Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 132 of 325
Found at i:39920030 original size:23 final size:23
Alignment explanation
Indices: 39919970--39920073 Score: 131
Period size: 23 Copynumber: 4.6 Consensus size: 23
39919960 TAGGAGTTAT
* *
39919970 AGAATAAGCCATAAAGGCTCCA-
1 AGAATATGCCACAAAGGCTCCAC
* *
39919992 AGAATATTCCATAAAGGCTCCAC
1 AGAATATGCCACAAAGGCTCCAC
39920015 AGAATATGCCACAAAGGCTCCAC
1 AGAATATGCCACAAAGGCTCCAC
* *
39920038 AGAATGTGCCACAAAGGCTTCAC
1 AGAATATGCCACAAAGGCTCCAC
*
39920061 AAAATATG-CACAA
1 AGAATATGCCACAA
39920074 CAGCTTTACA
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
22 25 0.34
23 48 0.66
ACGTcount: A:0.42, C:0.25, G:0.16, T:0.16
Consensus pattern (23 bp):
AGAATATGCCACAAAGGCTCCAC
Found at i:39925733 original size:42 final size:43
Alignment explanation
Indices: 39925686--39925907 Score: 120
Period size: 42 Copynumber: 5.2 Consensus size: 43
39925676 GAGGAGCACA
* * *
39925686 ATCACTTAAGCTCGCATG-GG-GAGGTTCGCTGATACACAGGTT
1 ATCACTTAAGCTC-CATGCGGAGAGCTCCGCTGATACACAGATT
* *
39925728 GTCACTTAAGCT-CATGCGGAGAGCTCCGTTGATACACAGATT
1 ATCACTTAAGCTCCATGCGGAGAGCTCCGCTGATACACAGATT
* * *** * *
39925770 ATCACTTAAGCT-CATGAGGGGAGCTTTACTGGTTACACTA-TTT
1 ATCACTTAAGCTCCATGCGGAGAGCTCCGCT-GATACAC-AGATT
* * * *
39925813 ATCACTTAAGCT-CATG-AGAGAGCTTCACTAATGACACA-ACTT
1 ATCACTTAAGCTCCATGCGGAGAGCTCCGCTGAT-ACACAGA-TT
* * * * * *
39925855 ATCACTTAAGCT-TAGGAGGGGAGCTTCGCTGATTACACAGCTT
1 ATCACTTAAGCTCCATGCGGAGAGCTCCGCTGA-TACACAGATT
*
39925898 ATCATTTAAG
1 ATCACTTAAG
39925908 TTCATGAAGA
Statistics
Matches: 143, Mismatches: 28, Indels: 17
0.76 0.15 0.09
Matches are distributed among these distances:
40 4 0.03
41 4 0.03
42 82 0.57
43 51 0.36
44 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (43 bp):
ATCACTTAAGCTCCATGCGGAGAGCTCCGCTGATACACAGATT
Found at i:39925821 original size:43 final size:43
Alignment explanation
Indices: 39925729--39925985 Score: 223
Period size: 43 Copynumber: 6.0 Consensus size: 43
39925719 ACACAGGTTG
* **** *
39925729 TCACTTAAGCTCATGCGGAGAGCTCCGTTGA-TACACAGA-TTA
1 TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACA-ACTTA
* ** * *
39925771 TCACTTAAGCTCATGAGGGGAGCTTTACTGGTTACACTATTTA
1 TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACAACTTA
* *
39925814 TCACTTAAGCTCATGA-GAGAGCTTCACTAATGACACAACTTA
1 TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACAACTTA
* * * ** * *
39925856 TCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACACAGCTTA
1 TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACAACTTA
* * * ** *
39925899 TCATTTAAGTTCATGAAGAGAATTTTGCTAATTACACAACTTA
1 TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACAACTTA
* * *
39925942 TCACTTAAACTCATGAGGAGAGCTTTTCTTATTACACAACTTA
1 TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACAACTTA
39925985 T
1 T
39925986 AAAACTGTTT
Statistics
Matches: 171, Mismatches: 41, Indels: 5
0.79 0.19 0.02
Matches are distributed among these distances:
42 58 0.34
43 113 0.66
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.32
Consensus pattern (43 bp):
TCACTTAAGCTCATGAGGAGAGCTTTACTAATTACACAACTTA
Found at i:39925891 original size:85 final size:85
Alignment explanation
Indices: 39925686--39925985 Score: 250
Period size: 85 Copynumber: 3.5 Consensus size: 85
39925676 GAGGAGCACA
* * * * * **
39925686 ATCACTTAAGC-TCGCATGGGGAGGTTCGCTGA-TACACAGGTTGTCACTTAAGCTCATGCGGAG
1 ATCACTTAAGCTTAGGA-GGGGAGCTTCGCTGATTACACAGCTTATCACTTAAGCTCATGAAGAG
* * *
39925749 AGCTCCGTTGATACACAGA-TT
65 AGCTTCGCTAATACACA-ACTT
* * ** * *
39925770 ATCACTTAAGCTCATGAGGGGAGCTTTACTGGTTACACTA-TTTATCACTTAAGCTCATG-AGAG
1 ATCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACAC-AGCTTATCACTTAAGCTCATGAAGAG
*
39925833 AGCTTCACTAATGACACAACTT
65 AGCTTCGCTAAT-ACACAACTT
* *
39925855 ATCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACACAGCTTATCATTTAAGTTCATGAAGAGA
1 ATCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACACAGCTTATCACTTAAGCTCATGAAGAGA
** *
39925920 ATTTTGCTAATTACACAACTT
66 GCTTCGCTAA-TACACAACTT
* * * * ** * *
39925941 ATCACTTAAACTCATGAGGAGAGCTTTTCTTATTACACAACTTAT
1 ATCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACACAGCTTAT
39925986 AAAACTGTTT
Statistics
Matches: 173, Mismatches: 35, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
84 35 0.20
85 79 0.46
86 58 0.34
87 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (85 bp):
ATCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACACAGCTTATCACTTAAGCTCATGAAGAGA
GCTTCGCTAATACACAACTT
Found at i:39925965 original size:86 final size:84
Alignment explanation
Indices: 39925760--39925985 Score: 247
Period size: 86 Copynumber: 2.6 Consensus size: 84
39925750 GCTCCGTTGA
* *
39925760 TACACAGA-TTATCACTTAAGCTCATGAGGGGAGCTTTACTGGTTACACTATTTATCACTTAAGC
1 TACACA-ACTTATCACTTAAGCTCATGAGGGGAGCTTTACTGATTACAC-ACTTATCACTTAAGC
*
39925824 TCATGAGAGAGCTTCACTAAT
64 TCATGAGAGAACTTCACTAAT
* * * ** * *
39925845 GACACAACTTATCACTTAAGCTTAGGAGGGGAGCTTCGCTGATTACACAGCTTATCATTTAAGTT
1 TACACAACTTATCACTTAAGCTCATGAGGGGAGCTTTACTGATTACACA-CTTATCACTTAAGCT
* **
39925910 CATGAAGAGAATTTTGCTAAT
65 CATG-AGAGAACTTCACTAAT
* * * *
39925931 TACACAACTTATCACTTAAACTCATGAGGAGAGCTTTTCTTATTACACAACTTAT
1 TACACAACTTATCACTTAAGCTCATGAGGGGAGCTTTACTGATTACAC-ACTTAT
39925986 AAAACTGTTT
Statistics
Matches: 116, Mismatches: 21, Indels: 7
0.81 0.15 0.05
Matches are distributed among these distances:
84 2 0.02
85 56 0.48
86 57 0.49
87 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (84 bp):
TACACAACTTATCACTTAAGCTCATGAGGGGAGCTTTACTGATTACACACTTATCACTTAAGCTC
ATGAGAGAACTTCACTAAT
Found at i:39929390 original size:49 final size:49
Alignment explanation
Indices: 39929330--39929472 Score: 205
Period size: 49 Copynumber: 2.9 Consensus size: 49
39929320 TTAGGGTAGT
* *
39929330 TTTATTGTACTATATTTTTCAAAATAACAACATCATGGATGTAGGCAGC
1 TTTATTGTACTATATTTTTCAGAATAACAACACCATGGATGTAGGCAGC
* * **
39929379 TTTATTATACTATATTTTTTAGAATAACAGGACCATGGATGTAGGCAGC
1 TTTATTGTACTATATTTTTCAGAATAACAACACCATGGATGTAGGCAGC
* * *
39929428 TTTATTGTACTATATTTTGCAGAATAACTACACCGTGGATGTAGG
1 TTTATTGTACTATATTTTTCAGAATAACAACACCATGGATGTAGG
39929473 TAGACTTCTC
Statistics
Matches: 81, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
49 81 1.00
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.37
Consensus pattern (49 bp):
TTTATTGTACTATATTTTTCAGAATAACAACACCATGGATGTAGGCAGC
Found at i:39929701 original size:24 final size:24
Alignment explanation
Indices: 39929674--39929766 Score: 134
Period size: 24 Copynumber: 3.9 Consensus size: 24
39929664 TTTCTCGAAG
*
39929674 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
**
39929698 ATTTATTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
39929722 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGTATAATAT
39929746 ATTT-GACATTTATTAGTATAA
1 ATTTAG-CATTTATTAGTATAA
39929767 AAATATTTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
23 1 0.02
24 62 0.98
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:39932580 original size:43 final size:43
Alignment explanation
Indices: 39932463--39932791 Score: 205
Period size: 43 Copynumber: 7.6 Consensus size: 43
39932453 ACAAAACTTC
* *
39932463 GCGGCGTTTTTTATACAAGCGCCGCTAAAGACCAGGACCTTTA
1 GCGGCGTTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTTTA
* * * * *
39932506 GCGGCG-CTCTTAAAAAAACGCCGCCAAAGACCAAGACCTTTA
1 GCGGCGTTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTTTA
39932548 GCGGCGTTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTTTA
1 GCGGCGTTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTTTA
* * * * * * * * *
39932591 GCAGCGCTTTTTATAAAAAACGCCACTATAGACCTGTACTTTTA
1 GCGGCGTTTTTTAT-AAAAGCGCCGCCAAAGACCAGGACCTTTA
* * * * * * * * *
39932635 GCGGTGCTTTTGTAAAAAAACGCCTCTATAGACCAAGAACTTTA
1 GCGGCG-TTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTTTA
* * * * * * * *
39932679 GCGGCG-CTTTTATAAAAAACGTCGCTATAGACCTGTACTTTTA
1 GCGGCGTTTTTTAT-AAAAGCGCCGCCAAAGACCAGGACCTTTA
* * * * * * *
39932722 GCGGCGCTTTTATATAAAAAACGCCGCTATAGACCTGTACTTTTA
1 GCGGCG-TTTTTTAT-AAAAGCGCCGCCAAAGACCAGGACCTTTA
* *
39932767 GCGGCGCTTTTGTA-AAAAACGCCGC
1 GCGGCG-TTTTTTATAAAAGCGCCGC
39932792 TAATTTGCCC
Statistics
Matches: 233, Mismatches: 47, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
42 39 0.17
43 88 0.38
44 54 0.23
45 52 0.22
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (43 bp):
GCGGCGTTTTTTATAAAAGCGCCGCCAAAGACCAGGACCTTTA
Found at i:39932793 original size:88 final size:88
Alignment explanation
Indices: 39932482--39932793 Score: 373
Period size: 88 Copynumber: 3.6 Consensus size: 88
39932472 TTTATACAAG
* * * * *
39932482 CGCCGCTAAAGACCAGGACCTTTAGCGGCGCTCTTA-AAAAAACGCCGCCAAAGACCAAG-ACCT
1 CGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTATAGACC-TGTACTT
* *
39932545 TTAGCGGCG-TTTTTTAT-AAAAG
65 TTAGCGGCGCTTTTATATAAAAAA
* * *
39932567 CGCCGCCAAAGACCAGGACCTTTAGCAGCGCTTTTTATAAAAAACGCCACTATAGACCTGTACTT
1 CGCCGCTAAAGACCAGGACCTTTAGCGGCGC-TTTTATAAAAAACGCCGCTATAGACCTGTACTT
* *
39932632 TTAGCGGTGCTTTTGTA-AAAAAA
65 TTAGCGGCGCTTTTATATAAAAAA
* * * * *
39932655 CGCCTCTATAGACCAAGAACTTTAGCGGCGCTTTTATAAAAAACGTCGCTATAGACCTGTACTTT
1 CGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTATAGACCTGTACTTT
39932720 TAGCGGCGCTTTTATATAAAAAA
66 TAGCGGCGCTTTTATATAAAAAA
* * * * *
39932743 CGCCGCTATAGACCTGTACTTTTAGCGGCGCTTTTGTAAAAAACGCCGCTA
1 CGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTA
39932794 ATTTGCCCAG
Statistics
Matches: 192, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
85 29 0.15
86 5 0.03
87 74 0.39
88 84 0.44
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (88 bp):
CGCCGCTAAAGACCAGGACCTTTAGCGGCGCTTTTATAAAAAACGCCGCTATAGACCTGTACTTT
TAGCGGCGCTTTTATATAAAAAA
Found at i:39933118 original size:21 final size:21
Alignment explanation
Indices: 39933094--39933134 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
39933084 GTTCTGCTCC
39933094 GCCTCCCTCGCTGCTGCCTCT
1 GCCTCCCTCGCTGCTGCCTCT
39933115 GCCTCCCTCGCTGCTGCCTC
1 GCCTCCCTCGCTGCTGCCTC
39933135 CGCTCTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.54, G:0.20, T:0.27
Consensus pattern (21 bp):
GCCTCCCTCGCTGCTGCCTCT
Found at i:39933724 original size:18 final size:18
Alignment explanation
Indices: 39933692--39933729 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
39933682 CTACATATAG
39933692 TAGTAAAAATATTATTTAA
1 TAGTAAAAATATTA-TTAA
*
39933711 TAGTAAAAA-GTTATTAA
1 TAGTAAAAATATTATTAA
39933728 TA
1 TA
39933730 CTTGATAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (18 bp):
TAGTAAAAATATTATTAA
Found at i:39940722 original size:133 final size:133
Alignment explanation
Indices: 39940484--39940735 Score: 486
Period size: 133 Copynumber: 1.9 Consensus size: 133
39940474 GAATTCAACA
39940484 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
39940549 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
39940614 ATT
131 ATT
* *
39940617 ATATAAAACGTGAGCAACAAGACAGTATTAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
1 ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
