Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 177 of 290
Found at i:60702542 original size:31 final size:31
Alignment explanation
Indices: 60702485--60702543 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
60702475 GTAAATACCC
* * *
60702485 AAAATTTGAGGGATTAAAGTGTAAATATGAA
1 AAAATTGGAGGGACTAAAGTGCAAATATGAA
60702516 AAAATTGGA-GGACTAATAGTGCAAATAT
1 AAAATTGGAGGGACTAA-AGTGCAAATAT
60702544 TTTAAGGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 6 0.25
31 18 0.75
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAATTGGAGGGACTAAAGTGCAAATATGAA
Found at i:60704849 original size:42 final size:42
Alignment explanation
Indices: 60704790--60704873 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
60704780 CGACAGAGGA
60704790 CTCCGAGGTGGCCACTCGAAGTAGTTTTTTTTTAAATATTAC
1 CTCCGAGGTGGCCACTCGAAGTAGTTTTTTTTTAAATATTAC
60704832 CTCCGAGGTGGCCACTCGAAGTAGTTTTTTTTTAAATATTAC
1 CTCCGAGGTGGCCACTCGAAGTAGTTTTTTTTTAAATATTAC
60704874 ACTTAAGAGT
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:0.19, G:0.19, T:0.38
Consensus pattern (42 bp):
CTCCGAGGTGGCCACTCGAAGTAGTTTTTTTTTAAATATTAC
Found at i:60707234 original size:43 final size:42
Alignment explanation
Indices: 60707154--60707237 Score: 116
Period size: 43 Copynumber: 2.0 Consensus size: 42
60707144 GCACCATACT
* *
60707154 AATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATC
1 AATGCCATAGCCCAGATATGGTCTTACATGAGATCTCATATC
*
60707196 AATGCCAATAGCCCAGCTATGGTCTTACATGA-AGTCTCATAT
1 AATGCC-ATAGCCCAGATATGGTCTTACATGAGA-TCTCATAT
60707238 TGCTGTCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 7 0.19
43 30 0.81
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
AATGCCATAGCCCAGATATGGTCTTACATGAGATCTCATATC
Found at i:60709606 original size:20 final size:20
Alignment explanation
Indices: 60709577--60709621 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
60709567 AGCACATGTA
* *
60709577 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAAATT
*
60709597 TTCATCAAATTTTACAAATT
1 TTCATAAAATTTTACAAATT
60709617 TTCAT
1 TTCAT
60709622 TTTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAAATT
Found at i:60710355 original size:410 final size:410
Alignment explanation
Indices: 60709595--60710839 Score: 2481
Period size: 410 Copynumber: 3.0 Consensus size: 410
60709585 ATTTTAGAAT
*
60709595 TTTTCATCAAATTTTACAAATTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
1 TTTTCATCAAATTTTACAACTTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
60709660 GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
66 GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
60709725 TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
131 TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
60709790 AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
196 AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
60709855 CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
261 CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
60709920 AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
326 AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
60709985 TTATCTTTTTCTATAAATTC
391 TTATCTTTTTCTATAAATTC
60710005 TTTTCATCAAATTTTACAACTTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
1 TTTTCATCAAATTTTACAACTTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
60710070 GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
66 GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
60710135 TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
131 TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
60710200 AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
196 AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
60710265 CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
261 CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
60710330 AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
326 AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
60710395 TTATCTTTTTCTATAAATTC
391 TTATCTTTTTCTATAAATTC
60710415 TTTTCATCAAATTTTACAACTTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
1 TTTTCATCAAATTTTACAACTTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
60710480 GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
66 GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
60710545 TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
131 TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
60710610 AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
196 AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
60710675 CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
261 CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
60710740 AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
326 AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
60710805 TTATCTTTTTCTATAAATTC
391 TTATCTTTTTCTATAAATTC
60710825 TTTTCATCAAATTTT
1 TTTTCATCAAATTTT
60710840 TTTATGCCTT
Statistics
Matches: 834, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
410 834 1.00
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.41
Consensus pattern (410 bp):
TTTTCATCAAATTTTACAACTTTTCATTTTAGTCCCTAAATCATGTTTTTGTCAAAAATCACTTA
GTAAAAGTTGTTTATCTATCAATAATCTTTCATTTTCTACCATAAATTTCTAATTTCCAGCATAA
TACATCCATGAACCATTTTCATACTTTGATAACTTTTCAAATTAATCCCTCAAATAGAGAGATTA
AGCTATCCCAATTTCAAAAATACCAAAAATACTAAAAACGGGACAAGAGAACTTACCCAATTTGG
CCTTGAAATCTTCTTTTCTCTCTCCTATGGTTTCCATGTGTTTTTAGGTTGAATATGATGAAAAT
AAGATGATATAAATTCTTTACATCTTTTAATTAATTAAGTTTTTTGGTATTTTCAATTTAGTCCA
TTATCTTTTTCTATAAATTC
Found at i:60714326 original size:20 final size:20
Alignment explanation
Indices: 60714301--60714344 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
60714291 AACTGTCTCT
60714301 ATTTGATTCCAATCAAATTG
1 ATTTGATTCCAATCAAATTG
** *
60714321 ATTTGATTTTATTCAAATTG
1 ATTTGATTCCAATCAAATTG
60714341 ATTT
1 ATTT
60714345 AAAGGTTCCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.50
Consensus pattern (20 bp):
ATTTGATTCCAATCAAATTG
Found at i:60717869 original size:30 final size:30
Alignment explanation
Indices: 60717809--60717879 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
60717799 AAAGTGATTA
* * *
60717809 TTATTTTTGTATACTTTAAATTTTATTTTT
1 TTATTTTTTTATACTTTAAAATATATTTTT
*
60717839 TTATTTTTTTATATTTTAAAA-ATATATTTT
1 TTATTTTTTTATACTTTAAAATATAT-TTTT
*
60717869 TTATGTTTTTA
1 TTATTTTTTTA
60717880 AAAGTTGAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 3 0.09
30 32 0.91
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (30 bp):
TTATTTTTTTATACTTTAAAATATATTTTT
Found at i:60717961 original size:24 final size:23
Alignment explanation
Indices: 60717929--60717975 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
60717919 TTTTAACTTT
* *
60717929 ATTTTTTTATTTTTTATAAATTTA
1 ATTTATTTAATTTTTATA-ATTTA
60717953 ATTTATTTAATTTTTATAATTTA
1 ATTTATTTAATTTTTATAATTTA
60717976 TAATATTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
ATTTATTTAATTTTTATAATTTA
Found at i:60718397 original size:2 final size:2
Alignment explanation
Indices: 60718390--60718415 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
60718380 GATTAAATGG
60718390 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
60718416 TTCACATGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60718717 original size:21 final size:21
Alignment explanation
Indices: 60718693--60718733 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60718683 TATTTAAATT
60718693 TAATTAACAATCT-AGATTAAC
1 TAATTAACAAT-TAAGATTAAC
*
60718714 TAATTAATAATTAAGATTAA
1 TAATTAACAATTAAGATTAA
60718734 GTTAGAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.51, C:0.07, G:0.05, T:0.37
Consensus pattern (21 bp):
TAATTAACAATTAAGATTAAC
Found at i:60720875 original size:18 final size:17
Alignment explanation
Indices: 60720845--60720891 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
60720835 TAAGGTTATG
*
60720845 GATTTAGGT-TTGCTTTT
1 GATTTA-GTATTGCTCTT
60720862 GCATTTAGTATTGCTCTT
1 G-ATTTAGTATTGCTCTT
*
60720880 GATTTATTATTG
1 GATTTAGTATTG
60720892 ATGATTTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 13 0.50
18 13 0.50
ACGTcount: A:0.17, C:0.09, G:0.19, T:0.55
Consensus pattern (17 bp):
GATTTAGTATTGCTCTT
Found at i:60729959 original size:47 final size:47
Alignment explanation
Indices: 60729893--60730246 Score: 433
Period size: 47 Copynumber: 7.3 Consensus size: 47
60729883 TACATGATAG
* * *
60729893 TATATGTGGTATGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
*
60729940 TATATGTGATAAGGCCTAATGG-C-ATGTGATGAATGTGAAAGTGTATATATA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG------TA
*
60729991 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
*
60730038 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG------TA
*
60730091 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
*
60730138 TATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTG--TA
* * * * * *
60730187 TATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
*
60730234 TAAATGTGATAAG
1 TATATGTGATAAG
60730247 TCCCGAAGGG
Statistics
Matches: 269, Mismatches: 22, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
45 18 0.07
46 1 0.00
47 122 0.45
49 40 0.15
51 24 0.09
52 1 0.00
53 63 0.23
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.29
Consensus pattern (47 bp):
TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAAAGTGTA
Found at i:60730111 original size:100 final size:100
Alignment explanation
Indices: 60729893--60730246 Score: 576
Period size: 100 Copynumber: 3.6 Consensus size: 100
60729883 TACATGATAG
* *
60729893 TATATGTGGTATGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
60729958 ATGG-C-ATGTGATGAATGTGAAAGTGTATATATA
66 ATGGCCGATGTGATGAATGTGAAAGTGTATATATA
60729991 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
60730056 ATGGCCGATGTGATGAATGTGAAAGTGTATATATA
66 ATGGCCGATGTGATGAATGTGAAAGTGTATATATA
60730091 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
60730156 ATGGCCGATGTGATGAATGTGAAAGTG----TATA
66 ATGGCCGATGTGATGAATGTGAAAGTGTATATATA
* * * * * * * *
60730187 TATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAG
60730247 TCCCGAAGGG
Statistics
Matches: 244, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
96 56 0.23
98 67 0.27
99 1 0.00
100 120 0.49
