Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 177 of 259
Found at i:57546728 original size:21 final size:22
Alignment explanation
Indices: 57546702--57546754 Score: 67
Period size: 21 Copynumber: 2.5 Consensus size: 22
57546692 TAATAATAAT
* *
57546702 AAATAATAAATAATA-CTAGTA
1 AAATAATAAATAATAGCAAATA
57546723 AAATAAT-AATAATAGCAAATA
1 AAATAATAAATAATAGCAAATA
57546744 AAATAA-AAATA
1 AAATAATAAATA
57546755 GCAATGAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (22 bp):
AAATAATAAATAATAGCAAATA
Found at i:57546766 original size:18 final size:18
Alignment explanation
Indices: 57546709--57546772 Score: 60
Period size: 18 Copynumber: 3.6 Consensus size: 18
57546699 AATAAATAAT
* *
57546709 AAATAATACTAGTAAA-A
1 AAATAATAATAGCAAATA
*
57546726 TAATAATAATAGCAAATA
1 AAATAATAATAGCAAATA
*
57546744 AAATAAAAATAGC-AATGA
1 AAATAATAATAGCAAAT-A
*
57546762 GAATAATAATA
1 AAATAATAATA
57546773 CTGATAACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
17 16 0.42
18 22 0.58
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (18 bp):
AAATAATAATAGCAAATA
Found at i:57549981 original size:27 final size:27
Alignment explanation
Indices: 57549949--57550000 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
57549939 TACTATGGAG
*
57549949 TAAAATTATATTTTAATCTAAAATTGA
1 TAAAATTATAATTTAATCTAAAATTGA
* **
57549976 TAAAATTTTAATTTCGTCTAAAATT
1 TAAAATTATAATTTAATCTAAAATT
57550001 ATTTGATATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (27 bp):
TAAAATTATAATTTAATCTAAAATTGA
Found at i:57550722 original size:14 final size:15
Alignment explanation
Indices: 57550703--57550732 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
57550693 TTTTATAGTT
57550703 TTTTGAAT-TTTTTA
1 TTTTGAATATTTTTA
57550717 TTTTGAATATTTTTA
1 TTTTGAATATTTTTA
57550732 T
1 T
57550733 AAATTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTTGAATATTTTTA
Found at i:57558321 original size:24 final size:24
Alignment explanation
Indices: 57558292--57558338 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
57558282 GTAAAAGCCG
57558292 ATAGAGTCGCACCTAAAAGGTAAT
1 ATAGAGTCGCACCTAAAAGGTAAT
57558316 ATAGAGTCGCACCTAAAAGGTAA
1 ATAGAGTCGCACCTAAAAGGTAA
57558339 GATAACCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (24 bp):
ATAGAGTCGCACCTAAAAGGTAAT
Found at i:57560315 original size:22 final size:22
Alignment explanation
Indices: 57560290--57560333 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
57560280 TAGTCATATA
57560290 ATAAATTATTAATATAATAAAT
1 ATAAATTATTAATATAATAAAT
* * *
57560312 ATAATTTATTATTTTAATAAAT
1 ATAAATTATTAATATAATAAAT
57560334 TATTTAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAATTATTAATATAATAAAT
Found at i:57560379 original size:16 final size:14
Alignment explanation
Indices: 57560353--57560393 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
57560343 TTTTAATTTT
57560353 ATTTT-AATAATAA
1 ATTTTAAATAATAA
57560366 ATTTTTAAAATAAT-A
1 A-TTTT-AAATAATAA
57560381 ATTTTAAATAATA
1 ATTTTAAATAATA
57560394 TTATTCACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 8 0.33
14 8 0.33
15 2 0.08
16 6 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
ATTTTAAATAATAA
Found at i:57560475 original size:21 final size:22
Alignment explanation
Indices: 57560435--57560475 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
57560425 TAATATTTTA
* *
57560435 ATAATATATATTTATTATAATT
1 ATAATATATATTAATAATAATT
57560457 ATAA-ATATATTAATAATAA
1 ATAATATATATTAATAATAA
57560476 ATGTTTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAATATATATTAATAATAATT
Found at i:57560934 original size:19 final size:21
Alignment explanation
Indices: 57560910--57560960 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
57560900 TATCTAAACA
57560910 CTAAAAAATATTAA-T-TTTT
1 CTAAAAAATATTAATTATTTT
*
57560929 CTAAAAAA-ATAAATTATTTT
1 CTAAAAAATATTAATTATTTT
*
57560949 CTAAAAATTATT
1 CTAAAAAATATT
57560961 TTTCGAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 4 0.15
19 9 0.35
20 11 0.42
21 2 0.08
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (21 bp):
CTAAAAAATATTAATTATTTT
Found at i:57560958 original size:14 final size:14
Alignment explanation
Indices: 57560939--57560976 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
57560929 CTAAAAAAAT
57560939 AAATTA-TTTTCTAA
1 AAATTATTTTTC-AA
*
57560953 AAATTATTTTTCGA
1 AAATTATTTTTCAA
57560967 AAATTATTTT
1 AAATTATTTT
57560977 GAATGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.39, C:0.05, G:0.03, T:0.53
Consensus pattern (14 bp):
AAATTATTTTTCAA
Found at i:57575861 original size:46 final size:46
Alignment explanation
Indices: 57575794--57576010 Score: 301
Period size: 46 Copynumber: 4.7 Consensus size: 46
57575784 TGGCAACCTG
*
57575794 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
** *
57575840 TGTGTAAGGTCATGGTTGAAAGATACCATGGCAACCTGATATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
*
57575886 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
* ** *
57575932 AGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATG-AAA
* * * *
57575978 TGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 TGTGTAAGACCATGGTTGAAAGATACCATGGCA
57576011 TCACGTCAAA
Statistics
Matches: 155, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 154 0.99
ACGTcount: A:0.39, C:0.15, G:0.24, T:0.22
Consensus pattern (46 bp):
TGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGACATGAAA
Found at i:57575996 original size:138 final size:130
Alignment explanation
Indices: 57575745--57576010 Score: 345
Period size: 138 Copynumber: 2.0 Consensus size: 130
57575735 ACTGTGCTCT
* *
57575745 CTGATATGAAATGTGTAAGACTATGGTTGAAAGATACCATGGCAACCTGTGTGTAAGACCATGGT
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGT
* * * ** * *
57575810 TGAAAGATACCATGGCAACCTGATATGAAATGTGTAAGGTCATGGTTGAAAGATACCATGGCAAC
66 TGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
*
57575875 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACGTGACATGAAAAGAATAAG
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTG---TG---AG--TAAG
57575940 ACCATGGTTGAAAGATACCATGGCAACATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACAC
58 ACCATGGTTGAAAGATACCATGGCAACATGACATG-AAATGAGTAAGACCATAGTTGAAAGACAC
*
57576004 TATGGCA
122 CATGGCA
57576011 TCACGTCAAA
Statistics
Matches: 116, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
130 47 0.41
133 2 0.02
136 1 0.01
137 1 0.01
138 65 0.56
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (130 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACCTGTGAGTAAGACCATGGT
TGAAAGATACCATGGCAACATGACATGAAATGAGTAAGACCATAGTTGAAAGACACCATGGCAAC
Found at i:57581038 original size:69 final size:69
Alignment explanation
Indices: 57580927--57581057 Score: 199
Period size: 69 Copynumber: 1.9 Consensus size: 69
57580917 TCATACGCAG
* * *
57580927 TCAGTGTAGTTAGCAGATATATGGCGAATCCCGGTAAAGAACATTGGAAAGCAGTTCAGTGGTAT
1 TCAGTGCAGTTAGCAGATACATGGCAAATCCCGGTAAAGAACATTGGAAAGCAGTTCAGTGGTAT
57580992 GCAT
66 GCAT
** * *
57580996 TCAGTGCAGTTATTAGATACATGGCAAATCCTGGTAAAGAACATTGGAAAGCAGTTTAGTGG
1 TCAGTGCAGTTAGCAGATACATGGCAAATCCCGGTAAAGAACATTGGAAAGCAGTTCAGTGG
57581058 ATTTTAATAT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.27
Consensus pattern (69 bp):
TCAGTGCAGTTAGCAGATACATGGCAAATCCCGGTAAAGAACATTGGAAAGCAGTTCAGTGGTAT
GCAT
Found at i:57586118 original size:21 final size:21
Alignment explanation
Indices: 57586092--57586132 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
57586082 ATCTGCTCAA
* *
57586092 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
57586113 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
57586133 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:57592075 original size:30 final size:30
Alignment explanation
Indices: 57592030--57592086 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
57592020 ATTTAATACG
*
57592030 AACTTTGGCAAAATTACATTTTTGCCCGTA
1 AACTTTGGCAAAATTACACTTTTGCCCGTA
* *
57592060 AACTTTTGCATAATTACACTTTTGCCC
1 AACTTTGGCAAAATTACACTTTTGCCC
57592087 CTAGGCTCGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.39
Consensus pattern (30 bp):
AACTTTGGCAAAATTACACTTTTGCCCGTA
Found at i:57595500 original size:26 final size:26
Alignment explanation
Indices: 57595471--57595520 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
57595461 GATTGTCACC
*
57595471 TTGTTTAACTGTCGATAGTCAACATA
1 TTGTTTAACTGACGATAGTCAACATA
57595497 TTGTTTAACTGACGATAGTCAACA
1 TTGTTTAACTGACGATAGTCAACA
57595521 CACAATCTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (26 bp):
TTGTTTAACTGACGATAGTCAACATA
Found at i:57598222 original size:26 final size:26
Alignment explanation
Indices: 57598193--57598245 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
57598183 CAAAAATTCA
57598193 AATATCTCATAAAATATAATTTATAT
1 AATATCTCATAAAATATAATTTATAT
57598219 AATATCTCATAAAATATAATTTATAT
1 AATATCTCATAAAATATAATTTATAT
57598245 A
1 A
57598246 CCTGTTTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.42
Consensus pattern (26 bp):
AATATCTCATAAAATATAATTTATAT
Found at i:57602678 original size:32 final size:32
Alignment explanation
Indices: 57602640--57602700 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
57602630 ATTTATACAC
57602640 TTTAGTCCCTAAGTTCAAAACTAACAATTCAT
1 TTTAGTCCCTAAGTTCAAAACTAACAATTCAT
57602672 TTTAGTCCCTAAGTTCAAAACTAACAATT
1 TTTAGTCCCTAAGTTCAAAACTAACAATT
57602701 TTCACTTTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (32 bp):
TTTAGTCCCTAAGTTCAAAACTAACAATTCAT
Found at i:57605774 original size:42 final size:42
Alignment explanation
Indices: 57605667--57605795 Score: 150
Period size: 42 Copynumber: 3.1 Consensus size: 42
57605657 CGAAGTAATC
** * * * *
57605667 ATACTGACATGTAAGTGCATTATCGAATGTACTGAAGCAAAT
1 ATACTGACACATAAGTGCATCATTGCATATACTGAAGCAAAT
57605709 ATACTGACACATAAGTGCATCATTGCATATACTGAAGCAAAT
1 ATACTGACACATAAGTGCATCATTGCATATACTGAAGCAAAT
* * * * * *
57605751 ATGCTGACACATAAGTGCGTCATTGGATATGCCGAAGCAATT
1 ATACTGACACATAAGTGCATCATTGCATATACTGAAGCAAAT
57605793 ATA
1 ATA
57605796 TTGGTATATA
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (42 bp):
ATACTGACACATAAGTGCATCATTGCATATACTGAAGCAAAT
Found at i:57607247 original size:41 final size:41
Alignment explanation
Indices: 57607100--57607259 Score: 178
Period size: 41 Copynumber: 3.9 Consensus size: 41
57607090 GCCTAGCAGG
* * *
