (20 bp):
AAAAACTCAAAATAATTTAT
Found at i:55999196 original size:21 final size:21
Alignment explanation
Indices: 55999157--55999196 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
55999147 TTCAATTCGC
*
55999157 CTTGACTCGAATTTCATTTCA
1 CTTGACTCGAATTTAATTTCA
55999178 CTTGACTCG-ATTTGAATTT
1 CTTGACTCGAATTT-AATTT
55999197 TTTCAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.23, C:0.20, G:0.12, T:0.45
Consensus pattern (21 bp):
CTTGACTCGAATTTAATTTCA
Found at i:56004091 original size:25 final size:25
Alignment explanation
Indices: 56004061--56004115 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
56004051 TCATCAAATT
56004061 AGAATGACATGTCACTTTCAGAATC
1 AGAATGACATGTCACTTTCAGAATC
* *
56004086 AGAATGACATTTCATTTTCAGAATC
1 AGAATGACATGTCACTTTCAGAATC
56004111 AGAAT
1 AGAAT
56004116 AGCATATCCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.31
Consensus pattern (25 bp):
AGAATGACATGTCACTTTCAGAATC
Found at i:56009810 original size:113 final size:112
Alignment explanation
Indices: 56009635--56010199 Score: 455
Period size: 114 Copynumber: 5.0 Consensus size: 112
56009625 TTTACCACGC
* * * *
56009635 AGCGCCGCAAAATATC-AAGACCAACACGCAGCGTTCTGGTCTTGATGTATATTGGC-ATTAGTG
1 AGCGCCGCAAAAGATCTTA-ACCAAAACGCAGAGTT-TGGTCTTGATGTATATT-GCAATTAGTG
* * *
56009698 GCGCTTATGAACAAACGCCGGTAATGTATAGTATTAGCGGCGCTTAGCGGA
63 GCGCTTATGAA-AAACGCCGCTAAAGTATAGTATTAGCGGCGCTTTGCGGA
* *
56009749 AGCGCCGCAAAAGATGTTAACCAAAACGCAGAGTTTAGTCTTGATGTATATTGCAATTAGTGGCG
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCAATTAGTGGCG
* * * *** *
56009814 CTTATAAAGAAAACGCCGCTAATGTATAGTATTAGCGGTGCAGGGCGTTA
66 CTTAT-GA-AAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTTGCG-GA
* * * * ** * **
56009864 AACGCCGCAAGATATCTTAATCAAAACGCACTGTTTTGGTCTTGATGTATACTATAATTAGTGGC
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGAG-TTTGGTCTTGATGTATATTGCAATTAGTGGC
* * * ** * *
56009929 GTTTATGGAAAACGCCAG-TAAAGGATAGT-TATAGCATCGTTTTGTGGTA
65 GCTTATGAAAAACGCC-GCTAAAGTATAGTAT-TAGCGGCGCTTTGCGG-A
* * * *
56009978 AGCGCCTCCAAATATCTTAACCAAAACGCAGAGTTTGGTCTTGA-GGAGTATTAG-AATTAGTGG
1 AGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTA-TATT-GCAATTAGTGG
* *
56010041 CGCTTGATGAAAAACGCCGCTAAAGTATA-TCATTAGCGGCG-TTTGTGTA
64 CGCTT-ATGAAAAACGCCGCTAAAGTATAGT-ATTAGCGGCGCTTTGCGGA
* * * * *
56010090 ACGCGCCGC-AAAGTATCTTAACCAAAACACAGCGTTTAGTTCTTGATGTATACTGGAATTAGTG
1 A-GCGCCGCAAAAG-ATCTTAACCAAAACGCAGAGTTT-GGTCTTGATGTATATTGCAATTAGTG
** * * * *
56010154 GCGCACATGGGAAAACGCCGCTGAAGCATAGTATTAGTGGCGCTTT
63 GCGCTTAT-GAAAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTT
56010200 TACCGAAACG
Statistics
Matches: 361, Mismatches: 67, Indels: 45
0.76 0.14 0.10
Matches are distributed among these distances:
112 9 0.02
113 97 0.27
114 186 0.52
115 37 0.10
116 32 0.09
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (112 bp):
AGCGCCGCAAAAGATCTTAACCAAAACGCAGAGTTTGGTCTTGATGTATATTGCAATTAGTGGCG
CTTATGAAAAACGCCGCTAAAGTATAGTATTAGCGGCGCTTTGCGGA
Found at i:56011257 original size:7 final size:7
Alignment explanation
Indices: 56011240--56011291 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
56011230 TTTACTGTTC
56011240 GGGGTTTT
1 GGGG-TTT
56011248 GGGGTTT
1 GGGGTTT
*
56011255 GGGATTT
1 GGGGTTT
*
56011262 AGGGTTT
1 GGGGTTT
**
56011269 ATGGTTT
1 GGGGTTT
*
56011276 AGGGTTT
1 GGGGTTT
56011283 GGGGTTT
1 GGGGTTT
56011290 GG
1 GG
56011292 TTTTTGAGGT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
7 34 0.89
8 4 0.11
ACGTcount: A:0.08, C:0.00, G:0.48, T:0.44
Consensus pattern (7 bp):
GGGGTTT
Found at i:56012032 original size:147 final size:147
Alignment explanation
