Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 156 of 198
Found at i:49351149 original size:18 final size:17
Alignment explanation
Indices: 49351126--49351192 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
49351116 TTAAAATTTA
49351126 TAAAAATATTCAAAAAAT
1 TAAAAATATT-AAAAAAT
*
49351144 TAAAAAT-TAAAAAAAAT
1 TAAAAATAT-TAAAAAAT
49351161 CT-AAAA-ATTAAAAAA-
1 -TAAAAATATTAAAAAAT
*
49351176 TAAAAA-ATAAAAAAAT
1 TAAAAATATTAAAAAAT
49351192 T
1 T
49351193 CATGAAAGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 1 0.02
15 12 0.29
16 7 0.17
17 13 0.32
18 8 0.20
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
TAAAAATATTAAAAAAT
Found at i:49353453 original size:16 final size:18
Alignment explanation
Indices: 49353422--49353454 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
49353412 TTATTTTAAA
49353422 ATATATATTTACATATAC
1 ATATATATTTACATATAC
49353440 ATATA-ATTTA-ATATA
1 ATATATATTTACATATA
49353455 ATTAATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (18 bp):
ATATATATTTACATATAC
Found at i:49358989 original size:38 final size:38
Alignment explanation
Indices: 49358938--49359015 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
49358928 TGGCTACTTT
*
49358938 AATTAGTAATTAAAGGTTTTATCTTTT-TCATGAATATG
1 AATTAGTAATTAAAGATTTTAT-TTTTATCATGAATATG
* *
49358976 AATTAGTAATTAAATATTTTATTTTTATTATGAATATG
1 AATTAGTAATTAAAGATTTTATTTTTATCATGAATATG
49359014 AA
1 AA
49359016 ATAATTTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 4 0.11
38 32 0.89
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (38 bp):
AATTAGTAATTAAAGATTTTATTTTTATCATGAATATG
Found at i:49366116 original size:20 final size:21
Alignment explanation
Indices: 49366075--49366118 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
49366065 TTGTGTACAA
*
49366075 TAAAAATGAACAAAATTGTGT
1 TAAAAATGAACAAAATTATGT
*
49366096 TAAAAATGAATAAAA-TATGT
1 TAAAAATGAACAAAATTATGT
49366116 TAA
1 TAA
49366119 CGAGGTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.57, C:0.02, G:0.11, T:0.30
Consensus pattern (21 bp):
TAAAAATGAACAAAATTATGT
Found at i:49370403 original size:31 final size:31
Alignment explanation
Indices: 49370365--49370496 Score: 140
Period size: 31 Copynumber: 4.2 Consensus size: 31
49370355 TTATATATCT
49370365 ATATACAAATCAAATTCGGCAATGTATAACC
1 ATATACAAATCAAATTCGGCAATGTATAACC
* *
49370396 ATATACAAATCAAATTCGGCAATATA-AATCT
1 ATATACAAATCAAATTCGGCAATGTATAA-CC
* * * * *
49370427 ATAAACAATTCAAATTCGACAATGTATATCT
1 ATATACAAATCAAATTCGGCAATGTATAACC
* ** *
49370458 ATAAACAAATCAAATTTAGCAATGTATAAAAC
1 ATATACAAATCAAATTCGGCAATGTAT-AACC
49370490 ATATACA
1 ATATACA
49370497 TTTAAATTCA
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
30 2 0.02
31 73 0.88
32 8 0.10
ACGTcount: A:0.49, C:0.16, G:0.07, T:0.28
Consensus pattern (31 bp):
ATATACAAATCAAATTCGGCAATGTATAACC
Found at i:49370466 original size:62 final size:62
Alignment explanation
Indices: 49370356--49370473 Score: 173
Period size: 62 Copynumber: 1.9 Consensus size: 62
49370346 GAGCTAGCTT
* * * *
49370356 TATATATCTATATACAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAA
1 TATAAATCTATAAACAAATCAAATTCGACAATGTATAACCATAAACAAATCAAATTCGGCAA
* * *
49370418 TATAAATCTATAAACAATTCAAATTCGACAATGTATATCTATAAACAAATCAAATT
1 TATAAATCTATAAACAAATCAAATTCGACAATGTATAACCATAAACAAATCAAATT
49370474 TAGCAATGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 49 1.00
ACGTcount: A:0.47, C:0.16, G:0.06, T:0.31
Consensus pattern (62 bp):
TATAAATCTATAAACAAATCAAATTCGACAATGTATAACCATAAACAAATCAAATTCGGCAA
Found at i:49370505 original size:62 final size:62
Alignment explanation
Indices: 49370363--49370494 Score: 156
Period size: 62 Copynumber: 2.1 Consensus size: 62
49370353 CTTTATATAT
* * * * * *
49370363 CTATATACAAATCAAATTCGGCAATGTATAACCATATACAAATCAAATTCGGCAATATAAAT
1 CTATAAACAATTCAAATTCGACAATGTATAACCATAAACAAATCAAATTCAGCAATATAAAA
* * *
49370425 CTATAAACAATTCAAATTCGACAATGTATATCTATAAACAAATCAAATTTAGCAATGTATAAAA
1 CTATAAACAATTCAAATTCGACAATGTATAACCATAAACAAATCAAATTCAGCAA--TATAAAA
49370489 CATATA
1 C-TATA
49370495 CATTTAAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 47 0.81
64 7 0.12
65 4 0.07
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (62 bp):
CTATAAACAATTCAAATTCGACAATGTATAACCATAAACAAATCAAATTCAGCAATATAAAA
Found at i:49371772 original size:17 final size:19
Alignment explanation
Indices: 49371750--49371785 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
49371740 TCATCCTCAA
49371750 AACCTT-AAATA-ATAAAC
1 AACCTTAAAATACATAAAC
49371767 AACCTTAAAATACATAAAC
1 AACCTTAAAATACATAAAC
49371786 CCAAAGAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 5 0.29
19 6 0.35
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.22
Consensus pattern (19 bp):
AACCTTAAAATACATAAAC
Found at i:49371824 original size:20 final size:20
Alignment explanation
Indices: 49371801--49371839 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
49371791 GAACCATAAA
49371801 CCTA-AAAAGAAAACCCTAAC
1 CCTAGAAAA-AAAACCCTAAC
*
49371821 CCTAGAAAACAAACCCTAA
1 CCTAGAAAAAAAACCCTAA
49371840 AAACTCTTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.54, C:0.31, G:0.05, T:0.10
Consensus pattern (20 bp):
CCTAGAAAAAAAACCCTAAC
Found at i:49374260 original size:31 final size:31
Alignment explanation
Indices: 49374223--49374305 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
49374213 TGAATTAAGA
* *
49374223 AATCATCGTTGTCGGGAAATCCG-GGGTGGT
1 AATCATCATTGTCGGGAAATCCGAGGGTGGC
* * *
49374253 AAGTCATCTTTGTAGGGAAA-CTGAGGGTGGC
1 AA-TCATCATTGTCGGGAAATCCGAGGGTGGC
*
49374284 AATCATCATTGTCGGGTAATCC
1 AATCATCATTGTCGGGAAATCC
49374306 AGGATGACAT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
30 18 0.43
31 24 0.57
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.28
Consensus pattern (31 bp):
AATCATCATTGTCGGGAAATCCGAGGGTGGC
Found at i:49382321 original size:4 final size:4
Alignment explanation
Indices: 49382312--49382336 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
49382302 CCTCTCCCTC
49382312 TCCA TCCA TCCA TCCA TCCA TCCA T
1 TCCA TCCA TCCA TCCA TCCA TCCA T
49382337 ATATATCCAT
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:0.48, G:0.00, T:0.28
Consensus pattern (4 bp):
TCCA
Found at i:49382695 original size:126 final size:122
Alignment explanation
Indices: 49382470--49382721 Score: 443
Period size: 126 Copynumber: 2.0 Consensus size: 122
49382460 CAAAGAATCT
*
49382470 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAATGGAAA
1 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAACGGAAA
49382535 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAAATACTTTTTATTTTCATTGGCATG
66 ACTAAAGGGGGAGAAAAATAGAAAGATAG-AAAAAAAATAC-TTTT-TTTT-ATTGGCATG
49382596 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAACGGAAA
1 CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAACGGAAA
*
49382661 ATTAAA-GGGGAGAAAAATAGAAAGATAGAAAAAAAATACTTTTTTTTATTGGCATG
66 ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATACTTTTTTTTATTGGCATG
49382717 CTTAG
1 CTTAG
49382722 TAGGAAAGAT
Statistics
Matches: 124, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
121 14 0.11
122 4 0.03
123 4 0.03
124 11 0.09
125 22 0.18
126 69 0.56
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.27
Consensus pattern (122 bp):
CTTAGAGGCATATTAACTTTAAGGCTTTGCTTGGTAAGGTGAAAAGAAAATTGGAAAAACGGAAA
ACTAAAGGGGGAGAAAAATAGAAAGATAGAAAAAAAATACTTTTTTTTATTGGCATG
Found at i:49392280 original size:13 final size:13
Alignment explanation
Indices: 49392262--49392317 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
49392252 TTAAAAAATC
49392262 ATAAAATTTATAA
1 ATAAAATTTATAA
*
49392275 ATAAAA-TTATTA
1 ATAAAATTTATAA
* *
49392287 A-AAAATTAAAAA
1 ATAAAATTTATAA
*
49392299 ATAAATTTTATAA
1 ATAAAATTTATAA
49392312 A-AAAAT
1 ATAAAAT
49392318 AAAAATTCTG
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
11 4 0.12
12 14 0.42
13 15 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (13 bp):
ATAAAATTTATAA
Found at i:49392304 original size:23 final size:25
Alignment explanation
Indices: 49392264--49392322 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
49392254 AAAAAATCAT
* *
49392264 AAAATTTATAAATAAAATTAT-TAA
1 AAAATTAAAAAATAAAATTATATAA
*
49392288 AAAATTAAAAAAT-AAATTTTATAA
1 AAAATTAAAAAATAAAATTATATAA
*
49392312 AAAAATAAAAA
1 AAAATTAAAAA
49392323 TTCTGATCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (25 bp):
AAAATTAAAAAATAAAATTATATAA
Found at i:49392921 original size:14 final size:14
Alignment explanation
Indices: 49392902--49392967 Score: 50
Period size: 13 Copynumber: 4.9 Consensus size: 14
49392892 AATTAATTAC
49392902 TAATTATAAAAATA
1 TAATTATAAAAATA
*
49392916 TAATTA-ACAAA-A
1 TAATTATAAAAATA
*
49392928 TAATT-TATATAATA
1 TAATTATA-AAAATA
*
49392942 TTAATTATATAAATA
1 -TAATTATAAAAATA
*
49392957 T-TTTATAAAAA
1 TAATTATAAAAA
49392968 AATATATAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
12 7 0.17
13 14 0.35
14 8 0.20
15 9 0.22
16 2 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
TAATTATAAAAATA
Found at i:49392935 original size:27 final size:28
Alignment explanation
