Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032253.1 Gossypioides kirkii chromosome KI_11
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: 55708359
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 180 of 182
Found at i:54951008 original size:18 final size:17
Alignment explanation
Indices: 54950972--54951030 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
54950962 GGCAACCCAA
*
54950972 TTATTTTTTTTATTTTT
1 TTATTTTTTTTATTATT
*
54950989 TTATTTTTCTTTCTTATT
1 TTATTTTT-TTTATTATT
*
54951007 TTA-TTTATTTATTCA-T
1 TTATTTTTTTTATT-ATT
54951023 TTATTTTT
1 TTATTTTT
54951031 GTCCAGGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 9 0.26
17 15 0.44
18 10 0.29
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (17 bp):
TTATTTTTTTTATTATT
Found at i:54951876 original size:105 final size:105
Alignment explanation
Indices: 54951707--54951897 Score: 242
Period size: 105 Copynumber: 1.8 Consensus size: 105
54951697 ATGTGTTAGA
* * * * *
54951707 CTGAGTAACTGGGGTAGAGTGCTTGGTTATCATTTCACTTCGCGTCAAAAGGGCTAATGCATTC-
1 CTGAGTAACCGGGATAGAGTGCTTGGGTATCATTTCACTTCACGTCAAAAGGGCTAATACATTCT
*
54951771 TACA-AAAAAAAAGAGAAGAAAAAAATTGAGAGCATGTTGGG
66 TAAAGAAAAAAAAG-GAA-AAAAAAATTGAGAGCATGTTGGG
* * * * * *
54951812 CTGAGTAACCGGGATAGAGTGTTTGGGTGTTATTTCATTTCACGTCAAAAGGTCTAATATATTCT
1 CTGAGTAACCGGGATAGAGTGCTTGGGTATCATTTCACTTCACGTCAAAAGGGCTAATACATTCT
54951877 TAAAGAAAAAAAAGGAAAAAA
66 TAAAGAAAAAAAAGGAAAAAA
54951898 TTCACAAAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
105 57 0.79
106 6 0.08
107 9 0.12
ACGTcount: A:0.38, C:0.12, G:0.24, T:0.27
Consensus pattern (105 bp):
CTGAGTAACCGGGATAGAGTGCTTGGGTATCATTTCACTTCACGTCAAAAGGGCTAATACATTCT
TAAAGAAAAAAAAGGAAAAAAAAATTGAGAGCATGTTGGG
Found at i:54952483 original size:19 final size:19
Alignment explanation
Indices: 54952461--54952505 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
54952451 TTATATTAGG
54952461 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
54952480 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
54952499 ATTTAAT
1 ATTTAAT
54952506 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:54952542 original size:14 final size:15
Alignment explanation
Indices: 54952510--54952542 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54952500 TTTAATTTAT
54952510 GTTTATCTTTTTGTA
1 GTTTATCTTTTTGTA
54952525 -TTTATCTTTTTG-A
1 GTTTATCTTTTTGTA
54952538 GTTTA
1 GTTTA
54952543 AATTGGATCC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.15, C:0.06, G:0.12, T:0.67
Consensus pattern (15 bp):
GTTTATCTTTTTGTA
Found at i:54953333 original size:16 final size:15
Alignment explanation
Indices: 54953309--54953338 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
54953299 CTTCTTTATT
54953309 TTATATTTCTTTTAA
1 TTATATTTCTTTTAA
54953324 TTATACTTTCTTTTA
1 TTATA-TTTCTTTTA
54953339 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
TTATATTTCTTTTAA
Found at i:54953344 original size:22 final size:21
Alignment explanation
Indices: 54953318--54953364 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
54953308 TTTATATTTC
*
54953318 TTTTAATTATACTTTCTTTTAT
1 TTTTAATTAT-CTTTCTTCTAT
* *
54953340 TTTTAATTCTGTTTCTTCTAT
1 TTTTAATTATCTTTCTTCTAT
54953361 TTTT
1 TTTT
54953365 CCTCAGATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTTAATTATCTTTCTTCTAT
Found at i:54955464 original size:14 final size:14
Alignment explanation
Indices: 54955442--54955495 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
54955432 AGATTTTATA
*
54955442 ACTTAAATTTTTAAT
1 ACTT-AATTTTTAAC
*
54955457 ACCTAATTTTTCAAC
1 ACTTAATTTTT-AAC
54955472 ACTTATATTTTTAAC
1 ACTTA-ATTTTTAAC
54955487 ACTTAATTT
1 ACTTAATTT
54955496 CTCAATTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 11 0.32
15 17 0.50
16 6 0.18
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (14 bp):
ACTTAATTTTTAAC
Found at i:54955476 original size:30 final size:30
Alignment explanation
Indices: 54955442--54955500 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
54955432 AGATTTTATA
* *
54955442 ACTTAAATTTTTAATACCTAATTTTTCAAC
1 ACTTAAATTTTTAACACCTAATTTCTCAAC
* *
54955472 ACTTATATTTTTAACACTTAATTTCTCAA
1 ACTTAAATTTTTAACACCTAATTTCTCAA
54955501 TTTATCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (30 bp):
ACTTAAATTTTTAACACCTAATTTCTCAAC
Found at i:54955983 original size:58 final size:60
Alignment explanation
Indices: 54955859--54955986 Score: 163
Period size: 58 Copynumber: 2.2 Consensus size: 60
54955849 ACTAATAGTC
* * *
54955859 ACCCAACTATTAGTAAATTTATTTTTGGTCATTTAACTAGGAAAAATTACAAAATGATCT
1 ACCCAACTATTAGTAAATTTATTTTTGATCACTAAACTAGGAAAAATTACAAAATGATCT
* * * * *
54955919 -CTCAACTATTAGTAAATTT-TTTTTGATCACTAAACTATGAAAAGTTACAACATGGT-T
1 ACCCAACTATTAGTAAATTTATTTTTGATCACTAAACTAGGAAAAATTACAAAATGATCT
54955976 ACCCAACTATT
1 ACCCAACTATT
54955987 CAATTTTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
57 1 0.02
58 39 0.67
59 18 0.31
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.37
Consensus pattern (60 bp):
ACCCAACTATTAGTAAATTTATTTTTGATCACTAAACTAGGAAAAATTACAAAATGATCT
Found at i:54956233 original size:189 final size:186
Alignment explanation
Indices: 54955915--54956276 Score: 564
Period size: 189 Copynumber: 1.9 Consensus size: 186
54955905 TTACAAAATG
* * *
54955915 ATCTCTCAACTATTAGTAAATTTTTTTTGATCACTAAACTATGAAAAGTTACAACATGGTTACCC
1 ATCTCTCAACTATTAGTAAATTTTTTTTGATCACTAAACTATAAAAAGTTACAAAATGATTACCC
*
54955980 AACTATTCAATTTTTTTCTTTTTTGGTTACCAGTTGACTAACATAAAAATGAAAATACTAAAAAA
66 AACTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATACTAAAAAA
* * *
54956045 TCCAAGATAGTTGGGTAACTAAAAAAATAGATAAATTAGTCATTATCTGTTAGATCA
131 TCCAAGATAATTGGGTAACT-AAAAAATAGACAAATTAATCATTATCTGTTAGATCA
* * * *
54956102 ATCTCTCAACTATTAGTAAGTTTATTTTTTGGTCACTTAACTATAAAAAGTTACAAAATGATTAT
1 ATCTCTCAACTATTAGTAA-ATT-TTTTTTGATCACTAAACTATAAAAAGTTACAAAATGATTAC
* *
54956167 CCAACTATTCAATTTTTTTTCTTTTTTGGTCATCAGTTGAC-AACATAAAAGTGAAAATACTAAA
64 CCAACTATTCAA-TTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATACTAAA
54956231 AAATCCAAGATAATTGGGTAACTAAAAAATAGACAAATTAATCATT
128 AAATCCAAGATAATTGGGTAACTAAAAAATAGACAAATTAATCATT
54956277 GTATGTTATA
Statistics
Matches: 159, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
187 19 0.12
188 23 0.14
189 91 0.57
190 26 0.16
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (186 bp):
ATCTCTCAACTATTAGTAAATTTTTTTTGATCACTAAACTATAAAAAGTTACAAAATGATTACCC
AACTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATACTAAAAAA
TCCAAGATAATTGGGTAACTAAAAAATAGACAAATTAATCATTATCTGTTAGATCA
Found at i:54956528 original size:14 final size:15
Alignment explanation
Indices: 54956501--54956531 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
54956491 TTTTTTAATA
54956501 GACTCGACTTGACTC
1 GACTCGACTTGACTC
54956516 GACTCGA-TTGACTC
1 GACTCGACTTGACTC
54956530 GA
1 GA
54956532 AATTTTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (15 bp):
GACTCGACTTGACTC
Found at i:54956642 original size:33 final size:33
Alignment explanation
Indices: 54956600--54956666 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
54956590 TAAAATAGGA
54956600 TTTGTCAACTTGACTAACTCAAATTTTTTTTAC
1 TTTGTCAACTTGACTAACTCAAATTTTTTTTAC
54956633 TTTGTCAACTTGACTAACTCAAATTTTTTTTAC
1 TTTGTCAACTTGACTAACTCAAATTTTTTTTAC
54956666 T
1 T
54956667 CGATTCGACT
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:0.27, C:0.18, G:0.06, T:0.49
Consensus pattern (33 bp):
TTTGTCAACTTGACTAACTCAAATTTTTTTTAC
Found at i:54957734 original size:62 final size:61
Alignment explanation
Indices: 54957660--54957775 Score: 180
Period size: 62 Copynumber: 1.9 Consensus size: 61
54957650 TATTAGGTAC
54957660 CTAATTAAAATTTTCTAGAAAC-TTAAAGGGAGAAATAAAATTTTCCAATAATTTTGGGTGGT
1 CTAATTAAAATTTTCTA-AAACTTTAAAGGGAGAAATAAAATTTTCCAA-AATTTTGGGTGGT
* * *
54957722 CTAATTAAAATTTTCTAAAACTTTCAAGGGATAAATAAATTTTTCCAAAATTTT
1 CTAATTAAAATTTTCTAAAACTTTAAAGGGAGAAATAAAATTTTCCAAAATTTT
54957776 AGAGGGAGGG
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
61 10 0.20
62 40 0.80
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.38
Consensus pattern (61 bp):
CTAATTAAAATTTTCTAAAACTTTAAAGGGAGAAATAAAATTTTCCAAAATTTTGGGTGGT
Found at i:54957782 original size:30 final size:30
Alignment explanation
Indices: 54957686--54957782 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 30
54957676 AGAAACTTAA
*
54957686 AGGGAGAAATAAAATTTTCCAATAATTTT-G
1 AGGGATAAATAAAATTTTCCAA-AATTTTAG
* * * * *
54957716 GGTGGTCTAATTAAAATTTTCTAAAACTTTCA-
1 AG-GG-ATAAATAAAATTTTCCAAAA-TTTTAG
*
54957748 AGGGATAAATAAATTTTTCCAAAATTTTAG
1 AGGGATAAATAAAATTTTCCAAAATTTTAG
54957778 AGGGA
1 AGGGA
54957783 GGGCCTAGCT
Statistics
Matches: 50, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
29 4 0.08
30 22 0.44
31 6 0.12
32 18 0.36
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.35
Consensus pattern (30 bp):
AGGGATAAATAAAATTTTCCAAAATTTTAG
Found at i:54963331 original size:42 final size:42
Alignment explanation
Indices: 54963284--54963367 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
54963274 GTTATAATTG
54963284 CATTTAGAATCTTTCGTATTTATATAGTTTTTGATAGTTTTT
1 CATTTAGAATCTTTCGTATTTATATAGTTTTTGATAGTTTTT
54963326 CATTTAGAATCTTTCGTATTTATATAGTTTTTGATAGTTTTT
1 CATTTAGAATCTTTCGTATTTATATAGTTTTTGATAGTTTTT
54963368 GATAGATTGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.24, C:0.07, G:0.12, T:0.57
Consensus pattern (42 bp):
CATTTAGAATCTTTCGTATTTATATAGTTTTTGATAGTTTTT
Found at i:54965161 original size:18 final size:18
Alignment explanation
Indices: 54965127--54965161 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54965117 TTAAATTTTG
*
54965127 TGAAAATTATAAGAATTT
1 TGAAAATTATAAAAATTT
*
54965145 TGAAAATTTTAAAAATT
1 TGAAAATTATAAAAATT
