Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr8
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: 56894857
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1173888 characters in sequence are not A, C, G, or T
File 183 of 185
Found at i:55853882 original size:34 final size:33
Alignment explanation
Indices: 55853824--55853922 Score: 139
Period size: 33 Copynumber: 2.9 Consensus size: 33
55853814 TAATATATAT
55853824 TTTTTA-AAATTTTAAATATATATTTTTGAAATTA
1 TTTTTATAAATTTTAAATAT-TATTTTT-AAATTA
55853858 TTTTTATAAATTTTAAATATTATTTTTAAATTA
1 TTTTTATAAATTTTAAATATTATTTTTAAATTA
*
55853891 TTTTT-TAAAATTTTAAATAGTATTTTTTAAAT
1 TTTTTAT-AAATTTTAAATATTA-TTTTTAAAT
55853923 ATTAAATATA
Statistics
Matches: 61, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
32 1 0.02
33 25 0.41
34 22 0.36
35 13 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (33 bp):
TTTTTATAAATTTTAAATATTATTTTTAAATTA
Found at i:55853899 original size:12 final size:11
Alignment explanation
Indices: 55853844--55853895 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
55853834 TTTAAATATA
55853844 TATTTTTGAAAT
1 TATTTTT-AAAT
55853856 TATTTTTATAA-
1 TATTTTTA-AAT
*
55853867 -ATTTTAAATAT
1 TATTTTTAA-AT
55853878 TATTTTTAAAT
1 TATTTTTAAAT
55853889 TATTTTT
1 TATTTTT
55853896 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
11 10 0.29
12 16 0.47
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (11 bp):
TATTTTTAAAT
Found at i:55853945 original size:22 final size:21
Alignment explanation
Indices: 55853818--55853946 Score: 93
Period size: 22 Copynumber: 5.9 Consensus size: 21
55853808 ATTTTATAAT
*
55853818 ATATATTTTTTAAAATTTTAA
1 ATATATTTTTTAAAATATTAA
* *
55853839 ATATATATTTTTGAAATTATT-T
1 ATATAT-TTTTT-AAAATATTAA
* **
55853861 TTATAAATTTTAAATATTATTTTTAA
1 ATATATTTTTTAAA-A-TA---TTAA
*
55853887 AT-TATTTTTTAAAATTTTAA
1 ATATATTTTTTAAAATATTAA
55853907 ATAGTATTTTTT-AAATATTAA
1 ATA-TATTTTTTAAAATATTAA
55853928 ATATATTTTTTAATAATAT
1 ATATATTTTTTAA-AATAT
55853947 AAAACATTTA
Statistics
Matches: 83, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
20 17 0.20
21 22 0.27
22 24 0.29
23 7 0.08
24 1 0.01
25 11 0.13
26 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATATATTTTTTAAAATATTAA
Found at i:55853949 original size:21 final size:20
Alignment explanation
Indices: 55853884--55853949 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
55853874 ATATTATTTT
*
55853884 TAAAT-TATTTTTTAAAATTT
1 TAAATATATTTTTTAAAA-TA
55853904 TAAATAGTATTTTTT-AAATA
1 TAAATA-TATTTTTTAAAATA
55853924 TTAAATATATTTTTTAATAATA
1 -TAAATATATTTTTTAA-AATA
55853946 TAAA
1 TAAA
55853950 ACATTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
20 14 0.35
21 14 0.35
22 12 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TAAATATATTTTTTAAAATA
Found at i:55853999 original size:136 final size:136
Alignment explanation
Indices: 55853854--55854160 Score: 358
Period size: 137 Copynumber: 2.3 Consensus size: 136
55853844 TATTTTTGAA
* *
55853854 ATTATTTTTATAA-ATTTTAAATATTATTTTTAAATTATTTTTTAAAATTTTAAATAGTATTTTT
1 ATTATTTTTATAATATTTTAAATA-TATTTTTAAATTATTTTATAAAATTTTAAAT-GTATTTTA
*
55853918 TAA-ATATTAAA-TAT-ATTTTTTAATAATATAAAACAT-TTAAATATTTTAAAGATATGACCTT
64 TAATATATTAAATTATAATTTTTAAATAATATAAAACATATT--AT-TTTTAAAGATATGACCTT
*
55853979 TTAAATTTATT
126 TCAAATTTATT
* * * * ** * *
55853990 ATTAGTTTTATAATATTTTAAATGTATATTTTAATTTGTTTTATAATTTTTTCAATTTATTTTAT
1 ATTATTTTTATAATATTTTAAATATAT-TTTTAAATTATTTTATAAAATTTTAAATGTATTTTAT
* * * * *
55854055 AATATTTTAAATTATAATTTTTAAATTATTTAAAATATATTATTTTTAAAGATATTACCTTTCAA
65 AATATATTAAATTATAATTTTTAAATAATATAAAACATATTATTTTTAAAGATATGACCTTTCAA
55854120 ATTTATT
130 ATTTATT
55854127 ATT-TTTTTATAATATTTTAAATAT-TTTTTAAATT
1 ATTATTTTTATAATATTTTAAATATATTTTTAAATT
55854161 TTAAATATAA
Statistics
Matches: 145, Mismatches: 20, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
134 8 0.06
135 1 0.01
136 43 0.30
137 68 0.47
138 5 0.03
139 18 0.12
140 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (136 bp):
ATTATTTTTATAATATTTTAAATATATTTTTAAATTATTTTATAAAATTTTAAATGTATTTTATA
ATATATTAAATTATAATTTTTAAATAATATAAAACATATTATTTTTAAAGATATGACCTTTCAAA
TTTATT
Found at i:55854047 original size:21 final size:20
Alignment explanation
Indices: 55854015--55854069 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
55854005 TTTTAAATGT
*
55854015 ATATTTTAATTTGTTTTATA
1 ATATTTTAATTTATTTTATA
*
55854035 ATTTTTTCAATTTATTTTATA
1 ATATTTT-AATTTATTTTATA
*
55854056 ATATTTTAAATTAT
1 ATATTTTAATTTAT
55854070 AATTTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (20 bp):
ATATTTTAATTTATTTTATA
Found at i:55854076 original size:14 final size:15
Alignment explanation
Indices: 55854051--55854083 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
55854041 TCAATTTATT
55854051 TTATAATATTTTAAA
1 TTATAATATTTTAAA
55854066 TTATAAT-TTTTAAA
1 TTATAATATTTTAAA
55854080 TTAT
1 TTAT
55854084 TTAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATAATATTTTAAA
Found at i:55854084 original size:24 final size:24
Alignment explanation
Indices: 55854049--55854104 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
55854039 TTTCAATTTA
*
55854049 TTTTATAATATTTTAAAT-TATAAT
1 TTTTA-AATATTTAAAATATATAAT
*
55854073 TTTTAAATTATTTAAAATATATTAT
1 TTTTAAA-TATTTAAAATATATAAT
55854098 TTTTAAA
1 TTTTAAA
55854105 GATATTACCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 14 0.50
25 12 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAAATATTTAAAATATATAAT
Found at i:55854151 original size:22 final size:20
Alignment explanation
Indices: 55854129--55854187 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 20
55854119 AATTTATTAT
55854129 TTTTTTATAATATTTTAAATA
1 TTTTTTATAA-ATTTTAAATA
55854150 -TTTTT-TAAATTTTAAATA
1 TTTTTTATAAATTTTAAATA
55854168 TAATTTTTATAAATTATTAA
1 T--TTTTTATAAATT-TTAA
55854188 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 10 0.30
19 3 0.09
20 5 0.15
21 5 0.15
22 6 0.18
23 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTTTTATAAATTTTAAATA
Found at i:55854174 original size:12 final size:13
Alignment explanation
Indices: 55854157--55854206 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 13
55854147 ATATTTTTTA
55854157 AATTTTAAATA-T
1 AATTTTAAATATT
55854169 AATTTTTATAAATTATT
1 AA--TTT-TAAA-TATT
55854186 AATTTTAAA-ATT
1 AATTTTAAATATT
55854198 AATTTTAAA
1 AATTTTAAA
55854207 GATATTCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
12 14 0.42
14 7 0.21
15 7 0.21
16 2 0.06
17 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTTTAAATATT
Found at i:55854260 original size:11 final size:11
Alignment explanation
Indices: 55854245--55854295 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
55854235 TTCAATATCT
*
55854245 TTAAAAACAAT
1 TTAAAAACAAA
55854256 TTAAAAATCATAA
1 TTAAAAA-CA-AA
55854269 TT-AAAA-AAA
1 TTAAAAACAAA
55854278 TTATAAAACAAA
1 TTA-AAAACAAA
55854290 TTAAAA
1 TTAAAA
55854296 TATACATTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
9 4 0.12
10 1 0.03
11 14 0.41
12 12 0.35
13 3 0.09
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (11 bp):
TTAAAAACAAA
Found at i:55854396 original size:20 final size:19
Alignment explanation
Indices: 55854371--55854456 Score: 90
Period size: 19 Copynumber: 4.6 Consensus size: 19
55854361 TTTTATATTA
*
55854371 TTAAAAATATATTTAATAT
1 TTAAAAATATATTTAAAAT
55854390 TTAAAAATAATATTTAAAAT
1 TTAAAAAT-ATATTTAAAAT
* *
55854410 TTAAAAAAATAATTT-CAA-
1 TTAAAAATAT-ATTTAAAAT
*
55854428 --AAATATATATTTAAAAT
1 TTAAAAATATATTTAAAAT
55854445 TTAAAAATATAT
1 TTAAAAATATAT
55854457 ATTATAAAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
15 4 0.07
16 8 0.15
19 21 0.39
20 21 0.39
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
TTAAAAATATATTTAAAAT
Found at i:55854402 original size:13 final size:13
Alignment explanation
Indices: 55854384--55854408 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55854374 AAAATATATT
55854384 TAATATTTAAAAA
1 TAATATTTAAAAA
55854397 TAATATTTAAAA
1 TAATATTTAAAA
55854409 TTTAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TAATATTTAAAAA
Found at i:55854417 original size:22 final size:20
Alignment explanation
Indices: 55854371--55854466 Score: 91
Period size: 20 Copynumber: 5.0 Consensus size: 20
55854361 TTTTATATTA
*
55854371 TTAAAAAT-ATATTTAATAT
1 TTAAAAATAATATTTAAAAT
55854390 TTAAAAATAATATTTAAAAT
1 TTAAAAATAATATTTAAAAT
55854410 TT-AAAA-AA-A--T--AAT
1 TTAAAAATAATATTTAAAAT
55854423 TTCAAAAATATATATTTAAAAT
1 TT-AAAAATA-ATATTTAAAAT
55854445 TTAAAAATATATATTATAAAAT
1 TTAAAAATA-ATATT-TAAAAT
55854467 ATTTCAAATG
Statistics
Matches: 65, Mismatches: 1, Indels: 19
0.76 0.01 0.22
Matches are distributed among these distances:
13 5 0.08
15 5 0.08
16 1 0.02
17 2 0.03
18 3 0.05
19 12 0.18
20 13 0.20
21 13 0.20
22 11 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAAAAATAATATTTAAAAT
Found at i:55854452 original size:21 final size:23
Alignment explanation
Indices: 55854420--55854466 Score: 80
Period size: 21 Copynumber: 2.1 Consensus size: 23
55854410 TTAAAAAAAT
55854420 AATTTCAAAAATATATATT-TAA
1 AATTTCAAAAATATATATTATAA
55854442 AATTT-AAAAATATATATTATAA
1 AATTTCAAAAATATATATTATAA
