Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D10
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: 65706892
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869813 characters in sequence are not A, C, G, or T
File 185 of 218
Found at i:55312606 original size:120 final size:120
Alignment explanation
Indices: 55312474--55312710 Score: 429
Period size: 120 Copynumber: 2.0 Consensus size: 120
55312464 ATAATCATAT
* * * *
55312474 TTTAACATAATTATTATTAAATGTAATTTAATAAGAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
*
55312539 AAATATTTTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATATAA
55312594 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
55312659 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATA
66 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATA
55312711 ACTGTTATTA
Statistics
Matches: 112, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (120 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATATAA
Found at i:55312719 original size:108 final size:107
Alignment explanation
Indices: 55312596--55312917 Score: 482
Period size: 108 Copynumber: 3.1 Consensus size: 107
55312586 AAATATAATT
*
55312596 TAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATTAA
1 TAAAATAA-TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
* *
55312661 ATATTTTTATATGAATTTACAAAAATCATAATATATAATACTA
65 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
*
55312704 TAAAATAACTGTTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
1 TAAAATAA-TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
55312769 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
65 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
* **
55312812 TAAAAT-ATAATT-TT-AA-A-AATTTATTATTAA-ATATAATTTAATAAAATTC--AATA-TAA
1 TAAAATAAT-ATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAA
*
55312868 TTATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
65 ATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
55312911 TAAAATA
1 TAAAATA
55312918 TAATTTAAAA
Statistics
Matches: 202, Mismatches: 10, Indels: 12
0.90 0.04 0.05
Matches are distributed among these distances:
99 51 0.25
100 4 0.02
102 19 0.09
103 10 0.05
104 1 0.00
105 2 0.01
106 3 0.01
107 3 0.01
108 109 0.54
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (107 bp):
TAAAATAATATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAA
TATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
Found at i:55312757 original size:99 final size:98
Alignment explanation
Indices: 55312660--55312927 Score: 337
Period size: 99 Copynumber: 2.6 Consensus size: 98
55312650 CTTAAAATTA
* * *
55312660 AATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATAACT-GTTATTAAAT
1 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAA-TAATT-TT-AA-
55312724 ATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
62 A-AATTTAATAAAAA-ATATAATTTAATAAAA---TTAATA-T
55312767 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAT-ATAATTTTAAAAA
1 -AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAATAATTTTAAAAA
* **
55312831 TTTATTATTAAATATAATTTAATAAAATTCAATAT
65 TTTAATAAAAAATATAATTTAATAAAATT-AATAT
55312866 AATTATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAT-ATAA-TTTAAAA
1 AA-TATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAATAATTTTAAAA
55312928 TAATCTACTT
Statistics
Matches: 151, Mismatches: 6, Indels: 16
0.87 0.03 0.09
Matches are distributed among these distances:
98 9 0.06
99 55 0.36
100 4 0.03
102 16 0.11
103 10 0.07
104 1 0.01
105 2 0.01
106 3 0.02
107 3 0.02
108 48 0.32
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (98 bp):
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATAATAATTTTAAAAAT
TTAATAAAAAATATAATTTAATAAAATTAATAT
Found at i:55312764 original size:120 final size:118
Alignment explanation
Indices: 55312474--55312756 Score: 350
Period size: 120 Copynumber: 2.3 Consensus size: 118
55312464 ATAATCATAT
* * ** * * *
55312474 TTTAACATAATTATTATTAAATGTAATTTAATAAGAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTAATAAAAAATATAATTTAATAA-AATATAT-ACTTAATAAAATTCTTAAAATT
*
55312539 AAATATTTTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
64 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATATAA
* ** *
55312594 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAAAATT
1 TTTAAAATAATTAATAAAAAATATAATTTAAT-AAAATATAT-ACTTAATAAAATTCTTAAAATT
**
55312659 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATAACTGT
64 AAATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAAT-A-TAA
55312716 TATTAAATATAATTTAATAAAAATATATAATTTAATAAAAT
1 T-TTAAA-ATAA-TTAATAAAAA-ATATAATTTAATAAAAT
55312757 TCTTAATATT
Statistics
Matches: 147, Mismatches: 9, Indels: 9
0.89 0.05 0.05
Matches are distributed among these distances:
120 109 0.74
121 3 0.02
122 2 0.01
123 5 0.03
124 4 0.03
125 12 0.08
126 12 0.08
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (118 bp):
TTTAAAATAATTAATAAAAAATATAATTTAATAAAATATATACTTAATAAAATTCTTAAAATTAA
ATATTTTTATATGAATTTACAAAAATCATAATATATAATACTATAAAATATAA
Found at i:55314425 original size:50 final size:50
Alignment explanation
Indices: 55314366--55314464 Score: 162
Period size: 50 Copynumber: 2.0 Consensus size: 50
55314356 ATAAATGCTT
* * *
55314366 GACATAAAGTGTTGAACTTTTGATTCATGATATTGAACTTAATTTTAATA
1 GACACAAAGTGTTCAACTTTTGATTCATGATATTAAACTTAATTTTAATA
*
55314416 GACACAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTTTAAT
1 GACACAAAGTGTTCAACTTTTGATTCATGATATTAAACTTAATTTTAAT
55314465 TTGTTTTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.41
Consensus pattern (50 bp):
GACACAAAGTGTTCAACTTTTGATTCATGATATTAAACTTAATTTTAATA
Found at i:55315998 original size:37 final size:36
Alignment explanation
Indices: 55315951--55316128 Score: 116
Period size: 38 Copynumber: 4.9 Consensus size: 36
55315941 TATTTTATAG
55315951 TATTATATATTATGATTTTAGTAAATTCATATAAGAA
1 TATTA-ATATTATGATTTTAGTAAATTCATATAAGAA
* * ****
55315988 TATTTAATATTAAGAATTTTATTAAATT-ATATATTTT
1 TA-TTAATATTATG-ATTTTAGTAAATTCATATAAGAA
* * * * * *
55316025 TATTAA-ATTAT-A-TTTAATAACA-ACTATTTTATAG
1 TATTAATATTATGATTTTAGTAA-ATTC-ATATAAGAA
55316059 TATTATATATTATGATTTTAGTAAATTCATATAAGAA
1 TATTA-ATATTATGATTTTAGTAAATTCATATAAGAA
* *
55316096 TATTTAATATTAAGAATTTTATTAAATT-ATATA
1 TA-TTAATATTATG-ATTTTAGTAAATTCATATA
55316129 TTTTATTAAA
Statistics
Matches: 107, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
32 7 0.07
33 2 0.02
34 9 0.08
35 5 0.05
36 9 0.08
37 37 0.35
38 38 0.36
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.49
Consensus pattern (36 bp):
TATTAATATTATGATTTTAGTAAATTCATATAAGAA
Found at i:55316131 original size:17 final size:17
Alignment explanation
Indices: 55316111--55316144 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
55316101 AATATTAAGA
55316111 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
55316128 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
55316145 TTAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:55316179 original size:108 final size:106
Alignment explanation
Indices: 55315841--55316155 Score: 502
Period size: 108 Copynumber: 3.0 Consensus size: 106
55315831 AAAGTAGATT
*
55315841 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT-ATATT--GAAT
1 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT
* * *
55315903 TTTATTAAATTATAT-TTAATAATAAA-T-T-TTTAA-AATT
66 TTTATTAAATTATATATT-TTATTAAATTATATTTAATAATA
55315940 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT
1 ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT
*
55316005 TTTATTAAATTATATATTTTTATTAAATTATATTTAATAACA
66 TTTATTAAATTATATA-TTTTATTAAATTATATTTAATAATA
55316047 ACTATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
1 A-TATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
55316112 TTTTATTAAATTATATATTTTATTAAATTATATTTAATAATA
65 TTTTATTAAATTATATATTTTATTAAATTATATTTAATAATA
55316154 AT
1 AT
55316156 TATGTTAAAA
Statistics
Matches: 200, Mismatches: 6, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
99 52 0.26
100 5 0.03
102 19 0.09
103 6 0.03
104 3 0.01
105 1 0.00
106 6 0.03
107 28 0.14
108 80 0.40
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (106 bp):
ATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAAT
TTTATTAAATTATATATTTTATTAAATTATATTTAATAATA
Found at i:55317322 original size:4 final size:4
Alignment explanation
Indices: 55317301--55317338 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
55317291 TCAAAATAAT
*
55317301 AATA AA-A AAGTA AGTA AATA AATA AATA AATA AATA AA
1 AATA AATA AA-TA AATA AATA AATA AATA AATA AATA AA
55317339 ATGAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.83
5 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:55317476 original size:12 final size:12
Alignment explanation
Indices: 55317456--55317490 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
55317446 AAAATAAAAA
55317456 ATATGTATATAG
1 ATATGTATATAG
*
55317468 ATATATATATAG
1 ATATGTATATAG
55317480 ATATGTATATA
1 ATATGTATATA
55317491 AATTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (12 bp):
ATATGTATATAG
Found at i:55317662 original size:37 final size:35
Alignment explanation
Indices: 55317588--55317663 Score: 89
Period size: 37 Copynumber: 2.1 Consensus size: 35
55317578 ATATATAAAG
* *
55317588 TATAAAAAGTATAGAAGTATGTATATGTACATATA
1 TATAAAAAGTATAAAAATATGTATATGTACATATA
* * *
55317623 TATAAATAAGTTATAAAAATATGTATGTGTATATGTA
1 TATAAA-AAG-TATAAAAATATGTATATGTACATATA
55317660 TATA
1 TATA
55317664 TATTATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 6 0.18
36 3 0.09
37 25 0.74
ACGTcount: A:0.47, C:0.01, G:0.13, T:0.38
Consensus pattern (35 bp):
TATAAAAAGTATAAAAATATGTATATGTACATATA
Found at i:55317848 original size:26 final size:27
Alignment explanation
Indices: 55317799--55317850 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
55317789 GGTATAAATG
*
55317799 AATAACTAATAATAAACATGATAATAA
1 AATAACTAATAATAAAAATGATAATAA
* *
55317826 AATAAC-AATATTAAAAATTATAATA
1 AATAACTAATAATAAAAATGATAATA
55317851 GAAAAAATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (27 bp):
AATAACTAATAATAAAAATGATAATAA
Found at i:55318527 original size:11 final size:10
Alignment explanation
Indices: 55318502--55318535 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
55318492 TAATATTTCG
*
55318502 AAAAAAATAA
1 AAAAAAACAA
55318512 AAAAAAACAA
1 AAAAAAACAA
55318522 AGAAAAAACAA
1 A-AAAAAACAA
55318533 AAA
1 AAA
55318536 TAAGAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:55319022 original size:16 final size:16
Alignment explanation
Indices: 55318997--55319034 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
55318987 TTGAATTACT
*
55318997 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
55319013 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
55319029 ATTACA
1 ATTACA
55319035 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:55325292 original size:26 final size:24
Alignment explanation
Indices: 55325252--55325302 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
55325242 TATTTTATAA
*
55325252 TTTTTATTTTTAAAAAATATGATT
1 TTTTTATTTTTAAAAAATATAATT
55325276 TTTTTATATTTTAAAAAATTATAATT
1 TTTTTAT-TTTTAAAAAA-TATAATT
55325302 T
1 T
55325303 GAAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 10 0.42
26 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTTATTTTTAAAAAATATAATT
Found at i:55329391 original size:29 final size:29
Alignment explanation
Indices: 55329335--55329393 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
55329325 TTTTAAAATT
**
55329335 TAAAAAATAATAAAAACTATTTTCAAAAA
1 TAAAAAATAATAAAAACTATTTAAAAAAA
* * *
55329364 TAAAAAATCATTAAAATTATTTAAAAAAA
1 TAAAAAATAATAAAAACTATTTAAAAAAA
55329393 T
1 T
55329394 TATAAAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (29 bp):
TAAAAAATAATAAAAACTATTTAAAAAAA
Found at i:55330020 original size:14 final size:15
Alignment explanation
Indices: 55329998--55330074 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
55329988 CAATCAAACA
55329998 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
55330012 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
55330027 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
55330047 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
55330061 ACGGAAAAT-ATTTT
1 CCAGAAAATCATTTT
55330075 ACTAGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 21 0.42
15 15 0.30
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.14, G:0.09, T:0.34
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:55330039 original size:20 final size:20
Alignment explanation
Indices: 55330014--55330053 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
55330004 AATATTTTCC
*
55330014 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
55330034 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
55330054 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:55330059 original size:34 final size:35
Alignment explanation
Indices: 55330002--55330068 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
55329992 CAAACACCAG
*
55330002 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
55330037 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
55330069 TATTTTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:55331000 original size:20 final size:18
Alignment explanation
Indices: 55330966--55331002 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
55330956 ATTGAATTAT
55330966 TCACAAGATTTATTTAAG
1 TCACAAGATTTATTTAAG
55330984 TCACTAAGATGTTATTTAA
1 TCAC-AAGAT-TTATTTAA
55331003 AAAAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TCACAAGATTTATTTAAG
Found at i:55335253 original size:2 final size:2
Alignment explanation
Indices: 55335246--55335314 Score: 120
Period size: 2 Copynumber: 34.0 Consensus size: 2
55335236 GTAGGGACGT
55335246 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
55335288 TA GA GA GA GA GA GA GA GA GA GA TGA GA
1 GA GA GA GA GA GA GA GA GA GA GA -GA GA
55335315 CACTTGAGTA
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 62 0.97
3 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.48, T:0.03
Consensus pattern (2 bp):
GA
Found at i:55342008 original size:43 final size:43
Alignment explanation
Indices: 55341947--55342031 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
55341937 ATATCCAAGC
*
55341947 CAAGGGTGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
1 CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
* * *
55341990 CAAGGATGGCGACAATAGTTTAATTATATTGCGTGACCATAG
1 CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAG
55342032 GATAGACAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (43 bp):
CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
Found at i:55354073 original size:64 final size:64
Alignment explanation
Indices: 55353972--55354096 Score: 241
Period size: 64 Copynumber: 2.0 Consensus size: 64
55353962 GACTCGGGAC
55353972 TTAGTTTGGGATCCTTCTCCCATGGGTAGGATAAAATTCAATGTGGCAGGGGTTGTTATGATAT
1 TTAGTTTGGGATCCTTCTCCCATGGGTAGGATAAAATTCAATGTGGCAGGGGTTGTTATGATAT
*
55354036 TTAGTTTGGGATCCTTCTCCCATGGGTGGGATAAAATTCAATGTGGCAGGGGTTGTTATGA
1 TTAGTTTGGGATCCTTCTCCCATGGGTAGGATAAAATTCAATGTGGCAGGGGTTGTTATGA
55354097 ATGAGATAAC
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.22, C:0.13, G:0.30, T:0.35
Consensus pattern (64 bp):
TTAGTTTGGGATCCTTCTCCCATGGGTAGGATAAAATTCAATGTGGCAGGGGTTGTTATGATAT
Found at i:55354680 original size:13 final size:13
Alignment explanation
Indices: 55354662--55354727 Score: 53
Period size: 13 Copynumber: 4.6 Consensus size: 13
55354652 GAACTTTCTT
55354662 TTTTTAATATATA
1 TTTTTAATATATA
55354675 TTTTTAA-ATATA
1 TTTTTAATATATA
55354687 TTTATTAAATTATATTA
1 TTT-TT-AA-TATA-TA
55354704 TTGTTCTTAATATATA
1 -T-TT-TTAATATATA
*
55354720 TTATTAAT
1 TTTTTAAT
55354728 CATAAGCTTA
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
12 8 0.18
13 14 0.32
14 3 0.07
15 1 0.02
16 5 0.11
17 6 0.14
18 3 0.07
19 4 0.09
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (13 bp):
TTTTTAATATATA
Found at i:55354684 original size:14 final size:14
Alignment explanation
Indices: 55354661--55354726 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
55354651 CGAACTTTCT
*
55354661 TTTTTTAATATATA
1 TTTTTAAATATATA
55354675 TTTTTAAATATAT-
1 TTTTTAAATATATA
*
55354688 TTATTAAATTATATTA
1 TTTTTAAA-TATA-TA
*
55354704 TTGTTCTTAATATATA
1 TT-TT-TAAATATATA
*
55354720 TTATTAA
1 TTTTTAA
55354727 TCATAAGCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
13 7 0.17
14 18 0.44
15 2 0.05
16 6 0.15
17 5 0.12
18 3 0.07
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.59
Consensus pattern (14 bp):
TTTTTAAATATATA
Found at i:55354685 original size:12 final size:12
Alignment explanation
Indices: 55354662--55354702 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
55354652 GAACTTTCTT
55354662 TTTTTAATATATA
1 TTTTTAA-ATATA
55354675 TTTTTAAATATA
1 TTTTTAAATATA
55354687 TTTATTAAATTATA
1 TTT-TTAAA-TATA
55354701 TT
1 TT
55354703 ATTGTTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.31
13 12 0.46
14 6 0.23
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTTTTAAATATA
Found at i:55355752 original size:22 final size:22
Alignment explanation
Indices: 55355694--55355752 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
55355684 CATTTATATC
*
55355694 ATAATTTCCAAAATTTAAATTT
1 ATAATTTCCATAATTTAAATTT
** * *
55355716 ATAA-ACCCCTGAATTTTAATTT
1 ATAATTTCCAT-AATTTAAATTT
55355738 ATAATTTCCATAATT
1 ATAATTTCCATAATT
55355753 AAGCCACCAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTTCCATAATTTAAATTT
Found at i:55356098 original size:22 final size:22
Alignment explanation
Indices: 55356047--55356091 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
55356037 TTTTTAAAAC
55356047 TTAGAATTAGTTGAATGCTAAA
1 TTAGAATTAGTTGAATGCTAAA
55356069 TTAGAATTAGTTGAATGCTAAA
1 TTAGAATTAGTTGAATGCTAAA
55356091 T
1 T
55356092 CTAAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (22 bp):
TTAGAATTAGTTGAATGCTAAA
Found at i:55360842 original size:20 final size:21
Alignment explanation
Indices: 55360817--55360904 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 21
55360807 GAATATTTAC
*
55360817 AATAATGCATAATAAAA-TAA
1 AATAATACATAATAAAAGTAA
*
55360837 AATAATACATGATAAAAGCATTACAA
1 AATAATACATAATAAAAG---T--AA
55360863 AATAATACATAATAAAA-TAA
1 AATAATACATAATAAAAGTAA
** *
55360883 AATAATGTAAAATAAAAGTAA
1 AATAATACATAATAAAAGTAA
55360904 A
1 A
55360905 TAAATAGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
20 31 0.56
21 4 0.07
22 1 0.02
24 1 0.02
26 18 0.33
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (21 bp):
AATAATACATAATAAAAGTAA
Found at i:55361799 original size:12 final size:12
Alignment explanation
Indices: 55361782--55361806 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55361772 TTCAATCACC
55361782 TTTCAATATTTT
1 TTTCAATATTTT
55361794 TTTCAATATTTT
1 TTTCAATATTTT
55361806 T
1 T
55361807 CTTTGTACTG
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCAATATTTT
Found at i:55362464 original size:16 final size:17
Alignment explanation
Indices: 55362438--55362473 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
55362428 GTATATATAC
*
55362438 ATACTTCTATACTTTAT
1 ATACTTCTATAATTTAT
55362455 ATACTT-TATAATTTAT
1 ATACTTCTATAATTTAT
55362471 ATA
1 ATA
55362474 TACGTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (17 bp):
ATACTTCTATAATTTAT
Found at i:55362491 original size:23 final size:23
Alignment explanation
Indices: 55362465--55362537 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
55362455 ATACTTTATA
55362465 ATTTATATATACGTTATACATAT
1 ATTTATATATACGTTATACATAT
*
55362488 ATTTTTATAATA--TATATACATAT
1 ATTTATAT-ATACGT-TATACATAT
* *
55362511 A--TACATATACG-TGTACATAT
1 ATTTATATATACGTTATACATAT
*
55362531 TTTTATA
1 ATTTATA
55362538 ACTTATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 13
0.67 0.11 0.23
Matches are distributed among these distances:
20 11 0.29
21 3 0.08
22 4 0.11
23 17 0.45
24 3 0.08
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTTATATATACGTTATACATAT
Found at i:55362562 original size:43 final size:43
Alignment explanation
Indices: 55362468--55362613 Score: 107
Period size: 47 Copynumber: 3.2 Consensus size: 43
55362458 CTTTATAATT
55362468 TATATATACGTTATACATATATTTTTATAATATATATACATATA
1 TATATATACGTTATACA-ATATTTTTATAATATATATACATATA
* * *
55362512 TACATATACG-TGTAC-ATATTTTTATAACTTATTTATATATATGTATA
1 TATATATACGTTATACAATATTTTTATAA--TA--TATATACA--TATA
* * * * *
55362559 TATACATACTTATATATTCTATATATTTTATAATTTATATACATATC
1 TATATATACGT-TATA--CAATAT-TTTTATAATATATATACATATA
55362606 TATATATA
1 TATATATA
55362614 TACATCTATA
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
41 12 0.15
43 6 0.08
44 9 0.11
45 7 0.09
47 21 0.27
49 10 0.13
51 2 0.03
52 4 0.05
53 8 0.10
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (43 bp):
TATATATACGTTATACAATATTTTTATAATATATATACATATA
Found at i:55362615 original size:53 final size:50
Alignment explanation
Indices: 55362527--55362625 Score: 126
Period size: 53 Copynumber: 1.9 Consensus size: 50
55362517 ATACGTGTAC
* * *
55362527 ATATTTTTATAACTTATTTATATATATGTATATATACATACTTATATATTCT
1 ATATTTTTATAACTTATATACATATATATATATATACAT-C-TATATATTCT
* *
55362579 ATATATTTTATAATTTATATACATATCTATATATATACATCTATATA
1 ATAT-TTTTATAACTTATATACATATATATATATATACATCTATATA
55362626 CATTTTTTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
51 6 0.15
52 5 0.12
53 30 0.73
ACGTcount: A:0.39, C:0.08, G:0.01, T:0.52
Consensus pattern (50 bp):
ATATTTTTATAACTTATATACATATATATATATATACATCTATATATTCT
Found at i:55363015 original size:21 final size:20
Alignment explanation
Indices: 55362984--55363028 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
55362974 TTGCTCATAT
*
55362984 TATTTTTATTCATATTAT-CA
1 TATTTTTATTC-CATTATGCA
55363004 TATTTATTATTCCATTATGCA
1 TATTT-TTATTCCATTATGCA
55363025 TATT
1 TATT
55363029 AACACCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTTATTCCATTATGCA
Found at i:55363301 original size:107 final size:107
Alignment explanation
Indices: 55363056--55363387 Score: 420
Period size: 107 Copynumber: 3.1 Consensus size: 107
55363046 AAGGAAAATT
* *
55363056 TTTCTAAA-TAAGGCAATGTTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTAATGTGCTGGGTT
1 TTTC-AAAGTAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
** * *
55363120 TCGATTTTTTTTTGTTCGACCAAATAGCCAAATATCCTTTTAAAA
65 TCGA--TTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
* * *
55363165 TTTTAAAGTAAGGA-AATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTGGGTT
1 TTTCAAAGTAA-GACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
*