Indices: 49392905--49392967 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
49392895 TAATTACTAA
49392905 TTATAAAAATA-TAATTA-ACAAAATAAT
1 TTATAAAAATATTAATTATA-AAAATAAT
* * *
49392932 TTAT-ATAATATTAATTATATAAATATT
1 TTATAAAAATATTAATTATAAAAATAAT
49392959 TTATAAAAA
1 TTATAAAAA
49392968 AATATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
26 5 0.17
27 20 0.69
28 4 0.14
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TTATAAAAATATTAATTATAAAAATAAT
Found at i:49392946 original size:15 final size:15
Alignment explanation
Indices: 49392902--49392958 Score: 52
Period size: 15 Copynumber: 4.1 Consensus size: 15
49392892 AATTAATTAC
*
49392902 TAATTATAAAAATA-
1 TAATTATATAAATAT
*
49392916 TAATTA-ACAAA-A-
1 TAATTATATAAATAT
49392928 TAATT-TATATAATAT
1 TAATTATATA-AATAT
49392943 TAATTATATAAATAT
1 TAATTATATAAATAT
49392958 T
1 T
49392959 TTATAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
12 8 0.22
13 6 0.17
14 7 0.19
15 11 0.31
16 4 0.11
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATTATATAAATAT
Found at i:49393472 original size:34 final size:32
Alignment explanation
Indices: 49393442--49393542 Score: 112
Period size: 34 Copynumber: 3.0 Consensus size: 32
49393432 AATAAATCAG
*
49393442 AGTTTAGAATTTTAAAAAAATTTAATTAAATTA
1 AGTTTAGAATTTTAAGAAAA-TTAATTAAATTA
** *
49393475 AGTTTTAAGGGTTTTAAGTAAATTAATTAAATTA
1 AG-TTT-AGAATTTTAAGAAAATTAATTAAATTA
*
49393509 AGGTTTAGATTTTTTAAGAAAATTAATTAAATTA
1 A-GTTTAGA-ATTTTAAGAAAATTAATTAAATTA
49393543 GGATTTAGGG
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
33 4 0.07
34 41 0.72
35 12 0.21
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.44
Consensus pattern (32 bp):
AGTTTAGAATTTTAAGAAAATTAATTAAATTA
Found at i:49393550 original size:34 final size:33
Alignment explanation
Indices: 49393434--49393560 Score: 105
Period size: 34 Copynumber: 3.7 Consensus size: 33
49393424 TTTTAAAAAA
* * *
49393434 TAAATCAGAGTTTAGA-ATTTTAAAAAAATTTAAT
1 TAAATTAG-GTTTAGATTTTTTAAGAAAA-TTAAT
* ** *
49393468 TAAATTAAGTTTTA-AGGGTTTTAAGTAAATTAAT
1 TAAATT-AGGTTTAGA-TTTTTTAAGAAAATTAAT
49393502 TAAATTAAGGTTTAGATTTTTTAAGAAAATTAAT
1 TAAATT-AGGTTTAGATTTTTTAAGAAAATTAAT
*
49393536 TAAATTAGGATTTAGGGTTTTTTAA
1 TAAATTAGG-TTTA-GATTTTTTAA
49393561 AAGTAATTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
33 4 0.05
34 52 0.68
35 21 0.27
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (33 bp):
TAAATTAGGTTTAGATTTTTTAAGAAAATTAAT
Found at i:49397215 original size:18 final size:18
Alignment explanation
Indices: 49397194--49397230 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
49397184 GACTGGGAAA
49397194 AGGAAACATATAAGGGTT
1 AGGAAACATATAAGGGTT
* *
49397212 AGGATACATATGAGGGTT
1 AGGAAACATATAAGGGTT
49397230 A
1 A
49397231 AGATACGCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.30, T:0.24
Consensus pattern (18 bp):
AGGAAACATATAAGGGTT
Found at i:49397235 original size:18 final size:18
Alignment explanation
Indices: 49397199--49397236 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
49397189 GGAAAAGGAA
*
49397199 ACATATAAGGGTTAGGAT
1 ACATATAAGGGTTAAGAT
*
49397217 ACATATGAGGGTTAAGAT
1 ACATATAAGGGTTAAGAT
49397235 AC
1 AC
49397237 GCATCTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.08, G:0.26, T:0.26
Consensus pattern (18 bp):
ACATATAAGGGTTAAGAT
Found at i:49397793 original size:7 final size:7
Alignment explanation
Indices: 49397781--49397806 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
49397771 TTATATATAT
49397781 AATACTA
1 AATACTA
49397788 AATACTA
1 AATACTA
49397795 AATACTA
1 AATACTA
49397802 AATAC
1 AATAC
49397807 AAAACAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:49401165 original size:44 final size:44
Alignment explanation
Indices: 49401102--49401240 Score: 260
Period size: 44 Copynumber: 3.2 Consensus size: 44
49401092 GAAAGAGCTA
*
49401102 TTATATTATTACCTAAAGGTAAAAAATTTGTCATTGATGATGCT
1 TTATATTATTACCTAAAGGTACAAAATTTGTCATTGATGATGCT
49401146 TTATATTATTACCTAAAGGTACAAAATTTGTCATTGATGATGCT
1 TTATATTATTACCTAAAGGTACAAAATTTGTCATTGATGATGCT
*
49401190 TTATATTATTACCTAAAGGTACAAAATTTGTCATTGATGATGTT
1 TTATATTATTACCTAAAGGTACAAAATTTGTCATTGATGATGCT
49401234 TTATATT
1 TTATATT
49401241 TCACTAAGTT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 93 1.00
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.43
Consensus pattern (44 bp):
TTATATTATTACCTAAAGGTACAAAATTTGTCATTGATGATGCT
Found at i:49409662 original size:19 final size:19
Alignment explanation
Indices: 49409638--49409686 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 19
49409628 ATTATGTTTT
49409638 TATATTATATTATTATTA-A
1 TATATTATATTA-TATTATA
49409657 TATATTATATTATATTATA
1 TATATTATATTATATTATA
49409676 TATATATATAT
1 TATAT-TATAT
49409687 ATCAAAAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.18
19 18 0.64
20 5 0.18
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATTATATTATATTATA
Found at i:49411724 original size:13 final size:14
Alignment explanation
Indices: 49411704--49411767 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
49411694 TTTGTATAAC
49411704 TTTTT-AAATTTT-
1 TTTTTAAAATTTTA
49411716 TTTTATAAAATTTTA
1 TTTT-TAAAATTTTA
*
49411731 TTTTTGAAATTGCTTAA
1 TTTTTAAAATT--TT-A
*
49411748 TTTATTTAAATTTTA
1 TTT-TTAAAATTTTA
49411763 TTTTT
1 TTTTT
49411768 GAATATTAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
12 4 0.09
13 1 0.02
14 15 0.35
15 8 0.19
16 4 0.09
17 4 0.09
18 7 0.16
ACGTcount: A:0.30, C:0.02, G:0.03, T:0.66
Consensus pattern (14 bp):
TTTTTAAAATTTTA
Found at i:49411816 original size:34 final size:35
Alignment explanation
Indices: 49411760--49411838 Score: 83
Period size: 34 Copynumber: 2.3 Consensus size: 35
49411750 TATTTAAATT
* *
49411760 TTATTTTT-GAATATTAATATTTTCT-AACTTTTA
1 TTATTTTTAAAATATTAACATTTTCTGAACTTTTA
* * *
49411793 -TATTTTATAAAATATTCACATTTTTTGAATTTTTA
1 TTATTTT-TAAAATATTAACATTTTCTGAACTTTTA
49411828 TTATTTTTAAA
1 TTATTTTTAAA
49411839 TTAGTTACTG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
32 6 0.16
33 1 0.03
34 13 0.35
35 11 0.30
36 6 0.16
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (35 bp):
TTATTTTTAAAATATTAACATTTTCTGAACTTTTA
Found at i:49413120 original size:32 final size:32
Alignment explanation
Indices: 49413083--49413147 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
49413073 CCTAACTCCA
49413083 CTACACACCTCACTTATGAGTTCCTTAGAACT
1 CTACACACCTCACTTATGAGTTCCTTAGAACT
*
49413115 CTACACATCTCACTTATGAGTTCCTTAGAACT
1 CTACACACCTCACTTATGAGTTCCTTAGAACT
49413147 C
1 C
49413148 ATTTACCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (32 bp):
CTACACACCTCACTTATGAGTTCCTTAGAACT
Found at i:49422427 original size:42 final size:40
Alignment explanation
Indices: 49422319--49422396 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
49422309 TACGTGGACG
*
49422319 CAAAACGCGCTGACGTCCACGCGATTTTCTGACACATCAA
1 CAAAACGCGCTGACGTCCACGCGATTTGCTGACACATCAA
49422359 CAAAACGCGCTGACGTCCACGCGATTTGCTGACACATC
1 CAAAACGCGCTGACGTCCACGCGATTTGCTGACACATC
49422397 CCCTCACATC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (40 bp):
CAAAACGCGCTGACGTCCACGCGATTTGCTGACACATCAA
Found at i:49422535 original size:20 final size:20
Alignment explanation
Indices: 49422499--49422540 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
49422489 AAAAATAGGG
49422499 CTTTTATGTGTAATTTGCCC
1 CTTTTATGTGTAATTTGCCC
*
49422519 CTTTT-TGTGGTATTTTGCCC
1 CTTTTATGT-GTAATTTGCCC
49422539 CT
1 CT
49422541 AATAATACAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.10, C:0.21, G:0.17, T:0.52
Consensus pattern (20 bp):
CTTTTATGTGTAATTTGCCC
Found at i:49424207 original size:9 final size:9
Alignment explanation
Indices: 49424179--49424236 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
49424169 TTGTTTTAAC
49424179 ATAATTTTTA
1 ATAA-TTTTA
49424189 ATATATTTTA
1 ATA-ATTTTA
49424199 ATAATTTTA
1 ATAATTTTA
49424208 ATAATTTATA
1 ATAATTT-TA
* *
49424218 TTTATTTTA
1 ATAATTTTA
49424227 A-AGATTTTA
1 ATA-ATTTTA
49424236 A
1 A
49424237 AAAAATAAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
9 22 0.54
10 18 0.44
11 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
ATAATTTTA
Found at i:49424208 original size:19 final size:18
Alignment explanation
Indices: 49424179--49424236 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
49424169 TTGTTTTAAC
49424179 ATAATTTTTAATATATTTTA
1 ATAA-TTTTAATA-ATTTTA
49424199 ATAATTTTAATAATTTATA
1 ATAATTTTAATAATTT-TA
* *
49424218 TTTATTTTAA-AGATTTTA
1 ATAATTTTAATA-ATTTTA
49424236 A
1 A
49424237 AAAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.21
19 22 0.67
20 4 0.12
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATAATTTTAATAATTTTA
Found at i:49424215 original size:17 final size:20
Alignment explanation
Indices: 49424179--49424214 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
49424169 TTGTTTTAAC
49424179 ATAATTTTTAATATATTTTA
1 ATAATTTTTAATATATTTTA
49424199 ATAA-TTTTAATA-ATTT
1 ATAATTTTTAATATATTT
49424215 ATATTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.25
19 8 0.50
20 4 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATAATTTTTAATATATTTTA
Found at i:49438626 original size:20 final size:19
Alignment explanation
Indices: 49438601--49438649 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
49438591 TTCGAGGATC
49438601 ATTTTGAAACAAATCAAAAA
1 ATTTTGAAA-AAATCAAAAA
* **
49438621 ATTTTGGAAAAATTGAAAA
1 ATTTTGAAAAAATCAAAAA
49438640 ATTTTGAAAA
1 ATTTTGAAAA
49438650 CAGGGGTCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.55, C:0.04, G:0.10, T:0.31
Consensus pattern (19 bp):
ATTTTGAAAAAATCAAAAA
Found at i:49439629 original size:9 final size:9
Alignment explanation
Indices: 49439615--49439640 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
49439605 AATTTAACTC
49439615 AATTTATAT
1 AATTTATAT
49439624 AATTTATAT
1 AATTTATAT
49439633 AATTTATA
1 AATTTATA
49439641 AAAGTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
AATTTATAT
Found at i:49452885 original size:15 final size:15
Alignment explanation
Indices: 49452867--49452915 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
49452857 CAAGATTAAT
*
49452867 ATGTGCAACATCAAC
1 ATGTGCAACATGAAC
* * *
49452882 ATGTACAACATGGAT
1 ATGTGCAACATGAAC
49452897 ATGTGCAACATGAAC
1 ATGTGCAACATGAAC
49452912 ATGT
1 ATGT
49452916 ACAGGATTGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (15 bp):
ATGTGCAACATGAAC
Found at i:49452885 original size:30 final size:30
Alignment explanation
Indices: 49452849--49452918 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
49452839 AATGAAGAGT
* * *
49452849 AACATGTCCAAGATTAATATGTGCAACATC
1 AACATGTACAACATGAATATGTGCAACATC
* *
49452879 AACATGTACAACATGGATATGTGCAACATG
1 AACATGTACAACATGAATATGTGCAACATC
49452909 AACATGTACA
1 AACATGTACA
49452919 GGATTGACAC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (30 bp):
AACATGTACAACATGAATATGTGCAACATC
Found at i:49463453 original size:9 final size:9
Alignment explanation
Indices: 49463441--49463470 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
49463431 AAAATTAATT
49463441 TTTTATATA
1 TTTTATATA
*
49463450 TTTTTTATA
1 TTTTATATA
49463459 TTTTATATA
1 TTTTATATA
49463468 TTT
1 TTT
49463471 ATAATACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (9 bp):
TTTTATATA
Found at i:49466815 original size:34 final size:35
Alignment explanation
Indices: 49466771--49466837 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
49466761 CAGTAAAATG
*
49466771 TTTTCCGTAAAATGATTT-CTAGAAAATATTTTAC
1 TTTTCCGTAAAACGATTTACTAGAAAATATTTTAC
*
49466805 TTTTCTGTAAAACGATTTACTAGAAAATATTTT
1 TTTTCCGTAAAACGATTTACTAGAAAATATTTT
49466838 CTACTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 16 0.53
35 14 0.47
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAACGATTTACTAGAAAATATTTTAC
Found at i:49467610 original size:7 final size:7
Alignment explanation
Indices: 49467598--49467628 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
49467588 TGAAGAGGCT
49467598 GCAGCCA
1 GCAGCCA
49467605 GCAGCCA
1 GCAGCCA
49467612 GCAGCCA
1 GCAGCCA
*
49467619 GCAACCA
1 GCAGCCA
49467626 GCA
1 GCA
49467629 ACCAACTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.32, C:0.42, G:0.26, T:0.00
Consensus pattern (7 bp):
GCAGCCA
Found at i:49468981 original size:43 final size:42
Alignment explanation
Indices: 49468934--49469077 Score: 177
Period size: 43 Copynumber: 3.4 Consensus size: 42
49468924 AAAACATGAC
49468934 CTTTAGCGGCGCTTTTATCACAAACACCGCTAAAAGCCATGTT
1 CTTTAGCGGCGCTTTTAT-ACAAACACCGCTAAAAGCCATGTT
* * *
49468977 CTTTAGAGGCGCTTTTATAACAAACACCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTTTAT-ACAAACACCGCTAAAAGCCATGTT
**
49469020 CTTTAGCGGCGCTTTTATAGCAAACGGCGCTAAAAGTACC--GTT
1 CTTTAGCGGCGCTTTTATA-CAAACACCGCTAAAAG--CCATGTT
49469063 CTTTAGCGGCG-TTTT
1 CTTTAGCGGCGCTTTT
49469078 GCAGAAAACG
Statistics
Matches: 89, Mismatches: 9, Indels: 7
0.85 0.09 0.07
Matches are distributed among these distances:
42 5 0.06
43 83 0.93
45 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGCTTTTATACAAACACCGCTAAAAGCCATGTT
Found at i:49474784 original size:13 final size:13
Alignment explanation
Indices: 49474766--49474829 Score: 60
Period size: 13 Copynumber: 4.8 Consensus size: 13
49474756 TAAGTATAAT
49474766 TAAGTTATGTATG
1 TAAGTTATGTATG
*
49474779 TAAGTTATGTATAAT
1 TAAGTTATGTAT--G
49474794 TAAGTTATGTATG
1 TAAGTTATGTATG
* *
49474807 TATGTGA-GTTAT-
1 TAAGTTATG-TATG
49474819 TAAGTTATGTA
1 TAAGTTATGTA
49474830 AGTTATGTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
12 8 0.20
13 21 0.51
15 12 0.29
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (13 bp):
TAAGTTATGTATG
Found at i:49474799 original size:15 final size:15
Alignment explanation
Indices: 49474759--49474805 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
49474749 TTAGGGATAA
49474759 GTATAATTAAGTTAT
1 GTATAATTAAGTTAT
*
49474774 GTAT--GTAAGTTAT
1 GTATAATTAAGTTAT
49474787 GTATAATTAAGTTAT
1 GTATAATTAAGTTAT
49474802 GTAT
1 GTAT
49474806 GTATGTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 12 0.43
15 16 0.57
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (15 bp):
GTATAATTAAGTTAT
Found at i:49474817 original size:32 final size:28
Alignment explanation
Indices: 49474759--49474829 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 28
49474749 TTAGGGATAA
49474759 GTATAATTAAGTTATGTATGTAAGTTAT
1 GTATAATTAAGTTATGTATGTAAGTTAT
* *
49474787 GTATAATTAAGTTATGTATGTATGTGA-
1 GTATAATTAAGTTATGTATGTAAGTTAT
49474814 GT-T-ATTAAGTTATGTA
1 GTATAATTAAGTTATGTA
49474830 AGTTATGTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
25 13 0.32
26 1 0.02
27 2 0.05
28 25 0.61
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (28 bp):
GTATAATTAAGTTATGTATGTAAGTTAT
Found at i:49474818 original size:17 final size:17
Alignment explanation
Indices: 49474771--49474837 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
49474761 ATAATTAAGT
49474771 TATGTATGTAAGTTATG
1 TATGTATGTAAGTTATG
*
49474788 TAT-AAT-TAAGTTATG
1 TATGTATGTAAGTTATG
*
49474803 TATGTATGTGAGTTAT-
1 TATGTATGTAAGTTATG
*
49474819 TAAGTTATGTAAGTTATG
1 TATG-TATGTAAGTTATG
49474837 T
1 T
49474838 GAGTTATGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
15 12 0.29
16 7 0.17
17 21 0.51
18 1 0.02
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.48
Consensus pattern (17 bp):
TATGTATGTAAGTTATG
Found at i:49474824 original size:8 final size:9
Alignment explanation
Indices: 49474775--49474845 Score: 71
Period size: 9 Copynumber: 8.4 Consensus size: 9
49474765 TTAAGTTATG
49474775 TATGTAAGT
1 TATGTAAGT
49474784 TATGT-A-T
1 TATGTAAGT
*
49474791 AAT-TAAGT
1 TATGTAAGT
*
49474799 TATGTATG-
1 TATGTAAGT
*
49474807 TATGTGAGT
1 TATGTAAGT
49474816 TAT-TAAGT
1 TATGTAAGT
49474824 TATGTAAGT
1 TATGTAAGT
*
49474833 TATGTGAGT
1 TATGTAAGT
49474842 TATG
1 TATG
49474846 ATATGATATG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
6 1 0.02
7 4 0.08
8 17 0.34
9 28 0.56
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (9 bp):
TATGTAAGT
Found at i:49474852 original size:5 final size:5
Alignment explanation
Indices: 49474842--49474903 Score: 117
Period size: 5 Copynumber: 12.6 Consensus size: 5
49474832 TTATGTGAGT
49474842 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
1 TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA TATGA
49474892 TATGA TAT-A TAT
1 TATGA TATGA TAT
49474904 AAGTTATTAA
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
4 4 0.07
5 53 0.93
ACGTcount: A:0.40, C:0.00, G:0.18, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:49475036 original size:9 final size:9
Alignment explanation
Indices: 49475014--49475150 Score: 111
Period size: 9 Copynumber: 15.0 Consensus size: 9
49475004 GATATATATA
49475014 TAAGTTAT-
1 TAAGTTATG
49475022 TAAGTTATG
1 TAAGTTATG
49475031 TAAGTTATG
1 TAAGTTATG
*
49475040 TGAGTTATG
1 TAAGTTATG
* *
49475049 ATATGATATATA
1 -TAAG-T-TATG
49475061 TAAGTTAT-
1 TAAGTTATG
*
49475069 TATGTTATG
1 TAAGTTATG
49475078 TAAGTTATG
1 TAAGTTATG
*
49475087 TGAGTTATG
1 TAAGTTATG
* *
49475096 ATATGATATATA
1 -TAAG-T-TATG
49475108 TAAGTTAT-
1 TAAGTTATG
49475116 TAAGTTATG
1 TAAGTTATG
*
49475125 TATG-TATG
1 TAAGTTATG
*
49475133 TCAGTTATG
1 TAAGTTATG
49475142 TAAGTTATG
1 TAAGTTATG
49475151 ATCTGATATA
Statistics
Matches: 103, Mismatches: 16, Indels: 19
0.75 0.12 0.14
Matches are distributed among these distances:
8 29 0.28
9 54 0.52
10 6 0.06
11 8 0.08
12 6 0.06
ACGTcount: A:0.34, C:0.01, G:0.20, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:49475076 original size:47 final size:47
Alignment explanation
Indices: 49474813--49475141 Score: 260
Period size: 47 Copynumber: 6.7 Consensus size: 47
49474803 TATGTATGTG
49474813 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATGATAT-
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATAT-ATATA
* * * * *
49474860 -G--A-TATGATATGATATGATATGAT-ATGATATGATATGATATATATA
1 AGTTATTAAGTTATG-TAAGTTATG-TGA-GTTATGATATGATATATATA
* *
49474905 AGTTATTAAGTTATCTATG-TATGTGAGTTATGTAAGTAATGACCTGCTATATATTTA
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATG--A-T-ATGA-----TATATA--TA
* ** * * *
49474962 TGTATTATGTAAGTTATGTGTCTGTTTTGTAAGTTATGGTATGATATATATATA
1 AG--TTAT-TAAGTTA--TGTAAGTTATGTGAGTTATGATATGAT--ATATATA