54965162 ATAATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TGAAAATTATAAAAATTT
Found at i:54965969 original size:18 final size:18
Alignment explanation
Indices: 54965935--54965969 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
54965925 TTAAATTTGG
*
54965935 TGAAAATTATAAGAATTT
1 TGAAAATTATAAAAATTT
*
54965953 TGAAAATTTTAAAAATT
1 TGAAAATTATAAAAATT
54965970 ATAATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TGAAAATTATAAAAATTT
Found at i:54970821 original size:27 final size:28
Alignment explanation
Indices: 54970778--54970865 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 28
54970768 CTTAAAAGTC
54970778 AAATTTTACAAATCACATTATTTTTTTC-A
1 AAATTTT-C-AATCACATTATTTTTTTCGA
54970807 AAATTTTCAATCACATTATTTTTATTCGA
1 AAATTTTCAATCACATTATTTTT-TTCGA
54970836 ATTCAGATTTTCATATCACATTATTTTTTT
1 A---A-ATTTTCA-ATCACATTATTTTTTT
54970866 TCTATTATAA
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
27 15 0.29
28 4 0.08
29 9 0.17
32 1 0.02
33 9 0.17
34 14 0.27
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (28 bp):
AAATTTTCAATCACATTATTTTTTTCGA
Found at i:54970879 original size:33 final size:31
Alignment explanation
Indices: 54970778--54970884 Score: 96
Period size: 33 Copynumber: 3.4 Consensus size: 31
54970768 CTTAAAAGTC
*
54970778 AAATTTTACAAATCACATTA-TTTTTTTCA--
1 AAATTTT-CATATCACATTATTTTTTTTCATT
*
54970807 AAATTTTCA-ATCACATTATTTTTATTCGAATT
1 AAATTTTCATATCACATTATTTTTTTTC--ATT
*
54970839 CAGATTTTCATATCACATTATTTTTTTTCTATT
1 -AAATTTTCATATCACATTATTTTTTTTC-ATT
*
54970872 ATAATTTTAATAT
1 A-AATTTTCATAT
54970885 TACTCTTGAT
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
27 9 0.14
28 9 0.14
29 7 0.11
30 1 0.02
32 1 0.02
33 20 0.31
34 17 0.27
ACGTcount: A:0.34, C:0.12, G:0.02, T:0.52
Consensus pattern (31 bp):
AAATTTTCATATCACATTATTTTTTTTCATT
Found at i:54970981 original size:20 final size:20
Alignment explanation
Indices: 54970952--54970990 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
54970942 TTTTGAATTC
*
54970952 TAAGAGTGCAATATATTTTA
1 TAAGAATGCAATATATTTTA
54970972 TAAGAATGCAATATATTTT
1 TAAGAATGCAATATATTTT
54970991 TCAAAATTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
TAAGAATGCAATATATTTTA
Found at i:54975681 original size:26 final size:27
Alignment explanation
Indices: 54975619--54975683 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
54975609 TATATGTGGA
54975619 AGCCTTTGTGGTTGTTCTGATATATATG
1 AGCCTTTGTGGTTGTTCTGA-ATATATG
* *
54975647 AGCCATTGTGGTTGTTCTG-ATATGTG
1 AGCCTTTGTGGTTGTTCTGAATATATG
*
54975673 AGTCTTTGTGG
1 AGCCTTTGTGG
54975684 CGGAATATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 15 0.45
28 18 0.55
ACGTcount: A:0.15, C:0.11, G:0.29, T:0.45
Consensus pattern (27 bp):
AGCCTTTGTGGTTGTTCTGAATATATG
Found at i:54977096 original size:18 final size:19
Alignment explanation
Indices: 54977075--54977124 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
54977065 AAAATTGTTA
*
54977075 AAAATTGTGAAT-ATAATT
1 AAAATTGTAAATAATAATT
54977093 AAAATTGTTAAATAATAATT
1 AAAATTG-TAAATAATAATT
54977113 AGAAATTGTAAA
1 A-AAATTGTAAA
54977125 AATGATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 7 0.25
19 4 0.14
20 11 0.39
21 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (19 bp):
AAAATTGTAAATAATAATT
Found at i:54977112 original size:20 final size:19
Alignment explanation
Indices: 54977075--54977121 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 19
54977065 AAAATTGTTA
*
54977075 AAAATTG-TGAATATAATT
1 AAAATTGTTAAATATAATT
54977093 AAAATTGTTAAATAATAATT
1 AAAATTGTTAAAT-ATAATT
54977113 AGAAATTGT
1 A-AAATTGT
54977122 AAAAATGATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 7 0.28
21 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
AAAATTGTTAAATATAATT
Found at i:54980353 original size:41 final size:41
Alignment explanation
Indices: 54980296--54980413 Score: 200
Period size: 41 Copynumber: 2.9 Consensus size: 41
54980286 TTACAATCTC
*
54980296 TTCTCGCGATGGGCGCGAGCATATTCAACTTCAACATAACT
1 TTCTCGCGATGGGCGCGAGCATATTCAACTTCAACAGAACT
*
54980337 TTCTCGCGATGGGCGCGAGCATATTCAACTTCAACAGAGCT
1 TTCTCGCGATGGGCGCGAGCATATTCAACTTCAACAGAACT
* *
54980378 TTCTCGCGATGGGCGCGAGCATATTCTACTTTAACA
1 TTCTCGCGATGGGCGCGAGCATATTCAACTTCAACA
54980414 ATACTAATTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 73 1.00
ACGTcount: A:0.25, C:0.26, G:0.22, T:0.27
Consensus pattern (41 bp):
TTCTCGCGATGGGCGCGAGCATATTCAACTTCAACAGAACT
Found at i:54983949 original size:2 final size:2
Alignment explanation
Indices: 54983942--54983975 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
54983932 AAGAAACAGG
54983942 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
54983976 ATGCATTGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:54986207 original size:15 final size:15
Alignment explanation
Indices: 54986189--54986222 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
54986179 ATAACTTAAA
*
54986189 TTTTTAATACCTAAT
1 TTTTTAACACCTAAT
*
54986204 TTTTTAACACTTAAT
1 TTTTTAACACCTAAT
54986219 TTTT
1 TTTT
54986223 CAATTTATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (15 bp):
TTTTTAACACCTAAT
Found at i:54987301 original size:60 final size:60
Alignment explanation
Indices: 54987175--54987304 Score: 165
Period size: 60 Copynumber: 2.2 Consensus size: 60
54987165 ACTAATAGTC
* *
54987175 ACCCAACTATTAGTAAATTTATTTTTGGTCATTTAACTAGGAAAAATTACAAAATGATCT
1 ACCCAACTATTAGTAAATTTATTTTTGGTCACTAAACTAGGAAAAATTACAAAATGATCT
* ** * * *
54987235 -CTCAACTATTAGTAAATTTATTTTTTGGTCACTAAACTTTGAAAAGTTACAACATGGT-T
1 ACCCAACTATTAGTAAATTTA-TTTTTGGTCACTAAACTAGGAAAAATTACAAAATGATCT
54987294 ACCCAACTATT
1 ACCCAACTATT
54987305 CAATTTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 20 0.34
60 39 0.66
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.38
Consensus pattern (60 bp):
ACCCAACTATTAGTAAATTTATTTTTGGTCACTAAACTAGGAAAAATTACAAAATGATCT
Found at i:54987556 original size:189 final size:189
Alignment explanation
Indices: 54987235--54987591 Score: 599
Period size: 188 Copynumber: 1.9 Consensus size: 189
54987225 AAAATGATCT
* * * * *
54987235 CTCAACTATTAGTAAATTTATTTTTTGGTCACTAAACTTTGAAAAGTTACAACATGGTTACCCAA
1 CTCAACTATTAGTAAATTTATTTTTTGATCACTAAACTATAAAAAGTTACAAAATGATTACCCAA
*
54987300 CTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATAGTCAAAAATC
66 CTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATACTCAAAAATC
54987365 CAAAATAA-TTGGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTGTATCAATCA
131 CAAAATAATTTGGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTGTATCAATCA
* *
54987423 CTCAACTATTAGTAAATTTATTTTTTGATCACTTAACTATAAAAAGTTACAAAATGATTATCCAA
1 CTCAACTATTAGTAAATTTATTTTTTGATCACTAAACTATAAAAAGTTACAAAATGATTACCCAA
* *
54987488 CTATTCAATTTTTTTTCTTTTTTGGTCATCAGTTGACTAACATAAAAGTGAAAATACTCAAAAAT
66 CTATTCAA-TTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATACTCAAAAAT
*
54987553 CCAAGATAATTTGGGTAACTAAAAAATAGATAAATTAGT
130 CCAAAATAATTTGGGTAACTAAAAAATAGATAAATTAGT
54987592 AATCGTATGT
Statistics
Matches: 156, Mismatches: 11, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
188 66 0.42
189 61 0.39
190 29 0.19
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (189 bp):
CTCAACTATTAGTAAATTTATTTTTTGATCACTAAACTATAAAAAGTTACAAAATGATTACCCAA
CTATTCAATTTTTTTCTTTTTTGGTCACCAGTTGACTAACATAAAAATGAAAATACTCAAAAATC
CAAAATAATTTGGGTAACTAAAAAATAGATAAATTAGTCATTATATGTTGTATCAATCA
Found at i:54990440 original size:16 final size:16
Alignment explanation
Indices: 54990419--54990461 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
54990409 TATAATAATA
54990419 ATTTTTATCTTATAAC
1 ATTTTTATCTTATAAC
* * *
54990435 ATTTTTATATTGTATC
1 ATTTTTATCTTATAAC
*
54990451 AATTTTATCTT
1 ATTTTTATCTT
54990462 GCTTTTAAGA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTTTTATCTTATAAC
Found at i:54992143 original size:30 final size:30
Alignment explanation
Indices: 54992109--54992172 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 30
54992099 CTAAACATCC
* *
54992109 TAGTAACTTAAAT-ACAACTTTTGAAT-AGTT
1 TAGT-ACTTAAATGAAAACTTTCGAATGA-TT
54992139 TAGTACTTAAATGAAAACTTTCGAATGATT
1 TAGTACTTAAATGAAAACTTTCGAATGATT
54992169 TAGT
1 TAGT
54992173 GACCATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.27
30 21 0.70
31 1 0.03
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (30 bp):
TAGTACTTAAATGAAAACTTTCGAATGATT
Found at i:54996605 original size:27 final size:27
Alignment explanation
Indices: 54996575--54996648 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
54996565 TTAACCCGTT
*
54996575 GACCCGAGTTGACTA-ACCCAACCTATA
1 GACCCGAGTTGA-TAGACCCAACCCATA
** *
54996602 GACCCGAGTTGATAGACCTGACCCATT
1 GACCCGAGTTGATAGACCCAACCCATA
*
54996629 GACCCGAGTTGATCGACCCA
1 GACCCGAGTTGATAGACCCA
54996649 TTGACTTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 2 0.05
27 37 0.95
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.19
Consensus pattern (27 bp):
GACCCGAGTTGATAGACCCAACCCATA
Found at i:54996664 original size:13 final size:13
Alignment explanation
Indices: 54996662--54996720 Score: 66
Period size: 13 Copynumber: 4.5 Consensus size: 13
54996652 ACTTTGACCA
*
54996662 TTGACCGTTGATT
1 TTGACCATTGATT
*
54996675 TTGACCTTTGATT
1 TTGACCATTGATT
54996688 TTGACCATTGATT
1 TTGACCATTGATT
* *
54996701 GTTGA-CTTTGACT
1 -TTGACCATTGATT
54996714 TTGACCA
1 TTGACCA
54996721 ATCATATCCT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
12 4 0.10
13 31 0.79
14 4 0.10
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (13 bp):
TTGACCATTGATT
Found at i:54996691 original size:26 final size:26
Alignment explanation
Indices: 54996649--54996720 Score: 92
Period size: 26 Copynumber: 2.7 Consensus size: 26
54996639 GATCGACCCA
* *
54996649 TTGACTTTGACCATTGACCGTTGATT-
1 TTGACTTTGA-CTTTGACCATTGATTG
*
