Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 90 of 97
Found at i:35455031 original size:26 final size:26
Alignment explanation
Indices: 35454999--35455078 Score: 126
Period size: 26 Copynumber: 3.1 Consensus size: 26
35454989 TACCTATAAG
35454999 TATGTGAAATATATGATTAACTAATA
1 TATGTGAAATATATGATTAACTAATA
*
35455025 TATGTGAAATATATGATTAGCTAATA
1 TATGTGAAATATATGATTAACTAATA
* *
35455051 TATGTGAAATATATTA-TAACTAACA
1 TATGTGAAATATATGATTAACTAATA
35455076 TAT
1 TAT
35455079 TCATTTTATT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 10 0.20
26 40 0.80
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (26 bp):
TATGTGAAATATATGATTAACTAATA
Found at i:35455275 original size:3 final size:3
Alignment explanation
Indices: 35455267--35455291 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35455257 CATGTAACTA
35455267 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
35455292 TCATTGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:35458510 original size:2 final size:2
Alignment explanation
Indices: 35458503--35458528 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35458493 TAAGTCTGGT
35458503 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
35458529 AGAGAGAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:35458533 original size:2 final size:2
Alignment explanation
Indices: 35458528--35458623 Score: 94
Period size: 2 Copynumber: 50.0 Consensus size: 2
35458518 GTGTGTGTGT
35458528 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G- GA G-
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * * * *
35458568 GA GA GA -A G- GA GG GA GA TGG GA G- GT GT TA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA -GA GA GA GA GA GA GA GA GA GA GA GA
*
35458608 GA GA GA GA GG GA GA GA
1 GA GA GA GA GA GA GA GA
35458624 ACAAGGGTAC
Statistics
Matches: 79, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
1 5 0.06
2 73 0.92
3 1 0.01
ACGTcount: A:0.43, C:0.00, G:0.53, T:0.04
Consensus pattern (2 bp):
GA
Found at i:35467608 original size:72 final size:72
Alignment explanation
Indices: 35467532--35467767 Score: 181
Period size: 72 Copynumber: 3.3 Consensus size: 72
35467522 TCATAGAGAG
* * *
35467532 GAAAAGAGATCAACATGGCACAATGACAATGAATTCGAGCCTAA-TTC-GAGAGATGATCGGTAT
1 GAAAAGAGATCAACAAGGCACAATGACAATGAATTCGAGCC-AAGGTCAG-GAGAAGATCGGTAT
35467595 AGAAGGGAA
64 AGAAGGGAA
* * * * * * * *
35467604 GAAAAAAGATCTAGAAGGCACAATGATAGTGACTTTGAGCCAAGGTCAGGAGAAGATCGTTATAG
1 GAAAAGAGATCAACAAGGCACAATGACAATGAATTCGAGCCAAGGTCAGGAGAAGATCGGTATAG
* *
35467669 GAGGGAT
66 AAGGGAA
* * ** ** * * * * *
35467676 GAAAAGAGATCTATAAGGCATGATGATGATGAATAT-GGGGCAAGGTTAAGAGAAGATCGTTATA
1 GAAAAGAGATCAACAAGGCACAATGACAATGAAT-TCGAGCCAAGGTCAGGAGAAGATCGGTATA
* *
35467740 GGAGGGAT
65 GAAGGGAA
*
35467748 GAAAAGAGATCAAAAAGGCA
1 GAAAAGAGATCAACAAGGCA
35467768 TGGTGATGAC
Statistics
Matches: 135, Mismatches: 26, Indels: 6
0.81 0.16 0.04
Matches are distributed among these distances:
71 2 0.01
72 131 0.97
73 2 0.01
ACGTcount: A:0.42, C:0.10, G:0.30, T:0.19
Consensus pattern (72 bp):
GAAAAGAGATCAACAAGGCACAATGACAATGAATTCGAGCCAAGGTCAGGAGAAGATCGGTATAG
AAGGGAA
Found at i:35467792 original size:72 final size:72
Alignment explanation
Indices: 35467639--35467794 Score: 224
Period size: 72 Copynumber: 2.2 Consensus size: 72
35467629 ATAGTGACTT
* * *
35467639 TGAGCCAAGGTCAGGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCTATAAGGCATGATGATG
1 TGAGCCAAGGTCAAGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCAAAAAGGCATGATGATG
*
35467704 ATGAATA
66 ATCAATA
* * * *
35467711 TGGGGCAAGGTTAAGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCAAAAAGGCATGGTGATG
1 TGAGCCAAGGTCAAGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCAAAAAGGCATGATGATG
35467776 A-CAAGTA
66 ATCAA-TA
35467783 TGAGCCAAGGTC