49475016 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATATATA
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATATATA
*
49475063 AGTTATTATGTTATGTAAGTTATGTGAGTTATGATATGATATATATA
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATATATA
* *
49475110 AGTTATTAAGTTATGTATG-TATGTCAGTTATG
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATG
49475142 TAAGTTATGA
Statistics
Matches: 229, Mismatches: 25, Indels: 57
0.74 0.08 0.18
Matches are distributed among these distances:
43 7 0.03
44 13 0.06
45 15 0.07
46 20 0.09
47 75 0.33
48 6 0.03
49 29 0.13
50 4 0.02
51 7 0.03
52 4 0.02
54 4 0.02
55 6 0.03
56 5 0.02
57 3 0.01
59 8 0.03
60 8 0.03
62 4 0.02
63 11 0.05
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.45
Consensus pattern (47 bp):
AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATATATA
Found at i:49475131 original size:205 final size:202
Alignment explanation
Indices: 49474813--49475182 Score: 541
Period size: 205 Copynumber: 1.8 Consensus size: 202
49474803 TATGTATGTG
*
49474813 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATGATATGATATGATATGATATGAT
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATGATATGATATGATATGATAAGAT
*
49474878 ATGATATGATATGATATGATATATATAAGTTATTAAGTTATCTATGTATGTGAGTTATGTAAGTA
66 ATGATATGATATGATATGATATATATAAGTTATTAAGTTATCTATGTATGTCAGTTATGTAAGTA
* * * *
49474943 ATGACCTGCTATATATTTATGTATTATGTAAGTTATGTGTCTGTTTTGTAAGTTATGGTATGATA
131 ATGACCTGATATATATATATATA-TATATAAGTTATGTGTCTGTTTTGTAAGTTATGGTATGATA
49475008 TATATATA
195 TATATATA
*
49475016 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATAT-ATATAAGTTATTATGTTATG-T
1 AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATGATAT--G--A-TATGATATGAT
* * *
49475079 AAGTTATG-TGA-GTTATGATATGATATATATAAGTTATTAAGTTATGTATGTATGTCAGTTATG
61 AAGATATGAT-ATGATATGATATGATATATATAAGTTATTAAGTTATCTATGTATGTCAGTTATG
* *
49475142 TAAGTTATGATCTGATATATATATATATATATATAAGTTAT
125 TAAGTAATGACCTGATATATATATATATATATATAAGTTAT
49475183 TAAGTTAAGA
Statistics
Matches: 149, Mismatches: 12, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
202 4 0.03
203 42 0.28
204 12 0.08
205 74 0.50
206 9 0.06
207 8 0.05
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.45
Consensus pattern (202 bp):
AGTTATTAAGTTATGTAAGTTATGTGAGTTATGATATGATATGATATGATATGATATGATAAGAT
ATGATATGATATGATATGATATATATAAGTTATTAAGTTATCTATGTATGTCAGTTATGTAAGTA
ATGACCTGATATATATATATATATATATAAGTTATGTGTCTGTTTTGTAAGTTATGGTATGATAT
ATATATA
Found at i:49475275 original size:9 final size:9
Alignment explanation
Indices: 49475233--49475345 Score: 59
Period size: 9 Copynumber: 12.4 Consensus size: 9
49475223 GGTATGAAAA
49475233 TTATGTAAG
1 TTATGTAAG
* *
49475242 TTGTGATATGG
1 TTATG-TA-AG
*
49475253 TTAT-TAAA
1 TTATGTAAG
49475261 TTATGTAAG
1 TTATGTAAG
*
49475270 TTATGTGAG
1 TTATGTAAG
*
49475279 TTATGTAAA
1 TTATGTAAG
* *
49475288 TTATATAAA
1 TTATGTAAG
*
49475297 TTATGTAAT
1 TTATGTAAG
* *
49475306 TTTTGATATG
1 TTATG-TAAG
* * *
49475316 ATATAT-AT
1 TTATGTAAG
49475324 TTATGTAAG
1 TTATGTAAG
*
49475333 TTATGTAAA
1 TTATGTAAG
49475342 TTAT
1 TTAT
49475346 ATATTCATTT
Statistics
Matches: 75, Mismatches: 24, Indels: 10
0.69 0.22 0.09
Matches are distributed among these distances:
8 8 0.11
9 57 0.76
10 6 0.08
11 4 0.05
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (9 bp):
TTATGTAAG
Found at i:49475617 original size:38 final size:38
Alignment explanation
Indices: 49475500--49475618 Score: 102
Period size: 38 Copynumber: 3.2 Consensus size: 38
49475490 GAAGAAATTG
*
49475500 AAATATAATTATTTTGTCTATATTTATCAAAATAAGTA
1 AAATATAATTAATTTGTCTATATTTATCAAAATAAGTA
** ** * * * **
49475538 AAATATAAAAAAATAAGACTTTAAGTTGGC--AA-AA-TA
1 AAATAT-AATTAATTTGTCTAT-ATTTATCAAAATAAGTA
49475574 AAATATAATTAATTTGTCTATATTTATCAAAATAAGTA
1 AAATATAATTAATTTGTCTATATTTATCAAAATAAGTA
49475612 AAATATA
1 AAATATA
49475619 TAGCTGAAGT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
34 4 0.07
35 9 0.16
36 10 0.18
37 4 0.07
38 17 0.30
39 8 0.14
40 4 0.07
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (38 bp):
AAATATAATTAATTTGTCTATATTTATCAAAATAAGTA
Found at i:49476305 original size:23 final size:24
Alignment explanation
Indices: 49476262--49476321 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
49476252 GAAAAACTAG
49476262 ATTGCTTCATTTGTTAATGGACAA
1 ATTGCTTCATTTGTTAATGGACAA
* *
49476286 ATTTCTTCATTT-TTAATGGACAG
1 ATTGCTTCATTTGTTAATGGACAA
49476309 ATTGCTTCATTTG
1 ATTGCTTCATTTG
49476322 AATTGATCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (24 bp):
ATTGCTTCATTTGTTAATGGACAA
Found at i:49478254 original size:7 final size:7
Alignment explanation
Indices: 49478242--49478491 Score: 76
Period size: 7 Copynumber: 34.9 Consensus size: 7
49478232 AAGGCTTAAT
49478242 CTAAACC
1 CTAAACC
49478249 CTAAACCC
1 CTAAA-CC
*
49478257 CTAACCC
1 CTAAACC
49478264 CTAAATCCC
1 CTAAA--CC
49478273 CTAAACC
1 CTAAACC
*
49478280 CTGAACC
1 CTAAACC
**
49478287 AAAAACC
1 CTAAACC
*
49478294 C-ACAACAT
1 CTA-AAC-C
49478302 CTAAACC
1 CTAAACC
*
49478309 TTAAACTC
1 CTAAAC-C
*
49478317 C--AGCC
1 CTAAACC
49478322 CTTAAACC
1 C-TAAACC
**
49478330 CTAAATA
1 CTAAACC
*
49478337 TTAAACC
1 CTAAACC
49478344 CTTAAACC
1 C-TAAACC
*
49478352 CTAAACT
1 CTAAACC
*
49478359 GTAAACC
1 CTAAACC
* *
49478366 ATAATCC
1 CTAAACC
49478373 CTAAACC
1 CTAAACC
*
49478380 CATAATCC
1 C-TAAACC
*
49478388 ATAAACC
1 CTAAACC
* **
49478395 TTAAATA
1 CTAAACC
*
49478402 GT-AACTC
1 CTAAAC-C
49478409 CTAAACC
1 CTAAACC
*
49478416 TTAAACC
1 CTAAACC
*
49478423 ATAAACC
1 CTAAACC
* * *
49478430 ATAATCT
1 CTAAACC
*
49478437 ATAAACC
1 CTAAACC
*
49478444 CTAAATC
1 CTAAACC
* *
49478451 TTAAAAC
1 CTAAACC
49478458 CTAAACC
1 CTAAACC
* *
49478465 ATATACC
1 CTAAACC
*
49478472 CTAGACC
1 CTAAACC
* *
49478479 ATCAACC
1 CTAAACC
49478486 CTAAAC
1 CTAAAC
49478492 TATAATGATA
Statistics
Matches: 172, Mismatches: 57, Indels: 28
0.67 0.22 0.11
Matches are distributed among these distances:
5 2 0.01
6 5 0.03
7 127 0.74
8 30 0.17
9 8 0.05
ACGTcount: A:0.43, C:0.34, G:0.02, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:49478363 original size:22 final size:23
Alignment explanation
Indices: 49478320--49478378 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
49478310 TAAACTCCAG
*
49478320 CCCTTAAACCCTAAA-TATTAAA
1 CCCTTAAACCCTAAACTAGTAAA
49478342 CCCTTAAACCCTAAACT-GTAAA
1 CCCTTAAACCCTAAACTAGTAAA
* *
49478364 -CCATAATCCCTAAAC
1 CCCTTAAACCCTAAAC
49478379 CCATAATCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
21 13 0.39
22 19 0.58
23 1 0.03
ACGTcount: A:0.42, C:0.32, G:0.02, T:0.24
Consensus pattern (23 bp):
CCCTTAAACCCTAAACTAGTAAA
Found at i:49478384 original size:15 final size:15
Alignment explanation
Indices: 49478360--49478394 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
49478350 CCCTAAACTG
*
49478360 TAAA-CCATAATCCC
1 TAAACCCATAATCCA
49478374 TAAACCCATAATCCA
1 TAAACCCATAATCCA
49478389 TAAACC
1 TAAACC
49478395 TTAAATAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.46, C:0.34, G:0.00, T:0.20
Consensus pattern (15 bp):
TAAACCCATAATCCA
Found at i:49478480 original size:49 final size:48
Alignment explanation
Indices: 49478360--49478480 Score: 125
Period size: 49 Copynumber: 2.4 Consensus size: 48
49478350 CCCTAAACTG
* **
49478360 TAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAATAGTAACTCC
1 TAAACCATAA-CCCTAAA-CCATAATCCATAAACCCTAAATAGTAAAACC
* * * **
49478410 TAAACCTTAAACCATAAACCATAATCTATAAACCCTAAATCTTAAAACC
1 TAAACCAT-AACCCTAAACCATAATCCATAAACCCTAAATAGTAAAACC
*
49478459 TAAACCATATACCCTAGACCAT
1 TAAACCATA-ACCCTAAACCAT
49478481 CAACCCTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.02
49 42 0.72
50 13 0.22
51 2 0.03
ACGTcount: A:0.45, C:0.29, G:0.02, T:0.24
Consensus pattern (48 bp):
TAAACCATAACCCTAAACCATAATCCATAAACCCTAAATAGTAAAACC
Found at i:49478833 original size:40 final size:39
Alignment explanation
Indices: 49478774--49478878 Score: 147
Period size: 40 Copynumber: 2.6 Consensus size: 39
49478764 TCTTTACGGT
*
49478774 GTTTTTCAAAGAGCACCGCTAATGCTCGACCTATAGCGGC
1 GTTTTTCAAA-AGCGCCGCTAATGCTCGACCTATAGCGGC
* * *
49478814 GTTTTTCAACAAGCGCCGCTAATGATCGACTTATAGTGGC
1 GTTTTTCAA-AAGCGCCGCTAATGCTCGACCTATAGCGGC
49478854 GTTTTTCAAAAAGCGCCGCTAATGC
1 GTTTTTC-AAAAGCGCCGCTAATGC
49478879 CACTAAAGCT
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 55 0.95
41 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.28
Consensus pattern (39 bp):
GTTTTTCAAAAGCGCCGCTAATGCTCGACCTATAGCGGC
Found at i:49479023 original size:114 final size:113
Alignment explanation
Indices: 49478815--49479085 Score: 341
Period size: 114 Copynumber: 2.4 Consensus size: 113
49478805 TATAGCGGCG
* * * * ** *
49478815 TTTTTCAACA-AGCGCCGCTAATGATCGACTTATAGTGGCGTTTTTCAAAAAGCGCCGCTAATGC
1 TTTTTCAA-AGAGCGCCACTAATGCTCAACCTATAACGGCATTTTTCAAAAAGCGCCGCTAATGC
* *
49478879 CACTAAAGCTCAACATAAAATGATGCCGTTGTGCTTAATTTTT-T-GCA
65 CACTAAAGCTCAACATAAAACGACGCCGTTGTGCTTAATTTTTATGGCA
* * *
49478926 GTGTTTTTCAAAGAGTGCCACTAATGCTCGACCTATAACGGTATTTTTCAAAAAGCGCCGCTAAT
1 ---TTTTTCAAAGAGCGCCACTAATGCTCAACCTATAACGGCATTTTTCAAAAAGCGCCGCTAAT
