Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 53 of 106
Found at i:20090840 original size:2 final size:2
Alignment explanation
Indices: 20090833--20090869 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
20090823 NNNNNNNNNN
*
20090833 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20090870 GTAAATATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20105985 original size:33 final size:33
Alignment explanation
Indices: 20105943--20106008 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
20105933 GCATTTCTAC
* *
20105943 CATTCCTTAAGTCCTTTTACATCTTAGAAACTA
1 CATTCCTTAAGTCATTTTACATCTCAGAAACTA
20105976 CATTCCTTAAGTCATTTTACATCTCAGAAACTA
1 CATTCCTTAAGTCATTTTACATCTCAGAAACTA
20106009 TCTTTAGGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (33 bp):
CATTCCTTAAGTCATTTTACATCTCAGAAACTA
Found at i:20106513 original size:31 final size:31
Alignment explanation
Indices: 20106478--20106581 Score: 79
Period size: 31 Copynumber: 3.2 Consensus size: 31
20106468 TATACATATG
20106478 CTCATGGCATTAATCATGCATACTTAATCAT
1 CTCATGGCATTAATCATGCATACTTAATCAT
* *
20106509 CTCATGTAGTATATGGAAT-ATACAT-CATATACAT-ATT
1 CTCATG--GCAT-T--AATCATGCATAC-T-TA-ATCA-T
*
20106546 CTCATGGCATTAATCATGCATACTTAATCAC
1 CTCATGGCATTAATCATGCATACTTAATCAT
20106577 CTCAT
1 CTCAT
20106582 ATGGTATATG
Statistics
Matches: 56, Mismatches: 5, Indels: 24
0.66 0.06 0.28
Matches are distributed among these distances:
31 13 0.23
32 6 0.11
33 9 0.16
34 4 0.07
35 9 0.16
36 6 0.11
37 9 0.16
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.36
Consensus pattern (31 bp):
CTCATGGCATTAATCATGCATACTTAATCAT
Found at i:20106526 original size:68 final size:67
Alignment explanation
Indices: 20106367--20106698 Score: 381
Period size: 68 Copynumber: 4.9 Consensus size: 67
20106357 CACATACATG
* *
20106367 CTTACTCATCTCATA-AGGTATATGGAATTTGCATCATATACATAATCTCATGGCATT--T-ATG
1 CTTAATCATCTCATATA-GTATATGGAATTTACATCATATACAT-ATCTCATGGCATTAATCATG
20106428 C-TA
64 CATA
* * *
20106431 GCTCAATCATCTCATGTAGTATATGGAATATACATCATATACATATGCTCATGGCATTAATCATG
1 -CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATAT-CTCATGGCATTAATCATG
20106496 CATA
64 CATA
* *
20106500 CTTAATCATCTCATGTAGTATATGGAATATACATCATATACATATTCTCATGGCATTAATCATGC
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATA-TCTCATGGCATTAATCATGC
20106565 ATA
65 ATA
* * * * *
20106568 CTTAATCACCTCATATGGTATATGGAATTTACATCATATACACCATC-CTATAGTA-TACATCAT
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACA-TATCTC-ATGGCATTA-ATCAT
20106631 GCATA
63 GCATA
* * * * *
20106636 CTTGATCATCTCATATGGTATATGGAATTTAAATCATATACATAATCTTATGGCATTCATCAT
1 CTTAATCATCTCATATAGTATATGGAATTTACATCATATACAT-ATCTCATGGCATTAATCAT
20106699 ACCAACATGC
Statistics
Matches: 233, Mismatches: 21, Indels: 23
0.84 0.08 0.08
Matches are distributed among these distances:
64 2 0.01
65 47 0.20
66 1 0.00
67 4 0.02
68 174 0.75
69 5 0.02
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (67 bp):
CTTAATCATCTCATATAGTATATGGAATTTACATCATATACATATCTCATGGCATTAATCATGCA
TA
Found at i:20107800 original size:72 final size:72
Alignment explanation
Indices: 20107683--20107817 Score: 209
Period size: 72 Copynumber: 1.9 Consensus size: 72
20107673 TATCGATATT
* *
20107683 TTATGAACATGTATTCATACATGTTCATCAAAAACACTTTTTGGGCTAAATGTATTGATACATCA
1 TTATGAACATGTATTCATACATGTTCATCAAAAACACTTTCTGGGCTAAATGTATCGATACATCA
20107748 TGAAACA
66 TGAAACA
* * *
20107755 TTATGAACATGTA-TCGATACATGTTCATCAGAGACCCTTTCTGGGCTAAATGTATCGATACAT
1 TTATGAACATGTATTC-ATACATGTTCATCAAAAACACTTTCTGGGCTAAATGTATCGATACAT
20107818 TTGAGACAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
71 2 0.04
72 55 0.96
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (72 bp):
TTATGAACATGTATTCATACATGTTCATCAAAAACACTTTCTGGGCTAAATGTATCGATACATCA
TGAAACA
Found at i:20108988 original size:21 final size:21
Alignment explanation
Indices: 20108958--20109037 Score: 101
Period size: 21 Copynumber: 3.9 Consensus size: 21
20108948 TTGGAAAAAT
20108958 TGTATCGATACATTATGAACA
1 TGTATCGATACATTATGAACA
* * **
20108979 TGTATTGATACATCACCAA-A
1 TGTATCGATACATTATGAACA
20108999 TGTATCGATACATTATGAACA
1 TGTATCGATACATTATGAACA
*
20109020 TGTATCCATACATT-TGAA
1 TGTATCGATACATTATGAA
20109038 ACAGAATGCA
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
20 20 0.41
21 29 0.59
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTATGAACA
Found at i:20112591 original size:15 final size:16
Alignment explanation
Indices: 20112573--20112616 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
20112563 AAATTTGTAA
20112573 AAAATTAATTAAA-AC
1 AAAATTAATTAAACAC
*
20112588 AAAATTAAAATAAACAC
1 AAAATT-AATTAAACAC
*
20112605 TAAATTAATTAA
1 AAAATTAATTAA
20112617 TAAACTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 6 0.25
16 11 0.46
17 7 0.29
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATTAATTAAACAC
Found at i:20112623 original size:17 final size:17
Alignment explanation
Indices: 20112574--20112626 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
20112564 AATTTGTAAA
*
20112574 AAATTAATT-A-AAACA
1 AAATTAATTAATAAACT
20112589 AAATTAA--AATAAACACT
1 AAATTAATTAAT-AA-ACT
20112606 AAATTAATTAATAAACT
1 AAATTAATTAATAAACT
20112623 AAAT
1 AAAT
20112627 AAGTTGAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
14 1 0.03
15 7 0.23
16 2 0.06
17 16 0.52
18 2 0.06
19 3 0.10
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (17 bp):
AAATTAATTAATAAACT
Found at i:20114050 original size:21 final size:19
Alignment explanation
Indices: 20114024--20114064 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
20114014 AATTTAAAAC
20114024 AAAATAACATAAAATTTAACT
1 AAAATAAC-TAAAA-TTAACT
*
20114045 AAAATAACTTAAATTAACT
1 AAAATAACTAAAATTAACT
20114064 A
1 A
20114065 CTCAACATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATAACTAAAATTAACT
Found at i:20116772 original size:35 final size:34
Alignment explanation
Indices: 20116723--20116831 Score: 129
Period size: 35 Copynumber: 3.2 Consensus size: 34
20116713 CCCAAAGTGA
20116723 TTTTTCAAAGGCTCAACCACAACCTTTCACAATGG
1 TTTTTCAAAGGCTCAACCACAACC-TTCACAATGG
*
20116758 TTTTTCACAA-GCTCAACCAAAACC--CA-AAGTGG
1 TTTTTCA-AAGGCTCAACCACAACCTTCACAA-TGG
20116790 TTTTTCAAAGGCTCAACCACAA-CTTACAACAATGG
1 TTTTTCAAAGGCTCAACCACAACCTT-C-ACAATGG
20116825 TTTTTCA
1 TTTTTCA
20116832 CGGGATCAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
31 5 0.08
32 23 0.36
34 1 0.02
35 31 0.48
36 4 0.06
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.28
Consensus pattern (34 bp):
TTTTTCAAAGGCTCAACCACAACCTTCACAATGG
Found at i:20116780 original size:67 final size:67
Alignment explanation
Indices: 20116664--20116851 Score: 254
Period size: 67 Copynumber: 2.8 Consensus size: 67
20116654 AGCTTTTATC
* * * * *
20116664 AGGCTCAGCCAAAACCTTTCACAATAGTTTTT-ACCAGGATTAACTAAAACCCAAAGTGATTTTT
1 AGGCTCAACCACAACCTTTCACAATGGTTTTTCA-CAGGATCAACCAAAACCCAAAGTGATTTTT
20116728 CAA
65 CAA
* * *
20116731 AGGCTCAACCACAACCTTTCACAATGGTTTTTCACAAGCTCAACCAAAACCCAAAGTGGTTTTTC
1 AGGCTCAACCACAACCTTTCACAATGGTTTTTCACAGGATCAACCAAAACCCAAAGTGATTTTTC
20116796 AA
66 AA
* *
20116798 AGGCTCAACCACAA-CTTACAACAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 AGGCTCAACCACAACCTTTC-ACAATGGTTTTTCACAGGATCAACCAAAACCCAA
20116852 CAACTAACTT
Statistics
Matches: 107, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
66 4 0.04
67 102 0.95
68 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (67 bp):
AGGCTCAACCACAACCTTTCACAATGGTTTTTCACAGGATCAACCAAAACCCAAAGTGATTTTTC
AA
Found at i:20116796 original size:32 final size:32
Alignment explanation
Indices: 20116709--20116851 Score: 128
Period size: 35 Copynumber: 4.3 Consensus size: 32
20116699 AGGATTAACT
*
20116709 AAAACCCAAAGTGATTTTTCAAAGGCTCAACC
1 AAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
*
20116741 ACAACCTTTCACAA-TGGTTTTTCACAA-GCTCAACC
1 AAAACC---CA-AAGTGGTTTTTCA-AAGGCTCAACC
20116776 AAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
1 AAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
* * * ** *
20116808 ACAACTTACAACAATGGTTTTTCACGGGATCAACC
1 AAAAC--CCAA-AGTGGTTTTTCAAAGGCTCAACC
20116843 AAAACCCAA
1 AAAACCCAA
20116852 CAACTAACTT
Statistics
Matches: 90, Mismatches: 11, Indels: 19
0.75 0.09 0.16
Matches are distributed among these distances:
31 4 0.04
32 29 0.32
33 3 0.03
34 3 0.03
35 47 0.52
36 4 0.04
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (32 bp):
AAAACCCAAAGTGGTTTTTCAAAGGCTCAACC
Found at i:20126691 original size:32 final size:32
Alignment explanation
Indices: 20126655--20126800 Score: 123
Period size: 35 Copynumber: 4.4 Consensus size: 32
20126645 TTTACCGGGA
*
20126655 TCAACTAAAACCTAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
* * *
20126687 TCAACCACAACCTTTCACAA-TAGTTTTTCACAGGC
1 TCAACCAAAACC--T-A-AAGTGGTTTTTCAAAGGC
* *
20126722 TCAACCAAAACCCAAAGTGATTTTTCAAAGGC
1 TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
* * ** *
20126754 TCAACCACAACCTGCAACAATGGTTTTTCACGGGA
1 TCAACCAAAACCT--AA-AGTGGTTTTTCAAAGGC
20126789 TCAACCAAAACC
1 TCAACCAAAACC
20126801 CAATAACTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
31 2 0.02
32 34 0.38
34 3 0.03
35 48 0.54
36 2 0.02
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCTAAAGTGGTTTTTCAAAGGC
Found at i:20126739 original size:67 final size:67
Alignment explanation
Indices: 20126628--20126803 Score: 257
Period size: 67 Copynumber: 2.6 Consensus size: 67
20126618 TCTTAGCCAA
* * *
20126628 AACCTTTCACAATAGTTTTT-ACCGGGATCAACTAAAACCTAAAGTGGTTTTTCAAAGGCTCAAC
1 AACCTTTCACAATAGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAAC
20126692 CAC
65 CAC
* *