54996675 TTGACCTTTGATTTTGACCATTGATTG
1 TTGA-CTTTGACTTTGACCATTGATTG
54996702 TTGACTTTGACTTTGACCA
1 TTGACTTTGACTTTGACCA
54996721 ATCATATCCT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 30 0.75
27 10 0.25
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.44
Consensus pattern (26 bp):
TTGACTTTGACTTTGACCATTGATTG
Found at i:54996695 original size:33 final size:32
Alignment explanation
Indices: 54996649--54996718 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 32
54996639 GATCGACCCA
*
54996649 TTGACTTTGACCATTGACCGTTGATTTTGACCT
1 TTGACTTTGACCATTGACCGTTGACTTTGA-CT
* **
54996682 TTGATTTTGACCATTGATTGTTGACTTTGACT
1 TTGACTTTGACCATTGACCGTTGACTTTGACT
54996714 TTGAC
1 TTGAC
54996719 CAATCATATC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 6 0.19
33 26 0.81
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (32 bp):
TTGACTTTGACCATTGACCGTTGACTTTGACT
Found at i:54998869 original size:23 final size:23
Alignment explanation
Indices: 54998842--54998895 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 23
54998832 TAAAATAAAA
54998842 AAAAAGAATAA-ACGGATTGAATTT
1 AAAAA-AATAATA-GGATTGAATTT
*
54998866 AAAAAAATAATAGGATTTAATTT
1 AAAAAAATAATAGGATTGAATTT
54998889 AAAAAAA
1 AAAAAAA
54998896 CAGAATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 22 0.79
24 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.26
Consensus pattern (23 bp):
AAAAAAATAATAGGATTGAATTT
Found at i:55001782 original size:17 final size:17
Alignment explanation
Indices: 55001756--55001788 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
55001746 GTTATTAGTA
55001756 AATTTTGAA-TAATATT
1 AATTTTGAATTAATATT
55001772 AATTATTGAATTAATAT
1 AATT-TTGAATTAATAT
55001789 GTTAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 5 0.33
18 6 0.40
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (17 bp):
AATTTTGAATTAATATT
Found at i:55008224 original size:37 final size:37
Alignment explanation
Indices: 55008124--55008224 Score: 87
Period size: 37 Copynumber: 2.6 Consensus size: 37
55008114 GACCTTGACT
* *
55008124 CGATGAGACACTGGGTGTCATTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTC---ACTTTACTTCGGATAGA-C
** ** *
55008165 CGATGAGGTACTGGGTACCACTTTACTTCGGCTAG-C
1 CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAC
55008201 CAGATGAGACACTGGGTGTCACTT
1 C-GATGAGACACTGGGTGTCACTT
55008225 ATTTGCTTCA
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
36 1 0.02
37 18 0.38
38 14 0.29
41 15 0.31
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.31
Consensus pattern (37 bp):
CGATGAGACACTGGGTGTCACTTTACTTCGGATAGAC
Found at i:55009532 original size:10 final size:10
Alignment explanation
Indices: 55009519--55009547 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
55009509 TTAATTTAAA
55009519 TATTTTTATT
1 TATTTTTATT
55009529 TA-TTTTATT
1 TATTTTTATT
55009538 TATTTTTATT
1 TATTTTTATT
55009548 GAGCCCAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TATTTTTATT
Found at i:55010252 original size:18 final size:18
Alignment explanation
Indices: 55010218--55010252 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55010208 TTAAATTTTG
*
55010218 TGAAAATTATAAGAATTT
1 TGAAAATTATAAAAATTT
*
55010236 TGAAAATTTTAAAAATT
1 TGAAAATTATAAAAATT
55010253 ATAATAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TGAAAATTATAAAAATTT
Found at i:55011015 original size:18 final size:18
Alignment explanation
Indices: 55010981--55011015 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55010971 TTAAATTTTG
*
55010981 TGAAAATTATAAGAATTT
1 TGAAAATTATAAAAATTT
*
55010999 TGAAAATTTTAAAAATT
1 TGAAAATTATAAAAATT
55011016 ATAAGAATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (18 bp):
TGAAAATTATAAAAATTT
Found at i:55017187 original size:20 final size:23
Alignment explanation
Indices: 55017148--55017188 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
55017138 TGAATATAAC
55017148 ATTTTATTGTGTTATAATAATGT
1 ATTTTATTGTGTTATAATAATGT
55017171 ATTTTA-TGT-TTAT-ATAAT
1 ATTTTATTGTGTTATAATAAT
55017189 ATTTAATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 4 0.22
22 3 0.17
23 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.10, T:0.59
Consensus pattern (23 bp):
ATTTTATTGTGTTATAATAATGT
Found at i:55017191 original size:18 final size:20
Alignment explanation
Indices: 55017141--55017192 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
55017131 TAAAAAGTGA
*
55017141 ATATAACATTTTATTGTGTT
1 ATATAATATTTTATTGTGTT
55017161 ATAATAATGTATTTTA-TGT-TT
1 AT-ATAA--TATTTTATTGTGTT
55017182 ATATAATATTT
1 ATATAATATTT
55017193 AATAGATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
18 5 0.18
20 6 0.21
21 8 0.29
22 3 0.11
23 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (20 bp):
ATATAATATTTTATTGTGTT
Found at i:55018714 original size:18 final size:18
Alignment explanation
Indices: 55018678--55018727 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
55018668 ATCTACCATT
*
55018678 TCATATTCCATTCCACATC
1 TCAT-TTCCATTTCACATC
*
55018697 TCATTTCCATTTCTCATC
1 TCATTTCCATTTCACATC
55018715 -C-TTTGCCATTTCA
1 TCATTT-CCATTTCA
55018728 ATATCAAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.11
17 8 0.30
18 12 0.44
19 4 0.15
ACGTcount: A:0.20, C:0.34, G:0.02, T:0.44
Consensus pattern (18 bp):
TCATTTCCATTTCACATC
Found at i:55019966 original size:3 final size:3
Alignment explanation
Indices: 55019958--55020000 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
55019948 TGTTTTCATT
55019958 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
55020001 AACATAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:55023619 original size:11 final size:12
Alignment explanation
Indices: 55023598--55023629 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
55023588 GGTTCATGTA
55023598 TCTTTAT-TTTT
1 TCTTTATCTTTT
55023609 TCTTT-TCTTTT
1 TCTTTATCTTTT
55023620 TCTTTATCTT
1 TCTTTATCTT
55023630 AACGTCTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.05
11 14 0.74
12 4 0.21
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTTTATCTTTT
Found at i:55046465 original size:96 final size:94
Alignment explanation
Indices: 55046263--55046465 Score: 239
Period size: 96 Copynumber: 2.1 Consensus size: 94
55046253 AAAGACATCT
* * *
55046263 AAACTCAAAAC-AAATTAAAAAAAAATGGAATCGACGAGCAAAAAGCGATCAATGGACCTTCGAG
1 AAACTCAAAACAAAATAAAAAAAAAATGGAATCGACGAGCAAAAAGCGATCAAGGGACCTTAGAG
55046327 CAGCGACAAAGGCACCGATAAACAACGTA
66 CAGCGACAAAGGCACCGATAAACAACGTA
* * ** * * *
55046356 AAA-ACAAATACAAAATAAAAATAAAAATGGAATTGATTAGCGAAAAAGTGATCGAGGGAGCTTA
1 AAACTCAAA-ACAAAATAAAAA-AAAAATGGAATCGACGAGC-AAAAAGCGATCAAGGGACCTTA
** * *
55046420 GTTCAGCGACAAATGCATCGATAAACAACGTA
63 GAGCAGCGACAAAGGCACCGATAAACAACGTA
55046452 AAACTCAAAACAAA
1 AAACTCAAAACAAA
55046466 TTCAAGAAAA
Statistics
Matches: 90, Mismatches: 15, Indels: 7
0.80 0.13 0.06
Matches are distributed among these distances:
92 4 0.04
93 5 0.06
94 8 0.09
95 16 0.18
96 53 0.59
97 4 0.04
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.15
Consensus pattern (94 bp):
AAACTCAAAACAAAATAAAAAAAAAATGGAATCGACGAGCAAAAAGCGATCAAGGGACCTTAGAG
CAGCGACAAAGGCACCGATAAACAACGTA
Found at i:55047993 original size:19 final size:18
Alignment explanation
Indices: 55047971--55048007 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
55047961 ATATTAATAA
*
55047971 TTTAATAATTTAAATATTT
1 TTTAAAAATTTAAA-ATTT
55047990 TTTAAAAATTTAAAATTT
1 TTTAAAAATTTAAAATTT
55048008 GAATAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTAAAAATTTAAAATTT
Found at i:55059054 original size:23 final size:23
Alignment explanation
Indices: 55059026--55059116 Score: 84
Period size: 23 Copynumber: 4.1 Consensus size: 23
55059016 TATTTTAATA
55059026 TATAAAATATTAATTTAAATATT
1 TATAAAATATTAATTTAAATATT
* *
55059049 TCT-AAATAATTAATATTAATTATT
1 TATAAAAT-ATTAAT-TTAAATATT
*
55059073 TATAAAAT-TTAA-TTAAA-ATA
1 TATAAAATATTAATTTAAATATT
* *
55059093 TATAAACTA-TATTTTAAATATT
1 TATAAAATATTAATTTAAATATT
55059115 TA
1 TA
55059117 AATATAACCA
Statistics
Matches: 54, Mismatches: 8, Indels: 13
0.72 0.11 0.17
Matches are distributed among these distances:
20 11 0.20
21 9 0.17
22 8 0.15
23 12 0.22
24 10 0.19
25 4 0.07
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (23 bp):
TATAAAATATTAATTTAAATATT
Found at i:55064053 original size:24 final size:24
Alignment explanation
Indices: 55064002--55064054 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
55063992 TATTTCAGTT
* *
55064002 AAATTCTATTTATTTATTTTAATT
1 AAATTCTATTTATTTATTTGAATC
*
55064026 AAATTCTATTTA-TTAGTTTGAGTC
1 AAATTCTATTTATTTA-TTTGAATC
55064050 AAATT
1 AAATT
55064055 TTTATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.55
Consensus pattern (24 bp):
AAATTCTATTTATTTATTTGAATC
Found at i:55065065 original size:18 final size:18
Alignment explanation
Indices: 55065044--55065078 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55065034 AAATTATTAT
*
55065044 AATTTTTAAAATTTTCAA
1 AATTCTTAAAATTTTCAA
*
55065062 AATTCTTATAATTTTCA
1 AATTCTTAAAATTTTCA
55065079 CAAAATTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (18 bp):
AATTCTTAAAATTTTCAA
Found at i:55066655 original size:95 final size:95
Alignment explanation
Indices: 55066492--55066679 Score: 277
Period size: 95 Copynumber: 2.0 Consensus size: 95
55066482 AAAACTTATT
* * * * * **
55066492 GTATTCCAACATAACAATCGATTCAAAAGGAGAAGAAGTAGTATTCTACCATAATAATTTATTTA
1 GTATTCCAACATAACAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTA
*
55066557 AACATATAAACAATCGATTCAAAAGAAGTA
66 AACATAAAAACAATCGATTCAAAAGAAGTA
* *
55066587 GTATTCTAACATAATAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTA
1 GTATTCCAACATAACAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTA
*
55066652 AACATAAAAACAATTGATTCAAAAGAAG