57607100 CTGTGTCGGTGTATAATATCAGGCCTATTGCCTAGCAAGCT
1 CTGTGCCGGTGTATAATATCAGGCCTATTGCCTAACAGGCT
* * * *
57607141 TTGTGCCGGTGTAAAATATCAGGCCTATTGCCTATCAGCCT
1 CTGTGCCGGTGTATAATATCAGGCCTATTGCCTAACAGGCT
* * * *
57607182 TTGTGCCGATGTATTATATCAGGCTTATTGCCTAACAGGCT
1 CTGTGCCGGTGTATAATATCAGGCCTATTGCCTAACAGGCT
* * *
57607223 CTGTGCCGGTGTATTATATTAGG-CTTTATGCCTAACA
1 CTGTGCCGGTGTATAATATCAGGCCTAT-TGCCTAACA
57607260 AATTTTATGT
Statistics
Matches: 101, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
40 2 0.02
41 99 0.98
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.34
Consensus pattern (41 bp):
CTGTGCCGGTGTATAATATCAGGCCTATTGCCTAACAGGCT
Found at i:57607255 original size:82 final size:80
Alignment explanation
Indices: 57607082--57607256 Score: 199
Period size: 82 Copynumber: 2.2 Consensus size: 80
57607072 GTGATATTCG
* * * * *
57607082 GGCTTTATGCCTAGCAGGCTGTGTCGGTGTATAATATCAGGCCTATTGCCTAGCAAGCTTTGTGC
1 GGCTTTATGCCTAGCAGCCTGTGCCGATGTATAATATCAGGCCTATTGCCTAACAAGCTCTGTGC
57607147 CGGTGTAAAATATCA
66 CGGTGTAAAATATCA
* * * * *
57607162 GGC-CTATTGCCTATCAGCCTTTGTGCCGATGTATTATATCAGGCTTATTGCCTAACAGGCTCTG
1 GGCTTTA-TGCCTAGCAGCC--TGTGCCGATGTATAATATCAGGCCTATTGCCTAACAAGCTCTG
** *
57607226 TGCCGGTGTATTATATTA
63 TGCCGGTGTAAAATATCA
57607244 GGCTTTATGCCTA
1 GGCTTTATGCCTA
57607257 ACAAATTTTA
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
79 2 0.03
80 13 0.17
82 60 0.78
83 2 0.03
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (80 bp):
GGCTTTATGCCTAGCAGCCTGTGCCGATGTATAATATCAGGCCTATTGCCTAACAAGCTCTGTGC
CGGTGTAAAATATCA
Found at i:57608796 original size:42 final size:42
Alignment explanation
Indices: 57608749--57608866 Score: 116
Period size: 42 Copynumber: 2.8 Consensus size: 42
57608739 AGATAAACTA
* *
57608749 AAGCAAATATATTGGAACATATA-TGCATCATCGGATATATCG
1 AAGCAAATATACT-GAACATATAGTGCATCATCGGATAAATCG
* * **
57608791 AAGCAATTATACT-AGCATATAAGTGCATCATAAGATAAATCG
1 AAGCAAATATACTGAACATAT-AGTGCATCATCGGATAAATCG
* *
57608833 AAGTAAATATACTAGCACATA-AGTGCATCATCGG
1 AAGCAAATATACT-GAACATATAGTGCATCATCGG
57608867 CTAATCAAAG
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
40 6 0.10
41 1 0.02
42 49 0.82
44 4 0.07
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.26
Consensus pattern (42 bp):
AAGCAAATATACTGAACATATAGTGCATCATCGGATAAATCG
Found at i:57609935 original size:18 final size:18
Alignment explanation
Indices: 57609904--57609954 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
57609894 CAAATAATTT
57609904 TTTTATTAAATAATAATA
1 TTTTATTAAATAATAATA
* *
57609922 TTTTAATAAGTAATAATA
1 TTTTATTAAATAATAATA
*
57609940 TTTTATTAATTAATA
1 TTTTATTAAATAATA
57609955 TTATAATAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTTTATTAAATAATAATA
Found at i:57609948 original size:21 final size:20
Alignment explanation
Indices: 57609896--57609954 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 20
57609886 ATGACTTTCA
*
57609896 AATAAT-TTTTTTATTAAAT
1 AATAATATTTTTTAATAAAT
*
57609915 AATAATA--TTTTAATAAGT
1 AATAATATTTTTTAATAAAT
*
57609933 AATAATATTTTATTAATTAAT
1 AATAATATTTT-TTAATAAAT
57609954 A
1 A
57609955 TTATAATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 16 0.50
19 6 0.19
20 2 0.06
21 8 0.25
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
AATAATATTTTTTAATAAAT
Found at i:57633349 original size:18 final size:18
Alignment explanation
Indices: 57633308--57633374 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
57633298 AAGTTTATAA
*
57633308 ATTTTAAATTTTTTTAAT
1 ATTTTTAATTTTTTTAAT
*
57633326 AATTTTAATGTTTTTT-AT
1 ATTTTTAAT-TTTTTTAAT
*
57633344 ATTTTT-ATTTTTACTAATT
1 ATTTTTAATTTTT-TTAA-T
57633363 ATCTTTTAATTT
1 AT-TTTTAATTT
57633375 CATAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 4 0.10
17 3 0.08
18 15 0.38
19 9 0.23
20 4 0.10
21 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (18 bp):
ATTTTTAATTTTTTTAAT
Found at i:57640274 original size:31 final size:31
Alignment explanation
Indices: 57640239--57640300 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
57640229 TGAATCGAGT
*
57640239 TTGTCAGCCATATCTAGATCAGTTCATCATA
1 TTGTCAACCATATCTAGATCAGTTCATCATA
57640270 TTGTCAACCATATCTAGATCAGTTCATCATA
1 TTGTCAACCATATCTAGATCAGTTCATCATA
57640301 GTTTTTATCG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.31, C:0.23, G:0.11, T:0.35
Consensus pattern (31 bp):
TTGTCAACCATATCTAGATCAGTTCATCATA
Found at i:57648669 original size:38 final size:38
Alignment explanation
Indices: 57648626--57648821 Score: 275
Period size: 38 Copynumber: 5.2 Consensus size: 38
57648616 AACACACTAG
57648626 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* ****
57648664 ACAGAAGCTCATAAGAGCTAATCCAACCGATTTTCCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* * *
57648702 ATAGAAGCTCATAAGAGCTAATCCAACCAAAACACCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* * *
57648740 ACAGAAGCTCATAAGAGTTGATCCAACCGAATCGCCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
* *
57648778 ACAAAAGCTCATAAGAGCTGATCCAACCGAAACGCCAA
1 ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
57648816 ACAGAA
1 ACAGAA
57648822 AGTATAACAC
Statistics
Matches: 137, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 137 1.00
ACGTcount: A:0.44, C:0.27, G:0.15, T:0.14
Consensus pattern (38 bp):
ACAGAAGCTCATAAGAGCTGATCCAACCGAAACACCAA
Found at i:57649800 original size:24 final size:23
Alignment explanation
Indices: 57649756--57649800 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
57649746 TTATTTTATT
* **
57649756 TTACTAATTATCTCTTTATTAAA
1 TTACTAATTACCTCTCAATTAAA
57649779 TTACTAATTTACCTCTCAATTA
1 TTACTAA-TTACCTCTCAATTA
57649801 TACATGCATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.33, C:0.18, G:0.00, T:0.49
Consensus pattern (23 bp):
TTACTAATTACCTCTCAATTAAA
Found at i:57655424 original size:9 final size:9
Alignment explanation
Indices: 57655382--57655441 Score: 52
Period size: 10 Copynumber: 6.6 Consensus size: 9
57655372 AAAAAAACTT
57655382 ATTTTTATGA
1 ATTTTTAT-A
*
57655392 GTTTTTAGTA
1 ATTTTTA-TA
*
57655402 ATTTTAATA
1 ATTTTTATA
57655411 ATTTTTAT-
1 ATTTTTATA
*
57655419 ATTTTTCTAA
1 ATTTTTAT-A
57655429 ATTTTTA-A
1 ATTTTTATA
57655437 ATTTT
1 ATTTT
57655442 AAAAATTAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
8 13 0.32
9 9 0.22
10 18 0.44
11 1 0.02
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:57655447 original size:17 final size:18
Alignment explanation
Indices: 57655393--57655448 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
57655383 TTTTTATGAG
*
57655393 TTTTTAGTAATTTTAATAA
1 TTTTTA-TAATTTTAAAAA
* **
57655412 TTTTTATATTTTTCTAAA
1 TTTTTATAATTTTAAAAA
57655430 TTTTTA-AATTTTAAAAA
1 TTTTTATAATTTTAAAAA
57655447 TT
1 TT
57655449 AATTAACTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 10 0.33
18 14 0.47
19 6 0.20
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTTATAATTTTAAAAA
Found at i:57658630 original size:26 final size:26
Alignment explanation
Indices: 57658594--57658677 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
57658584 TGATACAAAT
*
57658594 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
57658620 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
57658646 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
57658672 TGATAA
1 TGATAA
57658678 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:57661734 original size:19 final size:19
Alignment explanation
Indices: 57661691--57661730 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
57661681 TACAAAAATG
*
57661691 AAATTCAAAATAATTTCTA
1 AAATTCAAAATAATTTATA
57661710 AAATTCAAAAT-ATTTATA
1 AAATTCAAAATAATTTATA
57661728 AAA
1 AAA
57661731 ATTCCAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.35
Consensus pattern (19 bp):
AAATTCAAAATAATTTATA
Found at i:57662270 original size:74 final size:74
Alignment explanation
Indices: 57662156--57662303 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
57662146 ATCGAACTCT
57662156 CACCCCTAACTAGGTTGTTAAGTTTTTTTTTTTAAGTTCAACTAGCAAGCTCCAAGCGACAATTC
1 CACCCCTAACTAGGTTGTTAAGTTTTTTTTTTTAAGTTCAACTAGCAAGCTCCAAGCGACAATTC
57662221 AACGATCGG
66 AACGATCGG
57662230 CACCCCTAACTAGGTTGTTAAGTTTTTTTTTTTAAGTTCAACTAGCAAGCTCCAAGCGACAATTC
1 CACCCCTAACTAGGTTGTTAAGTTTTTTTTTTTAAGTTCAACTAGCAAGCTCCAAGCGACAATTC
57662295 AACGATCGG
66 AACGATCGG
57662304 TACAGTGGAC
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.32
Consensus pattern (74 bp):
CACCCCTAACTAGGTTGTTAAGTTTTTTTTTTTAAGTTCAACTAGCAAGCTCCAAGCGACAATTC
AACGATCGG
Found at i:57665707 original size:23 final size:23
Alignment explanation
Indices: 57665673--57665728 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
57665663 TGATACAAGG
* *
57665673 TTTTAATA-TTTTAAATTAATTT
1 TTTTTATATTTTTAAATTAATTA
**
57665695 TTTTTATATTTTTATCTTAATTA
1 TTTTTATATTTTTAAATTAATTA
57665718 TTTTTAT-TTTT
1 TTTTTATATTTT
57665729 ATTTATAATC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTTTATATTTTTAAATTAATTA
Found at i:57666189 original size:30 final size:30
Alignment explanation
Indices: 57666132--57666189 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
57666122 AATAGAAAAG
* * *
57666132 AACAAAAGAAAATTATTGCTTATAAATGTC
1 AACAAAAGAAAATAATGGCTTAAAAATGTC
57666162 AACAAAAGAAAATCAATGGC-TAAAAATG
1 AACAAAAGAAAAT-AATGGCTTAAAAATG
57666190 GAGTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 20 0.83
31 4 0.17
ACGTcount: A:0.55, C:0.10, G:0.12, T:0.22
Consensus pattern (30 bp):
AACAAAAGAAAATAATGGCTTAAAAATGTC
Found at i:57673116 original size:2 final size:2
Alignment explanation
Indices: 57673109--57673133 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
57673099 ACATAGCAAG
57673109 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
57673134 GCCCTACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57677463 original size:18 final size:18
Alignment explanation
Indices: 57677425--57677464 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
57677415 TATATTATTA
*
57677425 TTATTATTAGTATATGTT
1 TTATTATTAGTATATGAT
57677443 TTATTATTATGTATAT-AT
1 TTATTATTA-GTATATGAT
57677461 TTAT
1 TTAT
57677465 GTAGTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (18 bp):
TTATTATTAGTATATGAT
Found at i:57677476 original size:46 final size:45
Alignment explanation
Indices: 57677423--57677512 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
57677413 TTTATATTAT
*