1 TGAGCCAAGGTC
35467795 TAATGGAGAT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
71 2 0.03
72 70 0.97
ACGTcount: A:0.38, C:0.09, G:0.33, T:0.19
Consensus pattern (72 bp):
TGAGCCAAGGTCAAGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCAAAAAGGCATGATGATG
ATCAATA
Found at i:35467815 original size:72 final size:72
Alignment explanation
Indices: 35467639--35467824 Score: 189
Period size: 72 Copynumber: 2.6 Consensus size: 72
35467629 ATAGTGACTT
* * * * * * *
35467639 TGAGCCAAGGTCAGGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCTATAAGGCATGATGATG
1 TGAGCCAAGGTTAAGAGAAGATCATGACAGGAGGGATGAAAAGAGATCAAAAAGGCATGATGATG
*
35467704 ATGAATA
66 ATCAATA
* * * * * *
35467711 TGGGGCAAGGTTAAGAGAAGATCGTTATAGGAGGGATGAAAAGAGATCAAAAAGGCATGGTGATG
1 TGAGCCAAGGTTAAGAGAAGATCATGACAGGAGGGATGAAAAGAGATCAAAAAGGCATGATGATG
35467776 A-CAAGTA
66 ATCAA-TA
*
35467783 TGAGCCAAGGTCTAATG-G-AGATCATGACAGGAGGGAAGAAAA
1 TGAGCCAAGGT-TAA-GAGAAGATCATGACAGGAGGGATGAAAA
35467825 AAAATTAGTA
Statistics
Matches: 97, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
71 2 0.02
72 90 0.93
73 4 0.04
74 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.33, T:0.18
Consensus pattern (72 bp):
TGAGCCAAGGTTAAGAGAAGATCATGACAGGAGGGATGAAAAGAGATCAAAAAGGCATGATGATG
ATCAATA
Found at i:35475988 original size:25 final size:24
Alignment explanation
Indices: 35475949--35476020 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 24
35475939 ACTTTTAATA
*
35475949 AAATATTAATATTAAATTATAAAT
1 AAATATTAACATTAAATTATAAAT
35475973 AAATATTAACATTTAAATTATAAAT
1 AAATATTAACA-TTAAATTATAAAT
* * * *
35475998 TATTAATAA-AATAAATTATAAAT
1 AAATATTAACATTAAATTATAAAT
35476021 TATTCCTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
23 12 0.29
24 11 0.26
25 19 0.45
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATATTAACATTAAATTATAAAT
Found at i:35478712 original size:8 final size:8
Alignment explanation
Indices: 35478692--35478743 Score: 50
Period size: 8 Copynumber: 6.1 Consensus size: 8
35478682 TTTAATTTAA
*
35478692 TTTTAATT
1 TTTTTATT
35478700 TTTTTATT
1 TTTTTATT
35478708 TTTTTCATT
1 TTTTT-ATT
*
35478717 TATATTATT
1 T-TTTTATT
35478726 ATTTTTATT
1 -TTTTTATT
*
35478735 TATTTATT
1 TTTTTATT
35478743 T
1 T
35478744 ACATTTTATT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
8 20 0.54
9 13 0.35
10 4 0.11
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTATT
Found at i:35478730 original size:18 final size:17
Alignment explanation
Indices: 35478691--35478742 Score: 59
Period size: 18 Copynumber: 3.0 Consensus size: 17
35478681 GTTTAATTTA
* *
35478691 ATTTTAATTTTTTTATT
1 ATTTTCATTTATTTATT
*
35478708 TTTTTCATTTATATTATT
1 ATTTTCATTTAT-TTATT
*
35478726 ATTTTTATTTATTTATT
1 ATTTTCATTTATTTATT
35478743 TACATTTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
17 14 0.48
18 15 0.52
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (17 bp):
ATTTTCATTTATTTATT
Found at i:35478757 original size:32 final size:30
Alignment explanation
Indices: 35478682--35478753 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 30
35478672 ATTTTAGATG
*
35478682 TTTA-ATTTA-ATT-TTAATTTTTTTATTT
1 TTTACATTTATATTATTATTTTTTTTATTT
*
35478709 TTTTCATTTATATTATTATTTTTATTTATTT
1 TTTACATTTATATTATTATTTTT-TTTATTT
35478740 ATTTACATTT-TATT
1 -TTTACATTTATATT
35478754 TATTCATATG
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 3 0.08
28 5 0.14
29 3 0.08
30 7 0.19
31 11 0.30
32 8 0.22
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (30 bp):
TTTACATTTATATTATTATTTTTTTTATTT
Found at i:35478829 original size:69 final size:70
Alignment explanation
Indices: 35478750--35478887 Score: 208
Period size: 69 Copynumber: 2.0 Consensus size: 70
35478740 ATTTACATTT
*
35478750 TATTTATTCATATGTTTTAAATCTTTATAAATTTT-TTTCATAAATCTT-TACGAACCATAAATC