55363229 TCGATTTTTCCGTCCGACCATATAGCCAAATATCATTTTAAAA
65 TCGATTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
*
55363272 TTTCAAAGTAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTT
1 TTTCAAAGTAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* * ** * * * *
55363337 TGATTTCT-CGT-TTAGCCAAATAGCCAAATACCCTCTTAAAG
66 CGATTTTTCCGTCCGA-CCAAATAGCCAAATATCATTTTAAAA
55363378 TTTCAAAGTA
1 TTTCAAAGTA
55363388 TGGGTTTTGG
Statistics
Matches: 196, Mismatches: 23, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
105 1 0.01
106 36 0.18
107 98 0.50
108 3 0.02
109 57 0.29
110 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.35
Consensus pattern (107 bp):
TTTCAAAGTAAGACAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
Found at i:55366909 original size:33 final size:33
Alignment explanation
Indices: 55366871--55367127 Score: 237
Period size: 33 Copynumber: 7.8 Consensus size: 33
55366861 GGAGTAGAAA
* * *
55366871 CTGATGGGGTGGGTTATGTTGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * *** *
55366904 TTGATGGGGAGGGTGATGTTGAAGGAAAATGAA-
1 CTGATGGGGAGGGTGATGTAGAAGGGGTA-CAAG
* **
55366937 ATGATGATGAGGGTGATGTAGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * * * * *
55366970 TTGATAGGAAGGGTGATGTTGAAGGAGTAGAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* **
55367003 CTGATGTGGAAAGTGATGTAGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * * *
55367036 CTGATGAGGTGGGTAATGTAGATGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* *
55367069 CTGTTGGGGAGGGTGATGTAGAAGGGGTACAAA
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* *
55367102 CTGTTGGGGAGGGTGATGTTGAAGGG
1 CTGATGGGGAGGGTGATGTAGAAGGG
55367128 TAGAAGGTGA
Statistics
Matches: 177, Mismatches: 45, Indels: 4
0.78 0.20 0.02
Matches are distributed among these distances:
32 2 0.01
33 173 0.98
34 2 0.01
ACGTcount: A:0.28, C:0.04, G:0.44, T:0.24
Consensus pattern (33 bp):
CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
Found at i:55366961 original size:66 final size:65
Alignment explanation
Indices: 55366844--55367133 Score: 269
Period size: 66 Copynumber: 4.4 Consensus size: 65
55366834 ATGATTGCTA
* ** * * * * * *
55366844 GGGAGAGTGATGTTGGTGGAGTAGAAACTGATGGGGTGGGTTATGTTGAAGGGGTACAAGTTGAT
1 GGGAGGGTGATGTTGAAGGAGTAGAAGCTGAT-GTGAGGGTGATGTAGAAGGGGTACAAGCTGAT
55366909 G
65 G
** * *
55366910 GGGAGGGTGATGTTGAAGGAAAATGAA-ATGATGATGAGGGTGATGTAGAAGGGGTACAAGTTGA
1 GGGAGGGTGATGTTGAAGGAGTA-GAAGCTGATG-TGAGGGTGATGTAGAAGGGGTACAAGCTGA
*
55366974 TA
64 TG
* **
55366976 GGAAGGGTGATGTTGAAGGAGTAGAAGCTGATGTGGAAAGTGATGTAGAAGGGGTACAAGCTGAT
1 GGGAGGGTGATGTTGAAGGAGTAGAAGCTGATGT-GAGGGTGATGTAGAAGGGGTACAAGCTGAT
55367041 G
65 G
* * * * * * * * * * *
55367042 AGGTGGGTAATGTAGATGGGGTACAAGCTGTTGGGGAGGGTGATGTAGAAGGGGTACAAACTGTT
1 GGGAGGGTGATGTTGAAGGAGTAGAAGCTGAT-GTGAGGGTGATGTAGAAGGGGTACAAGCTGAT
55367107 G
65 G
55367108 GGGAGGGTGATGTTGAAGG-GTAGAAG
1 GGGAGGGTGATGTTGAAGGAGTAGAAG
55367134 GTGACGAGGA
Statistics
Matches: 180, Mismatches: 39, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
65 11 0.06
66 165 0.92
67 4 0.02
ACGTcount: A:0.29, C:0.03, G:0.44, T:0.23
Consensus pattern (65 bp):
GGGAGGGTGATGTTGAAGGAGTAGAAGCTGATGTGAGGGTGATGTAGAAGGGGTACAAGCTGATG
Found at i:55367127 original size:99 final size:99
Alignment explanation
Indices: 55366871--55367127 Score: 273
Period size: 99 Copynumber: 2.6 Consensus size: 99
55366861 GGAGTAGAAA
* * * * *
55366871 CTGATGGGGTGGGTTATGTTGAAGGGGTACAAGTTGATGGGGAGGGTGATGTTGAAGGAAAATGA
1 CTGATGGGGAGGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGGAAATCA
* *
55366936 AATGATGATGAGGGTGATGTAGAAGGGGTACAAG
66 AATGATGAGGAGGGTAATGTAGAAGGGGTACAAG
* * * * * * ** * **
55366970 TTGATAGGAAGGGTGATGTTGAAGGAGTAGAAGCTGATGTGGAAAGTGATGTAGAAGGGGTA-CA
1 CTGATGGGGAGGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGGAAATCA
* * *
55367034 AGCTGATGAGGTGGGTAATGTAGATGGGGTACAAG
66 A-ATGATGAGGAGGGTAATGTAGAAGGGGTACAAG
* * * *
55367069 CTGTTGGGGAGGGTGATGTAGAAGGGGTACAAACTGTTGGGGAGGGTGATGTTGAAGGG
1 CTGATGGGGAGGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGG
55367128 TAGAAGGTGA
Statistics
Matches: 123, Mismatches: 34, Indels: 2
0.77 0.21 0.01
Matches are distributed among these distances:
98 2 0.02
99 121 0.98
ACGTcount: A:0.28, C:0.04, G:0.44, T:0.24
Consensus pattern (99 bp):
CTGATGGGGAGGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGGAAATCA
AATGATGAGGAGGGTAATGTAGAAGGGGTACAAG
Found at i:55372013 original size:22 final size:22
Alignment explanation
Indices: 55371983--55372025 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
55371973 ACAGCAGAAC
* *
55371983 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
55372005 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
55372026 AACGCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:55372306 original size:43 final size:42
Alignment explanation
Indices: 55372115--55372409 Score: 292
Period size: 42 Copynumber: 7.0 Consensus size: 42
55372105 GCGCTTACAT
* *
55372115 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGGTTAT
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
** * * *
55372157 AAAAATGCGCCGCTAAAGATCATGTTCTTTAGTGACGCTTAC
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * **
55372199 AAATAAACGCCGCTAAAGAACATAATCTTTAGCGGCGCTTAG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
* * * *
55372241 AAATAAACGCTGATAAATATCATGTTCTTTAGCGGCGCTTAGG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA-G
* *
55372284 AAAAAAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTTTG
1 AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAG
** * * *
55372327 AGGAAAACGCCTCTAAA-AGTAATGTTCTATAGCGGCGCTT-G
1 AAAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG
**
55372368 TTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 -AAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
55372410 TTTCACAGAT
Statistics
Matches: 212, Mismatches: 35, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.01
42 140 0.66
43 68 0.32
44 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAG
Found at i:55372429 original size:18 final size:18
Alignment explanation
Indices: 55372406--55372443 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
55372396 TTTAGCGGCG
*
55372406 CTTATTTCACAGATGCCA
1 CTTATTTCACAAATGCCA
55372424 CTTATTTCACAAATGCCA
1 CTTATTTCACAAATGCCA
55372442 CT
1 CT
55372444 GTTTTGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (18 bp):
CTTATTTCACAAATGCCA
Found at i:55372921 original size:27 final size:21
Alignment explanation
Indices: 55372859--55372915 Score: 114
Period size: 21 Copynumber: 2.7 Consensus size: 21
55372849 GTTTCTATTG
55372859 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
55372880 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCGGCCT
55372901 CTGCTTCTCTCGCTG
1 CTGCTTCTCTCGCTG
55372916 TAGCTGTTGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCGGCCT
Found at i:55372927 original size:42 final size:42
Alignment explanation
Indices: 55372859--55372948 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
55372849 GTTTCTATTG
* * * *
55372859 CTGCTTCTCTCGCTGCGGCCTCTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCTCTGCTTCCCTCGCTGCCGCAT
* *
55372901 CTGCTTCTCTCGCTGTAG-CTGTTGCTTCCCTCGCTGCCGCAT
1 CTGCTTCTCTCGCTGCAGCCT-CTGCTTCCCTCGCTGCCGCAT
55372943 CTGCTT
1 CTGCTT
55372949 TAAGTTGCTG
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.02, C:0.40, G:0.22, T:0.36
Consensus pattern (42 bp):
CTGCTTCTCTCGCTGCAGCCTCTGCTTCCCTCGCTGCCGCAT
Found at i:55378418 original size:9 final size:9
Alignment explanation
Indices: 55378404--55378596 Score: 149
Period size: 9 Copynumber: 22.8 Consensus size: 9
55378394 AACTTATTTA
55378404 TTATGTAAG
1 TTATGTAAG
55378413 TTATGTAAG
1 TTATGTAAG
*
55378422 TTCTGTAAG
1 TTATGTAAG
55378431 TTATGTAAG
1 TTATGTAAG
*
55378440 CTATGTAAG
1 TTATGTAAG
*
55378449 TTGTGT-A-
1 TTATGTAAG
* *
55378456 TTATGAAAC
1 TTATGTAAG
55378465 TTATGTAAG
1 TTATGTAAG
*
55378474 TTATGT--C
1 TTATGTAAG
55378481 TTATGTAAG
1 TTATGTAAG
* *
55378490 TGATGTAAA
1 TTATGTAAG
*
55378499 ATATGT-A-
1 TTATGTAAG
55378506 TTATGTAAG
1 TTATGTAAG
*
55378515 TTATGTCAG
1 TTATGTAAG
*
55378524 TTGTGT-A-
1 TTATGTAAG
*
55378531 TTATGTAAA
1 TTATGTAAG
55378540 TTATGT-A-
1 TTATGTAAG
55378547 TTATGTAAG
1 TTATGTAAG
*
55378556 TTATGTAAT
1 TTATGTAAG
*
55378565 TTGTGT-A-
1 TTATGTAAG
*
55378572 TTATGTAAC
1 TTATGTAAG
* *
55378581 TTATTTAAT
1 TTATGTAAG
55378590 TTATGTA
1 TTATGTA
55378597 CGGTATGTGT
Statistics
Matches: 147, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
7 31 0.21
8 10 0.07
9 106 0.72
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:55378469 original size:25 final size:25
Alignment explanation
Indices: 55378397--55378553 Score: 131
Period size: 25 Copynumber: 6.3 Consensus size: 25
55378387 TAGGAATAAC
* *
55378397 TTATTTATTATGTAAGTTATGTAAG
1 TTATGTATTATGAAAGTTATGTAAG
* * *
55378422 TTCTGTAAGTTATGTAAGCTATGTAAG
1 TTATGT-A-TTATGAAAGTTATGTAAG
* *
55378449 TTGTGTATTATGAAACTTATGTAAG
1 TTATGTATTATGAAAGTTATGTAAG
* * * *
55378474 TTATGTCTTATGTAAGTGATGTAAA
1 TTATGTATTATGAAAGTTATGTAAG
* * *
55378499 ATATGTATTATGTAAGTTATGTCAG
1 TTATGTATTATGAAAGTTATGTAAG
*
55378524 TTGTGTATTATGTAAA-TTATGT-A-
1 TTATGTATTATG-AAAGTTATGTAAG
55378547 TTATGTA
1 TTATGTA
55378554 AGTTATGTAA
Statistics
Matches: 107, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
23 6 0.06
24 1 0.01
25 74 0.69
26 4 0.04
27 22 0.21
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.46
Consensus pattern (25 bp):
TTATGTATTATGAAAGTTATGTAAG
Found at i:55378483 original size:16 final size:16
Alignment explanation
Indices: 55378397--55378562 Score: 98
Period size: 16 Copynumber: 10.4 Consensus size: 16
55378387 TAGGAATAAC
*
55378397 TTATTTATTATGTAAG
1 TTATGTATTATGTAAG
*
55378413 TTATGTAAGTTCTGTAAG
1 TTATGT-A-TTATGTAAG
*
55378431 TTATGTAAGCTATGTAAG
1 TTATGT-A-TTATGTAAG
*
55378449 TTGTGTATTATG-AA-
1 TTATGTATTATGTAAG
*
55378463 --A---CTTATGTAAG
1 TTATGTATTATGTAAG
*
55378474 TTATGTCTTATGTAAG
1 TTATGTATTATGTAAG
* *
55378490 TGATGTAAAATATGT-A-
1 TTATGT--ATTATGTAAG
*
55378506 TTATGTAAGTTATGTCAG
1 TTATGT-A-TTATGTAAG
* *
55378524 TTGTGTATTATGTAAA
1 TTATGTATTATGTAAG
55378540 TTATGTATTATGTAAG
1 TTATGTATTATGTAAG
55378556 TTATGTA
1 TTATGTA
55378563 ATTTGTGTAT
Statistics
Matches: 118, Mismatches: 18, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
9 5 0.04
10 2 0.02
13 1 0.01
15 4 0.03
16 62 0.53
17 5 0.04
18 39 0.33
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.46
Consensus pattern (16 bp):
TTATGTATTATGTAAG
Found at i:55378506 original size:50 final size:50
Alignment explanation
Indices: 55378402--55378579 Score: 160
Period size: 50 Copynumber: 3.7 Consensus size: 50
55378392 ATAACTTATT
* ** *
55378402 TATTATGTAAGTTATGTAAGTTCTGTAAGTTATGTAAGCTATGTAAGTTGTG
1 TATTATGTAAGTTATGTAAGTTATGT-A-TTATGTAAGCTATGTAAAATATG
* * *
55378454 TATTATGAAACTTATGTAAGTTATGTCTTATGTAAG-TGATGTAAAATATG
1 TATTATGTAAGTTATGTAAGTTATGTATTATGTAAGCT-ATGTAAAATATG
* *
55378504 TATTATGTAAGTTATGTCAGTTGTGTATTATGTAA---A--T----TATG
1 TATTATGTAAGTTATGTAAGTTATGTATTATGTAAGCTATGTAAAATATG
* *
55378545 TATTATGTAAGTTATGTAATTTGTGTATTATGTAA
1 TATTATGTAAGTTATGTAAGTTATGTATTATGTAA
55378580 CTTATTTAAT
Statistics
Matches: 111, Mismatches: 14, Indels: 13
0.80 0.10 0.09
Matches are distributed among these distances:
41 37 0.33
45 1 0.01
47 1 0.01
49 1 0.01
50 48 0.43
52 23 0.21
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (50 bp):
TATTATGTAAGTTATGTAAGTTATGTATTATGTAAGCTATGTAAAATATG
Found at i:55378510 original size:41 final size:40
Alignment explanation
Indices: 55378465--55378579 Score: 133
Period size: 41 Copynumber: 2.8 Consensus size: 40
55378455 ATTATGAAAC
55378465 TTATGTAAGTTATGTC-TTATGTAAGTGATGTAAAATATGTA
1 TTATGTAAGTTATGTCATTATGT-A-TGATGTAAAATATGTA
* * *
55378506 TTATGTAAGTTATGTCAGTTGTGTATTATGTAAATTATGTA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAAAATATGTA
* * *
55378547 TTATGTAAGTTATGTAATTTGTGTATTATGTAA
1 TTATGTAAGTTATGTCA-TTATGTATGATGTAA
55378580 CTTATTTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 61 0.91
42 1 0.01
43 5 0.07
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.48
Consensus pattern (40 bp):
TTATGTAAGTTATGTCATTATGTATGATGTAAAATATGTA
Found at i:55378559 original size:25 final size:24
Alignment explanation
Indices: 55378403--55378596 Score: 99
Period size: 25 Copynumber: 7.7 Consensus size: 24
55378393 TAACTTATTT
* *
55378403 ATTATGTAAGTTATGTAAGTTCTGTA
1 ATTATGTAATTTATGT-A-TTATGTA
** *
55378429 AGTTATGTAAGCTATGTAAGTTGTGT-
1 A-TTATGTAATTTATGT-A-TTATGTA
* *
55378455 ATTATGAAACTTATGTAAGTTATGT-
1 ATTATGTAATTTATGT-A-TTATGTA
* * * *
55378480 CTTATGTAAGTGATGTAAAATATGT-
1 ATTATGTAATTTATGT--ATTATGTA
* *
55378505 ATTATGTAAGTTATGTCAGTTGTGT-
1 ATTATGTAATTTATGT-A-TTATGTA
*
55378530 ATTATGTAAATTATGTATTATGTA
1 ATTATGTAATTTATGTATTATGTA
*
55378554 AGTTATGTAATTTGTGTATTATGTA
1 A-TTATGTAATTTATGTATTATGTA
*
55378579 ACTTATTTAATTTATGTA
1 A-TTATGTAATTTATGTA
55378597 CGGTATGTGT
Statistics
Matches: 140, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
23 5 0.04
24 3 0.02
25 106 0.76
26 4 0.03
27 22 0.16
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (24 bp):
ATTATGTAATTTATGTATTATGTA
Found at i:55378798 original size:87 final size:86
Alignment explanation
Indices: 55378700--55379054 Score: 402
Period size: 87 Copynumber: 4.0 Consensus size: 86
55378690 CTTAAAAATT
*
55378700 TAATACTAATAAATTTA-ATATTTAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTAT
1 TAATACTAAT--ATTTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTAT
55378764 AGGTTATATTAAAACAATATTTA
64 AGGTTATATTAAAACAATATTTA
*
55378787 TAATACTAATAAATTTA-ATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTAT
1 TAATACTAAT--ATTTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTAT
55378851 AGGTTATATTAAAACAATATTTA
64 AGGTTATATTAAAACAATATTTA
* * * *
55378874 TAATACTAATA--TAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAAATT
1 TAATACTAATATTTAGATATTAAAACAATATTTATAATTATTTAGAAA---ACT--T-TTAAATT
* * * *
55378937 TAATA-CTAATA-TAGAAACCTTATAAATTTA
60 TTATAGGTTATATTA-AAA-C--A-ATATTTA
* * *
55378967 GAAAACT--TATATAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAG
1 TAATACTAATATTTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAG
55379030 GTTATATTAAAACAATATTTA
66 GTTATATTAAAACAATATTTA
55379051 TAAT
1 TAAT
55379055 TATTTAGAAA
Statistics
Matches: 229, Mismatches: 23, Indels: 35
0.80 0.08 0.12
Matches are distributed among these distances:
83 2 0.01
84 38 0.17
85 2 0.01
87 107 0.47
88 10 0.04
89 10 0.04
90 13 0.06
91 2 0.01
92 1 0.00
93 44 0.19
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.42
Consensus pattern (86 bp):
TAATACTAATATTTAGATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAG
GTTATATTAAAACAATATTTA
Found at i:55378827 original size:18 final size:18
Alignment explanation
Indices: 55378767--55378827 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
55378757 ATTTTATAGG
55378767 TTAT-ATTAAAACAATAT
1 TTATAATTAAAACAATAT
* *
55378784 TTATAA-TACTAATAA-AT
1 TTATAATTA-AAACAATAT
55378801 TTA-ATATTAAAACAATAT
1 TTATA-ATTAAAACAATAT
55378819 TTATAATTA
1 TTATAATTA
55378828 TTTAGAAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 11
0.69 0.08 0.22
Matches are distributed among these distances:
16 1 0.03
17 16 0.47
18 16 0.47
19 1 0.03
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTATAATTAAAACAATAT
Found at i:55378935 original size:15 final size:15
Alignment explanation
Indices: 55378915--55378947 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55378905 AGAATTATTT
*
55378915 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
55378930 ATAAATTTAATACTA
1 ATAAATTTAATACTA
55378945 ATA
1 ATA
55378948 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:55379013 original size:42 final size:46
Alignment explanation
Indices: 55378962--55379106 Score: 154
Period size: 52 Copynumber: 3.0 Consensus size: 46
55378952 AACCTTATAA
55378962 ATTTAGAAAACTT-A-TATA-G-ATATTAAAACAATATTTATAATT
1 ATTTAGAAAACTTAATTATAGGTATATTAAAACAATATTTATAATT
55379004 ATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAATATTTATAATT
1 ATTTAGAAAAC--TT-AA--TTATAGG-TATATTAAAACAATATTTATAATT
55379056 ATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAATATTTATAAT
1 ATTTAGAAAAC--TT-AA--TTATAGG-TATATTAAAACAATATTTATAAT
55379107 ACTAATATAG
Statistics
Matches: 93, Mismatches: 0, Indels: 10
0.90 0.00 0.10
Matches are distributed among these distances:
42 11 0.12
44 2 0.02
46 1 0.01
49 4 0.04
50 1 0.01
52 74 0.80
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (46 bp):
ATTTAGAAAACTTAATTATAGGTATATTAAAACAATATTTATAATT
Found at i:55379019 original size:21 final size:21
Alignment explanation
Indices: 55378962--55379023 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 21
55378952 AACCTTATAA
*
55378962 ATTTAGAAAACTTATATAGA-T
1 ATTTAGAAAACTTTTATA-ATT
*
55378983 A-TTA-AAACAATATTTATAATT
1 ATTTAGAAA-ACT-TTTATAATT
55379004 ATTTAGAAAACTTTTA-AATT
1 ATTTAGAAAACTTTTATAATT
55379024 TTATAGGTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 11
0.70 0.06 0.23
Matches are distributed among these distances:
19 3 0.09
20 10 0.30
21 12 0.36
22 5 0.15
23 3 0.09
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.42
Consensus pattern (21 bp):
ATTTAGAAAACTTTTATAATT
Found at i:55379037 original size:52 final size:52
Alignment explanation
Indices: 55378981--55379106 Score: 252
Period size: 52 Copynumber: 2.4 Consensus size: 52
55378971 ACTTATATAG
55378981 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTT
1 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTT
55379033 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTT
1 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTT
55379085 ATATTAAAACAATATTTATAAT
1 ATATTAAAACAATATTTATAAT
55379107 ACTAATATAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (52 bp):
ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTT
Found at i:55379050 original size:24 final size:24
Alignment explanation
Indices: 55379023--55379104 Score: 71
Period size: 24 Copynumber: 3.2 Consensus size: 24
55379013 ACTTTTAAAT
55379023 TTTATAGGTTATATTAAAACAATA
1 TTTATAGGTTATATTAAAACAATA
*
55379047 TTTATA-ATTAT-TTAGAAAACTTTTAA-A
1 TTTATAGGTTATATT--AAAAC----AATA
55379074 TTTTATAGGTTATATTAAAACAATA
1 -TTTATAGGTTATATTAAAACAATA
55379099 TTTATA
1 TTTATA
55379105 ATACTAATAT
Statistics
Matches: 46, Mismatches: 2, Indels: 20
0.68 0.03 0.29
Matches are distributed among these distances:
22 2 0.04
23 4 0.09
24 19 0.41
25 1 0.02
27 1 0.02
28 13 0.28
29 4 0.09
30 2 0.04
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (24 bp):
TTTATAGGTTATATTAAAACAATA
Found at i:55379089 original size:229 final size:229
Alignment explanation
Indices: 55378804--55379241 Score: 849
Period size: 229 Copynumber: 1.9 Consensus size: 229
55378794 AATAAATTTA
55378804 ATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATAGGTTATATTAAAACAAT
1 ATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATAGGTTATATTAAAACAAT
55378869 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
66 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
55378934 ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAGATATTAAAACAATATTTA
131 ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAGATATTAAAACAATATTTA
55378999 TAATTATTTAGAAAACTTTTAAATTTTATAGGTT
196 TAATTATTTAGAAAACTTTTAAATTTTATAGGTT
*
55379033 ATATTAAAACAATATTTATAATTATTTAGAAAACTTTTAAATTTTATAGGTTATATTAAAACAAT
1 ATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATAGGTTATATTAAAACAAT
*
55379098 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTTTTTATAAATTTAATAGTAATAA
66 ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
*
55379163 ATTTAATACTAATATAGAAACCTTATAAGTTTAGAAAACTTATATAGATATTAAAACAATATTTA
131 ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAGATATTAAAACAATATTTA
55379228 TAATTATTTAGAAA
196 TAATTATTTAGAAA
55379242 TGTTATCATT
Statistics
Matches: 206, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 206 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (229 bp):
ATATTAAAACAATATTTATAATTATTTAGAAAACATTTAAATTTTATAGGTTATATTAAAACAAT
ATTTATAATACTAATATAGATATTAAAACAATATTTAGAATTATTTATAAATTTAATAGTAATAA
ATTTAATACTAATATAGAAACCTTATAAATTTAGAAAACTTATATAGATATTAAAACAATATTTA
TAATTATTTAGAAAACTTTTAAATTTTATAGGTT
Found at i:55379164 original size:15 final size:15
Alignment explanation
Indices: 55379144--55379176 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
55379134 AGAATTTTTT
*
55379144 ATAAATTTAATAGTA
1 ATAAATTTAATACTA
55379159 ATAAATTTAATACTA
1 ATAAATTTAATACTA
55379174 ATA
1 ATA
55379177 TAGAAACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:55380572 original size:181 final size:188
Alignment explanation
Indices: 55380205--55380581 Score: 606
Period size: 195 Copynumber: 2.0 Consensus size: 188
55380195 TACGGAATAA
55380205 TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGA
1 TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGA
55380270 CGACTGCAAATGCGGGTTATAGAGCGACCGCCGGAGTGGAGCCGACTGCAATGACAGGGGGGATT
66 CGACTGCAAATGCGGGTTATAGAGCGACCGCCGGAGTGGAGCCGACTGCAATGACAGGGGGGATT
*
55380335 TGGGAATTTGGGGATTTAGGGAAATTAAATCGGGGAAACTGGGGGAATAGGAATTGGGGGAAAAT
131 TGGGAA------GATTTAGGGAAATT--ATCAGGGAAACTGGGGGAATAGGAATTGGGGGAAAAT
55380400 G
188 G
*
55380401 TGGGC-TTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTGAATAGAAGAAGTAGA
1 TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGA
55380465 CGACTGCAAATGCGGGTTATAGAGCGACCGCCGGAGTGGAGCCGACTGCAATGACAGGGGGGATT
66 CGACTGCAAATGCGGGTTATAGAGCGACCGCCGGAGTGGAGCCGACTGCAATGACAGGGGGGATT
*
55380530 TGGG-A-ATTT-GGG-AATT-T-AGGGAAACTGGGGGAATAGGAATTGGGGGGAAATG
131 TGGGAAGATTTAGGGAAATTATCAGGGAAACTGGGGGAATAGGAATTGGGGGAAAATG
55380582 AAATCGGGGA
Statistics
Matches: 178, Mismatches: 3, Indels: 15
0.91 0.02 0.08
Matches are distributed among these distances:
181 33 0.19
182 1 0.01
185 4 0.02
186 3 0.02
187 4 0.02
194 1 0.01
195 127 0.71
196 5 0.03
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (188 bp):
TGGGCTTTAATCCGAAGAAATATAACCTTAACCGAATAGAAGAAACACTAAATAGAAGAAGTAGA
CGACTGCAAATGCGGGTTATAGAGCGACCGCCGGAGTGGAGCCGACTGCAATGACAGGGGGGATT
TGGGAAGATTTAGGGAAATTATCAGGGAAACTGGGGGAATAGGAATTGGGGGAAAATG
Found at i:55380594 original size:24 final size:24
Alignment explanation
Indices: 55380565--55380618 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
55380555 TGGGGGAATA
55380565 GGAATTGGGGGGAA-ATGAAATCGG
1 GGAATTGGGGGGAATATGAAAT-GG
55380589 GGAATTGGGGGGAATATGAAATGG
1 GGAATTGGGGGGAATATGAAATGG
*
55380613 GAAATT
1 GGAATT