55854464 AAT
1 AAT
55854467 ATTTCAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTTCAAAAATATATATTATAA
Found at i:55854466 original size:35 final size:35
Alignment explanation
Indices: 55854385--55854468 Score: 106
Period size: 35 Copynumber: 2.5 Consensus size: 35
55854375 AAATATATTT
55854385 AATAT-TTA-AAAATA-ATATTTAAAATTTAAAAA
1 AATATATTATAAAATATATATTTAAAATTTAAAAA
55854417 AATA-ATT-TCAAAAATATATATTTAAAATTTAAAAA
1 AATATATTAT--AAAATATATATTTAAAATTTAAAAA
*
55854452 TATATATTATAAAATAT
1 AATATATTATAAAATAT
55854469 TTCAAATGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 11
0.79 0.02 0.20
Matches are distributed among these distances:
32 6 0.14
34 6 0.14
35 28 0.64
36 3 0.07
37 1 0.02
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (35 bp):
AATATATTATAAAATATATATTTAAAATTTAAAAA
Found at i:55854551 original size:10 final size:9
Alignment explanation
Indices: 55854544--55854608 Score: 51
Period size: 10 Copynumber: 6.9 Consensus size: 9
55854534 AGACAAAACT
55854544 TAAAAAAAG
1 TAAAAAAAG
*
55854553 TAAAAAAAAA
1 T-AAAAAAAG
* *
55854563 TGACAAAAG
1 TAAAAAAAG
55854572 TAAAGAAAAG
1 TAAA-AAAAG
55854582 TAAAAAGAA-
1 TAAAAA-AAG
*
55854591 AAAAACAAAG
1 TAAAA-AAAG
55854601 TAAAAAAA
1 TAAAAAAA
55854609 TAACAGGGTG
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
9 19 0.44
10 24 0.56
ACGTcount: A:0.77, C:0.03, G:0.11, T:0.09
Consensus pattern (9 bp):
TAAAAAAAG
Found at i:55854568 original size:29 final size:30
Alignment explanation
Indices: 55854526--55854608 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 30
55854516 ATAAATAAAT
*
55854526 AAAGATAAA-GACAAAACTTAAA-AAAAGTAA
1 AAAGA-AAATGACAAAA-GTAAAGAAAAGTAA
55854556 AAA-AAAATGACAAAAGTAAAGAAAAGTAA
1 AAAGAAAATGACAAAAGTAAAGAAAAGTAA
**
55854585 AAAGAAAAAAAC-AAAGTAAA-AAAA
1 AAAGAAAATGACAAAAGTAAAGAAAA
55854609 TAACAGGGTG
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 11 0.23
29 27 0.57
30 9 0.19
ACGTcount: A:0.75, C:0.05, G:0.11, T:0.10
Consensus pattern (30 bp):
AAAGAAAATGACAAAAGTAAAGAAAAGTAA
Found at i:55856078 original size:11 final size:11
Alignment explanation
Indices: 55856064--55856108 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
55856054 AGATAAATAT
55856064 TATTTTATTAA
1 TATTTTATTAA
*
55856075 TATTTTAATAAGA
1 TATTTT-ATTA-A
*
55856088 TATTTTATTAT
1 TATTTTATTAA
55856099 TATTTTATTA
1 TATTTTATTA
55856109 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55858339 original size:46 final size:46
Alignment explanation
Indices: 55858272--55859223 Score: 1744
Period size: 46 Copynumber: 20.7 Consensus size: 46
55858262 GGCAACCTGC
55858272 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858318 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858364 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858410 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858456 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858502 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858548 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858594 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858640 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858686 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858732 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858778 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858824 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858870 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858916 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55858962 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55859008 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
55859054 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
* * * *
55859100 GTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAA-AA
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATAT-AAGAT
** * * * * * *
55859146 GAATAAGACCATAGTTGAAAGATACCATGGCAACATGACAGAAAAT
1 GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
* * * *
55859192 GAGTAAGATCATAGTTGAAAGACACTATGGCA
1 GTGTAAGACCATGGTTGAAAGATACTATGGCA
55859224 TCACGTCAAA
Statistics
Matches: 890, Mismatches: 14, Indels: 4
0.98 0.02 0.00
Matches are distributed among these distances:
45 2 0.00
46 886 1.00
47 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.25
Consensus pattern (46 bp):
GTGTAAGACCATGGTTGAAAGATACTATGGCAACCTGATATAAGAT
Found at i:55861994 original size:40 final size:40
Alignment explanation
Indices: 55861757--55861983 Score: 393
Period size: 40 Copynumber: 5.7 Consensus size: 40
55861747 TCCTCGTTCA
* * * ** *
55861757 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55861796 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55861836 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55861876 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55861916 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
55861956 AATGCCTTCGGGACTTAACCCGGATTTA
1 AATGCCTTCGGGACTTAACCCGGATTTA
55861984 GTATATCGCA
Statistics
Matches: 181, Mismatches: 6, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
39 33 0.18
40 148 0.82
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:55862003 original size:40 final size:40
Alignment explanation
Indices: 55861755--55862059 Score: 368
Period size: 40 Copynumber: 7.7 Consensus size: 40
55861745 GCTCCTCGTT
* * * ** *
55861755 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
55861795 C-AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
55861834 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
55861874 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
*
55861914 CGAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
* **
55861954 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATA-TCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAACA-ACTCGCA
* ** * * *
55861994 CAAAGGCCTTC-GGATCTTAGTCCGGATATATTC-ACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCA
*
55862035 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
55862060 CAGCATTCAA
Statistics
Matches: 241, Mismatches: 17, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
39 37 0.15
40 192 0.80
41 12 0.05
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCA
Found at i:55862068 original size:41 final size:41
Alignment explanation
Indices: 55861991--55862068 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
55861981 TTAGTATATC
* * *
55861991 GCACAAAGGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
55862032 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAAGGCCTTC-GGATCTTAGCCCGGACA-CATTCA
55862069 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (41 bp):
GCACAAAGGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:55869155 original size:25 final size:25
Alignment explanation
Indices: 55869126--55869177 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
55869116 AAGAATAATT
*
55869126 TGAATATTTGATATTGCCTAATAAA
1 TGAATATATGATATTGCCTAATAAA
* *
55869151 TGAATATATGATATTGCTTAGTAAA
1 TGAATATATGATATTGCCTAATAAA
55869176 TG
1 TG
55869178 TCAAGCCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.06, G:0.15, T:0.40
Consensus pattern (25 bp):
TGAATATATGATATTGCCTAATAAA
Found at i:55869517 original size:27 final size:27
Alignment explanation
Indices: 55869487--55869541 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
55869477 TTGTATAAAG
55869487 ATAGTATTTCAAATGATTTGATGAGTA
1 ATAGTATTTCAAATGATTTGATGAGTA
55869514 ATAGTATTTCAAATGATTTGATGAGTA
1 ATAGTATTTCAAATGATTTGATGAGTA
55869541 A
1 A
55869542 AGCTCCAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (27 bp):
ATAGTATTTCAAATGATTTGATGAGTA
Found at i:55869866 original size:52 final size:52
Alignment explanation
Indices: 55869802--55869906 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
55869792 GAATATAAAG
55869802 AAGCGGTAAGTTAATTACCATGTTAGACGAATTTATTAAATATTAAATGTTT
1 AAGCGGTAAGTTAATTACCATGTTAGACGAATTTATTAAATATTAAATGTTT
* *
55869854 AAGCGGTAAGTTAATTACCATGTTATACGAATTTATTAAATATTACATGTTT
1 AAGCGGTAAGTTAATTACCATGTTAGACGAATTTATTAAATATTAAATGTTT
55869906 A
1 A
55869907 CTTTGTTTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (52 bp):
AAGCGGTAAGTTAATTACCATGTTAGACGAATTTATTAAATATTAAATGTTT
Found at i:55870965 original size:13 final size:13
Alignment explanation
Indices: 55870947--55870971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55870937 TTTACAGGGA
55870947 CATGCCCGTGTGC
1 CATGCCCGTGTGC
55870960 CATGCCCGTGTG
1 CATGCCCGTGTG
55870972 AAGGTGCTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.36, G:0.32, T:0.24
Consensus pattern (13 bp):
CATGCCCGTGTGC
Found at i:55884310 original size:45 final size:45
Alignment explanation
Indices: 55884261--55884411 Score: 162
Period size: 45 Copynumber: 3.4 Consensus size: 45
55884251 TCTTTAAACC
* *
55884261 ATGGTCTTACTCACTTCCATCTTGATGCCATAACATCTTTCAGCT
1 ATGGTCTTACTCACTTTCATCATGATGCCATAACATCTTTCAGCT
* ** * *
55884306 ATGGTATTACT-TGTTTCATCATGTTGCCATAACATCTTTCATCT
1 ATGGTCTTACTCACTTTCATCATGATGCCATAACATCTTTCAGCT
*** * * *
55884350 ATGGTCTTACTTGTTTTCATCATGATGTCATAGCATCTTTCGGCT
1 ATGGTCTTACTCACTTTCATCATGATGCCATAACATCTTTCAGCT
*