20126695 AACCTTTCACAATAGTTTTTCACAGGCTCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
1 AACCTTTCACAATAGTTTTTCACGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
20126760 AC
66 AC
* *
20126762 AACC-TGCAACAATGGTTTTTCACGGGATCAACCAAAACCCAA
1 AACCTTTC-ACAATAGTTTTTCACGGGATCAACCAAAACCCAA
20126804 TAACTAACTT
Statistics
Matches: 98, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
66 2 0.02
67 95 0.97
68 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (67 bp):
AACCTTTCACAATAGTTTTTCACGGGATCAACCAAAACCCAAAGTGATTTTTCAAAGGCTCAACC
AC
Found at i:20127627 original size:25 final size:25
Alignment explanation
Indices: 20127593--20127642 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20127583 TCTCCTTCAG
20127593 TGCAATTTTCCTATCAGTAGACAAA
1 TGCAATTTTCCTATCAGTAGACAAA
20127618 TGCAATTTTCCTATCAGTAGACAAA
1 TGCAATTTTCCTATCAGTAGACAAA
20127643 GGCATAATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (25 bp):
TGCAATTTTCCTATCAGTAGACAAA
Found at i:20131314 original size:24 final size:24
Alignment explanation
Indices: 20131282--20131336 Score: 110
Period size: 24 Copynumber: 2.3 Consensus size: 24
20131272 ATTATCCATC
20131282 CCATTCACCTCCATGCATGGCCAG
1 CCATTCACCTCCATGCATGGCCAG
20131306 CCATTCACCTCCATGCATGGCCAG
1 CCATTCACCTCCATGCATGGCCAG
20131330 CCATTCA
1 CCATTCA
20131337 ATTTACACTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.42, G:0.15, T:0.22
Consensus pattern (24 bp):
CCATTCACCTCCATGCATGGCCAG
Found at i:20134786 original size:31 final size:31
Alignment explanation
Indices: 20134735--20134832 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
20134725 ATTTCCTTAC
* ***
20134735 TTACCATTTGA-CCTTCCAAACTTTTCATCCT
1 TTACAATTTGATCCTT-CAAACTTTTCATAAA
*
20134766 TTACAATTT-AGTCCTTCAAACATTTCATAAA
1 TTACAATTTGA-TCCTTCAAACTTTTCATAAA
20134797 TTACAATTTGATCCTTC-AACTTGTTCAT-AA
1 TTACAATTTGATCCTTCAAACTT-TTCATAAA
20134827 TTACAA
1 TTACAA
20134833 CTTCACCCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
30 13 0.23
31 39 0.68
32 5 0.09
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.41
Consensus pattern (31 bp):
TTACAATTTGATCCTTCAAACTTTTCATAAA
Found at i:20135911 original size:46 final size:46
Alignment explanation
Indices: 20135848--20135937 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
20135838 TCACCCTATA
*
20135848 TTGTAATTGTTGGAGTAAGGATTATTCTACTATCTATTACCCATTG
1 TTGTAATTATTGGAGTAAGGATTATTCTACTATCTATTACCCATTG
* *
20135894 TTGTAATTATTGGAGTAAGGATTATTTTGCTATCTATTACCCAT
1 TTGTAATTATTGGAGTAAGGATTATTCTACTATCTATTACCCAT
20135938 AAATTGCACT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.27, C:0.12, G:0.17, T:0.44
Consensus pattern (46 bp):
TTGTAATTATTGGAGTAAGGATTATTCTACTATCTATTACCCATTG
Found at i:20139868 original size:22 final size:22
Alignment explanation
Indices: 20139840--20139883 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
20139830 TACTGAGTAC
20139840 TAAAATCTTATAACAAATTAAT
1 TAAAATCTTATAACAAATTAAT
20139862 TAAAATCTTATAACAAATTAAT
1 TAAAATCTTATAACAAATTAAT
20139884 CTTATTTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
TAAAATCTTATAACAAATTAAT
Found at i:20140580 original size:40 final size:40
Alignment explanation
Indices: 20140523--20140603 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
20140513 AATCCATGTC
*
20140523 AAAGAAAATAAACGAAACACAAAAGTAGAGAAAAAAACTA
1 AAAGAAAATAAAAGAAACACAAAAGTAGAGAAAAAAACTA
*
20140563 AAAGAAAATAAAAGAAACACAAAAGTAGGGAAAAAAACTA
1 AAAGAAAATAAAAGAAACACAAAAGTAGAGAAAAAAACTA
20140603 A
1 A
20140604 GTGTTGAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.70, C:0.09, G:0.14, T:0.07
Consensus pattern (40 bp):
AAAGAAAATAAAAGAAACACAAAAGTAGAGAAAAAAACTA
Found at i:20143163 original size:24 final size:25
Alignment explanation
Indices: 20143117--20143172 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
20143107 TTGGGTTCCT
*
20143117 TGTTTTGTTAATTGTGGATGGTTAA
1 TGTTTTGTTAAGTGTGGATGGTTAA
* *
20143142 TGTTTTGTTTAGT-TGGATGGTTGA
1 TGTTTTGTTAAGTGTGGATGGTTAA
20143166 TGTTTTG
1 TGTTTTG
20143173 ACAACCTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.55
Consensus pattern (25 bp):
TGTTTTGTTAAGTGTGGATGGTTAA
Found at i:20144015 original size:71 final size:69
Alignment explanation
Indices: 20143889--20144043 Score: 188
Period size: 71 Copynumber: 2.2 Consensus size: 69
20143879 AATGCTCAAT
* * *
20143889 CAAAAGTATCGAGACTTATGTAGTAAGTCTTGAGAATTTTCAACTTGAGAGCAAAAATTGAGCTT
1 CAAAAGTATCGAGACTTATGTAGTAAGTCTTGAGAATTTTCAACCTAAGAGCAAAAATTGA--TA
*
20143954 CAAGTG
64 CAAGAG
* * *
20143960 CAAAAGTATCGAGAGTTAAT-TCA-TAAGTCTTGAGACTTTTCAACCTAAGATCAAAAATTGATA
1 CAAAAGTATCGAGACTT-ATGT-AGTAAGTCTTGAGAATTTTCAACCTAAGAGCAAAAATTGATA
20144023 CAAGAG
64 CAAGAG
*
20144029 CAAAAGTATTGAGAC
1 CAAAAGTATCGAGAC
20144044 ACAAGGAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
69 19 0.26
71 51 0.70
72 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (69 bp):
CAAAAGTATCGAGACTTATGTAGTAAGTCTTGAGAATTTTCAACCTAAGAGCAAAAATTGATACA
AGAG
Found at i:20144135 original size:170 final size:172
Alignment explanation
Indices: 20143925--20144236 Score: 459
Period size: 170 Copynumber: 1.8 Consensus size: 172
20143915 GTCTTGAGAA
** * * *
20143925 TTTTCAACTTGAGAGCAAAAATTGAGCTTCAAGTGCAAAAGTATCGAGAGTTAATTCATAAGTCT
1 TTTTCAACTCAAGAGCAAAAATTGAGCTTAAAGTGCAAAAGTATCAAGACTTAATTCATAAGTCT
* * *
20143990 TGAGACTTTTCAACCTAAGATCAAAAATTGA-TACAAGAGCAAAAGTATTGAGACACAAGGAAAT
66 TGAGACCTTTCAACCCAAGATCAAAAATTGAGTACAAGAGCAAAAGTATTAAGACACAAGGAAAT
20144054 TTCAAAAGTATATAAACCTAATAAAAAAGTCTCAATCAAGTC
131 TTCAAAAGTATATAAACCTAATAAAAAAGTCTCAATCAAGTC
**
20144096 TTTTCAACTCAAGAGC-AAAATTGAGCTTTAAAG-GCAAAAGTATCAAGACTTTGTTCATAAGTC
1 TTTTCAACTCAAGAGCAAAAATTGAGC-TTAAAGTGCAAAAGTATCAAGACTTAATTCATAAGTC
* * *
20144159 TTGAGACCTTTCAACCCGAGATCAAAAATTGAGTTACAAGGGCAAAAGTATTAAGGCACAAGGAA
65 TTGAGACCTTTCAACCCAAGATCAAAAATTGAG-TACAAGAGCAAAAGTATTAAGACACAAGGAA
*
20144224 ATTTTAAAAGTAT
129 ATTTCAAAAGTAT
20144237 CAAGACCCAC
Statistics
Matches: 124, Mismatches: 14, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
170 65 0.52
171 19 0.15
172 40 0.32
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (172 bp):
TTTTCAACTCAAGAGCAAAAATTGAGCTTAAAGTGCAAAAGTATCAAGACTTAATTCATAAGTCT
TGAGACCTTTCAACCCAAGATCAAAAATTGAGTACAAGAGCAAAAGTATTAAGACACAAGGAAAT
TTCAAAAGTATATAAACCTAATAAAAAAGTCTCAATCAAGTC
Found at i:20148566 original size:2 final size:2
Alignment explanation
Indices: 20148559--20148588 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20148549 TTTACGTCTA
*
20148559 AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20148589 TTCAAATGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20149105 original size:25 final size:25
Alignment explanation
Indices: 20149080--20149151 Score: 90
Period size: 25 Copynumber: 2.8 Consensus size: 25
20149070 TTTATTTTTA
20149080 TTTCTTATTGGGCCATGCCCACTTAT
1 TTTC-TATTGGGCCATGCCCACTTAT
* ** *
20149106 TTTCTATTAGGTTATGCCCATTTAT
1 TTTCTATTGGGCCATGCCCACTTAT
20149131 TTTCTATTTGGGCCATGCCCA
1 TTTCTA-TTGGGCCATGCCCA
20149152 TTGTTTATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.44
Consensus pattern (25 bp):
TTTCTATTGGGCCATGCCCACTTAT
Found at i:20149176 original size:5 final size:5
Alignment explanation
Indices: 20149159--20149198 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
20149149 CCATTGTTTA
20149159 TTTTC TATTTC TTTTC TTTTC TTTTC TTTT- TCTTTC TTTT
1 TTTTC T-TTTC TTTTC TTTTC TTTTC TTTTC T-TTTC TTTT
20149199 TCTCTCTTCC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 1 0.03
5 25 0.78
6 6 0.19
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTC
Found at i:20149199 original size:10 final size:10
Alignment explanation
Indices: 20149160--20149206 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
20149150 CATTGTTTAT
*
20149160 TTTCTATTTC
1 TTTCTTTTTC
20149170 TTT-TCTTTTC
1 TTTCT-TTTTC
20149180 TTTTCTTTTTC
1 -TTTCTTTTTC
20149191 TTTCTTTTTC
1 TTTCTTTTTC
*
20149201 TCTCTT
1 TTTCTT
20149207 CCACCGTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 1 0.03
10 22 0.69
11 8 0.25
12 1 0.03
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:20149199 original size:16 final size:16
Alignment explanation
Indices: 20149160--20149201 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
20149150 CATTGTTTAT
*
20149160 TTTCTATTTC-TTTTC
1 TTTCTTTTTCTTTTTC
20149175 TTT-TCTTTTCTTTTTC
1 TTTCT-TTTTCTTTTTC
20149191 TTTCTTTTTCT
1 TTTCTTTTTCT
20149202 CTCTTCCACC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 1 0.04
15 7 0.30
16 14 0.61
17 1 0.04
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTTTTC
Found at i:20149201 original size:21 final size:21
Alignment explanation
Indices: 20149159--20149198 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20149149 CCATTGTTTA
20149159 TTTTCTATTTCTTTTCTTTTC
1 TTTTCTATTTCTTTTCTTTTC
*
20149180 TTTTCTTTTTC-TTTCTTTT
1 TTTTCTATTTCTTTTCTTTT
20149199 TCTCTCTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTCTATTTCTTTTCTTTTC
Found at i:20153428 original size:20 final size:20
Alignment explanation
Indices: 20153403--20153444 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
20153393 TAGTCCGACT
20153403 TCACTTTCCTCCACTCTTGG
1 TCACTTTCCTCCACTCTTGG
20153423 TCACTTTCCTCCACTCTTGG
1 TCACTTTCCTCCACTCTTGG
20153443 TC
1 TC
20153445 GAAGGAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.10, C:0.40, G:0.10, T:0.40
Consensus pattern (20 bp):
TCACTTTCCTCCACTCTTGG
Found at i:20156023 original size:25 final size:25
Alignment explanation
Indices: 20155995--20156056 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
20155985 CCATTTATTT
*
20155995 TTATTTCCTATTAGGCCATGCCCAC
1 TTATTTTCTATTAGGCCATGCCCAC
* * *