*
49478991 GCCACTAAAGCTCAACATAAAACGACGGCGTTGTGCTTAATTTTTAATGGCA
63 GCCACTAAAGCTCAACATAAAACGACGCCGTTGTGCTTAATTTTT-ATGGCA
* *
49479043 TTTTTCAAAGAGCGCCGCTAATGCTCAACCTATAGCGGCATTT
1 TTTTTCAAAGAGCGCCACTAATGCTCAACCTATAACGGCATTT
49479086 AACGACGGCG
Statistics
Matches: 137, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
113 1 0.01
114 132 0.96
116 1 0.01
117 3 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (113 bp):
TTTTTCAAAGAGCGCCACTAATGCTCAACCTATAACGGCATTTTTCAAAAAGCGCCGCTAATGCC
ACTAAAGCTCAACATAAAACGACGCCGTTGTGCTTAATTTTTATGGCA
Found at i:49479109 original size:75 final size:75
Alignment explanation
Indices: 49479011--49479156 Score: 238
Period size: 75 Copynumber: 1.9 Consensus size: 75
49479001 CTCAACATAA
*
49479011 AACGACGGCGTTGTGCTTAATTTTTAATGGCATTTTTCAAAGAGCGCCGCTAATGCTCAACCTAT
1 AACGACGGCGTTGTGCTTAATTTTTAATGGCATTTTTCAAAGAACGCCGCTAATGCTCAACCTAT
49479076 AGCGGCATTT
66 AGCGGCATTT
** * * *
49479086 AACGACGGCGTTGTGCTTAATTTTTTCTGTCGTTTTTCAAAGAACGCCGCTAATGCTCGACCTAT
1 AACGACGGCGTTGTGCTTAATTTTTAATGGCATTTTTCAAAGAACGCCGCTAATGCTCAACCTAT
49479151 AGCGGC
66 AGCGGC
49479157 GTTTTTCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
75 65 1.00
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (75 bp):
AACGACGGCGTTGTGCTTAATTTTTAATGGCATTTTTCAAAGAACGCCGCTAATGCTCAACCTAT
AGCGGCATTT
Found at i:49479174 original size:40 final size:40
Alignment explanation
Indices: 49479116--49479242 Score: 182
Period size: 40 Copynumber: 3.2 Consensus size: 40
49479106 TTTTTTCTGT
* *
49479116 CGTTTTTCAAAGAACGCCGCTAATGCTCGACCTATAGCGG
1 CGTTTTTCAAATAGCGCCGCTAATGCTCGACCTATAGCGG
*
49479156 CGTTTTTCAAATAGCGCCGCTAATGCTTGACCTATAGCGG
1 CGTTTTTCAAATAGCGCCGCTAATGCTCGACCTATAGCGG
* * * *
49479196 CGTTTTTCAAATAGCGTCGCTAAAGCCCGAGCTATAGCGG
1 CGTTTTTCAAATAGCGCCGCTAATGCTCGACCTATAGCGG
*
49479236 CTTTTTT
1 CGTTTTT
49479243 GTCCAAACGC
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 78 1.00
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (40 bp):
CGTTTTTCAAATAGCGCCGCTAATGCTCGACCTATAGCGG
Found at i:49481633 original size:24 final size:24
Alignment explanation
Indices: 49481588--49481634 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
49481578 TATATATACC
49481588 AATTCTATCAATATAAATTCAATA
1 AATTCTATCAATATAAATTCAATA
49481612 AATTC-ATCACATACTAAA-TCAAT
1 AATTCTATCA-ATA-TAAATTCAAT
49481635 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (24 bp):
AATTCTATCAATATAAATTCAATA
Found at i:49487569 original size:24 final size:25
Alignment explanation
Indices: 49487523--49487579 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 25
49487513 TAAAAATACT
49487523 AAAAATATTAAAATAAATATTTTCC
1 AAAAATATTAAAATAAATATTTTCC
**
49487548 AAAAA-ATTGAAAAT-AAT-TTTTTT
1 AAAAATATT-AAAATAAATATTTTCC
49487571 AAAAATATT
1 AAAAATATT
49487580 TATACTTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 9 0.32
24 9 0.32
25 10 0.36
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAAATATTAAAATAAATATTTTCC
Found at i:49502325 original size:16 final size:15
Alignment explanation
Indices: 49502304--49502361 Score: 53
Period size: 16 Copynumber: 3.7 Consensus size: 15
49502294 AAATAGTATT
49502304 AAAAATAAAATACCGA
1 AAAAATAAAATA-CGA
*** *
49502320 AAAAATATGTTTATGA
1 AAAAATA-AAATACGA
49502336 AAAAATAAAATACGAA
1 AAAAATAAAATACG-A
49502352 AAAAATAAAA
1 AAAAATAAAA
49502362 AACAAAAATA
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 3 0.09
16 27 0.84
17 2 0.06
ACGTcount: A:0.69, C:0.05, G:0.07, T:0.19
Consensus pattern (15 bp):
AAAAATAAAATACGA
Found at i:49502369 original size:16 final size:16
Alignment explanation
Indices: 49502335--49502369 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
49502325 TATGTTTATG
* *
49502335 AAAAAATAAAATACGA
1 AAAAAATAAAAAACAA
49502351 AAAAAATAAAAAACAA
1 AAAAAATAAAAAACAA
49502367 AAA
1 AAA
49502370 TAGTATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.83, C:0.06, G:0.03, T:0.09
Consensus pattern (16 bp):
AAAAAATAAAAAACAA
Found at i:49503035 original size:158 final size:157
Alignment explanation
Indices: 49502689--49503009 Score: 472
Period size: 157 Copynumber: 2.1 Consensus size: 157
49502679 NNNNTAATAC
*
49502689 TATTTTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTTTTTTTA
1 TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTTTTTTTA
* * *
49502754 TATAAATTTAGTAAAAAAGCCTCATTTTGGCCATTTGTTCGTATTTTTCTTATTCTCGGATTTTA
66 TATAAATTTAGTAAAAAACCCTCATTTTGGCCATTTGTTCGTATTTTTCTTATCCCCGGATTTTA
*
49502819 TTACTTTCAAAAAATATACTATTTTTG
131 TTACTTTCAAAAAATATACTATTTTCG
* *
49502846 TATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTGTTTTTT
1 TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGT-TTTTTT
* * *
49502911 ATATAAATTTAGTGAAAAACCCTTATTTTGGCCCTTTGTTTC-TA-TTTT-TT-TCCCCGGATTT
65 ATATAAATTTAGTAAAAAACCCTCATTTTGGCCATTTG-TTCGTATTTTTCTTATCCCCGGATTT
**
49502972 TATTACTTTCAGTAAATAT-CATATTTTCG
129 TATTACTTTCAAAAAATATAC-TATTTTCG
49503001 TATTTTATT
1 TATTTTATT
49503010 TCTTTTTGTA
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
154 1 0.01
155 42 0.28
156 2 0.01
157 59 0.40
158 42 0.28
159 3 0.02
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (157 bp):
TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTTTTTTTA
TATAAATTTAGTAAAAAACCCTCATTTTGGCCATTTGTTCGTATTTTTCTTATCCCCGGATTTTA
TTACTTTCAAAAAATATACTATTTTCG
Found at i:49503156 original size:27 final size:27
Alignment explanation
Indices: 49503109--49503172 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
49503099 AATAAAGGGG
* *
49503109 GGTGCCGCCTGTGGCAATGGCACC-TAT
1 GGTGCCGCCTCTGCCAATGGCACCAT-T
*
49503136 GGTGCCGCCTCTGCCACTGGCACCATT
1 GGTGCCGCCTCTGCCAATGGCACCATT
49503163 GGTGCCGCCT
1 GGTGCCGCCT
49503173 GTGGCAGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.11, C:0.36, G:0.31, T:0.22
Consensus pattern (27 bp):
GGTGCCGCCTCTGCCAATGGCACCATT
Found at i:49507589 original size:53 final size:53
Alignment explanation
Indices: 49507526--49507632 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
49507516 TCATGGTGTG
49507526 TTAGAATAAGACTCCGTTTGTTTCACTGAAAATAGCTTCCGAAAAATAATTTT
1 TTAGAATAAGACTCCGTTTGTTTCACTGAAAATAGCTTCCGAAAAATAATTTT
49507579 TTAGAATAAGACTCCGTTTGTTTCACTGAAAATAGCTTCCGAAAAATAATTTT
1 TTAGAATAAGACTCCGTTTGTTTCACTGAAAATAGCTTCCGAAAAATAATTTT
49507632 T
1 T
49507633 GGAAAATGAC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (53 bp):
TTAGAATAAGACTCCGTTTGTTTCACTGAAAATAGCTTCCGAAAAATAATTTT
Found at i:49508322 original size:19 final size:18
Alignment explanation
Indices: 49508300--49508360 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
49508290 AAAATAAATT
49508300 TTAAATATTAAATAATTTA
1 TTAAATATT-AATAATTTA
*
49508319 TTAAA-AATAATAAATTATA
1 TTAAATATTAAT-AATT-TA
49508338 TTAATTATATTAATAATTTA
1 TTAA--ATATTAATAATTTA
49508358 TTA
1 TTA
49508361 CATGACTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 3 0.09
18 6 0.17
19 11 0.31
20 5 0.14
21 5 0.14
22 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TTAAATATTAATAATTTA
Found at i:49509192 original size:42 final size:42
Alignment explanation
Indices: 49509122--49509212 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 42
49509112 CTGAAAACAT
** * * * *
49509122 GGGTCACACGACCGTGTCGTAGATCGTGTGCAAATCGAAATA
1 GGGTCACACGACCGTGTCACACACCGTGTACAAATCAAAATA
* *
49509164 GGGTCACACGATCGTGTCACACACCGTGTACAATTCAAAATA
1 GGGTCACACGACCGTGTCACACACCGTGTACAAATCAAAATA
*
49509206 AGGTCAC
1 GGGTCAC
49509213 GCGGTCATGT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (42 bp):
GGGTCACACGACCGTGTCACACACCGTGTACAAATCAAAATA
Found at i:49509744 original size:3 final size:3
Alignment explanation
Indices: 49509736--49509815 Score: 160
Period size: 3 Copynumber: 26.7 Consensus size: 3
49509726 CACAAACCAA
49509736 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49509784 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
49509816 AGCTACTGAA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:49512253 original size:40 final size:40
Alignment explanation
Indices: 49512177--49512256 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
49512167 GTAACAATTT
* * *
49512177 GGGCCTTAGCCCATCTCAGTACAGTATCATATATGCAGTA
1 GGGCCTTAGCCCATCACAGTAAAGTAGCATATATGCAGTA
49512217 GGGCCTTAGCCCATCACAGTATAAG-AGCA-ATCATGCAGTA
1 GGGCCTTAGCCCATCACAGTA-AAGTAGCATAT-ATGCAGTA
49512257 TTCAGTAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 2 0.06
40 31 0.89
41 2 0.06
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (40 bp):
GGGCCTTAGCCCATCACAGTAAAGTAGCATATATGCAGTA
Found at i:49523991 original size:22 final size:22
Alignment explanation
Indices: 49523963--49524068 Score: 140
Period size: 22 Copynumber: 4.8 Consensus size: 22
49523953 TTTATTGTTC
*
49523963 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTT
49523985 AAACATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
**
49524007 AGCCATGAGAGCTTAGTACGTT
1 AAACATGAGAGCTTAGTACGTT
** * * *
49524029 AGCCATGAGGGTTTAGTTCGTT
1 AAACATGAGAGCTTAGTACGTT
49524051 AAACATGAGAGCTTAGTA
1 AAACATGAGAGCTTAGTA
49524069 AAATGTCAAG
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 73 1.00