55884395 ATGGTTTTACTCA-TTTC
1 ATGGTCTTACTCACTTTC
55884412 TGTTATGTAA
Statistics
Matches: 87, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
44 41 0.47
45 46 0.53
ACGTcount: A:0.21, C:0.23, G:0.13, T:0.44
Consensus pattern (45 bp):
ATGGTCTTACTCACTTTCATCATGATGCCATAACATCTTTCAGCT
Found at i:55884344 original size:44 final size:45
Alignment explanation
Indices: 55884278--55884405 Score: 177
Period size: 44 Copynumber: 2.9 Consensus size: 45
55884268 TACTCACTTC
*
55884278 CATCTTGATGCCATAACATCTTTCAGCTATGGTATTACTTG-TTT
1 CATCATGATGCCATAACATCTTTCAGCTATGGTATTACTTGTTTT
* * *
55884322 CATCATGTTGCCATAACATCTTTCATCTATGGTCTTACTTGTTTT
1 CATCATGATGCCATAACATCTTTCAGCTATGGTATTACTTGTTTT
* * * *
55884367 CATCATGATGTCATAGCATCTTTCGGCTATGGTTTTACT
1 CATCATGATGCCATAACATCTTTCAGCTATGGTATTACT
55884406 CATTTCTGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
44 37 0.51
45 36 0.49
ACGTcount: A:0.21, C:0.21, G:0.14, T:0.44
Consensus pattern (45 bp):
CATCATGATGCCATAACATCTTTCAGCTATGGTATTACTTGTTTT
Found at i:55884909 original size:5 final size:5
Alignment explanation
Indices: 55884899--55884939 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
55884889 CTTTTGTGAA
*
55884899 AAAAT AAAAT AAAAT AAAAT -AAAG AAAAT AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
55884940 CACAAATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 3 0.09
5 30 0.91
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:55884928 original size:14 final size:14
Alignment explanation
Indices: 55884899--55884935 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
55884889 CTTTTGTGAA
*
55884899 AAAATAAAATAAAAT
1 AAAAT-AAAGAAAAT
55884914 AAAATAAAGAAAAT
1 AAAATAAAGAAAAT
55884928 AAAATAAA
1 AAAATAAA
55884936 ATAACACAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (14 bp):
AAAATAAAGAAAAT
Found at i:55889368 original size:5 final size:5
Alignment explanation
Indices: 55889358--55889397 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
55889348 ATTTGTGAAA
*
55889358 AAAAT AAAAT AAAAT AAAAT -AAAG AAAA- AAAAT AAAAT AA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA
55889398 CACAAATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
4 7 0.22
5 25 0.78
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (5 bp):
AAAAT
Found at i:55889373 original size:10 final size:10
Alignment explanation
Indices: 55889358--55889397 Score: 57
Period size: 9 Copynumber: 4.2 Consensus size: 10
55889348 ATTTGTGAAA
55889358 AAAATAAAAT
1 AAAATAAAAT
55889368 AAAATAAAAT
1 AAAATAAAAT
*
55889378 -AAAGAAAA-
1 AAAATAAAAT
55889386 AAAATAAAAT
1 AAAATAAAAT
55889396 AA
1 AA
55889398 CACAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 14 0.54
10 12 0.46
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:55889522 original size:38 final size:38
Alignment explanation
Indices: 55889478--55889551 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
55889468 AAAATTTGAA
*
55889478 TCAATACAAGAGGAATAGACTATGTTTATTTATAGGTT
1 TCAATACAAGAGGAATAGACTATGTCTATTTATAGGTT
55889516 TCAATACAAGAGGAATAGACTATGTCTATTTATAGG
1 TCAATACAAGAGGAATAGACTATGTCTATTTATAGG
55889552 CTTGTAAAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (38 bp):
TCAATACAAGAGGAATAGACTATGTCTATTTATAGGTT
Found at i:55893845 original size:22 final size:23
Alignment explanation
Indices: 55893810--55893874 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
55893800 GCTTACTATC
* *
55893810 CAGCACTTCGGTGCCTTCTG-AT
1 CAGCACTTCAGTGCCTACTGTAT
* *
55893832 CAGCACTTTAGTGCCTACTGTTT
1 CAGCACTTCAGTGCCTACTGTAT
*
55893855 AAGCACTTCAGTGCCTACTG
1 CAGCACTTCAGTGCCTACTG
55893875 GTATGGTGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.32
Consensus pattern (23 bp):
CAGCACTTCAGTGCCTACTGTAT
Found at i:55896914 original size:5 final size:5
Alignment explanation
Indices: 55896906--55896939 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
55896896 ATTTAATTAG
*
55896906 TAAAT TAAAT TAAAT TAAAT T-AAT TAAAA TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
55896940 AATATTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
TAAAT
Found at i:55896926 original size:15 final size:14
Alignment explanation
Indices: 55896906--55896939 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55896896 ATTTAATTAG
*
55896906 TAAATTAAATTAAAT
1 TAAATT-AATTAAAA
55896921 TAAATTAATTAAAA
1 TAAATTAATTAAAA
55896935 TAAAT
1 TAAAT
55896940 AATATTTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTAATTAAAA
Found at i:55899345 original size:42 final size:42
Alignment explanation
Indices: 55899298--55899383 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 42
55899288 TCCTTCTTTT
*
55899298 GTGGAAAAAATGTTA-TA-ATTTAAGTGCTAATTTTGTATTTAA
1 GTGGAAAAAATG-TAGTAGATTTAAG-GCTAATTTTGTACTTAA
* * *
55899340 GTGGAAATAATGTAGTAGTTTTAAGGTTAATTTTGTACTTAA
1 GTGGAAAAAATGTAGTAGATTTAAGGCTAATTTTGTACTTAA
55899382 GT
1 GT
55899384 CTACAATAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
41 2 0.05
42 30 0.79
43 6 0.16
ACGTcount: A:0.35, C:0.02, G:0.20, T:0.43
Consensus pattern (42 bp):
GTGGAAAAAATGTAGTAGATTTAAGGCTAATTTTGTACTTAA
Found at i:55908084 original size:17 final size:18
Alignment explanation
Indices: 55908052--55908086 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
55908042 TATGCACAAC
55908052 ATGTTCCATCCAGTTTCA
1 ATGTTCCATCCAGTTTCA
*
55908070 ATGTTCCA-GCAGTTTCA
1 ATGTTCCATCCAGTTTCA
55908087 GGTGCTGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (18 bp):
ATGTTCCATCCAGTTTCA
Found at i:55909922 original size:14 final size:14
Alignment explanation
Indices: 55909885--55909932 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
55909875 AATTTTCTAA
*
55909885 TAAAAATTCAGCAC
1 TAAAAATTCAGTAC
* *
55909899 TTATAAAATTTAGTAG
1 -TA-AAAATTCAGTAC
55909915 TAAAAATTCAGTAC
1 TAAAAATTCAGTAC
55909929 TAAA
1 TAAA
55909933 TTTTTCAGCG
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
14 14 0.52
15 4 0.15
16 9 0.33
ACGTcount: A:0.50, C:0.10, G:0.08, T:0.31
Consensus pattern (14 bp):
TAAAAATTCAGTAC
Found at i:55913383 original size:11 final size:11
Alignment explanation
Indices: 55913367--55913392 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
55913357 TGTAGAAGCC
55913367 GTATACTCAAT
1 GTATACTCAAT
55913378 GTATACTCAAT
1 GTATACTCAAT
55913389 GTAT
1 GTAT
55913393 CAGCTTTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (11 bp):
GTATACTCAAT
Found at i:55916331 original size:113 final size:113
Alignment explanation
Indices: 55916133--55916358 Score: 452
Period size: 113 Copynumber: 2.0 Consensus size: 113
55916123 TCAAGGTTCT
55916133 TCTGCCCCTTACAATGAAATTTAACACATATTTATAGGCAAAACAAAAGGGTAGCCGAATGGGTA
1 TCTGCCCCTTACAATGAAATTTAACACATATTTATAGGCAAAACAAAAGGGTAGCCGAATGGGTA
55916198 AAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
66 AAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
55916246 TCTGCCCCTTACAATGAAATTTAACACATATTTATAGGCAAAACAAAAGGGTAGCCGAATGGGTA
1 TCTGCCCCTTACAATGAAATTTAACACATATTTATAGGCAAAACAAAAGGGTAGCCGAATGGGTA
55916311 AAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
66 AAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
55916359 AATTATGCAT
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (113 bp):
TCTGCCCCTTACAATGAAATTTAACACATATTTATAGGCAAAACAAAAGGGTAGCCGAATGGGTA
AAATTGGAAGCCAAATTCGGCCATGGTGCTTCCTCAATTTGTTCCTTA
Found at i:55916386 original size:45 final size:45
Alignment explanation
Indices: 55916337--55916465 Score: 195
Period size: 45 Copynumber: 2.9 Consensus size: 45
55916327 TCGGCCATGG
*
55916337 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
* * * *
55916382 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
* *
55916427 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTG
55916466 TCCACCTCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
Found at i:55916600 original size:16 final size:16
Alignment explanation
Indices: 55916579--55916610 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
55916569 CATTCTGCAT
55916579 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
55916595 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
55916611 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:55917659 original size:29 final size:29
Alignment explanation
Indices: 55917617--55917678 Score: 106
Period size: 29 Copynumber: 2.1 Consensus size: 29
55917607 AAAACAATTC
*
55917617 AATTCTCGACATTCAATACCGTCAAATAT
1 AATTCGCGACATTCAATACCGTCAAATAT
*
55917646 AATTCGCGGCATTCAATACCGTCAAATAT
1 AATTCGCGACATTCAATACCGTCAAATAT
55917675 AATT
1 AATT
55917679 TGATTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (29 bp):
AATTCGCGACATTCAATACCGTCAAATAT
Found at i:55919571 original size:16 final size:17
Alignment explanation
Indices: 55919550--55919584 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55919540 TAGGGTTGAA
*
55919550 AAGAAA-GATTTAGAAG
1 AAGAAAGGATTGAGAAG
55919566 AAGAAAGGATTGAGAAG
1 AAGAAAGGATTGAGAAG
55919583 AA
1 AA
55919585 AGAACTGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.57, C:0.00, G:0.29, T:0.14
Consensus pattern (17 bp):
AAGAAAGGATTGAGAAG
Found at i:55926516 original size:31 final size:31
Alignment explanation