55380619 AGGGAATGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.35, C:0.02, G:0.43, T:0.20
Consensus pattern (24 bp):
GGAATTGGGGGGAATATGAAATGG
Found at i:55381188 original size:22 final size:22
Alignment explanation
Indices: 55381158--55381206 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
55381148 CCCTAAGTTT
*
55381158 AACCCGTAACCTTTATACTTTA
1 AACCCGTAACCTTTAAACTTTA
*
55381180 AACCTGTAACCTTTAAACTTTA
1 AACCCGTAACCTTTAAACTTTA
55381202 AACCC
1 AACCC
55381207 TAAACTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.33
Consensus pattern (22 bp):
AACCCGTAACCTTTAAACTTTA
Found at i:55381398 original size:53 final size:54
Alignment explanation
Indices: 55381278--55381400 Score: 157
Period size: 53 Copynumber: 2.3 Consensus size: 54
55381268 CTTAAATTAT
* *
55381278 AAACTAC-AAGCCCTAAAATACTAATTAATCCCAAACCCCAAACCGTTAACCAG
1 AAACTACTAAGCCCTAAAATACTAATTAATCCCAAACCCCAAAACGTTAACCAC
* *
55381331 AAGC-A-TCAAGCCCTAAAATACTAATTAATCCCAAACCCCAAAAC-TTAAACCCC
1 AAACTACT-AAGCCCTAAAATACTAATTAATCCCAAACCCCAAAACGTT-AACCAC
55381384 AAACTACTAA-CCCTAAA
1 AAACTACTAAGCCCTAAA
55381401 CCCAAGACAC
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
52 3 0.05
53 53 0.88
54 3 0.05
55 1 0.02
ACGTcount: A:0.46, C:0.33, G:0.04, T:0.17
Consensus pattern (54 bp):
AAACTACTAAGCCCTAAAATACTAATTAATCCCAAACCCCAAAACGTTAACCAC
Found at i:55382151 original size:189 final size:189
Alignment explanation
Indices: 55381843--55382235 Score: 578
Period size: 189 Copynumber: 2.1 Consensus size: 189
55381833 GCGTTTGAAC
*
55381843 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATATTTTGC
1 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
*
55381908 GGCGTTTTCATATAAGCGCCACTAAATGTAACATAGCTTAAGACAAACCACTGCGTTTTGTTAAG
66 GGCGTTTTCATATAAGCGCCACTAAATGTAACATAACTTAAGACAAACCACTGCGTTTTGTTAAG
* ** *
55381973 ATACGTTGCGGCGCTTTACCCAAAGCGCTGCTAAAT-ATATTCTTTAACGGCGTTTTCTA
131 ATACGTTGCGGCGCTTCACCCAAAGCGCCACT-AATGATATTCTATAACGGCGTTTTCTA
* * *
55382032 GTAAGCGCCACTAATTGAAGTATACATCGAGACCAAAATGGTGTGTTTTGGTTCAGATAGTTTGC
1 GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
*
55382097 GGCGTTTTGC-TATAAGCGCCACTAAATGTAACATAACTTCAA-ATGAAA-CACTGCGTTTTGTT
66 GGCGTTTT-CATATAAGCGCCACTAAATGTAACATAACTT-AAGA-CAAACCACTGCGTTTTGTT
* * ** * *
55382159 AAGGTACTTTGCGGCGCTTCGGCTAAAGCGCCACTAATGCTATTCTATAACGGCGTTTTCTA
128 AAGATACGTTGCGGCGCTTCACCCAAAGCGCCACTAATGATATTCTATAACGGCGTTTTCTA
55382221 GTAAGCGCCACTAAT
1 GTAAGCGCCACTAAT
55382236 ATAATCAAAA
Statistics
Matches: 184, Mismatches: 16, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
188 3 0.02
189 175 0.95
190 6 0.03
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (189 bp):
GTAAGCGCCACTAATTAAAGTATACATCGAGACCAAAACGGTGCGTTTTGGTTCAGATAGTTTGC
GGCGTTTTCATATAAGCGCCACTAAATGTAACATAACTTAAGACAAACCACTGCGTTTTGTTAAG
ATACGTTGCGGCGCTTCACCCAAAGCGCCACTAATGATATTCTATAACGGCGTTTTCTA
Found at i:55386403 original size:43 final size:44
Alignment explanation
Indices: 55386331--55386420 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 44
55386321 ACGTCGCTAA
*
55386331 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATT
1 CTTTAGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATT
* *
55386375 CTTTAGCGGCGC-TA-AGGAAATAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTACA-GAAAAAAACGCCGCTAAAGATCATATT
55386418 CTT
1 CTT
55386421 CATAAGCGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
42 1 0.02
43 30 0.71
44 11 0.26
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (44 bp):
CTTTAGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATT
Found at i:55386434 original size:28 final size:28
Alignment explanation
Indices: 55386394--55386448 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
55386384 CGCTAAGGAA
* *
55386394 ATAAACGCCGCTAAAGATCATGTTCTTC
1 ATAAACGCCGCTAAAGAACATGATCTTC
*
55386422 ATAAGCGCCGCTAAAGAACATGATCTT
1 ATAAACGCCGCTAAAGAACATGATCTT
55386449 TAGCGGCACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.25
Consensus pattern (28 bp):
ATAAACGCCGCTAAAGAACATGATCTTC
Found at i:55386488 original size:71 final size:71
Alignment explanation
Indices: 55386356--55386490 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
55386346 CAGAAAAAAA
* * *
55386356 CGCCGCTAAAGATCATATTCTTTAGCGGCGCTAAGGAAATAAACGCCGCTAAAGATCATGTTCTT
1 CGCCGCTAAAGAACATATTCTTTAGCGGCACTAAGGAAATAAACGCCGCTAAAGATAATGTTCTT
55386421 CATAAG
66 CATAAG
*
55386427 CGCCGCTAAAGAACATGA-TCTTTAGCGGCACTTAGGAAGA-AAACGCCGCTAAA-AGTAATGTT
1 CGCCGCTAAAGAACAT-ATTCTTTAGCGGCACTAAGGAA-ATAAACGCCGCTAAAGA-TAATGTT
55386489 CT
63 CT
55386491 ATAGCGGTGC
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
70 1 0.02
71 54 0.95
72 2 0.04
ACGTcount: A:0.33, C:0.22, G:0.21, T:0.24
Consensus pattern (71 bp):
CGCCGCTAAAGAACATATTCTTTAGCGGCACTAAGGAAATAAACGCCGCTAAAGATAATGTTCTT
CATAAG
Found at i:55386496 original size:43 final size:42
Alignment explanation
Indices: 55386427--55386540 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
55386417 TCTTCATAAG
* *
55386427 CGCCGCT-AAAGAACATGATCTTTAGCGGCACTTAGG-AAGAAAA
1 CGCCGCTAAAAGTA-ATGTTCTTTAGCGGCACTT-GGTAA-AAAA
* ** *
55386470 CGCCGCTAAAAGTAATGTTCTATAGCGGTGCTTGGTCAAAAA
1 CGCCGCTAAAAGTAATGTTCTTTAGCGGCACTTGGTAAAAAA
*
55386512 CGCCGCTAAAAGTAGTGTTCTTTAGCGGC
1 CGCCGCTAAAAGTAATGTTCTTTAGCGGC
55386541 GTTTATTTCA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
42 32 0.53
43 23 0.38
44 5 0.08
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.24
Consensus pattern (42 bp):
CGCCGCTAAAAGTAATGTTCTTTAGCGGCACTTGGTAAAAAA
Found at i:55386991 original size:21 final size:21
Alignment explanation
Indices: 55386967--55387038 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
55386957 TTCTTTTGAA
* *
55386967 CCTCTACTTCTCTCGCTGCGG
1 CCTCTGCTTCTCTCGCTGCAG
*
55386988 CCTCTGCTTCTCTCGCTGTAG
1 CCTCTGCTTCTCTCGCTGCAG
* * *
55387009 CCTCTGCTTCCCTCACTGCCG
1 CCTCTGCTTCTCTCGCTGCAG
55387030 CCTCTGCTT
1 CCTCTGCTT
55387039 TAAGTTGTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.04, C:0.44, G:0.17, T:0.35
Consensus pattern (21 bp):
CCTCTGCTTCTCTCGCTGCAG
Found at i:55388091 original size:25 final size:25
Alignment explanation
Indices: 55388063--55388322 Score: 235
Period size: 25 Copynumber: 10.4 Consensus size: 25
55388053 ATAAAGTAAA
*
55388063 TATGAAAATTATGTAAGTTATTTAT
1 TATGAAAATTATGTAAGTTATGTAT
*
55388088 TATGAAAATTATGTAAGTTGTGTAT
1 TATGAAAATTATGTAAGTTATGTAT
* *
55388113 TATGAAAATTATGCTATG-TAAG--T
1 TATGAAAATTATG-TAAGTTATGTAT
* * * *
55388136 TATGTAAGTCATATAAGTTATGTAT
1 TATGAAAATTATGTAAGTTATGTAT
* * *
55388161 TATGTAAGTTATGTAAGTTATTTAT
1 TATGAAAATTATGTAAGTTATGTAT
*
55388186 TATGAAAATTATGTAAGTTGTGTAT
1 TATGAAAATTATGTAAGTTATGTAT
* *
55388211 TATGAAAATTATGCTATG-TAAG--T
1 TATGAAAATTATG-TAAGTTATGTAT
* * * *
55388234 TATGTAAGTCATATAAGTTATGTAT
1 TATGAAAATTATGTAAGTTATGTAT
* * *
55388259 TATGTAAGTTATGTAAGTTATTTAT
1 TATGAAAATTATGTAAGTTATGTAT
*
55388284 TATGAAAATTAAGTAAGTTATGTAATT
1 TATGAAAATTATGTAAGTTATGT-A-T
55388311 TATGAATAATTA
1 TATGAA-AATTA
55388323 AAAAAATGTA
Statistics
Matches: 190, Mismatches: 34, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
22 6 0.03
23 26 0.14
25 139 0.73
26 7 0.04
27 7 0.04
28 5 0.03
ACGTcount: A:0.38, C:0.02, G:0.16, T:0.45
Consensus pattern (25 bp):
TATGAAAATTATGTAAGTTATGTAT
Found at i:55388139 original size:9 final size:9
Alignment explanation
Indices: 55388127--55388596 Score: 222
Period size: 9 Copynumber: 54.7 Consensus size: 9
55388117 AAAATTATGC
55388127 TATGTAAGT
1 TATGTAAGT
55388136 TATGTAAGT
1 TATGTAAGT
* *
55388145 CATATAAGT
1 TATGTAAGT
55388154 TATGT-A-T
1 TATGTAAGT
55388161 TATGTAAGT
1 TATGTAAGT
55388170 TATGTAAGT
1 TATGTAAGT
*
55388179 TAT-TTA-T
1 TATGTAAGT
* *
55388186 TATGAAAAT
1 TATGTAAGT
55388195 TATGTAAGT
1 TATGTAAGT
*
55388204 TGTGT-A-T
1 TATGTAAGT
55388211 TATG-AA--
1 TATGTAAGT
* * *
55388217 AAT-TATGC
1 TATGTAAGT
55388225 TATGTAAGT
1 TATGTAAGT
55388234 TATGTAAGT
1 TATGTAAGT
* *
55388243 CATATAAGT
1 TATGTAAGT
55388252 TATGT-A-T
1 TATGTAAGT
55388259 TATGTAAGT
1 TATGTAAGT
55388268 TATGTAAGT
1 TATGTAAGT
*
55388277 TAT-TTA-T
1 TATGTAAGT
* *
55388284 TATGAAAAT
1 TATGTAAGT
*
55388293 TAAGTAAGT
1 TATGTAAGT
*
55388302 TATGTAATT
1 TATGTAAGT
55388311 TATG-AA-T
1 TATGTAAGT
* **
55388318 AAT-TAAAAA
1 TATGT-AAGT
*
55388327 AATGTAAGT
1 TATGTAAGT
55388336 TATGTAAG-
1 TATGTAAGT
55388344 T-TGTAAGT
1 TATGTAAGT
55388352 TATGTAAGT
1 TATGTAAGT
*
55388361 TATGTATA-A
1 TATGTA-AGT
55388370 TAT-TAA-T
1 TATGTAAGT
55388377 TAAT-TAAGT
1 T-ATGTAAGT
*
55388386 TATGTAATT
1 TATGTAAGT
*
55388395 TATGTATTGCAT
1 TATGTA-AG--T
55388407 TAATGTAAGT
1 T-ATGTAAGT
*
55388417 TATGTAATT
1 TATGTAAGT
55388426 TATG-AA-T
1 TATGTAAGT
* **
55388433 AAT-TAAAAA
1 TATGT-AAGT
*
55388442 AATGTAAGT
1 TATGTAAGT
55388451 TATGTAAG-
1 TATGTAAGT
55388459 T-TGTAAGT
1 TATGTAAGT
*
55388467 TATGTAATT
1 TATGTAAGT
55388476 TATG-AA-T
1 TATGTAAGT
* **
55388483 AAT-TAAAAA
1 TATGT-AAGT
*
55388492 AATGTAAGT
1 TATGTAAGT
*
55388501 TATGTAATT
1 TATGTAAGT
*
55388510 TATGTTTAATAT
1 TATG--TAA-GT
55388522 TAATGTAAGT
1 T-ATGTAAGT
55388532 TATGTAAG-
1 TATGTAAGT
55388540 T-TGTAAGT
1 TATGTAAGT
55388548 TATGTAAGT
1 TATGTAAGT
*
55388557 TATGTATA-A
1 TATGTA-AGT
55388566 TAT-TAA-T
1 TATGTAAGT
55388573 TAAT-TAAGT
1 T-ATGTAAGT
55388582 TATGTAAGT
1 TATGTAAGT
55388591 TATGTA
1 TATGTA
55388597 TAATACTAAT
Statistics
Matches: 358, Mismatches: 56, Indels: 94
0.70 0.11 0.19
Matches are distributed among these distances:
6 3 0.01
7 56 0.16
8 49 0.14
9 222 0.62
10 9 0.03
11 6 0.02
12 5 0.01
13 8 0.02
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (9 bp):
TATGTAAGT
Found at i:55388166 original size:34 final size:34
Alignment explanation
Indices: 55388127--55388276 Score: 161
Period size: 34 Copynumber: 4.5 Consensus size: 34
55388117 AAAATTATGC
55388127 TATGTAAGTTATGTAAGTCATATAAGTTATGTAT
1 TATGTAAGTTATGTAAGTCATATAAGTTATGTAT
* * *
55388161 TATGTAAGTTATGTAAGTTAT-TTA-TTATGAAAAT
1 TATGTAAGTTATGTAAGTCATATAAGTTATG--TAT
* * * *
55388195 TATGTAAGTTGTGT-A-TTATGA-AAATTATG--C
1 TATGTAAGTTATGTAAGTCAT-ATAAGTTATGTAT
55388225 TATGTAAGTTATGTAAGTCATATAAGTTATGTAT
1 TATGTAAGTTATGTAAGTCATATAAGTTATGTAT
55388259 TATGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGT
55388277 TATTTATTAT
Statistics
Matches: 96, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
30 13 0.14
31 2 0.02
32 19 0.20
33 4 0.04
34 58 0.60
ACGTcount: A:0.35, C:0.02, G:0.18, T:0.45
Consensus pattern (34 bp):
TATGTAAGTTATGTAAGTCATATAAGTTATGTAT
Found at i:55388240 original size:98 final size:98
Alignment explanation
Indices: 55388071--55388366 Score: 461
Period size: 98 Copynumber: 3.0 Consensus size: 98
55388061 AATATGAAAA
55388071 TTATGTAAGTTATTTATTATGAAAATTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAGT
1 TTATGTAAGTTATTTATTATGAAAATTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAGT
55388136 TATGTAAGTCATATAAGTTATGTATTATGTAAG
66 TATGTAAGTCATATAAGTTATGTATTATGTAAG
55388169 TTATGTAAGTTATTTATTATGAAAATTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAGT
1 TTATGTAAGTTATTTATTATGAAAATTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAGT
55388234 TATGTAAGTCATATAAGTTATGTATTATGTAAG
66 TATGTAAGTCATATAAGTTATGTATTATGTAAG
* * ****
55388267 TTATGTAAGTTATTTATTATGAAAATTAAGTAAGTTATGTAATTTATGAATAATTAAAAAAATGT
1 TTATGTAAGTTATTTATTATGAAAATTATGTAAGTTGTGT-A-TTATGAA-AATT-ATGCTATGT
*