39940682 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
66 TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAAT
39940736 GGAATCACCA
Statistics
Matches: 117, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
133 117 1.00
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.20
Consensus pattern (133 bp):
ATATAAAACGTGAGCAACAAGACAGCAATAAACTCTTAAATCAATCTAAGTCCACACTAAACACA
TAAGTTGGATAGAAACATGAAAACAGACCAAAAGAACATCTAAATAACCAAAATATAACAATTTT
ATT
Found at i:39941824 original size:13 final size:13
Alignment explanation
Indices: 39941801--39941832 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
39941791 TTTTTTACCA
39941801 TAAAC-TATGAGG
1 TAAACATATGAGG
39941813 TAAACATATGAGG
1 TAAACATATGAGG
39941826 TAAACAT
1 TAAACAT
39941833 CTCTGTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (13 bp):
TAAACATATGAGG
Found at i:39944051 original size:22 final size:22
Alignment explanation
Indices: 39944003--39944045 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
39943993 ACTCTAAATT
* *
39944003 TAAAACCCTAAACCTGATACTC
1 TAAACCCCTAAACCTGAAACTC
*
39944025 TAAACCCCTAAACCTTAAACT
1 TAAACCCCTAAACCTGAAACT
39944046 ACAAACACAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.42, C:0.33, G:0.02, T:0.23
Consensus pattern (22 bp):
TAAACCCCTAAACCTGAAACTC
Found at i:39944578 original size:36 final size:38
Alignment explanation
Indices: 39944537--39944612 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 38
39944527 CTTCAATTAC
* * *
39944537 TAGTTAACTCCTAAACC-G-TAAATCTTAAACCATATA
1 TAGTTAACTCATAAACCTGCTAAACCCTAAACCATATA
39944573 TAGTTAACTCATAAACCTGCTTAAACCCTAAACCATATA
1 TAGTTAACTCATAAACCTGC-TAAACCCTAAACCATATA
39944612 T
1 T
39944613 CTTAAACTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 16 0.47
37 1 0.03
39 17 0.50
ACGTcount: A:0.41, C:0.24, G:0.05, T:0.30
Consensus pattern (38 bp):
TAGTTAACTCATAAACCTGCTAAACCCTAAACCATATA
Found at i:39944848 original size:41 final size:41
Alignment explanation
Indices: 39944791--39945091 Score: 430
Period size: 41 Copynumber: 7.4 Consensus size: 41
39944781 GTTCTATGAC
39944791 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* *
39944832 TTTTAGCGGCGTTTTACCGAAAGCGCTGCTAATGCTCTGTT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* *
39944873 TTTTAGCGGCATTTTACCGAAAGCGCAGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
* *
39944914 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-AT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
39944954 TTTTAGCGGCGTTTTACCCG-AAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTA-CCGAAAGCGCCGCTAATGCTCTGGT
* *
39944995 TTTTAGCGGCGTTTTACCCG-AAGCGCCGCTAATGATCTGTT
1 TTTTAGCGGCGTTTTA-CCGAAAGCGCCGCTAATGCTCTGGT
* * *
39945036 TTTTAGCGGCGTTTTACCTAAAGCACCGCTAATGATCT-GT
1 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
**
39945076 TTTTAGAAGCGTTTTA
1 TTTTAGCGGCGTTTTA
39945092 GTAAAAAACG
Statistics
Matches: 237, Mismatches: 20, Indels: 7
0.90 0.08 0.03
Matches are distributed among these distances:
40 51 0.22
41 186 0.78
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:39945011 original size:122 final size:122
Alignment explanation
Indices: 39944791--39945091 Score: 435
Period size: 122 Copynumber: 2.5 Consensus size: 122
39944781 GTTCTATGAC
*
39944791 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GTTTTTAGCGGCGTTTTACCGAAAGC
* * * *
39944856 GCTGCTAATGCTCTGTTTTTTAGCGGCATTTTA-CCGAAAGCGCAGCTAATGCTCTGGT
65 ACCGCTAATGCTCTGGTTTTTAGCGGCATTTTACCCG-AAGCGCAGCTAATGATCTGGT
*
39944914 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTATTTTTAGCGGCGTTTTACCCG-AAGC
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTTA-CCGAAAGC
* * *
39944978 ACCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCCGAAGCGCCGCTAATGATCTGTT
65 ACCGCTAATGCTCTGGTTTTTAGCGGCATTTTACCCGAAGCGCAGCTAATGATCTGGT
* * * **
39945036 TTTTAGCGGCGTTTTACCTAAAGCACCGCTAATGATCTGTTTTTAGAAGCGTTTTA
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTTA
39945092 GTAAAAAACG
Statistics
Matches: 161, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
122 118 0.73
123 43 0.27
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.34
Consensus pattern (122 bp):
TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGTTTTTAGCGGCGTTTTACCGAAAGCA
CCGCTAATGCTCTGGTTTTTAGCGGCATTTTACCCGAAGCGCAGCTAATGATCTGGT
Found at i:39945155 original size:163 final size:163
Alignment explanation
Indices: 39944791--39945155 Score: 464
Period size: 163 Copynumber: 2.2 Consensus size: 163
39944781 GTTCTATGAC
*
39944791 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
* * * * *
39944856 GCTGCTAATGCTCTGTTTTTTAGCGGCATTTTACCGAAAGCGCAGCTAATGCTCTGGTTTTTAGC
66 GCCGCTAATGATCTGTTTTTTAGCGGCATTTTACCGAAAGCACAGCTAATGATCTGGTTTTTAGA
* ** * *
39944921 GGCGTTTTACCCAAAGCGCCGCTAATGCTCTAT
131 AGCGTTTTACAAAAAACGCCGCTAATGCTATAT
* *
39944954 TTTTAGCGGCGTTTTACCCGAAGCACCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCCG-AAG
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTA-CCGAAAG
* * *
39945018 CGCCGCTAATGATCTGTTTTTTAGCGGCGTTTTACCTAAAGCACCGCTAATGATCT-GTTTTTAG
65 CGCCGCTAATGATCTGTTTTTTAGCGGCATTTTACCGAAAGCACAGCTAATGATCTGGTTTTTAG
* ** *
39945082 AAGCGTTTTAGTAAAAAACGCCGCTGTTGCTATGT
130 AAGCGTTTTA-CAAAAAACGCCGCTAATGCTATAT
* * ** * *
39945117 TTTTAGCGGCATTTTTCTTAAAACGCCGCTATTGCTCTG
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTG
39945156 TATTTTAAAA
Statistics
Matches: 172, Mismatches: 28, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
162 16 0.09
163 153 0.89
164 3 0.02
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (163 bp):
TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCGAAAGC
GCCGCTAATGATCTGTTTTTTAGCGGCATTTTACCGAAAGCACAGCTAATGATCTGGTTTTTAGA
AGCGTTTTACAAAAAACGCCGCTAATGCTATAT
Found at i:39945162 original size:41 final size:40
Alignment explanation
Indices: 39944791--39945162 Score: 420
Period size: 41 Copynumber: 9.1 Consensus size: 40
39944781 GTTCTATGAC
*
39944791 TTTTAGCGGCGTTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* *
39944832 TTTTAGCGGCGTTTTACCGAAAGCGCTGCTAATGCTCTGTT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTG-T
* * *
39944873 TTTTAGCGGCATTTTACCGAAAGCGCAGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
*
39944914 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTAT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
* *
39944954 TTTTAGCGGCGTTTTACCCGAAGCACCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCT-GT
* *
39944995 TTTTAGCGGCGTTTTACCCGAAGCGCCGCTAATGATCTGTT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTG-T
* * *
39945036 TTTTAGCGGCGTTTTACCTAAAGCACCGCTAATGATCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
** *** * ** *
39945076 TTTTAGAAGCGTTTTAGTAAAAAACGCCGCTGTTGCTATGT
1 TTTTAGCGGCGTTTTA-CCCAAAGCGCCGCTAATGCTCTGT
* * ** * *
39945117 TTTTAGCGGCATTTTTCTTAAAACGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
39945157 ATTTTA
1 -TTTTA
39945163 AAATTTTTGC
Statistics
Matches: 290, Mismatches: 35, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
40 73 0.25
41 216 0.74
42 1 0.00
ACGTcount: A:0.20, C:0.23, G:0.22, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTACCCAAAGCGCCGCTAATGCTCTGT
Found at i:39945489 original size:122 final size:121
Alignment explanation
Indices: 39945256--39945499 Score: 407
Period size: 122 Copynumber: 2.0 Consensus size: 121
39945246 CACACACGGT
* *
39945256 CTAGACACATGCCAGTGTCTACCCGTATGGACAAAAATAAGGCTATTTACCAAGCCATTTGCCAC
1 CTAGACACAAGCCAGTGTCTACCCGTATGGAAAAAAATAAGGCTATTTACCAAGCCATTTGCCAC
* *
39945321 CTTTACTCGCACCAACCTACACCACAACAAGCAACACCAATCCAAGCATTTATACA
66 ATTTACTCGCACCAACCTACACAACAACAAGCAACACCAATCCAAGCATTTATACA
* *
39945377 CTAGACACAAGCCCGTGTCTACCCGTGTGGAAAAAAATAAGGCTATTTACCAAGCCATTTTGCCA
1 CTAGACACAAGCCAGTGTCTACCCGTATGGAAAAAAATAAGGCTATTTACCAAGCCA-TTTGCCA
* *
39945442 CATTTACTTGCTCCAACCTACACAACAACAAGCAACACCAATCCAAGCATTTATACA
65 CATTTACTCGCACCAACCTACACAACAACAAGCAACACCAATCCAAGCATTTATACA
39945499 C
1 C
39945500 AACCAATTCA
Statistics
Matches: 114, Mismatches: 8, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
121 53 0.46
122 61 0.54
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.21
Consensus pattern (121 bp):
CTAGACACAAGCCAGTGTCTACCCGTATGGAAAAAAATAAGGCTATTTACCAAGCCATTTGCCAC
ATTTACTCGCACCAACCTACACAACAACAAGCAACACCAATCCAAGCATTTATACA
Found at i:39945517 original size:15 final size:15
Alignment explanation
Indices: 39945497--39945530 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39945487 AGCATTTATA
*
39945497 CACAACCAATTCAAC
1 CACAACCAAGTCAAC
*
39945512 CACAACCAAGTCATC
1 CACAACCAAGTCAAC
39945527 CACA
1 CACA
39945531 CATCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.41, G:0.03, T:0.12
Consensus pattern (15 bp):
CACAACCAAGTCAAC
Found at i:39946126 original size:20 final size:20
Alignment explanation
Indices: 39946098--39946141 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
39946088 TACCAACTTG
*
39946098 CAACTTACCATAATCTTTCA
1 CAACATACCATAATCTTTCA
* *
39946118 CAACATACCATAGTTTTTCA
1 CAACATACCATAATCTTTCA
39946138 CAAC
1 CAAC
39946142 TTAAACATTG
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:0.36, C:0.30, G:0.02, T:0.32
Consensus pattern (20 bp):
CAACATACCATAATCTTTCA
Found at i:39946348 original size:42 final size:42
Alignment explanation
Indices: 39946227--39946348 Score: 129
Period size: 43 Copynumber: 2.9 Consensus size: 42
39946217 TACCATACCA
* ** *
39946227 ATGCCATATCCCAGATATGGTCTTACATGGGATCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCATATCG
* * * *
39946269 ATGCCAATAACACAGCTATGGTCTTA-AAAAAAGTCTCATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACAAGAAA-TCTCATATCG
* *
39946312 ATGCCATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCA
39946349 ACTAACCCTA
Statistics
Matches: 63, Mismatches: 14, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
42 29 0.46
43 34 0.54
ACGTcount: A:0.32, C:0.23, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACAAGAAATCTCATATCG
Found at i:39956953 original size:18 final size:18
Alignment explanation
Indices: 39956932--39956971 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39956922 AAAGTTTTCA
* *
39956932 ATTTAAATTTAGTTTTTT
1 ATTTAAATTTACTTTTTG
*
39956950 ATTTAATTTTACTTTTTG
1 ATTTAAATTTACTTTTTG
39956968 ATTT
1 ATTT
39956972 TATAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.68
Consensus pattern (18 bp):
ATTTAAATTTACTTTTTG
Found at i:39957355 original size:16 final size:16
Alignment explanation
Indices: 39957334--39957368 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39957324 CTATCTTAAC
*
39957334 AACATGATGCCTAAAA
1 AACATGATGACTAAAA
*
39957350 AACATGATGATTAAAA
1 AACATGATGACTAAAA
39957366 AAC
1 AAC
39957369 CTAATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.54, C:0.14, G:0.11, T:0.20
Consensus pattern (16 bp):
AACATGATGACTAAAA
Found at i:39957679 original size:21 final size:21
Alignment explanation
Indices: 39957636--39957675 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39957626 AGAGAGAGCA
*
39957636 AGAAAACAATAAATGATAAAG