57677423 TATTATTATTAGTATATGTTTTA-TTAT-TATGTATATATTTATGTAG
1 TATTATTATTAGT-CAT-TTTTATTTATATATGTATATA-TTATGTAG
*
57677469 TATTATTATTAGTCATTTTTATTTCTATATGTATATATTATGTA
1 TATTATTATTAGTCATTTTTATTTATATATGTATATATTATGTA
57677513 AATATTTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 5 0.12
45 12 0.30
46 23 0.57
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (45 bp):
TATTATTATTAGTCATTTTTATTTATATATGTATATATTATGTAG
Found at i:57677481 original size:12 final size:12
Alignment explanation
Indices: 57677417--57677491 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 12
57677407 CCATTATTTA
*
57677417 TATTATTATTAT
1 TATTATTATTAG
*
57677429 TATTAGTA-TATG
1 TATTATTATTA-G
*
57677441 TTTTATTATTATG
1 TATTATTATTA-G
57677454 TATATATTTATGTAG
1 TAT-TA-TTAT-TAG
57677469 TATTATTATTAG
1 TATTATTATTAG
*
57677481 TCATTTTTATT
1 T-ATTATTATT
57677492 TCTATATGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
11 2 0.04
12 17 0.33
13 18 0.35
14 4 0.08
15 8 0.16
16 2 0.04
ACGTcount: A:0.29, C:0.01, G:0.08, T:0.61
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:57677626 original size:22 final size:24
Alignment explanation
Indices: 57677585--57677637 Score: 69
Period size: 22 Copynumber: 2.3 Consensus size: 24
57677575 TAATATTAAT
57677585 TTAT-TATTATTATATATTATTACG
1 TTATATATTATTATATATTATTA-G
57677609 -TATATATT-TTA-ATATTATTAG
1 TTATATATTATTATATATTATTAG
57677630 TTATATAT
1 TTATATAT
57677638 CTTTTATACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
21 1 0.04
22 16 0.59
23 6 0.22
24 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TTATATATTATTATATATTATTAG
Found at i:57677789 original size:22 final size:22
Alignment explanation
Indices: 57677764--57677829 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
57677754 ATCATTTCTA
57677764 ATATATATATTGTATATGTTTT
1 ATATATATATTGTATATGTTTT
*
57677786 ATATATAT-TATGTATATATTTT
1 ATATATATAT-TGTATATGTTTT
57677808 -TA-ATATTATTAGTTATATGTTT
1 ATATATA-TATT-G-TATATGTTT
57677830 CTTATACTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
20 3 0.08
21 5 0.14
22 21 0.57
23 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (22 bp):
ATATATATATTGTATATGTTTT
Found at i:57677840 original size:23 final size:23
Alignment explanation
Indices: 57677776--57677877 Score: 68
Period size: 23 Copynumber: 4.2 Consensus size: 23
57677766 ATATATATTG
57677776 TATATGTTTTATATATATTATGTA
1 TATATGTTTT-TATATATTATGTA
*
57677800 TATAT-TTTTAATATTATTA-GT-
1 TATATGTTTTTATA-TATTATGTA
*
57677821 TATATGTTTCTTATACTATTCCAGGTA
1 TATATGTTT-TTATA-TATT--ATGTA
*
57677848 CATAT-TTTTTATATCATCTTATGTA
1 TATATGTTTTTATAT-A--TTATGTA
57677873 TATAT
1 TATAT
57677878 TCTTAAATAC
Statistics
Matches: 62, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
21 5 0.08
22 8 0.13
23 17 0.27
24 6 0.10
25 15 0.24
26 5 0.08
27 6 0.10
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (23 bp):
TATATGTTTTTATATATTATGTA
Found at i:57678760 original size:130 final size:132
Alignment explanation
Indices: 57678426--57678889 Score: 354
Period size: 133 Copynumber: 3.5 Consensus size: 132
57678416 TTCGAAAGAG
* *
57678426 ATATTCGATTATTTTGAACAAACGAGAGATTGCAACCCAGCACGATAGGGCACT-ATTCCACGAA
1 ATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCA-TGATTCC-CGAA
**** * * * *
57678490 TTGCCAAACATCGAACATTTTTTTCTGTTTTAAAGAGTTTTTAGAAAACGTGAGTGAAATTCCGA
64 TTGCCAAACATCGAACATCGCATTCTGTTTTAAAGAGATTTTAGAAAACATGAGTGAAATACCAA
*
57678555 AGGG
129 AGGA
* * * * * * ** *
57678559 ATCTTCAATCATTTTGAACAAATGAAAAAGCGCAACCCAGCACGATAGGGC-TCGATTTTCAAAT
1 ATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCAT-GATTCCCGAAT
**
57678623 TGCCAAACATCGAATGTCGCATTC-GTTTTGAAA-A-ATTTTA-ATAAACATGAGTGAAA-ACCT
65 TGCCAAACATCGAACATCGCATTCTGTTTT-AAAGAGATTTTAGA-AAACATGAGTGAAATACC-
57678683 AAAGGA
127 AAAGGA
* *
57678689 ATATTCGATTGTTTTGAACAAACGAGAAATCACAACCCAGCACGATAGGGCATGATTCCCGAATT
1 ATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCATGATTCCCGAATT
** * ** * * * * ****
57678754 ATCAAACACCGATTATCGCCTT-TGTTTTAAA-AGATTTTTTTAGAAGATATGAATGAAATTTTG
66 GCCAAACATCGAACATCGCATTCTGTTTTAAAGAGA---TTTTAGAAAACATGAGTGAAATACCA
*
57678817 AAGGG
128 AAGGA
* * * * * * *
57678822 ATACTCGATTATTTTGAGCAAACGCA-AAATTGCAACCCAACACGTTAGGGAACGATTCCGCGAA
1 ATATTCGATTATTTTGAACAAACG-AGAAATCGCAACCCAGCACGATAGGGCATGATTCC-CGAA
57678886 TTGC
64 TTGC
57678890 TAAATATCAA
Statistics
Matches: 258, Mismatches: 58, Indels: 29
0.75 0.17 0.08
Matches are distributed among these distances:
129 7 0.03
130 96 0.37
131 8 0.03
132 25 0.10
133 114 0.44
134 8 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (132 bp):
ATATTCGATTATTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGGGCATGATTCCCGAATT
GCCAAACATCGAACATCGCATTCTGTTTTAAAGAGATTTTAGAAAACATGAGTGAAATACCAAAG
GA
Found at i:57681529 original size:44 final size:44
Alignment explanation
Indices: 57681481--57682297 Score: 888
Period size: 44 Copynumber: 18.2 Consensus size: 44
57681471 CTCAGGAACA
57681481 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
**
57681525 CCAAATCTGCTATCTTCGATCTGCTCTCTACCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
57681569 CCCAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
57681613 CCAAATCTGCTATCTTCGATCTGCTCTCTGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
57681657 CCAAATCTGTTATCTTCGATCTGCTCTTCGCCACTACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
57681701 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
57681745 CCAAATCTGCTATATTCGATCTGCTCTCCACCAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
** *
57681789 CCAAATCTGCTATCTTCGATCTGCTCTCCATCAACACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
57681833 CCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGAAG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
57681877 CCAAATCTGTTA-CTTTTGATCTGCTCTCTGCCAATACAGAGACG
1 CCAAATCTGCTATC-TTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
57681921 CCAAATCTGCTATCTTTGATCTACTCTCCGCCAATACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * ** * * ** * ** *
57681965 CCAAATCT-ATAAAGACGCCAAATCTGCTATCTTCGATCTGCTCT-CCGCCACT
1 CCAAATCTGCT--A-TCTTC-GATCTGC--TCTCCG--C--CAATACAGAGACG
* * * * *
57682017 ACAGAGATGCCAAAT-CTGTTGTCTTCGATCTGCTTTCCGCCACTACAGAGATG
1 CCA-A-AT--C---TGC---TATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * *
57682070 CCAAATCTGTTATCTTCGATCTTCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
57682114 CCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * *
57682158 CCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* *
57682202 CCAAATCTGCTATATTCGATCTGCTCTCCGCTAATACAGAGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
* * * *
57682246 CCAAATCTGCTATCTTCGATTTGCTCTCCACTACTACA-AGACG
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
57682289 CCAAATCTG
1 CCAAATCTG
57682298 TCTGTTCTTG
Statistics
Matches: 669, Mismatches: 80, Indels: 49
0.84 0.10 0.06
Matches are distributed among these distances:
43 16 0.02
44 600 0.90
45 2 0.00
46 2 0.00
47 5 0.01
49 6 0.01
51 3 0.00
52 9 0.01
53 8 0.01
54 3 0.00
56 5 0.01
58 6 0.01
59 3 0.00
62 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (44 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACG
Found at i:57681682 original size:132 final size:132
Alignment explanation
Indices: 57681481--57682297 Score: 1071
Period size: 132 Copynumber: 6.1 Consensus size: 132
57681471 CTCAGGAACA
57681481 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
** * *
57681546 TGCTCTCTACCAATACAGAGACGCCCAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
57681611 TG
131 TG
* * * *
57681613 CCAAATCTGCTATCTTCGATCTGCTCTCTGCCACTACAGAGATGCCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* *
57681678 TGCTCTTCGCCACTACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
57681743 TG
131 TG
* *
57681745 CCAAATCTGCTATATTCGATCTGCTCTCCACCAATACAGAGACGCCAAATCTGCTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
** * * *
57681810 TGCTCTCCATCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
*
57681875 AG
131 TG
* * * *
57681877 CCAAATCTGTTA-CTTTTGATCTGCTCTCTGCCAATACAGAGACGCCAAATCTGCTATCTTTGAT
1 CCAAATCTGCTATC-TTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
* *
57681941 CTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGACGCCAAATCTGCTATCTTCGATCTGC
65 CTGCTCTCCGCCAATACAGAGACGCCAAATC--T------G---------CTATCTTCGATCTGC
57682006 TCTCCGCCACTACAGAGATG
113 TCTCCGCCACTACAGAGATG
* * * * * *
57682026 CCAAATCTGTTGTCTTCGATCTGCTTTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* * * *
57682091 TTCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
57682156 TG
131 TG
* * * *
57682158 CCAAATCTGTTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGCTATATTCGATC
1 CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
* * * *
57682223 TGCTCTCCGCTAATACAGAGACGCCAAATCTGCTATCTTCGATTTGCTCTCCACTACTACA-AGA
66 TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
*
57682287 CG
131 TG
57682289 CCAAATCTG
1 CCAAATCTG
57682298 TCTGTTCTTG
Statistics
Matches: 604, Mismatches: 62, Indels: 39
0.86 0.09 0.06
Matches are distributed among these distances:
131 13 0.02
132 471 0.78
134 1 0.00
140 1 0.00
141 1 0.00
147 1 0.00
149 115 0.19
150 1 0.00
ACGTcount: A:0.25, C:0.32, G:0.15, T:0.28
Consensus pattern (132 bp):
CCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATC
TGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGA
TG
Found at i:57682011 original size:61 final size:61
Alignment explanation
Indices: 57681916--57682033 Score: 209
Period size: 61 Copynumber: 1.9 Consensus size: 61
57681906 GCCAATACAG
*
57681916 AGACGCCAAATCTGCTATCTTTGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
1 AGACGCCAAATCTGCTATCTTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
* *
57681977 AGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCT
1 AGACGCCAAATCTGCTATCTTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCT
57682034 GTTGTCTTCG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 54 1.00
ACGTcount: A:0.30, C:0.31, G:0.14, T:0.25
Consensus pattern (61 bp):
AGACGCCAAATCTGCTATCTTCGATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAA
Found at i:57682058 original size:105 final size:105
Alignment explanation
Indices: 57681876--57682077 Score: 289
Period size: 105 Copynumber: 1.9 Consensus size: 105