55388332 AAGTTATGTAAGT--TGTAAGTTATGTAAGTTATGTA
62 AAGTTATGTAAGTCATATAAGTTATGT-A-TTATGTA
55388367 TAATATTAAT
Statistics
Matches: 185, Mismatches: 7, Indels: 8
0.93 0.04 0.04
Matches are distributed among these distances:
98 136 0.74
99 1 0.01
100 18 0.10
101 5 0.03
102 25 0.14
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.44
Consensus pattern (98 bp):
TTATGTAAGTTATTTATTATGAAAATTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAGT
TATGTAAGTCATATAAGTTATGTATTATGTAAG
Found at i:55388300 original size:34 final size:35
Alignment explanation
Indices: 55388194--55388345 Score: 118
Period size: 34 Copynumber: 4.3 Consensus size: 35
55388184 ATTATGAAAA
* *
55388194 TTATGTAAGTTGTGTATTATGAAAATTATGCTATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTA----ATGTAAG
*
55388233 TTATGTAAGTCATAT-AAGTTATG--TATT-ATGTAAG
1 TTATGTAAGT--TATGAA-TTATGAAAATTAATGTAAG
**
55388267 TTATGTAAGTTATTTATTATGAAAATTAA-GTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
* * * *
55388301 TTATGTAATTTATGAATAATTAAAA-AAATGTAAG
1 TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
55388335 TTATGTAAGTT
1 TTATGTAAGTT
55388346 GTAAGTTATG
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
32 8 0.09
33 3 0.03
34 60 0.65
35 1 0.01
39 13 0.14
40 1 0.01
41 7 0.08
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.43
Consensus pattern (35 bp):
TTATGTAAGTTATGAATTATGAAAATTAATGTAAG
Found at i:55388350 original size:16 final size:16
Alignment explanation
Indices: 55388329--55388361 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55388319 ATTAAAAAAA
55388329 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
55388345 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
55388361 T
1 T
55388362 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:55388350 original size:50 final size:50
Alignment explanation
Indices: 55388296--55388507 Score: 203
Period size: 50 Copynumber: 3.9 Consensus size: 50
55388286 TGAAAATTAA
*
55388296 GTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
* *
55388346 GTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAGTTATGTAATTTATGT-A-TT
1 GTAAGTTATGTAAGTTATGAAT-A-ATTAA--AA--AA---ATGTAAGTTATGTAAGTT
* *
55388403 GCATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
1 G---TAA-GTTA----TGTAAGTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
*
55388461 GTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAA
1 GTAAGTTATGTAAGTTATGAATAATTAAAAAAATGTAAGTTATGTAA
55388508 TTTATGTTTA
Statistics
Matches: 135, Mismatches: 8, Indels: 38
0.75 0.04 0.21
Matches are distributed among these distances:
50 59 0.44
51 1 0.01
52 5 0.04
54 5 0.04
55 3 0.02
56 14 0.10
57 4 0.03
58 4 0.03
59 14 0.10
60 3 0.02
61 5 0.04
63 5 0.04
64 1 0.01
65 12 0.09
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.42
Consensus pattern (50 bp):
GTAAGTTATGTAAGTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTT
Found at i:55388356 original size:25 final size:25
Alignment explanation
Indices: 55388072--55388596 Score: 153
Period size: 25 Copynumber: 20.9 Consensus size: 25
55388062 ATATGAAAAT
* * *
55388072 TATGTAAGTTAT-TTATTATGAAAAT
1 TATGTAAGTTATGTAATTATG-TAAG
*
55388097 TATGTAAGTTGTGT-ATTATG-AA-
1 TATGTAAGTTATGTAATTATGTAAG
* * *
55388119 AAT-TATGCTATGTAAGTTATGTAAG
1 TATGTAAGTTATGTAA-TTATGTAAG
*
55388144 TCATATAAGTTATGT-ATTATGTAAG
1 T-ATGTAAGTTATGTAATTATGTAAG
* * *
55388169 TTATGTAAGTTAT-TTATTATGAAAAT
1 -TATGTAAGTTATGTAATTATG-TAAG
*
55388195 TATGTAAGTTGTGT-ATTATG-AA-
1 TATGTAAGTTATGTAATTATGTAAG
* * *
55388217 AAT-TATGCTATGTAAGTTATGTAAG
1 TATGTAAGTTATGTAA-TTATGTAAG
*
55388242 TCATATAAGTTATGT-ATTATGTAAG
1 T-ATGTAAGTTATGTAATTATGTAAG
* * *
55388267 TTATGTAAGTTAT-TTATTATGAAAAT
1 -TATGTAAGTTATGTAATTATG-TAAG
*
55388293 TAAGTAAGTTATGTAATTTATG-AA-
1 TATGTAAGTTATGTAA-TTATGTAAG
***
55388317 TAAT-TAAAAAAATGTAAGTTATGTAAG
1 T-ATGT-AAGTTATGTAA-TTATGTAAG
*
55388344 T-TGTAAGTTATGTAAGTTATGTATAA
1 TATGTAAGTTATGTAA-TTATGTA-AG
55388370 TAT-TAA-TTAAT-TAAGTTATGTAA-
1 TATGTAAGTT-ATGTAA-TTATGTAAG
* *
55388393 T-T-TATG-TAT-TGCATTAATGTAAG
1 TATGTAAGTTATGT-AATT-ATGTAAG
* * *
55388416 TTATGTAATTTATGAATAATTA--AAAA
1 -TATGTAAGTTATG--TAATTATGTAAG
* *
55388442 AATGTAAGTTATGTAAGT-TGTAAG
1 TATGTAAGTTATGTAATTATGTAAG
* * *
55388466 TTATGTAATTTATGAATAATTA--AAAA
1 -TATGTAAGTTATG--TAATTATGTAAG
* *
55388492 AATGTAAGTTATGTAATTTATGTTTAATAT
1 TATGTAAGTTATGTAA-TTATG--T-A-AG
*
55388522 TAATGTAAGTTATGTAAGT-TGTAAG
1 T-ATGTAAGTTATGTAATTATGTAAG
* *
55388547 TTATGTAAGTTATGTATAATAT-TAAT
1 -TATGTAAGTTATGTA-ATTATGTAAG
55388573 TAAT-TAAGTTATGTAAGTTATGTA
1 T-ATGTAAGTTATGTAA-TTATGTA
55388597 TAATACTAAT
Statistics
Matches: 379, Mismatches: 60, Indels: 121
0.68 0.11 0.22
Matches are distributed among these distances:
21 19 0.05
22 17 0.04
23 22 0.06
24 16 0.04
25 205 0.54
26 43 0.11
27 32 0.08
28 1 0.00
29 6 0.02
30 3 0.01
31 15 0.04
ACGTcount: A:0.39, C:0.01, G:0.16, T:0.44
Consensus pattern (25 bp):
TATGTAAGTTATGTAATTATGTAAG
Found at i:55388366 original size:34 final size:33
Alignment explanation
Indices: 55388225--55388596 Score: 113
Period size: 34 Copynumber: 11.2 Consensus size: 33
55388215 AAAATTATGC
*
55388225 TATGTAAGTTATGTAAGTCATATAAGTTATGT--AT
1 TATGTAAGTTATGTAA-T--TGTAAGTTATGTAAAT
* * *
55388259 TATGTAAGTTATGTAAGTTATTTA-TTATGAAAAT
1 TATGTAAGTTATGTAA-TT-GTAAGTTATGTAAAT
* * * *
55388293 TAAGTAAGTTATGTAATT-TATGAATAAT-TAAAAA
1 TATGTAAGTTATGTAATTGTA--AGTTATGT-AAAT
* *
55388327 AATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAA-TTGTAAGTTATGTAAAT
* * *
55388361 TATGTATA-ATAT-TAATTAATTAAGTTATGTAATT
1 TATGTA-AGTTATGTAATT--GTAAGTTATGTAAAT
*
55388395 TATGT-A-TTGCAT-TAA-TGTAAGTTATGTAATT
1 TATGTAAGTT--ATGTAATTGTAAGTTATGTAAAT
*** * *
55388426 TATGAATAA-TTAAAAAAATGTAAGTTATGT-AAG
1 TATG--TAAGTTATGTAATTGTAAGTTATGTAAAT
* * *
55388459 T-TGTAAGTTATGTAATT-TATGAATAAT-TAAAAA
1 TATGTAAGTTATGTAATTGTA--AGTTATGT-AAAT
* *
55388492 AATGTAAGTTATGTAATT-TATG-T-T-TAATAT
1 TATGTAAGTTATGTAATTGTAAGTTATGTAA-AT
*
55388522 TAATGTAAGTTATGTAAGTTGTAAGTTATGTAAGT
1 T-ATGTAAGTTATGTAA-TTGTAAGTTATGTAAAT
* * *
55388557 TATGTATA-ATAT-TAATTAATTAAGTTATGTAAGT
1 TATGTA-AGTTATGTAATT--GTAAGTTATGTAAAT
55388591 TATGTA
1 TATGTA
55388597 TAATACTAAT
Statistics
Matches: 261, Mismatches: 41, Indels: 72
0.70 0.11 0.19
Matches are distributed among these distances:
29 2 0.01
30 8 0.03
31 41 0.16
32 21 0.08
33 22 0.08
34 154 0.59
35 8 0.03
36 5 0.02
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (33 bp):
TATGTAAGTTATGTAATTGTAAGTTATGTAAAT
Found at i:55388438 original size:115 final size:115
Alignment explanation
Indices: 55388291--55388538 Score: 394
Period size: 115 Copynumber: 2.2 Consensus size: 115
55388281 TATTATGAAA
55388291 ATTAA-GTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTAT
1 ATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTAT
* * ** *
55388355 GTAAGTTATGTATAATATTAATTAAT-TAAGTTATGTAATTTATGTATT-GC
66 GTAAGTTATGAATAAT-TAAAAAAATGTAAGTTATGTAATTTATGT-TTAAC
55388405 ATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTAT
1 ATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTAT
* *
55388470 GTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAATTTATGTTTAAT
66 GTAAGTTATGAATAATTAAAAAAATGTAAGTTATGTAATTTATGTTTAAC
55388520 ATTAATGTAAGTTATGTAA
1 ATTAATGTAAGTTATGTAA
55388539 GTTGTAAGTT
Statistics
Matches: 124, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
114 13 0.10
115 111 0.90
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (115 bp):
ATTAATGTAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAAGTTGTAAGTTAT
GTAAGTTATGAATAATTAAAAAAATGTAAGTTATGTAATTTATGTTTAAC
Found at i:55388466 original size:81 final size:78
Alignment explanation
Indices: 55388381--55388618 Score: 248
Period size: 81 Copynumber: 2.9 Consensus size: 78
55388371 ATTAATTAAT
** **
55388381 TAAGTTATGTAATTTATGTATTGCATTAATGTAAGTTATGTAATTTATGAATAATTAA-AAAAAT
1 TAAGTTATGTAATTTATGTATTAAAAAAATGTAAGTTATGTAATTTATG--T--TTAATAAAAAT
55388445 GTAAGTTATGTAAGTTG
62 GTAAGTTATGTAAGTTG
**
55388462 TAAGTTATGTAATTTATGAATAATTAAAAAAATGTAAGTTATGTAATTTATGTTTAATATTAATG
1 TAAGTTATGTAATTTATG--T-ATTAAAAAAATGTAAGTTATGTAATTTATGTTTAATAAAAATG
55388527 TAAGTTATGTAAGTTG
63 TAAGTTATGTAAGTTG
* * * **
55388543 TAAGTTATGTAAGTTATGTA-TAATATTAATTAAT-TAAGTTATGTAAGTTATGTATAATACTAA
1 TAAGTTATGTAATTTATGTATTAA-A--AA--AATGTAAGTTATGTAATTTATGTTTAATAAAAA
55388606 TGTAAGTTATGTA
61 TGTAAGTTATGTA
55388619 TTATATAATA
Statistics
Matches: 138, Mismatches: 10, Indels: 18
0.83 0.06 0.11
Matches are distributed among these distances:
77 3 0.02
78 2 0.01
79 1 0.01
80 6 0.04
81 95 0.69
82 4 0.03
83 1 0.01
84 26 0.19
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (78 bp):
TAAGTTATGTAATTTATGTATTAAAAAAATGTAAGTTATGTAATTTATGTTTAATAAAAATGTAA
GTTATGTAAGTTG
Found at i:55388546 original size:16 final size:16
Alignment explanation
Indices: 55388525--55388557 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
55388515 TTAATATTAA
55388525 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
55388541 TGTAAGTTATGTAAGT
1 TGTAAGTTATGTAAGT
55388557 T
1 T
55388558 ATGTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.24, T:0.45
Consensus pattern (16 bp):
TGTAAGTTATGTAAGT
Found at i:55388550 original size:47 final size:43
Alignment explanation
Indices: 55388407--55388596 Score: 156
Period size: 43 Copynumber: 4.4 Consensus size: 43
55388397 TGTATTGCAT
* * * **
55388407 TAATGTAAGTTATGTAATTTATGAATAAT-TAAAAAAATGTAAG
1 TAATGTAAGTTATGTAAGTTATGTATAATATTAATTAAT-TAAG
* * * *
55388450 TTATGTAAG-T-TGTAAGTTATGTA-ATTTATGAA-TAATTAAAA
1 TAATGTAAGTTATGTAAGTTATGTATA-ATATTAATTAATT-AAG
* * * *
55388491 AAATGTAAGTTATGTAATTTATGTTTAATATTAATGTAAGTTATG
1 TAATGTAAGTTATGTAAGTTATGTATAATATTAAT-TAA-TTAAG
55388536 TAAGTTGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
1 TAA--TGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
*
55388581 TTATGTAAGTTATGTA
1 TAATGTAAGTTATGTA
55388597 TAATACTAAT
Statistics
Matches: 116, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
40 2 0.02
41 24 0.21
42 5 0.04
43 37 0.32
44 1 0.01
45 12 0.10
46 5 0.04
47 30 0.26
ACGTcount: A:0.41, C:0.00, G:0.15, T:0.44
Consensus pattern (43 bp):
TAATGTAAGTTATGTAAGTTATGTATAATATTAATTAATTAAG
Found at i:55388611 original size:22 final size:21
Alignment explanation
Indices: 55388583--55388627 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
55388573 TAATTAAGTT
55388583 ATGTAAGTTATGTATAATACTA
1 ATGTAAGTTATGTATAATA-TA
*
55388605 ATGTAAGTTATGTATTATATA
1 ATGTAAGTTATGTATAATATA
55388626 AT
1 AT
55388628 AACAGCGTCG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.40, C:0.02, G:0.13, T:0.44
Consensus pattern (21 bp):
ATGTAAGTTATGTATAATATA
Found at i:55391304 original size:16 final size:16
Alignment explanation
Indices: 55391259--55391314 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
55391249 TAAATCTCAC
*
55391259 ATCTTTTATTTATT-T
1 ATCTTTTATTAATTGT
* *
55391274 ATTTATTTCTTAATTGT
1 ATCT-TTTATTAATTGT
55391291 ATCTTTTATTAATTGT
1 ATCTTTTATTAATTGT
55391307 ATCTTTTA
1 ATCTTTTA
55391315 ATTACTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
15 3 0.09
16 27 0.79
17 4 0.12
ACGTcount: A:0.23, C:0.07, G:0.04, T:0.66
Consensus pattern (16 bp):
ATCTTTTATTAATTGT
Found at i:55393670 original size:63 final size:66
Alignment explanation