66 AACATAAAAACAATCGATTCAAAAGAAG
55066680 CAATGCTCCA
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
95 82 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.26
Consensus pattern (95 bp):
GTATTCCAACATAACAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTA
AACATAAAAACAATCGATTCAAAAGAAGTA
Found at i:55066695 original size:95 final size:95
Alignment explanation
Indices: 55066496--55066700 Score: 257
Period size: 95 Copynumber: 2.1 Consensus size: 95
55066486 CTTATTGTAT
* * * * * * **
55066496 TCCAACATAACAATCGATTCAAAAGGAGAAGAAGTAGTATTCTACCATAATAATTTATTTAAACA
1 TCCAACATAATAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTAAACA
* * * *
55066561 TATAAACAATCGATTCAAAAGAAGTAGTAT
66 TAAAAACAATCGATTCAAAAGAAGCAATAC
*
55066591 TCTAACATAATAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTAAACA
1 TCCAACATAATAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTAAACA
* *
55066656 TAAAAACAATTGATTCAAAAGAAGCAATGC
66 TAAAAACAATCGATTCAAAAGAAGCAATAC
*
55066686 TCCATCATAACTAAT
1 TCCAACATAA-TAAT
55066701 TAAAAATATA
Statistics
Matches: 92, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
95 88 0.96
96 4 0.04
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.25
Consensus pattern (95 bp):
TCCAACATAATAATCGATTCAAAAGAAAAAGAAGAAGTATTCCACCATAACAATCAATTTAAACA
TAAAAACAATCGATTCAAAAGAAGCAATAC
Found at i:55071925 original size:20 final size:19
Alignment explanation
Indices: 55071892--55071930 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
55071882 TTGTAGAAAA
55071892 AAAAATATATATATATATT
1 AAAAATATATATATATATT
*
55071911 AAAAATTTATGATATATATT
1 AAAAATATAT-ATATATATT
55071931 TTTTATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (19 bp):
AAAAATATATATATATATT
Found at i:55075923 original size:4 final size:4
Alignment explanation
Indices: 55075914--55075964 Score: 68
Period size: 4 Copynumber: 12.8 Consensus size: 4
55075904 TTTGTTGCCA
* *
55075914 ATGT ATGT ATGT ATGG ATAG- ATGT ATGT ATGT ATCT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
55075962 ATG
1 ATG
55075965 GTTGGATGGA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
3 1 0.02
4 40 0.95
5 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.45
Consensus pattern (4 bp):
ATGT
Found at i:55075939 original size:16 final size:16
Alignment explanation
Indices: 55075918--55075984 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
55075908 TTGCCAATGT
55075918 ATGTATGTATGGATAG
1 ATGTATGTATGGATAG
* **
55075934 ATGTATGTATGTATCT
1 ATGTATGTATGGATAG
* *
55075950 ATGTATGTATGTATGG
1 ATGTATGTATGGATAG
* * *
55075966 TTGGATGGATGGATAG
1 ATGTATGTATGGATAG
55075982 ATG
1 ATG
55075985 GATAGATGTA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.27, C:0.01, G:0.31, T:0.40
Consensus pattern (16 bp):
ATGTATGTATGGATAG
Found at i:55081093 original size:174 final size:171
Alignment explanation
Indices: 55080792--55081167 Score: 474
Period size: 174 Copynumber: 2.2 Consensus size: 171
55080782 TTTTTTTTTT
* *
55080792 TTTTAGAAAGAAATTTTAATTATTAAGCTAGTGCTAATTAGTATAATTCTTGATTAATCCTCTGA
1 TTTTAGAAAGAAATTTTAATTATTAAGCTAGT-CTAATTAGTATAACTCTTGACTAATCCTCTGA
* *
55080857 ATTGTGATTTGCGGATATTGTTTAGCTGTAAAAAGTTTTTGATTGAGTAATGGAAGTAATGCTTA
65 ATTGTAATTTGCGGATATTATTTAGCTGTAAAAAGTTTTTGATTGAGTAATGGAAGTAATGCTTA
* * * *
55080922 ATGAGCTTGTTATGAATTTG-GATTTGTTCACAAAACGGTGAATAAA
130 ATGACCTTATTATGAATTTGAG-TTCGTTCAC--AA--GTGAACAAA
* * * * *
55080968 TTTTAGAAAGGAAGTTTAATT-TTAAGCTAGT-TGATTATTATAACTCTTGACTGATCCTCTGAA
1 TTTTAGAAAGAAATTTTAATTATTAAGCTAGTCTAATTAGTATAACTCTTGACTAATCCTCTG-A
* * *
55081031 ATT-TAATTTGC-GATGTATTATTTAGCTGTAAAATGTTTTTGATTGAGTGATGGAATTAATGCT
65 ATTGTAATTTGCGGA--TATTATTTAGCTGTAAAAAGTTTTTGATTGAGTAATGGAAGTAATGCT
55081094 TAATGACCTTATTATGAATTTGAGTTCGTTCACAAGTGAACAAA
128 TAATGACCTTATTATGAATTTGAGTTCGTTCACAAGTGAACAAA
* *
55081138 TTTTAGAAAGTAATTTTAATTATTACGCTA
1 TTTTAGAAAGAAATTTTAATTATTAAGCTA
55081168 TTAACGATTA
Statistics
Matches: 176, Mismatches: 19, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
170 27 0.15
171 7 0.04
172 4 0.02
173 32 0.18
174 76 0.43
175 11 0.06
176 19 0.11
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (171 bp):
TTTTAGAAAGAAATTTTAATTATTAAGCTAGTCTAATTAGTATAACTCTTGACTAATCCTCTGAA
TTGTAATTTGCGGATATTATTTAGCTGTAAAAAGTTTTTGATTGAGTAATGGAAGTAATGCTTAA
TGACCTTATTATGAATTTGAGTTCGTTCACAAGTGAACAAA
Found at i:55081190 original size:52 final size:52
Alignment explanation
Indices: 55081134--55081236 Score: 134
Period size: 52 Copynumber: 2.0 Consensus size: 52
55081124 CACAAGTGAA
* * * *
55081134 CAAATTTTAGAAAGTAATTTTAATTATTACGCTATTAACGATTAATATAATC
1 CAAATTTTAGAAAGAAATTTCAATTATTAAGCTAGTAACGATTAATATAATC
* * * *
55081186 CAAATTTTGGAAGGAAATTTCAATTGTTAAGCTAGTAATGATTAATATAAT
1 CAAATTTTAGAAAGAAATTTCAATTATTAAGCTAGTAACGATTAATATAAT
55081237 TTTTTATTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.39
Consensus pattern (52 bp):
CAAATTTTAGAAAGAAATTTCAATTATTAAGCTAGTAACGATTAATATAATC
Found at i:55086843 original size:6 final size:6
Alignment explanation
Indices: 55086832--55086877 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
55086822 TTGGTCCTTC
55086832 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATG
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATG
55086878 ATGTTGCATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:55090619 original size:6 final size:6
Alignment explanation
Indices: 55090608--55090647 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
55090598 AATGAATGTA
55090608 CATGGG CATGGG CATGGG CATGGG CATGGG CATGGG CATG
1 CATGGG CATGGG CATGGG CATGGG CATGGG CATGGG CATG
55090648 ACACAAATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.17, G:0.47, T:0.17
Consensus pattern (6 bp):
CATGGG
Found at i:55091214 original size:89 final size:89
Alignment explanation
Indices: 55091063--55091236 Score: 249
Period size: 89 Copynumber: 2.0 Consensus size: 89
55091053 ATTTTACCAA
* * * * * * *
55091063 ACTAATTGTACTAACTAAACAGATGACCAAATTGTACTACATTAAAATATAGGGGTTAAATCTCA
1 ACTAATTGTACTAACCAAACAGAAGACCAAAATATACTAAATGAAAATATAGGAGTTAAATCTCA
*
55091128 AATATAAATAAAATAGAGAATTCT
66 AATATAAACAAAATAGAGAATTCT
* *
55091152 ACTAATTGTACTAACCAAATAGAAGACCAAAATATAGTAAATGAAAATATAGGAGTTAAATCTCA
1 ACTAATTGTACTAACCAAACAGAAGACCAAAATATACTAAATGAAAATATAGGAGTTAAATCTCA
*
55091217 AATATAAACAAAGTAGAGAA
66 AATATAAACAAAATAGAGAA
55091237 ACCAAAATCA
Statistics
Matches: 74, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
89 74 1.00
ACGTcount: A:0.51, C:0.11, G:0.12, T:0.26
Consensus pattern (89 bp):
ACTAATTGTACTAACCAAACAGAAGACCAAAATATACTAAATGAAAATATAGGAGTTAAATCTCA
AATATAAACAAAATAGAGAATTCT
Found at i:55092655 original size:20 final size:20
Alignment explanation
Indices: 55092630--55092667 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
55092620 ACACTTTATG
55092630 AAATAA-AAAATTAAAATTTT
1 AAATAATAAAA-TAAAATTTT
55092650 AAATAATAAAATAAAATT
1 AAATAATAAAATAAAATT
55092668 ATATATTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
AAATAATAAAATAAAATTTT
Found at i:55092733 original size:21 final size:21
Alignment explanation
Indices: 55092682--55092735 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
55092672 ATTTTCACTT
***
55092682 AAAAATAAATTTTCTTTTTGA
1 AAAAATAAATTTTAAATTTGA
55092703 AAATAATAAATTTTAAATTTGA
1 AAA-AATAAATTTTAAATTTGA
55092725 AAAAATAAATT
1 AAAAATAAATT
55092736 AACTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.41
Consensus pattern (21 bp):
AAAAATAAATTTTAAATTTGA
Found at i:55095393 original size:14 final size:14
Alignment explanation
Indices: 55095354--55095393 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
55095344 TTGTTTCACT
*
55095354 AAAATAATTTTCGA
1 AAAATAATTTTTGA
*
55095368 AAAATAATTTTTGG
1 AAAATAATTTTTGA
*
55095382 TAAATAATTTTT
1 AAAATAATTTTT
55095394 TTTTTGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (14 bp):
AAAATAATTTTTGA
Found at i:55100770 original size:19 final size:18
Alignment explanation
Indices: 55100746--55100782 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
55100736 TAATATATTA
55100746 TTTAATATTAGAATTTGAT
1 TTTAATATT-GAATTTGAT
*
55100765 TTTAATATTTAATTTGAT
1 TTTAATATTGAATTTGAT
55100783 ACTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.57
Consensus pattern (18 bp):
TTTAATATTGAATTTGAT
Found at i:55100771 original size:31 final size:31
Alignment explanation
Indices: 55100735--55100799 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
55100725 TATTAATGGG
*
55100735 TTAATATATT-ATTTAATA-TTAGAATTTGATT
1 TTAATAT-TTAATTTAATACTTA-AATTTAATT
*
55100766 TTAATATTTAATTTGATACTTAAATTTAATT
1 TTAATATTTAATTTAATACTTAAATTTAATT
55100797 TTA
1 TTA
55100800 GTGTTCAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 2 0.07
31 25 0.83
32 3 0.10
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (31 bp):
TTAATATTTAATTTAATACTTAAATTTAATT
Found at i:55100778 original size:18 final size:19
Alignment explanation
Indices: 55100744--55100797 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
55100734 GTTAATATAT
*
55100744 TATTTAATATTAGAATTTGA
1 TATTTAATATT-TAATTTGA
55100764 T-TTTAATATTTAATTTGA
1 TATTTAATATTTAATTTGA
*
55100782 TACTTAA-ATTTAATTT
1 TATTTAATATTTAATTT
55100798 TAGTGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 17 0.55
19 13 0.42
20 1 0.03
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
TATTTAATATTTAATTTGA
Found at i:55101248 original size:64 final size:64
Alignment explanation
Indices: 55101147--55101287 Score: 255
Period size: 64 Copynumber: 2.2 Consensus size: 64
55101137 AAATGATTTG
* *
55101147 AACTTGAAATGACCCTAAATCACTCAAACTCAAAATAATCCAAATTCACAATTACTTGAATCTC
1 AACTTGAAATGACCCTAAATCACTCAAACTCAAAATAATCCAAACTCACAATTACTTGAATCAC
*
55101211 AACTTGAAATGACCCTAAATCACTCAAACTCGAAATAATCCAAACTCACAATTACTTGAATCAC