1 AGAAAACAATAAATAATAAAG
*
39957657 AGAAAATAATAAA-AATAAA
1 AGAAAACAATAAATAATAAA
39957676 AGAGGTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.72, C:0.03, G:0.10, T:0.15
Consensus pattern (21 bp):
AGAAAACAATAAATAATAAAG
Found at i:39959486 original size:50 final size:50
Alignment explanation
Indices: 39959432--39959566 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
39959422 ATGAGATTTT
* * *
39959432 ATGTAAGACCATATTTGGGACATGACATTAACATTGATATATGTGATCCC
1 ATGTAAGACCATATTTGGGACATGACATTGACATCGATATATGTGAACCC
* * * * *
39959482 ATGTAAGACCATGTCTGGGACATGACATTGGCATCGATATGTGTGAACCT
1 ATGTAAGACCATATTTGGGACATGACATTGACATCGATATATGTGAACCC
* * *
39959532 ATGTAAGACCGTATTTGGGATATGGCATTGACATC
1 ATGTAAGACCATATTTGGGACATGACATTGACATC
39959567 TTACTATGTG
Statistics
Matches: 71, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.30
Consensus pattern (50 bp):
ATGTAAGACCATATTTGGGACATGACATTGACATCGATATATGTGAACCC
Found at i:39961299 original size:20 final size:20
Alignment explanation
Indices: 39961274--39961311 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39961264 GTTTATTCGC
*
39961274 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
39961294 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
39961312 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:39962968 original size:27 final size:27
Alignment explanation
Indices: 39962937--39963005 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
39962927 AGCGTAGATC
39962937 ACGAAATTACCCCTAAAGAGCAAAATT
1 ACGAAATTACCCCTAAAGAGCAAAATT
39962964 ACGAAATTACCCCTAAAGAGCAAAATT
1 ACGAAATTACCCCTAAAGAGCAAAATT
*
39962991 ACCGATA-TACCCCTA
1 A-CGAAATTACCCCTA
39963006 GGGTTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (27 bp):
ACGAAATTACCCCTAAAGAGCAAAATT
Found at i:39969275 original size:20 final size:20
Alignment explanation
Indices: 39969250--39969287 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
39969240 GTTTATTCGC
*
39969250 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
39969270 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
39969288 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:39970944 original size:27 final size:27
Alignment explanation
Indices: 39970913--39970981 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
39970903 AGCGTAGATC
39970913 ACGAAATTACCCCTAAAGAGCAAAATT
1 ACGAAATTACCCCTAAAGAGCAAAATT
39970940 ACGAAATTACCCCTAAAGAGCAAAATT
1 ACGAAATTACCCCTAAAGAGCAAAATT
*
39970967 ACCGATA-TACCCCTA
1 A-CGAAATTACCCCTA
39970982 GGGTTTAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.45, C:0.26, G:0.10, T:0.19
Consensus pattern (27 bp):
ACGAAATTACCCCTAAAGAGCAAAATT
Found at i:39971667 original size:105 final size:105
Alignment explanation
Indices: 39971520--39971708 Score: 378
Period size: 105 Copynumber: 1.8 Consensus size: 105
39971510 ACTAAATTGA
39971520 ATAAATTGCAAAACTTGTGTTCTAGAAGTATTTTGCATAAAATTGAATTAGATTATTAATTAGAG
1 ATAAATTGCAAAACTTGTGTTCTAGAAGTATTTTGCATAAAATTGAATTAGATTATTAATTAGAG
39971585 GTCCTTAAAGAGTAATTTTACTAATTTTACCAATTAGATT
66 GTCCTTAAAGAGTAATTTTACTAATTTTACCAATTAGATT
39971625 ATAAATTGCAAAACTTGTGTTCTAGAAGTATTTTGCATAAAATTGAATTAGATTATTAATTAGAG
1 ATAAATTGCAAAACTTGTGTTCTAGAAGTATTTTGCATAAAATTGAATTAGATTATTAATTAGAG
39971690 GTCCTTAAAGAGTAATTTT
66 GTCCTTAAAGAGTAATTTT
39971709 TTAATGTTTT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 84 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (105 bp):
ATAAATTGCAAAACTTGTGTTCTAGAAGTATTTTGCATAAAATTGAATTAGATTATTAATTAGAG
GTCCTTAAAGAGTAATTTTACTAATTTTACCAATTAGATT
Found at i:39971989 original size:46 final size:46
Alignment explanation
Indices: 39971936--39972111 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
39971926 TATTTGGGCA
39971936 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
39971982 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
39972029 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
39972075 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39972112 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:39972091 original size:93 final size:93
Alignment explanation
Indices: 39971932--39972103 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
39971922 GGGATATTTG
* *
39971932 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39971997 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
39972025 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39972090 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
39972104 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:39975084 original size:15 final size:15
Alignment explanation
Indices: 39975064--39975132 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
39975054 GTATCTTGGG
39975064 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
39975079 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
39975094 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
39975109 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
39975124 TTTCTTTAT
1 TTTCTTTAT
39975133 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:39975133 original size:30 final size:30
Alignment explanation
Indices: 39975055--39975142 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
39975045 CATAGTATCG
* * * *
39975055 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
39975085 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
39975115 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
39975143 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:39977578 original size:46 final size:46
Alignment explanation
Indices: 39977525--39977700 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
39977515 TATTTGGGCA
39977525 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
39977571 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
39977618 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
39977664 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
39977701 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:39977680 original size:93 final size:93
Alignment explanation
Indices: 39977521--39977692 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
39977511 GGGATATTTG
* *
39977521 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39977586 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
39977614 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
39977679 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
39977693 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:39980962 original size:27 final size:26
Alignment explanation
Indices: 39980906--39980962 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
39980896 CAACCTTAAC
* *
39980906 CCTAGGGGTATATCAGTAATTTTACT
1 CCTAGGGGTAAATCAGTAATTTTACA
*
39980932 CCTAGGGGTAAATCTA-TAAATTTTCCA
1 CCTAGGGGTAAATC-AGT-AATTTTACA
39980959 CCTA
1 CCTA
39980963 TAAAGGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (26 bp):
CCTAGGGGTAAATCAGTAATTTTACA
Found at i:39988318 original size:27 final size:26
Alignment explanation
Indices: 39988279--39988397 Score: 105
Period size: 27 Copynumber: 4.4 Consensus size: 26
39988269 TGGCTGCCAG
* *
39988279 AACAGATATTGTGATAGAGTCACCAA
1 AACAGATATTGTGACAGAGCCACCAA
* *
39988305 ATACAGATATTGTGGCAGAGCCACCAG
1 A-ACAGATATTGTGACAGAGCCACCAA
* *
39988332 AACAGATATTTGTGGCATAGCCACCAGA
1 AACAGATA-TTGTGACAGAGCCACCA-A
* *
39988360 AATAGATATTTGTGGCATG-GCCACCAGA
1 AACAGATA-TTGTGACA-GAGCCACCA-A
39988388 AACAGATATT
1 AACAGATATT
39988398 TGTAGCATGG
Statistics
Matches: 80, Mismatches: 9, Indels: 7
0.83 0.09 0.07
Matches are distributed among these distances:
26 8 0.10
27 40 0.50
28 32 0.40
ACGTcount: A:0.37, C:0.18, G:0.22, T:0.23
Consensus pattern (26 bp):
AACAGATATTGTGACAGAGCCACCAA
Found at i:39988375 original size:28 final size:28
Alignment explanation
Indices: 39988299--39988413 Score: 155
Period size: 28 Copynumber: 4.2 Consensus size: 28
39988289 GTGATAGAGT
*
39988299 CACCA-AATACAGATA-TTGTGGCAGAGC
1 CACCAGAA-ACAGATATTTGTGGCATAGC
39988326 CACCAG-AACAGATATTTGTGGCATAGC
1 CACCAGAAACAGATATTTGTGGCATAGC
* *
39988353 CACCAGAAATAGATATTTGTGGCATGGC
1 CACCAGAAACAGATATTTGTGGCATAGC
* *
39988381 CACCAGAAACAGATATTTGTAGCATGGC
1 CACCAGAAACAGATATTTGTGGCATAGC
39988409 CACCA
1 CACCA
39988414 AAATGCTTCC
Statistics
Matches: 80, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 7 0.09
27 23 0.29
28 50 0.62
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (28 bp):
CACCAGAAACAGATATTTGTGGCATAGC
Found at i:39988399 original size:56 final size:53
Alignment explanation
Indices: 39988275--39988417 Score: 159
Period size: 56 Copynumber: 2.6 Consensus size: 53
39988265 AGCATGGCTG
* *
39988275 CCAGAACAGATA-TTGT-G-ATAGAGTCACCAAATACAGATATTGTGGCAGAGCCA
1 CCAGAACAGATATTTGTAGCAT--AGCCACCAAA-ATAGATATTGTGGCAGAGCCA
*
39988328 CCAGAACAGATATTTGTGGCATAGCCACCAGAAATAGATATTTGTGGCATG-GCCA
1 CCAGAACAGATATTTGTAGCATAGCCACCA-AAATAGATA-TTGTGGCA-GAGCCA
*
39988383 CCAGAAACAGATATTTGTAGCATGGCCACCAAAAT
1 CCAG-AACAGATATTTGTAGCATAGCCACCAAAAT
39988418 GCTTCCTCCA
Statistics
Matches: 79, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
53 12 0.15
54 17 0.22
55 23 0.29
56 27 0.34
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (53 bp):
CCAGAACAGATATTTGTAGCATAGCCACCAAAATAGATATTGTGGCAGAGCCA
Found at i:39988547 original size:26 final size:27
Alignment explanation
Indices: 39988518--39988581 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 27
39988508 CAAAATCAAC
*
39988518 CCTAGGGGTATAACGGTCATTTT-ACA
1 CCTAGGGGTATAACGGTAATTTTCACA
* *
39988544 CCTAGGGGTATAATGGTAATTTTCATA
1 CCTAGGGGTATAACGGTAATTTTCACA
*
39988571 CTTAGGGGTAT
1 CCTAGGGGTAT
39988582 TTTAGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 21 0.64
27 12 0.36
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (27 bp):
CCTAGGGGTATAACGGTAATTTTCACA
Found at i:40000531 original size:20 final size:20
Alignment explanation
Indices: 40000502--40000539 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40000492 AAATGATGTA
40000502 AAAACCCAAGTTTTCCCTAT
1 AAAACCCAAGTTTTCCCTAT
*
40000522 AAAACTCAAGTTTTCCCT
1 AAAACCCAAGTTTTCCCT
40000540 TTTTATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (20 bp):
AAAACCCAAGTTTTCCCTAT
Found at i:40007324 original size:29 final size:29
Alignment explanation
Indices: 40007283--40007434 Score: 145
Period size: 29 Copynumber: 5.3 Consensus size: 29
40007273 ATGAGCATGA
40007283 ATAT-AATGTGATTTGGG-CTAGATGGGCC
1 ATATAAATGTGA-TTGGGCCTAGATGGGCC
* *
40007311 ATATAAATGAGATTGGGCCTA-ATGTGCC
1 ATATAAATGTGATTGGGCCTAGATGGGCC
*
40007339 ATATGAATGTGAATTGGGCCT-GATGGGCC
1 ATATAAATGTG-ATTGGGCCTAGATGGGCC
* * * *
40007368 ACATGAACGTGAATTGGGTC-AGATGGGCC
1 ATATAAATGTG-ATTGGGCCTAGATGGGCC
* *
40007397 ATATAAGTGAGATTGGGCCTAG-TGGGCC
1 ATATAAATGTGATTGGGCCTAGATGGGCC
*
40007425 ATATACATGT
1 ATATAAATGT
40007435 ATGTAGGGGT
Statistics
Matches: 101, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
28 44 0.44
29 57 0.56
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (29 bp):
ATATAAATGTGATTGGGCCTAGATGGGCC
Found at i:40009615 original size:48 final size:48
Alignment explanation