20156020 TTATTTTCTATTGGGTCATGCCCAT
1 TTATTTTCTATTAGGCCATGCCCAC
20156045 TTATTTTCTATT
1 TTATTTTCTATT
20156057 TATTTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.11, T:0.48
Consensus pattern (25 bp):
TTATTTTCTATTAGGCCATGCCCAC
Found at i:20156240 original size:34 final size:34
Alignment explanation
Indices: 20156192--20156316 Score: 196
Period size: 34 Copynumber: 3.7 Consensus size: 34
20156182 CACTATGCTG
*
20156192 TCCAATTTTCCTGCACAAATTGGTAGCAAACAGC
1 TCCAATTTTTCTGCACAAATTGGTAGCAAACAGC
*
20156226 TCCAATTTCTCTGCACAAATTGGTAGCAAACAGC
1 TCCAATTTTTCTGCACAAATTGGTAGCAAACAGC
** **
20156260 TCCAATTTTTCTGCACAAATTGGCGGCAAACAAT
1 TCCAATTTTTCTGCACAAATTGGTAGCAAACAGC
20156294 TCCAATTTTTCTGCACAAATTGG
1 TCCAATTTTTCTGCACAAATTGG
20156317 CATCAAGCAG
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 84 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (34 bp):
TCCAATTTTTCTGCACAAATTGGTAGCAAACAGC
Found at i:20156317 original size:34 final size:34
Alignment explanation
Indices: 20156192--20156337 Score: 193
Period size: 34 Copynumber: 4.3 Consensus size: 34
20156182 CACTATGCTG
* *
20156192 TCCAATTTTCCTGCACAAATTGGTAGCAAACAGC
1 TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
* *
20156226 TCCAATTTCTCTGCACAAATTGGTAGCAAACAGC
1 TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
* **
20156260 TCCAATTTTTCTGCACAAATTGGCGGCAAACAAT
1 TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
* *
20156294 TCCAATTTTTCTGCACAAATTGGCATCAAGCAGC
1 TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
**
20156328 TTAAATTTTT
1 TCCAATTTTT
20156338 AGCAGCAAAA
Statistics
Matches: 98, Mismatches: 14, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 98 1.00
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (34 bp):
TCCAATTTTTCTGCACAAATTGGCAGCAAACAGC
Found at i:20157791 original size:42 final size:42
Alignment explanation
Indices: 20157725--20157812 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
20157715 TGTTGATATG
*
20157725 GACCCGACTATGTGCAAGTAGGAGTGTACATAAGCCGATGAT
1 GACCCGACTATGTGCAAGTAGGAGTGCACATAAGCCGATGAT
* ** *
20157767 GACCCGGCTATGTGTGAGTGGGAGTGCACATAAGCCGATGAT
1 GACCCGACTATGTGCAAGTAGGAGTGCACATAAGCCGATGAT
20157809 GACC
1 GACC
20157813 TAGCCATGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.27, C:0.20, G:0.32, T:0.20
Consensus pattern (42 bp):
GACCCGACTATGTGCAAGTAGGAGTGCACATAAGCCGATGAT
Found at i:20157850 original size:43 final size:42
Alignment explanation
Indices: 20157734--20157850 Score: 137
Period size: 42 Copynumber: 2.8 Consensus size: 42
20157724 GGACCCGACT
* * * * *
20157734 ATGTGCAAGTAGGAGTGTACATAAGCCGATGATGACCCGGCT
1 ATGTGCTAGTGGGAGTGCACATAAGCCGATGATGACCCAGCC
*
20157776 ATGTG-TGAGTGGGAGTGCACATAAGCCGATGATGACCTAGCC
1 ATGTGCT-AGTGGGAGTGCACATAAGCCGATGATGACCCAGCC
* *
20157818 ATGTGCTAGTGGGCAGTGCACATGAGCTGATGA
1 ATGTGCTAGTGGG-AGTGCACATAAGCCGATGA
20157851 CAATAGCAGA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
42 46 0.72
43 18 0.28
ACGTcount: A:0.26, C:0.18, G:0.33, T:0.22
Consensus pattern (42 bp):
ATGTGCTAGTGGGAGTGCACATAAGCCGATGATGACCCAGCC
Found at i:20165281 original size:3 final size:3
Alignment explanation
Indices: 20165273--20165299 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20165263 TAAATATAGT
20165273 TAC TAC TAC TAC TAC TAC TAC TAC TAC
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC
20165300 CACCACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TAC
Found at i:20166288 original size:14 final size:14
Alignment explanation
Indices: 20166269--20166296 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
20166259 CAAAACAAAA
20166269 AATTTGCATATGTT
1 AATTTGCATATGTT
20166283 AATTTGCATATGTT
1 AATTTGCATATGTT
20166297 TTAGTTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (14 bp):
AATTTGCATATGTT
Found at i:20166811 original size:42 final size:43
Alignment explanation
Indices: 20166764--20166894 Score: 147
Period size: 43 Copynumber: 3.1 Consensus size: 43
20166754 CACCATCCCA
* * * ** *
20166764 TCATCATCAGCTCATGTGTACTCCCTACTCGCACAT-GGCTGG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* * *
20166806 TCATCACCAGTTTATGCACACTCCCTACTCGCACATAACCGGG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* * *
20166849 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGAG
1 TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
20166892 TCA
1 TCA
20166895 ATATCATTAC
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 30 0.41
43 43 0.59
ACGTcount: A:0.22, C:0.36, G:0.17, T:0.25
Consensus pattern (43 bp):
TCATCATCAGCTTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:20193843 original size:67 final size:68
Alignment explanation
Indices: 20193691--20193859 Score: 277
Period size: 67 Copynumber: 2.5 Consensus size: 68
20193681 ATATATACAT
* * * *
20193691 ATATAATTTTTGTTATTATAAATTAATAAAAACTACATATACTATATATATATTATATATATAGT
1 ATATAATTTTTGTTTTTGTAAATCAATAAAAATTACATATAC-ATATATATATTATATATATAGT
20193756 TTGC
65 TTGC
*
20193760 ATATAATTTTTATTTTTGTAAATCAATAAAAATTACATATAC-TATATATATTATATATATAGTT
1 ATATAATTTTTGTTTTTGTAAATCAATAAAAATTACATATACATATATATATTATATATATAGTT
20193824 TGC
66 TGC
20193827 ATATAATTTTTGTTTTTGTAAATCAATAAAAAT
1 ATATAATTTTTGTTTTTGTAAATCAATAAAAAT
20193860 AATGGATATA
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
67 57 0.61
69 37 0.39
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (68 bp):
ATATAATTTTTGTTTTTGTAAATCAATAAAAATTACATATACATATATATATTATATATATAGTT
TGC
Found at i:20196406 original size:40 final size:40
Alignment explanation
Indices: 20196362--20196456 Score: 154
Period size: 40 Copynumber: 2.4 Consensus size: 40
20196352 ATGCTTTAAC
* * *
20196362 CTTGAAAAGGCAGTGATGTTGTTAGGTTGTGCTTGCTCCT
1 CTTGAAAAGGCAGTGACGTTGTGAGGTTGTGCTTGATCCT
*
20196402 CTTGAAAAGGCAATGACGTTGTGAGGTTGTGCTTGATCCT
1 CTTGAAAAGGCAGTGACGTTGTGAGGTTGTGCTTGATCCT
20196442 CTTGAAAAGGCAGTG
1 CTTGAAAAGGCAGTG
20196457 TTTGAGTAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.22, C:0.15, G:0.31, T:0.33
Consensus pattern (40 bp):
CTTGAAAAGGCAGTGACGTTGTGAGGTTGTGCTTGATCCT
Found at i:20196826 original size:44 final size:46
Alignment explanation
Indices: 20196774--20196967 Score: 203
Period size: 44 Copynumber: 3.9 Consensus size: 46
20196764 AGTTTATAAT
*
20196774 TAAAATTTTAATTTAATTTTTAAATTAAAAATATTAA-TTT-TTTA
1 TAAAATTTTAATTTAATTTTTAAATTTAAAATATTAATTTTATTTA
*
20196818 TAAAATTTTAATTTGATTTTTAAATTTAAAATATTAAATTTTTTATAATGTA
1 TAAAATTTTAATTTAATTTTTAAATTTAAAATATT-AA--TTTTAT--T-TA
20196870 TAATTTTAATTTTAATTTAATTTTTAAATTTAAAATATTAATTTTATAATTTA
1 TAA----AATTTTAATTTAATTTTTAAATTTAAAATATTAA-TTT-T-ATTTA
20196923 TATTAACATTTTAATTTAATTTTTTAAATTTAAAATATTAATTTT
1 TA--AA-ATTTTAATTTAA-TTTTTAAATTTAAAATATTAATTTT
20196968 TTATAATTTA
Statistics
Matches: 129, Mismatches: 3, Indels: 29
0.80 0.02 0.18
Matches are distributed among these distances:
44 33 0.26
45 2 0.02
48 3 0.02
49 1 0.01
51 3 0.02
52 20 0.16
53 25 0.19
54 5 0.04
55 4 0.03
56 33 0.26
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (46 bp):
TAAAATTTTAATTTAATTTTTAAATTTAAAATATTAATTTTATTTA
Found at i:20196878 original size:24 final size:22
Alignment explanation
Indices: 20196786--20196882 Score: 53
Period size: 23 Copynumber: 4.4 Consensus size: 22
20196776 AAATTTTAAT
20196786 TTAA-TTTTTAAAT-TAAAAATA
1 TTAATTTTTTAAATGT-AAAATA
*
20196807 TTAATTTTTT--A--TAAAATT
1 TTAATTTTTTAAATGTAAAATA
*
20196825 TTAATTTGATTTTTAAATTTAAAATA
1 TTAA--T--TTTTTAAATGTAAAATA
* *
20196851 TTAAATTTTTTATAATGTATAATT
1 TT-AATTTTTTA-AATGTAAAATA
20196875 TTAATTTT
1 TTAATTTT
20196883 AATTTAATTT
Statistics
Matches: 60, Mismatches: 5, Indels: 20
0.71 0.06 0.24
Matches are distributed among these distances:
18 9 0.15
19 1 0.02
20 2 0.03
21 4 0.07
22 10 0.17
23 12 0.20
24 11 0.18
25 1 0.02
26 8 0.13
27 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTAATTTTTTAAATGTAAAATA
Found at i:20196881 original size:56 final size:55
Alignment explanation
Indices: 20196821--20196989 Score: 247
Period size: 53 Copynumber: 3.1 Consensus size: 55
20196811 TTTTTTATAA
* *
20196821 AATTTTAATTTGATTTTTAAATTTAAAATATTAAATTTTTTATAATGTATAATTTT
1 AATTTTAATTTAATTTTTAAATTTAAAATATT-AATTTTTTATAATTTATAATTTT
*
20196877 AATTTTAATTTAATTTTTAAATTTAAAATATTAA--TTTTATAATTTAT-A-TTA
1 AATTTTAATTTAATTTTTAAATTTAAAATATTAATTTTTTATAATTTATAATTTT
20196928 ACATTTTAATTTAATTTTTTAAATTTAAAATATTAATTTTTTATAATTTATAATTTAT
1 A-ATTTTAATTTAA-TTTTTAAATTTAAAATATTAATTTTTTATAATTTATAATTT-T
20196986 AATT
1 AATT
20196990 AAAAACTAAA
Statistics
Matches: 102, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
51 3 0.03
52 13 0.13
53 33 0.32
55 15 0.15
56 32 0.31
57 5 0.05
58 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (55 bp):
AATTTTAATTTAATTTTTAAATTTAAAATATTAATTTTTTATAATTTATAATTTT
Found at i:20196881 original size:100 final size:105
Alignment explanation
Indices: 20196768--20196989 Score: 312
Period size: 100 Copynumber: 2.1 Consensus size: 105
20196758 ATTCAAAGTT
**
20196768 TATAATTAAAATTTTAATTTAATTTTTAAATTAAAAATATTAA-TT-T-TTTATA-AA-ATTTTA
1 TATAATTTTAATTTTAATTTAATTTTTAAATTAAAAATATTAATTTATATTTATATAACATTTTA
*
20196828 ATTTGA-TTTTTAAATTTAAAATATTAAATTTTTTATAATG
66 ATTTAATTTTTTAAATTTAAAATATT-AATTTTTTATAATG
*
20196868 TATAATTTTAATTTTAATTTAATTTTTAAATTTAAAATATTAATTTTATAATTTATATTAACATT
1 TATAATTTTAATTTTAATTTAATTTTTAAATTAAAAATATTAA-TTTAT-ATTTATA-TAACATT
*
20196933 TTAATTTAATTTTTTAAATTTAAAATATTAATTTTTTATAATT
63 TTAATTTAATTTTTTAAATTTAAAATATTAATTTTTTATAATG
20196976 TATAATTTATAATT
1 TATAATTT-TAATT
20196990 AAAAACTAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
100 40 0.37
102 2 0.02
103 1 0.01
105 6 0.06
107 2 0.02
108 32 0.30
109 24 0.22