1 AACTTGAAATGACCCTAAATCACTCAAACTCAAAATAATCCAAACTCACAATTACTTGAATCAC
55101275 AACTTGAAATGAC
1 AACTTGAAATGAC
55101288 TCATACTTGA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 74 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (64 bp):
AACTTGAAATGACCCTAAATCACTCAAACTCAAAATAATCCAAACTCACAATTACTTGAATCAC
Found at i:55102808 original size:19 final size:19
Alignment explanation
Indices: 55102781--55102817 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55102771 AATTTAAATA
55102781 TATTCAATTATAATTATAT
1 TATTCAATTATAATTATAT
*
55102800 TATTTAATTATAATTATA
1 TATTCAATTATAATTATA
55102818 CTTAATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTCAATTATAATTATAT
Found at i:55103329 original size:31 final size:31
Alignment explanation
Indices: 55103294--55103353 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
55103284 TTAATATCAG
* *
55103294 AATTTGATTTTAATATTCGATTTGGTACTTA
1 AATTTAATTTTAATATTCAATTTGGTACTTA
* *
55103325 AATTTAATTTTATTGTTCAATTTGGTACT
1 AATTTAATTTTAATATTCAATTTGGTACT
55103354 CAAACCAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.12, T:0.53
Consensus pattern (31 bp):
AATTTAATTTTAATATTCAATTTGGTACTTA
Found at i:55104576 original size:30 final size:30
Alignment explanation
Indices: 55104536--55104608 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
55104526 AGTATATATC
* *
55104536 TTTATAATTTTTAAAAAATTAGA-TCAAAAT
1 TTTATTATTTTTAAAAAATTAAAGT-AAAAT
* *
55104566 TTTATTA-TTTTAAAAGATTAAAGTATAAT
1 TTTATTATTTTTAAAAAATTAAAGTAAAAT
*
55104595 TTTATTATTATTAA
1 TTTATTATTTTTAA
55104609 TTTAAAATTT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 24 0.67
30 12 0.33
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (30 bp):
TTTATTATTTTTAAAAAATTAAAGTAAAAT
Found at i:55110769 original size:45 final size:46
Alignment explanation
Indices: 55110652--55110773 Score: 183
Period size: 47 Copynumber: 2.7 Consensus size: 46
55110642 TTTTTTGAAA
*
55110652 AAAAACTATATAAATTTATTTGTGGTCCTTAATTTTAATTTCTTTT
1 AAAAACCATATAAATTTATTTGTGGTCCTTAATTTTAATTTCTTTT
* * *
55110698 AAAAGAACATATAATTTTTTTTGTGGTCCTTAATTTTAATTT-TTTT
1 AAAA-ACCATATAAATTTATTTGTGGTCCTTAATTTTAATTTCTTTT
*
55110744 GAAAACCATATAAATTTATTTGTGGTCCTT
1 AAAAACCATATAAATTTATTTGTGGTCCTT
55110774 CAAATTATCA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
45 23 0.34
46 11 0.16
47 33 0.49
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (46 bp):
AAAAACCATATAAATTTATTTGTGGTCCTTAATTTTAATTTCTTTT
Found at i:55112549 original size:34 final size:34
Alignment explanation
Indices: 55112506--55112600 Score: 156
Period size: 34 Copynumber: 2.8 Consensus size: 34
55112496 CTAATATTTA
55112506 ATTTTTAGTTCGTGGTCCTTGACTTTTTTTTATC
1 ATTTTTAGTTCGTGGTCCTTGACTTTTTTTTATC
*
55112540 ATTTTTAGTTCGTGGTCCTTTGACTTTTTTTTTTC
1 ATTTTTAGTTCGTGGTCC-TTGACTTTTTTTTATC
*
55112575 A-TTTTAGTTCGTGGTCCTTGAATTTT
1 ATTTTTAGTTCGTGGTCCTTGACTTTT
55112601 GATATCAACC
Statistics
Matches: 58, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
33 8 0.14
34 34 0.59
35 16 0.28
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.59
Consensus pattern (34 bp):
ATTTTTAGTTCGTGGTCCTTGACTTTTTTTTATC
Found at i:55112987 original size:14 final size:15
Alignment explanation
Indices: 55112968--55112996 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
55112958 AAAGCTTTAG
55112968 TTTTGAT-ATTGTAA
1 TTTTGATGATTGTAA
55112982 TTTTGATGATTGTAA
1 TTTTGATGATTGTAA
55112997 ATTACTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (15 bp):
TTTTGATGATTGTAA
Found at i:55115543 original size:314 final size:316
Alignment explanation
Indices: 55114969--55115589 Score: 932
Period size: 314 Copynumber: 2.0 Consensus size: 316
55114959 CCGAACCTCT
55114969 TAACAAGAACAAAGGCTCCATCAATGGTTTTGAGTTTTGAAACCATCCTATCAATACATAAGAAC
1 TAACAAGAACAAAGGCTCCATCAATGGTTTTGAGTTTTGAAACCATCCTATCAATACATAAGAAC
* * * *
55115034 CAATGTAAATGAGGATCCACTGAGCTTTTATTAGATTTGTCATGCACACACTTCATACTAAATAG
66 CAAAGCAAATGAGGATCCAATGAGCTTTTATTAGATTTGTCATGCACACACGTCATACTAAATAG
* * * * ** * * *
55115099 AAATGGAAAGTATTGGAACCAATGTTTTCATGGCATCGGTTTAGAGTTCTCGGCAATGTTGTTCT
131 AAATGGAAAGTATTGGAACCAATGTTTTCATAGAATCGGGTCAGAGTTCTCACCAATGCTGCTCC
* *
55115164 GAGTCTTCATTTTTCTTGAACTATCCGTGTTTGACATAGATCTGAACACAAATACAAGGATGAGT
196 GAGTCTTCATTTTTCTTGAACTATCCATGTCTGACATAGATCTGAACACAAATACAAGGATGAGT
*
55115229 CTCTAAATACATGAACAACAAAACATAC-T-CATATATACTAACACTCGAGGTTCC
261 CTCTAAAGACATGAACAACAAAACATACATCCATATATACTAACACTCGAGGTTCC
55115283 TAACAAGAACACAA-GCTCCATCAATGG-TTTGAGTTCTTGAAACCATCCTATCAATACATAAGA
1 TAACAAGAACA-AAGGCTCCATCAATGGTTTTGAGTT-TTGAAACCATCCTATCAATACATAAGA
55115346 ACCAAAGCAAATGAGGATCCAATGAGCTTTTATTAGATTTGTCATGCA-ACACGTCATACTAAAT
64 ACCAAAGCAAATGAGGATCCAATGAGCTTTTATTAGATTTGTCATGCACACACGTCATACTAAAT
* * * *
55115410 AGAAAT-GTAAGTATTGTAA-GAGATGTTTTCATAGAATCGGGTCAGAGTTCTCACCTATGCTGC
129 AGAAATGGAAAGTATTGGAACCA-ATGTTTTCATAGAATCGGGTCAGAGTTCTCACCAATGCTGC
* *
55115473 TCCGAGTCTTCATTTTTCTTTAACTATCCATGTCTGACATATATCTGAACACAAATACAAGGATA
193 TCCGAGTCTTCATTTTTCTTGAACTATCCATGTCTGACATAGATCTGAACACAAATACAAGG--A
55115538 TGAGTCTCTAAAGACATGAACAACAAAACATACATACCCATATATACTAACA
256 TGAGTCTCTAAAGACATGAACAACAAAACATACAT--CCATATATACTAACA
55115590 ACTGAGCACA
Statistics
Matches: 276, Mismatches: 22, Indels: 14
0.88 0.07 0.04
Matches are distributed among these distances:
311 1 0.00
312 100 0.36
313 29 0.11
314 129 0.47
315 3 0.01
318 14 0.05
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (316 bp):
TAACAAGAACAAAGGCTCCATCAATGGTTTTGAGTTTTGAAACCATCCTATCAATACATAAGAAC
CAAAGCAAATGAGGATCCAATGAGCTTTTATTAGATTTGTCATGCACACACGTCATACTAAATAG
AAATGGAAAGTATTGGAACCAATGTTTTCATAGAATCGGGTCAGAGTTCTCACCAATGCTGCTCC
GAGTCTTCATTTTTCTTGAACTATCCATGTCTGACATAGATCTGAACACAAATACAAGGATGAGT
CTCTAAAGACATGAACAACAAAACATACATCCATATATACTAACACTCGAGGTTCC
Found at i:55133007 original size:29 final size:31
Alignment explanation
Indices: 55132974--55133031 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
55132964 TTTACCAAAT
*
55132974 AAATTTT-T-AATATAAATTCAACACTTATA
1 AAATTTTATCAATAAAAATTCAACACTTATA
*
55133003 AAATTTTATCAATAAAAATTCAATACTTA
1 AAATTTTATCAATAAAAATTCAACACTTA
55133032 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.28
30 1 0.04
31 17 0.68
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATTTTATCAATAAAAATTCAACACTTATA
Found at i:55136103 original size:5 final size:5
Alignment explanation
Indices: 55136093--55136123 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
55136083 AATTTGTGCT
55136093 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
55136124 CTCATGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Found at i:55139929 original size:17 final size:17
Alignment explanation
Indices: 55139907--55139944 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
55139897 TTAGGGACCA
55139907 AAATGAATCCAATTACT
1 AAATGAATCCAATTACT
55139924 AAATGAATCCAATTACT
1 AAATGAATCCAATTACT
55139941 AAAT
1 AAAT
55139945 AAAAGGACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.05, T:0.29
Consensus pattern (17 bp):
AAATGAATCCAATTACT
Found at i:55147184 original size:22 final size:23
Alignment explanation
Indices: 55147126--55147187 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
55147116 CCTGAATAAG
*
55147126 TTATTTTGTTGTTAT-TTTCTTA
1 TTATTTTGTTGTTATATTGCTTA
* ** *
55147148 CTATTTTACTATTATATTGC-TA
1 TTATTTTGTTGTTATATTGCTTA
55147170 TTATTTTGTTGTTATATT
1 TTATTTTGTTGTTATATT
55147188 TTGGATATTA
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.19, C:0.06, G:0.08, T:0.66
Consensus pattern (23 bp):
TTATTTTGTTGTTATATTGCTTA
Found at i:55149228 original size:82 final size:82
Alignment explanation
Indices: 55149060--55149209 Score: 232
Period size: 82 Copynumber: 1.8 Consensus size: 82
55149050 CCTGCTGCAC
* * *
55149060 TAATTATGCTGTACAAAACAAGGAATTTCACCTAATTACCTAACAGTCTAATAGTTTTTTCAATC
1 TAATTATGCTGTACAAAACAAGGAATTTCACCTAATTACCAAACAGTCCAATAGTTTTTTCAACC
*
55149125 TAATGCAATCTCAGAAA
66 TAATGCAATCTCACAAA
*
55149142 TAATTATGCTGTACAAAACAAGGAATTTCACCTAATTACCAAATAGTCCAATCA-TTTTTTC-AC
1 TAATTATGCTGTACAAAACAAGGAATTTCACCTAATTACCAAACAGTCCAAT-AGTTTTTTCAAC
55149205 CTAAT
65 CTAAT
55149210 TATTTACTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
81 6 0.10
82 56 0.89
83 1 0.02
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (82 bp):
TAATTATGCTGTACAAAACAAGGAATTTCACCTAATTACCAAACAGTCCAATAGTTTTTTCAACC
TAATGCAATCTCACAAA
Found at i:55153253 original size:18 final size:19
Alignment explanation
Indices: 55153221--55153267 Score: 64
Period size: 18 Copynumber: 2.6 Consensus size: 19
55153211 TCACTCTCAA
55153221 CAAAA-ATTTAAAAAAA-T
1 CAAAATATTTAAAAAAATT
*
55153238 CAAAATATTTATAAAAATT
1 CAAAATATTTAAAAAAATT
55153257 CAAAAT-TTTAA
1 CAAAATATTTAA
55153268 TTTTTTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.19
18 14 0.54
19 7 0.27
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (19 bp):
CAAAATATTTAAAAAAATT
Found at i:55153259 original size:19 final size:18
Alignment explanation
Indices: 55153221--55153267 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
55153211 TCACTCTCAA
55153221 CAAAA-ATTTAAAAAAAT
1 CAAAATATTTAAAAAAAT
*
55153238 CAAAATATTTATAAAAATT
1 CAAAATATTTA-AAAAAAT
55153257 CAAAAT-TTTAA
1 CAAAATATTTAA
55153268 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
17 6 0.22
18 9 0.33
19 12 0.44
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (18 bp):
CAAAATATTTAAAAAAAT
Found at i:55156563 original size:59 final size:61
Alignment explanation
Indices: 55156454--55156577 Score: 157
Period size: 59 Copynumber: 2.1 Consensus size: 61
55156444 TAATTGTTTA
* * * *
55156454 ATTTATATTAGATATTGTAATTATTTAAGTTTATTTTTTACTTAATTAATATTTAGATACT
1 ATTTATATTAGATATTGAAATTATTTAACTTTATTTTATACTAAATTAATATTTAGATACT
*
55156515 ATTTATATTTA-AGTATTGAAATTATTTAACTTT-TTTTAT-C-AAATTAATATTTAGATGCT