ACGTcount: A:0.31, C:0.09, G:0.30, T:0.29
Consensus pattern (100 bp):
TATATGTGATAAGGCCTAATGGCCGACGTGATGAATGTGAGAGTGTATATATGTGATAAGGCCTA
ATGGCCGATGTGATGAATGTGAAAGTGTATATATA
Found at i:60730421 original size:37 final size:37
Alignment explanation
Indices: 60730365--60730443 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
60730355 CCGAGCTCTA
* *
60730365 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
60730402 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
60730439 AAGAC
1 AAGAC
60730444 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:60734885 original size:27 final size:25
Alignment explanation
Indices: 60734854--60734912 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
60734844 ACACATGAAA
*
60734854 TCTTAAATCAACTTTTCAAAAATACTT
1 TCTTAAATC-ACTTTTCAAAAACAC-T
* * *
60734881 TCTTACATCATTTTTCAAGAACACT
1 TCTTAAATCACTTTTCAAAAACACT
60734906 TCTTAAA
1 TCTTAAA
60734913 AGTAATGCTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
25 7 0.26
26 12 0.44
27 8 0.30
ACGTcount: A:0.37, C:0.20, G:0.02, T:0.41
Consensus pattern (25 bp):
TCTTAAATCACTTTTCAAAAACACT
Found at i:60736975 original size:15 final size:14
Alignment explanation
Indices: 60736955--60736986 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
60736945 ATTTCATTAC
60736955 TTATTATAAATATAT
1 TTATTATAAATAT-T
60736970 TTATTATAAATATT
1 TTATTATAAATATT
60736984 TTA
1 TTA
60736987 CATATTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTATTATAAATATT
Found at i:60754579 original size:13 final size:13
Alignment explanation
Indices: 60754561--60754602 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
60754551 AATATATATA
60754561 TTAAATCTATTAC
1 TTAAATCTATTAC
* *
60754574 TTAAATATGTTAC
1 TTAAATCTATTAC
60754587 TTAAATAC-ATTAC
1 TTAAAT-CTATTAC
60754600 TTA
1 TTA
60754603 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.45
Consensus pattern (13 bp):
TTAAATCTATTAC
Found at i:60754669 original size:36 final size:36
Alignment explanation
Indices: 60754627--60754738 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 36
60754617 TACTTATATG
60754627 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
* *
60754663 TAAAATTTAAGTA----AGTT---TAC-TTA--TATG
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTA-C
60754690 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
1 TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
60754726 TAAAATTTAAGTA
1 TAAAATTTAAGTA
60754739 AGTTTACATA
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
26 2 0.03
27 13 0.21
28 3 0.05
29 3 0.05
31 3 0.05
32 3 0.05
34 3 0.05
35 3 0.05
36 26 0.43
37 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (36 bp):
TAAAATTTAAGTATGTTACTTAAATACATTACTTAC
Found at i:60754695 original size:63 final size:63
Alignment explanation
Indices: 60754574--60754756 Score: 320
Period size: 63 Copynumber: 3.0 Consensus size: 63
60754564 AATCTATTAC
*
60754574 TTAAATATGTTACTTAAATACATTACTTACTAAAA-TT---TAAGTTTACTTATATGTAAAAT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
60754633 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
*
60754696 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACATATATGTAAA
1 TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAA
60754757 CTTACATAAT
Statistics
Matches: 118, Mismatches: 2, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
59 34 0.29
60 2 0.02
63 82 0.69
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (63 bp):
TTAAGTATGTTACTTAAATACATTACTTACTAAAATTTAAGTAAGTTTACTTATATGTAAAAT
Found at i:60754826 original size:44 final size:37
Alignment explanation
Indices: 60754774--60754863 Score: 155
Period size: 37 Copynumber: 2.4 Consensus size: 37
60754764 AATACATTAC
60754774 AACTTACATAATACATAACTT-TAAAATTTTTTATATA
1 AACTTACATAATACATAACTTAT-AAATTTTTTATATA
*
60754811 AACTTACATAATACATAACTTATAATTTTTTTATATA
1 AACTTACATAATACATAACTTATAAATTTTTTATATA
60754848 AACTTACATAATACAT
1 AACTTACATAATACAT
60754864 TTAACTTACA
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 50 0.98
38 1 0.02
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (37 bp):
AACTTACATAATACATAACTTATAAATTTTTTATATA
Found at i:60754879 original size:9 final size:9
Alignment explanation
Indices: 60754848--60755317 Score: 341
Period size: 9 Copynumber: 52.0 Consensus size: 9
60754838 TTTTTATATA
60754848 AACTTACAT
1 AACTTACAT
60754857 AA--TACATTT
1 AACTTACA--T
60754866 AACTTACAT
1 AACTTACAT
60754875 AACTTACAT
1 AACTTACAT
*
60754884 AACTTACAC
1 AACTTACAT
60754893 AACTTACAT
1 AACTTACAT
60754902 AACCTT-CAT
1 AA-CTTACAT
60754911 AA--TACATTT
1 AACTTACA--T
60754920 AACTTACAT
1 AACTTACAT
60754929 AACTTACAT
1 AACTTACAT
60754938 AACTTACAT
1 AACTTACAT
* *
60754947 AA--TGCAA
1 AACTTACAT
60754954 AACTTACAT
1 AACTTACAT
60754963 AACAACTTACAT
1 ---AACTTACAT
*
60754975 AACATACAT
1 AACTTACAT
* **
60754984 TACTTTGAT
1 AACTTACAT
60754993 AACTTACAT
1 AACTTACAT
*
60755002 AACTTACAG
1 AACTTACAT
* *
60755011 AA--TGCAA
1 AACTTACAT
60755018 AACTTACAT
1 AACTTACAT
*
60755027 AAC-AAC-T
1 AACTTACAT
*
60755034 TACTTACAT
1 AACTTACAT
*
60755043 AACATACAT
1 AACTTACAT
* *
60755052 TACTTAAAT
1 AACTTACAT
* *
60755061 TATTTACAT
1 AACTTACAT
60755070 AA--TACAT
1 AACTTACAT
60755077 AACTTAGTACAT
1 AAC-T--TACAT
*
60755089 AATTTACAT
1 AACTTACAT
60755098 AA--TACAT
1 AACTTACAT
*
60755105 AACTTAGTACAC
1 AAC-T--TACAT
60755117 AACTTACAT
1 AACTTACAT
* *
60755126 AATTTTTTC-T
1 AA--CTTACAT
60755136 AAATTGCTTACAT
1 -AA---CTTACAT
* *
60755149 AAATTATAT
1 AACTTACAT
60755158 AACTTACAT
1 AACTTACAT
60755167 AACTTACATT
1 AACTTACA-T
*
60755177 AA-TTAAAT
1 AACTTACAT
60755185 AACTTACAT
1 AACTTACAT
60755194 AACTTACAT
1 AACTTACAT
60755203 AACTTACAT
1 AACTTACAT
*
60755212 ATCTTACAT
1 AACTTACAT
60755221 AACTTACAT
1 AACTTACAT
* *
60755230 AAATTAAAT
1 AACTTACAT
60755239 AACTTACAT
1 AACTTACAT
60755248 AACTTACAT
1 AACTTACAT
60755257 AACTTACAT
1 AACTTACAT
*
60755266 AAATTACAT
1 AACTTACAT
60755275 AACTTACAT
1 AACTTACAT
60755284 AACTTACAT
1 AACTTACAT
60755293 AA--TACAT
1 AACTTACAT
*
60755300 AACCTT-CCT
1 AA-CTTACAT
60755309 AACTTACAT
1 AACTTACAT
60755318 TATTGTTTAA
Statistics
Matches: 367, Mismatches: 54, Indels: 80
0.73 0.11 0.16
Matches are distributed among these distances:
6 1 0.00
7 40 0.11
8 10 0.03
9 263 0.72
10 8 0.02
11 15 0.04
12 29 0.08
13 1 0.00
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:60754971 original size:12 final size:12
Alignment explanation
Indices: 60754954--60754978 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60754944 CATAATGCAA
60754954 AACTTACATAAC
1 AACTTACATAAC
60754966 AACTTACATAAC
1 AACTTACATAAC
60754978 A
1 A
60754979 TACATTACTT
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:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (12 bp):
AACTTACATAAC
Found at i:60755006 original size:64 final size:64
Alignment explanation
Indices: 60754865--60755078 Score: 235
Period size: 64 Copynumber: 3.3 Consensus size: 64
60754855 ATAATACATT
* *
60754865 TAACTTACATAACTTACATAACTTACACAACTTACATAAC--CTT-CAT-A-ATACATTTAACTT
1 TAACTTACATAACTTACATAA--TGCAAAACTTACATAACAACTTACATAACATACA-TT-ACTT
60754925 ACA
62 ACA
**
60754928 TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACATAACATACATTACTTTGA
1 TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACATAACATACATTACTTACA
*
60754992 TAACTTACATAACTTACAGAATGCAAAACTTACATAACAACTTACTTACATAACATACATTACTT
1 TAACTTACATAACTTACATAATGCAAAACTTACATAAC-A---ACTTACATAACATACATTACTT
*
60755057 AAA
62 ACA
* *
60755060 TTATTTACATAA--TACATAA
1 TAACTTACATAACTTACATAA
60755079 CTTAGTACAT
Statistics
Matches: 132, Mismatches: 10, Indels: 15
0.84 0.06 0.10
Matches are distributed among these distances:
61 15 0.11
63 24 0.18
64 45 0.34
65 4 0.03
66 11 0.08
68 33 0.25
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (64 bp):
TAACTTACATAACTTACATAATGCAAAACTTACATAACAACTTACATAACATACATTACTTACA
Found at i:60755038 original size:16 final size:18
Alignment explanation
Indices: 60755019--60755057 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
60755009 AGAATGCAAA
60755019 ACTTACATAACA-AC-TT
1 ACTTACATAACATACATT
60755035 ACTTACATAACATACATT
1 ACTTACATAACATACATT
60755053 ACTTA
1 ACTTA
60755058 AATTATTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 12 0.57
17 2 0.10
18 7 0.33
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (18 bp):
ACTTACATAACATACATT
Found at i:60755100 original size:28 final size:28
Alignment explanation
Indices: 60755062--60755128 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
60755052 TACTTAAATT
*
60755062 ATTTACATAATACATAACTTAGTACATA
1 ATTTACATAATACATAACTTAGTACACA
60755090 ATTTACATAATACATAACTTAGTACACA
1 ATTTACATAATACATAACTTAGTACACA
*
60755118 ACTTACATAAT
1 ATTTACATAAT
60755129 TTTTTCTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (28 bp):
ATTTACATAATACATAACTTAGTACACA
Found at i:60758009 original size:21 final size:21
Alignment explanation
Indices: 60757983--60758051 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
60757973 CAACAACTTA
* *
60757983 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCGCAGCGAGAG
* **
60758004 AAGCAGATGCTACAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
60758025 AAGCAGAGGCCGCAGCGAGAG
1 AAGCAGAGGCCGCAGCGAGAG
60758046 AAGCAG
1 AAGCAG
60758052 CAATAGAAGC
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.35, C:0.20, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCGCAGCGAGAG
Found at i:60758666 original size:44 final size:42
Alignment explanation
Indices: 60758456--60758726 Score: 291
Period size: 42 Copynumber: 6.4 Consensus size: 42
60758446 ATTTTTTAAA
* **
60758456 AAAGCGCCGCTAAAGAACACT-A-CTATTAGTGGCG-TTTTTGA
1 AAAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTTC
* * *
60758497 ACAAGCGCCGC-AATAGAACATTA-CTTTTAGCGGCGTTTTCCTCC
1 A-AAGCGCCGCTAA-AGAACATGATC-TTTAGCGGCGTTTT-TTTC
60758541 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
60758583 AAAGCGCCGCTAAAGTACATGATCTTTTGCGGCGTTTTTTTC
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
* *
60758625 AAAGCGCCGCTAAAGAACATGATCTCTGTAGCGGTGTTTTTTCC
1 AAAGCGCCGCTAAAGAACATGATCT-T-TAGCGGCGTTTTTTTC
* * *
60758669 TAAGCGCCGCTAAAGAACATGATCTTTAGCGGCATTTTTTCTG
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTT-TC
* *
60758712 TAAGCGCCGCAAAAG