Indices: 55393603--55393727 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 66
55393593 TTTTGAAAAA
* * * * * *
55393603 ATATAATTTATTAAGAAACTAAAAGTTAGA-TTAAATATATATGT-AAAA-AATATTTAAATGTA
1 ATATAATTGATCAAGAAACTAAAAATTAAACCTAAATATATATATGAAAAGAATATTTAAATGTA
55393665 T
66 T
*
55393666 ATATAATTGATCAATAAACTAAAAATTAAACCCTAAATATATATATGAAAAGAATATTTAAA
1 ATATAATTGATCAAGAAACTAAAAATTAAA-CCTAAATATATATATGAAAAGAATATTTAAA
55393728 AATATTAATA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
63 25 0.49
65 12 0.24
66 4 0.08
67 10 0.20
ACGTcount: A:0.54, C:0.05, G:0.06, T:0.34
Consensus pattern (66 bp):
ATATAATTGATCAAGAAACTAAAAATTAAACCTAAATATATATATGAAAAGAATATTTAAATGTA
T
Found at i:55394524 original size:14 final size:15
Alignment explanation
Indices: 55394505--55394537 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
55394495 ATAGTATTGT
55394505 ATTTTATAT-ATATA
1 ATTTTATATGATATA
*
55394519 ATTTTATGTGATATA
1 ATTTTATATGATATA
55394534 ATTT
1 ATTT
55394538 ACATAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTTTATATGATATA
Found at i:55394568 original size:20 final size:20
Alignment explanation
Indices: 55394540--55394586 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
55394530 TATAATTTAC
*
55394540 ATAATATATA-TAAATAAAAT
1 ATAAAATATACTAAA-AAAAT
*
55394560 ATAAAATATACTACAAAAAT
1 ATAAAATATACTAAAAAAAT
55394580 ATAAAAT
1 ATAAAAT
55394587 GGGTTAGGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 21 0.88
21 3 0.12
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
ATAAAATATACTAAAAAAAT
Found at i:55395360 original size:38 final size:39
Alignment explanation
Indices: 55395309--55395390 Score: 148
Period size: 38 Copynumber: 2.1 Consensus size: 39
55395299 AAAATTAAAA
*
55395309 AAAAAAGTATTTTAAAAGTATTTTAAAATT-AAAAAATT
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
55395347 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
1 AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
55395386 AAAAA
1 AAAAA
55395391 TTAAAATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 29 0.69
39 13 0.31
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (39 bp):
AAAAAAGTATTTTAAAAATATTTTAAAATTAAAAAAATT
Found at i:55395368 original size:11 final size:12
Alignment explanation
Indices: 55395310--55395374 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 12
55395300 AAATTAAAAA
55395310 AAAAAGTATTTT
1 AAAAAGTATTTT
55395322 -AAAAGTATTTT
1 AAAAAGTATTTT
** * *
55395333 AAAATTAAAAAATTA
1 -AAA--AAGTATTTT
55395348 AAAAAGTATTTT
1 AAAAAGTATTTT
55395360 AAAAA-TATTTT
1 AAAAAGTATTTT
55395371 AAAA
1 AAAA
55395375 TTAAAAAAAT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
11 21 0.51
12 10 0.24
13 2 0.05
14 3 0.07
15 5 0.12
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (12 bp):
AAAAAGTATTTT
Found at i:55401946 original size:13 final size:13
Alignment explanation
Indices: 55401928--55401977 Score: 64
Period size: 13 Copynumber: 3.8 Consensus size: 13
55401918 TCTTCATTGT
55401928 TTTTGAAAAGTGC
1 TTTTGAAAAGTGC
*
55401941 TTTTGAAAAGTAC
1 TTTTGAAAAGTGC
** *
55401954 TTTTGGGAAGTGT
1 TTTTGAAAAGTGC
55401967 TTTTGAAAAGT
1 TTTTGAAAAGT
55401978 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.30, C:0.04, G:0.24, T:0.42
Consensus pattern (13 bp):
TTTTGAAAAGTGC
Found at i:55403488 original size:24 final size:23
Alignment explanation
Indices: 55403430--55403489 Score: 61
Period size: 24 Copynumber: 2.6 Consensus size: 23
55403420 CTATTTTCCA
*
55403430 TTATTT-AATATAAAGGTTTTTT
1 TTATTTAAATATAAAGGGTTTTT
*
55403452 TTA-TGAAATATATAAGGGGTTTTT
1 TTATTTAAATATA-AA-GGGTTTTT
55403476 TTATTTAACATATA
1 TTATTTAA-ATATA
55403490 TTTGTGTCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 1 0.03
22 9 0.30
23 2 0.07
24 10 0.33
25 3 0.10
26 5 0.17
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.52
Consensus pattern (23 bp):
TTATTTAAATATAAAGGGTTTTT
Found at i:55405407 original size:13 final size:14
Alignment explanation
Indices: 55405389--55405417 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
55405379 AACCTTTGAC
55405389 CCTTGAACC-CAAA
1 CCTTGAACCTCAAA
55405402 CCTTGAACCTCAAA
1 CCTTGAACCTCAAA
55405416 CC
1 CC
55405418 CCTAACCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.34, C:0.41, G:0.07, T:0.17
Consensus pattern (14 bp):
CCTTGAACCTCAAA
Found at i:55407155 original size:31 final size:29
Alignment explanation
Indices: 55407092--55407159 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
55407082 CTAGCGGCTC
* *
55407092 AGTGACTAAAATGTAACATTTCAAACACA
1 AGTGACTAAAATGTAACATTACAAACAAA
55407121 AGTGACTAAAATGTAAC-TTGAGACAAACAAA
1 AGTGACTAAAATGTAACATT---ACAAACAAA
55407152 AGTGACTA
1 AGTGACTA
55407160 TTTTAATAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 2 0.06
29 17 0.50
31 15 0.44
ACGTcount: A:0.49, C:0.15, G:0.15, T:0.22
Consensus pattern (29 bp):
AGTGACTAAAATGTAACATTACAAACAAA
Found at i:55409493 original size:3 final size:3
Alignment explanation
Indices: 55409487--55409518 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
55409477 ATGATGAATC
55409487 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
55409519 GGTTTAGGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:55409972 original size:20 final size:20
Alignment explanation
Indices: 55409927--55409965 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
55409917 AACTGCTCTT
*
55409927 TTTTTTTATTGTTTTCTTGC
1 TTTTTTTATTGTTTTATTGC
55409947 TTTTTTTATTGTTTTATTG
1 TTTTTTTATTGTTTTATTG
55409966 TTATTTTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.05, G:0.10, T:0.77
Consensus pattern (20 bp):
TTTTTTTATTGTTTTATTGC
Found at i:55411071 original size:42 final size:42
Alignment explanation
Indices: 55411012--55411097 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
55411002 AGGAAAAATA
*
55411012 GTACTACATCGTGTATTTACTCCTCCTCAGGGCACATCACAT
1 GTACTACATCGTGTATTTACTCCCCCTCAGGGCACATCACAT
*
55411054 GTACTACATCGTGTATTTACTCCCCCTCAGGGTACATCACAT
1 GTACTACATCGTGTATTTACTCCCCCTCAGGGCACATCACAT
55411096 GT
1 GT
55411098 TATCTTATAC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.31
Consensus pattern (42 bp):
GTACTACATCGTGTATTTACTCCCCCTCAGGGCACATCACAT
Found at i:55416027 original size:20 final size:20
Alignment explanation
Indices: 55416002--55416041 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55415992 AATATTTTCT
* *
55416002 AGTAAATCATTTTACAGAAA
1 AGTAAAACAGTTTACAGAAA
*
55416022 AGTAAAACAGTTTGCAGAAA
1 AGTAAAACAGTTTACAGAAA
55416042 TCATTTTACG
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:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (20 bp):
AGTAAAACAGTTTACAGAAA
Found at i:55417442 original size:16 final size:16
Alignment explanation
Indices: 55417422--55417474 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
55417412 TTGGTTCGCT
* *
55417422 GTAATGGAATAGAGGT
1 GTAATGGAATACAGGC
55417438 GTAATGGAATACAGGC
1 GTAATGGAATACAGGC
55417454 GTAATGGAATACAGGC
1 GTAATGGAATACAGGC
55417470 GTAAT
1 GTAAT
55417475 AGGTAATCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.32, T:0.23
Consensus pattern (16 bp):
GTAATGGAATACAGGC
Found at i:55417774 original size:61 final size:61
Alignment explanation
Indices: 55417709--55417906 Score: 228
Period size: 61 Copynumber: 3.3 Consensus size: 61
55417699 TTATTATTAA
*
55417709 ATATAAT-TTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAAT
1 ATATAATATT-ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATAATAAT
* * * * * ** *
55417770 ATATAATATTATAAAA-T-GTAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAAAAT
1 ATATAATATTATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATAATAAT
*
55417829 ATATAAT-TTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATTATAAT
1 ATATAATATT-ATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATAATAAT
55417890 ATATAATATTATAAAAT
1 ATATAATATTATAAAAT
55417907 ATAATTTAAA
Statistics
Matches: 110, Mismatches: 18, Indels: 18
0.75 0.12 0.12
Matches are distributed among these distances:
58 4 0.04
59 35 0.32
60 16 0.15
61 49 0.45
62 6 0.05
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (61 bp):
ATATAATATTATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATAATAAT
Found at i:55417830 original size:59 final size:59
Alignment explanation
Indices: 55417767--55417955 Score: 222
Period size: 59 Copynumber: 3.2 Consensus size: 59
55417757 CTAAAATCAT
*
55417767 AATATATAATATTATAAAATGTAATTTAAAATAATTATTATTAAATATAATTTAATAAA
1 AATATATAATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAA
* * * * * ** * *
55417826 AATATATAAT-TTAATAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATTAT
1 AATATATAATATT-ATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAA
55417887 AATATATAATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAA
1 AATATATAATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAA
55417946 AATATATAAT
1 AATATATAAT
55417956 TCCCCCACGT
Statistics
Matches: 104, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
58 4 0.04
59 45 0.43
60 16 0.15
61 35 0.34
62 4 0.04
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (59 bp):
AATATATAATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAA
Found at i:55417866 original size:120 final size:120
Alignment explanation
Indices: 55417709--55417956 Score: 478
Period size: 120 Copynumber: 2.1 Consensus size: 120
55417699 TTATTATTAA
55417709 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
*
55417774 AATATTATAAAATGTAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
66 AATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
*
55417829 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATTATAATATAT
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
55417894 AATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
66 AATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
55417949 ATATAATT
1 ATATAATT
55417957 CCCCCACGTT
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 126 1.00
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (120 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATAT
AATATTATAAAATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAAT
Found at i:55417902 original size:15 final size:15
Alignment explanation
Indices: 55417882--55417951 Score: 60
Period size: 15 Copynumber: 4.9 Consensus size: 15
55417872 ATTTACTAAA
*
55417882 ATTATAATATATAAT
1 ATTATAAAATATAAT
55417897 ATTATAAAATAT-A-
1 ATTATAAAATATAAT
*
55417910 ATT-TAAAATA-ATT
1 ATTATAAAATATAAT
*
55417923 ATTATTAAATATAAT
1 ATTATAAAATATAAT
55417938 -TTAATAAAAATATA
1 ATT-AT-AAAATATA
55417952 TAATTCCCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
12 7 0.16
13 6 0.14
14 9 0.20
15 15 0.34
16 7 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATTATAAAATATAAT
Found at i:55420175 original size:23 final size:23
Alignment explanation
Indices: 55420149--55420201 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
55420139 ATAAGTGCCA
*
55420149 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
*
55420172 CACTGATATGTAATCGAAGCTAC
1 CACTGATATGTAACCGAAGCTAC
55420195 CACTGAT
1 CACTGAT
55420202 CAATAACACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAACCGAAGCTAC
Found at i:55420469 original size:19 final size:19
Alignment explanation
Indices: 55420434--55420470 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
55420424 TTCCACATTC