1 TATTTATTCATATGTTTTAAATCTTTATAAATTTTCTTTCATAAAT-TTATACAAACCATAAATC
35478813 ATATTC
65 ATATTC
* * * *
35478819 TATTTATTCATATTTTTTAAATCTTTATAGATTTTCTTTCATAAATTTATACAAATCATCAATCA
1 TATTTATTCATATGTTTTAAATCTTTATAAATTTTCTTTCATAAATTTATACAAACCATAAATCA
35478884 TATT
66 TATT
35478888 TTTTGTCTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
69 35 0.56
70 27 0.44
ACGTcount: A:0.35, C:0.12, G:0.02, T:0.51
Consensus pattern (70 bp):
TATTTATTCATATGTTTTAAATCTTTATAAATTTTCTTTCATAAATTTATACAAACCATAAATCA
TATTC
Found at i:35484182 original size:2 final size:2
Alignment explanation
Indices: 35484175--35484209 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
35484165 CATTATAATT
35484175 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35484210 TCGTGTTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:35486090 original size:13 final size:13
Alignment explanation
Indices: 35486072--35486096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35486062 GGAAAATAGG
35486072 ATTTTATAAAATA
1 ATTTTATAAAATA
35486085 ATTTTATAAAAT
1 ATTTTATAAAAT
35486097 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:35492007 original size:19 final size:19
Alignment explanation
Indices: 35491983--35492020 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35491973 CAGAAAATAC
35491983 GTTGCAGGTGGTCCCGACT
1 GTTGCAGGTGGTCCCGACT
35492002 GTTGCAGGTGGTCCCGACT
1 GTTGCAGGTGGTCCCGACT
35492021 ATGGCTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.37, T:0.26
Consensus pattern (19 bp):
GTTGCAGGTGGTCCCGACT
Found at i:35499539 original size:12 final size:12
Alignment explanation
Indices: 35499522--35499577 Score: 67
Period size: 12 Copynumber: 4.5 Consensus size: 12
35499512 CCCTTCGGTA
35499522 ATATATAAATAC
1 ATATATAAATAC
35499534 ATATATACATATAC
1 ATATATA-A-ATAC
*
35499548 ATATATATATAC
1 ATATATAAATAC
* *
35499560 ATATACATATAC
1 ATATATAAATAC
35499572 ATATAT
1 ATATAT
35499578 GTATGTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
12 27 0.69
13 1 0.03
14 11 0.28
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATATAAATAC
Found at i:35499547 original size:6 final size:6
Alignment explanation
Indices: 35499536--35499576 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
35499526 ATAAATACAT
*
35499536 ATATAC ATATAC ATATAT ATATAC ATATAC ATATAC ATATA
1 ATATAC ATATAC ATATAC ATATAC ATATAC ATATAC ATATA
35499577 TGTATGTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (6 bp):
ATATAC
Found at i:35499555 original size:18 final size:18
Alignment explanation
Indices: 35499524--35499576 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
35499514 CTTCGGTAAT
* *
35499524 ATATAAATACATATATAC
1 ATATACATATATATATAC
35499542 ATATACATATATATATAC
1 ATATACATATATATATAC
*
35499560 ATATACATATACATATA
1 ATATACATATATATATA
35499577 TGTATGTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.36
Consensus pattern (18 bp):
ATATACATATATATATAC
Found at i:35499586 original size:16 final size:16
Alignment explanation
Indices: 35499567--35499602 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
35499557 TACATATACA
35499567 TATACATATATGTATG
1 TATACATATATGTATG
**
35499583 TATATGTATATGTATG
1 TATACATATATGTATG
35499599 TATA
1 TATA
35499603 TGTATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.14, T:0.47
Consensus pattern (16 bp):
TATACATATATGTATG
Found at i:35499588 original size:10 final size:10
Alignment explanation
Indices: 35499575--35499613 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
35499565 CATATACATA
* *
35499575 TATGTATGTA
1 TATGTATATG
35499585 TATGTATATG
1 TATGTATATG
35499595 TATGTATATG
1 TATGTATATG
*
35499605 TATATATAT
1 TATGTATAT
35499614 CCAGAACTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (10 bp):
TATGTATATG
Found at i:35499603 original size:16 final size:16