1 AAAGCGCCGCTAAAG
60758727 TTAGCGACGT
Statistics
Matches: 200, Mismatches: 19, Indels: 20
0.84 0.08 0.08
Matches are distributed among these distances:
41 4 0.02
42 103 0.51
43 51 0.25
44 42 0.21
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (42 bp):
AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTC
Found at i:60758682 original size:86 final size:84
Alignment explanation
Indices: 60758456--60758726 Score: 291
Period size: 86 Copynumber: 3.2 Consensus size: 84
60758446 ATTTTTTAAA
* **
60758456 AAAGCGCCGCTAAAGAACACT-A-CTATTAGTGGCG-TTTTTGAACAAGCGCCGC-AATAGAACA
1 AAAGCGCCGCTAAAGAACA-TGATCT-TTAGCGGCGTTTTTTCCA-AAGCGCCGCTAA-AGAACA
* * *
60758517 TTA-CTTTTAGCGGCGTTTTCCTCC
62 TGATCTTTT-GCGGCGTTTT-TTTC
* *
60758541 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTCAAAGCGCCGCTAAAGTACATGAT
1 AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGAT
60758606 CTTTTGCGGCGTTTTTTTC
66 CTTTTGCGGCGTTTTTTTC
* *
60758625 AAAGCGCCGCTAAAGAACATGATCTCTGTAGCGGTGTTTTTTCCTAAGCGCCGCTAAAGAACATG
1 AAAGCGCCGCTAAAGAACATGATCT-T-TAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATG
* * *
60758690 ATCTTTAGCGGCATTTTTTCTG
64 ATCTTTTGCGGCGTTTTTT-TC
* *
60758712 TAAGCGCCGCAAAAG
1 AAAGCGCCGCTAAAG
60758727 TTAGCGACGT
Statistics
Matches: 162, Mismatches: 16, Indels: 14
0.84 0.08 0.07
Matches are distributed among these distances:
84 28 0.17
85 55 0.34
86 65 0.40
87 14 0.09
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (84 bp):
AAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTCCAAAGCGCCGCTAAAGAACATGAT
CTTTTGCGGCGTTTTTTTC
Found at i:60762688 original size:40 final size:40
Alignment explanation
Indices: 60762590--60762892 Score: 396
Period size: 40 Copynumber: 7.6 Consensus size: 40
60762580 TCCTCGTTCA
* * * * *
60762590 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
60762629 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
60762669 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
60762709 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
60762749 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
60762789 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
60762829 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
60762869 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
60762893 CAGCATTCAA
Statistics
Matches: 240, Mismatches: 20, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 195 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:60771819 original size:40 final size:39
Alignment explanation
Indices: 60771721--60771983 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
60771711 TCCTCGTTCA
* * * *
60771721 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
60771760 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
60771799 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
60771839 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
60771879 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
60771919 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
60771960 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
60771984 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:60771943 original size:120 final size:119
Alignment explanation
Indices: 60771721--60771983 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
60771711 TCCTCGTTCA
* * *
60771721 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
60771786 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
60771839 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
60771904 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
60771960 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
60771984 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:60771992 original size:41 final size:41
Alignment explanation
Indices: 60771915--60771992 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
60771905 TTTGTATCTC
* * *
60771915 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
60771956 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
60771993 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:60781230 original size:23 final size:23
Alignment explanation
Indices: 60781199--60781274 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
60781189 AGTGTTATTG
*
60781199 ATCAGTGGTAGTTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
60781222 TTCAGTGGTAGCTACGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
60781245 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
60781268 ATCAGTG
1 ATCAGTG
60781275 TGGCACTTAT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:60788059 original size:23 final size:23
Alignment explanation
Indices: 60788033--60788077 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
60788023 GTGTTATTTA
*
60788033 TCAGTGGTAGCTTCAGCTACATT
1 TCAGTGGTAGCTACAGCTACATT
60788056 TCAGTGGTAGCTACAGCTACAT
1 TCAGTGGTAGCTACAGCTACAT
60788078 ATCGGTAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
TCAGTGGTAGCTACAGCTACATT
Found at i:60788891 original size:11 final size:11
Alignment explanation
Indices: 60788875--60788899 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
60788865 GAATTTAAAA
60788875 ATTCATAATTG
1 ATTCATAATTG
60788886 ATTCATAATTG
1 ATTCATAATTG
60788897 ATT
1 ATT
60788900 AGTGAGTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (11 bp):
ATTCATAATTG
Found at i:60794564 original size:45 final size:45
Alignment explanation
Indices: 60794488--60794596 Score: 146
Period size: 45 Copynumber: 2.4 Consensus size: 45
60794478 GACAATCAAC
* *
60794488 GATGCCATAGCATCTTTCAGTTATGGCCCTACCCATTTCAGTCAT
1 GATGTCATAGCATCTTTCAGCTATGGCCCTACCCATTTCAGTCAT
* * * * * *
60794533 GATGTCATAACATCTTTTAGCTATGGTCCTACTCATTTTAGTCTT
1 GATGTCATAGCATCTTTCAGCTATGGCCCTACCCATTTCAGTCAT
60794578 GATGTCATAGCATCTTTCA
1 GATGTCATAGCATCTTTCA
60794597 ACTACGGTCT
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (45 bp):
GATGTCATAGCATCTTTCAGCTATGGCCCTACCCATTTCAGTCAT
Found at i:60794614 original size:45 final size:45
Alignment explanation
Indices: 60794521--60794618 Score: 124
Period size: 45 Copynumber: 2.2 Consensus size: 45
60794511 TGGCCCTACC
* * * * *
60794521 CATTTCAGTCATGATGTCATAACATCTTTTAGCTATGGTCCTACT
1 CATTTTAGTCATGATGTCATAACATCTTTCAACTACGGTCCTAAT
* * *
60794566 CATTTTAGTCTTGATGTCATAGCATCTTTCAACTACGGTCTTAAT
1 CATTTTAGTCATGATGTCATAACATCTTTCAACTACGGTCCTAAT
60794611 CATTTTAG
1 CATTTTAG
60794619 GCATACAACC
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.42
Consensus pattern (45 bp):
CATTTTAGTCATGATGTCATAACATCTTTCAACTACGGTCCTAAT
Found at i:60798526 original size:24 final size:24
Alignment explanation
Indices: 60798457--60798526 Score: 77
Period size: 24 Copynumber: 2.9 Consensus size: 24
60798447 CATGCCCATT
60798457 TTCACAGCTCGTGTGAGCATTTATA
1 TTCACAGCTCGTGTGAGCA-TTATA
* * ** * *
60798482 ATCATAGCTCAAGAGATCATTATA
1 TTCACAGCTCGTGTGAGCATTATA
60798506 TTCACAGCTCGTGTGAGCATT
1 TTCACAGCTCGTGTGAGCATT
60798527 GTTATCCCAC
Statistics
Matches: 33, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 20 0.61
25 13 0.39
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (24 bp):
TTCACAGCTCGTGTGAGCATTATA
Found at i:60803612 original size:20 final size:20
Alignment explanation
Indices: 60803583--60803632 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
60803573 CTTGAGTAAA
*
60803583 TTGAAGATTT-ATGATAGAT
1 TTGAATATTTGATGATAGAT
*
60803602 TATGAATATTTGATGTTAGAT
1 T-TGAATATTTGATGATAGAT
*
60803623 TTTAATATTT
1 TTGAATATTT
60803633 TATAAAGTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 16 0.62
21 9 0.35
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (20 bp):
TTGAATATTTGATGATAGAT
Found at i:60804296 original size:43 final size:43
Alignment explanation
Indices: 60804200--60804362 Score: 163
Period size: 43 Copynumber: 3.8 Consensus size: 43
60804190 AGGGTTTCTA
*
60804200 AGATTACGTGTAAGACCATATCTGGGATA-TGGCATCGATATG
1 AGATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATG
* * **
60804242 AGAATT-TGTGTAAGACCATGTCTGGGACATTCACATCGATATG
1 AG-ATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATG
* * ** * *
60804285 TGATTTCGTGTAAGACCATGGCTGGG-CTATTGGCATCGGTACG
1 AGATTACGTGTAAGACCATATCTGGGAC-ATTGGCATCGATATG
* *
60804328 AGATTACATGTAAGACCATATCTGGGATA-TGGCAT
1 AGATTACGTGTAAGACCATATCTGGGACATTGGCAT
60804363 TGTTACGGTA
Statistics
Matches: 98, Mismatches: 18, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
42 32 0.33
43 66 0.67
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (43 bp):
AGATTACGTGTAAGACCATATCTGGGACATTGGCATCGATATG
Found at i:60807317 original size:17 final size:17
Alignment explanation
Indices: 60807295--60807328 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
60807285 TTTGGTGTGT
60807295 TGGTTAGATTTGTATAA
1 TGGTTAGATTTGTATAA
60807312 TGGTTAGATTTGTATAA
1 TGGTTAGATTTGTATAA
60807329 CCATTTGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.47
Consensus pattern (17 bp):
TGGTTAGATTTGTATAA
Found at i:60811083 original size:78 final size:78
Alignment explanation
Indices: 60810954--60811109 Score: 303
Period size: 78 Copynumber: 2.0 Consensus size: 78
60810944 GAAGTATCTC
60810954 CTCTTCTTCGAGAATTTCCCGCACAAAGTGATAGCGAACGTCTATGTGCTTCGTTCGTGCATGAA
1 CTCTTCTTCGAGAATTTCCCGCACAAAGTGATAGCGAACGTCTATGTGCTTCGTTCGTGCATGAA
*
60811019 AGACTTGATTCTT
66 AAACTTGATTCTT
60811032 CTCTTCTTCGAGAATTTCCCGCACAAAGTGATAGCGAACGTCTATGTGCTTCGTTCGTGCATGAA
1 CTCTTCTTCGAGAATTTCCCGCACAAAGTGATAGCGAACGTCTATGTGCTTCGTTCGTGCATGAA
60811097 AAACTTGATTCTT
66 AAACTTGATTCTT
60811110 TGCTAAATGA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 77 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (78 bp):
CTCTTCTTCGAGAATTTCCCGCACAAAGTGATAGCGAACGTCTATGTGCTTCGTTCGTGCATGAA
AAACTTGATTCTT
Found at i:60812370 original size:21 final size:21
Alignment explanation
Indices: 60812324--60812363 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
60812314 GGAAATCCTT
*
60812324 TTCACCTGCTGCGGAGTACAC
1 TTCACCTGCTGCGAAGTACAC
60812345 TTCACCTGCTGCGAAGTAC
1 TTCACCTGCTGCGAAGTAC
60812364 TACTCACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.33, G:0.23, T:0.25
Consensus pattern (21 bp):
TTCACCTGCTGCGAAGTACAC
Found at i:60820315 original size:27 final size:27
Alignment explanation
Indices: 60820284--60820461 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