55420434 AATATTAATTCACATTTCA
1 AATATTAATTCACATTTCA
55420453 AATA-TAATTCACAATTTC
1 AATATTAATTCAC-ATTTC
55420471 TAAAAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.43, C:0.16, G:0.00, T:0.41
Consensus pattern (19 bp):
AATATTAATTCACATTTCA
Found at i:55429461 original size:15 final size:15
Alignment explanation
Indices: 55429441--55429490 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
55429431 TGTAGTTGAA
55429441 GATGACGACGACAAC
1 GATGACGACGACAAC
* *
55429456 GATGACGACGACGAT
1 GATGACGACGACAAC
* *
55429471 GATGACGATGACAAG
1 GATGACGACGACAAC
55429486 GATGA
1 GATGA
55429491 AGATGATGCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.32, T:0.12
Consensus pattern (15 bp):
GATGACGACGACAAC
Found at i:55432946 original size:15 final size:15
Alignment explanation
Indices: 55432891--55432947 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
55432881 AAAGTTTTAT
*
55432891 TAATAGTTATATAATA
1 TAATAG-TATATAATG
55432907 TAATAGTATAGT-ATAG
1 TAATAGTATA-TAAT-G
55432923 T-ATAGTATATAATG
1 TAATAGTATATAATG
*
55432937 TAATACTATAT
1 TAATAGTATAT
55432948 GTATTAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.09
15 24 0.69
16 8 0.23
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.42
Consensus pattern (15 bp):
TAATAGTATATAATG
Found at i:55432958 original size:30 final size:29
Alignment explanation
Indices: 55432888--55432958 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 29
55432878 TTAAAAGTTT
*
55432888 TATTAATAGTTATATAATATAATAGTATAG
1 TATTAATAG-TATATAATATAATACTATAG
*
55432918 TA-TAGTATAGTATATAATGTAATACTATATG
1 TATTA--ATAGTATATAATATAATACTATA-G
55432949 TATTAATAGT
1 TATTAATAGT
55432959 TATGTAGTAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
29 2 0.06
30 24 0.69
31 7 0.20
32 2 0.06
ACGTcount: A:0.44, C:0.01, G:0.11, T:0.44
Consensus pattern (29 bp):
TATTAATAGTATATAATATAATACTATAG
Found at i:55434720 original size:30 final size:29
Alignment explanation
Indices: 55434671--55434742 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
55434661 ACGAATAAAA
*
55434671 ATATATAAATATAAATAAA-TAAATATTTTT
1 ATATATAAAT-TAAATAAATTAAATA-ATTT
*
55434701 ATATGTAAATTAAATTAAATTAAATAATTT
1 ATATATAAATTAAA-TAAATTAAATAATTT
*
55434731 ATATTTAAATTA
1 ATATATAAATTA
55434743 TTGAATATGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 4 0.11
30 27 0.73
31 6 0.16
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (29 bp):
ATATATAAATTAAATAAATTAAATAATTT
Found at i:55435206 original size:20 final size:20
Alignment explanation
Indices: 55435158--55435206 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
55435148 ATTAAAGGGG
55435158 AAATTAAATCAATTTGATTA
1 AAATTAAATCAATTTGATTA
*
55435178 AAATCAAATCTAA-TTGATTA
1 AAATTAAATC-AATTTGATTA
*
55435198 GAATTAAAT
1 AAATTAAAT
55435207 AAAATCAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 23 0.92
21 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (20 bp):
AAATTAAATCAATTTGATTA
Found at i:55437876 original size:43 final size:43
Alignment explanation
Indices: 55437827--55438178 Score: 467
Period size: 43 Copynumber: 8.3 Consensus size: 43
55437817 TTTTAGAAAT
* * * * ***
55437827 AAACGCCGCTAAAGATCAAGATCTTTAGCAGCGCTTTTTTTAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
55437870 AAACGCCACTATAGATCAAGACCTTTAGCGGCGC-TTTCCCAA
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
55437912 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* *
55437955 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGC-TTTCCCAA
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
*
55437997 AAACGCCGCTATAGATCAGGACCTTTAGCGACGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* ** *
55438040 AAACGCCGCTATAGATCAAGACCTTTAGCAACACTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* ** * *
55438083 AAACGCCGCTATAAATCAGGACCTTTAGTTGCACTTTTCCCAT
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
**
55438126 AAACGCCGCTATAGATC-GGACCTTTAGCGGCGCTTTTTTCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
55438168 AAACGCCGCTA
1 AAACGCCGCTA
55438179 AAAGTGCCAT
Statistics
Matches: 275, Mismatches: 32, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
42 105 0.38
43 170 0.62
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
Found at i:55437928 original size:85 final size:84
Alignment explanation
Indices: 55437827--55438161 Score: 456
Period size: 85 Copynumber: 3.9 Consensus size: 84
55437817 TTTTAGAAAT
* * * *** *
55437827 AAACGCCGCTAAAGATCAAGATCTTTAGCAGCGCTTTTTTTACAAACGCCACTATAGATCAAGAC
1 AAACGCCGCTATAGATCAGGACCTTTAGC-GCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
55437892 CTTTAGCGGCGCTTTCCCAA
65 CTTTAGCGGCGCTTTCCCAA
* *
55437912 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAGGAT
1 AAACGCCGCTATAGATCAGGACCTTTAGC-GCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
55437977 CTTTAGCGGCGCTTTCCCAA
65 CTTTAGCGGCGCTTTCCCAA
55437997 AAACGCCGCTATAGATCAGGACCTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCG-CGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
** * *
55438062 CTTTAGCAACACTTTTCCCAC
65 CTTTAGCGGCGC-TTTCCCAA
* * * * *
55438083 AAACGCCGCTATAAATCAGGACCTTTAGTTGCACTTTTCCCATAAACGCCGCTATAGATC-GGAC
1 AAACGCCGCTATAGATCAGGACCTTTAG-CGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
55438147 CTTTAGCGGCGCTTT
65 CTTTAGCGGCGCTTT
55438162 TTTCACAAAC
Statistics
Matches: 223, Mismatches: 24, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
84 4 0.02
85 157 0.70
86 61 0.27
87 1 0.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (84 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACC
TTTAGCGGCGCTTTCCCAA
Found at i:55438036 original size:128 final size:129
Alignment explanation
Indices: 55437827--55438178 Score: 476
Period size: 128 Copynumber: 2.8 Consensus size: 129
55437817 TTTTAGAAAT
* * *** * * *
55437827 AAACGCCGCTAAAGATCAAGATCTTTAGCAGCGCTTTTTTTACAAACGCCACTATAGATCAAGAC
1 AAACGCCGCTATAGATCAGGATCTTTAGCAGCGCTTTTCCCAAAAACGCCGCTATAGATCAGGAC
* * ** *
55437892 CTTTAGCGGCGC-TTTCCCAAAAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCAACACTTTTCCCAC
*
55437955 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGC-TTTCCCAAAAACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCAGGATCTTTAGCAGCGCTTTTCCCAAAAACGCCGCTATAGATCAGGAC
*
55438019 CTTTAGCGACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCAACACTTTTCCCAC
66 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCAACACTTTTCCCAC
* * ** * *
55438083 AAACGCCGCTATAAATCAGGACCTTTAGTTGCACTTTTCCCATAAACGCCGCTATAGATC-GGAC
1 AAACGCCGCTATAGATCAGGATCTTTAGCAGCGCTTTTCCCAAAAACGCCGCTATAGATCAGGAC
**
55438147 CTTTAGCGGCGCTTTTTTCACAAACGCCGCTA
66 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
55438179 AAAGTGCCAT
Statistics
Matches: 198, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
127 35 0.18
128 139 0.70
129 24 0.12
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.25
Consensus pattern (129 bp):
AAACGCCGCTATAGATCAGGATCTTTAGCAGCGCTTTTCCCAAAAACGCCGCTATAGATCAGGAC
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCAACACTTTTCCCAC
Found at i:55441198 original size:57 final size:57
Alignment explanation
Indices: 55441085--55441198 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
55441075 CTCCACTCCA
* **
55441085 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
55441142 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
55441199 TCTTCAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 48 0.94
58 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Found at i:55442751 original size:18 final size:19
Alignment explanation
Indices: 55442728--55442764 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
55442718 TTGAATCCCT
55442728 AACCCTAAACCT-TAACCC
1 AACCCTAAACCTCTAACCC
*
55442746 AACCCTAAATCTCTAACCC
1 AACCCTAAACCTCTAACCC
55442765 TTAAATATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (19 bp):
AACCCTAAACCTCTAACCC
Found at i:55443030 original size:20 final size:20
Alignment explanation
Indices: 55442990--55443032 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
55442980 ATCTTAAATT
*
55442990 AACCATATATATATACTCTA
1 AACCATATATATAAACTCTA
55443010 AACCATATATATTAAAC-CTA
1 AACCATATATA-TAAACTCTA
55443030 AAC
1 AAC
55443033 TATAATGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
AACCATATATATAAACTCTA
Found at i:55443950 original size:41 final size:41
Alignment explanation
Indices: 55443791--55443950 Score: 250
Period size: 41 Copynumber: 3.9 Consensus size: 41
55443781 TTTTATTATT
* *
55443791 ATTAGCGGCGCTTTTTCAAAAAACGCTGCTAAAGG-TCGAGC
1 ATTAGCGGCGCTTTTTC-AAAAACGCCGCTAAAGGCCCGAGC
* * * *
55443832 ACTAGAGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
55443873 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
55443914 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCC
55443951 CAAAAACTCA
Statistics
Matches: 108, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
40 16 0.15
41 92 0.85
ACGTcount: A:0.29, C:0.28, G:0.24, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:55444036 original size:39 final size:39
Alignment explanation
Indices: 55443993--55444121 Score: 143
Period size: 40 Copynumber: 3.3 Consensus size: 39
55443983 GGCTTTTTGC
* *
55443993 GGCGCTTTTTAAAAAACACCGCTAATGCTTATTTTTAGT
1 GGCGCTTTTTAAAAAGCGCCGCTAATGCTTATTTTTAGT
** * ** *
55444032 GGCGCTTTCCAAAAAGCGCCGCTAATGCTCGACCTTTAGC
1 GGCGCTTTTTAAAAAGCGCCGCTAATGCT-TATTTTTAGT
55444072 GGCG-TTTTTATAAAAGCGCCGCTAATGCTTGATTTTTAGT
1 GGCGCTTTTTA-AAAAGCGCCGCTAATGCTT-ATTTTTAGT
*
55444112 GGCGTTTTTT
1 GGCGCTTTTT
55444122 GTCTAAACGC
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 29 0.40
40 38 0.53
41 5 0.07
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (39 bp):
GGCGCTTTTTAAAAAGCGCCGCTAATGCTTATTTTTAGT
Found at i:55448424 original size:41 final size:42
Alignment explanation
Indices: 55448377--55448460 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
55448367 GCTTAAGACT
55448377 TAAAACTTAATATATTTAT-TTTTTATTTACATAGTTTTTTA
1 TAAAACTTAATATATTTATCTTTTTATTTACATAGTTTTTTA
55448418 TAAAACTTAATATATTTATCTTTTTATTTACATAGTTTTTTA
1 TAAAACTTAATATATTTATCTTTTTATTTACATAGTTTTTTA
55448460 T
1 T
55448461 TGAAGCAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 19 0.45
42 23 0.55
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (42 bp):
TAAAACTTAATATATTTATCTTTTTATTTACATAGTTTTTTA
Found at i:55450573 original size:37 final size:37
Alignment explanation
Indices: 55450523--55450598 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
55450513 TGAAGAGGGC
55450523 GGCTTTGAAATAGGAGAAAGGGTTGGGTGGAAATGAA
1 GGCTTTGAAATAGGAGAAAGGGTTGGGTGGAAATGAA
*
55450560 GGCTTTGAAATAGGAGAAAGGGTTGGGTGGGAATGAA
1 GGCTTTGAAATAGGAGAAAGGGTTGGGTGGAAATGAA
55450597 GG
1 GG
55450599 AAGCGTTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.03, G:0.43, T:0.21
Consensus pattern (37 bp):
GGCTTTGAAATAGGAGAAAGGGTTGGGTGGAAATGAA
Found at i:55451724 original size:28 final size:28
Alignment explanation
Indices: 55451684--55451743 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
55451674 TAGCTACATA
55451684 ATAAAATAAAGTAAGAATATTATTTTAT
1 ATAAAATAAAGTAAGAATATTATTTTAT
55451712 ATAAAATAAAGTAAGAATATTATTTTAT
1 ATAAAATAAAGTAAGAATATTATTTTAT
55451740 ATAA
1 ATAA
55451744 TTTTTCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (28 bp):
ATAAAATAAAGTAAGAATATTATTTTAT
Done.