Indices: 55926475--55926551 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
55926465 GAAAAGTGAA
* *
55926475 AGTGATAAGTGGTAGCTTCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
* *
55926506 AGTGAAAAGTGGTAACTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
*
55926537 AGTGACAAGTGGTAG
1 AGTGAAAAGTGGTAG
55926552 TACCGGCTAC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCAGCTACCTGATC
Found at i:55926692 original size:130 final size:129
Alignment explanation
Indices: 55926542--55926784 Score: 405
Period size: 130 Copynumber: 1.9 Consensus size: 129
55926532 TGATCAGTGA
55926542 CAAGTGGTAGTACCGGCTACAAGTGACAAGTGATTTCCGTACAAGACCATATCTGGGATATGGCA
1 CAAGTGGTAGTACCGGCTACAAGTGACAAGTGATTTCCGTACAAGACCATATCTGGGATATGGCA
* * * *
55926607 TCGGTGTGATATATGCTACTGTATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATT
66 TCAGTGAGATATATGATAC-GTATAAGACCATAGCTGGGATATGGCATCAGTGAGATATGTGATT
55926672 CAAGTGGTAGTACCGGCTACAAGTGACAAGTGATTTCCGTACAAGACCATATCTGGGATATGGCA
1 CAAGTGGTAGTACCGGCTACAAGTGACAAGTGATTTCCGTACAAGACCATATCTGGGATATGGCA
* * * *
55926737 TCAGTGAGATATGTGATTCGTGTAAGACCATAGCTGGGCTATGGCATC
66 TCAGTGAGATATATGATACGTATAAGACCATAGCTGGGATATGGCATC
55926785 GATATATGAA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
129 26 0.25
130 79 0.75
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (129 bp):
CAAGTGGTAGTACCGGCTACAAGTGACAAGTGATTTCCGTACAAGACCATATCTGGGATATGGCA
TCAGTGAGATATATGATACGTATAAGACCATAGCTGGGATATGGCATCAGTGAGATATGTGATT
Found at i:55926814 original size:42 final size:43
Alignment explanation
Indices: 55926756--55926870 Score: 162
Period size: 42 Copynumber: 2.7 Consensus size: 43
55926746 TATGTGATTC
*
55926756 GTGTAAGACCATAGCTGGGCTATGGCATCGA-TATATGAATAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* *
55926798 GTGTAAGACCATAGCTGGGCTATGACATC-ATTATGTGAAGAT
1 GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
* **
55926840 GTGTAAGACCATAGTTGAACTATGGCATCGA
1 GTGTAAGACCATAGCTGGGCTATGGCATCGA
55926871 GAAAACGAAG
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 62 0.97
43 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (43 bp):
GTGTAAGACCATAGCTGGGCTATGGCATCGATTATATGAAGAT
Found at i:55931646 original size:8 final size:8
Alignment explanation
Indices: 55931633--55931663 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
55931623 AATATTAATA
55931633 ATAAGAAC
1 ATAAGAAC
55931641 ATAAGAAC
1 ATAAGAAC
55931649 ATAAGAAC
1 ATAAGAAC
55931657 ATAAGAA
1 ATAAGAA
55931664 ATGAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.65, C:0.10, G:0.13, T:0.13
Consensus pattern (8 bp):
ATAAGAAC
Found at i:55938775 original size:11 final size:11
Alignment explanation
Indices: 55938761--55938805 Score: 54
Period size: 11 Copynumber: 3.9 Consensus size: 11
55938751 AGATAAATAT
55938761 TATTTTATTAA
1 TATTTTATTAA
*
55938772 TATTTTAATAATA
1 TATTTT-ATTA-A
*
55938785 TATTTTATTAT
1 TATTTTATTAA
55938796 TATTTTATTA
1 TATTTTATTA
55938806 GTATATAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 16 0.55
12 6 0.21
13 7 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:55938788 original size:24 final size:24
Alignment explanation
Indices: 55938756--55938811 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
55938746 TAATTAGATA
55938756 AATATTATTTTATTAATATTTTAAT
1 AATA-TATTTTATTAATATTTTAAT
* *
55938781 AATATATTTTATTATTATTTTATT
1 AATATATTTTATTAATATTTTAAT
*
55938805 AGTATAT
1 AATATAT
55938812 AAAGAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 24 0.86
25 4 0.14
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AATATATTTTATTAATATTTTAAT
Found at i:55942508 original size:104 final size:104
Alignment explanation
Indices: 55942383--55942934 Score: 512
Period size: 104 Copynumber: 5.3 Consensus size: 104
55942373 GCTAACTCAA
* *
55942383 AGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAATGTAGGTCTGC
1 AGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAACGTAGGTCCGC
* * * * *
55942448 AAGTTGTTTGGGAGATGCAATCTTAAATCAGCT-ACTTAG
66 GAGCTATTTGGGAGTTGCAATCTTAAAT-AGTTAACTTAG
* ** *
55942487 AGAGATATAGGTT-CCAGTCTTAAATCAAATAACCTTTAAACATCA-ATTGGGAACGTAGGTCCA
1 AGAGATATAGGTTGCGA-TCTTAAATCAGCTAACCTTTAAACATCATATTGGGAACGTAGGTCCG
** * * *
55942550 CGATTTTTTTGGGAGTTGCGAA-CTTAAATAAATTAACTCAG
65 CGAGCTATTTGGGAGTTGC-AATCTTAAAT-AGTTAACTTAG
* * * * * *
55942591 AGAGATATAGG-TACGATCTTAAATCAGCTAACCTTTAAACTTCA-ACTGGTAACATAGGTCCGT
1 AGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAACGTAGGTCCGC
**
55942654 GAGCTATTTGGGAGTTG-AGATCTTAAATAAACTAACTTAG
66 GAGCTATTTGGGAGTTGCA-ATCTTAAAT-AGTTAACTTAG
* * * * * *
55942694 AGAGATTTAGGTTGCGATATTAAATCAGCTAACCTTTAAATATCAT-CTGAGAACGTAGGTCCGT
1 AGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAACGTAGGTCCGC
* * *
55942758 GAGCTATTTGGGAGTTGCGATATTAAATATGTTAACTCAG
66 GAGCTATTTGGGAGTTGCAATCTTAAATA-GTTAACTTAG
* * * * * * * * * *
55942798 AGAAATTTAGGTTACGATTTTAAATCAACTAATCTTTAAACAT--TAGTTGGGAATGTAAGTTCA
1 AGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATA-TTGGGAACGTAGGTCCG
* * **
55942861 CAAGCTGTTTGGGAGTTGTGATCTTAAATATGTTAACTTAG
65 CGAGCTATTTGGGAGTTGCAATCTTAAATA-GTTAACTTAG
* *
55942902 AGAGATTTAGGTTGCGATCTTAAATCAGGTAAC
1 AGAGATATAGGTTGCGATCTTAAATCAGCTAAC
55942935 TCAGAGAGAT
Statistics
Matches: 371, Mismatches: 65, Indels: 24
0.81 0.14 0.05
Matches are distributed among these distances:
101 1 0.00
102 2 0.01
103 123 0.33
104 245 0.66
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (104 bp):
AGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAACGTAGGTCCGC
GAGCTATTTGGGAGTTGCAATCTTAAATAGTTAACTTAG
Found at i:55942622 original size:207 final size:207
Alignment explanation
Indices: 55942375--55942928 Score: 613
Period size: 207 Copynumber: 2.7 Consensus size: 207
55942365 TTAACTTTGC
* *
55942375 TAACTCAAAGAGATATAGGTTGCGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAATGT
1 TAACTCAGAGAGATATAGGTTACGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAATGT
* * * *
55942440 AGGTCTGCAAGTTGTTTGGGAGATGCAATCTTAAATCAGCT-ACTTAGAGAGATATAGGTT-CCA
66 AGGTCTGCAAGCTGTTTGGGAGTTG-AATCTTAAAT-AGCTAACTTAGAGAGATTTAGGTTGCGA
* ** *
55942503 GTCTTAAATCAAATAACCTTTAAACATCAAT-TGGGAACGTAGGTCCACGATTTTTTTGGGAGTT
129 -TCTTAAATCAAATAACCTTTAAACATC-ATCTGAGAACGTAGGTCCACGAGCTATTTGGGAGTT
55942567 GCGA-ACTTAAATAAAT
192 GCGATA-TTAAATAAAT
* * * **
55942583 TAACTCAGAGAGATATAGG-TACGATCTTAAATCAGCTAACCTTTAAACTTCA-ACTGGTAACAT
1 TAACTCAGAGAGATATAGGTTACGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAATGT
* ** * *
55942646 AGGTCCGTGAGCTATTTGGGAGTTGAGATCTTAAATAAACTAACTTAGAGAGATTTAGGTTGCGA
66 AGGTCTGCAAGCTGTTTGGGAGTTGA-ATCTTAAAT-AGCTAACTTAGAGAGATTTAGGTTGCGA
* ** * **
55942711 TATTAAATCAGCTAACCTTTAAATATCATCTGAGAACGTAGGTCCGTGAGCTATTTGGGAGTTGC
129 TCTTAAATCAAATAACCTTTAAACATCATCTGAGAACGTAGGTCCACGAGCTATTTGGGAGTTGC
**
55942776 GATATTAAATATGT
194 GATATTAAATAAAT
* * * * *
55942790 TAACTCAGAGAAATTTAGGTTACGATTTTAAATCAACTAATCTTTAAACAT--TAGTTGGGAATG
1 TAACTCAGAGAGATATAGGTTACGATCTTAAATCAGCTAACCTTTAAACATCATA-TTGGGAATG
* * * *
55942853 TAAGT-TCACAAGCTGTTTGGGAGTTGTGATCTTAAATATGTTAACTTAGAGAGATTTAGGTTGC
65 TAGGTCT-GCAAGCTGTTTGGGAGTTG-AATCTTAAATA-GCTAACTTAGAGAGATTTAGGTTGC
55942917 GATCTTAAATCA
127 GATCTTAAATCA
55942929 GGTAACTCAG
Statistics
Matches: 286, Mismatches: 49, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
205 1 0.00
206 40 0.14
207 130 0.45
208 115 0.40
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (207 bp):
TAACTCAGAGAGATATAGGTTACGATCTTAAATCAGCTAACCTTTAAACATCATATTGGGAATGT
AGGTCTGCAAGCTGTTTGGGAGTTGAATCTTAAATAGCTAACTTAGAGAGATTTAGGTTGCGATC
TTAAATCAAATAACCTTTAAACATCATCTGAGAACGTAGGTCCACGAGCTATTTGGGAGTTGCGA
TATTAAATAAAT
Found at i:55942935 original size:37 final size:37
Alignment explanation
Indices: 55942875--55942952 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
55942865 CTGTTTGGGA
* * *
55942875 GTTGTGATCTTAAATATGTTAACTTAGAGAGATTTAG
1 GTTGCGATCTTAAATATGGTAACTCAGAGAGATTTAG
55942912 GTTGCGATCTTAAATCA-GGTAACTCAGAGAGATTTAG
1 GTTGCGATCTTAAAT-ATGGTAACTCAGAGAGATTTAG
55942949 GTTG
1 GTTG
55942953 TTATCATTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 36 0.97
38 1 0.03
ACGTcount: A:0.31, C:0.09, G:0.24, T:0.36
Consensus pattern (37 bp):
GTTGCGATCTTAAATATGGTAACTCAGAGAGATTTAG
Found at i:55947235 original size:20 final size:21
Alignment explanation
Indices: 55947196--55947235 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
55947186 TGTGTTTGCT
* *
55947196 TTCCGTTTAGCTCTTATGAGC
1 TTCCGTTTAACTCATATGAGC
55947217 TTCCG-TTAACTCATATGAG
1 TTCCGTTTAACTCATATGAG
55947236 TTTCAGTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TTCCGTTTAACTCATATGAGC
Found at i:55954092 original size:21 final size:22
Alignment explanation
Indices: 55954066--55954133 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 22
55954056 AATTAGTTAC
55954066 AATCCAAATCTAAATTTAAATT
1 AATCCAAATCTAAATTTAAATT
*
55954088 -ATCCAAATAATAAATTTAAATT
1 AATCCAAAT-CTAAATTTAAATT
*
55954110 AATTCAAAATCTTAAATTTCAAAT
1 AA-TCCAAATC-TAAATTT-AAAT
55954134 ATGTTAAATC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 8 0.21
22 12 0.32
23 1 0.03
24 13 0.34
25 4 0.11
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (22 bp):