Indices: 40009504--40009883 Score: 268
Period size: 48 Copynumber: 7.9 Consensus size: 48
40009494 AAAGGGTAAG
* * *
40009504 ATGTCGATGCCATG-TCCTAGACATGGTCTTACACTGGTTCTCATA-TATCG
1 ATGTCGATGCCATGTTCC-AAACATGGTCTTACACTGG--CTCATACAAT-A
* ** ** * * *
40009554 GTGTTAATGCCATGCCCCAGACATGGTCTTATACTTGCTCATACAATA
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATACAATA
* ** * * *
40009602 AAGTCGATGCCATGTTCCAAACATAATCTTACATTGACTC--ACATATCG
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATACA-AT-A
* * * ** * *
40009650 AGGCCGATGCCATGTCCCAGGCATGGTCTTACACTAGCTC-TCATAATA
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCAT-ACAATA
* *
40009698 ATGTCGAGGCTATGTTCCAAACAT-GTCTTACACTGGCTCATACAATA
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATACAATA
* * *
40009745 ATGTCGATGCCATATTCCGAACATGGTCTTACACTGGCTCATACAACA
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATACAATA
* * * *** * *
40009793 ATGCCGATGCCATGTTCCAAACATGGTTTTATACTGGCTCACGTATTG
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATACAATA
* * * ** *
40009841 AGGCCGATGCCATGTCCCAGGCTTGGTCTTACACTGGCTCATA
1 ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATA
40009884 TATAACCCTA
Statistics
Matches: 254, Mismatches: 68, Indels: 18
0.75 0.20 0.05
Matches are distributed among these distances:
46 3 0.01
47 41 0.16
48 174 0.69
49 4 0.02
50 30 0.12
51 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (48 bp):
ATGTCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCATACAATA
Found at i:40009676 original size:96 final size:94
Alignment explanation
Indices: 40009560--40009883 Score: 339
Period size: 96 Copynumber: 3.4 Consensus size: 94
40009550 ATCGGTGTTA
* * * *
40009560 ATGCCATGCCCCAGACATGGTCTTATACTTGCTCATACAATAAAGTCGATGCCATGTTCCAAACA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACAATAATGTCGATGCCATGTTCCAAACA
* * *
40009625 TAATCTTACATTGACTCACATATCGAGGCCG
66 T-GTCTTACACTGGCTCACATAT-GAGGCCG
* * * * *
40009656 ATGCCATGTCCCAGGCATGGTCTTACACTAGCTC-TCATAATAATGTCGAGGCTATGTTCCAAAC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCAT-ACAATAATGTCGATGCCATGTTCCAAAC
* * *
40009720 ATGTCTTACACTGGCTCATACA-ATAATGTCG
65 ATGTCTTACACTGGCTC--ACATATGAGGCCG
* * * *
40009751 ATGCCATATTCC-GAACATGGTCTTACACTGGCTCATACAACAATGCCGATGCCATGTTCCAAAC
1 ATGCCATGTCCCAG-ACATGGTCTTACACTGGCTCATACAATAATGTCGATGCCATGTTCCAAAC
* * *
40009815 ATGGTTTTATACTGGCTCACGTATTGAGGCCG
65 AT-GTCTTACACTGGCTCACATA-TGAGGCCG
* *
40009847 ATGCCATGTCCCAGGCTTGGTCTTACACTGGCTCATA
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATA
40009884 TATAACCCTA
Statistics
Matches: 186, Mismatches: 33, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
94 3 0.02
95 71 0.38
96 108 0.58
97 4 0.02
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.28
Consensus pattern (94 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCATACAATAATGTCGATGCCATGTTCCAAACA
TGTCTTACACTGGCTCACATATGAGGCCG
Found at i:40014740 original size:39 final size:40
Alignment explanation
Indices: 40014651--40014910 Score: 408
Period size: 39 Copynumber: 6.7 Consensus size: 40
40014641 CTACTTGCTC
40014651 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
40014691 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACT-GCACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
*
40014730 AATGCCTTC-GGACTTAGCCCGATTATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
*
40014769 AATGCCTTC-GGACTTAGCCCGGTTATAGTAACTCACACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
*
40014808 AATGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
** * *
40014847 AATGCCTTCGGG-CTTAG-CCGAAT-TAGTCACTAGCACA
1 AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
40014884 AATGCCTTCGGGACTTAGCCCGGTTAT
1 AATGCCTTCGGGACTTAGCCCGGTTAT
40014911 CATCCGAATA
Statistics
Matches: 205, Mismatches: 10, Indels: 10
0.91 0.04 0.04
Matches are distributed among these distances:
37 24 0.12
38 33 0.16
39 111 0.54
40 37 0.18
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACA
Found at i:40022652 original size:39 final size:39
Alignment explanation
Indices: 40022598--40022849 Score: 332
Period size: 39 Copynumber: 6.4 Consensus size: 39
40022588 AAACCAAGTA
* * * *
40022598 CCTTCGGAATTTAGCCGGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCGGATATAG-TAACTCGCACAAATG
*
40022637 CCTTCGGGACTTAGCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
*
40022676 CCTTCGGGACTTAGCCCGATTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCGGA-TATAGTAACTCGCACAAATG
*
40022716 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
*
40022756 CCTTC-GGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
* *
40022795 CCTTCGGG-CTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAG-CCGGATA-TAGTAACTCGCACAAATG
40022834 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
40022850 CGGTTATCAT
Statistics
Matches: 193, Mismatches: 14, Indels: 12
0.88 0.06 0.05
Matches are distributed among these distances:
38 2 0.01
39 122 0.63
40 66 0.34
41 3 0.02
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
Found at i:40022710 original size:40 final size:40
Alignment explanation
Indices: 40022631--40022856 Score: 336
Period size: 39 Copynumber: 5.7 Consensus size: 40
40022621 GCTACTTGCT
*
40022631 CAAATGCCTTCGGGACTTAG-CCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
40022670 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
*
40022710 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
*
40022750 CAAATGCCTTC-GGACTTAGCCCGGA-TATAGTAACTCACA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
* * *
40022789 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCC-GATTATAGTAACTCGCA
*
40022828 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGATTAT
40022857 CATCCGAATA
Statistics
Matches: 172, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
39 91 0.53
40 81 0.47
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGATTATAGTAACTCGCA
Found at i:40022728 original size:79 final size:80
Alignment explanation
Indices: 40022631--40022856 Score: 354
Period size: 79 Copynumber: 2.9 Consensus size: 80
40022621 GCTACTTGCT
40022631 CAAATGCCTTCGGGACTTAG-CCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
*
40022695 TTATAGTAACTCGCA
66 TTATAGTAACTCACA
40022710 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTC-GGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCC-G
40022774 A-TATAGTAACTCACA
65 ATTATAGTAACTCACA
* * *
40022789 CAAATGCCTTCGGG-CTTAGCCCGG-AATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCG
*
40022852 GTTAT
65 ATTAT
40022857 CATCCGAATA
Statistics
Matches: 137, Mismatches: 5, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
77 1 0.01
78 32 0.23
79 72 0.53
80 32 0.23
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAGCCCGA
TTATAGTAACTCACA
Found at i:40025422 original size:39 final size:39
Alignment explanation
Indices: 40025372--40025616 Score: 330
Period size: 39 Copynumber: 6.3 Consensus size: 39
40025362 GTGTGAGATA
* *
40025372 TATATCCGGGCTAATTCCCAAAGGCATTCGTGTTGGTGT
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
* *
40025411 TATATCTGGGCTAAGTCCCAAAGGCATTCATGCTGGTGT
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
* ** *
40025450 TATATTCGGGCTAAGTCCTGAAGCCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
**
40025489 TATATCCGGGCTAAGTCCCGGAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
*
40025528 TATACCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
*** * *
40025567 TATATCCGGGCTAAGTCTTGAAGGC-TTTGTGCTGGTAT
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
*
40025605 TACATCCGGGCT
1 TATATCCGGGCT
40025617 TAAAGTTTCG
Statistics
Matches: 182, Mismatches: 24, Indels: 1
0.88 0.12 0.00
Matches are distributed among these distances:
38 22 0.12
39 160 0.88
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (39 bp):
TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGT
Found at i:40025578 original size:117 final size:116
Alignment explanation
Indices: 40025372--40025616 Score: 364
Period size: 117 Copynumber: 2.1 Consensus size: 116
40025362 GTGTGAGATA
* * * *
40025372 TATATCCGGGCTAATTCCCAAAGGCATTCGTGTTGGTGTTATATCTGGGCTAAGTCCCAAAGGCA
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGTTATACCCGGGCTAAGTCCCAAAGGCA
* *
40025437 TTCATGCTGGTGTTATATTCGGGCTAAGTCCTGAAGCCATTCGTGCTGGTGT
66 TTCATGCTGGTGTTATATCCGGGCTAAGTCCTGAAGCC-TTCGTGCTGGTAT
**
40025489 TATATCCGGGCTAAGTCCCGGAGGCATTCGTGCTGGTGTTATACCCGGGCTAAGTCCCAAAGGCA
1 TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGTTATACCCGGGCTAAGTCCCAAAGGCA
* * * *
40025554 TTCGTGCTGGTGTTATATCCGGGCTAAGTCTTGAAGGCTTTGTGCTGGTAT
66 TTCATGCTGGTGTTATATCCGGGCTAAGTCCTGAAGCCTTCGTGCTGGTAT
*
40025605 TACATCCGGGCT
1 TATATCCGGGCT
40025617 TAAAGTTTCG
Statistics
Matches: 115, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
116 22 0.19
117 93 0.81
ACGTcount: A:0.19, C:0.22, G:0.28, T:0.31
Consensus pattern (116 bp):
TATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTGTTATACCCGGGCTAAGTCCCAAAGGCA
TTCATGCTGGTGTTATATCCGGGCTAAGTCCTGAAGCCTTCGTGCTGGTAT
Found at i:40028153 original size:48 final size:48
Alignment explanation
Indices: 40028080--40028258 Score: 152
Period size: 48 Copynumber: 3.7 Consensus size: 48
40028070 ATACTAGGGT
*
40028080 TATGTGAGCCAGTGTAAGATC-ATGTTTGGAACATGGAATCAACCTTGA
1 TATGTGAGCCAATGTAAGA-CAATGTTTGGAACATGGAATCAACCTTGA
* * *** *
40028128 TATGTGAGCCAATGTAAGACAATGTTTGGGACATGGCATTGGCCTCGA
1 TATGTGAGCCAATGTAAGACAATGTTTGGAACATGGAATCAACCTTGA
* * * *
40028176 TATGTGAGCCAGTATAAGA-ATATGTTTGGAACAT-GACATCAACATTTA
1 TATGTGAGCCAATGTAAGACA-ATGTTTGGAACATGGA-ATCAACCTTGA
* * *
40028224 TATGAGAGCTAGA-GTAAGACCATGTCTTGG-ACATG
1 TATGTGAGCCA-ATGTAAGACAATGT-TTGGAACATG
40028259 CCATGGCCTC
Statistics
Matches: 102, Mismatches: 22, Indels: 13
0.74 0.16 0.09
Matches are distributed among these distances:
47 3 0.03
48 95 0.93
49 4 0.04
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (48 bp):
TATGTGAGCCAATGTAAGACAATGTTTGGAACATGGAATCAACCTTGA
Found at i:40028256 original size:96 final size:95
Alignment explanation
Indices: 40028080--40028359 Score: 298
Period size: 96 Copynumber: 2.9 Consensus size: 95
40028070 ATACTAGGGT
* * *
40028080 TATGTGAGCCAGTGTAAG-ATCATGTTTGGAACATGGA-ATCAACCTTGATATGTGAGCCA-ATG
1 TATGTGAGCCAGTGTAAGAAT-ATGTTTGGAACAT-GACATCAACATTTATATGAGAGCCAGA-G
* *
40028142 TAAGACAATGTTTGGGACATGGCATTGGCCTCGA
63 TAAGACCATGTTT-GGACATGGCATTGGCCTCAA
* *
40028176 TATGTGAGCCAGTATAAGAATATGTTTGGAACATGACATCAACATTTATATGAGAGCTAGAGTAA
1 TATGTGAGCCAGTGTAAGAATATGTTTGGAACATGACATCAACATTTATATGAGAGCCAGAGTAA
*
40028241 GACCATGTCTTGGACATGCCA-TGGCCTCAA
66 GACCATGT-TTGGACATGGCATTGGCCTCAA
* * * ** * * * *
40028271 CATGTGGGCTAGTGTAAGACCATGTTTGGAACATGGCATCGACACTGATATATGAGAGCCAGTGT
1 TATGTGAGCCAGTGTAAGAATATGTTTGGAACATGACATCAACA-T-TTATATGAGAGCCAGAGT
*
40028336 AAGACCATGATTGGGACATGGCAT
64 AAGACCATG-TTTGGACATGGCAT
40028360 CGGCATCTTA
Statistics
Matches: 155, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
95 46 0.30
96 69 0.45
97 39 0.25