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.56
Consensus pattern (105 bp):
TATAATTTTAATTTTAATTTAATTTTTAAATTAAAAATATTAATTTATATTTATATAACATTTTA
ATTTAATTTTTTAAATTTAAAATATTAATTTTTTATAATG
Found at i:20196927 original size:18 final size:19
Alignment explanation
Indices: 20196886--20196979 Score: 51
Period size: 18 Copynumber: 5.0 Consensus size: 19
20196876 TAATTTTAAT
20196886 TTAATTTTTA-AATTTAAAATA
1 TTAATTTTTATAATTT---ATA
20196907 TTAA-TTTTATAATTTATA
1 TTAATTTTTATAATTTATA
**
20196925 TTAACATTT-TAATTTA-A
1 TTAATTTTTATAATTTATA
20196942 -T--TTTTTA-AATTTAAAATA
1 TTAATTTTTATAATTT---ATA
20196960 TTAATTTTTTATAATTTATA
1 TTAA-TTTTTATAATTTATA
20196980 ATTTATAATT
Statistics
Matches: 58, Mismatches: 3, Indels: 25
0.67 0.03 0.29
Matches are distributed among these distances:
14 8 0.14
16 1 0.02
17 2 0.03
18 15 0.26
19 4 0.07
20 8 0.14
21 9 0.16
22 6 0.10
23 5 0.09
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATTTTTATAATTTATA
Found at i:20207298 original size:21 final size:21
Alignment explanation
Indices: 20207274--20207315 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20207264 ATCTTTTTTA
*
20207274 ATATAAATAATTAAATTATTT
1 ATATAAACAATTAAATTATTT
20207295 ATATAAACAATTAAATTATTT
1 ATATAAACAATTAAATTATTT
20207316 GTAAGAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAAACAATTAAATTATTT
Found at i:20216584 original size:20 final size:20
Alignment explanation
Indices: 20216527--20216589 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
20216517 TATATACCCA
*
20216527 TCATCATCATC-TCACCAAC
1 TCATCATCATCATCACCAGC
*
20216546 CCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
20216566 TCATCATCATCATCACCAGC
1 TCATCATCATCATCACCAGC
20216586 TCAT
1 TCAT
20216590 GCGCACTCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.30, C:0.41, G:0.03, T:0.25
Consensus pattern (20 bp):
TCATCATCATCATCACCAGC
Found at i:20216636 original size:43 final size:43
Alignment explanation
Indices: 20216588--20216706 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
20216578 TCACCAGCTC
** * *
20216588 ATGCGCACTCCCTACTCGCACATGGCTGGGTCATCAC-CGGGTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATC-CTCGGCTT
20216631 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
* *
20216674 ATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 ATGCGCACTCCCTACTCGCACATAACCGGGTCA
20216707 ACATAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCGCACATAACCGGGTCATCCTCGGCTT
Found at i:20219229 original size:15 final size:15
Alignment explanation
Indices: 20219209--20219238 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
20219199 CTCTGCCCCT
20219209 GCTTGCAAGTAAGGA
1 GCTTGCAAGTAAGGA
20219224 GCTTGCAAGTAAGGA
1 GCTTGCAAGTAAGGA
20219239 TTATTTTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.20
Consensus pattern (15 bp):
GCTTGCAAGTAAGGA
Found at i:20220416 original size:23 final size:23
Alignment explanation
Indices: 20220389--20220489 Score: 82
Period size: 25 Copynumber: 4.3 Consensus size: 23
20220379 ATTTATTTTT
*
20220389 ATTTTATTTTTTAAATATTAATA
1 ATTTTATTATTTAAATATTAATA
*
20220412 ATTTTTAATTAATTAAAATATTAATA
1 A-TTTT-ATT-ATTTAAATATTAATA
* *
20220438 A-TTAATTATTTAAATATCAAT-
1 ATTTTATTATTTAAATATTAATA
*
20220459 ATTTTACTATAATTTAATTATTAAT-
1 ATTTTA-T-T-ATTTAAATATTAATA
20220484 ATTTTA
1 ATTTTA
20220490 ATTAATAATA
Statistics
Matches: 63, Mismatches: 8, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
21 1 0.02
22 15 0.24
23 5 0.08
24 7 0.11
25 21 0.33
26 14 0.22
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTTATTATTTAAATATTAATA
Found at i:20220490 original size:40 final size:41
Alignment explanation
Indices: 20220432--20220525 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 41
20220422 AATTAAAATA
*
20220432 TTAATAATTAATTATTTAAAT-ATCAATATTTTA-CTATAAT
1 TTAATTATTAATTATTTAAATAAT-AATATTTTATCTATAAT
* *
20220472 TTAATTATTAA-TATTTTAATTAATAATATTTTATTTATAAT
1 TTAATTATTAATTA-TTTAAATAATAATATTTTATCTATAAT
20220513 TTAA-TATT-ATTAT
1 TTAATTATTAATTAT
20220526 GATTAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
39 4 0.09
40 31 0.66
41 12 0.26
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (41 bp):
TTAATTATTAATTATTTAAATAATAATATTTTATCTATAAT
Found at i:20220491 original size:15 final size:15
Alignment explanation
Indices: 20220397--20220509 Score: 67
Period size: 15 Copynumber: 7.7 Consensus size: 15
20220387 TTATTTTATT
*
20220397 TTTTAAATATTAATAA
1 TTTTAATTATTAAT-A
*
20220413 TTTTTAATTAATTAAAA
1 -TTTTAATT-ATTAATA
* *
20220430 TATTAATAATTAAT-
1 TTTTAATTATTAATA
* *
20220444 TATTTAAATATCAATA
1 T-TTTAATTATTAATA
*
20220460 TTTT-ACTA-T-A-A
1 TTTTAATTATTAATA
20220471 -TTTAATTATTAATA
1 TTTTAATTATTAATA
*
20220485 TTTTAATTAATAATA
1 TTTTAATTATTAATA
*
20220500 TTTTATTTAT
1 TTTTAATTAT
20220510 AATTTAATAT
Statistics
Matches: 73, Mismatches: 15, Indels: 18
0.69 0.14 0.17
Matches are distributed among these distances:
10 3 0.04
11 4 0.05
12 2 0.03
13 1 0.01
14 5 0.07
15 38 0.52
16 7 0.10
17 8 0.11
18 5 0.07
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (15 bp):
TTTTAATTATTAATA
Found at i:20220491 original size:48 final size:49
Alignment explanation
Indices: 20220388--20220493 Score: 121
Period size: 48 Copynumber: 2.2 Consensus size: 49
20220378 TATTTATTTT
* *
20220388 TATTTT-ATTTTTTAAATATTAATAATTTTTAATTAATTAAAATATTAA
1 TATTTTAATTATTTAAATATCAATAATTTTTAATTAATTAAAATATTAA
* * * *
20220436 TA-ATTAATTATTTAAATATCAAT-A-TTTTACTATAATTTAATTATTAA
1 TATTTTAATTATTTAAATATCAATAATTTTTAAT-TAATTAAAATATTAA
20220483 TATTTTAATTA
1 TATTTTAATTA
20220494 ATAATATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
46 6 0.12
47 18 0.38
48 24 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (49 bp):
TATTTTAATTATTTAAATATCAATAATTTTTAATTAATTAAAATATTAA
Found at i:20220591 original size:16 final size:16
Alignment explanation
Indices: 20220566--20220596 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20220556 ATTCATACTC
20220566 ATTAAAAATTTAATAT
1 ATTAAAAATTTAATAT
*
20220582 ATTAATAATTTAATA
1 ATTAAAAATTTAATA
20220597 AATAAAACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATTAAAAATTTAATAT
Found at i:20220637 original size:16 final size:16
Alignment explanation
Indices: 20220618--20220655 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20220608 AATAGTTTAA
20220618 AATATAATATTATAAT
1 AATATAATATTATAAT
**
20220634 AATATGTTATTATAAT
1 AATATAATATTATAAT
20220650 AA-ATAA
1 AATATAA
20220656 CAGTAAGTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATATAATATTATAAT
Found at i:20221240 original size:32 final size:32
Alignment explanation
Indices: 20221199--20221309 Score: 116
Period size: 32 Copynumber: 3.4 Consensus size: 32
20221189 CATTGTTGTA
*
20221199 GGTTGTGGTTGAGCCTTTAAAAAATCACTTTG
1 GGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
* ** *
20221231 GGTTTTGGTTGAGCCCGTGAAAAACCA-TTGTG
1 GGTTGTGGTTGAGCCTTTGAAAAATCACTT-TG
*
20221263 AAAGGTTGTGGTTGAGCTTTTGAAAAATCACTTTG
1 ---GGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
*
20221298 GGTTTTGGTTGA
1 GGTTGTGGTTGA
20221310 TCCCGGTAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 10
0.75 0.13 0.12
Matches are distributed among these distances:
31 2 0.03
32 35 0.56
35 24 0.38
36 2 0.03
ACGTcount: A:0.23, C:0.11, G:0.29, T:0.37
Consensus pattern (32 bp):
GGTTGTGGTTGAGCCTTTGAAAAATCACTTTG
Found at i:20221269 original size:67 final size:67
Alignment explanation
Indices: 20221163--20221336 Score: 262
Period size: 67 Copynumber: 2.6 Consensus size: 67
20221153 TAGTTGTTGA
*
20221163 GTTTTGGTTGATCCCGTGAGAAAAACCATTGTTG-TAGGTTGTGGTTGAGCCTTTAAAAAATCAC
1 GTTTTGGTTGATCCCGT--GAAAAACCATTG-TGAAAGGTTGTGGTTGAGCCTTTAAAAAATCAC
20221227 TTTGG
63 TTTGG
* * *
20221232 GTTTTGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCTTTTGAAAAATCACTTT
1 GTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTAAAAAATCACTTT
20221297 GG
66 GG
20221299 GTTTTGGTTGATCCCG-GTAAAAACCATTGTGAAAGGTT
1 GTTTTGGTTGATCCCGTG-AAAAACCATTGTGAAAGGTT
20221337 TTGGCTAAGC
Statistics
Matches: 98, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
66 3 0.03
67 79 0.81
69 16 0.16
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (67 bp):
GTTTTGGTTGATCCCGTGAAAAACCATTGTGAAAGGTTGTGGTTGAGCCTTTAAAAAATCACTTT
GG
Found at i:20221277 original size:35 final size:33
Alignment explanation
Indices: 20221167--20221330 Score: 104
Period size: 32 Copynumber: 4.8 Consensus size: 33
20221157 TGTTGAGTTT
*
20221167 TGGTTGATCCCGTGAGAAAAACCATTGTTGTAGGTTG
1 TGGTTGAGCCCGT--GAAAAACCATTG-TG-AGGTTG
** * * *
20221204 TGGTTGAGCCTTTAAAAAATCACTT-TG-GGTTT
1 TGGTTGAGCCCGTGAAAAACCA-TTGTGAGGTTG
20221236 TGGTTGAGCCCGTGAAAAACCATTGTGAAAGGTTG
1 TGGTTGAGCCCGTGAAAAACCATTGTG--AGGTTG
*** * *
20221271 TGGTTGAGCTTTTGAAAAATCACTT-TG-GGTTT
1 TGGTTGAGCCCGTGAAAAACCA-TTGTGAGGTTG
*
20221303 TGGTTGATCCCG-GTAAAAACCATTGTGA
1 TGGTTGAGCCCGTG-AAAAACCATTGTGA
20221331 AAGGTTTTGG
Statistics
Matches: 97, Mismatches: 21, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
31 5 0.05
32 45 0.46
34 2 0.02
35 31 0.32
36 4 0.04
37 10 0.10
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (33 bp):
TGGTTGAGCCCGTGAAAAACCATTGTGAGGTTG
Found at i:20227297 original size:43 final size:43
Alignment explanation
Indices: 20227236--20227371 Score: 193
Period size: 43 Copynumber: 3.2 Consensus size: 43
20227226 AACCGGCTCA
*
20227236 TCATCATCGACTTATGCGCACTCCCTACTCGCACATAGCCGGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
*
20227279 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCAGG
1 TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
* * ** *
20227322 TCATCATCAGCTCATGTACACTCCC-ACATCGCACATAGCTGGG