AATCCAAATCTAAATTTAAATT
Found at i:55954101 original size:22 final size:21
Alignment explanation
Indices: 55954067--55954110 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
55954057 ATTAGTTACA
*
55954067 ATCCAAATCTAAATTTAAATT
1 ATCCAAATATAAATTTAAATT
55954088 ATCCAAATAATAAATTTAAATT
1 ATCCAAAT-ATAAATTTAAATT
55954110 A
1 A
55954111 ATTCAAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (21 bp):
ATCCAAATATAAATTTAAATT
Found at i:55954181 original size:15 final size:16
Alignment explanation
Indices: 55954161--55954190 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
55954151 AAAACTTTAA
55954161 AAATAAT-AATTTCAT
1 AAATAATAAATTTCAT
55954176 AAATAATAAATTTCA
1 AAATAATAAATTTCA
55954191 AAGTTACCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATAATAAATTTCAT
Found at i:55954638 original size:24 final size:22
Alignment explanation
Indices: 55954611--55954659 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
55954601 TCTTAGATTT
*
55954611 TTATGTTTTAAATATATTAATATA
1 TTAT-TTTTAAATATA-AAATATA
*
55954635 TTA-TTTTAATTATAAAATATA
1 TTATTTTTAAATATAAAATATA
55954656 TTAT
1 TTAT
55954660 ATTATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.41
22 10 0.45
24 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTTTTAAATATAAAATATA
Found at i:55954655 original size:21 final size:22
Alignment explanation
Indices: 55954629--55954669 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
55954619 TAAATATATT
*
55954629 AATATATTATTTTA-ATTATAA
1 AATATATTATATTATATTATAA
55954650 AATATATTATATTATATTAT
1 AATATATTATATTATATTAT
55954670 TATGTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
AATATATTATATTATATTATAA
Found at i:55954863 original size:19 final size:19
Alignment explanation
Indices: 55954810--55954891 Score: 64
Period size: 19 Copynumber: 4.5 Consensus size: 19
55954800 ATAAACAAAT
55954810 GAAACAAATGAAATA-AAAA
1 GAAACAAA-GAAATAGAAAA
* *
55954829 GAAATAAA-AGATAGAAAA
1 GAAACAAAGAAATAGAAAA
* *
55954847 GAAACAAAGAAACAGAATA
1 GAAACAAAGAAATAGAAAA
* *
55954866 G-AA-AACGAAATAGGAAA
1 GAAACAAAGAAATAGAAAA
*
55954883 GAAAGAAAG
1 GAAACAAAG
55954892 GAGAAAAGAA
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
17 15 0.31
18 15 0.31
19 18 0.38
ACGTcount: A:0.70, C:0.05, G:0.18, T:0.07
Consensus pattern (19 bp):
GAAACAAAGAAATAGAAAA
Found at i:55955859 original size:21 final size:21
Alignment explanation
Indices: 55955833--55955878 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
55955823 CCTCGAGTTG
*
55955833 ATTAGGCACTATATGTGTCAT
1 ATTAGGCACCATATGTGTCAT
* *
55955854 ATTAGGCACCATGTGTGTCGT
1 ATTAGGCACCATATGTGTCAT
55955875 ATTA
1 ATTA
55955879 TTACTTCTGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (21 bp):
ATTAGGCACCATATGTGTCAT
Found at i:55956335 original size:31 final size:31
Alignment explanation
Indices: 55956297--55956355 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
55956287 GAGTATATCT
*
55956297 ATACTCAGCGTGTGGTTGTTTTCGTGCGATG
1 ATACTCAGCGTGTGGTTGTTTACGTGCGATG
55956328 ATACTCAGCGTGTGGTTGTTTACGTGCG
1 ATACTCAGCGTGTGGTTGTTTACGTGCG
55956356 CAGATCAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.14, C:0.17, G:0.32, T:0.37
Consensus pattern (31 bp):
ATACTCAGCGTGTGGTTGTTTACGTGCGATG
Found at i:55957729 original size:24 final size:21
Alignment explanation
Indices: 55957682--55957734 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 21
55957672 TGATATTACA
55957682 TTATTATTATTTTCTTTCTAT
1 TTATTATTATTTTCTTTCTAT
* *
55957703 TTATTATT-TTTT-TTCCTTT
1 TTATTATTATTTTCTTTCTAT
55957722 TTATT-TTATTTTC
1 TTATTATTATTTTC
55957735 GAATTTGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 4 0.14
21 8 0.29
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTATTATTTTCTTTCTAT
Found at i:55958436 original size:15 final size:14
Alignment explanation
Indices: 55958410--55958445 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
55958400 TATATTTTTG
55958410 TTATACTTATATATA
1 TTATA-TTATATATA
55958425 TGTATATTATATATA
1 T-TATATTATATATA
55958440 TTATAT
1 TTATAT
55958446 AGTATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 11 0.55
16 4 0.20
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATATTATATATA
Found at i:55958781 original size:17 final size:17
Alignment explanation
Indices: 55958759--55958821 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
55958749 TTAAATATTG
55958759 TATTTTTATTATGTATA
1 TATTTTTATTATGTATA
* * *
55958776 TATTTTTAATACGGATA
1 TATTTTTATTATGTATA
*
55958793 CATTTTTTATTACTCGTATA
1 TA-TTTTTATTA-T-GTATA
55958813 TATATTTTA
1 TAT-TTTTA
55958822 ATATTATTTT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
17 15 0.44
18 8 0.24
19 1 0.03
20 10 0.29
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.57
Consensus pattern (17 bp):
TATTTTTATTATGTATA
Found at i:55959197 original size:15 final size:14
Alignment explanation
Indices: 55959162--55959197 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 14
55959152 TTAATTTTAC
55959162 TTTTATTATTATCA
1 TTTTATTATTATCA
55959176 TTATTATTATTATCA
1 TT-TTATTATTATCA
55959191 TATTTAT
1 T-TTTAT
55959198 ACTTATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 2 0.10
15 17 0.85
16 1 0.05
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTATTATTATCA
Found at i:55959414 original size:3 final size:3
Alignment explanation
Indices: 55959406--55959459 Score: 60
Period size: 3 Copynumber: 18.3 Consensus size: 3
55959396 TATCTCTAAC
55959406 TAT TAT TAT TAT T-T TA- TAT ATAT TAT TAT CTA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TAT TAT TAT
*
55959450 TAC TAT TAT T
1 TAT TAT TAT T
55959460 CTTTATTGTC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
2 6 0.14
3 33 0.75
4 5 0.11
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:55960518 original size:40 final size:39
Alignment explanation
Indices: 55960442--55960519 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
55960432 AATTTACAAT
* *
55960442 AAAAAAAACTAAAAAAAAATTAAAATTTATTCGAATTTA
1 AAAAAAAACTAAAAAAAAATTAAAATTCATCCGAATTTA
*
55960481 AAAAAATAACTAAAATAAAATTAAAATTCA-CCAGAATTT
1 AAAAAA-AACTAAAAAAAAATTAAAATTCATCC-GAATTT
55960520 CCCTCACTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 7 0.21
40 27 0.79
ACGTcount: A:0.63, C:0.08, G:0.03, T:0.27
Consensus pattern (39 bp):
AAAAAAAACTAAAAAAAAATTAAAATTCATCCGAATTTA
Found at i:55961251 original size:46 final size:46
Alignment explanation
Indices: 55961198--55961289 Score: 150
Period size: 46 Copynumber: 2.0 Consensus size: 46
55961188 CCAATGCTTC
*
55961198 GTCTATTAATTGCAAATTATTTGGTCACGGA-GTCAATCCACTAAAA
1 GTCTATTAATTGCAAATTATTTGGTCA-GAAGGTCAATCCACTAAAA
*
55961244 GTCTATTAATTGCAAATTATTTGGTCATAAGGTCAATCCACTAAAA
1 GTCTATTAATTGCAAATTATTTGGTCAGAAGGTCAATCCACTAAAA
55961290 ATATCATGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 1 0.02
46 42 0.98
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (46 bp):
GTCTATTAATTGCAAATTATTTGGTCAGAAGGTCAATCCACTAAAA
Found at i:55963860 original size:20 final size:20
Alignment explanation
Indices: 55963835--55963874 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
55963825 CGGACAGAAG
55963835 AAAGCTGAACACTTTTTTTT
1 AAAGCTGAACACTTTTTTTT
55963855 AAAGCTGAACACTTTTTTTT
1 AAAGCTGAACACTTTTTTTT
55963875 TCCCTTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
AAAGCTGAACACTTTTTTTT
Found at i:55968789 original size:14 final size:14
Alignment explanation
Indices: 55968767--55968813 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
55968757 ATAATTTATT
*
55968767 TTAATTTTTTATAG
1 TTAAATTTTTATAG
*
55968781 TTAAA-TTTTAT-T
1 TTAAATTTTTATAG
55968793 TTAAATTTTTTATAG
1 TTAAA-TTTTTATAG
55968808 TTAAAT
1 TTAAAT
55968814 ATTCTTTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
12 5 0.19
13 6 0.22
14 11 0.41
15 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (14 bp):
TTAAATTTTTATAG
Found at i:55968789 original size:15 final size:15
Alignment explanation
Indices: 55968769--55968813 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
55968759 AATTTATTTT
55968769 AATTTTTTATAGTTA
1 AATTTTTTATAGTTA
*
55968784 AA--TTTTAT-TTTA
1 AATTTTTTATAGTTA
55968796 AATTTTTTATAGTTA
1 AATTTTTTATAGTTA
55968811 AAT
1 AAT
55968814 ATTCTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.20
13 6 0.24
14 6 0.24
15 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (15 bp):
AATTTTTTATAGTTA
Found at i:55968807 original size:27 final size:27
Alignment explanation
Indices: 55968761--55968822 Score: 99
Period size: 27 Copynumber: 2.3 Consensus size: 27
55968751 GAAATTATAA
55968761 TTTATTTT-AATTTTTTATAGTTAAAT
1 TTTATTTTAAATTTTTTATAGTTAAAT
55968787 TTTATTTTAAATTTTTTATAGTTAAAT
1 TTTATTTTAAATTTTTTATAGTTAAAT
* *
55968814 ATTCTTTTA
1 TTTATTTTA
55968823 TAACAATGAT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
26 8 0.24
27 25 0.76
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.65
Consensus pattern (27 bp):
TTTATTTTAAATTTTTTATAGTTAAAT
Found at i:55974570 original size:51 final size:51
Alignment explanation
Indices: 55974489--55974592 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
55974479 TGCTGTGGAG
* *
55974489 TATGATGAACTGTCAAGTGTCTCATGATCCCTTCTGACTTGCACAATCTAT