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.27
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTT
Found at i:49525745 original size:18 final size:16
Alignment explanation
Indices: 49525727--49525798 Score: 58
Period size: 18 Copynumber: 4.4 Consensus size: 16
49525717 TAAAACAATA
49525727 TTATATTAA-TTATAT
1 TTATATTAATTTATAT
* * * * *
49525742 ATATGTTAAATAATAA
1 TTATATTAATTTATAT
49525758 TTAT-TTATATTTATAT
1 TTATATTA-ATTTATAT
49525774 TTATATTTATATTTATAT
1 TTATA-TTA-ATTTATAT
49525792 TTATATT
1 TTATATT
49525799 TATATTAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
15 10 0.22
16 16 0.36
17 2 0.04
18 17 0.38
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (16 bp):
TTATATTAATTTATAT
Found at i:49525770 original size:6 final size:6
Alignment explanation
Indices: 49525759--49525804 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
49525749 AAATAATAAT
49525759 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
49525805 AAATCACTAA
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:0.00, T:0.67
Consensus pattern (6 bp):
TATTTA
Found at i:49526506 original size:20 final size:20
Alignment explanation
Indices: 49526480--49526553 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
49526470 TTTAATTTAT
49526480 TAATATTTAAATAAATTACA
1 TAATATTTAAATAAATTACA
* * *
49526500 TAGTATTTAATACAAATTATTTA
1 TAATATTTAA-ATAAATTA--CA
*
49526523 TATTAATCTTAAATAAATTACA
1 TAAT-AT-TTAAATAAATTACA
49526545 TAATATTTA
1 TAATATTTA
49526554 TTATTAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 12 0.29
21 9 0.21
22 4 0.10
23 4 0.10
24 9 0.21
25 4 0.10
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.45
Consensus pattern (20 bp):
TAATATTTAAATAAATTACA
Found at i:49526535 original size:45 final size:46
Alignment explanation
Indices: 49526477--49526567 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
49526467 CATTTTAATT
* *
49526477 TATTAATATTTAAATAAATTACATAGTATTTAATACAAATTATTTA
1 TATTAATACTTAAATAAATTACATAATATTTAATACAAATTATTTA
* **
49526523 TATTAAT-CTTAAATAAATTACATAATATTTATTATTAATTATTTA
1 TATTAATACTTAAATAAATTACATAATATTTAATACAAATTATTTA
49526568 AACTTTGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 33 0.82
46 7 0.17
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (46 bp):
TATTAATACTTAAATAAATTACATAATATTTAATACAAATTATTTA
Found at i:49531024 original size:17 final size:19
Alignment explanation
Indices: 49530988--49531024 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
49530978 TTTTTCCAGA
*
49530988 AAATCTTGATAATTTCAAT
1 AAATCTTGATAATGTCAAT
49531007 AAATCTTGA-AA-GTCAAT
1 AAATCTTGATAATGTCAAT
49531024 A
1 A
49531025 TTAATTCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 2 0.12
19 9 0.53
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (19 bp):
AAATCTTGATAATGTCAAT
Found at i:49541369 original size:41 final size:42
Alignment explanation
Indices: 49541308--49541392 Score: 138
Period size: 41 Copynumber: 2.0 Consensus size: 42
49541298 TCAAAAAAAA
49541308 TTCAAAAATCCCAAAAATATTTTCCATT-TTCATTTTTAATTT
1 TTCAAAAATCCCAAAAATATTTTCC-TTCTTCATTTTTAATTT
*
49541350 TTCAAAAAT-CCAAAAATATTTTCCTTCTTTATTTTTAATTT
1 TTCAAAAATCCCAAAAATATTTTCCTTCTTCATTTTTAATTT
49541391 TT
1 TT
49541393 GTTATTGCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
40 2 0.05
41 30 0.73
42 9 0.22
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (42 bp):
TTCAAAAATCCCAAAAATATTTTCCTTCTTCATTTTTAATTT
Found at i:49545702 original size:21 final size:19
Alignment explanation
Indices: 49545678--49545719 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
49545668 GTAACTTTTA
49545678 ATGTTTACATTATAATATTAT
1 ATGTTTA-ATT-TAATATTAT
*
49545699 ATGTTTAATTTAATTTTAT
1 ATGTTTAATTTAATATTAT
49545718 AT
1 AT
49545720 AAATTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 3 0.15
21 7 0.35
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
ATGTTTAATTTAATATTAT
Found at i:49545744 original size:15 final size:16
Alignment explanation
Indices: 49545715--49545744 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
49545705 AATTTAATTT
49545715 TATATAAATTACATAC
1 TATATAAATTACATAC
49545731 TATATAAA-TACATA
1 TATATAAATTACATA
49545745 TGATAAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (16 bp):
TATATAAATTACATAC
Found at i:49550240 original size:2 final size:2
Alignment explanation
Indices: 49550233--49550279 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
49550223 TCATCTTTCT
* *
49550233 TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC GC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
49550275 TC TC T
1 TC TC T
49550280 GTCACTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.04, T:0.47
Consensus pattern (2 bp):
TC
Found at i:49555025 original size:2 final size:2
Alignment explanation
Indices: 49555018--49555049 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49555008 ATTTCAGGTT
49555018 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
49555050 ATATGTGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:49555105 original size:3 final size:3
Alignment explanation
Indices: 49555097--49555121 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49555087 AAGAGAAAGA
49555097 AGG AGG AGG AGG AGG AGG AGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG A
49555122 TAGTATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.64, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:49555858 original size:3 final size:3
Alignment explanation
Indices: 49555850--49555878 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
49555840 TGAAAAGGCT
49555850 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
49555879 TAACAGTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:49557390 original size:22 final size:22
Alignment explanation
Indices: 49557350--49557391 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
49557340 CATAATTATT
* * *
49557350 TTTATAATATGATTTTTTTTAA
1 TTTATAATATAAATATTTTTAA
49557372 TTTATAATATAAATATTTTT
1 TTTATAATATAAATATTTTT
49557392 TACCATAACC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTATAATATAAATATTTTTAA
Found at i:49558011 original size:10 final size:9
Alignment explanation
Indices: 49557990--49558114 Score: 81
Period size: 10 Copynumber: 13.0 Consensus size: 9
49557980 TAATATAAAC
49557990 TTATAAAAA
1 TTATAAAAA
49557999 TTATAATAAA
1 TTATAA-AAA
49558009 TTATAAAAA
1 TTATAAAAA
49558018 TTAT-AAAA
1 TTATAAAAA
49558026 TTAATAAAATA
1 TT-ATAAAA-A
* **
49558037 TATTTAAGATT
1 T-TATAA-AAA
49558048 TTATAAAAA
1 TTATAAAAA
* *
49558057 TGTATTAAAT
1 T-TATAAAAA
49558067 TCTATAAAAA
1 T-TATAAAAA
*
49558077 TCATAAAAA
1 TTATAAAAA
* *
49558086 GTATTAAAA
1 TTATAAAAA
*
49558095 TTAATATAAAC
1 TT-ATA-AAAA
49558106 TTATAAAAA
1 TTATAAAAA
49558115 CATATATAAA
Statistics
Matches: 88, Mismatches: 19, Indels: 18
0.70 0.15 0.14
Matches are distributed among these distances:
8 6 0.07
9 34 0.39
10 35 0.40
11 11 0.12
12 2 0.02
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
TTATAAAAA
Found at i:49558021 original size:28 final size:30
Alignment explanation
Indices: 49557963--49558123 Score: 81
Period size: 29 Copynumber: 5.5 Consensus size: 30
49557953 TATTAAATGT
* *
49557963 TAAAAATATATTAATATTAATATAAACTTA
1 TAAAAATATAATAATATTAATATAAAATTA
49557993 TAAAAATTATAATAA-ATT-ATA-AAAATTA
1 TAAAAA-TATAATAATATTAATATAAAATTA
* * *
49558021 T-AAAAT-TAATAA-AATATATTTAAGATTTTA
1 TAAAAATATAATAATATTA-ATATAA-A-ATTA
* * * *
49558051 TAAAAATGTATTAA-ATT-CTATAAAAATCA
1 TAAAAATATAATAATATTAATAT-AAAATTA
* *
49558080 TAAAAAGTAT--TAAAATTAATATAAACTTA
1 TAAAAA-TATAATAATATTAATATAAAATTA
*
49558109 TAAAAACATATATAA
1 TAAAAATATA-ATAA
49558124 AAGAACATTA
Statistics
Matches: 100, Mismatches: 16, Indels: 29
0.69 0.11 0.20
Matches are distributed among these distances:
25 8 0.08
26 1 0.01
27 6 0.06
28 14 0.14
29 26 0.26
30 21 0.21
31 17 0.17
32 7 0.07
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (30 bp):
TAAAAATATAATAATATTAATATAAAATTA
Found at i:49558074 original size:20 final size:18
Alignment explanation
Indices: 49557985--49558114 Score: 75
Period size: 19 Copynumber: 6.8 Consensus size: 18
49557975 AATATTAATA
*
49557985 TAAACTTATAAAAATTAT
1 TAAATTTATAAAAATTAT
49558003 AATAAA-TTATAAAAATTAT
1 --TAAATTTATAAAAATTAT
* *
49558022 AAAATTAAT-AAAATATATT
1 TAAATTTATAAAAAT-TA-T
49558041 TAAGATTTTATAAAAATGTAT
1 TAA-A-TTTATAAAAAT-TAT
*
49558062 TAAATTCTATAAAAATCAT
1 TAAATT-TATAAAAATTAT
* ** *
49558081 AAAAAGTATTAAAATTAAT
1 TAAATTTATAAAAATT-AT
*
49558100 ATAAACTTATAAAAA
1 -TAAATTTATAAAAA
49558115 CATATATAAA
Statistics
Matches: 86, Mismatches: 15, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
17 8 0.09
18 13 0.15
19 25 0.29
20 25 0.29
21 8 0.09
22 7 0.08
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.36
Consensus pattern (18 bp):
TAAATTTATAAAAATTAT
Found at i:49578083 original size:2 final size:2
Alignment explanation
Indices: 49578076--49578113 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
49578066 GGTAGTTCAA
49578076 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49578114 GCAATTGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49584129 original size:5 final size:5