Indices: 56011881--56012158 Score: 332
Period size: 147 Copynumber: 1.9 Consensus size: 147
56011871 ATTATGTTTA
* * *
56011881 TTGAAATGTTGTCGTTTTTGTCT-AT-TATATTACTGGCG-TTTGTCGGAAACGCCACAACATTG
1 TTGAAACGTTGTCG-TTTTGT-TAATGT-TATTACTGGCGTTTTATCGAAAACGCCACAACATTG
* ****
56011943 -GGTAAACTGTTGGGGAAACGGGTTCGTTTTGAGTTATAGTTAGTGGCGCTTTA-CTTAAAACGC
63 AGGT-AACTGTTGAGGAAACGACCGCGTTTTGAGTTATAGTTAGTGGCGC-TTAGCTTAAAACGC
56012006 CGCAAAAATGTTCAAACATTTG
126 CGCAAAAATGTTCAAACATTTG
* * **
56012028 TTGAAACGTTGTCGTTTTGTTAATGTTATTAGTGGCGTTTTATCGAAAACGCCACGAGTTTGAGG
1 TTGAAACGTTGTCGTTTTGTTAATGTTATTACTGGCGTTTTATCGAAAACGCCACAACATTGAGG
* * * *
56012093 TAAGTGTTGATGAAGCGACCGCGTTTTGAGTTATAGTTAGTGGCGCTTAGTTTAAAACGCCGCAA
66 TAACTGTTGAGGAAACGACCGCGTTTTGAGTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAA
56012158 A
131 A
56012159 TTTTTGACCT
Statistics
Matches: 110, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
145 1 0.01
146 21 0.19
147 85 0.77
148 3 0.03
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (147 bp):
TTGAAACGTTGTCGTTTTGTTAATGTTATTACTGGCGTTTTATCGAAAACGCCACAACATTGAGG
TAACTGTTGAGGAAACGACCGCGTTTTGAGTTATAGTTAGTGGCGCTTAGCTTAAAACGCCGCAA
AAATGTTCAAACATTTG
Found at i:56013399 original size:27 final size:27
Alignment explanation
Indices: 56013361--56013419 Score: 100
Period size: 27 Copynumber: 2.2 Consensus size: 27
56013351 ATTTACTCCT
*
56013361 AATTTAAAATTATTTTCCATGCATTCC
1 AATTTAAAATTATTTTCCATACATTCC
*
56013388 AATTTAAAATTATTTTCCATACATTCT
1 AATTTAAAATTATTTTCCATACATTCC
56013415 AATTT
1 AATTT
56013420 TTTTGCTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.15, G:0.02, T:0.47
Consensus pattern (27 bp):
AATTTAAAATTATTTTCCATACATTCC
Found at i:56018660 original size:42 final size:42
Alignment explanation
Indices: 56018614--56018732 Score: 211
Period size: 42 Copynumber: 2.8 Consensus size: 42
56018604 TAAGAATAAA
* *
56018614 CGCCGCTAAAGAACATGATTTTTAGCGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
*
56018656 CGCCGCTAAAGAACATGGTCTTTAACGGCGTTTTTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
56018698 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTT
56018733 GTTTGTAAAC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.34
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAG
Found at i:56021024 original size:2 final size:2
Alignment explanation
Indices: 56021017--56021053 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
56021007 ACATTGCATA
56021017 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
56021054 GTTAGCTGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56026753 original size:30 final size:30
Alignment explanation
Indices: 56026690--56026754 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
56026680 AATAGTTTAT
* *
56026690 ATTTTTATAATTTTTAAAGAATTAAATTAA
1 ATTTTTATAATTTTTAAAGAATCAAAGTAA
* *
56026720 ATTTTTATCATTTTTAAA-AGTCAAAGTATA
1 ATTTTTATAATTTTTAAAGAATCAAAGTA-A
56026750 ATTTT
1 ATTTT
56026755 ACCATTACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.51
Consensus pattern (30 bp):
ATTTTTATAATTTTTAAAGAATCAAAGTAA
Found at i:56026755 original size:29 final size:30
Alignment explanation
Indices: 56026687--56026760 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 30
56026677 TTTAATAGTT
* * * *
56026687 TATATTTTTATAATTTTTAAAGAATTAAAT
1 TATAATTTTATCATTTTTAAAGAATCAAAG
*
56026717 TA-AATTTTTATCATTTTTAAA-AGTCAAAG
1 TATAA-TTTTATCATTTTTAAAGAATCAAAG
*
56026746 TATAATTTTACCATT
1 TATAATTTTATCATT
56026761 ACTAAATTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
29 17 0.47
30 19 0.53
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (30 bp):
TATAATTTTATCATTTTTAAAGAATCAAAG
Done.