60820274 TAAATTGTAC
60820284 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
60820311 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60820337 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
60820365 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
60820393 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60820420 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
60820447 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
60820462 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:60820398 original size:82 final size:81
Alignment explanation
Indices: 60820285--60820440 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
60820275 AAATTGTACA
* *
60820285 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
60820349 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
60820366 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
60820431 TGCGAGTTGA
65 TGCGAATTGA
60820441 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:60820452 original size:82 final size:81
Alignment explanation
Indices: 60820281--60820461 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
60820271 GATTAAATTG
* *
60820281 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
60820346 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
60820362 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
60820426 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
60820444 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
60820462 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:60828378 original size:27 final size:27
Alignment explanation
Indices: 60828347--60828524 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
60828337 TAAATTGTAC
60828347 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
60828374 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60828400 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
60828428 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
60828456 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
60828483 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
60828510 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
60828525 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:60828461 original size:82 final size:81
Alignment explanation
Indices: 60828348--60828503 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
60828338 AAATTGTACA
* *
60828348 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
60828412 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
60828429 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
60828494 TGCGAGTTGA
65 TGCGAATTGA
60828504 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:60828515 original size:82 final size:81
Alignment explanation
Indices: 60828344--60828524 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
60828334 GATTAAATTG
* *
60828344 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
60828409 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
60828425 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
60828489 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
60828507 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
60828525 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:60833959 original size:57 final size:57
Alignment explanation
Indices: 60833897--60834130 Score: 389
Period size: 57 Copynumber: 4.1 Consensus size: 57
60833887 ACTTTAAACA
** * *
60833897 TCATATTCTAACATCAATCCATAAGATCATACCAATTTCACAAAGTTCATTTCCATG
1 TCATATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATG
60833954 TCATATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATG
1 TCATATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATG
60834011 TCATATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATG
1 TCATATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATG
* *
60834068 TCATATTCTATTATCAATCTATAATATCATACCCATTTCACACAA-TTCATTTCAATG
1 TCATATTCTATTATCAATCTATAATATCATACCAATTTCACA-AAGTTCATTTCCATG
*
60834125 TTATAT
1 TCATAT
60834131 AAAATTAGTT
Statistics
Matches: 169, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
57 167 0.99
58 2 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.39
Consensus pattern (57 bp):
TCATATTCTATTATCAATCTATAATATCATACCAATTTCACAAAGTTCATTTCCATG
Found at i:60846527 original size:27 final size:27
Alignment explanation
Indices: 60846497--60846674 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
60846487 ATATTGAGCC
* *
60846497 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
60846524 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
60846551 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
60846579 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
60846606 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
60846633 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
60846660 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
60846675 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:60846609 original size:55 final size:54
Alignment explanation
Indices: 60846497--60846674 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
60846487 ATATTGAGCC
* * * * *
60846497 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
60846551 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
60846606 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
60846660 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
60846675 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:60851262 original size:45 final size:45
Alignment explanation
Indices: 60851198--60851284 Score: 140
Period size: 45 Copynumber: 1.9 Consensus size: 45
60851188 CAGATCCTCG
* *
60851198 GTGGATTCAGCACATAGCAACCACCTTA-TTAATCAATGATGTCCA
1 GTGGAATCAGCACATAGCAACCACCTTACTT-ATCAAAGATGTCCA
60851243 GTGGAATCAGCACATAGCAACCACCTTACTTATCAAAGATGT
1 GTGGAATCAGCACATAGCAACCACCTTACTTATCAAAGATGT
60851285 TCGGTTCACA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
45 37 0.95
46 2 0.05
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.25
Consensus pattern (45 bp):
GTGGAATCAGCACATAGCAACCACCTTACTTATCAAAGATGTCCA
Found at i:60851353 original size:51 final size:50
Alignment explanation
Indices: 60851286--60851481 Score: 198
Period size: 51 Copynumber: 3.9 Consensus size: 50
60851276 CAAAGATGTT
* * *
60851286 CGGTTCACATAGTAGCCTACACATAGTACTACACATGTGACCATTACCAT-
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCA-TACCATC
* * * *
60851336 CGGATACACGTAGTAGCCTACACATAGTACTACACACATGATCGAAACTATC
1 CGG-TACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCATACCATC
* * * * * * *
60851388 CGGTACGCATAGTAGCCTGCACATAGTACAACACATGCGACC-TATCATTC
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATACCA-TC
* *
60851438 CGGTACACGTAGTAGCCTGCACATACTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCAT
60851482 CACTTTCACT
Statistics
Matches: 117, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
49 2 0.02
50 42 0.36
51 68 0.58
52 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.22
Consensus pattern (50 bp):
CGGTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATACCATC
Found at i:60852625 original size:306 final size:306
Alignment explanation
Indices: 60852072--60852682 Score: 1222
Period size: 306 Copynumber: 2.0 Consensus size: 306
60852062 GGACTCCAAA
60852072 TACGTAAAGAACATTAAAAACGTGGCTTGGAATCACTTACTATGGATCTTAGAAGCTTGAAAACC
1 TACGTAAAGAACATTAAAAACGTGGCTTGGAATCACTTACTATGGATCTTAGAAGCTTGAAAACC
60852137 CTAACTATGGCTTCTCCCCTTGTAAAATTCGGCCATGGGGTTGAAGATGATGAAATTTTTGCCTA
66 CTAACTATGGCTTCTCCCCTTGTAAAATTCGGCCATGGGGTTGAAGATGATGAAATTTTTGCCTA
60852202 TTTTCTCTTTTTAATTCATTTTAATTACCAAATTACCAAAATGTCCTTAACTTAAAAATATCCTA
131 TTTTCTCTTTTTAATTCATTTTAATTACCAAATTACCAAAATGTCCTTAACTTAAAAATATCCTA
60852267 TTTCACTTATCTCATGTCCATTTTTGTCCACCAACTTGACCAATGGTTTAATTACAATATAAGGA
196 TTTCACTTATCTCATGTCCATTTTTGTCCACCAACTTGACCAATGGTTTAATTACAATATAAGGA
60852332 CCTCCAATTTAAAATTTTATAACAATTGGACACCTCTAACATGTAG
261 CCTCCAATTTAAAATTTTATAACAATTGGACACCTCTAACATGTAG
60852378 TACGTAAAGAACATTAAAAACGTGGCTTGGAATCACTTACTATGGATCTTAGAAGCTTGAAAACC
1 TACGTAAAGAACATTAAAAACGTGGCTTGGAATCACTTACTATGGATCTTAGAAGCTTGAAAACC
60852443 CTAACTATGGCTTCTCCCCTTGTAAAATTCGGCCATGGGGTTGAAGATGATGAAATTTTTGCCTA
66 CTAACTATGGCTTCTCCCCTTGTAAAATTCGGCCATGGGGTTGAAGATGATGAAATTTTTGCCTA
60852508 TTTTCTCTTTTTAATTCATTTTAATTACCAAATTACCAAAATGTCCTTAACTTAAAAATATCCTA
131 TTTTCTCTTTTTAATTCATTTTAATTACCAAATTACCAAAATGTCCTTAACTTAAAAATATCCTA
60852573 TTTCACTTATCTCATGTCCATTTTTGTCCACCAACTTGACCAATGGTTTAATTACAATATAAGGA
196 TTTCACTTATCTCATGTCCATTTTTGTCCACCAACTTGACCAATGGTTTAATTACAATATAAGGA
60852638 CCTCCAATTTAAAATTTTATAACAATTGGACACCTCTAACATGTA
261 CCTCCAATTTAAAATTTTATAACAATTGGACACCTCTAACATGTA
60852683 AAACTCAACT
Statistics
Matches: 305, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
306 305 1.00
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (306 bp):
TACGTAAAGAACATTAAAAACGTGGCTTGGAATCACTTACTATGGATCTTAGAAGCTTGAAAACC
CTAACTATGGCTTCTCCCCTTGTAAAATTCGGCCATGGGGTTGAAGATGATGAAATTTTTGCCTA
TTTTCTCTTTTTAATTCATTTTAATTACCAAATTACCAAAATGTCCTTAACTTAAAAATATCCTA
TTTCACTTATCTCATGTCCATTTTTGTCCACCAACTTGACCAATGGTTTAATTACAATATAAGGA
CCTCCAATTTAAAATTTTATAACAATTGGACACCTCTAACATGTAG
Found at i:60853695 original size:24 final size:25
Alignment explanation
Indices: 60853668--60853714 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
60853658 AAGACCATGC
*
60853668 GAGCCAATAA-CGGGTAGCTCTGAA
1 GAGCCAATAATCGGGAAGCTCTGAA
*
60853692 GAGCCATTAATCGGGAAGCTCTG
1 GAGCCAATAATCGGGAAGCTCTG
60853715 GATAGCCATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (25 bp):
GAGCCAATAATCGGGAAGCTCTGAA
Found at i:60853711 original size:25 final size:24
Alignment explanation
Indices: 60853668--60853723 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
60853658 AAGACCATGC
* *
60853668 GAGCCAATAACGGGTAGCTCTGAA
1 GAGCCATTAACGGGAAGCTCTGAA
*
60853692 GAGCCATTAATCGGGAAGCTCTGGA
1 GAGCCATTAA-CGGGAAGCTCTGAA
*
60853717 TAGCCAT
1 GAGCCAT
60853724 ATATCAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 9 0.33
25 18 0.67
ACGTcount: A:0.30, C:0.21, G:0.29, T:0.20
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCTGAA
Found at i:60853733 original size:25 final size:25
Alignment explanation