1 ATTTATA-TTAGA-TATTGAAATTATTTAACTTTATTTTATACTAAATTAATATTTAGATACT
55156574 ATTT
1 ATTT
55156578 TGTATTAGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
59 21 0.38
60 1 0.02
61 13 0.23
62 21 0.38
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (61 bp):
ATTTATATTAGATATTGAAATTATTTAACTTTATTTTATACTAAATTAATATTTAGATACT
Found at i:55156997 original size:19 final size:20
Alignment explanation
Indices: 55156955--55157000 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
55156945 TTTAATTTCG
55156955 AAAAATTTAATAATTAAATA
1 AAAAATTTAATAATTAAATA
55156975 AAAAATTTAATAATTAAATA
1 AAAAATTTAATAATTAAATA
55156995 AAAAAT
1 AAAAAT
55157001 CAATAATTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAATTTAATAATTAAATA
Found at i:55164028 original size:186 final size:186
Alignment explanation
Indices: 55163710--55164082 Score: 530
Period size: 186 Copynumber: 2.0 Consensus size: 186
55163700 ATCAACCTAG
* ** * *
55163710 AAGGGATTTCACTCCTTTTCCTTAGTAATCACTACTCAACCTATTGTTAATATCAAAGATTGCTC
1 AAGGGATTTCACTCCTTTTCCTTAGTAATCACAACTCAACCTACAGTTAACATCAAAGATAGCTC
*
55163775 TGACTCTTCGATTTTCATGAAATACATTTGTCCTATACAAATTCAAACACAAATATCTAAAACTT
66 CGACTCTTCGATTTTCATGAAATACATTTGTCCTATACAAATTCAAACACAAATATCTAAAACTT
* * * ***
55163840 AGACCCAAATCCAAGCAATATAGATATCAAGCACAAGATTCATGGCAACTAGGCCA
131 AGACCCAAATACAAGCAACATAGATATCAAACACAAGATTCAAACCAACTAGGCCA
* * *
55163896 AAGGGATTTCACTCCTTTTCCTTAGTAATCACAACTCACCCTACAGTTAGCATCATAGATAGCTC
1 AAGGGATTTCACTCCTTTTCCTTAGTAATCACAACTCAACCTACAGTTAACATCAAAGATAGCTC
* * * * * * *
55163961 CGACTCTTCGGTTTTCATGAAATCCATTTGTCCTATACATATTCGAACACGAGTATCTAACACTT
66 CGACTCTTCGATTTTCATGAAATACATTTGTCCTATACAAATTCAAACACAAATATCTAAAACTT
* *
55164026 AGACCCAAATACAAGCAACATAGATATCAAACACTAGGTTCAAACCAACTAGGCCA
131 AGACCCAAATACAAGCAACATAGATATCAAACACAAGATTCAAACCAACTAGGCCA
55164082 A
1 A
55164083 GCAATCAACC
Statistics
Matches: 163, Mismatches: 24, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
186 163 1.00
ACGTcount: A:0.35, C:0.24, G:0.12, T:0.29
Consensus pattern (186 bp):
AAGGGATTTCACTCCTTTTCCTTAGTAATCACAACTCAACCTACAGTTAACATCAAAGATAGCTC
CGACTCTTCGATTTTCATGAAATACATTTGTCCTATACAAATTCAAACACAAATATCTAAAACTT
AGACCCAAATACAAGCAACATAGATATCAAACACAAGATTCAAACCAACTAGGCCA
Found at i:55170130 original size:12 final size:13
Alignment explanation
Indices: 55170107--55170144 Score: 53
Period size: 12 Copynumber: 3.1 Consensus size: 13
55170097 TATTTATATC
*
55170107 ACTTTCAATTTCA
1 ACTTTCACTTTCA
55170120 AC-TTCACTTTC-
1 ACTTTCACTTTCA
55170131 ACTTTCACTTTCA
1 ACTTTCACTTTCA
55170144 A
1 A
55170145 TTTTGATCAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
11 2 0.09
12 17 0.77
13 3 0.14
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (13 bp):
ACTTTCACTTTCA
Found at i:55172868 original size:9 final size:9
Alignment explanation
Indices: 55172854--55172880 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55172844 CAAGAATATT
55172854 TGATTTAAC
1 TGATTTAAC
55172863 TGATTTAAC
1 TGATTTAAC
55172872 TGATTTAAC
1 TGATTTAAC
55172881 ACTTATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.44
Consensus pattern (9 bp):
TGATTTAAC
Found at i:55182431 original size:31 final size:32
Alignment explanation
Indices: 55182376--55182436 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
55182366 TCATGCTATT
* *
55182376 TTTTTGAATTTTTTATATACTTTTAAAATTAA
1 TTTTTAAATTTTTGATATACTTTTAAAATTAA
* *
55182408 TTTTTAAATTTTTGA-ATATTTTTATAATT
1 TTTTTAAATTTTTGATATACTTTTAAAATT
55182437 TGTAAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (32 bp):
TTTTTAAATTTTTGATATACTTTTAAAATTAA
Found at i:55183568 original size:27 final size:27
Alignment explanation
Indices: 55183526--55183595 Score: 88
Period size: 27 Copynumber: 2.6 Consensus size: 27
55183516 AAATAAATAT
55183526 AAAAAATT-ACTCGAATTACCCGAATTA
1 AAAAAATTAACT-GAATTACCCGAATTA
* * *
55183553 ATAGAATTAACTGAATTGCCCGAATTA
1 AAAAAATTAACTGAATTACCCGAATTA
*
55183580 AAAAAATTAACCGAAT
1 AAAAAATTAACTGAAT
55183596 GAAAGTATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
27 33 0.92
28 3 0.08
ACGTcount: A:0.49, C:0.16, G:0.10, T:0.26
Consensus pattern (27 bp):
AAAAAATTAACTGAATTACCCGAATTA
Found at i:55203275 original size:74 final size:74
Alignment explanation
Indices: 55203196--55203344 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
55203186 TTGATTTTTT
55203196 TTAAAAAAATTATTTTTTAGAATTTTTTAAATTATTTATTGGTGTAACGTATAAGACAAACAATG
1 TTAAAAAAATTATTTTTTAGAATTTTTTAAATTATTTATTGGTGTAACGTATAAGACAAACAATG
55203261 TAATGTTAA
66 TAATGTTAA
55203270 TTAAAAAAATTATTTTTTAGAATTTTTTAAATTATTTATTGGTGTAACGTATAAGACAAACAATG
1 TTAAAAAAATTATTTTTTAGAATTTTTTAAATTATTTATTGGTGTAACGTATAAGACAAACAATG
*
55203335 TCATGTTAA
66 TAATGTTAA
55203344 T
1 T
55203345 ATGAAAATAC
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.44
Consensus pattern (74 bp):
TTAAAAAAATTATTTTTTAGAATTTTTTAAATTATTTATTGGTGTAACGTATAAGACAAACAATG
TAATGTTAA
Found at i:55203770 original size:46 final size:46
Alignment explanation
Indices: 55203703--55203794 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
55203693 CAGGTTACAT
55203703 TCCGAGATATTTCCACTATTCGATTGTTCATAATCCTATAATTCTA
1 TCCGAGATATTTCCACTATTCGATTGTTCATAATCCTATAATTCTA
55203749 TCCGAGATATTTCCACTATTCGATTGTTCATAATCCTATAATTCTA
1 TCCGAGATATTTCCACTATTCGATTGTTCATAATCCTATAATTCTA
55203795 AGAATTATTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (46 bp):
TCCGAGATATTTCCACTATTCGATTGTTCATAATCCTATAATTCTA
Found at i:55204675 original size:23 final size:24
Alignment explanation
Indices: 55204631--55204675 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
55204621 ATTGAAACCA
*
55204631 TTAATTGACACATAAAATTTTATG
1 TTAATTGACACATAAAACTTTATG
55204655 TTAATTGA-A-ATGAAAACTTTA
1 TTAATTGACACAT-AAAACTTTA
55204676 AAGAAAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 2 0.11
23 9 0.47
24 8 0.42
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (24 bp):
TTAATTGACACATAAAACTTTATG
Found at i:55211179 original size:16 final size:17
Alignment explanation
Indices: 55211158--55211198 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
55211148 GTTAGAGTGT
*
55211158 AATTTTATTAATT-TAA
1 AATTTTATCAATTATAA
55211174 AATTTTATCAATTATAA
1 AATTTTATCAATTATAA
55211191 AATATTTA
1 AAT-TTTA
55211199 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 12 0.55
17 6 0.27
18 4 0.18
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTTATCAATTATAA
Found at i:55217451 original size:21 final size:19
Alignment explanation
Indices: 55217425--55217474 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 19
55217415 ATATTAATCT
55217425 TAATATTTTTTATGATTATA
1 TAATATTTTTTATGATT-TA
* * *
55217445 TATATATATATTATGATTTT
1 TA-ATATTTTTTATGATTTA
55217465 TAATATTTTT
1 TAATATTTTT
55217475 ATAAGAAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 6 0.25
20 5 0.21
21 13 0.54
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (19 bp):
TAATATTTTTTATGATTTA
Found at i:55218903 original size:51 final size:54
Alignment explanation
Indices: 55218838--55218950 Score: 153
Period size: 55 Copynumber: 2.1 Consensus size: 54
55218828 TCACTAACAG
** *
55218838 TCATCCAACTATTAAT-A-TTTTT-TTA-TCAGACTATAAAAAACTACAAAATGA
1 TCATCCAAAAATTAATAATTTTTTGTTACTCA-ACTATAAAAAACTACAAAATAA
55218889 TCATCCAAAAATTAATAATTTTTTTGTTACTCAACTATAAAAAACTACAAAATAA
1 TCATCCAAAAATTAATAA-TTTTTTGTTACTCAACTATAAAAAACTACAAAATAA
55218944 TCATCCA
1 TCATCCA
55218951 GTTATTCAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
51 14 0.26
52 1 0.02
54 5 0.09
55 31 0.57
56 3 0.06
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.35
Consensus pattern (54 bp):
TCATCCAAAAATTAATAATTTTTTGTTACTCAACTATAAAAAACTACAAAATAA
Found at i:55220947 original size:166 final size:169
Alignment explanation
Indices: 55220666--55221085 Score: 632
Period size: 166 Copynumber: 2.5 Consensus size: 169
55220656 TATGGACCAA
55220666 AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
1 AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
*
55220731 TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCGAGACGTCTTCAATGG-T-TCTAACA
66 TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCGAGACGTCTTCAAGGGTTCTCTAACA
55220794 GCAGCTATTGTGAACTTAC-AAATTTCTCCATAAACACT
131 GCAGCTATTGTGAACTTACAAAATTTCTCCATAAACACT
** * *
55220832 AGTTAATTAGAACGAGGAATAAGACCACAAAACAAAGCAAGCACAACATACAAACATGATACAAG
1 AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
* * * * *
55220897 TTTGTTTTGCTAAAATCGAGTGCAACCGCCAATGTTTTTGAGATGTCTTCAAGGGTTCTCTAACA
66 TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCGAGACGTCTTCAAGGGTTCTCTAACA
*
55220962 GCAGCTATTGTGAACTTACAAAATTTCTCCATAAGCACT
131 GCAGCTATTGTGAACTTACAAAATTTCTCCATAAACACT
* * *
55221001 AGATAATTAGAATGAGGAA-AAGGACCATGAAACAAAGGTTGCAAACACAACATACAATCATGAC
1 AGTTAATTAGAACGAGGAATAA-GACCATGAAACAAA----GCAAACACAACATACAAACATGAC
*
55221065 ACAAGTTTGTTTAGCTAAAAT
61 ACAAGTTTGTTTTGCTAAAAT
55221086 TGCATATAAC
Statistics
Matches: 227, Mismatches: 19, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
166 110 0.48
167 1 0.00
168 28 0.12
169 47 0.21
173 41 0.18
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.25
Consensus pattern (169 bp):
AGTTAATTAGAACGAGGAATAAGACCATGAAACAAAGCAAACACAACATACAAACATGACACAAG
TTTGTTTTGCTAAAATCAAATGCAACAGCCAATGTTTTCGAGACGTCTTCAAGGGTTCTCTAACA
GCAGCTATTGTGAACTTACAAAATTTCTCCATAAACACT
Found at i:55244636 original size:189 final size:190
Alignment explanation
Indices: 55244000--55244690 Score: 809
Period size: 192 Copynumber: 3.6 Consensus size: 190
55243990 TATACTGGCA
* * ** * *
55244000 TAACACTCTCTAGAAAAGAATGTTCAGAACCTAGAAACTGATGTCTTTAGGAGTAGC-AGTGTGA
1 TAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAACCGATGTCTTTACGAGTAGCTA-TGTGA
* ** ** * * * * * * *