1 TATGACGAACTGTCAAGTGTCTCATAATCCCTTCTGACTTGCACAATCTAT
55974540 TATGACGAACTGTCAAGTGTCTCATAATCCCTTCTGACTTGCACAATCTAT
1 TATGACGAACTGTCAAGTGTCTCATAATCCCTTCTGACTTGCACAATCTAT
55974591 TA
1 TA
55974593 AACTCATCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (51 bp):
TATGACGAACTGTCAAGTGTCTCATAATCCCTTCTGACTTGCACAATCTAT
Found at i:55989221 original size:20 final size:20
Alignment explanation
Indices: 55989196--55989235 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55989186 ACAGCATTCA
*
55989196 ATAGCTAATCTTTAGGGATT
1 ATAGCTAATCTTTAGAGATT
* *
55989216 ATAGCTGATTTTTAGAGATT
1 ATAGCTAATCTTTAGAGATT
55989236 CTAATTAGAG
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:0.30, C:0.07, G:0.20, T:0.42
Consensus pattern (20 bp):
ATAGCTAATCTTTAGAGATT
Found at i:55994192 original size:46 final size:46
Alignment explanation
Indices: 55994115--55994226 Score: 158
Period size: 46 Copynumber: 2.5 Consensus size: 46
55994105 TCTGTTATTA
* *
55994115 ATCTTATTCGCATGTTAAGCATGTCACTGTGTTAATTTATAATGAG
1 ATCTGATTCGCATGTTAAGCATGTCAATGTGTTAATTTATAATGAG
* *
55994161 ATCTGATTCTCATGTTAAGCATGTCAATGTGTTAATTTGTAATGAG
1 ATCTGATTCGCATGTTAAGCATGTCAATGTGTTAATTTATAATGAG
*
55994207 ATC---TTCGCATGTAAAGCATG
1 ATCTGATTCGCATGTTAAGCATG
55994227 CCAACCAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
43 15 0.25
46 45 0.75
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (46 bp):
ATCTGATTCGCATGTTAAGCATGTCAATGTGTTAATTTATAATGAG
Found at i:55997895 original size:37 final size:37
Alignment explanation
Indices: 55997845--55997920 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
55997835 TTTTGACATC
55997845 AGACGCAGTTATCTTCATTGTTCTTTTATGTAGTTTT
1 AGACGCAGTTATCTTCATTGTTCTTTTATGTAGTTTT
55997882 AGACGCAGTTATCTTCATTGTTCTTTTATGTAGTTTT
1 AGACGCAGTTATCTTCATTGTTCTTTTATGTAGTTTT
55997919 AG
1 AG
55997921 TTGAACTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (37 bp):
AGACGCAGTTATCTTCATTGTTCTTTTATGTAGTTTT
Found at i:56000771 original size:33 final size:33
Alignment explanation
Indices: 56000734--56000800 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
56000724 CAAGCAACTT
56000734 ATAAAAACAAATTCCAAGGAGGAGAATTATATG
1 ATAAAAACAAATTCCAAGGAGGAGAATTATATG
56000767 ATAAAAACAAATTCCAAGGAGGAGAATTATATG
1 ATAAAAACAAATTCCAAGGAGGAGAATTATATG
56000800 A
1 A
56000801 GAGCATAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (33 bp):
ATAAAAACAAATTCCAAGGAGGAGAATTATATG
Found at i:56004330 original size:20 final size:20
Alignment explanation
Indices: 56004305--56004345 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
56004295 TAAAAAACAA
56004305 TTAATTCACAATTTAGTTCT
1 TTAATTCACAATTTAGTTCT
56004325 TTAATTCACAATTTAGTTCT
1 TTAATTCACAATTTAGTTCT
56004345 T
1 T
56004346 AAACTTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (20 bp):
TTAATTCACAATTTAGTTCT
Found at i:56009444 original size:27 final size:28
Alignment explanation
Indices: 56009386--56009442 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
56009376 TTACCGTAGG
* *
56009386 TTCAAATCTTTTTTATTCATCAAGTACT
1 TTCAAATCTTTTTGAGTCATCAAGTACT
*
56009414 TTCAAATCTTTTTGAGTCATTAAGTACT
1 TTCAAATCTTTTTGAGTCATCAAGTACT
56009442 T
1 T
56009443 CAGACATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (28 bp):
TTCAAATCTTTTTGAGTCATCAAGTACT
Found at i:56023995 original size:14 final size:13
Alignment explanation
Indices: 56023963--56023996 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
56023953 TGAAAATATT
56023963 AAAACAATAATTA
1 AAAACAATAATTA
*
56023976 ACAACACATAATTA
1 AAAACA-ATAATTA
56023990 AAAACAA
1 AAAACAA
56023997 GAACAAGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.68, C:0.15, G:0.00, T:0.18
Consensus pattern (13 bp):
AAAACAATAATTA
Found at i:56026307 original size:6 final size:6
Alignment explanation
Indices: 56026227--56026319 Score: 91
Period size: 6 Copynumber: 15.5 Consensus size: 6
56026217 GAAAACAAAC
* * * * *
56026227 TAAACA TAAAAA GAAAAA T-AAAA -AAAAG TAAAAG TATAAA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
* *
56026273 TAAAAGA TAAAAGA TAAAAA TAAAAA TAAACA TAAACA TAAAAA TAA
1 TAAAA-A TAAAA-A TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAA
56026320 TCAGACTCAA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
5 7 0.09
6 55 0.73
7 13 0.17
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.16
Consensus pattern (6 bp):
TAAAAA
Found at i:56028024 original size:26 final size:28
Alignment explanation
Indices: 56027981--56028032 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 28
56027971 TAACCAAAGA
56027981 AATAATTAAGAATGAAAAGAAAAAAATAT
1 AATAATTAAGAATGAAAA-AAAAAAATAT
*
56028010 AATAA-TAA-AAT-AAAAATAAAAAT
1 AATAATTAAGAATGAAAAAAAAAAAT
56028033 CTAAAGTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
25 7 0.32
26 4 0.18
27 3 0.14
28 3 0.14
29 5 0.23
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (28 bp):
AATAATTAAGAATGAAAAAAAAAAATAT
Found at i:56028713 original size:20 final size:20
Alignment explanation
Indices: 56028688--56028732 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
56028678 TTGTTTCTCT
56028688 CACGCCCGTGTGGTATACCA
1 CACGCCCGTGTGGTATACCA
*
56028708 CACGCCCGTGTGGTATCCCA
1 CACGCCCGTGTGGTATACCA
56028728 CACGC
1 CACGC
56028733 TAGTGTGTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.18, C:0.40, G:0.24, T:0.18
Consensus pattern (20 bp):
CACGCCCGTGTGGTATACCA
Found at i:56028738 original size:20 final size:20
Alignment explanation
Indices: 56028688--56028739 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
56028678 TTGTTTCTCT
*
56028688 CACGCCCGTGTGGTATACCA
1 CACGCCAGTGTGGTATACCA
* *
56028708 CACGCCCGTGTGGTATCCCA
1 CACGCCAGTGTGGTATACCA
*
56028728 CACGCTAGTGTG
1 CACGCCAGTGTG
56028740 TCCGAACACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.35, G:0.27, T:0.21
Consensus pattern (20 bp):
CACGCCAGTGTGGTATACCA
Found at i:56031925 original size:22 final size:22
Alignment explanation
Indices: 56031900--56031943 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56031890 GATAAGTTAG
56031900 TAAATTATAATAAAAATAAAAA
1 TAAATTATAATAAAAATAAAAA
* *
56031922 TAAATTGTATTAAAAATAAAAA
1 TAAATTATAATAAAAATAAAAA
56031944 ATAGCTAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (22 bp):
TAAATTATAATAAAAATAAAAA
Found at i:56036111 original size:42 final size:42
Alignment explanation
Indices: 56036064--56036169 Score: 153
Period size: 42 Copynumber: 2.5 Consensus size: 42
56036054 TTTGGGTTAC
* *
56036064 TGAGACTATGTGTAAGACCATATCTGGGATATGGAATCAATA
1 TGAGACTATGTGTAAGACCATATCTAGGATATAGAATCAATA
56036106 TGAGACTATGTGTAAGA-CAGTATCTAGGATATAGAATCAATA
1 TGAGACTATGTGTAAGACCA-TATCTAGGATATAGAATCAATA
*
56036148 TGAGAGT-TCGTGTAAGACCATA
1 TGAGACTAT-GTGTAAGACCATA
56036170 GTTAAGCTGT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
41 3 0.05
42 53 0.91
43 2 0.03
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (42 bp):
TGAGACTATGTGTAAGACCATATCTAGGATATAGAATCAATA
Found at i:56040965 original size:14 final size:15
Alignment explanation
Indices: 56040941--56040973 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
56040931 TCATTGTCTA
56040941 ATAATTTATAACAAT
1 ATAATTTATAACAAT
56040956 ATAA-TTATAACAAT
1 ATAATTTATAACAAT
56040970 ATAA
1 ATAA
56040974 GTGGATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAATTTATAACAAT
Found at i:56048483 original size:180 final size:180
Alignment explanation
Indices: 56048011--56049189 Score: 1510
Period size: 180 Copynumber: 6.6 Consensus size: 180
56048001 ACCTTTAGGA
* * * *
56048011 AGATGAGG-TTGATAGGTTAAATCTGCTCTATTGCTGATACATGGAGATAAGATTCACCAT-T-T
1 AGATAAGGCTTGAT-GGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGT
** ** * * *
56048073 TCA-ATCTGCTCCATTGCCACTTCAGGGAGATAAGATCCTCAA-CCATCAGTCTGCTTCCTTGCT
65 GAAGATCTGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATTC-TCAGTCTGCTTCCTTGCT
* * * *
56048136 ACCTCAGGAAGACAATACTTATTCTTCAACCTGCTCTCTTGCTACTTCAGAG
129 ACCTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
* * * * * *
56048188 AGATGAGGCTGGA-GGTAAAATCTGCTCCATTGCTGATACATGGAAATAAGATTCACAATCTGCG
1 AGATAAGGCTTGATGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGTG
* * * * *
56048252 AAGATCTGTTCCTCTGCAA-TCTCAGGGATATAAAATCTTCAATTCTCAGTCTGTTTCCTTGCTA
66 AAGATCTGCTCCGCTGCAACT-TCAGGGAGATAAGATCTTCAATTCTCAGTCTGCTTCCTTGCTA
* *
56048316 CCTCAGGAAGATAAGACTTATTCTTCAATCTGCTCTCTTGCTACCTCAGAG
130 CCTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
*
56048367 AGATAAGGCTTGATGGTAAAATCTTCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGTG
1 AGATAAGGCTTGATGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGTG
* *
56048432 AAGATCTACTCCGCTGCAACTTCAGGGAGATAAGATCTTTAATTCTCAGTCTGCTTCCTTGCTAC
66 AAGATCTGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATTCTCAGTCTGCTTCCTTGCTAC
* * * * *
56048497 CTTAGGAAGATAAGACTCATTCTTCAACCTGTTCTCTTACTCCCTCAGTG
131 CTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
* * * * *
56048547 AGATAAGGCTTGGTGGTAAAATCTGCTTCATTGTCGATACATGGAGATAAGATTCACCATCAGCG
1 AGATAAGGCTTGATGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGTG
* * *
56048612 AAGATCTGCTCCGCTGCAA-TCTCAGGGAGATAAAATTTTCAA-TCTTCAGTCTGTTTCCTTGCT