Alignment explanation
Indices: 49584119--49584143 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
49584109 TATAAAATAT
49584119 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
49584144 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:49590170 original size:28 final size:28
Alignment explanation
Indices: 49590135--49590206 Score: 110
Period size: 28 Copynumber: 2.6 Consensus size: 28
49590125 AAAAATAAAA
* *
49590135 ATTTACCAAAATACTA-CAAGTTTTTTTT
1 ATTTACCAAAATA-TATAAACTTTTTTTT
49590163 ATTTACCAAAATATATAAACTTTTTTTT
1 ATTTACCAAAATATATAAACTTTTTTTT
49590191 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
49590207 CAAAAAAAAC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
27 2 0.05
28 39 0.95
ACGTcount: A:0.40, C:0.12, G:0.01, T:0.46
Consensus pattern (28 bp):
ATTTACCAAAATATATAAACTTTTTTTT
Found at i:49590310 original size:51 final size:51
Alignment explanation
Indices: 49590234--49590336 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
49590224 AAAAAAAAAC
49590234 TTGACAAAAAAAAATCAGACTGAAGTGACATCTCACTGGTCACGCCAATGG
1 TTGACAAAAAAAAATCAGACTGAAGTGACATCTCACTGGTCACGCCAATGG
49590285 TTGACAAAAAAAAATCAGACTGAAGTGACATCTCACTGGTCACGCCAATGG
1 TTGACAAAAAAAAATCAGACTGAAGTGACATCTCACTGGTCACGCCAATGG
49590336 T
1 T
49590337 ATTGGCGGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.20
Consensus pattern (51 bp):
TTGACAAAAAAAAATCAGACTGAAGTGACATCTCACTGGTCACGCCAATGG
Found at i:49590367 original size:27 final size:27
Alignment explanation
Indices: 49590328--49590430 Score: 161
Period size: 27 Copynumber: 3.8 Consensus size: 27
49590318 CACTGGTCAC
** *
49590328 GCCAATGGTATTGGCGGCACCAAAGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
**
49590355 GCCAAAACCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
49590382 GCCAATGCCATTGGCGGCACCAATGGT
1 GCCAATGCCATTGGCGGCACCAATGGT
49590409 GCCAATGCCATTGGCGGCACCA
1 GCCAATGCCATTGGCGGCACCA
49590431 GTTGGTGTTA
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.25, C:0.29, G:0.29, T:0.17
Consensus pattern (27 bp):
GCCAATGCCATTGGCGGCACCAATGGT
Found at i:49590482 original size:4 final size:4
Alignment explanation
Indices: 49590473--49590570 Score: 71
Period size: 4 Copynumber: 24.5 Consensus size: 4
49590463 GCAGAAGGAG
* * *
49590473 AGAA AGAA AGAA AGAA AGGAG AGGA AGAA AGAAA AGGAA AG-G AGAA GAGAA
1 AGAA AGAA AGAA AGAA A-GAA AGAA AGAA AG-AA A-GAA AGAA AGAA -AGAA
* *
49590524 A-AA AGGAA AGAA AG-A AG-A AGAA A-AA AGAA AGAA GGAA GGAA AGAA
1 AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA
49590569 AG
1 AG
49590571 GGAAAGGAGA
Statistics
Matches: 77, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
3 14 0.18
4 46 0.60
5 16 0.21
6 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:49590491 original size:21 final size:21
Alignment explanation
Indices: 49590467--49590593 Score: 97
Period size: 21 Copynumber: 6.0 Consensus size: 21
49590457 GTGGGGGCAG
49590467 AAGGAGAGAAAGAAAGAAAGA
1 AAGGAGAGAAAGAAAGAAAGA
*
49590488 AAGGAGAGGAAGAAAGAAAAGGA
1 AAGGAGAGAAAGAAAG-AAA-GA
*
49590511 AAGGAGAAGAGAAAAAAGGAAAGA
1 AAGGAG-AGA-AAGAAA-GAAAGA
*
49590535 AAGAAGAAGAAA-AAAGAAAG-
1 AAGGAG-AGAAAGAAAGAAAGA
*
49590555 AAGGA-AGGAAAGAAAG--GGA
1 AAGGAGA-GAAAGAAAGAAAGA
*
49590574 AAGGAGA-AGAGAAA-AAAGA
1 AAGGAGAGAAAGAAAGAAAGA
49590593 A
1 A
49590594 GAAGAAGAAG
Statistics
Matches: 87, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
18 8 0.09
19 12 0.14
20 9 0.10
21 20 0.23
22 6 0.07
23 10 0.11
24 13 0.15
25 8 0.09
26 1 0.01
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (21 bp):
AAGGAGAGAAAGAAAGAAAGA
Found at i:49590502 original size:17 final size:15
Alignment explanation
Indices: 49590480--49590570 Score: 71
Period size: 17 Copynumber: 5.7 Consensus size: 15
49590470 GAGAGAAAGA
49590480 AAGAAAGAAAGGAGAGG
1 AAGAAAGAAA-GA-AGG
49590497 AAGAAAGAAAAGGAAAGG
1 AAGAAAG-AAA-G-AAGG
*
49590515 -AGAAGAGAAAAAAGG
1 AAGAA-AGAAAGAAGG
49590530 AAAGAAAG-AAGAA-G
1 -AAGAAAGAAAGAAGG
*
49590544 AAAAAAGAAAGAAGG
1 AAGAAAGAAAGAAGG
49590559 AAGGAAAGAAAG
1 AA-GAAAGAAAG
49590571 GGAAAGGAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
13 6 0.10
14 6 0.10
15 11 0.18
16 10 0.16
17 18 0.29
18 10 0.16
19 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAGAAGG
Found at i:49590554 original size:51 final size:52
Alignment explanation
Indices: 49590497--49590599 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 52
49590487 AAAGGAGAGG
49590497 AAGAAAGAA-AAGGAAAGGAGAAGAGAAA-A-AAG-GAAAGAAAGAAGAAGAAAA
1 AAGAAAGAAGAAGGAAA-GA-AAGAGAAAGAGAAGAGAAA-AAAGAAGAAGAAAA
*
49590548 AAGAAAGAAGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAGAAGAAGAA
1 AAGAAAGAA-GAAGGAAAGAAAGAGAAA-GAGAAGAGAAAAAAGAAGAAGAA
49590600 GAAGAGGGAA
Statistics
Matches: 45, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
51 16 0.36
52 2 0.04
53 8 0.18
54 15 0.33
55 4 0.09
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (52 bp):
AAGAAAGAAGAAGGAAAGAAAGAGAAAGAGAAGAGAAAAAAGAAGAAGAAAA
Found at i:49590578 original size:63 final size:62
Alignment explanation
Indices: 49590476--49590604 Score: 192
Period size: 63 Copynumber: 2.1 Consensus size: 62
49590466 GAAGGAGAGA
49590476 AAGAAAGAAAGAAAGGAGAGGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGGAAAGAAAGAAG
1 AAGAAAGAAAGAAAGGAGAGGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAA-G-AAG-AAGAAG
*
49590541 AAGAAA-AAAGAAA-GA-AGGAAGGAAAGAAAGGGAAAGGAGAAGAGAAAAAAGAAGAAGAAG
1 AAGAAAGAAAGAAAGGAGAGGAA-GAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAG
49590601 AAGA
1 AAGA
49590605 GGGAAGAAAG
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
60 10 0.16
61 3 0.05
62 6 0.10
63 30 0.48
64 7 0.11
65 6 0.10
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (62 bp):
AAGAAAGAAAGAAAGGAGAGGAAGAAAGAAAAGGAAAGGAGAAGAGAAAAAAGAAGAAGAAG
Found at i:49590581 original size:29 final size:30
Alignment explanation
Indices: 49590494--49590586 Score: 91
Period size: 33 Copynumber: 3.0 Consensus size: 30
49590484 AAGAAAGGAG
*
49590494 AGGAA-GAAAGAAAAGGAAAGGAGAAGAGA
1 AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
** **
49590523 AAAAAGGAAAGAAAGAAGAAGAAAAAAGAA-AGA
1 AGGAAGGAAAGAAAG--G--GAAAGGAGAAGAGA
49590556 AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
1 AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
49590586 A
1 A
49590587 AAAAGAAGAA
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
29 11 0.22
30 12 0.24
31 1 0.02
32 1 0.02
33 16 0.33
34 8 0.16
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (30 bp):
AGGAAGGAAAGAAAGGGAAAGGAGAAGAGA
Found at i:49590957 original size:13 final size:13
Alignment explanation
Indices: 49590939--49590963 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49590929 GAAAATAAAT
49590939 AAATGCGAAAAAG
1 AAATGCGAAAAAG
49590952 AAATGCGAAAAA
1 AAATGCGAAAAA
49590964 TGTACATGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.08, G:0.20, T:0.08
Consensus pattern (13 bp):
AAATGCGAAAAAG
Found at i:49593672 original size:36 final size:36
Alignment explanation
Indices: 49593628--49593733 Score: 101
Period size: 26 Copynumber: 3.3 Consensus size: 36
49593618 AAATAATAAA
49593628 CAAAATAATACACACTAAAATTATTAATTTTATACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
**
49593664 ---ACGAAT--A-A-T---ATTATTAATTTTATACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
49593690 CAAAATAATACACACTAAAATTATTAA-TTT-TACT
1 CAAAATAATACACACTAAAATTATTAATTTTATACT
*
49593724 AAAAATAATA
1 CAAAATAATA
49593734 ACTAACTATA
Statistics
Matches: 55, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
26 17 0.31
29 5 0.09
30 1 0.02
31 2 0.04
32 1 0.02
33 5 0.09
34 13 0.24
35 3 0.05
36 8 0.15
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (36 bp):
CAAAATAATACACACTAAAATTATTAATTTTATACT
Found at i:49593889 original size:3 final size:3
Alignment explanation
Indices: 49593881--49593975 Score: 190
Period size: 3 Copynumber: 31.7 Consensus size: 3
49593871 TCTTCATACT
49593881 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
49593929 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
49593976 TAATAATAAT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 92 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:49593980 original size:3 final size:3
Alignment explanation
Indices: 49593974--49594032 Score: 100
Period size: 3 Copynumber: 19.3 Consensus size: 3
49593964 CAACAACAAC
49593974 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
49594022 ATT AACT AAT A
1 AAT AA-T AAT A
49594033 CTTTTATTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:49594289 original size:27 final size:27
Alignment explanation
Indices: 49594251--49594317 Score: 107
Period size: 27 Copynumber: 2.5 Consensus size: 27
49594241 ATAATACGAG
49594251 TGGTGCCGCCAATGGCATTGGCACCAT
1 TGGTGCCGCCAATGGCATTGGCACCAT
** *
49594278 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGCATTGGCACCAT
49594305 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
49594318 ACTATTGGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.15, C:0.28, G:0.30, T:0.27