1 TCATCATCGGCTTATGCGCACTCCCTAC-TCGCACATAGCCGGG
20227365 TCATCAT
1 TCATCAT
20227372 TATCACACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
42 2 0.02
43 82 0.98
ACGTcount: A:0.23, C:0.36, G:0.17, T:0.24
Consensus pattern (43 bp):
TCATCATCGGCTTATGCGCACTCCCTACTCGCACATAGCCGGG
Found at i:20228480 original size:2 final size:2
Alignment explanation
Indices: 20228473--20228502 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
20228463 ACAACATAAG
20228473 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
20228503 TGTCAAAACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:20228557 original size:22 final size:23
Alignment explanation
Indices: 20228532--20228575 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
20228522 TAAGTCCAAC
20228532 TTTCTTTCTTTCTTTTC-CTCCA
1 TTTCTTTCTTTCTTTTCTCTCCA
20228554 TTTCTTTCTTTCTTTTCTCTCC
1 TTTCTTTCTTTCTTTTCTCTCC
20228576 TTGGCTCGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTCTTTCTTTCTTTTCTCTCCA
Found at i:20228662 original size:60 final size:59
Alignment explanation
Indices: 20228554--20228679 Score: 171
Period size: 60 Copynumber: 2.1 Consensus size: 59
20228544 TTTTCCTCCA
* * * *
20228554 TTTCTTTCTTTCTTTTCTCTCCTTGGCTCGGCTGAACTTCCTTCTCTCTTTTTCTTTCC
1 TTTCTTCCTTTCTTTTCTCTCATTGGCTCGGCTAAACTCCCTTCTCTCTTTTTCTTTCC
* * *
20228613 TTTCTTCCTTCTCTTTTCTCTCATTGGTTTGGCTAAACTCCCTTTTCTCTTTTTCTTTCC
1 TTTCTTCCTT-TCTTTTCTCTCATTGGCTCGGCTAAACTCCCTTCTCTCTTTTTCTTTCC
*
20228673 TTCCTTC
1 TTTCTTC
20228680 TCCTTCCTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 9 0.16
60 49 0.84
ACGTcount: A:0.05, C:0.32, G:0.07, T:0.56
Consensus pattern (59 bp):
TTTCTTCCTTTCTTTTCTCTCATTGGCTCGGCTAAACTCCCTTCTCTCTTTTTCTTTCC
Found at i:20228708 original size:19 final size:18
Alignment explanation
Indices: 20228656--20228714 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 18
20228646 TAAACTCCCT
20228656 TTTCTCTTT-TTCTTTCC
1 TTTCTCTTTCTTCTTTCC
20228673 -TTC-CTTCTCCTTCCTTTCC
1 TTTCTCTT-T-CTT-CTTTCC
*
20228692 TTTCTCCTTTCTTCTTTCT
1 TTTCT-CTTTCTTCTTTCC
20228711 TTTC
1 TTTC
20228715 ATCTCGGCTT
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
15 3 0.09
16 4 0.12
18 2 0.06
19 15 0.44
20 6 0.18
21 1 0.03
22 3 0.09
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTCTCTTTCTTCTTTCC
Found at i:20233668 original size:19 final size:19
Alignment explanation
Indices: 20233644--20233707 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
20233634 TGCCCGGGTG
20233644 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGCA
**** **
20233663 CACGATG-GCACTGACTGTG
1 CACGATGTGGGGGGA-TGCA
20233682 CACGATGTGGGGGGATGCA
1 CACGATGTGGGGGGATGCA
20233701 CACGATG
1 CACGATG
20233708 ACTCCGGCTA
Statistics
Matches: 31, Mismatches: 12, Indels: 4
0.66 0.26 0.09
Matches are distributed among these distances:
18 3 0.10
19 25 0.81
20 3 0.10
ACGTcount: A:0.22, C:0.20, G:0.41, T:0.17
Consensus pattern (19 bp):
CACGATGTGGGGGGATGCA
Found at i:20233683 original size:38 final size:39
Alignment explanation
Indices: 20233641--20233742 Score: 143
Period size: 38 Copynumber: 2.6 Consensus size: 39
20233631 GAGTGCCCGG
* *
20233641 GTGCACGATGTGGGGGGATGCACACGATGGCACTGAC-T
1 GTGCACGATGTGGGGGGATGCACACGATGACACCGACAT
* *
20233679 GTGCACGATGTGGGGGGATGCACACGATGACTCCGGCTAT
1 GTGCACGATGTGGGGGGATGCACACGATGACACCGAC-AT
*
20233719 GTGCACGATGTGGGGGAATGCACA
1 GTGCACGATGTGGGGGGATGCACA
20233743 TGAGTCGGAT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
38 33 0.58
40 24 0.42
ACGTcount: A:0.22, C:0.21, G:0.39, T:0.19
Consensus pattern (39 bp):
GTGCACGATGTGGGGGGATGCACACGATGACACCGACAT
Found at i:20251229 original size:20 final size:20
Alignment explanation
Indices: 20251203--20251248 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
20251193 AATCTGACTT
* *
20251203 TTTTTCACTTGTTTCCTTGAA
1 TTTTACACTT-TTCCCTTGAA
20251224 TTTTCACACTTTTCCCTTGAA
1 TTTT-ACACTTTTCCCTTGAA
20251245 TTTT
1 TTTT
20251249 TCCACCTAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.15, C:0.22, G:0.07, T:0.57
Consensus pattern (20 bp):
TTTTACACTTTTCCCTTGAA
Found at i:20251250 original size:22 final size:22
Alignment explanation
Indices: 20251208--20251248 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20251198 GACTTTTTTT
*
20251208 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
20251230 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
20251249 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:20254761 original size:40 final size:38
Alignment explanation
Indices: 20254714--20254793 Score: 97
Period size: 38 Copynumber: 2.1 Consensus size: 38
20254704 CATGTGCCTT
** * *
20254714 CCCCCACATTGTGCACATAGTCGGTGCCATCGTGTGCATC
1 CCCCCACATCATGCACA-A-TCAGTGCCATCGTGTACATC
*
20254754 CCCCCACATCATGCACAATTAGTGCCATCGTGTACATC
1 CCCCCACATCATGCACAATCAGTGCCATCGTGTACATC
20254792 CC
1 CC
20254794 TCCCCTCACA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 19 0.54
39 1 0.03
40 15 0.43
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.24
Consensus pattern (38 bp):
CCCCCACATCATGCACAATCAGTGCCATCGTGTACATC
Found at i:20254937 original size:2 final size:2
Alignment explanation
Indices: 20254930--20254963 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20254920 CATGCACAAC
20254930 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20254964 CATCATAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20262031 original size:40 final size:38
Alignment explanation
Indices: 20261978--20262071 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 38
20261968 ATTTGCATTG
* *
20261978 CCCCACATCGTGCACATAGCCGGCGCCATCGTGTGCATCC
1 CCCCACATCGTGCACA-A-CCAGCGCCATCGTGTACATCC
* * *
20262018 CCCCACATTGTGCACAATCAGTGCCATCGTGTACATCC
1 CCCCACATCGTGCACAACCAGCGCCATCGTGTACATCC
20262056 CCCCACATCGTGCACA
1 CCCCACATCGTGCACA
20262072 CGGGCACTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
38 32 0.67
39 1 0.02
40 15 0.31
ACGTcount: A:0.21, C:0.41, G:0.18, T:0.19
Consensus pattern (38 bp):
CCCCACATCGTGCACAACCAGCGCCATCGTGTACATCC
Found at i:20263004 original size:19 final size:19
Alignment explanation
Indices: 20262956--20263005 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
20262946 TGGAAGAAGA
*
20262956 AGAAGGAGAAGAAGCTGCT
1 AGAAGGAGAAGAAGCTACT
*
20262975 AG-AGAATGAAGAAGCTACT
1 AGAAGGA-GAAGAAGCTACT
*
20262994 GGAAGGAGAAGA
1 AGAAGGAGAAGA
20263006 TATTTATAGC
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.46, C:0.08, G:0.36, T:0.10
Consensus pattern (19 bp):
AGAAGGAGAAGAAGCTACT
Found at i:20269026 original size:58 final size:58
Alignment explanation
Indices: 20268929--20269041 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
20268919 TGAGTACAAA
* *
20268929 GTGGAAGAGCCTTAAATAATTGTTTATAATCCTAAACATTCATTTCCACCTACTTTTT
1 GTGGAAGAGCATTAAATAATTGTTTATAATCCTAAACATTCATTCCCACCTACTTTTT
** * * * *
20268987 GTGGAAGAGCATTTCATAGTTGTTTATAATCTTATACATTTATTCCCACCTACTT
1 GTGGAAGAGCATTAAATAATTGTTTATAATCCTAAACATTCATTCCCACCTACTT
20269042 AACAAAAAAG
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.41
Consensus pattern (58 bp):
GTGGAAGAGCATTAAATAATTGTTTATAATCCTAAACATTCATTCCCACCTACTTTTT
Found at i:20269084 original size:18 final size:19
Alignment explanation
Indices: 20269063--20269101 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
20269053 TAATGCTTAT
20269063 GAAC-AAATTAAGATGGTA
1 GAACAAAATTAAGATGGTA
20269081 GAACAAAATTAAGATGGTA
1 GAACAAAATTAAGATGGTA
20269100 GA
1 GA
20269102 GGTAGTGGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (19 bp):
GAACAAAATTAAGATGGTA
Found at i:20271741 original size:26 final size:26
Alignment explanation
Indices: 20271711--20271766 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
20271701 TCTCTCTTTG
**
20271711 TCTATCTCTTGCCATATCATCGTCGA
1 TCTATCTCTCACCATATCATCGTCGA
*
20271737 TCTATCTCTCACCATATCATCGTTGA
1 TCTATCTCTCACCATATCATCGTCGA
20271763 TCTA
1 TCTA
20271767 CAAACCAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.21, C:0.30, G:0.09, T:0.39
Consensus pattern (26 bp):
TCTATCTCTCACCATATCATCGTCGA
Found at i:20272017 original size:27 final size:27
Alignment explanation
Indices: 20271982--20272043 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
20271972 TTGAACATGG
* *
20271982 CATGGCGTGTAACAACATGTTTTTT-TA
1 CATGACGTGTAACAACAT-TTTTTTGAA
**
20272009 CATGACGTGTATTAACATTTTTTTGAA
1 CATGACGTGTAACAACATTTTTTTGAA
20272036 CATGACGT
1 CATGACGT
20272044 ATAGTAAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.20
27 24 0.80
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (27 bp):
CATGACGTGTAACAACATTTTTTTGAA
Found at i:20272196 original size:27 final size:27
Alignment explanation
Indices: 20272156--20272224 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
20272146 TAGAATTTTT
* * **
20272156 TTTTTCAAAAATGGTGTATAGCAAACTA
1 TTTTTC-AACATGGTGTATAGAAAAAAA
* * *
20272184 TTTTTGAACATGGCGTGTAGAAAAAAA
1 TTTTTCAACATGGTGTATAGAAAAAAA
20272211 TTTTTCAACATGGT
1 TTTTTCAACATGGT
20272225 AACGACATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
27 27 0.84
28 5 0.16
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.36
Consensus pattern (27 bp):
TTTTTCAACATGGTGTATAGAAAAAAA
Found at i:20272354 original size:26 final size:26
Alignment explanation
Indices: 20272278--20272356 Score: 77
Period size: 26 Copynumber: 3.0 Consensus size: 26
20272268 ATATGGCATG
*
20272278 CAACATTTTTTCTACATGGCATGTAA
1 CAACATTTTTTCAACATGGCATGTAA
* * * * *
20272304 CAGCTTTTTTTTTTAAAATGACATGTAA
1 CAAC--ATTTTTTCAACATGGCATGTAA
*
20272332 TAACATTTTTTCAACATGGCATGTA
1 CAACATTTTTTCAACATGGCATGTA
20272357 GCAAAATGTT
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
26 20 0.51
28 19 0.49