98 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (95 bp):
TATGTGAGCCAGTGTAAGAATATGTTTGGAACATGACATCAACATTTATATGAGAGCCAGAGTAA
GACCATGTTTGGACATGGCATTGGCCTCAA
Found at i:40036179 original size:48 final size:48
Alignment explanation
Indices: 40036097--40036475 Score: 327
Period size: 48 Copynumber: 7.9 Consensus size: 48
40036087 ATACTAGGGT
* * **
40036097 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCATTAGCCTCGA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA
* * * * * *
40036145 TATGTAAACCAGTGTAAGACCAAGTCTGGGACATGGCATCAGCCTCAA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA
* * * * *
40036193 TATG-AGAGCTAGAGTAAGACCATGTCTAGG-ACATGACATCGGCATCGA
1 TATGTA-AGCCAGTGTAAGACCATGT-TTGGAACATGGCATCGGCCTCGA
* * * * *
40036241 TATCTGAGCCAGTGTAAGACCAT-TTCTAGAACATAGCATCGGGCTCGA
1 TATGTAAGCCAGTGTAAGACCATGTT-TGGAACATGGCATCGGCCTCGA
* * * * **
40036289 TAAGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA
* * *
40036337 TATG-AGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCCTCAA
1 TATGTA-AGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA
* * * * *
40036385 CATGTAGGCTAGTGTAAGACCATGTTTGGAACATGGCATTGACACT-GA
1 TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGC-CTCGA
* * *
40036433 TATATGAGAGCCAGTGTAAGACCATGTTTGGGACATGACATCG
1 TATGT-A-AGCCAGTGTAAGACCATGTTTGGAACATGGCATCG
40036476 ACATCTTACC
Statistics
Matches: 262, Mismatches: 58, Indels: 20
0.77 0.17 0.06
Matches are distributed among these distances:
46 1 0.00
47 3 0.01
48 220 0.84
49 8 0.03
50 30 0.11
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (48 bp):
TATGTAAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGGCCTCGA
Found at i:40036280 original size:96 final size:96
Alignment explanation
Indices: 40036097--40036475 Score: 383
Period size: 96 Copynumber: 3.9 Consensus size: 96
40036087 ATACTAGGGT
* * * * *
40036097 TATGTGAGCTAGTGTAAGACCATGTTTGGAACATGGCAT-TAGCCTCGATATGTAAACCAGTGTA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGA-CATCGATATGTGAGCCAGTGTA
** *
40036161 AGACCAAGTCTGGGACATGGCATCAGCCTCAA
65 AGACCATTTCTGGGACATGGCATCGGCCTCAA
* * * * *
40036193 TATGAGAGCTAGAGTAAGACCATGTCTAGG-ACATGACATCGGCATCGATATCTGAGCCAGTGTA
1 TATGAGAGCTAGTGTAAGACCATGT-TTGGAACATGGCATCGACATCGATATGTGAGCCAGTGTA
* * * * *
40036257 AGACCATTTCTAGAACATAGCATCGGGCTCGA
65 AGACCATTTCTGGGACATGGCATCGGCCTCAA
* * * ** * *
40036289 TAAGTGAGCCAGTGTAAGACCATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAA
1 TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGACATCGATATGTGAGCCAGTGTAA
40036354 GACCATGTT-TGGGACATGGCATCGGCCTCAA
66 GACCAT-TTCTGGGACATGGCATCGGCCTCAA
* * *
40036385 CATGTAG-GCTAGTGTAAGACCATGTTTGGAACATGGCATTGACA-CTGATATATGAGAGCCAGT
1 TATG-AGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGACATC-G--ATATGTGAGCCAGT
*
40036448 GTAAGACCATGTT-TGGGACATGACATCG
62 GTAAGACCAT-TTCTGGGACATGGCATCG
40036476 ACATCTTACC
Statistics
Matches: 231, Mismatches: 44, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
95 3 0.01
96 182 0.79
97 6 0.03
98 40 0.17
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (96 bp):
TATGAGAGCTAGTGTAAGACCATGTTTGGAACATGGCATCGACATCGATATGTGAGCCAGTGTAA
GACCATTTCTGGGACATGGCATCGGCCTCAA
Found at i:40036361 original size:144 final size:143
Alignment explanation
Indices: 40036101--40036480 Score: 424
Period size: 144 Copynumber: 2.6 Consensus size: 143
40036091 TAGGGTTATG
* * * *
40036101 TGAGCTAGTGTAAGACCATGTTTGGAACATGGCATTAGCCTCGATATGTAAACCAGTGTAAGACC
1 TGAGCTAGTGTAAGACCATGTTTGGAACATGGCA-TAGACTCGATAAGTGAGCCAGTGTAAGACC
* * *
40036166 AAGTCTGGGACATGGCATC-AGCCTCAATATGAGAGCTAGAGTAAGACCATGTCTAGGACATGAC
65 ATGTTTGGGACATGGCATCGA-CATCAATATGAGAGCTAGAGTAAGACCATGTCTAGGACATGAC
* *
40036230 ATCGGCATCGATATC
129 ATCGGCATCAACATC
* * * * *
40036245 TGAGCCAGTGTAAGACCAT-TTCTAGAACATAGCATCGGGCTCGATAAGTGAGCCAGTGTAAGAC
1 TGAGCTAGTGTAAGACCATGTT-TGGAACATGGCAT-AGACTCGATAAGTGAGCCAGTGTAAGAC
* ** * * * *
40036309 CATGTTTGGAACATGGCATCGACATTTATATGAGAGCTAGTGTAAGACCATGTTTGGGACATGGC
64 CATGTTTGGGACATGGCATCGACATCAATATGAGAGCTAGAGTAAGACCATGTCTAGGACATGAC
* *
40036374 ATCGGCCTCAACATG
129 ATCGGCATCAACATC
* * *
40036389 T-AGGCTAGTGTAAGACCATGTTTGGAACATGGCATTGACACTGATATATGAGAGCCAGTGTAAG
1 TGA-GCTAGTGTAAGACCATGTTTGGAACATGGCATAGACTC-GATA-A-GTGAGCCAGTGTAAG
*
40036453 ACCATGTTTGGGACATGACATCGACATC
62 ACCATGTTTGGGACATGGCATCGACATC
40036481 TTACCCTTTT
Statistics
Matches: 196, Mismatches: 32, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
143 7 0.04
144 146 0.74
145 4 0.02
146 39 0.20
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (143 bp):
TGAGCTAGTGTAAGACCATGTTTGGAACATGGCATAGACTCGATAAGTGAGCCAGTGTAAGACCA
TGTTTGGGACATGGCATCGACATCAATATGAGAGCTAGAGTAAGACCATGTCTAGGACATGACAT
CGGCATCAACATC
Found at i:40037719 original size:21 final size:21
Alignment explanation
Indices: 40037669--40037729 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
40037659 GTTAAGAGGA
* *
40037669 CACACGGGCATGTTGCCCTCC
1 CACACGGGCGTGTTGCCCTTC
* *
40037690 CATATGGGCGTGTTGCCCTTC
1 CACACGGGCGTGTTGCCCTTC
*
40037711 CACACGGGCGT-CTGCCCTT
1 CACACGGGCGTGTTGCCCTT
40037730 GTTTGCTTTG
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 7 0.21
21 26 0.79
ACGTcount: A:0.11, C:0.38, G:0.26, T:0.25
Consensus pattern (21 bp):
CACACGGGCGTGTTGCCCTTC
Found at i:40044534 original size:45 final size:46
Alignment explanation
Indices: 40044371--40044545 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
40044361 TGGTTGAGCA
*
40044371 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
40044417 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
40044462 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
40044510 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40044546 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 37 0.33
46 29 0.26
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:40051845 original size:46 final size:45
Alignment explanation
Indices: 40051795--40051968 Score: 187
Period size: 46 Copynumber: 3.8 Consensus size: 45
40051785 TGGTTGAGCA
40051795 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
40051841 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAA-T--G
*
40051886 CATCCGAACT-GTTGAGTTGAGT-CGAGTTCACTTATGGATGTGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG-GAATG
* * *
40051932 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40051969 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
44 6 0.06
45 22 0.21
46 58 0.54
47 8 0.07
48 4 0.04
49 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.30
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGGAATG
Found at i:40051949 original size:91 final size:93
Alignment explanation
Indices: 40051792--40051961 Score: 290
Period size: 91 Copynumber: 1.8 Consensus size: 93
40051782 GGATGGTTGA
* *
40051792 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40051857 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
40051885 GCATCCGAACT-GTTGAGTTGAGT-CGAGTTCACTTATGGATGTGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
40051948 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
40051962 CTTATGGGCG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
91 50 0.68
92 12 0.16
93 11 0.15
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:40060261 original size:93 final size:93
Alignment explanation
Indices: 40060154--40060325 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
40060144 GCCCATAAGT
* * * *
40060154 GAACTCGGACTCAACTCAATGAGCTCGGTCGTTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40060219 CGAGCTCGGATGCCTAGTTACATCTTTC
66 CGAGCTCGGATGCCTAGTTACATCTTTC
*
40060247 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
40060312 CGAGTTCGGATGCC
66 CGAGCTCGGATGCC
40060326 CAAATATCCT
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGCTCGGATGCCTAGTTACATCTTTC
Found at i:40060321 original size:46 final size:46
Alignment explanation
Indices: 40060146--40060321 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
40060136 TGTAACCCGC
* * * *
40060146 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGTCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
40060192 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--ATGC-CTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGC-A--T
* *** *
40060238 ACATCTTTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGT-GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
*
40060285 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
40060322 TGCCCAAATA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 2 0.02
46 69 0.63
47 32 0.29
49 4 0.04
50 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCAT
Found at i:40060340 original size:46 final size:44
Alignment explanation
Indices: 40060197--40060340 Score: 116
Period size: 46 Copynumber: 3.1 Consensus size: 44
40060187 TGCATCCATA
* *
40060197 AGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGT-TACATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCA-TAT-C--CT
* * *
40060244 -TTCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGC--ATCCAT
1 AGT-GAACTCGGACTCAACTCAACGAGTTCGG--ATGCCCATATCC-T
40060289 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCAAATATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCC--ATATCCT
40060336 AGTGA
1 AGTGA
40060341 CATGTCACTT
Statistics
Matches: 78, Mismatches: 8, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
44 5 0.06
45 1 0.01
46 35 0.45
47 30 0.38
48 4 0.05
49 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (44 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCCATATCCT
Found at i:40062560 original size:96 final size:96
Alignment explanation
Indices: 40062350--40062728 Score: 415
Period size: 96 Copynumber: 3.9 Consensus size: 96
40062340 AAAGGGTAAG
* * * * * * * *
40062350 ATGCTGATGCCATG-TCCTAGACATGATCTTACACTGGTTTTCATATAT-TAGTGCCGATGTCAA
1 ATGCCGATGCCATGTTCC-AAACATGGTCTTACACTGG--CTCACATATCAAG-GCCGATGCCAT
* *
40062413 GTCTCAGACATGGTCTTATACT-GACTCATACAACA
62 GTCCCAGACATGGTCTTACACTAG-CTCATACAACA
* *
40062448 ATGCCGATGCCATGTTCCAAACATGATCTTACACTGGCTCACATATCAAGGCCAATGCCATGTCC
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCCGATGCCATGTCC
*
40062513 CAGACATGGTCTTACACTAGCTC-TCATAACA
66 CAGACATGGTCTTACACTAGCTCAT-ACAACA
* * * * * * * * *
40062544 ATGCCGAGGCCATGTTCCAAACACGGTCTTACACTGGCTCATACAACAATGTCGATGGCATGTTC
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCCGATGCCATGTCC
* *
40062609 CAAATATGGTCTTACACTAGCTCATACAACA
66 CAGACATGGTCTTACACTAGCTCATACAACA
* * * *
40062640 ATGCCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCACGTATCGAGGCCGATGCCATGTCC
1 ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCCGATGCCATGTCC
*
40062705 CAGACATGGTCTTACACTGGCTCA
66 CAGACATGGTCTTACACTAGCTCA
40062729 CATATAACCC
Statistics
Matches: 235, Mismatches: 41, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
95 1 0.00
96 196 0.83
97 4 0.02
98 31 0.13
99 3 0.01
ACGTcount: A:0.27, C:0.27, G:0.18, T:0.27
Consensus pattern (96 bp):
ATGCCGATGCCATGTTCCAAACATGGTCTTACACTGGCTCACATATCAAGGCCGATGCCATGTCC
CAGACATGGTCTTACACTAGCTCATACAACA