55244064 ACTCATGACTTGTATACTTTTGTAATGAAATGTTTTTGCTGTCTAGAGCATCCTTTTGATCGAAA
65 ATTTGTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCCTTTTGATTGAAG
* * * * *
55244129 CCATATTCATGTTCAGCTGCCTATTATGAACTTGAATGAATGAAGCACATTGCTATACGGACG
130 CCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAG-ACA-TGTTGTACCGACG
** * * **
55244192 TTGCACCCTCTAGAAAAGAATGTTTA-AAACCGAGAAACCGATGTCTTTACGAGCAGAGATGTGA
1 TAACACCCTCTAGAAAAGAATGTTTAGAACCCG-GAAACCGATGTCTTTACGAGTAGCTATGTGA
* * * * * * * *
55244256 ATCTGCGACTTATATGCATTTATAATGAAAAGTTTTCGATGTCTAGGGCACTCGTTTTGGTTGAA
65 ATTTGTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCAC-CCTTTTGATTGAA
* *
55244321 GCCATATTCATGTTCTACTGCATATTATGAACTTGAATGAATGAA-ACATGTTGTATATC-AGCG
129 GCCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAGACATGTTG--TACCGA-CG
* *
55244384 TAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAAACGATGTCTTTACGAGTAGGTATGTGAA
1 TAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAACCGATGTCTTTACGAGTAGCTATGTGAA
* * *
55244449 TTTGTGACGCATATGCTTTTATAATGAAATGTTTTC-AGTGTCTAAAGCACCCTTTTGATTGCAG
66 TTTGTGACTCATATGCTTTTATAATGAAATGTTTTCGA-TGTCTAGAGCACCCTTTTGATTGAAG
* *
55244513 CTATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAGA-ATGTTGTGCCGACG
130 CCATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAGACATGTTGTACCGACG
* * *
55244573 CAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAACCAATGTCTTTATGAGTAGCTATGTGAA
1 TAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAACCGATGTCTTTACGAGTAGCTATGTGAA
*
55244638 TTTGTGACTCATATGCTTTTATACTGAAATGTTTTCGATGTCTAGAGCACCCT
66 TTTGTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCCT
55244691 GCTTTATATT
Statistics
Matches: 422, Mismatches: 66, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
189 112 0.27
190 5 0.01
191 67 0.16
192 181 0.43
193 57 0.14
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (190 bp):
TAACACCCTCTAGAAAAGAATGTTTAGAACCCGGAAACCGATGTCTTTACGAGTAGCTATGTGAA
TTTGTGACTCATATGCTTTTATAATGAAATGTTTTCGATGTCTAGAGCACCCTTTTGATTGAAGC
CATATTCATGTTCTGCTGCATATTATGAACTTGAATGAATGAAGACATGTTGTACCGACG
Found at i:55247870 original size:55 final size:55
Alignment explanation
Indices: 55247798--55247909 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 55
55247788 GTCCCTCCTA
* *
55247798 AAAAAATTTAAGCAATTTAATTTCTGTCAATTTCGAAAGTGAACAAACTAAGGAT
1 AAAAAATTTAAGCAATTTAATCTCTATCAATTTCGAAAGTGAACAAACTAAGGAT
* * * *
55247853 AAAAATTTTGAGCAATTTAATCTCTATCAATTTTGAAAGTGAGCAAACTAAGGAT
1 AAAAAATTTAAGCAATTTAATCTCTATCAATTTCGAAAGTGAACAAACTAAGGAT
55247908 AA
1 AA
55247910 TGAATCATGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (55 bp):
AAAAAATTTAAGCAATTTAATCTCTATCAATTTCGAAAGTGAACAAACTAAGGAT
Found at i:55251536 original size:121 final size:121
Alignment explanation
Indices: 55251322--55251566 Score: 447
Period size: 121 Copynumber: 2.0 Consensus size: 121
55251312 TTATGATTTG
*
55251322 TATGTCATGGAAATTATTTTTTAAAATTATTAAATATTTGTTTTAGGATTCAAAATTTAGGGTTT
1 TATGTCATGGAAATTATTTTTTAAAATTATTAAATATTTATTTTAGGATTCAAAATTTAGGGTTT
55251387 GATCAAAAATTATAAATTTGAAAGGAAATAATTGTAATTTGATTTG-ATCATATATA
66 GATCAAAAATTATAAATTTGAAAGGAAATAATTGTAATTTGATTTGAAT-ATATATA
*
55251443 TATGTCATGGAAATTATTTTTTAAAATTATTAAATATTTATTTTAGGATTCAAAATTTATGGTTT
1 TATGTCATGGAAATTATTTTTTAAAATTATTAAATATTTATTTTAGGATTCAAAATTTAGGGTTT
*
55251508 GATCAAAAATTATAATTTTGAAAGGAAATAATTGTAATTTGATTTGAATATATATA
66 GATCAAAAATTATAAATTTGAAAGGAAATAATTGTAATTTGATTTGAATATATATA
55251564 TAT
1 TAT
55251567 ATCAAATTAT
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
121 118 0.98
122 2 0.02
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (121 bp):
TATGTCATGGAAATTATTTTTTAAAATTATTAAATATTTATTTTAGGATTCAAAATTTAGGGTTT
GATCAAAAATTATAAATTTGAAAGGAAATAATTGTAATTTGATTTGAATATATATA
Found at i:55251840 original size:22 final size:23
Alignment explanation
Indices: 55251807--55251855 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
55251797 TTCTTCTATC
*
55251807 TAAAATTGATAACATAATTAATT
1 TAAAATTGATAAAATAATTAATT
**
55251830 TAAAA-TGATAAAATTTTTAATT
1 TAAAATTGATAAAATAATTAATT
55251852 TAAA
1 TAAA
55251856 TTTTTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
TAAAATTGATAAAATAATTAATT
Found at i:55251922 original size:84 final size:83
Alignment explanation
Indices: 55251829--55251990 Score: 200
Period size: 84 Copynumber: 1.9 Consensus size: 83
55251819 CATAATTAAT
* * * * *
55251829 TTAAAATGATAAAATTTTTAATTTAAATTTTTTTATAATTTATAAAAATTTAAATTA-ATAATAA
1 TTAAAATGATAAAA-ATTTAATTTAAA-TCTTTTAAAATTTATAAAAATATAAATTATAAAATAA
*
55251893 TAAAATTGTATTTTAGTGTG
64 TAAAATTATATTTTAGTGTG
* * **
55251913 TTAAAATGATAAAAATTTGATTTTAATCTTTTAAAATTTATAAAGGTATAAATTATTAAAATAAT
1 TTAAAATGATAAAAATTTAATTTAAATCTTTTAAAATTTATAAAAATATAAATTA-TAAAATAAT
55251978 AAAATTATATTTT
65 AAAATTATATTTT
55251991 TATTATCATA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 24 0.36
83 9 0.14
84 33 0.50
ACGTcount: A:0.47, C:0.01, G:0.06, T:0.47
Consensus pattern (83 bp):
TTAAAATGATAAAAATTTAATTTAAATCTTTTAAAATTTATAAAAATATAAATTATAAAATAATA
AAATTATATTTTAGTGTG
Found at i:55252810 original size:31 final size:31
Alignment explanation
Indices: 55252775--55252843 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
55252765 AAAAAAAAAC
55252775 TCAATGACTTAGA-TAAAAATTTTCGAATAGT
1 TCAATGACTTA-ATTAAAAATTTTCGAATAGT
* *
55252806 TCAATGACTTAATTGAAAATTTTTGAATAGT
1 TCAATGACTTAATTAAAAATTTTCGAATAGT
*
55252837 TTAATGA
1 TCAATGA
55252844 TAATTTTGTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (31 bp):
TCAATGACTTAATTAAAAATTTTCGAATAGT
Found at i:55259891 original size:9 final size:9
Alignment explanation
Indices: 55259877--55259947 Score: 50
Period size: 9 Copynumber: 8.6 Consensus size: 9
55259867 GCAAATGATT
55259877 TTAAAATTA
1 TTAAAATTA
55259886 TTAAAATTA
1 TTAAAATTA
55259895 TT----TT-
1 TTAAAATTA
55259899 TTAAAA-TA
1 TTAAAATTA
55259907 -TAAAATTA
1 TTAAAATTA
55259915 TTAAAATTA
1 TTAAAATTA
*
55259924 TTTTTAAA-TA
1 --TTAAAATTA
*
55259934 ATAAAATTA
1 TTAAAATTA
55259943 TTAAA
1 TTAAA
55259948 TAATTTTAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 20
0.67 0.06 0.28
Matches are distributed among these distances:
4 2 0.04
5 2 0.04
7 6 0.12
8 6 0.12
9 25 0.52
10 2 0.04
11 5 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:55259897 original size:20 final size:20
Alignment explanation
Indices: 55259869--55259925 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
55259859 CCACTTTAGC
*
55259869 AAATGATTTTAAAATTATTA
1 AAATTATTTTAAAATTATTA
55259889 AAATTATTTTTTAAAA-TA-TA
1 AAATTA--TTTTAAAATTATTA
55259909 AAATTA--TTAAAATTATT
1 AAATTATTTTAAAATTATT
55259926 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 1 0.03
20 13 0.41
21 2 0.06
22 8 0.25
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AAATTATTTTAAAATTATTA
Found at i:55259937 original size:28 final size:29
Alignment explanation
Indices: 55259878--55259947 Score: 117
Period size: 28 Copynumber: 2.4 Consensus size: 29
55259868 CAAATGATTT
55259878 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
55259907 TAAAATTATTAAAATTA-TTTTT-AAATAA
1 TAAAATTATTAAAATTATTTTTTAAAAT-A
55259935 TAAAATTATTAAA
1 TAAAATTATTAAA
55259948 TAATTTTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
27 4 0.10
28 19 0.47
29 17 0.43
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:55273071 original size:31 final size:31
Alignment explanation
Indices: 55273004--55273195 Score: 135
Period size: 31 Copynumber: 6.3 Consensus size: 31
55272994 AAAATCGAAT
* * *
55273004 TTTTAAAAA-TTTAA-AGACTTATTTAGAAT
1 TTTTAAAAATTTTAAGAGACTTAATTAAAAC
*
55273033 TTTTAAAAATTTTAAGAGACATAATTAAAAC
1 TTTTAAAAATTTTAAGAGACTTAATTAAAAC
* * * * *
55273064 TTTTAAAAATTTTAAAAGGCATGA-TAAAAGA
1 TTTTAAAAATTTTAAGAGACTTAATTAAAA-C
* * * * *
55273095 TTTTCAAAATTTTGAGAGA-TCCAATTACAAT
1 TTTTAAAAATTTTAAGAGACT-TAATTAAAAC
* * * *
55273126 TTTTGAAACTTTTGAA-AGACTTAACTAATAC
1 TTTTAAAAATTTT-AAGAGACTTAATTAAAAC
* *
55273157 TTTTAGAAATTTTAAGAGGCTTAATTAAAA-
1 TTTTAAAAATTTTAAGAGACTTAATTAAAAC
55273187 TTTTAAAAA
1 TTTTAAAAA
55273196 GTTTCAAAGG
Statistics
Matches: 123, Mismatches: 32, Indels: 15
0.72 0.19 0.09
Matches are distributed among these distances:
29 9 0.07
30 20 0.16
31 88 0.72
32 6 0.05
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (31 bp):
TTTTAAAAATTTTAAGAGACTTAATTAAAAC
Found at i:55278989 original size:158 final size:158
Alignment explanation
Indices: 55278700--55279015 Score: 404
Period size: 158 Copynumber: 2.0 Consensus size: 158
55278690 TATCATATAG
* * * * *
55278700 TGCTCACACGAGTTGTGGAATGGATCTGCTCACACGAGCTGTGGGTTGAGATAAAAAGCTACACG
1 TGCTCACACGAGCTATGGAATGGATCTGCTCACACGAGCTATGAGTCGAGATAAAAAGCTACACG
* * * * * *
55278765 ATGCTGCTCACAAGAGTTGTGGAGAATCCGCAACATATGTCGGATCTCAGCCATTTGTAGGTCAT
66 ATGCTGCTCACAAGAGCTGTGAAAAATCCACAACATATGTCGGATCTCAGCCATTGGTAGGACAT
* * *
55278830 CTAATA-TCAGCACCCTTATAACATGTAA
131 CTAAGACT-AACACCCATATAACATGTAA
* * *
55278858 TGCTCACACGAGCTATGTAATGGGTCTGCTCACACGAGCTATGAGTCGAGATGATAAA-CTACAC
1 TGCTCACACGAGCTATGGAATGGATCTGCTCACACGAGCTATGAGTCGAGAT-AAAAAGCTACAC
* * *
55278922 GATGCTGCTCATACA-AGCTGTGAAAAATTCACAACATATGTTGGATCTCAGCCATTGGTAGGAC
65 GATGCTGCTCACA-AGAGCTGTGAAAAATCCACAACATATGTCGGATCTCAGCCATTGGTAGGAC
55278986 ATCTAAGACTAACACCCATATAACATGTAA
129 ATCTAAGACTAACACCCATATAACATGTAA
55279016 ATCCCAAAAC
Statistics
Matches: 135, Mismatches: 20, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
158 129 0.96
159 6 0.04
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (158 bp):
TGCTCACACGAGCTATGGAATGGATCTGCTCACACGAGCTATGAGTCGAGATAAAAAGCTACACG
ATGCTGCTCACAAGAGCTGTGAAAAATCCACAACATATGTCGGATCTCAGCCATTGGTAGGACAT
CTAAGACTAACACCCATATAACATGTAA
Found at i:55282470 original size:4 final size:4
Alignment explanation