57681866 ATACAGAGAA
* * * *
57681876 GCCAAATCTGTTACTTTTGATCTGCTCTCTGCCAATACAGAGACGCCAAATCTGCTATCTTTGAT
1 GCCAAATCTGCTACTTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
57681941 CTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGAC
66 CTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGAC
* * * *
57681981 GCCAAATCTGCTA-TCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTGTCTTCGA
1 GCCAAATCTGCTACT-TTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGA
* * *
57682045 TCTGCTTTCCGCCACTACAGAGATGCCAAATCT
65 TCTACTCTCCGCCAATACAGAGATGCCAAATCT
57682078 GTTATCTTCG
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
104 1 0.01
105 84 0.99
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.29
Consensus pattern (105 bp):
GCCAAATCTGCTACTTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCGAT
CTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGAC
Found at i:57682163 original size:237 final size:237
Alignment explanation
Indices: 57681744--57682209 Score: 693
Period size: 237 Copynumber: 2.0 Consensus size: 237
57681734 CTACAGAGAT
57681744 GCCAAATCTGCTATATTCGATCTGCTCTCCACCAATACAGAGACGCCAAATCTGCTATCTTCGAT
1 GCCAAATCTGCTATATTCGATCTGCTCTCCACCAATACAGAGACGCCAAATCTGCTATCTTCGAT
* *
57681809 CTGCTCTCCATCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCTGCCAATACAGAG
66 CTGCTCTCCAGCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAG
* * *
57681874 AAGCCAAATCTGTTACTTTTGATCTGCTCTCTGCCAATACAGAGACGCCAAATCTGCTATCTTTG
131 AAGCCAAATCTGTTACTTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCG
57681939 ATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGAC
196 ATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGAC
* * * * * *
57681981 GCCAAATCTGCTATCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTGTCTTCGAT
1 GCCAAATCTGCTATATTCGATCTGCTCTCCACCAATACAGAGACGCCAAATCTGCTATCTTCGAT
* * * * * *
57682046 CTGCTTTCC-GCCACTACAGAGATGCCAAATCTGTTATCTTCGATCTTCTCTCCGCCACTACAGA
66 CTGCTCTCCAGCAAC-ACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGA
* * * *
57682110 GATGCCAAATCTGTTA-TCTTCGATCTGCTCTCCGCCACTACAGAGATGCCAAATCTGTTATCTT
130 GAAGCCAAATCTGTTACT-TTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTT
* *
57682174 CGATCTGCTCTCCGCCACTACAGAGATGCCAAATCT
194 CGATCTACTCTCCGCCAATACAGAGATGCCAAATCT
57682210 GCTATATTCG
Statistics
Matches: 204, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
236 4 0.02
237 200 0.98
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (237 bp):
GCCAAATCTGCTATATTCGATCTGCTCTCCACCAATACAGAGACGCCAAATCTGCTATCTTCGAT
CTGCTCTCCAGCAACACAGAGACGCCAAATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAG
AAGCCAAATCTGTTACTTTCGATCTGCTCTCCGCCAATACAGAGACGCCAAATCTGCTATCTTCG
ATCTACTCTCCGCCAATACAGAGATGCCAAATCTATAAAGAC
Found at i:57682680 original size:131 final size:128
Alignment explanation
Indices: 57682477--57682845 Score: 440
Period size: 131 Copynumber: 2.8 Consensus size: 128
57682467 TCGAGAAGAT
* * *
57682477 AAGACCTACAATCGTCAGCCCACTTCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
1 AAGA-CTACAATCCTCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
* * * * *
57682542 TCGCTGCATCTTCAGGAAGCCAAGATTTATCGTCTTTGAT-TTGCCTCACTGCAA-CTTCAGGGA
65 TCACTGCAACTTCAGGAAGCCAAGA-TT-CCGTCTTCGATCTGGCC-CACTGCAATCTT-AGGGA
*
57682605 GAC
126 AAC
* *
57682608 GAGATCTACAATCCTCAGCCTACTCCACTACAACTTTAGAGAGCTAGGACTTGCTTAAATCTGCT
1 AAGA-CTACAATCCTCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCT
* * *
57682673 TTACTGCAACATCAGGAAGCCTAGATTCCGTCTTCGATCTGGCCCACTGCAATCTTAGGGAAAC
65 TCACTGCAACTTCAGGAAGCCAAGATTCCGTCTTCGATCTGGCCCACTGCAATCTTAGGGAAAC
* * * *
57682737 AAGACTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTA-GAATGGTGGCTTAAATCTA
1 AAGACTACAATCCTCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACT--T-GCTTAAATCTG
57682801 CTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTG
63 CTTCACTGCAACTTCAGGAAGC-CAAGATT--CCGTCTTCGATCTG
57682846 TTTCACTGTA
Statistics
Matches: 207, Mismatches: 23, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
127 3 0.01
128 38 0.18
129 28 0.14
130 44 0.21
131 80 0.39
132 14 0.07
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (128 bp):
AAGACTACAATCCTCAGCCTACTCCACTACAACTTTAGGGAGCTAGGACTTGCTTAAATCTGCTT
CACTGCAACTTCAGGAAGCCAAGATTCCGTCTTCGATCTGGCCCACTGCAATCTTAGGGAAAC
Found at i:57682984 original size:132 final size:132
Alignment explanation
Indices: 57682841--57683197 Score: 597
Period size: 132 Copynumber: 2.7 Consensus size: 132
57682831 GCCGTCTTCG
* * *
57682841 ATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCGCTGCAACTTT
1 ATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTC
* *
57682906 AGGGAAACAAGATCTGGAATTTTAGCCTACTCCACTGCAACTTTAGGGAGCTAGGTTGGTGGCTT
66 AGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTT
57682971 AA
131 AA
* * * *
57682973 ATCTGTTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTTGATCTGCTTCACTGTAACTTC
1 ATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTC
*
57683038 AGGGAAACAAGATCTGAAATTTTAGCCTACTCTACTACAACTTTAGGGAGCTAGGTTGGTGGCTT
66 AGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTT
57683103 AA
131 AA
*
57683105 ATCTGCTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTC
1 ATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTC
* *
57683170 AGGGAAACAAAATCTAAAATTTTAGCCT
66 AGGGAAACAAGATCTGAAATTTTAGCCT
57683198 CATAGGCCCA
Statistics
Matches: 208, Mismatches: 17, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 208 1.00
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.32
Consensus pattern (132 bp):
ATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGCAACTTC
AGGGAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGGTGGCTT
AA
Found at i:57682996 original size:177 final size:177
Alignment explanation
Indices: 57682666--57683036 Score: 518
Period size: 177 Copynumber: 2.1 Consensus size: 177
57682656 ACTTGCTTAA
* * * *
57682666 ATCTGCTTTACTGCAACATCAGGAAGC-CTAGATT--CCGTCTTCGATCTGGCCCACTGCAATCT
1 ATCTGCTTCACTGTAACTTTAGGAAGCTC-AGATTCGCCGTCTTCGATCTGGCCCACTGCAATCT
*
57682728 TAGGGAAACAAGACTATAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCT
65 TAGGGAAACAAGACTAGAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCT
57682793 TAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCG
130 TAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCG
* *** *
57682841 ATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCGCTGCAA-CTT
1 ATCTGCTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGGCCCACTGCAATC-T
* * * **
57682905 TAGGGAAACAAGATCTGGAAT-TTTAGCCTACTCCACTGCAACTTTAGGGAGCTAGGTTGGTGGC
65 TAGGGAAACAAGA-CTAGAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGC
** *
57682969 TTAAATCTGTTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTTG
129 TTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCG
57683018 ATCTGCTTCACTGTAACTT
1 ATCTGCTTCACTGTAACTT
57683037 CAGGGAAACA
Statistics
Matches: 172, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
175 27 0.16
176 2 0.01
177 138 0.80
178 5 0.03
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (177 bp):
ATCTGCTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGGCCCACTGCAATCTT
AGGGAAACAAGACTAGAATCTTCAGCCTACTCCACTACAACTTTAGGGAGCTAGAATGGTGGCTT
AAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCG
Found at i:57683158 original size:45 final size:45
Alignment explanation
Indices: 57682791--57683168 Score: 220
Period size: 45 Copynumber: 8.5 Consensus size: 45
57682781 AGAATGGTGG
* * *
57682791 CTTAAATCTACTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
* * *
57682836 CTTCGATCTGTTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
* * * * * ***
57682881 CTTCGATCTGTTTCGCTGCAACTTTAGGGAAAC-AAGA-TCTGGAAT
1 CTTAGATCTGCTTCACTGCAACTTTA-GGAAGCTCAGATTC-GCCGT
* * * * * * ** *
57682926 TTTAG-CCTACTCCACTGCAACTTTAGGGAGCT-AGGTT-GGTGG
1 CTTAGATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
* * *
57682968 CTTAAATCTGTTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
* * * * * ***
57683013 CTTTGATCTGCTTCACTGTAACTTCAGGGAAAC-AAGA-TCTGAAAT
1 CTTAGATCTGCTTCACTGCAACTTTA-GGAAGCTCAGATTC-GCCGT
* * * * * * ** *
57683058 TTTAG-CCTAC-TCTACTACAACTTTAGGGAGCT-AGGTT-GGTGG
1 CTTAGATCTGCTTC-ACTGCAACTTTAGGAAGCTCAGATTCGCCGT
* *
57683100 CTTAAATCTGCTTCACTGTAACTTTAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
*
57683145 CTTCGATCTGCTTCACTGCAACTT
1 CTTAGATCTGCTTCACTGCAACTT
57683169 CAGGGAAACA
Statistics
Matches: 242, Mismatches: 75, Indels: 32
0.69 0.21 0.09
Matches are distributed among these distances:
42 9 0.04
43 54 0.22
44 43 0.18
45 126 0.52
46 10 0.04
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (45 bp):
CTTAGATCTGCTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
Found at i:57686853 original size:5 final size:5
Alignment explanation
Indices: 57686843--57686903 Score: 58
Period size: 5 Copynumber: 12.6 Consensus size: 5
57686833 AATGCAAATG
* *
57686843 ATGCA ATGCA ATGCA ATGTAA AT--T ATGCA ATGCA ATGCA ATGCAA ATG--
1 ATGCA ATGCA ATGCA ATG-CA ATGCA ATGCA ATGCA ATGCA ATGC-A ATGCA
57686891 ATGCA ATGCA ATG
1 ATGCA ATGCA ATG
57686904 TAAATGCATG
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
3 5 0.11
5 35 0.74
6 7 0.15
ACGTcount: A:0.41, C:0.15, G:0.20, T:0.25
Consensus pattern (5 bp):
ATGCA
Found at i:57686857 original size:19 final size:18
Alignment explanation
Indices: 57686833--57686909 Score: 60
Period size: 19 Copynumber: 4.6 Consensus size: 18
57686823 TGGGAAATTT
57686833 AATGCAAATGATGCAATGC
1 AATGCAAATG-TGCAATGC
*
57686852 AATGC-AATGT-AAAT--
1 AATGCAAATGTGCAATGC
*
57686866 TATGC-AA--TGCAATGC
1 AATGCAAATGTGCAATGC
57686881 AATGCAAATGATGCAATGC
1 AATGCAAATG-TGCAATGC
*
57686900 AATGTAAATG
1 AATGCAAATG
57686910 CATGGGATGA
Statistics
Matches: 46, Mismatches: 5, Indels: 14
0.71 0.08 0.22
Matches are distributed among these distances:
12 1 0.02
13 3 0.07
14 6 0.13
15 4 0.09
16 5 0.11
17 1 0.02
18 4 0.09
19 22 0.48
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (18 bp):
AATGCAAATGTGCAATGC
Found at i:57686865 original size:24 final size:24
Alignment explanation
Indices: 57686833--57686903 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
57686823 TGGGAAATTT
57686833 AATGCAAATGATGCAATGCAATGC
1 AATGCAAATGATGCAATGCAATGC
* *
57686857 AATGTAAATTATGCAATGCAATGC