Found at i:40062729 original size:48 final size:48
Alignment explanation
Indices: 40062350--40062732 Score: 361
Period size: 48 Copynumber: 7.9 Consensus size: 48
40062340 AAAGGGTAAG
* * * * * * **
40062350 ATGCTGATGCCATGTCCTAGACATGATCTTACACTGGTTTTCATATATTA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGG--CTCACATAACA
* * * * * * * * *
40062400 GTGCCGATGTCAAGTCTCAGACATGGTCTTATACTGACTCATACAACA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
* * *
40062448 ATGCCGATGCCATGTTCCAAACATGATCTTACACTGGCTCACATATCA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
* * * * *
40062496 AGGCCAATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATAACA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
* * * * *
40062544 ATGCCGAGGCCATGTTCCAAACACGGTCTTACACTGGCTCATACAACA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
* * * * * * *
40062592 ATGTCGATGGCATGTTCCAAATATGGTCTTACACTAGCTCATACAACA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
* * * *
40062640 ATGCCGATGCCATGTCCCAAACATGGTCTTACATTGGCTCACGTATCG
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
* *
40062688 AGGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACATA
1 ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATA
40062733 TAACCCTAGT
Statistics
Matches: 269, Mismatches: 64, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
48 241 0.90
50 28 0.10
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (48 bp):
ATGCCGATGCCATGTCCCAAACATGGTCTTACACTGGCTCACATAACA
Found at i:40072842 original size:68 final size:68
Alignment explanation
Indices: 40072692--40072849 Score: 169
Period size: 68 Copynumber: 2.3 Consensus size: 68
40072682 CTAGCCAATT
* * *
40072692 TATCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACACATGCGACCTAGCTACA
1 TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACA
**
40072757 TTTA
65 CATA
* * *
40072761 TCTCTCCCGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTA
1 TATCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTA
40072823 CTACATA
63 C-ACATA
40072830 GTATCTCGTAGCTCTCTTGT
1 -TATCTCGTAGCTCTCTTGT
40072850 ACACATGATG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
68 36 0.48
69 7 0.09
70 6 0.08
71 26 0.35
ACGTcount: A:0.21, C:0.29, G:0.16, T:0.34
Consensus pattern (68 bp):
TATCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACAC
ATA
Found at i:40075136 original size:16 final size:16
Alignment explanation
Indices: 40075106--40075143 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
40075096 TAGTAAATTG
40075106 GAAGCTCGTTTGGATT
1 GAAGCTCGTTTGGATT
40075122 AGAAGCTCG-TTGGATT
1 -GAAGCTCGTTTGGATT
40075138 GAAGCT
1 GAAGCT
40075144 TGGCGAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 6 0.29
16 7 0.33
17 8 0.38
ACGTcount: A:0.24, C:0.13, G:0.32, T:0.32
Consensus pattern (16 bp):
GAAGCTCGTTTGGATT
Found at i:40075946 original size:46 final size:46
Alignment explanation
Indices: 40075876--40076093 Score: 296
Period size: 46 Copynumber: 4.7 Consensus size: 46
40075866 ATGCATAGTG
* * * *
40075876 TCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTA
* * ** * * *
40075922 TCATTCAACCAAGGTCTTATTCATTTCCCATCACGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTA
*
40075968 TCTTTCAACCATGGTCTTAAACA-TTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTA
40076014 TCTTTCAACCATGGTCTTACACA-TTTCATATCAGGTTGCCATGGTA
1 TCTTTCAACCATGGTCTTACACATTTTC-TATCAGGTTGCCATGGTA
40076060 TCTTTCAACCATGGTCTTACACATTTTCTATCAG
1 TCTTTCAACCATGGTCTTACACATTTTCTATCAG
40076094 AGAGCACACT
Statistics
Matches: 154, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
45 3 0.02
46 147 0.95
47 4 0.03
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (46 bp):
TCTTTCAACCATGGTCTTACACATTTTCTATCAGGTTGCCATGGTA
Found at i:40079520 original size:40 final size:40
Alignment explanation
Indices: 40079475--40079641 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
40079465 CGGAATATAA
40079475 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40079515 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40079555 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40079595 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40079634 CCGGATAT
1 CCGGATAT
40079642 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40079625 original size:80 final size:79
Alignment explanation
Indices: 40079491--40079641 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
40079481 ATAATCACGT
*
40079491 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
40079556 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
40079571 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
40079634 CCGGATAT
64 CCGGATAT
40079642 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40080490 original size:17 final size:19
Alignment explanation
Indices: 40080467--40080512 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40080457 AAGAAGCATG
40080467 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40080485 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40080503 AATCATGCTC
1 AATCATGCTC
40080513 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40087530 original size:40 final size:40
Alignment explanation
Indices: 40087485--40087651 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
40087475 CGGAATATAA
40087485 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40087525 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
40087565 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40087605 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40087644 CCGGATAT
1 CCGGATAT
40087652 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40087635 original size:80 final size:79
Alignment explanation
Indices: 40087501--40087651 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
40087491 ATAATCACGT
*
40087501 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
40087566 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
40087581 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
40087644 CCGGATAT
64 CCGGATAT
40087652 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:40088500 original size:17 final size:19
Alignment explanation
Indices: 40088477--40088522 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40088467 AAGAAGCATG
40088477 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40088495 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40088513 AATCATGCTC
1 AATCATGCTC
40088523 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40089454 original size:11 final size:11
Alignment explanation
Indices: 40089438--40089489 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
40089428 TATACTAAAT
40089438 AAATAATAATA
1 AAATAATAATA
*
40089449 AAATAAT-ATT
1 AAATAATAATA
* *
40089459 AAATATCTCATA
1 AAATA-ATAATA
*
40089471 AAATATTAATA
1 AAATAATAATA
40089482 AAATAATA
1 AAATAATA
40089490 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:40115159 original size:6 final size:6
Alignment explanation
Indices: 40115148--40115176 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
40115138 TTTAAAATCA
40115148 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA
40115177 AAGAGTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTAT
Found at i:40118842 original size:31 final size:28
Alignment explanation
Indices: 40118766--40118845 Score: 96
Period size: 25 Copynumber: 2.9 Consensus size: 28
40118756 ACAAATTTTT
40118766 AAAAAAT-TCATAGTTGGGTGAC--AAA
1 AAAAAATCTCATAGTTGGGTGACTAAAA
*
40118791 AAAAAATC-CATAATTGGGTGACTAAAA
1 AAAAAATCTCATAGTTGGGTGACTAAAA
40118818 AATAAAATGACTCATAGTTGGGTGACTA
1 AA-AAAAT--CTCATAGTTGGGTGACTA
40118846 GTGATTAGAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 20 0.43
27 5 0.11
28 5 0.11
30 1 0.02
31 15 0.33
ACGTcount: A:0.46, C:0.10, G:0.19, T:0.25
Consensus pattern (28 bp):
AAAAAATCTCATAGTTGGGTGACTAAAA
Found at i:40120365 original size:30 final size:31
Alignment explanation
Indices: 40120296--40120367 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 31
40120286 AAAATGTTAA
* * *
40120296 TGAGTGGCTGATTTGTCACTTTTCGATAATG
1 TGAGTGACTGATTTATCACTTTTCGAAAATG
* * *
40120327 TTAGTGACTGTTTTATCATTTTTCGAAAAT-
1 TGAGTGACTGATTTATCACTTTTCGAAAATG
40120357 TGAGTGACTGA
1 TGAGTGACTGA
40120368 ATTGAAACCA
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 9 0.27
31 24 0.73
ACGTcount: A:0.24, C:0.11, G:0.22, T:0.43
Consensus pattern (31 bp):
TGAGTGACTGATTTATCACTTTTCGAAAATG
Found at i:40122725 original size:63 final size:63
Alignment explanation
Indices: 40122657--40122787 Score: 217
Period size: 63 Copynumber: 2.1 Consensus size: 63
40122647 CCCTTATTCT
* *
40122657 TTTTTCTTCGAAAAGAAAAAGGAAAAAGAAGAAAAAATTATTTTTCTCTCTTTATCTACTTAG
1 TTTTTCTTCGAAAAGAAAAAGGAAAAAGAAGAAAAAATTATTTTTCTCTCTCTATCCACTTAG
* * *
40122720 TTTTTCTTTGAAAAGAAAAAGGAAAAAGAAGAAAAAATTGTTTTTCTCTCTCTATCCACTTGG
1 TTTTTCTTCGAAAAGAAAAAGGAAAAAGAAGAAAAAATTATTTTTCTCTCTCTATCCACTTAG
40122783 TTTTT
1 TTTTT
40122788 ATTTTATTAT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.38
Consensus pattern (63 bp):
TTTTTCTTCGAAAAGAAAAAGGAAAAAGAAGAAAAAATTATTTTTCTCTCTCTATCCACTTAG
Found at i:40124141 original size:46 final size:44
Alignment explanation
Indices: 40124091--40124179 Score: 108
Period size: 46 Copynumber: 2.0 Consensus size: 44
40124081 AGAAATAGAA
40124091 AAATGGAAAACA-TTCAGAAATAATTATGGTTTTCTCCAAAATGGAG
1 AAATGG-AAACATTTCAGAAATAA-TATGGTTTTCT-CAAAATGGAG
* * * *
40124137 AAATGGAATCATTTGAGAATTAATGTGGTTTTCTCAAAATGGA
1 AAATGGAAACATTTCAGAAATAATATGGTTTTCTCAAAATGGA
40124180 AATTGAAATG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 9 0.24
45 14 0.37
46 15 0.39
ACGTcount: A:0.40, C:0.09, G:0.19, T:0.31
Consensus pattern (44 bp):
AAATGGAAACATTTCAGAAATAATATGGTTTTCTCAAAATGGAG
Found at i:40128369 original size:22 final size:21
Alignment explanation
Indices: 40128331--40128377 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
40128321 TGTAATTTAA
*
40128331 TTTAATTATTTTATTGTTATAT
1 TTTAATTATATTATTG-TATAT
*
40128353 TTTAATTAATATT-TTGTATTT
1 TTTAATT-ATATTATTGTATAT
40128374 TTTA
1 TTTA
40128378 TATATAGGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 8 0.36
22 10 0.45
23 4 0.18
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (21 bp):
TTTAATTATATTATTGTATAT
Found at i:40139564 original size:15 final size:14
Alignment explanation
Indices: 40139539--40139595 Score: 69
Period size: 15 Copynumber: 3.9 Consensus size: 14
40139529 CGATGAATTT
*
40139539 ATTGAATTTATATGG
1 ATTGAA-TTATATTG
*
40139554 ATTGAGATTATTTTG
1 ATTGA-ATTATATTG
40139569 ATTGAATTTATATTG
1 ATTGAA-TTATATTG
40139584 ATTGAATTATAT
1 ATTGAATTATAT
40139596 AATATATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.19
15 29 0.78
16 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (14 bp):
ATTGAATTATATTG
Found at i:40139996 original size:23 final size:23
Alignment explanation
Indices: 40139966--40140052 Score: 101
Period size: 21 Copynumber: 4.0 Consensus size: 23
40139956 GCTTTATCGA
* *
40139966 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