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (26 bp):
CAACATTTTTTCAACATGGCATGTAA
Found at i:20273262 original size:39 final size:39
Alignment explanation
Indices: 20273173--20273388 Score: 267
Period size: 39 Copynumber: 5.6 Consensus size: 39
20273163 TCAACTCAGC
* ** * *
20273173 TCATGTGCACTCCCACATTGCACATAGC-TA-AT-ATCC
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
20273209 TCATGTGCACTCCCACACTGCACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
20273248 TCATGTGCTTTCCCACACCACACATGGCATATATCATCA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* * *
20273287 TCATGTACTCTCTCACACCGCACATGGCATATATCATTA
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
20273326 TCATGTGCTCTCCCACACCACACATGGCATATATCATCG
1 TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
* *
20273365 GCGTGTGCTCTCCCACACCGCACA
1 TCATGTGCTCTCCCACACCGCACA
20273389 CTACCGGCAC
Statistics
Matches: 157, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
36 26 0.17
37 2 0.01
38 2 0.01
39 127 0.81
ACGTcount: A:0.26, C:0.35, G:0.12, T:0.26
Consensus pattern (39 bp):
TCATGTGCTCTCCCACACCGCACATGGCATATATCATCA
Found at i:20274593 original size:26 final size:26
Alignment explanation
Indices: 20274537--20274595 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
20274527 GGCCGGCCAT
* *
20274537 AAGGAAAGAACAAGAGAGAAAATAGA
1 AAGGAAAGAACAAAAGAGAAAATACA
* *
20274563 GAGGAAAGGAAGAAAAGAGAAAA-ACA
1 AAGGAAA-GAACAAAAGAGAAAATACA
20274589 AAGGAAA
1 AAGGAAA
20274596 ACTAGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 14 0.52
27 13 0.48
ACGTcount: A:0.66, C:0.03, G:0.29, T:0.02
Consensus pattern (26 bp):
AAGGAAAGAACAAAAGAGAAAATACA
Found at i:20277234 original size:19 final size:21
Alignment explanation
Indices: 20277194--20277239 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
20277184 ATGAAGAATC
*
20277194 AAGAGAAGAAAGAAAAGGGAA
1 AAGAGAAGAAAGAAAAGAGAA
20277215 AAGA-AAGAAAGAAAA-AGAA
1 AAGAGAAGAAAGAAAAGAGAA
20277234 AAGAGA
1 AAGAGA
20277240 TCGATTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 12 0.52
21 4 0.17
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGAGAAGAAAGAAAAGAGAA
Found at i:20280291 original size:44 final size:44
Alignment explanation
Indices: 20280241--20280354 Score: 124
Period size: 44 Copynumber: 2.6 Consensus size: 44
20280231 AATTTCGAGT
* * * *
20280241 AAATGTATCAATACATTGAGGC-AATGTATCGATACATTTTAGCC
1 AAATGTATCGATACATTGAGCCAAATGTATCAATACA-TTGAGCC
* *
20280285 AAATGTATCGATACATTTTAGCCAAATGTATCAATACATTGAGGC
1 AAATGTATCGATACA-TTGAGCCAAATGTATCAATACATTGAGCC
*
20280330 -AATGTATCGATACATTTTAGCCAAA
1 AAATGTATCGATACA-TTGAGCCAAA
20280355 ATACTCACTA
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
44 39 0.63
45 10 0.16
46 13 0.21
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (44 bp):
AAATGTATCGATACATTGAGCCAAATGTATCAATACATTGAGCC
Found at i:20280292 original size:23 final size:23
Alignment explanation
Indices: 20280241--20280354 Score: 146
Period size: 23 Copynumber: 5.1 Consensus size: 23
20280231 AATTTCGAGT
* * *
20280241 AAATGTATCAATACA-TTGAGGC
1 AAATGTATCGATACATTTTAGCC
20280263 -AATGTATCGATACATTTTAGCC
1 AAATGTATCGATACATTTTAGCC
20280285 AAATGTATCGATACATTTTAGCC
1 AAATGTATCGATACATTTTAGCC
* * *
20280308 AAATGTATCAATACA-TTGAGGC
1 AAATGTATCGATACATTTTAGCC
20280330 -AATGTATCGATACATTTTAGCC
1 AAATGTATCGATACATTTTAGCC
20280352 AAA
1 AAA
20280355 ATACTCACTA
Statistics
Matches: 79, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
21 26 0.33
22 15 0.19
23 38 0.48
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.32
Consensus pattern (23 bp):
AAATGTATCGATACATTTTAGCC
Found at i:20287939 original size:60 final size:59
Alignment explanation
Indices: 20287846--20287991 Score: 193
Period size: 60 Copynumber: 2.4 Consensus size: 59
20287836 TAGGAGACCA
* * * * * *
20287846 AAACAGAAAGTTTTTCGCTACAGTGAGATTCAATCTCACTGCAGCGAAATTGTAACTCAG
1 AAACAGAAAG-TTTTCGCTGCAGCGAAATTCAATCTCACTGCAGCAAAACTGCAACTCAG
* *
20287906 AAACAGAAAGTTTCTCGCTGCAGCGAAATTCAATCTCGCTGTAGCAAAACTGCAACTCAG
1 AAACAGAAAGTTT-TCGCTGCAGCGAAATTCAATCTCACTGCAGCAAAACTGCAACTCAG
20287966 AAACAGAAAGTATTTCGCTGCAGCGA
1 AAACAGAAAGT-TTTCGCTGCAGCGA
20287992 GAATGTATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
59 3 0.04
60 71 0.93
61 2 0.03
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.23
Consensus pattern (59 bp):
AAACAGAAAGTTTTCGCTGCAGCGAAATTCAATCTCACTGCAGCAAAACTGCAACTCAG
Found at i:20287999 original size:21 final size:21
Alignment explanation
Indices: 20287970--20288015 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
20287960 ACTCAGAAAC
*
20287970 AGAAAGTATTTCGCTGCAGCG
1 AGAAAGTATTTCGCTGCAACG
*
20287991 AGAATGTATTTCGCTGCAACG
1 AGAAAGTATTTCGCTGCAACG
20288012 AGAA
1 AGAA
20288016 GCTACAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (21 bp):
AGAAAGTATTTCGCTGCAACG
Found at i:20288457 original size:43 final size:43
Alignment explanation
Indices: 20288380--20288489 Score: 112
Period size: 43 Copynumber: 2.6 Consensus size: 43
20288370 TCACCAGCTC
* ** * ** *
20288380 ATGCGCACTCTTTACTCGCACATGGCTGGATCATCATCGGGTT
1 ATGCGCACTCCTTACTCGCACATAACCGGATCATCATCGACTA
* * * *
20288423 ATGCGTACTCCTTACTCGCACATAACCGGGTCATCTTCTACTA
1 ATGCGCACTCCTTACTCGCACATAACCGGATCATCATCGACTA
*
20288466 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCTTACTCGCACATA
20288490 GCTGAGTCAA
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (43 bp):
ATGCGCACTCCTTACTCGCACATAACCGGATCATCATCGACTA
Found at i:20290355 original size:19 final size:19
Alignment explanation
Indices: 20290318--20290357 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
20290308 GGGTTTTAGA
*
20290318 GAGAAACCCTCGACTAGTT
1 GAGAAACCCTCGACCAGTT
*
20290337 GAGAAACCCTCGTCCAGTT
1 GAGAAACCCTCGACCAGTT
20290356 GA
1 GA
20290358 TAATTTGAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (19 bp):
GAGAAACCCTCGACCAGTT
Found at i:20294745 original size:37 final size:37
Alignment explanation
Indices: 20294695--20294774 Score: 151
Period size: 37 Copynumber: 2.2 Consensus size: 37
20294685 AAGATGTTCA
*
20294695 CAATGCTTCATATTAGGTCATAATAGACAAAATTTCC
1 CAATGCTTCATATTAGGTCATAATAGAAAAAATTTCC
20294732 CAATGCTTCATATTAGGTCATAATAGAAAAAATTTCC
1 CAATGCTTCATATTAGGTCATAATAGAAAAAATTTCC
20294769 CAATGC
1 CAATGC
20294775 CGTTTACAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (37 bp):
CAATGCTTCATATTAGGTCATAATAGAAAAAATTTCC
Found at i:20295351 original size:15 final size:15
Alignment explanation
Indices: 20295331--20295362 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20295321 GTTATTACAC
20295331 GCCATGCCTTAGTAG
1 GCCATGCCTTAGTAG
*
20295346 GCCATGCTTTAGTAG
1 GCCATGCCTTAGTAG
20295361 GC
1 GC
20295363 AATTGTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.28, T:0.28
Consensus pattern (15 bp):
GCCATGCCTTAGTAG
Found at i:20295389 original size:31 final size:31
Alignment explanation
Indices: 20295347--20295525 Score: 106
Period size: 31 Copynumber: 5.9 Consensus size: 31
20295337 CCTTAGTAGG
* * *
20295347 CCATGCTTTAGTAGGCAATTGTTGTTACACA
1 CCATGCCTTAGTAGACAATTGTTGCTACACA
* *
20295378 CCATGCCTTAGTAGGCAATTGTTGCTACATGA
1 CCATGCCTTAGTAGACAATTGTTGCTACA-CA
* * * **
20295410 -CATGCC-TA-T-TAC--TGTATTGTTACATG
1 CCATGCCTTAGTAGACAAT-TGTTGCTACACA
* *
20295436 CCATAG--GTAGTAGAC-ATCTGTTGTTACACA
1 CCAT-GCCTTAGTAGACAAT-TGTTGCTACACA
* *
20295466 CCATGCCTTAGTACACAATTGTTGCTACACG
1 CCATGCCTTAGTAGACAATTGTTGCTACACA
***
20295497 TTTTGCCTTAGTAGACAATTGTTGCTACA
1 CCATGCCTTAGTAGACAATTGTTGCTACA
20295526 TGTTATCCCT
Statistics
Matches: 115, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
26 1 0.01
27 13 0.11
28 3 0.03
29 4 0.03
30 16 0.14
31 75 0.65
32 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (31 bp):
CCATGCCTTAGTAGACAATTGTTGCTACACA
Found at i:20295537 original size:31 final size:31
Alignment explanation
Indices: 20295471--20295550 Score: 115
Period size: 31 Copynumber: 2.6 Consensus size: 31
20295461 ACACACCATG
* * *
20295471 CCTTAGTACACAATTGTTGCTACACGTTTTG
1 CCTTAGTAGACAATTGTTGCTACACGTTATC
*
20295502 CCTTAGTAGACAATTGTTGCTACATGTTATC
1 CCTTAGTAGACAATTGTTGCTACACGTTATC
*
20295533 CCTTAGTAGGCAATTGTT
1 CCTTAGTAGACAATTGTT
20295551 ACATGCCCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (31 bp):
CCTTAGTAGACAATTGTTGCTACACGTTATC
Found at i:20297251 original size:29 final size:29
Alignment explanation
Indices: 20297212--20297282 Score: 97
Period size: 29 Copynumber: 2.4 Consensus size: 29
20297202 AATAACTTAG
* *
20297212 TATTGGTATGGCATGTAACTTACAATATA
1 TATTGGCATGGCATGTAACTAACAATATA
**
20297241 TATTGGCATGGTGTGTAACTAACAATATA
1 TATTGGCATGGCATGTAACTAACAATATA
*
20297270 TATAGGCATGGCA
1 TATTGGCATGGCA
20297283 CTTAGCAACA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.34
Consensus pattern (29 bp):
TATTGGCATGGCATGTAACTAACAATATA
Found at i:20299964 original size:38 final size:38
Alignment explanation
Indices: 20299902--20300026 Score: 175
Period size: 38 Copynumber: 3.4 Consensus size: 38
20299892 TGATGTGGGT
20299902 GGGAGTG--CATG-TGATGATATTGAAATGTGCGAGTA
1 GGGAGTGCACATGATGATGATATTGAAATGTGCGAGTA
20299937 GGGAGTGCACATGATGATGATATTGAAATGTGCGAGTA
1 GGGAGTGCACATGATGATGATATTGAAATGTGCGAGTA
* *** * *
20299975 GGGAGTGTACATGATGATGATATTGCCTTGTGAGTGTA
1 GGGAGTGCACATGATGATGATATTGAAATGTGCGAGTA
20300013 GGGAGTGCACATGA
1 GGGAGTGCACATGA
20300027 GCTGAGTGTG
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
35 7 0.09
37 4 0.05
38 69 0.86
ACGTcount: A:0.28, C:0.08, G:0.36, T:0.28
Consensus pattern (38 bp):
GGGAGTGCACATGATGATGATATTGAAATGTGCGAGTA
Found at i:20302321 original size:29 final size:29
Alignment explanation
Indices: 20302285--20302460 Score: 132