Indices: 60853683--60853811 Score: 70
Period size: 25 Copynumber: 5.2 Consensus size: 25
60853673 AATAACGGGT
*
60853683 AGCTCTGAAGAGCCATTAATCGGGA
1 AGCTCTGAAGAGCCATTAATCAGGA
* *
60853708 AGCTCTGGATAGCCA-TATATCAGGA
1 AGCTCTGAAGAGCCATTA-ATCAGGA
* * *
60853733 AG-T-TCAAGCGAGCTA-T-ATCGGGA
1 AGCTCTGAA--GAGCCATTAATCAGGA
* * *
60853756 AGCTCCGTAGAGCTATTAATCAGGA
1 AGCTCTGAAGAGCCATTAATCAGGA
** *
60853781 AGCTCACAAAGAGCCTTTAATCAGGA
1 AGCTC-TGAAGAGCCATTAATCAGGA
*
60853807 CGCTC
1 AGCTC
60853812 ATAAGTGCTG
Statistics
Matches: 79, Mismatches: 17, Indels: 15
0.71 0.15 0.14
Matches are distributed among these distances:
23 16 0.20
24 5 0.06
25 38 0.48
26 20 0.25
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.22
Consensus pattern (25 bp):
AGCTCTGAAGAGCCATTAATCAGGA
Found at i:60864535 original size:40 final size:40
Alignment explanation
Indices: 60864483--60864598 Score: 205
Period size: 40 Copynumber: 2.9 Consensus size: 40
60864473 GTAAATTATA
*
60864483 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
* *
60864523 CCCTAATTGCACTTACGTGCCCCTGTTTGTACTTCAGTGC
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
60864563 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCA
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCA
60864599 ACACCCATGA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.14, C:0.33, G:0.18, T:0.35
Consensus pattern (40 bp):
CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
Found at i:60864596 original size:20 final size:20
Alignment explanation
Indices: 60864483--60864587 Score: 124
Period size: 20 Copynumber: 5.2 Consensus size: 20
60864473 GTAAATTATA
60864483 CCCTGATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
* * *
60864503 CCCTGTTTGTACTT-CGGTAC
1 CCCTGATTGCACTTAC-GTGC
*
60864523 CCCTAATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
* *
60864543 CCCTGTTTGTACTT-CAGTGC
1 CCCTGATTGCACTTAC-GTGC
60864563 CCCTGATTGCACTTACGTGC
1 CCCTGATTGCACTTACGTGC
60864583 CCCTG
1 CCCTG
60864588 TTTGTACTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
19 2 0.03
20 65 0.94
21 2 0.03
ACGTcount: A:0.13, C:0.34, G:0.19, T:0.33
Consensus pattern (20 bp):
CCCTGATTGCACTTACGTGC
Found at i:60864614 original size:40 final size:40
Alignment explanation
Indices: 60864483--60864614 Score: 185
Period size: 40 Copynumber: 3.3 Consensus size: 40
60864473 GTAAATTATA
* *
60864483 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTAC
1 CCCTGAATGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
*
60864523 CCCT-AATTGCACTTACGTGCCCCTGTTTGTACTTCAGTGC
1 CCCTGAA-TGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
* **
60864563 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAACAC
1 CCCTGAATGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
*
60864603 CCATGAATGCAC
1 CCCTGAATGCAC
60864615 ATCGGTTCCC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 1 0.01
40 79 0.98
41 1 0.01
ACGTcount: A:0.17, C:0.33, G:0.17, T:0.33
Consensus pattern (40 bp):
CCCTGAATGCACTTACGTGCCCCTGTTTGTACTTCAGTAC
Found at i:60864649 original size:80 final size:80
Alignment explanation
Indices: 60864483--60864636 Score: 204
Period size: 80 Copynumber: 1.9 Consensus size: 80
60864473 GTAAATTATA
*** * * *
60864483 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCGGTACCCCTAATTGCACTTACGTGCCCCTG
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAACACCCATAATTGCACATACGTGCCCCTA
*
60864548 TTTGTACTTCAGTGC
66 TTTGCACTTCAGTGC
*
60864563 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAACACCCATGAA-TGCACAT-CGGTTCCCC
1 CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAACACCCAT-AATTGCACATAC-GTGCCCC
60864626 TATTTGCACTT
64 TATTTGCACTT
60864637 TGATTCCCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
79 1 0.02
80 61 0.95
81 2 0.03
ACGTcount: A:0.16, C:0.33, G:0.17, T:0.34
Consensus pattern (80 bp):
CCCTGATTGCACTTACGTGCCCCTGTTTGTACTTCAACACCCATAATTGCACATACGTGCCCCTA
TTTGCACTTCAGTGC
Found at i:60866342 original size:12 final size:12
Alignment explanation
Indices: 60866325--60866350 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
60866315 GCAGTTACAT
60866325 GGCCTAGCACAC
1 GGCCTAGCACAC
60866337 GGCCTAGCACAC
1 GGCCTAGCACAC
60866349 GG
1 GG
60866351 GCTTGTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.38, G:0.31, T:0.08
Consensus pattern (12 bp):
GGCCTAGCACAC
Found at i:60867643 original size:18 final size:17
Alignment explanation
Indices: 60867616--60867659 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
60867606 TAATCATCAT
60867616 TTTATTTAAACTTT-AAC
1 TTTATTTAAA-TTTAAAC
60867633 TTTAGTTTAAATTTAAAC
1 TTTA-TTTAAATTTAAAC
*
60867651 TTTAATTAA
1 TTTATTTAA
60867660 GTTAAAAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (17 bp):
TTTATTTAAATTTAAAC
Found at i:60867668 original size:24 final size:24
Alignment explanation
Indices: 60867619--60867666 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
60867609 TCATCATTTT
* *
60867619 ATTTAAACTTTAACTTTAGTTTAA
1 ATTTAAACTTTAACTTAAGTTAAA
60867643 ATTTAAACTTTAA-TTAAGTTAAA
1 ATTTAAACTTTAACTTAAGTTAAA
60867666 A
1 A
60867667 ATCTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTTAAACTTTAACTTAAGTTAAA
Found at i:60871907 original size:85 final size:85
Alignment explanation
Indices: 60871764--60871942 Score: 358
Period size: 85 Copynumber: 2.1 Consensus size: 85
60871754 GGCCGGCCAT
60871764 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
60871829 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
60871849 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
1 GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
60871914 GTAAGGATTAATAAAATAAA
66 GTAAGGATTAATAAAATAAA
60871934 GAGCATGGG
1 GAGCATGGG
60871943 CAATAAAATA
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.27, T:0.26
Consensus pattern (85 bp):
GAGCATGGGTGGACAAGATGTTATGGCTAAAAACATGTCATAAACATGTTGGGGTAGTGCATTAT
GTAAGGATTAATAAAATAAA
Found at i:60876739 original size:57 final size:57
Alignment explanation
Indices: 60876671--60876785 Score: 162
Period size: 57 Copynumber: 2.0 Consensus size: 57
60876661 ACTCATCTCA
* *
60876671 AATATCATATTCTATCATCAATCCATAAGA-TAATAC-CAATTTCACATAGTTCATTTC
1 AATATCATATTCTATCATCAATCCATAAGAGT-ATACAC-ATTTCACACAATTCATTTC
* *
60876728 AATATCATATTCTATTATCAATCTATAAGAGTATACACATTTCACACAATTCATTTC
1 AATATCATATTCTATCATCAATCCATAAGAGTATACACATTTCACACAATTCATTTC
60876785 A
1 A
60876786 TTGTTATATC
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
57 50 0.96
58 2 0.04
ACGTcount: A:0.39, C:0.20, G:0.03, T:0.37
Consensus pattern (57 bp):
AATATCATATTCTATCATCAATCCATAAGAGTATACACATTTCACACAATTCATTTC
Found at i:60878878 original size:4 final size:4
Alignment explanation
Indices: 60878871--60878905 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
60878861 TTTTTCTTTC
*
60878871 AATA AATA AATA TATA AATA AA-A AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA
60878906 TATTAAGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 3 0.11
4 25 0.89
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:60881338 original size:78 final size:75
Alignment explanation
Indices: 60881204--60881389 Score: 237
Period size: 78 Copynumber: 2.4 Consensus size: 75
60881194 TACGTGAAGT
* * *
60881204 CTTTGTGGTGAATTATCTGATAAGCCTTTGTGGCAAATCATCTAATAAGCCTTTGTGGTGCTGAA
1 CTTTATGGTGAATCATCTGATAAGCCTTTGTGGCAAATCATCTAATAAGCCTTTGT-G-GC-AAA
*
60881269 TCATCTAATAAGC
63 TCATCTAATAAAC
* * * *
60881282 CTTTATGGTGAATCATTTGATAAGCCTTTGTGGCGAATCATCTGATAAGCCTTTGTGGCAAATTA
1 CTTTATGGTGAATCATCTGATAAGCCTTTGTGGCAAATCATCTAATAAGCCTTTGTGGCAAATCA
*
60881347 TCTGATAAAC
66 TCTAATAAAC
* * *
60881357 CTCTATGGTGAATCATCTGATAAGTCTCTGTGG
1 CTTTATGGTGAATCATCTGATAAGCCTTTGTGG
60881390 TGTATTGTAT
Statistics
Matches: 95, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
75 41 0.43
76 2 0.02
77 1 0.01
78 51 0.54
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (75 bp):
CTTTATGGTGAATCATCTGATAAGCCTTTGTGGCAAATCATCTAATAAGCCTTTGTGGCAAATCA
TCTAATAAAC
Found at i:60881390 original size:25 final size:25
Alignment explanation
Indices: 60881204--60881391 Score: 205
Period size: 25 Copynumber: 7.4 Consensus size: 25
60881194 TACGTGAAGT
*
60881204 CTTTGTGGTGAATTATCTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
** *
60881229 CTTTGTGGCAAATCATCTAATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
*
60881254 CTTTGTGGTGCTGAATCATCTAATAAGC
1 CTTTGT-G-G-TGAATCATCTGATAAGC
* *
60881282 CTTTATGGTGAATCATTTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
*
60881307 CTTTGTGGCGAATCATCTGATAAGC
1 CTTTGTGGTGAATCATCTGATAAGC
** * *
60881332 CTTTGTGGCAAATTATCTGATAAAC
1 CTTTGTGGTGAATCATCTGATAAGC
* * *
60881357 CTCTATGGTGAATCATCTGATAAGT
1 CTTTGTGGTGAATCATCTGATAAGC
*
60881382 CTCTGTGGTG
1 CTTTGTGGTG
60881392 TATTGTATGA
Statistics
Matches: 137, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
25 113 0.82
26 2 0.01
27 2 0.01
28 20 0.15
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (25 bp):
CTTTGTGGTGAATCATCTGATAAGC
Found at i:60891261 original size:48 final size:48
Alignment explanation
Indices: 60891205--60891303 Score: 198
Period size: 48 Copynumber: 2.1 Consensus size: 48
60891195 GCTTTCATTA
60891205 GCCATTCTCCAACACAAAAAGGCTATAAATGTTATTCACCTACCTTAC
1 GCCATTCTCCAACACAAAAAGGCTATAAATGTTATTCACCTACCTTAC
60891253 GCCATTCTCCAACACAAAAAGGCTATAAATGTTATTCACCTACCTTAC
1 GCCATTCTCCAACACAAAAAGGCTATAAATGTTATTCACCTACCTTAC
60891301 GCC
1 GCC
60891304 GAATGTTTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.34, C:0.30, G:0.09, T:0.26
Consensus pattern (48 bp):
GCCATTCTCCAACACAAAAAGGCTATAAATGTTATTCACCTACCTTAC
Found at i:60891347 original size:38 final size:38
Alignment explanation
Indices: 60891304--60891382 Score: 140
Period size: 38 Copynumber: 2.1 Consensus size: 38
60891294 ACCTTACGCC
*
60891304 GAATGTTTATCTCTCGGGATGTTACCTTTTTTGAGAAT
1 GAATGTTTATCTCTCGAGATGTTACCTTTTTTGAGAAT
*
60891342 GAATGTTTATCTCTCGAGATGTTACCTTTTTTTAGAAT
1 GAATGTTTATCTCTCGAGATGTTACCTTTTTTGAGAAT
60891380 GAA
1 GAA
60891383 CCATACTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (38 bp):
GAATGTTTATCTCTCGAGATGTTACCTTTTTTGAGAAT
Found at i:60893517 original size:13 final size:13
Alignment explanation
Indices: 60893499--60893524 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60893489 CTTAGGAAGT