40139989 TCAGGCACCTCATGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
40140010 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
40140032 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
40140053 ACTGATTAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 34 0.62
22 2 0.04
23 19 0.35
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:40141714 original size:2 final size:2
Alignment explanation
Indices: 40141707--40141742 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40141697 TATGATATGC
40141707 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40141743 TCTATGAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40143337 original size:50 final size:49
Alignment explanation
Indices: 40143217--40143382 Score: 176
Period size: 50 Copynumber: 3.3 Consensus size: 49
40143207 TGTGAGAACA
* *
40143217 CATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAGATGGTTTTAGGTTACG
1 CATGTGTAGTACTA-GTGCAGGCTACTACGTGTATAAGATGG--TTAGG-T-CG
*
40143271 C--GTGTAGTACTAAGTGCAGGCTACTACGTGTACT-AGATAGTTAGGTCG
1 CATGTGTAGTACT-AGTGCAGGCTACTACGTGTA-TAAGATGGTTAGGTCG
* * *
40143319 CATGTGTAGTACTGAGTGCAGGCTACCACGTGTATCAGATGGTTAGGTCA
1 CATGTGTAGTACT-AGTGCAGGCTACTACGTGTATAAGATGGTTAGGTCG
*
40143369 CGTGTGTAGTACTA
1 CATGTGTAGTACTA
40143383 AGTAGATAGT
Statistics
Matches: 99, Mismatches: 8, Indels: 15
0.81 0.07 0.12
Matches are distributed among these distances:
48 3 0.03
49 3 0.03
50 58 0.59
52 32 0.32
53 2 0.02
54 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.33
Consensus pattern (49 bp):
CATGTGTAGTACTAGTGCAGGCTACTACGTGTATAAGATGGTTAGGTCG
Found at i:40143352 original size:26 final size:25
Alignment explanation
Indices: 40143271--40143352 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 25
40143261 TTAGGTTACG
*
40143271 CGTGTAGTACTAAGTGCAGGCTACTA
1 CGTGTAGTACT-AGTGCAGGCTACCA
* * *
40143297 CGTGTACTAGATAGT-TAGG-T-CGCA
1 CGTGTAGTA-CTAGTGCAGGCTAC-CA
*
40143321 TGTGTAGTACTGAGTGCAGGCTACCA
1 CGTGTAGTACT-AGTGCAGGCTACCA
40143347 CGTGTA
1 CGTGTA
40143353 TCAGATGGTT
Statistics
Matches: 41, Mismatches: 9, Indels: 12
0.66 0.15 0.19
Matches are distributed among these distances:
23 2 0.05
24 12 0.29
25 6 0.15
26 19 0.46
27 2 0.05
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.28
Consensus pattern (25 bp):
CGTGTAGTACTAGTGCAGGCTACCA
Found at i:40143398 original size:31 final size:31
Alignment explanation
Indices: 40143355--40143416 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
40143345 CACGTGTATC
* *
40143355 AGATGGTTAGGTCACGTGTGTAGTACTAAGT
1 AGATAGTTAGGTCACATGTGTAGTACTAAGT
*
40143386 AGATAGTTAGGTCGCATGTGTAGTACTAAGT
1 AGATAGTTAGGTCACATGTGTAGTACTAAGT
40143417 GCAGGCTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.10, G:0.31, T:0.32
Consensus pattern (31 bp):
AGATAGTTAGGTCACATGTGTAGTACTAAGT
Found at i:40143499 original size:132 final size:131
Alignment explanation
Indices: 40143272--40143517 Score: 350
Period size: 132 Copynumber: 1.9 Consensus size: 131
40143262 TAGGTTACGC
* * * * * *
40143272 GTGTAGTACTAAGTGCAGGCTACTACGTGTACTAGATAGTTAGGTCGCATGTGTAGTACTGAGTG
1 GTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATACTTAGATCACATGTGTAGTACTAAGTG
*
40143337 CAGGCTACCACGTGTATCAGATGGTTAGGTCACGTGTGTAGTACTAAGTAGATAGTTAGGTCGCA
66 CAGGCTACCACGTGTATCAGATGGTAAGGTCACGTGTGTAGTACTAAGTAGATAGTTAGGTCGCA
40143402 T
131 T
* * * *
40143403 GTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCA-ATCACGTGTGTCGTACTAAG
1 GTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGAT-ACTT-AGATCACATGTGTAGTACTAAG
* *
40143467 TGCAGGCTACTACGTGTATCAGATGGTAAGGTCATGTGTGTAGTACTAAGT
64 TGCAGGCTACCACGTGTATCAGATGGTAAGGTCACGTGTGTAGTACTAAGT
40143518 GTAGGCTACT
Statistics
Matches: 100, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
131 33 0.33
132 66 0.66
133 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (131 bp):
GTGTAGTACTAAGTGCAGGCTACTACGCGTACCAGATACTTAGATCACATGTGTAGTACTAAGTG
CAGGCTACCACGTGTATCAGATGGTAAGGTCACGTGTGTAGTACTAAGTAGATAGTTAGGTCGCA
T
Found at i:40143524 original size:50 final size:49
Alignment explanation
Indices: 40143393--40143589 Score: 171
Period size: 49 Copynumber: 4.0 Consensus size: 49
40143383 AGTAGATAGT
* * * * * **
40143393 TAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACT
1 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT--GG
* * *
40143444 TCA-ATCACGTGTGTCGTACTAAGTGCAGGCTACTACGTGTATCAGATGG
1 T-AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG
* * * * *
40143493 TAAGGTCATGTGTGTAGTACTAAGTGTAGGCTACTACATGTACCGGATTG
1 T-AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG
* * * * *
40143543 TTGGTCGCATGTGTAGTGCTAAGTGCAGGCTACTATGTGTACCAGAT
1 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGAT
40143590 AGCTTCGGTT
Statistics
Matches: 116, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
49 39 0.34
50 39 0.34
51 37 0.32
52 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.30
Consensus pattern (49 bp):
TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATGG
Found at i:40143573 original size:49 final size:50
Alignment explanation
Indices: 40143394--40143589 Score: 155
Period size: 50 Copynumber: 3.9 Consensus size: 50
40143384 GTAGATAGTT
* *** * **
40143394 AGGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTTCA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAT--GGT-A
* * * *
40143447 A--TCACGTGTGTCGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTA
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTA
** * * *
40143495 AGGTCATGTGTGTAGTACTAAGTGTAGGCTACTACATGTACCGGATTGT-
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTA
* * * **
40143544 TGGTCGCATGTGTAGTGCTAAGTGCAGGCTACTATGTGTACCAGAT
1 AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGAT
40143590 AGCTTCGGTT
Statistics
Matches: 116, Mismatches: 25, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
48 2 0.02
49 38 0.33
50 39 0.34
51 36 0.31
53 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (50 bp):
AGGTCACATGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATGGTA
Found at i:40143810 original size:16 final size:15
Alignment explanation
Indices: 40143789--40143818 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40143779 GAATGGAGTA
40143789 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
40143805 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
40143819 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:40149042 original size:26 final size:26
Alignment explanation
Indices: 40149013--40149094 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
40149003 TGATACAAAT
*
40149013 TGATAATGGGTTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
40149039 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40149065 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
40149091 TGAT
1 TGAT
40149095 TGGAATTTCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:40153369 original size:18 final size:18
Alignment explanation
Indices: 40153346--40153431 Score: 100
Period size: 18 Copynumber: 4.7 Consensus size: 18
40153336 GAACGATTAT
*
40153346 TTATTCAGTAACAGTCAA
1 TTATTCAGTAACAATCAA
*
40153364 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAATCAA
* * *
40153382 TTATTCAATAATAATCAG
1 TTATTCAGTAACAATCAA
* *
40153400 TTATTCTGTAACAATTAAA
1 TTATTCAGTAACAA-TCAA
40153419 TTATTCAGTAACA
1 TTATTCAGTAACA
40153432 GTCGATCTTT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
18 41 0.75
19 14 0.25
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (18 bp):
TTATTCAGTAACAATCAA
Found at i:40153387 original size:36 final size:37
Alignment explanation
Indices: 40153346--40153434 Score: 117
Period size: 36 Copynumber: 2.4 Consensus size: 37
40153336 GAACGATTAT
*
40153346 TTATTCAGTAACAGTCAATTATTCGGTAACAA-TCAA
1 TTATTCAGTAACAGTCAATTATTCGGTAACAATTAAA
* * * * *
40153382 TTATTCAATAATAATCAGTTATTCTGTAACAATTAAA
1 TTATTCAGTAACAGTCAATTATTCGGTAACAATTAAA
40153419 TTATTCAGTAACAGTC
1 TTATTCAGTAACAGTC
40153435 GATCTTTCCA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
36 27 0.63
37 16 0.37
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (37 bp):
TTATTCAGTAACAGTCAATTATTCGGTAACAATTAAA
Found at i:40153628 original size:47 final size:47
Alignment explanation
Indices: 40153559--40153662 Score: 163
Period size: 47 Copynumber: 2.2 Consensus size: 47
40153549 CAGTAACAGT
* * * *
40153559 AACAGTAGCAATACGGTACACAGAGTACCTCATTGGAACAAATCCGG
1 AACAGTAACAATACGGTACACAGAGTACCTAATCGGAACAAATCCGA
40153606 AACAGTAACAATACGGTACACAGAGTACCTAATCGGAACAAATCCGA
1 AACAGTAACAATACGGTACACAGAGTACCTAATCGGAACAAATCCGA
*
40153653 AATAGTAACA
1 AACAGTAACA
40153663 GTAACGATAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 52 1.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.16
Consensus pattern (47 bp):
AACAGTAACAATACGGTACACAGAGTACCTAATCGGAACAAATCCGA
Found at i:40161885 original size:15 final size:14
Alignment explanation
Indices: 40161865--40161948 Score: 78
Period size: 14 Copynumber: 5.6 Consensus size: 14
40161855 CTAAAAAAAT
40161865 TATAAAAAATTTATA
1 TATAAAAAA-TTATA
*
40161880 TATAAAAAATTATT
1 TATAAAAAATTATA
*
40161894 TTTAAAAAACTTAATA
1 TATAAAAAA-TT-ATA
* *
40161910 TATAAAAATTTAAAA
1 TATAAAAAATT-ATA
*
40161925 CTATAAAAAAATATA
1 -TATAAAAAATTATA
40161940 TATAAAAAA
1 TATAAAAAA
40161949 CAAACCCTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 21 0.37
15 18 0.32
16 18 0.32
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (14 bp):
TATAAAAAATTATA
Found at i:40162325 original size:11 final size:11
Alignment explanation
Indices: 40162292--40162334 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
40162282 GGGTGAAAAT
40162292 AATTATATAATA
1 AATTATATAA-A
* *
40162304 AATTTTTTAAA
1 AATTATATAAA
40162315 AATTATATAAA
1 AATTATATAAA
*
40162326 AGTTATATA
1 AATTATATA
40162335 TGTATAGTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
AATTATATAAA
Found at i:40163513 original size:48 final size:46
Alignment explanation
Indices: 40163432--40163527 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 46
40163422 ATGAACAAAT
* * *
40163432 ATTCATCTAATTTGTTGAATCTCTCTATTACATTGCTCCTTATGAG
1 ATTCATCTAATTTGATAAATCTCTCTATTACATTGCTCCGTATGAG
40163478 ATTCATCTAATTATTGATAAATCTCTCTATTACATTGCTCCGTATGAG
1 ATTCATCTAA-T-TTGATAAATCTCTCTATTACATTGCTCCGTATGAG
40163526 AT
1 AT
40163528 GCTTCATAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 10 0.22
47 1 0.02
48 34 0.76
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (46 bp):
ATTCATCTAATTTGATAAATCTCTCTATTACATTGCTCCGTATGAG
Found at i:40164392 original size:25 final size:27
Alignment explanation
Indices: 40164346--40164395 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
40164336 AATAGAAGTT
* *
40164346 TTAAAATATTTTATTTTTATAAAATTA
1 TTAAAATATTTTAATTTAATAAAATTA
40164373 TTAAAA-A-TTTAATTTAATAAAAT
1 TTAAAATATTTTAATTTAATAAAAT
40164396 CATATATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 1 0.05
27 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAAAATATTTTAATTTAATAAAATTA
Found at i:40169194 original size:40 final size:40
Alignment explanation