1 AATGCAAATGATGCAATGCAATGC
57686881 AATGCAAATGATGCAATGCAATG
1 AATGCAAATGATGCAATGCAATG
57686904 TAAATGCATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (24 bp):
AATGCAAATGATGCAATGCAATGC
Found at i:57688808 original size:130 final size:132
Alignment explanation
Indices: 57688456--57688800 Score: 328
Period size: 130 Copynumber: 2.6 Consensus size: 132
57688446 TAAAATACGC
* * * *
57688456 GTGAAATTCCGAAA-GAGATATTCGATTATTTTGAACAAACGAGAGATTGCAACCCAGCACGATA
1 GTGAAATACC-AAAGGA-ATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATA
**** *
57688520 GGGCACT-ATTCCCCGAATTGCCAAACATCAAACATTTTTTTCTGTTTTAAAGAGTTTTTAGAAA
64 GGGCA-TGATT-CCCGAATTGCCAAACATCAAACATCACATTCTGTTTTAAAGAGATTTTAGAAA
*
57688584 ACGTGA
127 ACATGA
* * * * * * * *
57688590 GTGAAATTCCGAAGGGATCTTCGATCGTTTTGAACAAATGAAAAAGCGCAACCCAGCACGATAGG
1 GTGAAATACCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGG
** * * * *
57688655 GC-TCGATTTTCAAATTGCCAAACATCGAACGTCACATTC-GTTTTGAAA-A-ATTTTA-ATAAG
66 GCAT-GATTCCCGAATTGCCAAACATCAAACATCACATTCTGTTTT-AAAGAGATTTTAGA-AAA
57688715 CATGA
128 CATGA
* *
57688720 GTGAAA-ACCTAAAGGAATATTCGATTGTTTTGAACAAGCGAGAAATCACAACCCAGCACGATAG
1 GTGAAATACC-AAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATAG
57688784 GGCATGATTCCCGAATT
65 GGCATGATTCCCGAATT
57688801 ATCAAACAGC
Statistics
Matches: 169, Mismatches: 35, Indels: 18
0.76 0.16 0.08
Matches are distributed among these distances:
129 3 0.02
130 74 0.44
131 8 0.05
132 25 0.15
133 48 0.28
134 11 0.07
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (132 bp):
GTGAAATACCAAAGGAATATTCGATTGTTTTGAACAAACGAGAAATCGCAACCCAGCACGATAGG
GCATGATTCCCGAATTGCCAAACATCAAACATCACATTCTGTTTTAAAGAGATTTTAGAAAACAT
GA
Found at i:57701589 original size:11 final size:11
Alignment explanation
Indices: 57701573--57701599 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
57701563 CAAGCAAATG
57701573 AGAACGACAAA
1 AGAACGACAAA
57701584 AGAACGACAAA
1 AGAACGACAAA
57701595 AGAAC
1 AGAAC
57701600 AATCAGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.19, G:0.19, T:0.00
Consensus pattern (11 bp):
AGAACGACAAA
Found at i:57702838 original size:44 final size:44
Alignment explanation
Indices: 57702774--57702933 Score: 241
Period size: 44 Copynumber: 3.6 Consensus size: 44
57702764 TTATGCCTAA
*
57702774 AAAAAGAGATCAATGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
1 AAAAA-AGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
57702819 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
1 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
* * *
57702863 AAAAAGGATCAAGGTGAAAACCCAAAAAGGGCGTCTTGATTAAC
1 AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
* *
57702907 ACAAAAGAT-TAGGATGAAAACCCGAAA
1 AAAAAAGATCAAGG-TGAAAACCCGAAA
57702934 TGGCGTTCTA
Statistics
Matches: 106, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
43 3 0.03
44 98 0.92
45 5 0.05
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (44 bp):
AAAAAAGATCAAGGTGAAAACCCGAAAAGGGCGTCTTGATGAAC
Found at i:57703942 original size:77 final size:75
Alignment explanation
Indices: 57703725--57703942 Score: 276
Period size: 75 Copynumber: 2.9 Consensus size: 75
57703715 TTCTGTTTTC
* * * * * *
57703725 AAAAATCAACTCATATTGCGAGAGGTCAGTTGAGTCTCAAGACAAGTTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTTAATTTC
* *
57703790 CGTCTTTCAA
66 TGTCATTCAA
* *
57703800 AAAAATCAATTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTAATTTTAATTTC
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTTAATTTC
57703865 TGTTCATT-AA
66 TG-TCATTCAA
* * * *
57703875 AAAAATCAACTCATATTGTGAGATGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGTT
1 AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGG--ACACGTTGAGGTATTTTTAATT
57703940 TCT
64 TCT
57703943 ATCAACTCAT
Statistics
Matches: 124, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 98 0.79
76 4 0.03
77 22 0.18
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (75 bp):
AAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGTTGAGGTATTTTTAATTTC
TGTCATTCAA
Found at i:57703980 original size:64 final size:64
Alignment explanation
Indices: 57703879--57704008 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
57703869 CATTAAAAAA
* * * * *
57703879 ATCAACTCATATTGTGAGATGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTAGTTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACGCTGAGGTATTTTCAATTTCT
*
57703943 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACATGCTGAGGTATTTTCAATTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACGCTGAGGTATTTTCAATTTCT
57704007 AT
1 AT
57704009 TTTTTTAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (64 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACACGCTGAGGTATTTTCAATTTCT
Found at i:57704117 original size:90 final size:89
Alignment explanation
Indices: 57703943--57704104 Score: 245
Period size: 90 Copynumber: 1.8 Consensus size: 89
57703933 TTTAGTTTCT
* * * *
57703943 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGTCACATGCTGAGGTATTTTCAATTTCTA
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACACGCCGAGGTATTTTCAAATTC-A
*
57704008 TTTTTTTAAATTAGGTTTTTCAAAA
65 TGTTTTTAAATTAGGTTTTTCAAAA
* *
57704033 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCCACACGCCGAGGTCTTTTCAAATTC-T
1 ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACACGCCGAGGTATTTTCAAATTCAT
57704097 GTTTTTAA
66 GTTTTTAA
57704105 TTTCTGTTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
88 8 0.12
90 57 0.88
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (89 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGACCCTCGGGCCACACGCCGAGGTATTTTCAAATTCAT
GTTTTTAAATTAGGTTTTTCAAAA
Found at i:57704118 original size:15 final size:15
Alignment explanation
Indices: 57704098--57704134 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
57704088 TCAAATTCTG
*
57704098 TTTTTAATTTCTGTT
1 TTTTTAATTTCTATT
57704113 TTTTTAATTTCTATT
1 TTTTTAATTTCTATT
57704128 TTTTTAA
1 TTTTTAA
57704135 AAAATCAACT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTAATTTCTATT
Found at i:57704416 original size:55 final size:56
Alignment explanation
Indices: 57704283--57704430 Score: 237
Period size: 56 Copynumber: 2.7 Consensus size: 56
57704273 TCTATTCGCC
*
57704283 AAAAATCGACTCATATTGTGAGAAGTGAGTTGAGCCTTTTAGTCTCTGATTTTTCA
1 AAAAATCGACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAGTCTCTGATTTTTCA
57704339 AAAAATCGACTCATATTGCGAGAAGT-AGGTTGAGCCTTTTAGTCTCTG-TTTTTCA
1 AAAAATCGACTCATATTGCGAGAAGTGA-GTTGAGCCTTTTAGTCTCTGATTTTTCA
* * *
57704394 AAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCT
1 AAAAATCGACTCATATTGCGAGAAGTGAGTTGAGCCT
57704431 CAGGTCACAC
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
55 40 0.47
56 46 0.53
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (56 bp):
AAAAATCGACTCATATTGCGAGAAGTGAGTTGAGCCTTTTAGTCTCTGATTTTTCA
Found at i:57704651 original size:19 final size:19
Alignment explanation
Indices: 57704627--57704673 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
57704617 TTGAAATTAC
57704627 AAGTTGTAGCGGAACCCTG
1 AAGTTGTAGCGGAACCCTG
57704646 AAGTTGTAGCGGAACCCTG
1 AAGTTGTAGCGGAACCCTG
57704665 AAGTTGTAG
1 AAGTTGTAG
57704674 TGGAGCGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.17, G:0.32, T:0.23
Consensus pattern (19 bp):
AAGTTGTAGCGGAACCCTG
Found at i:57706122 original size:3 final size:3
Alignment explanation
Indices: 57706116--57706215 Score: 53
Period size: 3 Copynumber: 31.7 Consensus size: 3
57706106 ATTTTTTTAA
* * *
57706116 TAT TATT TAT TAT T-T TATT TAC CAT TAT T-T ATAT TAT TAA TAT TAT
1 TAT TA-T TAT TAT TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT
* * *
57706162 TAT TAT TAG TA- TAT GTTT TAT TAT TAT GTAT ATACT TAT GTAG TAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT -TA-T TAT -TAT TAT
57706208 TAT TAT TA
1 TAT TAT TA
57706216 GTCGTTTTTA
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
2 5 0.07
3 51 0.68
4 18 0.24
5 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:57706362 original size:22 final size:24
Alignment explanation
Indices: 57706325--57706373 Score: 68
Period size: 22 Copynumber: 2.1 Consensus size: 24
57706315 ATTAATTTTT
57706325 TATTATTATATATTATTACG-TATA
1 TATTATTATATATTATTA-GTTATA
57706349 TATT-TTA-ATATTATTAGTTATA
1 TATTATTATATATTATTAGTTATA
57706371 TAT
1 TAT
57706374 CTTTTATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.04
22 16 0.67
23 3 0.12
24 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (24 bp):
TATTATTATATATTATTAGTTATA
Found at i:57706527 original size:22 final size:22
Alignment explanation
Indices: 57706502--57706568 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
57706492 TCATTTCTAA
57706502 TATATATATATTGTATATGTTT
1 TATATATATATTGTATATGTTT
*
57706524 TATATATAT-TATGTATATATTT
1 TATATATATAT-TGTATATGTTT
57706546 T-TA-ATATTATTAGTTATATGTTT
1 TATATATA-TATT-G-TATATGTTT
57706569 CTTATACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
20 3 0.08
21 5 0.13
22 22 0.58
23 8 0.21
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (22 bp):
TATATATATATTGTATATGTTT
Found at i:57706579 original size:23 final size:23
Alignment explanation
Indices: 57706502--57706616 Score: 69
Period size: 23 Copynumber: 4.8 Consensus size: 23
57706492 TCATTTCTAA
*
57706502 TATATATATAT-TGTATATGTTTT
1 TATATAT-TATGTATATATGTTTT
57706525 ATATATATTATGTATATAT-TTTT
1 -TATATATTATGTATATATGTTTT
*
57706548 AATATTATTA-GT-TATATGTTTCT
1 TATA-TATTATGTATATATGTTT-T
* *
57706571 TATACTATTCCAGGTACATAT-TTTT
1 TATA-TATT--ATGTATATATGTTTT
57706596 TATATCATCTTATGTATATAT
1 TATAT-A--TTATGTATATAT
57706617 TCTTAAATAC
Statistics
Matches: 73, Mismatches: 7, Indels: 21
0.72 0.07 0.21
Matches are distributed among these distances:
21 5 0.07
22 8 0.11
23 20 0.27
24 14 0.19
25 15 0.21
26 5 0.07
27 6 0.08
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (23 bp):
TATATATTATGTATATATGTTTT
Found at i:57714104 original size:22 final size:22
Alignment explanation
Indices: 57714078--57714147 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
57714068 TCCAATACTA
57714078 AAATCACCACATTACCAAGATC
1 AAATCACCACATTACCAAGATC
* *
57714100 AAATCGA--A-AGTA-C-AGTCATA
1 AAATC-ACCACATTACCAAG--ATC
57714120 AAATCACCACATTACCAAGATC
1 AAATCACCACATTACCAAGATC
57714142 AAATCA
1 AAATCA
57714148 GAAGTACAGT
Statistics