Indices: 55282456--55282487 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
55282446 AACTGTTAAT
55282456 ATAA TATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATA
55282488 TTCATGGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAA
Found at i:55284512 original size:28 final size:28
Alignment explanation
Indices: 55284472--55284529 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
55284462 AAAGATTCGG
55284472 AATTTCATCCCTATATTTAATTTGATTT
1 AATTTCATCCCTATATTTAATTTGATTT
*
55284500 AATTTGATCCCTATATTTAATTTGATTT
1 AATTTCATCCCTATATTTAATTTGATTT
55284528 AA
1 AA
55284530 ATTACTGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.52
Consensus pattern (28 bp):
AATTTCATCCCTATATTTAATTTGATTT
Found at i:55289823 original size:21 final size:21
Alignment explanation
Indices: 55289783--55289832 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
55289773 CATTAAATTG
* *
55289783 AAAAAATAACTCTTAGTATA-
1 AAAAAATAAATCTAAGTATAT
*
55289803 AAGAAAATAAATCTAATTATAT
1 AA-AAAATAAATCTAAGTATAT
55289825 AAAAAATA
1 AAAAAATA
55289833 TTAACTCGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAAATAAATCTAAGTATAT
Found at i:55294018 original size:18 final size:19
Alignment explanation
Indices: 55293981--55294018 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
55293971 TTGTAAAATA
**
55293981 TTTATTATATTATATTATT
1 TTTATTATATTATACAATT
55294000 TTTA-TATATTATACAATT
1 TTTATTATATTATACAATT
55294018 T
1 T
55294019 GTAACACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTATTATATTATACAATT
Found at i:55298436 original size:31 final size:32
Alignment explanation
Indices: 55298400--55298460 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
55298390 TTAGACTAAA
55298400 TTTGAGTATAAAAAATTTGA-TTTGAGATTGT
1 TTTGAGTATAAAAAATTTGAGTTTGAGATTGT
* **
55298431 TTTGAGTTTAAATCATTTGAGTTTGAGATT
1 TTTGAGTATAAAAAATTTGAGTTTGAGATT
55298461 TGAGTTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 17 0.65
32 9 0.35
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (32 bp):
TTTGAGTATAAAAAATTTGAGTTTGAGATTGT
Found at i:55298737 original size:29 final size:29
Alignment explanation
Indices: 55298705--55298781 Score: 77
Period size: 29 Copynumber: 2.6 Consensus size: 29
55298695 TTAAAAAAAC
*
55298705 TTAAACCTCCAAAATTTT-AGATATTTTAA
1 TTAAACCTCCAAAATTTTGA-AAATTTTAA
*
55298734 TTAAACC-CTCAGAATTTTGAAAATTTTAA
1 TTAAACCTC-CAAAATTTTGAAAATTTTAA
*
55298763 TTACAACTTCCCAAAATTT
1 TTA-AACCT-CCAAAATTT
55298782 AACGGCATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
28 1 0.03
29 26 0.67
30 4 0.10
31 7 0.18
32 1 0.03
ACGTcount: A:0.40, C:0.17, G:0.04, T:0.39
Consensus pattern (29 bp):
TTAAACCTCCAAAATTTTGAAAATTTTAA
Found at i:55299118 original size:4 final size:4
Alignment explanation
Indices: 55299109--55299178 Score: 81
Period size: 4 Copynumber: 18.0 Consensus size: 4
55299099 ATATAATGTA
* * *
55299109 TATG TATG TATG TATG TATG TATG TAGG TATG CATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
55299157 -A-G TGTG TATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG
55299179 AGTGTGTATG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 1 0.02
3 1 0.02
4 54 0.96
ACGTcount: A:0.24, C:0.04, G:0.29, T:0.43
Consensus pattern (4 bp):
TATG
Found at i:55299170 original size:22 final size:22
Alignment explanation
Indices: 55299115--55299193 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
55299105 TGTATATGTA
* *
55299115 TGTATGTATGTATGTATGTAGGTA
1 TGTATGCATGTATGTATG-A-GTG
*
55299139 TGCATGCATGTATGTATGAGTG
1 TGTATGCATGTATGTATGAGTG
55299161 TGTATGCATGTATGTATGAGTG
1 TGTATGCATGTATGTATGAGTG
55299183 TGTATGCATGT
1 TGTATGCATGT
55299194 GTGGAACTTC
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 34 0.67
23 1 0.02
24 16 0.31
ACGTcount: A:0.23, C:0.05, G:0.30, T:0.42
Consensus pattern (22 bp):
TGTATGCATGTATGTATGAGTG
Found at i:55299196 original size:12 final size:12
Alignment explanation
Indices: 55299110--55299193 Score: 86
Period size: 12 Copynumber: 7.3 Consensus size: 12
55299100 TATAATGTAT
*
55299110 ATGTATGTATGT
1 ATGTATGTATGC
*
55299122 ATGTATGTATGT
1 ATGTATGTATGC
* *
55299134 AGGTATGCATGC
1 ATGTATGTATGC
55299146 ATGTATGTATG-
1 ATGTATGTATGC
*
55299157 A-GTGTGTATGC
1 ATGTATGTATGC
55299168 ATGTATGTATG-
1 ATGTATGTATGC
*
55299179 A-GTGTGTATGC
1 ATGTATGTATGC
55299190 ATGT
1 ATGT
55299194 GTGGAACTTC
Statistics
Matches: 60, Mismatches: 8, Indels: 8
0.79 0.11 0.11
Matches are distributed among these distances:
10 16 0.27
11 4 0.07
12 40 0.67
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.42
Consensus pattern (12 bp):
ATGTATGTATGC
Found at i:55299705 original size:32 final size:32
Alignment explanation
Indices: 55299669--55299752 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
55299659 CTTGTCAAAA
55299669 CTTTTGAAAATTCTCATTAAACCCTC-AATTTT
1 CTTTTGAAAATT-TCATTAAACCCTCAAATTTT
* *
55299701 CTTTTGAAAATTTTAATTAAATCTCTCAAATTTT
1 CTTTTGAAAA-TTTCATTAAA-CCCTCAAATTTT
55299735 C--TTG-AAATTTCATTAAAC
1 CTTTTGAAAATTTCATTAAAC
55299753 TCTTAGAATT
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
29 1 0.02
30 9 0.20
31 3 0.07
32 20 0.43
33 6 0.13
34 7 0.15
ACGTcount: A:0.35, C:0.17, G:0.04, T:0.45
Consensus pattern (32 bp):
CTTTTGAAAATTTCATTAAACCCTCAAATTTT
Found at i:55303412 original size:2 final size:2
Alignment explanation
Indices: 55303405--55303443 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
55303395 TATAATTGCT
55303405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55303444 GTAAATAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:55306687 original size:222 final size:222
Alignment explanation
Indices: 55306268--55307336 Score: 1479
Period size: 222 Copynumber: 4.8 Consensus size: 222
55306258 ATATATCGCA
* *
55306268 TATGGTACTTTCGTTGCTCTAGC-TCGTGTGAAAGAAAAGACTCGTTTAGTCCTTAGAATCGATT
1 TATGGTACTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
* **
55306332 TTATGCATTGAGGTTCTGAGAGTCAAATGCTGCTTCCATCCATTGTCGATATGCCGGTTATTTTT
66 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCTGTTGTCGATATGCCGGTTATTTTT
* * *
55306397 GTGTGAATCTTGTGGCGTCTGATATTAGTTCTTAACAAGATGTTGCGTTTGCTCACTCATCGTTA
131 GTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTA
*
55306462 AACCGAACCTTCATCGTACTTATTGTG
196 AACCGAACCTTCATCGTACTTATCGTG
* * *
55306489 TATGGTTCTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGATTTGTTTAGTCCTTAGAATCGATT
1 TATGGTACTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
* * * *
55306554 TTGTGCATCGAGGTTCTGTGAGTCAAATGCTGCTTCCATCTGTTGTCAATATGCCAGTTATTTTT
66 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCTGTTGTCGATATGCCGGTTATTTTT
* * ** *
55306619 GTGTGAATCTTGTTGTGTCTGATGTTAGTTCTTAACAAGATGTCATGTTTGCTCCCTCATCATTA
131 GTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTA
*
55306684 AACCGAACCTTCATCGTACTTATTGTG
196 AACCGAACCTTCATCGTACTTATCGTG
** *
55306711 TATCATACTTTCGTTTCTCTAGCGTCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
1 TATGGTACTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
*
55306776 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCAATCCT-TTGTC-AGTATGCCGGTTATTT
66 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCAT-CTGTTGTCGA-TATGCCGGTTATTT
55306839 TTGTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGT
129 TTGTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGT
* *
55306904 TAAACCAAACCTTCATCGTACTTATCGTA
194 TAAACCGAACCTTCATCGTACTTATCGTG
* * * * * * * * *
55306933 TATGATACTTTCATTTTTATAGCATCATATGAAAGCAAGGACTCATTTAGTCCTTACAATCGATT
1 TATGGTACTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
* * * * *
55306998 TTATGCATCGAGGTTCTAAGAGTCAAATGCTGCTTCCATCCGTTGTTGATATGCTGCTTATTTTT
66 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCTGTTGTCGATATGCCGGTTATTTTT
*
55307063 GTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTCGCTCCCTCATCGTTA
131 GTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTA
*
55307128 AACCGAACCTTCATTGTACTTATCGTG
196 AACCGAACCTTCATCGTACTTATCGTG
** *
55307155 TATGGTACTTTCGTTTCTCTAGTGTCGTGTGAAAGCAAAGACTCGTTTAGTCCTT----TCGGTT
1 TATGGTACTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
* * * * * * *
55307216 TTATGCATCAAGGTTCTGAGGGTCAAATGTTGC-TCCTATCTGTTGTTGATATTCTGGTGTTTTT
66 TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCC-ATCTGTTGTCGATATGC-CG-GTTATT
* ** * * * *
55307280 TTGTGTGTGAATATTGTTATGTCCGATTTTAGTTCTTAACAAGATATCGTGTTTGCT
128 TT-TGTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCT
55307337 GTTCTCGAAA
Statistics
Matches: 753, Mismatches: 86, Indels: 18
0.88 0.10 0.02
Matches are distributed among these distances:
217 3 0.00
218 49 0.07
219 1 0.00
220 6 0.01
221 69 0.09
222 622 0.83
223 3 0.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.40
Consensus pattern (222 bp):
TATGGTACTTTCGTTTCTCTAGCATCGTGTGAAAGCAAAGACTCGTTTAGTCCTTAGAATCGATT
TTATGCATCGAGGTTCTGAGAGTCAAATGCTGCTTCCATCTGTTGTCGATATGCCGGTTATTTTT
GTGTGAATCTTGTTGCGTCTGATATTAGTTCTTAACAAGATGTTGTGTTTGCTCCCTCATCGTTA
AACCGAACCTTCATCGTACTTATCGTG
Found at i:55308579 original size:12 final size:12
Alignment explanation
Indices: 55308562--55308586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55308552 GTCAATTTAA
55308562 AATATGAATTGG
1 AATATGAATTGG
55308574 AATATGAATTGG
1 AATATGAATTGG
55308586 A
1 A
55308587 CTTAGTGCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (12 bp):
AATATGAATTGG
Found at i:55308757 original size:17 final size:17
Alignment explanation
Indices: 55308737--55308769 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
55308727 AATATTACTT
*
55308737 TAATGTAAGCATTAAAA
1 TAATGTAAACATTAAAA
55308754 TAATGTAAACATTAAA
1 TAATGTAAACATTAAA
55308770 TATTAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.09, T:0.30
Consensus pattern (17 bp):
TAATGTAAACATTAAAA
Done.