60893499 TACTGATTTTTAG
1 TACTGATTTTTAG
60893512 TACTGATTTTTAG
1 TACTGATTTTTAG
60893525 GGATTGTTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
TACTGATTTTTAG
Found at i:60893776 original size:3 final size:3
Alignment explanation
Indices: 60893756--60893831 Score: 80
Period size: 3 Copynumber: 25.3 Consensus size: 3
60893746 ACAATTTAAG
* * * * * * *
60893756 AAT AAT ATT AAT ATT AAT AAT AAT GAT GAT GAT GAT GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
60893804 AAT AAT AAT AAT AAT AAT AAA AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
60893832 GAAATCTAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:60894504 original size:32 final size:31
Alignment explanation
Indices: 60894442--60894502 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
60894432 CTTATTTAAA
60894442 CCAAATTTTTTCTAAAAACTTCATTTTTTTC
1 CCAAATTTTTTCTAAAAACTTCATTTTTTTC
60894473 CCAAATTTTTTCTAAAAACTTCATTTTTTT
1 CCAAATTTTTTCTAAAAACTTCATTTTTTT
60894503 TCTTCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (31 bp):
CCAAATTTTTTCTAAAAACTTCATTTTTTTC
Found at i:60897133 original size:28 final size:28
Alignment explanation
Indices: 60897077--60897133 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
60897067 CTTTACTTTT
**
60897077 CCCCAAAACTTTTACTCCCTCACTTTCC
1 CCCCAAAACTTTTACTCCCTCACCATCC
*
60897105 CCCCAAAACTTTTACTATCCTC-CCATCC
1 CCCCAAAACTTTTACT-CCCTCACCATCC
60897133 C
1 C
60897134 ACCCCCTTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.23, C:0.47, G:0.00, T:0.30
Consensus pattern (28 bp):
CCCCAAAACTTTTACTCCCTCACCATCC
Found at i:60898039 original size:21 final size:22
Alignment explanation
Indices: 60898015--60898056 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
60898005 ACATGTATGC
60898015 AAAATTAAAAT-TAATTTTTTA
1 AAAATTAAAATATAATTTTTTA
*
60898036 AAAATTAAAATATATTTTTTT
1 AAAATTAAAATATAATTTTTT
60898057 TATATTTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AAAATTAAAATATAATTTTTTA
Found at i:60905439 original size:3 final size:3
Alignment explanation
Indices: 60905431--60905458 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
60905421 AATTAGGCAA
60905431 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
60905459 AAACAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:60905977 original size:7 final size:6
Alignment explanation
Indices: 60905941--60905975 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
60905931 TTTTGTATTT
60905941 TTTTAA TTTTAA TTTTAA TTTTAA TTTTTAA TTTT
1 TTTTAA TTTTAA TTTTAA TTTTAA -TTTTAA TTTT
60905976 TATAATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (6 bp):
TTTTAA
Found at i:60911387 original size:30 final size:31
Alignment explanation
Indices: 60911351--60911409 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
60911341 ATTTTTATGC
* *
60911351 TTTTATACTTTT-TGACTTTTTAAAATAATT
1 TTTTATAATTTTATGAATTTTTAAAATAATT
60911381 TTTTATAATTTTATGAATTTTTAAAATAA
1 TTTTATAATTTTATGAATTTTTAAAATAA
60911410 AAAAAAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (31 bp):
TTTTATAATTTTATGAATTTTTAAAATAATT
Found at i:60914889 original size:9 final size:8
Alignment explanation
Indices: 60914858--60914913 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 8
60914848 TTTTAATAAA
60914858 AATTTTAT
1 AATTTTAT
*
60914866 AATTTTAA
1 AATTTTAT
60914874 AATTTTTAT
1 AA-TTTTAT
60914883 AACTTTTAT
1 AA-TTTTAT
*
60914892 ATTTTTAAT
1 AATTTT-AT
60914901 AATTTTA-
1 AATTTTAT
60914908 AATTTT
1 AATTTT
60914914 TAAAAGAGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 6 0.15
8 14 0.34
9 21 0.51
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (8 bp):
AATTTTAT
Found at i:60914914 original size:8 final size:8
Alignment explanation
Indices: 60914860--60914917 Score: 53
Period size: 8 Copynumber: 6.9 Consensus size: 8
60914850 TTAATAAAAA
60914860 TTTTATAAT
1 TTTTA-AAT
*
60914869 TTTAAAAT
1 TTTTAAAT
*
60914877 TTTTATAAC
1 TTTTA-AAT
*
60914886 TTTTATAT
1 TTTTAAAT
*
60914894 TTTTAATAA
1 TTTTAA-AT
60914903 TTTTAAAT
1 TTTTAAAT
60914911 TTTTAAA
1 TTTTAAA
60914918 AGAGCTTAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
8 21 0.54
9 18 0.46
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (8 bp):
TTTTAAAT
Found at i:60914916 original size:17 final size:16
Alignment explanation
Indices: 60914860--60914915 Score: 76
Period size: 17 Copynumber: 3.3 Consensus size: 16
60914850 TTAATAAAAA
60914860 TTTTATAATTTTAAAAT
1 TTTTATAATTTT-AAAT
*
60914877 TTTTATAACTTTTATAT
1 TTTTATAA-TTTTAAAT
60914894 TTTTAATAATTTTAAAT
1 TTTT-ATAATTTTAAAT
60914911 TTTTA
1 TTTTA
60914916 AAAGAGCTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 1 0.03
17 26 0.74
18 8 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTATAATTTTAAAT
Found at i:60915361 original size:30 final size:27
Alignment explanation
Indices: 60915312--60915366 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 27
60915302 AAAGATATAA
60915312 ACTATTAAAATAATAAAATTATATTTTT
1 ACTATTAAAATAATAAAATTA-ATTTTT
60915340 ACTATTATAAA-AATTACAAATTAATTT
1 ACTATTA-AAATAA-TA-AAATTAATTT
60915367 CACCCCTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 9 0.38
29 9 0.38
30 6 0.25
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
ACTATTAAAATAATAAAATTAATTTTT
Found at i:60920399 original size:21 final size:21
Alignment explanation
Indices: 60920375--60920424 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
60920365 AGGGTCTAGG
60920375 CCGTGTGACTGAGGAACACAC
1 CCGTGTGACTGAGGAACACAC
* ** *
60920396 CCGTATGACTGAGGGTCACGC
1 CCGTGTGACTGAGGAACACAC
60920417 CCGTGTGA
1 CCGTGTGA
60920425 GCAAGCTGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.28, G:0.32, T:0.18
Consensus pattern (21 bp):
CCGTGTGACTGAGGAACACAC
Found at i:60935082 original size:8 final size:8
Alignment explanation
Indices: 60935060--60935094 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
60935050 TGAGTGTCTT
60935060 TAAAA-GG
1 TAAAATGG
*
60935067 TAACATGG
1 TAAAATGG
60935075 TAAAATGG
1 TAAAATGG
60935083 TAAAATGG
1 TAAAATGG
60935091 TAAA
1 TAAA
60935095 TAAGGATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 4 0.16
8 21 0.84
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (8 bp):
TAAAATGG
Found at i:60937144 original size:12 final size:12
Alignment explanation
Indices: 60937127--60937156 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
60937117 TCAATTTGTT
60937127 ACACGGCCTAGC
1 ACACGGCCTAGC
*
60937139 ACACGGCCTGGC
1 ACACGGCCTAGC
60937151 ACACGG
1 ACACGG
60937157 GCGTGTGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:60937172 original size:13 final size:13
Alignment explanation
Indices: 60937151--60937204 Score: 63
Period size: 13 Copynumber: 4.2 Consensus size: 13
60937141 ACGGCCTGGC
60937151 ACACGGGCGTGTG
1 ACACGGGCGTGTG
* *
60937164 ACCCGGGCGTGAG
1 ACACGGGCGTGTG
**
60937177 ACACGATCGTGTG
1 ACACGGGCGTGTG
*
60937190 ACACGGTCGTGTG
1 ACACGGGCGTGTG
60937203 AC
1 AC
60937205 CCTACTATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.19, C:0.26, G:0.39, T:0.17
Consensus pattern (13 bp):
ACACGGGCGTGTG
Found at i:60938423 original size:30 final size:30
Alignment explanation
Indices: 60938356--60938695 Score: 169
Period size: 30 Copynumber: 11.3 Consensus size: 30
60938346 TCATTGGCTA
* *
60938356 ATGAAAAGGGATAGCTTCGGTTATCAAAATA
1 ATGAAAAGGGATAGCTTCGGCTATC-AAATT
* *
60938387 ATGAAAAGGGATTGCCTCGGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * * *
60938417 ATGAAAAGGGAT-GGTAACGAAAC-ATC-AATA
1 ATGAAAAGGGATAGCT-TCG--GCTATCAAATT
* * * * * **
60938447 ATGAAAAGGGAT-GGTGACGACCATCGAACA
1 ATGAAAAGGGATAGCT-TCGGCTATCAAATT
* *
60938477 ATGAAAAGGGATAGCTCCGGCTATCGAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * * *
60938507 GTGATAAGGGATAGCTTCAGTTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * *
60938537 GTGAAAAGGGATAACTTCAGCTATCAAATT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * *
60938567 ATGAAAAGGGAT-GGTGAT-GGCCATC-AATA
1 ATGAAAAGGGATAGCT--TCGGCTATCAAATT
* * * * *
60938596 ATGAAAAGGGAT-GGTGACGACCATCAAATA
1 ATGAAAAGGGATAGCT-TCGGCTATCAAATT
* * *
60938626 ATGAAAAGGGATAGCTTCGACTATCGAGTT
1 ATGAAAAGGGATAGCTTCGGCTATCAAATT
* * **
60938656 GCTG-AAAGGGATAGCTTCAGG-TATCGAGCT
1 -ATGAAAAGGGATAGCTTC-GGCTATCAAATT
60938686 ATGAAAAGGG
1 ATGAAAAGGG
60938696 TTGGGACAAC
Statistics
Matches: 250, Mismatches: 45, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
28 2 0.01
29 31 0.12
30 183 0.73
31 33 0.13
32 1 0.00
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (30 bp):
ATGAAAAGGGATAGCTTCGGCTATCAAATT
Found at i:60938608 original size:29 final size:30
Alignment explanation
Indices: 60938559--60938637 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 30
60938549 AACTTCAGCT
* * *
60938559 ATCAAATTATGAAAAGGGATGGTGATGGCC
1 ATCAAATAATGAAAAGGGATGGTGACGACC
60938589 ATC-AATAATGAAAAGGGATGGTGACGACC
1 ATCAAATAATGAAAAGGGATGGTGACGACC
60938618 ATCAAATAATGAAAAGGGAT
1 ATCAAATAATGAAAAGGGAT
60938638 AGCTTCGACT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 26 0.58
30 19 0.42
ACGTcount: A:0.43, C:0.10, G:0.27, T:0.20
Consensus pattern (30 bp):
ATCAAATAATGAAAAGGGATGGTGACGACC
Found at i:60938633 original size:149 final size:151
Alignment explanation
Indices: 60938360--60938680 Score: 459
Period size: 149 Copynumber: 2.1 Consensus size: 151
60938350 TGGCTAATGA
* ** *
60938360 AAAGGGATAGCTTCGGTTATCAAAATAATGAAAAGGGATTGCCTCGGCTATCAAATTATGAAAAG
1 AAAGGGATAGCTTCAGTTATCAAAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAG
*
60938425 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCGAACAATGAAAAGGGATA
66 GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATA
*
60938490 GCTCCGGCTATCGAATTG-TG
131 GCTCCGACTATCGAATTGCTG
** *
60938510 ATAAGGGATAGCTTCAGTTATC-AAATTGTGAAAAGGGATAACTTCAGCTATCAAATTATGAAAA
1 A-AAGGGATAGCTTCAGTTATCAAAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAA
* * ** *
60938574 GGGATGGTGATG-GCCATCAATAATGAAAAGGGATGGTGACGACCATCAAATAATGAAAAGGGAT
65 GGGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGAT
* *
60938638 AGCTTCGACTATCGAGTTGCTG
130 AGCTCCGACTATCGAATTGCTG
*
60938660 AAAGGGATAGCTTCAGGTATC
1 AAAGGGATAGCTTCAGTTATC
60938681 GAGCTATGAA
Statistics
Matches: 152, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
149 83 0.55
150 50 0.33
151 19 0.12