Matches: 36, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 10 0.28
21 2 0.06
22 16 0.44
23 2 0.06
24 2 0.06
ACGTcount: A:0.49, C:0.26, G:0.07, T:0.19
Consensus pattern (22 bp):
AAATCACCACATTACCAAGATC
Found at i:57714135 original size:42 final size:42
Alignment explanation
Indices: 57714076--57714160 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
57714066 ATTCCAATAC
57714076 TAAAATCACCACATTACCAAGATCAAATC-GAAAGTACAGTCA
1 TAAAATCACCACATTACCAAGATCAAATCAG-AAGTACAGTCA
57714118 TAAAATCACCACATTACCAAGATCAAATCAGAAGTACAGTCA
1 TAAAATCACCACATTACCAAGATCAAATCAGAAGTACAGTCA
57714160 T
1 T
57714161 GCTTATAATG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.47, C:0.24, G:0.09, T:0.20
Consensus pattern (42 bp):
TAAAATCACCACATTACCAAGATCAAATCAGAAGTACAGTCA
Found at i:57717528 original size:20 final size:20
Alignment explanation
Indices: 57717505--57717542 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
57717495 TACTTTGCTT
57717505 AAAGTATCGATACCTTTAAC
1 AAAGTATCGATACCTTTAAC
* *
57717525 AAAGTTTCGATATCTTTA
1 AAAGTATCGATACCTTTA
57717543 TTCTGGTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
AAAGTATCGATACCTTTAAC
Found at i:57726194 original size:4 final size:4
Alignment explanation
Indices: 57726185--57726209 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57726175 TGTATAAGTT
57726185 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
57726210 AATAATTCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:57734419 original size:75 final size:75
Alignment explanation
Indices: 57734296--57734445 Score: 282
Period size: 75 Copynumber: 2.0 Consensus size: 75
57734286 GTTTGCCATT
*
57734296 GAAGTTGAAAAGTGATCCGAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
1 GAAGTTGAAAAGTGATCCAAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
57734361 TAAAATGAAG
66 TAAAATGAAG
*
57734371 GAAGTTGAAAAGTGATCCAAAAGAAAACTTTTTAAGAACTCTATTAAAAGTTGCTTATGAAAAGA
1 GAAGTTGAAAAGTGATCCAAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
57734436 TAAAATGAAG
66 TAAAATGAAG
57734446 AATTAATAGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (75 bp):
GAAGTTGAAAAGTGATCCAAAAGAAAACTTTTTAAGAACGCTATTAAAAGTTGCTTATGAAAAGA
TAAAATGAAG
Found at i:57734871 original size:17 final size:17
Alignment explanation
Indices: 57734860--57734914 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 17
57734850 ATTAATTATT
57734860 TTTTAAAATTAAAAATA
1 TTTTAAAATTAAAAATA
*
57734877 TTTTAAAATTTAAAATTA
1 TTTTAAAA-TTAAAAATA
*
57734895 TTTAAAATATATAAAAATA
1 TTTTAAA-AT-TAAAAATA
57734914 T
1 T
57734915 CAATTAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 8 0.25
18 15 0.47
19 9 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTAAAATTAAAAATA
Found at i:57734889 original size:18 final size:18
Alignment explanation
Indices: 57734860--57734914 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
57734850 ATTAATTATT
57734860 TTTTAAAA-TTAAAAATA
1 TTTTAAAATTTAAAAATA
*
57734877 TTTTAAAATTTAAAATTA
1 TTTTAAAATTTAAAAATA
57734895 -TTTAAAATATATAAAAATA
1 TTTTAAAAT-T-TAAAAATA
57734914 T
1 T
57734915 CAATTAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 16 0.50
18 9 0.28
19 7 0.22
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAATTTAAAAATA
Found at i:57742284 original size:18 final size:19
Alignment explanation
Indices: 57742248--57742285 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
57742238 TTGAAGCTTT
*
57742248 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTATTATAC
57742267 ATTTTAAT-TTTATTATAC
1 ATTTTAATATTTATTATAC
57742285 A
1 A
57742286 CATTTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTAATATTTATTATAC
Found at i:57742290 original size:20 final size:19
Alignment explanation
Indices: 57742248--57742292 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
57742238 TTGAAGCTTT
*
57742248 ATTTTAATATTTTTTATAC
1 ATTTTAATATTTTTTACAC
57742267 ATTTTAAT-TTTATTATACAC
1 ATTTTAATATTT-TT-TACAC
57742287 ATTTTA
1 ATTTTA
57742293 TTACTTCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 3 0.13
19 10 0.43
20 10 0.43
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTAATATTTTTTACAC
Found at i:57745053 original size:20 final size:19
Alignment explanation
Indices: 57745009--57745053 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
57744999 GCTAGGTTTG
*
57745009 ATATATTTTCTTTTTTATTA
1 ATAT-TTTTCTTTTTTATGA
*
57745029 TTATTTTTCTTTTTTAATGA
1 ATATTTTTCTTTTTT-ATGA
57745049 ATATT
1 ATATT
57745054 ACTATCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.69
Consensus pattern (19 bp):
ATATTTTTCTTTTTTATGA
Found at i:57750830 original size:15 final size:16
Alignment explanation
Indices: 57750812--57750885 Score: 55
Period size: 15 Copynumber: 4.6 Consensus size: 16
57750802 TAAAATTTCA
57750812 ATAAA-TAAAAAATAT
1 ATAAATTAAAAAATAT
**
57750827 ATAAAATTATTAAATAT
1 AT-AAATTAAAAAATAT
*
57750844 -TAAATTAAAAATTAT
1 ATAAATTAAAAAATAT
*
57750859 ATAATATTTTAAAAAAAAT
1 ATAA-A--TTAAAAAATAT
57750878 -TAAATTAA
1 ATAAATTAA
57750886 TATGAGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
15 17 0.37
16 7 0.15
17 10 0.22
18 3 0.07
19 9 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
ATAAATTAAAAAATAT
Found at i:57750853 original size:32 final size:30
Alignment explanation
Indices: 57750813--57750871 Score: 82
Period size: 32 Copynumber: 1.9 Consensus size: 30
57750803 AAAATTTCAA
57750813 TAAATAAAAAATATATAAAATTATTAAATAT
1 TAAATAAAAAATATATAAAATT-TTAAATAT
* *
57750844 TAAATTAAAAATTATATAATATTTTAAA
1 TAAA-TAAAAAATATATAAAATTTTAAA
57750872 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (30 bp):
TAAATAAAAAATATATAAAATTTTAAATAT
Found at i:57750857 original size:22 final size:22
Alignment explanation
Indices: 57750829--57750888 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
57750819 AAAAATATAT
57750829 AAAATTAT-TAA-ATATTAAATTA
1 AAAATTATATAATATATTAAA--A
*
57750851 AAAATTATATAATATTTTAAAA
1 AAAATTATATAATATATTAAAA
*
57750873 AAAATTAAATTAATAT
1 AAAATTATA-TAATAT
57750889 GAGTTTGTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 17 0.52
23 9 0.27
24 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTATATAATATATTAAAA
Found at i:57753463 original size:8 final size:8
Alignment explanation
Indices: 57753452--57753488 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
57753442 AGTTTTTTTT
57753452 TTTTTTAC
1 TTTTTTAC
57753460 TTTTTTAC
1 TTTTTTAC
57753468 TTTTTTAC
1 TTTTTTAC
57753476 TTTTTTGAC
1 TTTTTT-AC
57753485 TTTT
1 TTTT
57753489 ATTTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 22 0.79
9 6 0.21
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.76
Consensus pattern (8 bp):
TTTTTTAC
Found at i:57753488 original size:15 final size:15
Alignment explanation
Indices: 57753453--57753497 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
57753443 GTTTTTTTTT
57753453 TTTTTACTTTTTTAC
1 TTTTTACTTTTTTAC
57753468 TTTTTTACTTTTTTGAC
1 -TTTTTACTTTTTT-AC
*
57753485 -TTTTATTTTTTTA
1 TTTTTACTTTTTTA
57753498 TGTTTTGTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 1 0.04
15 11 0.41
16 13 0.48
17 2 0.07
ACGTcount: A:0.13, C:0.09, G:0.02, T:0.76
Consensus pattern (15 bp):
TTTTTACTTTTTTAC
Found at i:57753503 original size:22 final size:22
Alignment explanation
Indices: 57753462--57753522 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
57753452 TTTTTTACTT
* *
57753462 TTTTACTTTTTTACTTTTTTGAC
1 TTTTATTTTTTTA-TGTTTTGAC
*
57753485 TTTTATTTTTTTATGTTTTGTC
1 TTTTATTTTTTTATGTTTTGAC
57753507 TTTTATCTTTATTTAT
1 TTTTAT-TTT-TTTAT
57753523 TTATTTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.39
23 15 0.45
24 5 0.15
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTATTTTTTTATGTTTTGAC
Found at i:57753598 original size:24 final size:23
Alignment explanation
Indices: 57753556--57753617 Score: 65
Period size: 26 Copynumber: 2.7 Consensus size: 23
57753546 AAAATTTGAA
*
57753556 ATATATATTTGAAATATTTTATTAAT
1 ATATATATTT-TAATATTTTA--AAT
57753582 ATATATATTTTAA-ATTTTAAAT
1 ATATATATTTTAATATTTTAAAT
*
57753604 ATAT-TTTTTTAATA
1 ATATATATTTTAATA
57753618 ATATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.21
22 8 0.24
24 6 0.18
25 2 0.06
26 10 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (23 bp):
ATATATATTTTAATATTTTAAAT
Found at i:57753904 original size:26 final size:28
Alignment explanation
Indices: 57753852--57753907 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
57753842 AAATGAATTT
*
57753852 ATTTAAATATATATATTAAAAAATAAAA
1 ATTTAAATATATAAATTAAAAAATAAAA
*
57753880 ATTTAAAT-T-TAAATTAAAAATTAAAA
1 ATTTAAATATATAAATTAAAAAATAAAA
57753906 AT
1 AT
57753908 ATATATTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 17 0.65
27 1 0.04
28 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (28 bp):
ATTTAAATATATAAATTAAAAAATAAAA
Found at i:57754324 original size:19 final size:21
Alignment explanation
Indices: 57754278--57754326 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
57754268 TTTAAAAATC
*
57754278 ATAATTTAA-AATATTATAAA
1 ATAATTAAATAATATTATAAA
57754298 ATAAATTAAATAATATT-TAAA
1 AT-AATTAAATAATATTATAAA
57754319 AT-ATTAAA
1 ATAATTAAA
57754327 AAACTAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 12 0.46
22 6 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAATTAAATAATATTATAAA
Found at i:57754410 original size:21 final size:23
Alignment explanation
Indices: 57754386--57754435 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
57754376 TTATATTATT
*
57754386 AAAAATAT-ATATT-AATATTTA
1 AAAAATATAATATTCAAAATTTA
*
57754407 AAAAA-ATAATATTCAAAATTTT
1 AAAAATATAATATTCAAAATTTA
57754429 AAAAATA
1 AAAAATA
57754436 ATTTAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 11 0.46
23 1 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (23 bp):
AAAAATATAATATTCAAAATTTA
Found at i:57754436 original size:21 final size:20
Alignment explanation
Indices: 57754384--57754443 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 20
57754374 TTTTATATTA
*
57754384 TTAAAAATATATATTAATATT
1 TTAAAAATA-ATATTAAAATT
*
57754405 TAAAAAAATAATATTCAAAATT
1 T-TAAAAATAATATT-AAAATT
57754427 TTAAAAATAAT-TTAAAA
1 TTAAAAATAATATTAAAA
57754444 ATAATTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 4 0.12
20 2 0.06
21 15 0.44
22 13 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAAAATAATATTAAAATT
Found at i:57754442 original size:11 final size:11
Alignment explanation
Indices: 57754408--57754450 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
57754398 TAATATTTAA
57754408 AAAAATAATATT
1 AAAAATAAT-TT
*
57754420 CAAAAT--TTT
1 AAAAATAATTT
57754429 AAAAATAATTT
1 AAAAATAATTT
57754440 AAAAATAATTT
1 AAAAATAATTT
57754451 TTAAAATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.26
10 1 0.04
11 14 0.52
12 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAAATAATTT
Found at i:57754449 original size:23 final size:23
Alignment explanation
Indices: 57754424--57754502 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 23
57754414 AATATTCAAA
*
57754424 ATTTTAAAAATAATTTAAAAATA-
1 ATTTTAAAAAT-ATTTAAATATAG
* * *
57754447 ATTTTTAAAATTTTTAAATATAT
1 ATTTTAAAAATATTTAAATATAG
*
57754470 ATATTATAAAATATTTCAAATATAG
1 ATTTTA-AAAATATTT-AAATATAG
57754495 ATTTTAAA
1 ATTTTAAA
57754503 TTTTTTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
22 9 0.20
23 14 0.31
24 10 0.22
25 12 0.27
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
ATTTTAAAAATATTTAAATATAG
Found at i:57754528 original size:10 final size:9
Alignment explanation
Indices: 57754515--57754618 Score: 50
Period size: 10 Copynumber: 11.2 Consensus size: 9
57754505 TTTTAAAATT
57754515 AATAACAAAA
1 AATAA-AAAA
*
57754525 AATAAATAA
1 AATAAAAAA
*
57754534 AAT-AAATA
1 AATAAAAAA
* *
57754542 CA-AAATAA
1 AATAAAAAA
57754550 AATAAGAAAA
1 AATAA-AAAA
*
57754560 AATATAAAA
1 AATAAAAAA
**
57754569 CTTAAAAAA
1 AATAAAAAA
*
57754578 ATTAAAGAAA
1 AATAAA-AAA
* *
57754588 AAGACAAAA
1 AATAAAAAA
*
57754597 GATAATAAAA
1 AATAA-AAAA
57754607 AAGTAAAAAA
1 AA-TAAAAAA
57754617 AA
1 AA
57754619 AGTGAAAGAT
Statistics
Matches: 68, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
8 8 0.12
9 28 0.41
10 29 0.43
11 3 0.04
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.15
Consensus pattern (9 bp):
AATAAAAAA
Found at i:57758331 original size:20 final size:20
Alignment explanation
Indices: 57758306--57758349 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
57758296 TAAGATACGG
57758306 TGAAGG-AAAAGAAATAACTT
1 TGAAGGTAAAAGAAATAA-TT
**
57758326 TGAAGGTAAAATTAATAATT
1 TGAAGGTAAAAGAAATAATT
57758346 TGAA
1 TGAA
57758350 TTCATTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.18, T:0.27
Consensus pattern (20 bp):
TGAAGGTAAAAGAAATAATT
Found at i:57759128 original size:31 final size:31
Alignment explanation
Indices: 57759084--57759142 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
57759074 AATTTGGACC
*
57759084 AAAATAAATTTTAAGTGCTGAAGTGAATCTT
1 AAAATAAAGTTTAAGTGCTGAAGTGAATCTT
* * *
57759115 AAAATTAAGTTTAAGTGCTTAATTGAAT
1 AAAATAAAGTTTAAGTGCTGAAGTGAAT
57759143 AAAAAATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.37
Consensus pattern (31 bp):
AAAATAAAGTTTAAGTGCTGAAGTGAATCTT
Found at i:57763757 original size:18 final size:19
Alignment explanation
Indices: 57763730--57763779 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
57763720 TTTATTACAT
*
57763730 TTTA-TTTTTGTTTT-TAG
1 TTTATTTTTTGTTTTCTAA
57763747 TTTATTTTTTGTTTTCTAA
1 TTTATTTTTTGTTTTCTAA
57763766 TTT-TTCTTTTGTTT
1 TTTATT-TTTTGTTT
57763780 GCTTTTGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 4 0.14
18 12 0.41
19 13 0.45
ACGTcount: A:0.10, C:0.04, G:0.08, T:0.78
Consensus pattern (19 bp):
TTTATTTTTTGTTTTCTAA
Found at i:57768841 original size:22 final size:21
Alignment explanation
Indices: 57768816--57768858 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
57768806 CATTATTAAC
*
57768816 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATT-ATTTT
*
57768838 ATAATAAATTTTGATTATTTT
1 ATAATAAATTTTAATTATTTT
57768859 CGACAGATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (21 bp):
ATAATAAATTTTAATTATTTT
Found at i:57771213 original size:19 final size:18
Alignment explanation
Indices: 57771189--57771234 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
57771179 TTTGTTTTAC
*
57771189 TTTCTTTTTATTTTTTATT
1 TTTCTTTTTA-TGTTTATT
57771208 TTTCTTTTTATGTTTATT
1 TTTCTTTTTATGTTTATT
*
57771226 TTTATTTTT
1 TTTCTTTTT
57771235 TTAGACTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.11, C:0.04, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTCTTTTTATGTTTATT
Found at i:57771235 original size:7 final size:6
Alignment explanation
Indices: 57771193--57771234 Score: 57
Period size: 6 Copynumber: 6.8 Consensus size: 6
57771183 TTTTACTTTC
* *
57771193 TTTTTA TTTTTTA TTTTTC TTTTTA TGTTTA TTTTTA TTTTT
1 TTTTTA -TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTT
57771235 TTAGACTTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:57771270 original size:25 final size:25
Alignment explanation
Indices: 57771224--57771271 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
57771214 TTTATGTTTA
* *
57771224 TTTTTATTTTTTTAGACTTATTTCT
1 TTTTTATCTTTTGAGACTTATTTCT
57771249 TTTTTATCTTTTGA-ACTATATTT
1 TTTTTATCTTTTGAGACT-TATTT
57771272 AATTTTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTTTATCTTTTGAGACTTATTTCT
Found at i:57771277 original size:25 final size:25
Alignment explanation
Indices: 57771223--57771277 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
57771213 TTTTATGTTT
* * *
57771223 ATTTTTATTTTTTTAGACTTATTTC
1 ATTTTTATCTTTTGAGACTTATTTA
*
57771248 TTTTTTATCTTTTGA-ACTATATTTA
1 ATTTTTATCTTTTGAGACT-TATTTA
57771273 ATTTT
1 ATTTT
57771278 ATGTTTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (25 bp):
ATTTTTATCTTTTGAGACTTATTTA
Found at i:57774932 original size:25 final size:25
Alignment explanation
Indices: 57774835--57774924 Score: 153
Period size: 25 Copynumber: 3.6 Consensus size: 25
57774825 TTCCGAGTCA
*
57774835 TATAACGGGAAGTTCATGTGAGCTG
1 TATAACGGGAAGCTCATGTGAGCTG
*
57774860 TATAACGGGAAGCTCATGTGAGCTA
1 TATAACGGGAAGCTCATGTGAGCTG
57774885 TATAACGGGAAGCTCATGTGAGCTG
1 TATAACGGGAAGCTCATGTGAGCTG
*
57774910 TATAACAGGAAGCTC
1 TATAACGGGAAGCTC
57774925 TTGCGAGCCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 61 1.00
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (25 bp):
TATAACGGGAAGCTCATGTGAGCTG
Found at i:57774946 original size:25 final size:25
Alignment explanation
Indices: 57774918--57775040 Score: 106
Period size: 25 Copynumber: 4.9 Consensus size: 25
57774908 TGTATAACAG
*
57774918 GAAGCTCTTGCGAGCCAAATATCGA
1 GAAGCTCTTGAGAGCCAAATATCGA
** * *
57774943 GAAGCTCAAGAGAGCC-ATTAATCGG
1 GAAGCTCTTGAGAGCCAAAT-ATCGA
* * * *
57774968 GAAGCTCGTGAAAGCTAAATAAT-GG
1 GAAGCTCTTGAGAGCCAAAT-ATCGA
* * *
57774993 GAAACTCTTAAGAGCCAAGTATCGA
1 GAAGCTCTTGAGAGCCAAATATCGA
57775018 GAAGCTCTTGAGAGCCAAATATC
1 GAAGCTCTTGAGAGCCAAATATC
57775041 AGGACGCTTA
Statistics
Matches: 75, Mismatches: 20, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
24 4 0.05
25 66 0.88
26 5 0.07
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
GAAGCTCTTGAGAGCCAAATATCGA
Found at i:57774947 original size:50 final size:50
Alignment explanation
Indices: 57774819--57774950 Score: 174
Period size: 50 Copynumber: 2.6 Consensus size: 50
57774809 TGTAAACGGA
* * * *
57774819 AAGCTCTTCCGAGTCATATAACGGGAAGTTCATGTGAGCTGTATAACGGG
1 AAGCTCTTGCGAGCCATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
* * *
57774869 AAGCTCATGTGAGCTATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
1 AAGCTCTTGCGAGCCATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
* * *
57774919 AAGCTCTTGCGAGCCAAATATCGAGAAGCTCA
1 AAGCTCTTGCGAGCCATATAACGGGAAGCTCA
57774951 AGAGAGCCAT
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (50 bp):
AAGCTCTTGCGAGCCATATAACGGGAAGCTCATGTGAGCTGTATAACAGG
Found at i:57774947 original size:75 final size:75
Alignment explanation
Indices: 57774868--57775034 Score: 174
Period size: 75 Copynumber: 2.2 Consensus size: 75
57774858 TGTATAACGG
* * * ** ** * **
57774868 GAAGCTCATGTGAGCTATATAA-CGGGAAGCTCATGTGAGCTGTATAACAGGAAGCTCTTGCGAG
1 GAAGCTCAAGAGAGCCAT-TAATCGGGAAGCTCATGAAAGCTAAATAACAGGAAACTCTTAAGAG
57774932 CCAAATATCGA
65 CCAAATATCGA
* **
57774943 GAAGCTCAAGAGAGCCATTAATCGGGAAGCTCGTGAAAGCTAAATAATGGGAAACTCTTAAGAGC
1 GAAGCTCAAGAGAGCCATTAATCGGGAAGCTCATGAAAGCTAAATAACAGGAAACTCTTAAGAGC
*
57775008 CAAGTATCGA
66 CAAATATCGA
**
57775018 GAAGCTCTTGAGAGCCA
1 GAAGCTCAAGAGAGCCA
57775035 AATATCAGGA
Statistics
Matches: 75, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
74 3 0.04
75 72 0.96
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.20
Consensus pattern (75 bp):
GAAGCTCAAGAGAGCCATTAATCGGGAAGCTCATGAAAGCTAAATAACAGGAAACTCTTAAGAGC
CAAATATCGA
Found at i:57781508 original size:31 final size:30
Alignment explanation
Indices: 57781473--57781549 Score: 73
Period size: 31 Copynumber: 2.5 Consensus size: 30
57781463 GTTAAAGATA
57781473 AAATTGATACTCGAATTTATTTATTTCTCCT
1 AAATTGATACTCGAATTT-TTTATTTCTCCT
* * * * * *
57781504 AAATTGGTACTTGTGATTTTTTTTTTGTTCT
1 AAATTGATACTCG-AATTTTTTATTTCTCCT
*
57781535 AGATTGATACTCGAA
1 AAATTGATACTCGAA
57781550 CTTGTATTAG
Statistics
Matches: 35, Mismatches: 10, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
30 1 0.03
31 30 0.86
32 4 0.11
ACGTcount: A:0.26, C:0.12, G:0.13, T:0.49
Consensus pattern (30 bp):
AAATTGATACTCGAATTTTTTATTTCTCCT
Found at i:57782037 original size:191 final size:193
Alignment explanation
Indices: 57781678--57782053 Score: 477
Period size: 192 Copynumber: 2.0 Consensus size: 193
57781668 GAAAAATAAT
* ** * * *
57781678 GAGGTATAAGAGGACGTCACGTGGCAGTGTGCGATTAGCTAGCACTGCCACGTCAGCAAAAAAAT
1 GAGGTATAAGAGGACGTCACGCGGCAGCATGCGATTAGCTAACAATACCACGTCAGC-AAAAAAT
* ** ** * **
57781743 TAACGTTCTTAGTCTCAGGTATCAATATAGTGGACAAAAAAAAGTTTGGGTATCAATCTGGGAAA
65 TAACGTTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATAAATCTGAAAAA
* * * *
57781808 AAAAATCATAAGTATCAATTTGGGAGAAATGGACAAATTCGAGTACCAATTTTATTAAGAAAAG
130 AAAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
* * *
57781872 GAGGTATAAGAGGACGTCACGCGGCGGCATGTGATTGGCTAACAATACCACGTCAGC-AAAAATT
1 GAGGTATAAGAGGACGTCACGCGGCAGCATGCGATTAGCTAACAATACCACGTCAGCAAAAAATT
* * * * *
57781936 AACGTTGTTAGTCTTAAGTATCGATATAGCAGACAGAAAAAATTTTGAATATAAATCT-AAAAAA
66 AACGTTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATAAATCTGAAAAAA
* *
57782000 AAAACCATAAGTATAAATTTGGGAGAAGTGAACAAATTCGAATACTAATTTTAT
131 AAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTAT
57782054 ATTTAACCCT
Statistics