Consensus pattern (27 bp):
TGGTGCCGCCAATGGCATTGGCACCAT
Found at i:49594325 original size:27 final size:27
Alignment explanation
Indices: 49594251--49594326 Score: 100
Period size: 27 Copynumber: 2.8 Consensus size: 27
49594241 ATAATACGAG
49594251 TGGTGCCGCCAATGGC-ATTGGCACCAT
1 TGGTGCCGCCAAT-GCTATTGGCACCAT
* * *
49594278 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGCTATTGGCACCAT
*
49594305 TGGTGCCGCCAATACTATTGGC
1 TGGTGCCGCCAATGCTATTGGC
49594327 GTGACCAGTG
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGCTATTGGCACCAT
Found at i:49594427 original size:28 final size:28
Alignment explanation
Indices: 49594387--49594462 Score: 107
Period size: 28 Copynumber: 2.7 Consensus size: 28
49594377 TTTTGGTTTT
*
49594387 TTTATATATTTTGGTAAATAAAAAAAAG
1 TTTATATATTTTGGTAAATAAAAAAAAA
*
49594415 TTTATATATTTTGATAAATAAAAAAAAA
1 TTTATATATTTTGGTAAATAAAAAAAAA
* *
49594443 CTTGTAGTATTTTGGTAAAT
1 TTTATA-TATTTTGGTAAAT
49594463 TTTTATTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
28 30 0.71
29 12 0.29
ACGTcount: A:0.46, C:0.01, G:0.11, T:0.42
Consensus pattern (28 bp):
TTTATATATTTTGGTAAATAAAAAAAAA
Found at i:49600266 original size:40 final size:38
Alignment explanation
Indices: 49600222--49600299 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
49600212 TTGTCATATG
**
49600222 ACATTAATTTAAAATACGATTATTGTAGCTTAAAAAACTT
1 ACATTAATGCAAAATA--ATTATTGTAGCTTAAAAAACTT
* *
49600262 ACATTAATGCGACATAATTATTGTAGCTTAAAAAACTT
1 ACATTAATGCAAAATAATTATTGTAGCTTAAAAAACTT
49600300 GACCTACAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 22 0.65
40 12 0.35
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.36
Consensus pattern (38 bp):
ACATTAATGCAAAATAATTATTGTAGCTTAAAAAACTT
Found at i:49603480 original size:22 final size:21
Alignment explanation
Indices: 49603455--49603502 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
49603445 TTTTCACAAA
49603455 CAAATCCTATCTAATTTCCTTC
1 CAAATCCTATC-AATTTCCTTC
* *
49603477 CAAAATTCTCTCAATTTCCTTC
1 C-AAATCCTATCAATTTCCTTC
49603499 CAAA
1 CAAA
49603503 ATTCTCTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 3 0.13
22 12 0.52
23 8 0.35
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (21 bp):
CAAATCCTATCAATTTCCTTC
Found at i:49603503 original size:22 final size:22
Alignment explanation
Indices: 49603467--49603512 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
49603457 AATCCTATCT
49603467 AATTTCCTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
49603489 AATTTCCTTCCAAAATTCTCTC
1 AATTTCCTTCCAAAATTCTCTC
49603511 AA
1 AA
49603513 ACTCTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTTCCTTCCAAAATTCTCTC
Found at i:49603520 original size:30 final size:30
Alignment explanation
Indices: 49603484--49603542 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
49603474 TTCCAAAATT
* *
49603484 CTCTCAATTTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
49603514 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
49603543 TTTCCTTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:49603561 original size:22 final size:22
Alignment explanation
Indices: 49603514--49603555 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
49603504 TTCTCTCAAA
49603514 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
*
49603536 CTCTCAATTTCCTTCCAAAA
1 CTCTCAAATTCCTTCCAAAA
49603556 ATCTCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:49603595 original size:17 final size:18
Alignment explanation
Indices: 49603570--49603603 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
49603560 CTAAAATCCA
49603570 TATTAAATTTC-TTTTTC
1 TATTAAATTTCATTTTTC
*
49603587 TATTCAATTTCATTTTT
1 TATTAAATTTCATTTTT
49603604 TAAGATAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.65
Consensus pattern (18 bp):
TATTAAATTTCATTTTTC
Found at i:49603633 original size:31 final size:30
Alignment explanation
Indices: 49603598--49603663 Score: 105
Period size: 31 Copynumber: 2.2 Consensus size: 30
49603588 ATTCAATTTC
* *
49603598 ATTTTTTAAGATAATTTTAAATATTTTTTAT
1 ATTTTTTAAAATAATTTTAAAT-TTTTTAAT
49603629 ATTTTTTAAAATAATTTTAAATTTTTTAAT
1 ATTTTTTAAAATAATTTTAAATTTTTTAAT
49603659 ATTTT
1 ATTTT
49603664 CAACAATGGC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (30 bp):
ATTTTTTAAAATAATTTTAAATTTTTTAAT
Found at i:49603635 original size:20 final size:20
Alignment explanation
Indices: 49603598--49603663 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 20
49603588 ATTCAATTTC
*
49603598 ATTTTTTAAGATAATTTTAAAT
1 ATTTTTTAA-AT-TTTTTAAAT
*
49603620 ATTTTTTATATTTTTTAAA-
1 ATTTTTTAAATTTTTTAAAT
*
49603639 ATAATTTTAAATTTTTT-AAT
1 AT-TTTTTAAATTTTTTAAAT
49603659 ATTTT
1 ATTTT
49603664 CAACAATGGC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
19 6 0.16
20 21 0.57
21 2 0.05
22 8 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
ATTTTTTAAATTTTTTAAAT
Found at i:49607507 original size:123 final size:124
Alignment explanation
Indices: 49607279--49607593 Score: 569
Period size: 123 Copynumber: 2.5 Consensus size: 124
49607269 CCACGAGGGC
* **
49607279 GCAATTTTATACTATTTGCTCAGAAATTTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
1 GCAATTTAATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
*
49607344 AAATCGCGTCCACGAGGGCTCGATTTCACAATTTCTTCTCAAATATCATCCTGGTAGAA
66 AAATCGCGTCCACGAAGGCTCGATTTCACAATTTCTTCTCAAATATCATCCTGGTAGAA
* *
49607403 GCGATTTAATACTATTTGCTCAGAAACGTCAAAAAAAA-TATTTCTTACATGATCAACTGTAGCG
1 GCAATTTAATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
49607467 AAATCGCGTCCACGAAGGCTCGATTTCACAATTTCTTCTCAAATATCATCCTGGTAGAA
66 AAATCGCGTCCACGAAGGCTCGATTTCACAATTTCTTCTCAAATATCATCCTGGTAGAA
49607526 GCAATTTAATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
1 GCAATTTAATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
49607591 AAA
66 AAA
49607594 CCCTAAAAAG
Statistics
Matches: 182, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
123 120 0.66
124 62 0.34
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (124 bp):
GCAATTTAATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
AAATCGCGTCCACGAAGGCTCGATTTCACAATTTCTTCTCAAATATCATCCTGGTAGAA
Found at i:49612712 original size:6 final size:7
Alignment explanation
Indices: 49612697--49612721 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
49612687 TCAAGTTGGA
49612697 TTTTATT
1 TTTTATT
49612704 TTTTATT
1 TTTTATT
49612711 TTTTATT
1 TTTTATT
49612718 TTTT
1 TTTT
49612722 CTTAATCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:49614833 original size:13 final size:13
Alignment explanation
Indices: 49614815--49614846 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49614805 TTTCCAGCAA
49614815 TTATGAATTTATT
1 TTATGAATTTATT
49614828 TTATGAATTTATT
1 TTATGAATTTATT
*
49614841 TGATGA
1 TTATGA
49614847 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:49615051 original size:50 final size:50
Alignment explanation
Indices: 49614940--49615144 Score: 284
Period size: 50 Copynumber: 4.0 Consensus size: 50
49614930 CATTTGGGTA
* *
49614940 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATC
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C
*
49614994 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATGGGCACCGAGAC
1 A--AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* * *
49615046 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
* *
49615096 GAGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGA
1 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGA
49615145 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
50 90 0.65
52 2 0.01
53 4 0.03
54 1 0.01
55 2 0.01
56 39 0.28
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (50 bp):
AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAC
Found at i:49615136 original size:100 final size:103
Alignment explanation
Indices: 49614940--49615144 Score: 326
Period size: 100 Copynumber: 2.0 Consensus size: 103
49614930 CATTTGGGTA
49614940 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCC
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC-TGAGA--ATGAGAGGTCC
49615005 CATGTAAGACCATGTATGGGACATGGCATGGGCACCGAGAC
63 CATGTAAGACCATGTATGGGACATGGCATGGGCACCGAGAC
* * *
49615046 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GAG-ATGAGAGGTCCCCT
1 AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCAT
*
49615108 GTAAGACCATGTCTGGGACATGGCATGGGCACCGAGA
66 GTAAGACCATGTATGGGACATGGCATGGGCACCGAGA
49615145 NNNNNNNNNN
Statistics
Matches: 95, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
100 49 0.52
103 3 0.03
105 2 0.02
106 41 0.43
ACGTcount: A:0.27, C:0.22, G:0.31, T:0.20
Consensus pattern (103 bp):
AAGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTGAGAATGAGAGGTCCCAT
GTAAGACCATGTATGGGACATGGCATGGGCACCGAGAC
Found at i:49634637 original size:13 final size:13
Alignment explanation
Indices: 49634619--49634650 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49634609 TTTCCAGCAA
49634619 TTATGAATTTATT
1 TTATGAATTTATT
49634632 TTATGAATTTATT
1 TTATGAATTTATT
*
49634645 TGATGA
1 TTATGA
49634651 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Done.