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (151 bp):
AAAGGGATAGCTTCAGTTATCAAAATAATGAAAAGGGATAACCTCAGCTATCAAATTATGAAAAG
GGATGGTAACGAAACATCAATAATGAAAAGGGATGGTGACGACCATCAAACAATGAAAAGGGATA
GCTCCGACTATCGAATTGCTG
Found at i:60938666 original size:119 final size:120
Alignment explanation
Indices: 60938355--60938710 Score: 289
Period size: 119 Copynumber: 3.0 Consensus size: 120
60938345 ATCATTGGCT
* *** * * * *
60938355 AATGAAAAGGGATAGCTTCGGTTATCAAAATAATGAAAAGGGATTGCCTCGGCTATCAAATTATG
1 AATGAAAAGGGATAGCTACGACCATC-AAATAATGAAAAGGGATAGCTTCAGCTATCAAATTGTG
** *
60938420 AAAAGGGATGGTAAC-GAAAC-ATC-AA-TAATGAAAAGGGATGGTGACGACCATCGAAC
65 AAAAGGGA---TAACTTCAGCTATCAAACT-ATGAAAAGGGATGGTGACGACCATCGAAC
* * * * ** * *
60938476 AATGAAAAGGGATAGCTCCGGCTATCGAATTGTGATAAGGGATAGCTTCAGTTATCAAATTGTGA
1 AATGAAAAGGGATAGCTACGACCATCAAATAATGAAAAGGGATAGCTTCAGCTATCAAATTGTGA
* * * *
60938541 AAAGGGATAACTTCAGCTATCAAATTATGAAAAGGGATGGTGATGGCCATC-AAT
66 AAAGGGATAACTTCAGCTATCAAACTATGAAAAGGGATGGTGACGACCATCGAAC
* * *
60938595 AATGAAAAGGGAT-GGTGACGACCATCAAATAATGAAAAGGGATAGCTTC-GACTATCGAGTTGC
1 AATGAAAAGGGATAGCT-ACGACCATCAAATAATGAAAAGGGATAGCTTCAG-CTATCAAATTG-
* * * * * *
60938658 TG-AAAGGGATAGCTTCAGGTATCGAGCTATGAAAAGGGTTGG-GACAACCATCG
63 TGAAAAGGGATAACTTCAGCTATCAAACTATGAAAAGGGATGGTGACGACCATCG
60938711 TGATTTTTAT
Statistics
Matches: 190, Mismatches: 37, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
117 4 0.02
118 12 0.06
119 85 0.45
120 64 0.34
121 25 0.13
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.22
Consensus pattern (120 bp):
AATGAAAAGGGATAGCTACGACCATCAAATAATGAAAAGGGATAGCTTCAGCTATCAAATTGTGA
AAAGGGATAACTTCAGCTATCAAACTATGAAAAGGGATGGTGACGACCATCGAAC
Found at i:60947816 original size:10 final size:9
Alignment explanation
Indices: 60947803--60947844 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
60947793 AACAAAACCC
60947803 AAAAAAAACG
1 AAAAAAAA-G
60947813 AAAAGAAAAG
1 AAAA-AAAAG
60947823 AAAAAAAA-
1 AAAAAAAAG
*
60947831 AGAAAAAAG
1 AAAAAAAAG
60947840 AAAAA
1 AAAAA
60947845 GAAAACCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
8 7 0.25
9 8 0.29
10 9 0.32
11 4 0.14
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:60958331 original size:16 final size:16
Alignment explanation
Indices: 60958305--60958343 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
60958295 TTATTTCCCA
60958305 ATTTAATTTAATTTTTG
1 ATTT-ATTTAATTTTTG
*
60958322 ATTTATTTAATTTTTT
1 ATTTATTTAATTTTTG
60958338 ATTTAT
1 ATTTAT
60958344 GCTATTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
ATTTATTTAATTTTTG
Found at i:60964149 original size:14 final size:14
Alignment explanation
Indices: 60964130--60964158 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
60964120 TAGAAAAAAA
60964130 AAGACTAAATGCTT
1 AAGACTAAATGCTT
60964144 AAGACTAAATGCTT
1 AAGACTAAATGCTT
60964158 A
1 A
60964159 CTCAATAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.14, G:0.14, T:0.28
Consensus pattern (14 bp):
AAGACTAAATGCTT
Found at i:60968634 original size:15 final size:15
Alignment explanation
Indices: 60968614--60968691 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
60968604 TTTATGGAAA
60968614 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
60968629 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
60968643 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
60968659 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
60968673 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
60968689 ATC
1 ATC
60968692 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:60968651 original size:30 final size:30
Alignment explanation
Indices: 60968610--60968691 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
60968600 CATATTTATG
*
60968610 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
60968640 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
60968670 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
60968692 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:60974883 original size:24 final size:24
Alignment explanation
Indices: 60974851--60974933 Score: 87
Period size: 24 Copynumber: 3.5 Consensus size: 24
60974841 TCCTGAAACC
60974851 ATGAAAAGGTTGAAAAGGAT-CCGA
1 ATGAAAAGGTTGAAAAGGATACC-A
* *
60974875 ATGAAAAGGCTGAAAAGGTTACCA
1 ATGAAAAGGTTGAAAAGGATACCA
* ** *
60974899 TTGAAAAGGTCAAAAAGGATATCA
1 ATGAAAAGGTTGAAAAGGATACCA
*
60974923 ATGAAATGGTT
1 ATGAAAAGGTT
60974934 ATTATATCAA
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
24 45 0.96
25 2 0.04
ACGTcount: A:0.46, C:0.08, G:0.25, T:0.20
Consensus pattern (24 bp):
ATGAAAAGGTTGAAAAGGATACCA
Found at i:60977657 original size:15 final size:15
Alignment explanation
Indices: 60977637--60977665 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
60977627 CAACCCAAAT
60977637 AATCAATAATAATTA
1 AATCAATAATAATTA
60977652 AATCAATAATAATT
1 AATCAATAATAATT
60977666 GAACTGAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (15 bp):
AATCAATAATAATTA
Found at i:60983889 original size:26 final size:27
Alignment explanation
Indices: 60983831--60983893 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
60983821 CTACCTACAG
60983831 TAGTTTCAGAATATCATAACATATAAC
1 TAGTTTCAGAATATCATAACATATAAC
* * *
60983858 -AATTTCAGAATATCATAGCATGT-AC
1 TAGTTTCAGAATATCATAACATATAAC
60983883 TAGTTTCAGAA
1 TAGTTTCAGAA
60983894 CACTTACAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (27 bp):
TAGTTTCAGAATATCATAACATATAAC
Found at i:60991794 original size:24 final size:24
Alignment explanation
Indices: 60991762--60991817 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
60991752 ATTTCCGAAA
60991762 CAATGAAAAGGTCGAAAAGGATAC
1 CAATGAAAAGGTCGAAAAGGATAC
*
60991786 CAATGAAAAGGTCGAAAAGGATAT
1 CAATGAAAAGGTCGAAAAGGATAC
*
60991810 TAATGAAA
1 CAATGAAA
60991818 TGGTTATTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.52, C:0.09, G:0.23, T:0.16
Consensus pattern (24 bp):
CAATGAAAAGGTCGAAAAGGATAC
Found at i:60992141 original size:18 final size:18
Alignment explanation
Indices: 60992120--60992160 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
60992110 TTGGTTTGGT
60992120 GTTTGTGTTTGATACTTA
1 GTTTGTGTTTGATACTTA
60992138 GTTTGTGTTTGATACTTA
1 GTTTGTGTTTGATACTTA
60992156 GTTTG
1 GTTTG
60992161 GTGACAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.15, C:0.05, G:0.24, T:0.56
Consensus pattern (18 bp):
GTTTGTGTTTGATACTTA
Found at i:60995701 original size:27 final size:27
Alignment explanation
Indices: 60995655--60996123 Score: 527
Period size: 27 Copynumber: 17.4 Consensus size: 27
60995645 GGTATAACAA
*
60995655 TCATTTTACCCTAT-GGGGGTATTTCAG
1 TCATTTTACCCT-TCGAGGGTATTTCAG
* *
60995682 TCATTTTACCCTTCAAGGGTATTTCAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
60995709 TCATTTTCCCCTTCGAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
60995736 TCA-TTTACCTTTCAAGGGTATTT-TG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
60995761 ATCATTTTATCCTTCGGGGGTATTTCAA
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* *
60995789 TTATTTTACCCTTCGGGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
60995816 TTATTTTACCCTTCAAGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * * *
60995843 CCATTTTACCCTTCAAGGGTATTTTAA
1 TCATTTTACCCTTCGAGGGTATTTCAG
* * *
60995870 TCATTTTACCTTTTGAGGGTATTGCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
60995897 TCATTTTACCCTTCGAGGGTATTTC-G
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
60995923 ATCATTTCACCCTTCAAGGGTATTTC-G
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* *
60995950 ATCATTTTATCCTTCGGGGGTATTTCAG
1 -TCATTTTACCCTTCGAGGGTATTTCAG
* **
60995978 TCATTTTACCCTT-TAGGGGTATTTTGG
1 TCATTTTACCCTTCGA-GGGTATTTCAG
*
60996005 TCATTTTACCCCTCGAGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
60996032 TCATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
* *
60996059 TCATTTTACCCTTCGGGGGTATTTCGG
1 TCATTTTACCCTTCGAGGGTATTTCAG
*
60996086 TCATTTTACCCTTCGGGGGTATTTCAG
1 TCATTTTACCCTTCGAGGGTATTTCAG
60996113 TCATTTTACCC
1 TCATTTTACCC
60996124 ATGAATCGTA
Statistics
Matches: 377, Mismatches: 57, Indels: 16
0.84 0.13 0.04
Matches are distributed among these distances:
25 1 0.00
26 22 0.06
27 352 0.93
28 2 0.01
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (27 bp):
TCATTTTACCCTTCGAGGGTATTTCAG
Found at i:60995863 original size:81 final size:81
Alignment explanation
Indices: 60995671--60996123 Score: 584
Period size: 81 Copynumber: 5.6 Consensus size: 81
60995661 TACCCTATGG
* * * *
60995671 GGGTATTTCAGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTCCCCTTCGAGGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
*
60995736 TCA-TTTACCTTTCAA
66 TCATTTTACCCTTCAA
* * * ** *
60995751 GGGTATTTTGATCATTTTATCCTTCGGGGGTATTTCAATTATTTTACCCTTCGGGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
*
60995816 TTATTTTACCCTTCAA
66 TCATTTTACCCTTCAA
* * * * * *
60995832 GGGTATTTCGGCCATTTTACCCTTCAAGGGTATTTTAATCATTTTACCTTTTGAGGGTATTGCAG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
*
60995897 TCATTTTACCCTTCGA
66 TCATTTTACCCTTCAA
* * * *
60995913 GGGTATTTCGATCATTTCACCCTTCAAGGGTATTTCGATCATTTTATCCTTCGGGGGTATTTCAG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
* *
60995978 TCATTTTACCCTTTAG
66 TCATTTTACCCTTCAA
* * * * *
60995994 GGGTATTTTGGTCATTTTACCCCTCGAGGGTATTTCAGTCATTTTACCCTTCGGGGGTATTTCGG
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
**
60996059 TCATTTTACCCTTCGG
66 TCATTTTACCCTTCAA
** *
60996075 GGGTATTTCGGTCATTTTACCCTTCGGGGGTATTTCAGTCATTTTACCC
1 GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCC
60996124 ATGAATCGTA
Statistics
Matches: 319, Mismatches: 53, Indels: 1
0.86 0.14 0.00
Matches are distributed among these distances:
80 57 0.18
81 262 0.82
ACGTcount: A:0.18, C:0.21, G:0.19, T:0.42
Consensus pattern (81 bp):
GGGTATTTCGGTCATTTTACCCTTCAAGGGTATTTCAATCATTTTACCCTTCGGGGGTATTTCAG
TCATTTTACCCTTCAA
Found at i:60998574 original size:19 final size:18
Alignment explanation
Indices: 60998550--60998603 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 18
60998540 CATGTGGCAG
*
60998550 AAAATATAAAAAAATGCTA
1 AAAATATAAAAAAAT-ATA
*
60998569 AAAATATAAAAGAATATA
1 AAAATATAAAAAAATATA
60998587 AAAATATTAGAAAAAAT
1 AAAATA-TA-AAAAAAT
60998604 TATATAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.27