Matches: 154, Mismatches: 28, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
191 52 0.34
192 54 0.35
194 48 0.31
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (193 bp):
GAGGTATAAGAGGACGTCACGCGGCAGCATGCGATTAGCTAACAATACCACGTCAGCAAAAAATT
AACGTTCTTAGTCTCAAGTATCAATATAGCAGACAAAAAAAAGTTTGAATATAAATCTGAAAAAA
AAAACCATAAGTATAAATTTGGGAGAAATGAACAAATTCGAATACCAATTTTATTAAGAAAAG
Found at i:57786319 original size:20 final size:20
Alignment explanation
Indices: 57786294--57786336 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
57786284 AAAATTATAC
57786294 TTTTAAAACTA-ATTTAATTT
1 TTTTAAAA-TATATTTAATTT
*
57786314 TTTTAAAATATTTTTAATTT
1 TTTTAAAATATATTTAATTT
57786334 TTT
1 TTT
57786337 AATTTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAAAATATATTTAATTT
Found at i:57788925 original size:23 final size:23
Alignment explanation
Indices: 57788898--57788942 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
57788888 CCCGTTACAT
*
57788898 GGCTCTTTGTGAGCTTCCTGATA
1 GGCTCTTCGTGAGCTTCCTGATA
57788921 GGCTCTTCGTGAGCTTCCTGAT
1 GGCTCTTCGTGAGCTTCCTGAT
57788943 TAAAAGTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.11, C:0.24, G:0.27, T:0.38
Consensus pattern (23 bp):
GGCTCTTCGTGAGCTTCCTGATA
Found at i:57789035 original size:23 final size:26
Alignment explanation
Indices: 57789007--57789064 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
57788997 AGCCCGGATA
57789007 AGCTTCCTGA-TAA-G-CTCTTTGTG
1 AGCTTCCTGATTAATGACTCTTTGTG
*
57789030 AGCTTCCCGATTAATGACTCTTTGTG
1 AGCTTCCTGATTAATGACTCTTTGTG
57789056 AGCTTCCTG
1 AGCTTCCTG
57789065 TTATATGGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 9 0.30
24 3 0.10
25 1 0.03
26 17 0.57
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (26 bp):
AGCTTCCTGATTAATGACTCTTTGTG
Found at i:57795752 original size:21 final size:21
Alignment explanation
Indices: 57795693--57795753 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
57795683 GATTATATGA
* * *
57795693 ATTGGATTGAATATTGATTAT
1 ATTGAATTGATTATTGAATAT
57795714 ATTGAATTGATT-TATGAATAT
1 ATTGAATTGATTAT-TGAATAT
57795735 ATGTGAATTG-TTATTGAAT
1 AT-TGAATTGATTATTGAAT
57795754 TGAAATTAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
20 1 0.03
21 25 0.74
22 8 0.24
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (21 bp):
ATTGAATTGATTATTGAATAT
Found at i:57796611 original size:45 final size:45
Alignment explanation
Indices: 57796547--57796786 Score: 381
Period size: 45 Copynumber: 5.3 Consensus size: 45
57796537 CTGTTACCGC
*
57796547 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATTTTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
57796592 TACTGCTACTATTACCGATTCGACACTTTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
57796637 TACTGCTACTGTTACCGATTCGGCACTGTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
57796682 TACTGTTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * * *
57796727 TACTGTTACCGTTACCGATTCAGCACTTTGTGTGTTGAATACTGT
1 TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
57796772 TACTGTTACTGTTAC
1 TACTGCTACTGTTAC
57796787 TATTACTGTT
Statistics
Matches: 182, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 182 1.00
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.41
Consensus pattern (45 bp):
TACTGCTACTGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:57796777 original size:6 final size:6
Alignment explanation
Indices: 57796766--57796808 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
57796756 GTGTGTTGAA
*
57796766 TACTGT TACTGT TACTGT TACTAT TACTGT TACTGT TACTGT T
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT T
57796809 CCGGATTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.19, C:0.16, G:0.14, T:0.51
Consensus pattern (6 bp):
TACTGT
Found at i:57796995 original size:18 final size:18
Alignment explanation
Indices: 57796972--57797254 Score: 180
Period size: 18 Copynumber: 15.3 Consensus size: 18
57796962 AAAGGTATAA
*
57796972 AATAATTGATTATTACTG
1 AATAATTGATTGTTACTG
57796990 AATAATTGATTGTTACTG
1 AATAATTGATTGTTACTG
* *
57797008 GATAATTGACTGTTACT-
1 AATAATTGATTGTTACTG
*
57797025 AGAT-ATTAGACTGTTACTG
1 A-ATAATT-GATTGTTACTG
* * *
57797044 AATAACTGAATATTACTG
1 AATAATTGATTGTTACTG
**
57797062 AATAATTGATCATTACTG
1 AATAATTGATTGTTACTG
* *
57797080 AATAACTGATTGTCACTG
1 AATAATTGATTGTTACTG
* * *
57797098 AATGAA-TGACTGCTACTA
1 AAT-AATTGATTGTTACTG
* *
57797116 AATAACTTAATAGTTACTG
1 AATAA-TTGATTGTTACTG
57797135 AAT-ATCTGATT-TTACTG
1 AATAAT-TGATTGTTACTG
*
57797152 AATAATTGACTGTTACTGG
1 AATAATTGATTGTTACT-G
* *
57797171 ATAACCGATCAATTGATCGATACTG
1 ---A---AT-AATTGATTGTTACTG
* * * *
57797196 AATAACTGGTTATTATTG
1 AATAATTGATTGTTACTG
*
57797214 AATAATTGATTGTTACCG
1 AATAATTGATTGTTACTG
* *
57797232 AATAACTGACTGTTACTG
1 AATAATTGATTGTTACTG
57797250 AATAA
1 AATAA
57797255 ATAATTATTC
Statistics
Matches: 204, Mismatches: 43, Indels: 36
0.72 0.15 0.13
Matches are distributed among these distances:
17 19 0.09
18 151 0.74
19 18 0.09
22 2 0.01
25 3 0.01
26 11 0.05
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (18 bp):
AATAATTGATTGTTACTG
Found at i:57801525 original size:317 final size:320
Alignment explanation
Indices: 57800931--57801613 Score: 848
Period size: 317 Copynumber: 2.1 Consensus size: 320
57800921 CAACGGTTTT
*
57800931 CTAATAGGG-AGGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTG
1 CTAATAGGGCA-GCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTC
* *
57800995 TTACATTTTATTAAAGAGAGAACATATATTCAGTAATGGAGTCCTTCTGTGGTGGGGGAAGGGCA
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCTATGGTGGGGGAAGGGCA
* * * *
57801060 AGGGCAGTCTACTCGTTGTCAGGTTGCAATAAGAAATGAAAACTAGTCATTGGAGGGAACACAAG
130 AGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAG
** * * *
57801125 GCTAGAGGAGAGTGGCTTTGCATACGAGCCTTACTCTATAGGCTCATCAGAGTGCTACAGCTAGC
195 GCTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGCACATCAGAGTGCTACAACTAGC
* *
57801190 ACTTTGAAGCCCGCTGAAAAACAGATG--TGCTCTACTAGCGCGCAATGG-TTTGAAGCTTTG
260 ACTTTGAAGCCAGCTGAAAAACAGATGCTTG--CTACTAGCGCGCAATGGTTTTCAAGCTTTG
* * * *** * ** *
57801250 CTGATAGGGCAGCTTTATGCTTATTCAATAATTGTGGTATTGCCTTGGATTTTCTGTTTAGGTTC
1 CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACG-TTGTCCATGTAGGTTC
*
57801315 TTACATTTTATTAAATAAAGAACATATATTCAGTAATGGAGTCCTTAC-ATGGTGGGGGAAGGGC
65 TTACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTT-CTATGGTGGGGGAAGGGC
** * * *
57801379 AAGGGCAG-C-A-TCCTTGTTGGGTTGAAACAAGAAACGGAAACTAGTCGTTGGAGGGAACACGA
129 AAGGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAA
* * * * *
57801441 GGCTTGTGGA-ATGTGG-TTCCACATAAGAGCCTTACTCTATAGTG-ACGTTAGTGTGCTACAAC
194 GGCTAGAGGAGA-GTGGCTT-CACATAAGAGCCTTACTCTATAG-GCACATCAGAGTGCTACAAC
* * * *
57801503 TAGCACTTTGAAGCCAGCTGAAAAACTGATGCTTGCTATTGGTGCGCAATGGTTTTCAAGCTTTG
256 TAGCACTTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGTTTTCAAGCTTTG
*
57801568 CTAATAGGGCAGCTTTATTGCTTATTCGATAATTGTGCCATTGCCA
1 CTAATAGGGCAGCTTTA-TGCTTATTCGATAATTGTGGCATTGCCA
57801614 GCATTTTCCA
Statistics
Matches: 310, Mismatches: 44, Indels: 20
0.83 0.12 0.05
Matches are distributed among these distances:
316 3 0.01
317 131 0.42
318 29 0.09
319 67 0.22
320 79 0.25
321 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.30
Consensus pattern (320 bp):
CTAATAGGGCAGCTTTATGCTTATTCGATAATTGTGGCATTGCCAACGTTGTCCATGTAGGTTCT
TACATTTTATTAAAGAAAGAACATATATTCAGTAATGGAGTCCTTCTATGGTGGGGGAAGGGCAA
GGGCAGTCTACTCCTTGTCAGGTTGAAACAAGAAACGAAAACTAGTCATTGGAGGGAACACAAGG
CTAGAGGAGAGTGGCTTCACATAAGAGCCTTACTCTATAGGCACATCAGAGTGCTACAACTAGCA
CTTTGAAGCCAGCTGAAAAACAGATGCTTGCTACTAGCGCGCAATGGTTTTCAAGCTTTG
Found at i:57803839 original size:14 final size:15
Alignment explanation
Indices: 57803820--57803848 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57803810 GATTTGCAAC
57803820 AGTTAAATT-TATTA
1 AGTTAAATTATATTA
57803834 AGTTAAATTATATTA
1 AGTTAAATTATATTA
57803849 TTTTCAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (15 bp):
AGTTAAATTATATTA
Found at i:57807466 original size:28 final size:28
Alignment explanation
Indices: 57807419--57807472 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
57807409 AGTCTCTTCA
*
57807419 TGTTAAAAATTCTATTCATTTAATTATC
1 TGTTAAAAATTCTATCCATTTAATTATC
*
57807447 TGTTAAAAATT-TCATCCATTTTATTA
1 TGTTAAAAATTCT-ATCCATTTAATTA
57807473 GAATTAATCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.35, C:0.11, G:0.04, T:0.50
Consensus pattern (28 bp):
TGTTAAAAATTCTATCCATTTAATTATC
Found at i:57811752 original size:14 final size:13
Alignment explanation
Indices: 57811730--57811760 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
57811720 AGTTTGGCAA
57811730 TTTTTTATTTTAT
1 TTTTTTATTTTAT
57811743 TTTTTATATTTTAT
1 TTTTT-TATTTTAT
57811757 TTTT
1 TTTT
57811761 ATACAAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
TTTTTTATTTTAT
Found at i:57811759 original size:13 final size:13
Alignment explanation
Indices: 57811729--57811763 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
57811719 AAGTTTGGCA
57811729 ATTTTT-TATTTT
1 ATTTTTATATTTT
57811741 ATTTTTTATATTTT
1 A-TTTTTATATTTT
57811755 ATTTTTATA
1 ATTTTTATA
57811764 CAAAGATACC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 1 0.05
13 13 0.62
14 7 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
ATTTTTATATTTT
Found at i:57813385 original size:24 final size:24
Alignment explanation
Indices: 57813337--57813398 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 24
57813327 ACCTCTTTGT
* *
57813337 TTGAACCGTTATATCAATCATTTC
1 TTGAACCATTATATCAATCAGTTC
* *
57813361 TTGAACCATTATATCGATTAGTTC
1 TTGAACCATTATATCAATCAGTTC
* *
57813385 TTGGACTATTATAT
1 TTGAACCATTATAT
57813399 TGATCAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.29, C:0.16, G:0.11, T:0.44
Consensus pattern (24 bp):
TTGAACCATTATATCAATCAGTTC
Found at i:57816934 original size:31 final size:31
Alignment explanation
Indices: 57816899--57816961 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
57816889 TTCATGGAGC
*
57816899 TAAGGTCCAAAATATGGAAGAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
57816930 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
1 TAAGGTCCAAAATATAGAAGAAACAGGTGTT
57816961 T
1 T
57816962 CCACAACTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.43, C:0.10, G:0.24, T:0.24
Consensus pattern (31 bp):
TAAGGTCCAAAATATAGAAGAAACAGGTGTT
Done.