66 AAGATCTGCTCCGCTGCAACT-TCAGGGAGATAAGATCTTCAATTC-TCAGTCTGCTTCCTTGCT
* *
56048675 ACTTCAGGAAGATAAGACTTATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
129 ACCTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
* * *
56048727 AGATAAGGCTTGGTGGTAAAATCTGCTCCATTGCTGATACATGGAGATAAGATTCACCATCTGTA
1 AGATAAGGCTTGATGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGTG
* * * *
56048792 AAGATCTGCTCCGCTGTAACTTTAGGGAGATAAGATCTTTAATTCTCAGTCTGTTTCCTTGCTAC
66 AAGATCTGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATTCTCAGTCTGCTTCCTTGCTAC
* *
56048857 CTCAAGAAGATAAGACTCATTCCTCAACCTGCTCTCTTGCTACCTCAGAG
131 CTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
* * *
56048907 AAATAAGG-TT-AGTGGTAAAATCTACTCCATTGCCGATACATGGAAATAAGATTCACCAT-T-T
1 AGATAAGGCTTGA-TGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGT
** * * ** * * *
56048968 -TCGATTTGCTCCGCTAC-TGTTTAGAGAGATAAAATCTTCAATTCTCAGTCTGCTTCCTTGCTA
65 GAAGATCTGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATTCTCAGTCTGCTTCCTTGCTA
* *
56049031 CCTCAAGAAGATAAGACTCACTCTTCAACCTGCTCTCTTGCTACCTCAGAG
130 CCTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
* * *
56049082 AGATGAGG-TT-AGTGGTAAAATCTGCTCCATTACCGATACATGGAGATAAGATTCACCATCTGC
1 AGATAAGGCTTGA-TGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGT
* *
56049145 GAAGATCTACTCCGCTGCAACTTCAGGGGGATAAGATCTTCAATT
65 GAAGATCTGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATT
56049190 TTTACTCATG
Statistics
Matches: 875, Mismatches: 110, Indels: 32
0.86 0.11 0.03
Matches are distributed among these distances:
175 143 0.16
176 55 0.06
177 10 0.01
178 18 0.02
179 175 0.20
180 470 0.54
181 4 0.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (180 bp):
AGATAAGGCTTGATGGTAAAATCTGCTCCATTGCCGATACATGGAGATAAGATTCACCATCTGTG
AAGATCTGCTCCGCTGCAACTTCAGGGAGATAAGATCTTCAATTCTCAGTCTGCTTCCTTGCTAC
CTCAGGAAGATAAGACTCATTCTTCAACCTGCTCTCTTGCTACCTCAGAG
Found at i:56049349 original size:64 final size:63
Alignment explanation
Indices: 56049247--56049437 Score: 301
Period size: 64 Copynumber: 3.0 Consensus size: 63
56049237 TTCATTTTAT
* ** * *
56049247 ATGCTTATGCCAAATAATTGGATGTTATGATCAAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGCTTATGTCAAATAATTGGATGCCATGATCAAAATGAACCAAATGCTCCTAACTAAATGTG
56049310 ATGCTTATGTCAAATAATTAGGATGCCATGATCAAAATGAACCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGTCAAATAATT-GGATGCCATGATCAAAATGAACCAAATGCTCCTAACTAAATGTG
* *
56049374 ATGCTTATGTCAAATAATTTGGATGCCATAATCAAAATGAACCAAATGTTCCTAACTAAATGTG
1 ATGCTTATGTCAAATAA-TTGGATGCCATGATCAAAATGAACCAAATGCTCCTAACTAAATGTG
56049438 TTATGAATGA
Statistics
Matches: 119, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
63 18 0.15
64 99 0.83
65 2 0.02
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (63 bp):
ATGCTTATGTCAAATAATTGGATGCCATGATCAAAATGAACCAAATGCTCCTAACTAAATGTG
Found at i:56055939 original size:12 final size:12
Alignment explanation
Indices: 56055909--56055942 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
56055899 TATATATTTT
56055909 AAAATT-ATATA
1 AAAATTAATATA
56055920 AAAA-TAATATA
1 AAAATTAATATA
56055931 AAAATTAATATA
1 AAAATTAATATA
56055943 GACGGGCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 1 0.05
11 13 0.62
12 7 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:56058727 original size:27 final size:27
Alignment explanation
Indices: 56058685--56058738 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
56058675 GAATGGACAA
56058685 AGAATCTAATTCTTAAAGGTGTATAGT
1 AGAATCTAATTCTTAAAGGTGTATAGT
56058712 AGAATCTAAATT-TTAAAGGTGTATAGT
1 AGAATCT-AATTCTTAAAGGTGTATAGT
56058739 CTATTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.39, C:0.06, G:0.19, T:0.37
Consensus pattern (27 bp):
AGAATCTAATTCTTAAAGGTGTATAGT
Found at i:56061568 original size:8 final size:8
Alignment explanation
Indices: 56061555--56061579 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
56061545 AATAATTAAT
56061555 TTTTAAAA
1 TTTTAAAA
56061563 TTTTAAAA
1 TTTTAAAA
56061571 TTTTAAAA
1 TTTTAAAA
56061579 T
1 T
56061580 ATATATAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTTTAAAA
Found at i:56064237 original size:24 final size:24
Alignment explanation
Indices: 56064205--56064252 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
56064195 ATATGACATG
56064205 TTAGAATAGAGAAACTAGCTTGAA
1 TTAGAATAGAGAAACTAGCTTGAA
56064229 TTAGAATAGAGAAACTAGCTTGAA
1 TTAGAATAGAGAAACTAGCTTGAA
56064253 AACACGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (24 bp):
TTAGAATAGAGAAACTAGCTTGAA
Found at i:56064928 original size:19 final size:19
Alignment explanation
Indices: 56064906--56064949 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
56064896 CATGTATTTG
56064906 TGTGGTATGAATGGTGGTT
1 TGTGGTATGAATGGTGGTT
* *
56064925 TGTGGTGTGATTGGTGGTT
1 TGTGGTATGAATGGTGGTT
*
56064944 GGTGGT
1 TGTGGT
56064950 TGGTAAGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.09, C:0.00, G:0.48, T:0.43
Consensus pattern (19 bp):
TGTGGTATGAATGGTGGTT
Found at i:56067606 original size:8 final size:8
Alignment explanation
Indices: 56067586--56067617 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
56067576 TAAAATTAGG
56067586 TAAATATA
1 TAAATATA
56067594 T--ATATA
1 TAAATATA
56067600 TAAATATA
1 TAAATATA
56067608 TAAATATA
1 TAAATATA
56067616 TA
1 TA
56067618 TATAATTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
6 6 0.27
8 16 0.73
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TAAATATA
Found at i:56080377 original size:43 final size:42
Alignment explanation
Indices: 56080240--56080403 Score: 161
Period size: 43 Copynumber: 3.8 Consensus size: 42
56080230 CATAGGATTC
* ** *
56080240 CGATATGTGATTTCGTGTAAGACCACGCCTGGGACGTTGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTTTGGGAC-ATGGCAT
* * * *
56080283 CGAT-TTGAGATTTACGTGTAAGGCCATGTTTGGGACATCGACAT
1 CGATATT-TGATTT-CGTGTAAGACCACGTTTGGGACAT-GGCAT
**
56080327 CG-TATTTGATTTCGTGTAAGACCTTGTTTGGGACAATGGCAT
1 CGATATTTGATTTCGTGTAAGACCACGTTTGGGAC-ATGGCAT
* *
56080369 CGATATTTGATTACATGTAAGACCACGTTTGGGAC
1 CGATATTTGATTTCGTGTAAGACCACGTTTGGGAC
56080404 GTTGGCGTTG
Statistics
Matches: 99, Mismatches: 16, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
42 27 0.27
43 46 0.46
44 26 0.26
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
CGATATTTGATTTCGTGTAAGACCACGTTTGGGACATGGCAT
Found at i:56080622 original size:46 final size:46
Alignment explanation
Indices: 56080567--56080679 Score: 176
Period size: 46 Copynumber: 2.5 Consensus size: 46
56080557 TATGTACATT
56080567 TGTGA-ACATATGTTATATGTGAATGAATTATGATCAAATGAGCCA
1 TGTGAGACATATGTTATATGTGAATGAATTATGATCAAATGAGCCA
* *
56080612 TGTGAGACATATGTTATATGTGAATGAATTATGATGAAATGAGCTA
1 TGTGAGACATATGTTATATGTGAATGAATTATGATCAAATGAGCCA
* *
56080658 TATGAGACATATG-GATATGTGA
1 TGTGAGACATATGTTATATGTGA
56080680 TTGTATTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 13 0.21
46 50 0.79
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (46 bp):
TGTGAGACATATGTTATATGTGAATGAATTATGATCAAATGAGCCA
Found at i:56081998 original size:157 final size:157
Alignment explanation
Indices: 56081781--56082095 Score: 612
Period size: 157 Copynumber: 2.0 Consensus size: 157
56081771 TTAGTCCCGA
56081781 ATGCATGATTAGAGCCTTGTATGCTTGATTTAAGTACATATTGAGTGTGATTGAATGATATTGAT
1 ATGCATGATTAGAGCCTTGTATGCTTGATTTAAGTACATATTGAGTGTGATTGAATGATATTGAT
56081846 TGAGAAAAGATGTTATCGGATAAATGATTGTTCTGAACTGAGTTATAAGTCTAGTAATACCTTTT
66 TGAGAAAAGATGTTATCGGATAAATGATTGTTCTGAACTGAGTTATAAGTCTAGTAATACCTTTT
*
56081911 AACCTATTCCTGCGACGGTTACAGGTT
131 AACCTATTCCTGCGACGGTTACAAGTT
56081938 ATGCATGATTAGAGCCTTGTATGCTTGATTTAAGTACATATTGAGTGTGATTGAATGATATTGAT
1 ATGCATGATTAGAGCCTTGTATGCTTGATTTAAGTACATATTGAGTGTGATTGAATGATATTGAT
*
56082003 TGAGATAAGATGTTATCGGATAAATGATTGTTCTGAACTGAGTTATAAGTCTAGTAATACCTTTT
66 TGAGAAAAGATGTTATCGGATAAATGATTGTTCTGAACTGAGTTATAAGTCTAGTAATACCTTTT
56082068 AACCTATTCCTGCGACGGTTACAAGTT
131 AACCTATTCCTGCGACGGTTACAAGTT
56082095 A
1 A
56082096 GGGGTGTTAC
Statistics
Matches: 156, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 156 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.37
Consensus pattern (157 bp):
ATGCATGATTAGAGCCTTGTATGCTTGATTTAAGTACATATTGAGTGTGATTGAATGATATTGAT
TGAGAAAAGATGTTATCGGATAAATGATTGTTCTGAACTGAGTTATAAGTCTAGTAATACCTTTT
AACCTATTCCTGCGACGGTTACAAGTT
Found at i:56087941 original size:55 final size:55
Alignment explanation
Indices: 56087819--56087949 Score: 149
Period size: 55 Copynumber: 2.4 Consensus size: 55
56087809 TGTGTATGTA
* ** *
56087819 TGTC-CACGCCCATGTTGTTTTCTCAGTCTTGACCATGGGTAGCGAGCACCGGTG
1 TGTCGCACGCCCGTGTTGTTTTCTCAGTCTTGACCATGGGTAGCGAGCACAAGCG
* * * ** *
56087873 TGTTGCACACCCGTGTTGTTTTCTCAGTTTTGACCAT-GGTCTCTAGACACAAGCG
1 TGTCGCACGCCCGTGTTGTTTTCTCAGTCTTGACCATGGGTAGCGAG-CACAAGCG
56087928 TGTCGCACGCCCGTGTTGTTTT
1 TGTCGCACGCCCGTGTTGTTTT
56087950 GATAGATTCA
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 9 0.14
55 54 0.86
ACGTcount: A:0.15, C:0.27, G:0.25, T:0.34
Consensus pattern (55 bp):
TGTCGCACGCCCGTGTTGTTTTCTCAGTCTTGACCATGGGTAGCGAGCACAAGCG
Found at i:56092083 original size:13 final size:13