Alignment explanation
Indices: 35499573--35499609 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
35499563 TACATATACA
35499573 TATATGTATGTATATG
1 TATATGTATGTATATG
35499589 TATATGTATGTATATG
1 TATATGTATGTATATG
35499605 TATAT
1 TATAT
35499610 ATATCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.51
Consensus pattern (16 bp):
TATATGTATGTATATG
Found at i:35500833 original size:12 final size:12
Alignment explanation
Indices: 35500798--35500827 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
35500788 AACAGAGTGC
35500798 ATTGTCAACATG
1 ATTGTCAACATG
35500810 ATTGTCAACATG
1 ATTGTCAACATG
35500822 ATTGTC
1 ATTGTC
35500828 TCCATGCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (12 bp):
ATTGTCAACATG
Found at i:35504946 original size:3 final size:3
Alignment explanation
Indices: 35504931--35504967 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
35504921 ATATATTTAC
* *
35504931 ATT ATT ATC ATT ATT ATT TTT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
35504968 AGACATGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:35514114 original size:2 final size:2
Alignment explanation
Indices: 35514107--35514149 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
35514097 CATCAAAATT
35514107 TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35514146 TA TA
1 TA TA
35514150 ATTCAATTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.08
2 35 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:35514131 original size:19 final size:19
Alignment explanation
Indices: 35514107--35514149 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
35514097 CATCAAAATT
35514107 TATATATATAATATATATA
1 TATATATATAATATATATA
*
35514126 TATATATATATTATATATA
1 TATATATATAATATATATA
35514145 -ATATA
1 TATATA
35514150 ATTCAATTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATAATATATATA
Found at i:35514568 original size:23 final size:24
Alignment explanation
Indices: 35514531--35514575 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
35514521 TTTTTTATTA
35514531 ATTAATATATAAATT-AATAATTT
1 ATTAATATATAAATTAAATAATTT
* *
35514554 ATTAATTTATCAATTAAATAAT
1 ATTAATATATAAATTAAATAAT
35514576 ATCTCAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 13 0.68
24 6 0.32
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAATATATAAATTAAATAATTT
Found at i:35514715 original size:2 final size:2
Alignment explanation
Indices: 35514708--35514736 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35514698 TGATGTGTAC
35514708 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
35514737 TTGAAAGGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35520916 original size:22 final size:23
Alignment explanation
Indices: 35520886--35520928 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
35520876 ATTTTAAATT
35520886 ATTAAAAATATTTA-ATTTTTTA
1 ATTAAAAATATTTATATTTTTTA
* *
35520908 ATTATAAATTTTTATATTTTT
1 ATTAAAAATATTTATATTTTT
35520929 ATTTTGAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTAAAAATATTTATATTTTTTA
Found at i:35546966 original size:5 final size:5
Alignment explanation
Indices: 35546956--35546980 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35546946 TGAAATTTCA
35546956 ATGAT ATGAT ATGAT ATGAT ATGAT
1 ATGAT ATGAT ATGAT ATGAT ATGAT
35546981 CATAGTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (5 bp):
ATGAT
Found at i:35557695 original size:2 final size:2
Alignment explanation
Indices: 35557688--35557739 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
35557678 TTGATATCTC
35557688 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35557730 AT AT AT AT AT
1 AT AT AT AT AT
35557740 CCCTTGTGTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35558623 original size:29 final size:28
Alignment explanation
Indices: 35558565--35558632 Score: 84