Indices: 40169104--40169288 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
40169094 TTGAATGATG
* *
40169104 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
*
40169143 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
* * *
40169184 TTCGGGCTAAG-CCCGAAGGCATTTGTGGGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40169223 TCCGGGTTAAGTCCCGAAGGCATTTATGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
40169262 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
40169289 AACGAGTAGC
Statistics
Matches: 123, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 35 0.28
40 78 0.63
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:40169240 original size:79 final size:81
Alignment explanation
Indices: 40169105--40169288 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 81
40169095 TGAATGATGT
* *
40169105 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
* *
40169169 GTGCGAGTTACTA-ATT
66 ATGCGAGTTACTATA-A
* * * **
40169185 TCGGGCTAAG-CCCGAAGGCATTTGTG-GGAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCATT
40169247 TATGCGAGTTACTATAA
65 TATGCGAGTTACTATAA
*
40169264 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40169289 AACGAGTAGC
Statistics
Matches: 89, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
78 1 0.01
79 58 0.65
80 30 0.34
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (81 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
ATGCGAGTTACTATAA
Found at i:40169319 original size:79 final size:79
Alignment explanation
Indices: 40169156--40169321 Score: 178
Period size: 79 Copynumber: 2.1 Consensus size: 79
40169146 CGGACTAAGA
* ** ***
40169156 TCCGAAGGCATTTGTGCGAGTTACTAATTTCGGGCTAAGCCCGAAGGCATTTGTGGGAGTTACTA
1 TCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
*
40169221 AATCCGGGTTAAGT
66 AATCCGGGTTAAAT
* *
40169235 CCCGAAGGCATTTATGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAG
1 TCCGAAGGCATTTATGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-
*
40169298 CTATA-CAC-GGTTAAAT
63 CTAAATC-CGGGTTAAAT
40169314 TCCGAAGG
1 TCCGAAGG
40169322 TACGTGATTT
Statistics
Matches: 72, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
78 2 0.03
79 48 0.67
80 22 0.31
ACGTcount: A:0.27, C:0.20, G:0.27, T:0.27
Consensus pattern (79 bp):
TCCGAAGGCATTTATGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTA
AATCCGGGTTAAAT
Found at i:40173993 original size:22 final size:22
Alignment explanation
Indices: 40173949--40173993 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
40173939 TTAATCATTA
* * **
40173949 TTATTTAGTATCAGTCATTTAT
1 TTATTCAGTAACAGTCAAATAT
40173971 TTATTCAGTAACAGTCAAATAT
1 TTATTCAGTAACAGTCAAATAT
40173993 T
1 T
40173994 CGGCAGCAGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.47
Consensus pattern (22 bp):
TTATTCAGTAACAGTCAAATAT
Found at i:40175224 original size:17 final size:17
Alignment explanation
Indices: 40175192--40175234 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40175182 CTTTTTCGTT
40175192 TTTTCATTCTCTTTTTC
1 TTTTCATTCTCTTTTTC
* * *
40175209 TTTTCTTTCTTTTTTTT
1 TTTTCATTCTCTTTTTC
40175226 TGTTTCATT
1 T-TTTCATT
40175235 TACTTTTATG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.05, C:0.16, G:0.02, T:0.77
Consensus pattern (17 bp):
TTTTCATTCTCTTTTTC
Found at i:40175225 original size:13 final size:16
Alignment explanation
Indices: 40175190--40175226 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
40175180 CCCTTTTTCG
40175190 TTTTTTCATTCTCTTT
1 TTTTTTCATTCTCTTT
40175206 TTCTTTTC-TT-TCTTT
1 TT-TTTTCATTCTCTTT
40175221 TTTTTT
1 TTTTTT
40175227 GTTTCATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTCATTCTCTTT
Found at i:40192794 original size:43 final size:43
Alignment explanation
Indices: 40192733--40192884 Score: 164
Period size: 43 Copynumber: 3.5 Consensus size: 43
40192723 ATAGGATTCT
40192733 GATATGAGATTTCATGTAAGACCACATCTGGGACGTTGGCATC
1 GATATGAGATTTCATGTAAGACCACATCTGGGACGTTGGCATC
* *
40192776 GATATGAGATTTCATGTAAGATCACATCTGGGACGTTGGCATA
1 GATATGAGATTTCATGTAAGACCACATCTGGGACGTTGGCATC
* * * * * ** * **
40192819 TATTTGAAATTTACGTGTAAAACCATGTCTGGGACATCAGCATC
1 GATATGAGATTT-CATGTAAGACCACATCTGGGACGTTGGCATC
40192863 G-TAT-ATGATTTCATGTAAGACC
1 GATATGA-GATTTCATGTAAGACC
40192885 CTGTCTGAGA
Statistics
Matches: 88, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
42 10 0.11
43 56 0.64
44 22 0.25
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.31
Consensus pattern (43 bp):
GATATGAGATTTCATGTAAGACCACATCTGGGACGTTGGCATC
Found at i:40192890 original size:42 final size:42
Alignment explanation
Indices: 40192829--40192926 Score: 101
Period size: 42 Copynumber: 2.3 Consensus size: 42
40192819 TATTTGAAAT
* * *
40192829 TTACGTGTAAAACCATGTCTGGGAC-ATCAGCATCGTATA-TGA
1 TTACATGTAAGACCATGTCTGAGACAAT-AGCATC-TATATTGA
* * *
40192871 TTTCATGTAAGACCCTGTCTGAGACAATGGCATCTATATTTGA
1 TTACATGTAAGACCATGTCTGAGACAATAGCATCTATA-TTGA
40192914 TTACATGTAAGAC
1 TTACATGTAAGAC
40192927 TAGGTCAGGG
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
41 4 0.09
42 25 0.54
43 17 0.37
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGAGACAATAGCATCTATATTGA
Found at i:40203574 original size:5 final size:5
Alignment explanation
Indices: 40203564--40203597 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
40203554 GATATTGAGA
40203564 AAAAT AAAAT AAAAT AAAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT -AAAAT AAAAT AAAAT AAA
40203598 GAACACACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:40203584 original size:16 final size:16
Alignment explanation
Indices: 40203563--40203597 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
40203553 GGATATTGAG
40203563 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
40203579 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
40203595 AAA
1 AAA
40203598 GAACACACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:40216376 original size:12 final size:12
Alignment explanation
Indices: 40216361--40216386 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40216351 ACTAAACACT
40216361 AAAGAAAACCCA
1 AAAGAAAACCCA
40216373 AAAGAAAACCCA
1 AAAGAAAACCCA
40216385 AA
1 AA
40216387 CAAAATTAAA
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:0.69, C:0.23, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAGAAAACCCA
Found at i:40219884 original size:21 final size:20
Alignment explanation
Indices: 40219854--40219893 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40219844 AAAAACTTGT
40219854 ATAACTATCATCAAACATTC
1 ATAACTATCATCAAACATTC
*
40219874 ATAATCTATCATCAATCATT
1 ATAA-CTATCATCAAACATT
40219894 AACATACATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
ATAACTATCATCAAACATTC
Found at i:40223512 original size:93 final size:93
Alignment explanation
Indices: 40223400--40223571 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
40223390 TGCCCATAAG
* *
40223400 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40223465 ACGAGTTCGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
40223493 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
40223558 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
40223572 TCAACCATCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40223568 original size:46 final size:46
Alignment explanation
Indices: 40223393--40223568 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
40223383 TGTAACCTGC
* * *
40223393 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* *
40223439 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
40223489 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40223532 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
40223569 TGCTCAACCA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 63 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.21, T:0.20
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40225529 original size:30 final size:30
Alignment explanation
Indices: 40225485--40225572 Score: 92
Period size: 30 Copynumber: 3.0 Consensus size: 30
40225475 CAAAGATAAC
40225485 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
40225514 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
40225544 AAGAGATCCAGGATAAA-AAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
40225573 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
29 17 0.35
30 32 0.65
ACGTcount: A:0.58, C:0.16, G:0.16, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:40225533 original size:15 final size:15
Alignment explanation
Indices: 40225485--40225560 Score: 84
Period size: 15 Copynumber: 5.1 Consensus size: 15
40225475 CAAAGATAAC
*
40225485 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
40225499 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
40225514 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
40225529 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
40225544 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
40225559 AA
1 AA
40225561 AAACCCAAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
14 9 0.17
15 42 0.81
16 1 0.02
ACGTcount: A:0.58, C:0.14, G:0.17, T:0.11
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:40228678 original size:93 final size:93
Alignment explanation
Indices: 40228519--40228689 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
40228509 GCCCATAAGT
* *
40228519 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40228584 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
40228612 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
40228677 CGAGTTCGGATGC
66 CGAGTTCGGATGC
40228690 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:40228686 original size:46 final size:46
Alignment explanation
Indices: 40228511--40228686 Score: 225
Period size: 46 Copynumber: 3.8 Consensus size: 46
40228501 TGTAACCCGC
* * *
40228511 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
40228557 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
* *
40228607 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40228650 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40228687 TGCTCAACCA
Statistics
Matches: 112, Mismatches: 9, Indels: 18
0.81 0.06 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 64 0.57
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40235607 original size:40 final size:39
Alignment explanation
Indices: 40235496--40235645 Score: 140
Period size: 40 Copynumber: 3.8 Consensus size: 39
40235486 TTAATCACGT
* * *
40235496 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * *
40235536 GCACGAATGCCTTCGGGCCTTAGCCCGGATATAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* *** *
40235576 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAA-TGCCTTCGGGTCTTAGCCCGGATATAACAACTA
* * *
40235616 GCATATTGTCTTCGGG-CTTAGCCCGGATAT
1 GCACAATGCCTTCGGGTCTTAGCCCGGATAT
40235646 CATTCAATTT
Statistics
Matches: 91, Mismatches: 18, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
38 13 0.14
39 11 0.12
40 67 0.74
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (39 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATATAACAACTA
Done.