Alignment explanation
Indices: 56092065--56092090 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
56092055 GCTTGACAGG
56092065 GACACGCCCATGT
1 GACACGCCCATGT
56092078 GACACGCCCATGT
1 GACACGCCCATGT
56092091 TCGATTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.23, T:0.15
Consensus pattern (13 bp):
GACACGCCCATGT
Found at i:56098508 original size:61 final size:60
Alignment explanation
Indices: 56098439--56098578 Score: 208
Period size: 60 Copynumber: 2.3 Consensus size: 60
56098429 TTTGAATATT
* *
56098439 AAATTGATAGAATTTGTAAATGTGAAGAGTTAAATTTATTAAATTATTTAGAAGTAGGATC
1 AAATTGATAAAATTTGTAAATGTGAAGA-TTAAATTTATTAAATTACTTAGAAGTAGGATC
* * *
56098500 AAATTGATAAAATTTATAAATGTGAAGATTAAATTTATTGAATTACTTAGAATTAGGATC
1 AAATTGATAAAATTTGTAAATGTGAAGATTAAATTTATTAAATTACTTAGAAGTAGGATC
* *
56098560 AAATTAATAAAATATGTAA
1 AAATTGATAAAATTTGTAA
56098579 GTATTGAGGG
Statistics
Matches: 71, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
60 45 0.63
61 26 0.37
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.37
Consensus pattern (60 bp):
AAATTGATAAAATTTGTAAATGTGAAGATTAAATTTATTAAATTACTTAGAAGTAGGATC
Found at i:56098513 original size:30 final size:30
Alignment explanation
Indices: 56098470--56098572 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
56098460 GTGAAGAGTT
*
56098470 AAATTTATTAAATTATTTAGAAGTAGGATC
1 AAATTTATAAAATTATTTAGAAGTAGGATC
* * * *
56098500 AAATTGATAAAATT-TATA-AATGTGAAGATT
1 AAATTTATAAAATTATTTAGAA-GT-AGGATC
** * *
56098530 AAATTTATTGAATTACTTAGAATTAGGATC
1 AAATTTATAAAATTATTTAGAAGTAGGATC
*
56098560 AAATTAATAAAAT
1 AAATTTATAAAAT
56098573 ATGTAAGTAT
Statistics
Matches: 53, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
28 2 0.04
29 5 0.09
30 41 0.77
31 3 0.06
32 2 0.04
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.38
Consensus pattern (30 bp):
AAATTTATAAAATTATTTAGAAGTAGGATC
Found at i:56103723 original size:17 final size:17
Alignment explanation
Indices: 56103701--56103735 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
56103691 AAGGGCTATG
56103701 ATTAAGGACTGAGTTCT
1 ATTAAGGACTGAGTTCT
56103718 ATTAAGGACTGAGTTCT
1 ATTAAGGACTGAGTTCT
56103735 A
1 A
56103736 CTGTATGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (17 bp):
ATTAAGGACTGAGTTCT
Found at i:56109837 original size:46 final size:46
Alignment explanation
Indices: 56109730--56109857 Score: 150
Period size: 46 Copynumber: 2.7 Consensus size: 46
56109720 CCACATTATG
* *
56109730 AGAGCCAGTGTAAGACCATGTCTGAGACATGGCATCAGCATTGAGACA
1 AGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCAGCATCGAGACA
* * ** *
56109778 AGTGCAAGTGTAAGACATGTCTGGGACATGCATTGGCCTCGAGACA
1 AGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGACA
*
56109824 TA-AGCCAGTGTAAGACATGTCTGGAACATGCATC
1 -AGAGCCAGTGTAAGACATGTCTGGGACATGCATC
56109858 GGCTAAGAGG
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 41 0.60
47 14 0.21
48 13 0.19
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.21
Consensus pattern (46 bp):
AGAGCCAGTGTAAGACATGTCTGGGACATGCATCAGCATCGAGACA
Found at i:56111826 original size:17 final size:16
Alignment explanation
Indices: 56111797--56111843 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
56111787 AAACAAGTGG
56111797 AAGTG-AATGAAGTGACC
1 AAGTGAAAT-AAGTG-CC
*
56111814 AAGTGAAATAAGTGCT
1 AAGTGAAATAAGTGCC
*
56111830 AAGAGAAATAAGTG
1 AAGTGAAATAAGTG
56111844 GTAAGCAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 14 0.52
17 10 0.37
18 3 0.11
ACGTcount: A:0.47, C:0.06, G:0.28, T:0.19
Consensus pattern (16 bp):
AAGTGAAATAAGTGCC
Found at i:56111839 original size:16 final size:16
Alignment explanation
Indices: 56111818--56111848 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56111808 GTGACCAAGT
56111818 GAAATAAGTGCTAAGA
1 GAAATAAGTGCTAAGA
*
56111834 GAAATAAGTGGTAAG
1 GAAATAAGTGCTAAG
56111849 CAAAGTAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.29, T:0.19
Consensus pattern (16 bp):
GAAATAAGTGCTAAGA
Found at i:56115106 original size:12 final size:12
Alignment explanation
Indices: 56115091--56115121 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
56115081 TTCTCTTTTA
56115091 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
56115103 TTTTTCTTTCTC
1 TTTTTCTTTCCC
56115115 TTTTTCT
1 TTTTTCT
56115122 CCCCTGCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:56115222 original size:16 final size:16
Alignment explanation
Indices: 56115201--56115231 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
56115191 TTTATTATTT
56115201 TATTAACATAATATAA
1 TATTAACATAATATAA
*
56115217 TATTAATATAATATA
1 TATTAACATAATATA
56115232 TTAAAATATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAACATAATATAA
Found at i:56118842 original size:9 final size:9
Alignment explanation
Indices: 56118828--56118853 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
56118818 TTTATGCCAT
56118828 TTTTACAAC
1 TTTTACAAC
56118837 TTTTACAAC
1 TTTTACAAC
56118846 TTTTACAA
1 TTTTACAA
56118854 AATGGTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.46
Consensus pattern (9 bp):
TTTTACAAC
Found at i:56119873 original size:23 final size:23
Alignment explanation
Indices: 56119836--56119889 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
56119826 CCATTCCCAC
56119836 TTGAGAG-ATTATTTGCAAAGTT
1 TTGAGAGTATTATTTGCAAAGTT
56119858 TTGAGAGTATTATTTGCAAAGTT
1 TTGAGAGTATTATTTGCAAAGTT
56119881 TTGAGAGTA
1 TTGAGAGTA
56119890 GCCACTTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 7 0.23
23 24 0.77
ACGTcount: A:0.31, C:0.04, G:0.24, T:0.41
Consensus pattern (23 bp):
TTGAGAGTATTATTTGCAAAGTT
Found at i:56124329 original size:6 final size:6
Alignment explanation
Indices: 56124301--56124352 Score: 59
Period size: 6 Copynumber: 8.2 Consensus size: 6
56124291 TTTAAGTGAA
* *
56124301 TATTTT TAATTATT TATTGT TATTTT TATTTT TGTTTT TATTTTT TATTTT
1 TATTTT T-ATT-TT TATTTT TATTTT TATTTT TATTTT TA-TTTT TATTTT
56124352 T
1 T
56124353 TTCACTCTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
6 24 0.62
7 12 0.31
8 3 0.08
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (6 bp):
TATTTT
Found at i:56132107 original size:42 final size:42
Alignment explanation
Indices: 56132048--56132132 Score: 161
Period size: 42 Copynumber: 2.0 Consensus size: 42
56132038 GCATGTCCAG
56132048 CACCTCTGCCAGGTGCCCCACGTCCCCGTCCGTTACCATTGC
1 CACCTCTGCCAGGTGCCCCACGTCCCCGTCCGTTACCATTGC
*
56132090 CACCTCTGCCAGTTGCCCCACGTCCCCGTCCGTTACCATTGC
1 CACCTCTGCCAGGTGCCCCACGTCCCCGTCCGTTACCATTGC
56132132 C
1 C
56132133 CACGACCTCT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.12, C:0.48, G:0.18, T:0.22
Consensus pattern (42 bp):
CACCTCTGCCAGGTGCCCCACGTCCCCGTCCGTTACCATTGC
Found at i:56134476 original size:31 final size:31
Alignment explanation
Indices: 56134438--56134501 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
56134428 CCTTTTCATA
56134438 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
** *
56134469 TTTCATATTTCATATTACTGGGTCGAAGCCT
1 TTTCATATTTCATAACACTGGGCCGAAGCCT
56134500 TT
1 TT
56134502 ACTGTAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.22, G:0.16, T:0.39
Consensus pattern (31 bp):
TTTCATATTTCATAACACTGGGCCGAAGCCT
Found at i:56134746 original size:24 final size:24
Alignment explanation
Indices: 56134709--56134789 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
56134699 CTAGAGGTCT
*
56134709 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
56134734 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
56134758 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
56134781 AGCCCTTTT
1 AGCCCTTTT
56134790 GCACTTCCTC
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
23 23 0.43
24 27 0.50
25 4 0.07
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:56134770 original size:23 final size:23
Alignment explanation
Indices: 56134716--56134788 Score: 128
Period size: 23 Copynumber: 3.1 Consensus size: 23
56134706 TCTAGCCTCT
*
56134716 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
56134739 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
56134763 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
56134786 TTT
1 TTT
56134789 TGCACTTCCT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 26 0.54
24 22 0.46
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:56134882 original size:20 final size:20
Alignment explanation
Indices: 56134837--56134883 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
56134827 TTATGAATAC
56134837 ACCATGTGCATATCATACAT
1 ACCATGTGCATATCATACAT
**
56134857 GTCATGTGCATATCATACAT
1 ACCATGTGCATATCATACAT
56134877 ACCATGT
1 ACCATGT
56134884 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (20 bp):
ACCATGTGCATATCATACAT
Found at i:56135402 original size:8 final size:8
Alignment explanation
Indices: 56135389--56135424 Score: 63
Period size: 8 Copynumber: 4.5 Consensus size: 8
56135379 AAATGCCAGA
56135389 ATTTCGGC
1 ATTTCGGC
56135397 ATTTCGGC
1 ATTTCGGC
56135405 ATTTCGGC
1 ATTTCGGC
*
56135413 TTTTCGGC
1 ATTTCGGC
56135421 ATTT
1 ATTT
56135425 ATCGCTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.11, C:0.22, G:0.22, T:0.44
Consensus pattern (8 bp):
ATTTCGGC
Done.