Period size: 29 Copynumber: 6.3 Consensus size: 29
20302275 AATAACTTAG
* * *
20302285 TATTGGCATGGAATGTAACTTACAACATA
1 TATTGGCATGGCATGTAACTAACAATATA
* *
20302314 TATTGGCATGGCGTGTAACTGACAATATA
1 TATTGGCATGGCATGTAACTAACAATATA
* *
20302343 TATAGGCATGTCATGTAACTAACAATATA
1 TATTGGCATGGCATGTAACTAACAATATA
* * * *
20302372 TATAGGAATGTCATG----TAAC-ATA-G
1 TATTGGCATGGCATGTAACTAACAATATA
* * * * *
20302395 CATTGCCATGGCATGTACCTTACAATATC
1 TATTGGCATGGCATGTAACTAACAATATA
* *
20302424 TATT-GCATGGCGTGTAACTGACAATATA
1 TATTGGCATGGCATGTAACTAACAATATA
*
20302452 TATAGGCAT
1 TATTGGCAT
20302461 AGTGTGTGAT
Statistics
Matches: 116, Mismatches: 24, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
23 10 0.09
24 3 0.03
25 4 0.03
27 3 0.03
28 25 0.22
29 71 0.61
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (29 bp):
TATTGGCATGGCATGTAACTAACAATATA
Found at i:20302584 original size:36 final size:31
Alignment explanation
Indices: 20302509--20302588 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
20302499 AGAATTCTAT
20302509 TTGTTGGTGTGGTGTGTAGCAACATTTGGTA
1 TTGTTGGTGTGGTGTGTAGCAACATTTGGTA
20302540 TTGTTGGTGTGGTGTGTAGCAACATTTGGTA
1 TTGTTGGTGTGGTGTGTAGCAACATTTGGTA
**
20302571 TTGTTGGCATGGTGTGTA
1 TTGTTGGTGTGGTGTGTA
20302589 AGAAGTCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.15, C:0.06, G:0.36, T:0.42
Consensus pattern (31 bp):
TTGTTGGTGTGGTGTGTAGCAACATTTGGTA
Found at i:20305664 original size:69 final size:67
Alignment explanation
Indices: 20305545--20305697 Score: 175
Period size: 69 Copynumber: 2.3 Consensus size: 67
20305535 TGATTGTTGT
** * * *
20305545 AGGTTGTGGTTGAGCCTTGGAAAAACCATTTTGGGTTTTAGTTTAGCCCGT-AAAGAACTAGTG-
1 AGGTTGTGGTTGAGCCTTAAAAAAACCACTTTGGGTTTTAGTTGAGCCCGTGAAA-AACCAGTGC
20305608 TAAA
65 T-AA
* * *
20305612 AGGTTGTGGTTGAGCCTTAAAAAAAAACCACTTTGGGTTTTGGTTGATCCCGTGAAAAACCATTG
1 AGGTTGTGGTTGAGCCTT--AAAAAAACCACTTTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTG
20305677 CTAA
64 CTAA
*
20305681 AGGTTGTGGCTGAGCCT
1 AGGTTGTGGTTGAGCCT
20305698 ACGAAAAGCC
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
67 18 0.25
69 51 0.70
70 4 0.05
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.31
Consensus pattern (67 bp):
AGGTTGTGGTTGAGCCTTAAAAAAACCACTTTGGGTTTTAGTTGAGCCCGTGAAAAACCAGTGCT
AA
Found at i:20309790 original size:19 final size:19
Alignment explanation
Indices: 20309763--20309800 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20309753 CCATTTAACT
* *
20309763 TATTGGAGTATGATTTGAG
1 TATTAGAGTATAATTTGAG
20309782 TATTAGAGTATAATTTGAG
1 TATTAGAGTATAATTTGAG
20309801 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.26, T:0.42
Consensus pattern (19 bp):
TATTAGAGTATAATTTGAG
Found at i:20317109 original size:29 final size:28
Alignment explanation
Indices: 20317048--20317111 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
20317038 TCATAGCATA
* * *
20317048 CTCATTTAAGTGCCAACATATGCACTAT
1 CTCATTCATGTGCCAACATATGCACTAG
20317076 CTCATTCATGTGCCAAACATATGCAC-AG
1 CTCATTCATGTGCC-AACATATGCACTAG
20317104 CATCATTC
1 C-TCATTC
20317112 GAGTCTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 14 0.45
29 17 0.55
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (28 bp):
CTCATTCATGTGCCAACATATGCACTAG
Found at i:20321861 original size:28 final size:30
Alignment explanation
Indices: 20321783--20321880 Score: 80
Period size: 30 Copynumber: 3.3 Consensus size: 30
20321773 AAAATCCTTG
**
20321783 GTTGCTACACGCCAGCCCTAAAAA--TTATTA
1 GTTGCTACACGCCATACCTAAAAACCTTA--A
** *
20321813 GTTGCTATGCGCCATACCTAATAA-C-TAA
1 GTTGCTACACGCCATACCTAAAAACCTTAA
*
20321841 GTTGTTACACGCCATGA-CTAAAAACCTTAA
1 GTTGCTACACGCCAT-ACCTAAAAACCTTAA
20321871 GTTGCTACAC
1 GTTGCTACAC
20321881 ACTAAACAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
28 19 0.35
29 2 0.04
30 33 0.61
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.28
Consensus pattern (30 bp):
GTTGCTACACGCCATACCTAAAAACCTTAA
Found at i:20322334 original size:27 final size:27
Alignment explanation
Indices: 20322298--20322519 Score: 136
Period size: 27 Copynumber: 8.2 Consensus size: 27
20322288 GCGTGTCGTA
* *
20322298 TTTTCTCAACATGGCATATAACAACAT
1 TTTTTTCAACATGGCATGTAACAACAT
20322325 TTTTTTCAACATGGCATGTAACAGTA-AT
1 TTTTTTCAACATGGCATGTAACA--ACAT
* *
20322353 TTATTT-AAAATGGCATGTAGA-AA-AT
1 TTTTTTCAACATGGCATGTA-ACAACAT
* * *
20322378 ATTTTTGAACATGGCATATAGCAACAACA-
1 TTTTTTCAACATGGC--AT-GTAACAACAT
* * * *
20322407 TCTTTCCAACATGGCATGTAACGAC-C
1 TTTTTTCAACATGGCATGTAACAACAT
* *
20322433 TTTTTT-AACATGGCATGTAACAATAA
1 TTTTTTCAACATGGCATGTAACAACAT
* * * **
20322459 TTTTTCCAAAATGGCATTTAGTAAC-T
1 TTTTTTCAACATGGCATGTAACAACAT
* *
20322485 TATTTTGAACATGGCATGTAACAACAAT
1 TTTTTTCAACATGGCATGTAACAAC-AT
20322513 ATTTTTT
1 -TTTTTT
20322520 GTAATAACCT
Statistics
Matches: 146, Mismatches: 34, Indels: 28
0.70 0.16 0.13
Matches are distributed among these distances:
25 23 0.16
26 40 0.27
27 49 0.34
28 12 0.08
29 21 0.14
30 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.36
Consensus pattern (27 bp):
TTTTTTCAACATGGCATGTAACAACAT
Found at i:20322391 original size:53 final size:51
Alignment explanation
Indices: 20322325--20322518 Score: 149
Period size: 53 Copynumber: 3.6 Consensus size: 51
20322315 ATAACAACAT
* *
20322325 TTTTTTCAACATGGCATGTAACAGTAATTTATTTAAAATGGCATGTAGAAAA
1 TTTTTTGAACATGGCATGTAACAATAATTT-TTTAAAATGGCATGTAGAAAA
* * * ** * **
20322377 TATTTTTGAACATGGCATATAGCAACAACATCTTTCCAACATGGCATGTA-ACGACC
1 T-TTTTTGAACATGGCATGTAACAA-TA-AT-TTTTTAAAATGGCATGTAGA--AAA
* * * *
20322433 TTTTTT-AACATGGCATGTAACAATAATTTTTCCAAAATGGCATTTAGTAAC
1 TTTTTTGAACATGGCATGTAACAATAATTTTT-TAAAATGGCATGTAGAAAA
*
20322484 TTATTTTGAACATGGCATGTAACAACAATATTTTT
1 TT-TTTTGAACATGGCATGTAACAATAAT-TTTTT
20322519 TGTAATAACC
Statistics
Matches: 111, Mismatches: 20, Indels: 21
0.73 0.13 0.14
Matches are distributed among these distances:
51 7 0.06
52 19 0.17
53 40 0.36
54 21 0.19
55 20 0.18
56 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (51 bp):
TTTTTTGAACATGGCATGTAACAATAATTTTTTAAAATGGCATGTAGAAAA
Found at i:20322450 original size:107 final size:110
Alignment explanation
Indices: 20322299--20322511 Score: 283
Period size: 107 Copynumber: 2.0 Consensus size: 110
20322289 CGTGTCGTAT
* * *
20322299 TTTCTCAACATGGCATATAACAACATTTTTTTCAACATGGCATGTAACAGTAATTTATT-TAAAA
1 TTTCTCAACATGGCATATAACAACACTTTTTTCAACATGGCATGTAACAATAATTT-TTCCAAAA
*
20322363 TGGCATGTAGAAAA-TATTTTTGAACATGGCATATAGCAACAACATC
65 TGGCATGTAGAAAATTA-TTTTGAACATGGCATATAACAACAACATC
* *
20322409 TTTC-CAACATGGCATGTAACGAC-CTTTTTT-AACATGGCATGTAACAATAATTTTTCCAAAAT
1 TTTCTCAACATGGCATATAACAACACTTTTTTCAACATGGCATGTAACAATAATTTTTCCAAAAT
* * * *
20322471 GGCATTTAGTAACTTATTTTGAACATGGCATGTAACAACAA
66 GGCATGTAGAAAATTATTTTGAACATGGCATATAACAACAA
20322512 TATTTTTTGT
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
106 2 0.02
107 60 0.66
108 8 0.09
109 17 0.19
110 4 0.04
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (110 bp):
TTTCTCAACATGGCATATAACAACACTTTTTTCAACATGGCATGTAACAATAATTTTTCCAAAAT
GGCATGTAGAAAATTATTTTGAACATGGCATATAACAACAACATC
Found at i:20322549 original size:97 final size:96
Alignment explanation
Indices: 20322430--20322606 Score: 218
Period size: 97 Copynumber: 1.8 Consensus size: 96
20322420 GCATGTAACG
* *
20322430 ACCTTTTTTAACATGGCATGTAACAATAATTTT-TCCAAAATGGCAT-T-TAGTAAC-TTATTTT
1 ACCTTTTTTAACATGACATGTAACAAT--TTTTGTCCAAAAT--CATGTGTAGCAACATTATTTT
*
20322491 GAACATGGCATGTAACAACAATATTTTTTGTAATA
62 GAACATGGCATGGAACAACAATATTTTTTGTAATA
** * *
20322526 ACCTTTTTTCAACATGATGTGTAACAATTTTTGTCCAAAATTATGTGTAGCAACATTTTTTTGAA
1 ACCTTTTTT-AACATGACATGTAACAATTTTTGTCCAAAATCATGTGTAGCAACATTATTTTGAA
20322591 CATGGCATGGAACAAC
65 CATGGCATGGAACAAC
20322607 TTGTTTTCAA
Statistics
Matches: 69, Mismatches: 7, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
94 2 0.03
95 5 0.07
96 23 0.33
97 39 0.57
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (96 bp):
ACCTTTTTTAACATGACATGTAACAATTTTTGTCCAAAATCATGTGTAGCAACATTATTTTGAAC
ATGGCATGGAACAACAATATTTTTTGTAATA
Found at i:20327540 original size:15 final size:15
Alignment explanation
Indices: 20327520--20327560 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
20327510 TTCTTAAAAC
*
20327520 AACTTTAAAATCGAA
1 AACTTTAAAATCCAA
20327535 AACTTTAAAATCCAA
1 AACTTTAAAATCCAA
*
20327550 AGCTTTAAAAT
1 AACTTTAAAAT
20327561 AAAAATCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.51, C:0.15, G:0.05, T:0.29
Consensus pattern (15 bp):
AACTTTAAAATCCAA
Found at i:20336457 original size:43 final size:43
Alignment explanation
Indices: 20336370--20336541 Score: 240
Period size: 43 Copynumber: 4.0 Consensus size: 43
20336360 TTGTGTGATA
* * *
20336370 ATGATGACCC-AGCTATGTGTGTGT-GGGAGTGAACATGAGCTG
1 ATGATGACCCGA-CCATGTGTGAGTAGGGAGTGCACATGAGCTG
*
20336412 ATGATGACCCGACCATGTGTGAGTAGGGAGTGCACATGAGTTG
1 ATGATGACCCGACCATGTGTGAGTAGGGAGTGCACATGAGCTG
* * *
20336455 ATGATGACCCGGCCATGTGTGAGCAGGGAGTACACATGAGCTG
1 ATGATGACCCGACCATGTGTGAGTAGGGAGTGCACATGAGCTG
* *
20336498 ATGATGACCCGGCCATGTGTGAGTAGGAAGTGCACATGAGCTG
1 ATGATGACCCGACCATGTGTGAGTAGGGAGTGCACATGAGCTG
20336541 A
1 A
20336542 GTGTAAAGGG
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
42 20 0.17
43 97 0.83
ACGTcount: A:0.26, C:0.17, G:0.35, T:0.22
Consensus pattern (43 bp):
ATGATGACCCGACCATGTGTGAGTAGGGAGTGCACATGAGCTG
Found at i:20343823 original size:43 final size:42
Alignment explanation
Indices: 20343747--20343875 Score: 170
Period size: 43 Copynumber: 3.0 Consensus size: 42
20343737 TTGTGTGATA
20343747 ATGATGACCCAGCTATGTGCATGTGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGCATGTGGGAGTGCACATGAGCTG
* * *