19 16 0.53
20 6 0.20
ACGTcount: A:0.70, C:0.02, G:0.06, T:0.22
Consensus pattern (18 bp):
AAAATATAAAAAAATATA
Found at i:61000356 original size:6 final size:6
Alignment explanation
Indices: 61000345--61000370 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
61000335 CATACATATC
61000345 GATGAA GATGAA GATGAA GATGAA GA
1 GATGAA GATGAA GATGAA GATGAA GA
61000371 AAGAAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GATGAA
Found at i:61003511 original size:27 final size:27
Alignment explanation
Indices: 61003481--61003658 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
61003471 ATATTGAGTC
* * * *
61003481 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
61003508 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61003535 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
61003563 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
61003590 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
61003617 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
61003644 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
61003659 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:61003620 original size:82 final size:81
Alignment explanation
Indices: 61003502--61003657 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
61003492 TGCTATATAA
* *
61003502 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
61003567 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
61003584 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
61003648 CACTTAGTGC
65 CACTTAGTGC
61003658 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:61021375 original size:16 final size:16
Alignment explanation
Indices: 61021356--61021394 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
61021346 TTTTAATAAA
61021356 ATTAAAACGAATTGTT
1 ATTAAAACGAATTGTT
**
61021372 ATTAAAATTAATTGTT
1 ATTAAAACGAATTGTT
*
61021388 AGTAAAA
1 ATTAAAA
61021395 TTATCAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (16 bp):
ATTAAAACGAATTGTT
Found at i:61021377 original size:22 final size:22
Alignment explanation
Indices: 61021328--61021382 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
61021318 TTTAATTAAA
** * *
61021328 ATTAAAATTAAAATTATTTTTT
1 ATTAAAATTAAAACGAATTGTT
*
61021350 AATAAAATTAAAACGAATTGTT
1 ATTAAAATTAAAACGAATTGTT
61021372 ATTAAAATTAA
1 ATTAAAATTAA
61021383 TTGTTAGTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.42
Consensus pattern (22 bp):
ATTAAAATTAAAACGAATTGTT
Found at i:61021395 original size:16 final size:16
Alignment explanation
Indices: 61021365--61021397 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
61021355 AATTAAAACG
*
61021365 AATTGTTATTAAAATT
1 AATTGTTAGTAAAATT
61021381 AATTGTTAGTAAAATT
1 AATTGTTAGTAAAATT
61021397 A
1 A
61021398 TCAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (16 bp):
AATTGTTAGTAAAATT
Found at i:61021476 original size:59 final size:59
Alignment explanation
Indices: 61021408--61021547 Score: 262
Period size: 59 Copynumber: 2.4 Consensus size: 59
61021398 TCAAATTATT
*
61021408 AATTGTTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
61021467 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
1 AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
*
61021526 AATTATTATTTGTATTAATTGT
1 AATTATTAATTGTATTAATTGT
61021548 ATTAATTGTT
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 79 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (59 bp):
AATTATTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCA
Found at i:61040389 original size:40 final size:40
Alignment explanation
Indices: 61040299--61040523 Score: 269
Period size: 40 Copynumber: 5.7 Consensus size: 40
61040289 TTGAATGATG
* * * *
61040299 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * * * *
61040339 TTCGGACTAAGAT-CCAAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61040379 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61040418 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
61040458 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
* *
61040499 -CCGGGTTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
61040524 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 18, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
39 33 0.20
40 119 0.73
41 10 0.06
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:61040541 original size:80 final size:79
Alignment explanation
Indices: 61040355--61040546 Score: 230
Period size: 80 Copynumber: 2.4 Consensus size: 79
61040345 CTAAGATCCA
** * *
61040355 AAGGCATTTGTGCGAGAT-ACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAAT
1 AAGGCATTTGAACGAG-TGACTAAATCCGGGTTAAGCCCGAAGGCATTGGTGCGAGTTACTAAAT
61040419 CCGGGTTAAGTCCCG
65 CCGGGTTAAGTCCCG
** * *
61040434 AAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 AAGGCATTTGAACGAGTGACTAAATCCGGGTTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
*
61040499 -CCGGGTTATGTCCCG
64 TCCGGGTTAAGTCCCG
*
61040514 AAGGCATTTGAACGAG-GAGCTATATCC-GGTTAA
1 AAGGCATTTGAACGAGTGA-CTAAATCCGGGTTAA
61040547 ATTTCGAGTT
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
78 1 0.01
79 38 0.38
80 60 0.59
81 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (79 bp):
AAGGCATTTGAACGAGTGACTAAATCCGGGTTAAGCCCGAAGGCATTGGTGCGAGTTACTAAATC
CGGGTTAAGTCCCG
Found at i:61040608 original size:40 final size:40
Alignment explanation
Indices: 61040551--61040628 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 40
61040541 GGTTAAATTT
*
61040551 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTG
1 CGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTG
*
61040591 CGAGTTACTATAA-CCGGGCTATGTCCCGAAGGCATTTG
1 CGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATTTG
61040629 AACGAGGAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 33 0.94
41 2 0.06
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTTGTG
Found at i:61040628 original size:105 final size:105
Alignment explanation
Indices: 61040446--61040658 Score: 417
Period size: 105 Copynumber: 2.0 Consensus size: 105
61040436 GGCATTTGTG
*
61040446 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGTTATGTC
1 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
61040511 CCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTT
66 CCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTT
61040551 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
61040616 CCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTT
66 CCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTT
61040656 CGA
1 CGA
61040659 AGGTACGTGA
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
105 107 1.00
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.28
Consensus pattern (105 bp):
CGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
CCGAAGGCATTTGAACGAGGAGCTATATCCGGTTAAATTT
Found at i:61040642 original size:40 final size:40
Alignment explanation
Indices: 61040551--61040647 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 40
61040541 GGTTAAATTT
* * **
61040551 CGAGTTACTA-AATCCGGGTTAAGTCCCGAAGGCATTTGTG
1 CGAGTGACTATAA-CCGGGCTAAGTCCCGAAGGCATTTGAA
* *
61040591 CGAGTTACTATAACCGGGCTATGTCCCGAAGGCATTTGAA
1 CGAGTGACTATAACCGGGCTAAGTCCCGAAGGCATTTGAA
*
61040631 CGAG-GAGCTATATCCGG
1 CGAGTGA-CTATAACCGG
61040648 TTAAATTTCG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 1 0.02
40 46 0.94
41 2 0.04
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
CGAGTGACTATAACCGGGCTAAGTCCCGAAGGCATTTGAA
Found at i:61040727 original size:50 final size:50
Alignment explanation
Indices: 61040670--61040769 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
61040660 GGTACGTGAT
*
61040670 TTGGGAATGAATGATCTTGCTGTAAAAATTTCAGTTAATACTCTAGAAAC
1 TTGGGAATGAATGATCTTGCTGTAAAAATTTCAGTAAATACTCTAGAAAC
61040720 TTGGGAATGAATGATCTTGCTGTAAAAATTTCAGTAAATACTCTAGAAAC
1 TTGGGAATGAATGATCTTGCTGTAAAAATTTCAGTAAATACTCTAGAAAC
61040770 ATCCCAACAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (50 bp):
TTGGGAATGAATGATCTTGCTGTAAAAATTTCAGTAAATACTCTAGAAAC
Found at i:61041052 original size:195 final size:195
Alignment explanation
Indices: 61040720--61041090 Score: 724
Period size: 195 Copynumber: 1.9 Consensus size: 195
61040710 CTCTAGAAAC
*
61040720 TTGGGAATGAATGATCTTGCTGTAAAAATTTCAGTAAATACTCTAGAAACATCCCAACATTGAGG
1 TTGGGAATGAATGATCTTACTGTAAAAATTTCAGTAAATACTCTAGAAACATCCCAACATTGAGG
61040785 TATGTTTCGTATGTGCTTGAATTTAGTTGAGCCCTTACAAATAAGTATTCGCTCAGTTGATAAAC
66 TATGTTTCGTATGTGCTTGAATTTAGTTGAGCCCTTACAAATAAGTATTCGCTCAGTTGATAAAC
61040850 GAGCTACCGGCCTTTGGCTAAGTTGATCTTTTGTGTATGTACATAAAATTCCGAAGGTACGTGAA
131 GAGCTACCGGCCTTTGGCTAAGTTGATCTTTTGTGTATGTACATAAAATTCCGAAGGTACGTGAA
*
61040915 TTGGGAATGAATGATCTTACTGTAAAAATTTCAGTAAATACTCTAGAAATATCCCAACATTGAGG
1 TTGGGAATGAATGATCTTACTGTAAAAATTTCAGTAAATACTCTAGAAACATCCCAACATTGAGG
61040980 TATGTTTCGTATGTGCTTGAATTTAGTTGAGCCCTTACAAATAAGTATTCGCTCAGTTGATAAAC
66 TATGTTTCGTATGTGCTTGAATTTAGTTGAGCCCTTACAAATAAGTATTCGCTCAGTTGATAAAC
61041045 GAGCTACCGGCCTTTGGCTAAGTTGATCTTTTGTGTATGTACATAA
131 GAGCTACCGGCCTTTGGCTAAGTTGATCTTTTGTGTATGTACATAA
61041091 GGGTTGGTAA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
195 174 1.00
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (195 bp):
TTGGGAATGAATGATCTTACTGTAAAAATTTCAGTAAATACTCTAGAAACATCCCAACATTGAGG
TATGTTTCGTATGTGCTTGAATTTAGTTGAGCCCTTACAAATAAGTATTCGCTCAGTTGATAAAC
GAGCTACCGGCCTTTGGCTAAGTTGATCTTTTGTGTATGTACATAAAATTCCGAAGGTACGTGAA
Found at i:61041275 original size:78 final size:78
Alignment explanation
Indices: 61041187--61041339 Score: 279
Period size: 78 Copynumber: 2.0 Consensus size: 78
61041177 GTGCTGGAAT
*
61041187 TCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCCGTTTCTTTGATCCTCTGTTTTATAGA
1 TCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCCGTTTCTTTGATCCTCTATTTTATAGA
61041252 TTTTGGTTCTCCA
66 TTTTGGTTCTCCA
* *
61041265 TCCTTGCTCAAAACTTAGTAAGCATAAATTGCTTACTTCGTTTCTTTGATCCTCTATTTTATAGA
1 TCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCCGTTTCTTTGATCCTCTATTTTATAGA
61041330 TTTTGGTTCT
66 TTTTGGTTCT
61041340 TCAGCTATCG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.22, C:0.21, G:0.12, T:0.45
Consensus pattern (78 bp):
TCCTTGCTCAAAACTTACTAAGCATAAATTGCTTACTCCGTTTCTTTGATCCTCTATTTTATAGA
TTTTGGTTCTCCA
Done.