20343789 ATGATGGCCCAACTATGTGCTATGTGGGAGTGCACATGAGCTA
1 ATGATGACCCAGCTATGTGC-ATGTGGGAGTGCACATGAGCTG
* * *
20343832 ATGATGACTCGGCCATGTGCGA-GTAGGGAGTGCACATGAGCTG
1 ATGATGACCCAGCTATGTGC-ATGT-GGGAGTGCACATGAGCTG
20343875 A
1 A
20343876 GTGTGAAGGA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
42 20 0.27
43 55 0.73
ACGTcount: A:0.25, C:0.19, G:0.33, T:0.23
Consensus pattern (42 bp):
ATGATGACCCAGCTATGTGCATGTGGGAGTGCACATGAGCTG
Found at i:20346234 original size:43 final size:43
Alignment explanation
Indices: 20346186--20346295 Score: 132
Period size: 43 Copynumber: 2.6 Consensus size: 43
20346176 TTCCCAGCTC
** *
20346186 ATGCGCACTCCCTACTCACACATGGCTAGGTCATCACCGAG-TT
1 ATGCGCACTCCCTACTCACACATAACCAGGTCATCACCG-GCTT
* * * *
20346229 ATGCGCACTTCTTACTCACACATAACCGGGTCATCATCGGCTT
1 ATGCGCACTCCCTACTCACACATAACCAGGTCATCACCGGCTT
*
20346272 ATGCGCACTCCCTACTCGCACATA
1 ATGCGCACTCCCTACTCACACATA
20346296 GCTGAGTCAA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.24, C:0.35, G:0.16, T:0.25
Consensus pattern (43 bp):
ATGCGCACTCCCTACTCACACATAACCAGGTCATCACCGGCTT
Found at i:20362335 original size:37 final size:37
Alignment explanation
Indices: 20362293--20362367 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
20362283 TTGTTTATCT
20362293 ATTTCTAGTGTTACTAAAGTAGAGAAACGAAATAGCC
1 ATTTCTAGTGTTACTAAAGTAGAGAAACGAAATAGCC
*
20362330 ATTTCTAGTGTTACTAAAGTAGAGAAATGAAATAGCC
1 ATTTCTAGTGTTACTAAAGTAGAGAAACGAAATAGCC
20362367 A
1 A
20362368 ATCAAATGGC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.12, G:0.19, T:0.28
Consensus pattern (37 bp):
ATTTCTAGTGTTACTAAAGTAGAGAAACGAAATAGCC
Found at i:20362940 original size:54 final size:54
Alignment explanation
Indices: 20362859--20363017 Score: 210
Period size: 54 Copynumber: 2.9 Consensus size: 54
20362849 ATGGTGATAC
* * ** * *
20362859 TGTCCGGCTATGTGCATAATGTAGTGGGCTGCACATGAGCTGGGTGAGATGGGA
1 TGTCCAGCTATATGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
* *
20362913 TGTCCAGCTATATTCACGATGTGGTGGGATGCACATGAGCAGGGTGAGATGGGA
1 TGTCCAGCTATATGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
* * * *
20362967 TGTCCGGGTATGTGCACGATGTGGTGGGATGCACATGAGTTGGGTGAGATG
1 TGTCCAGCTATATGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATG
20363018 CACATGATGA
Statistics
Matches: 91, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.26
Consensus pattern (54 bp):
TGTCCAGCTATATGCACGATGTGGTGGGATGCACATGAGCTGGGTGAGATGGGA
Found at i:20370440 original size:22 final size:22
Alignment explanation
Indices: 20370398--20370438 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
20370388 TACCTTTTGT
*
20370398 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
20370420 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
20370439 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:20375327 original size:2 final size:2
Alignment explanation
Indices: 20375315--20375360 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
20375305 ACCATATACC
* *
20375315 AT AT AT GT AT AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20375357 AT AT
1 AT AT
20375361 CANNNNNNNN
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20375427 original size:2 final size:2
Alignment explanation
Indices: 20375415--20375456 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
20375405 NNNNNNNNNC
*
20375415 AT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20375457 CAATCATCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20375544 original size:42 final size:42
Alignment explanation
Indices: 20375497--20375622 Score: 171
Period size: 42 Copynumber: 3.0 Consensus size: 42
20375487 CATCTCATAT
** * *
20375497 GCAACGGCTTATGCACACTCCCACTTGCACATAGCTGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* *
20375539 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCAGGTTA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
* **
20375581 GCAACGACTTATGTGCACTCCTGCTCGCACATAGCCGGGTCA
1 GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
20375623 ATATCATTAC
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 73 1.00
ACGTcount: A:0.23, C:0.33, G:0.22, T:0.21
Consensus pattern (42 bp):
GCAACGGCTTATGTGCACTCCCACTCGCACATAGCCGGGTCA
Found at i:20384331 original size:11 final size:11
Alignment explanation
Indices: 20384298--20384332 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
20384288 CCTAGGGTTC
20384298 TTGTTCTTCCT
1 TTGTTCTTCCT
20384309 TT-TTCTTCCT
1 TTGTTCTTCCT
*
20384319 TTGTTCTTACT
1 TTGTTCTTCCT
20384330 TTG
1 TTG
20384333 GCCGGCCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.03, C:0.23, G:0.09, T:0.66
Consensus pattern (11 bp):
TTGTTCTTCCT
Found at i:20386507 original size:52 final size:52
Alignment explanation
Indices: 20386432--20386686 Score: 345
Period size: 52 Copynumber: 4.9 Consensus size: 52
20386422 CACACTTGCA
* * *
20386432 CATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCACGCA
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCT
* * *
20386484 CATGGCATATATCATCAGTGTGTGCATTCATACAGCACACCACTATCACG-T
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCT
* *
20386535 CATGGTATATATCATCAGTGTATGCACTCACACAGCACACCACTATCATG-T
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCT
* * * *
20386586 CATGGTATAAATCATTAGTGTGTGCACTCACATATCACACCACTATCAC-CGT
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGC-T
* * *
20386638 TATGGTATATATCGTCAGTGTGTGCACTCACACAACACACCACTATCAC
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCAC
20386687 TGTCATGTGC
Statistics
Matches: 180, Mismatches: 21, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
51 89 0.49
52 91 0.51
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (52 bp):
CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCACGCT
Found at i:20386643 original size:103 final size:102
Alignment explanation
Indices: 20386432--20386693 Score: 362
Period size: 103 Copynumber: 2.5 Consensus size: 102
20386422 CACACTTGCA
* * * * *
20386432 CATGGCATATATCATCAGTGTGTGCACTCACATAGCACACCACTATCACGCACATGGCATATATC
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCATG-TCATGGCATAAATC
* *
20386497 ATCAGTGTGTGCATTCATACAGCACACCACTATCACGT
65 ATCAGTGTGTGCACTCACACAGCACACCACTATCACGT
* *
20386535 CATGGTATATATCATCAGTGTATGCACTCACACAGCACACCACTATCATGTCATGGTATAAATCA
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCATGTCATGGCATAAATCA
* * *
20386600 TTAGTGTGTGCACTCACATATCACACCACTATCACCGT
66 TCAGTGTGTGCACTCACACAGCACACCACTATCA-CGT
* * *
20386638 TATGGTATATATCGTCAGTGTGTGCACTCACACAACACACCACTATCACTGTCATG
1 CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCA-TGTCATG
20386694 TGCACTCCCA
Statistics
Matches: 141, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
102 41 0.29
103 93 0.66
104 7 0.05
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (102 bp):
CATGGTATATATCATCAGTGTGTGCACTCACACAGCACACCACTATCATGTCATGGCATAAATCA
TCAGTGTGTGCACTCACACAGCACACCACTATCACGT
Found at i:20387524 original size:19 final size:19
Alignment explanation
Indices: 20387477--20387529 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
20387467 AAGAGTTAGG
*
20387477 AGAAGGAAGAAGCAAGAAAA
1 AGAAGGAA-AAGAAAGAAAA
* *
20387497 AGAAAGAAAAGAAAGGAAA
1 AGAAGGAAAAGAAAGAAAA
*
20387516 ATAAGGAAAAGAAA
1 AGAAGGAAAAGAAA
20387530 ATAAAAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 21 0.75
20 7 0.25
ACGTcount: A:0.70, C:0.02, G:0.26, T:0.02
Consensus pattern (19 bp):
AGAAGGAAAAGAAAGAAAA
Found at i:20388509 original size:25 final size:25
Alignment explanation
Indices: 20388451--20388510 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
20388441 GTGGTTGCAA
*
20388451 CCACGTATATCAACTCATGACCTAG
1 CCACGTATATCAACCCATGACCTAG
* * *
20388476 CCACATATATCAACCCATGGCCTTG
1 CCACGTATATCAACCCATGACCTAG
*
20388501 CCATGTATAT
1 CCACGTATAT
20388511 ATCACAGACC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.30, C:0.32, G:0.12, T:0.27
Consensus pattern (25 bp):
CCACGTATATCAACCCATGACCTAG
Found at i:20398480 original size:48 final size:49
Alignment explanation
Indices: 20398364--20398506 Score: 211
Period size: 48 Copynumber: 2.9 Consensus size: 49
20398354 TATTGACTCA
* *
20398364 GCTATGTACGAGTAAGGAGTACG-AGTAAGCCGATGATGATGATGACCCG
1 GCTATGTGCGAGTAAGGAGTGCGCA-TAAGCCGATGATGATGATGACCCG
*
20398413 GCTATGTGCGAGTAGGGAGTGCGCATAAGCCGATGATGAT-ATGACCCG
1 GCTATGTGCGAGTAAGGAGTGCGCATAAGCCGATGATGATGATGACCCG
*
20398461 TCTATGTGCGAGTAAGGAGTGCGCATAAGCCGATGATG-TCGATGAC
1 GCTATGTGCGAGTAAGGAGTGCGCATAAGCCGATGATGAT-GATGAC
20398507 TCCAACTATG
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
47 1 0.01
48 44 0.51
49 40 0.47
50 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.22
Consensus pattern (49 bp):
GCTATGTGCGAGTAAGGAGTGCGCATAAGCCGATGATGATGATGACCCG
Found at i:20409038 original size:27 final size:27
Alignment explanation
Indices: 20408990--20409067 Score: 104
Period size: 27 Copynumber: 2.9 Consensus size: 27
20408980 TTCTAATTGG
*
20408990 GCCATGCCCA-TTTTCTTTCTTGTTTA
1 GCCATGCCCATTTTTCTTTCTTGTTCA
* *
20409016 GCCATACCCATTTTTCTTTCTTGTTCG
1 GCCATGCCCATTTTTCTTTCTTGTTCA
* *
20409043 GTCATGCCCATTTTTTTTTCTTGTT
1 GCCATGCCCATTTTTCTTTCTTGTT
20409068 ACTTTCTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
26 9 0.20
27 36 0.80
ACGTcount: A:0.10, C:0.26, G:0.12, T:0.53
Consensus pattern (27 bp):
GCCATGCCCATTTTTCTTTCTTGTTCA
Found at i:20409837 original size:2 final size:2
Alignment explanation
Indices: 20409830--20409876 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
20409820 GAGCTTCACC
20409830 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
20409872 TA TA T
1 TA TA T
20409877 TATTATTATT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.