Period size: 27 Copynumber: 2.4 Consensus size: 28
35558555 TGATTTGATG
* *
35558565 AAACATGACATAAAAGATGACATGAC-A
1 AAACACGATATAAAAGATGACATGACAA
35558592 AAACACGATATAAAAGATATGACATGACAA
1 AAACACGATATAAAAG--ATGACATGACAA
35558622 AATACACGATA
1 AA-ACACGATA
35558633 AGTGACGATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 14 0.40
29 10 0.29
30 3 0.09
31 8 0.23
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.16
Consensus pattern (28 bp):
AAACACGATATAAAAGATGACATGACAA
Found at i:35562092 original size:2 final size:2
Alignment explanation
Indices: 35562085--35562136 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
35562075 GCTGACCTTT
35562085 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35562127 GA GA GA GA GA
1 GA GA GA GA GA
35562137 TGGAGGTAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35576357 original size:64 final size:63
Alignment explanation
Indices: 35576234--35576361 Score: 168
Period size: 64 Copynumber: 2.0 Consensus size: 63
35576224 ACTCACGTTT
* * * * *
35576234 TCAATTTCTAAACCTGTTAGTAAGTCCAACTTTACAAAAAAAACAGTCAATCCATATTTTTCCA
1 TCAATATCTAAACCTATTAGTAAATCCAACTTTACAAAAAAAACAATCAATCCACA-TTTTCCA
* *
35576298 TCAATATCTAAACCTATTAGTAAATCCAACTTTACAAAAGAACCAATCAA-CTCACATTTTCCA
1 TCAATATCTAAACCTATTAGTAAATCCAACTTTACAAAAAAAACAATCAATC-CACATTTTCCA
35576361 T
1 T
35576362 TAGTCAAATT
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
63 9 0.16
64 47 0.84
ACGTcount: A:0.41, C:0.23, G:0.05, T:0.31
Consensus pattern (63 bp):
TCAATATCTAAACCTATTAGTAAATCCAACTTTACAAAAAAAACAATCAATCCACATTTTCCA
Found at i:35577276 original size:85 final size:85
Alignment explanation
Indices: 35577116--35577282 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 85
35577106 AATGGGGCTT
* * * * *
35577116 TCAGAGTTAACCACGTGAAGGGTATAGAGAGTGAAAGGGAAAAGATGTTGAAGCAAGAAGAGAGA
1 TCAGAGTTAACCACGTGAAGGGCAAAGAGAGAGAAAGGAAAAAGATGTTGAAGCAAGAAGAGACA
35577181 AAGAGAGGGGTGCAAAGGGG
66 AAGAGAGGGGTGCAAAGGGG
* * * **
35577201 TCAGAGTTATCCGCGTGAAGGGCAAATAGAGAGAAAGAGAAAAAGATGTTGAAGCAA-ATTAG-C
1 TCAGAGTTAACCACGTGAAGGGCAAAGAGAGAGAAAG-GAAAAAGATGTTGAAGCAAGAAGAGAC
35577264 AAAGAGAGGGGGTGCAAAG
65 AAAGAGA-GGGGTGCAAAG
35577283 AGGTTCGTGT
Statistics
Matches: 70, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
84 7 0.10
85 45 0.64
86 18 0.26
ACGTcount: A:0.42, C:0.08, G:0.36, T:0.14
Consensus pattern (85 bp):
TCAGAGTTAACCACGTGAAGGGCAAAGAGAGAGAAAGGAAAAAGATGTTGAAGCAAGAAGAGACA
AAGAGAGGGGTGCAAAGGGG
Found at i:35577790 original size:22 final size:23
Alignment explanation
Indices: 35577759--35577810 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
35577749 ATAATTTCTT
*
35577759 TCTTTTTTTGTTCTTTT-AGTTA
1 TCTTTATTTGTTCTTTTAAGTTA
35577781 TCTTTATTTGTTCTTTTAAGTTA
1 TCTTTATTTGTTCTTTTAAGTTA
*
35577804 TTTTTAT
1 TCTTTAT
35577811 AATACGTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 16 0.59
23 11 0.41
ACGTcount: A:0.13, C:0.08, G:0.08, T:0.71
Consensus pattern (23 bp):
TCTTTATTTGTTCTTTTAAGTTA
Found at i:35582480 original size:19 final size:19
Alignment explanation
Indices: 35582458--35582497 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
35582448 ATATTCAAGA
*
35582458 AATGTGTAGTTTGTCAACC
1 AATGTATAGTTTGTCAACC
*
35582477 AATGTATGGTTTGTCAACC
1 AATGTATAGTTTGTCAACC
35582496 AA
1 AA
35582498 GAAAGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (19 bp):
AATGTATAGTTTGTCAACC
Found at i:35594064 original size:19 final size:19
Alignment explanation
Indices: 35594027--35594064 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
35594017 TTAGATATTA
*
35594027 GTTTTTCTTTTTTTATTTT
1 GTTTTTCTTTTATTATTTT
35594046 GTTTTTCGTTTTATT-TTTT
1 GTTTTTC-TTTTATTATTTT
35594065 ATAATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.05, C:0.05, G:0.08, T:0.82
Consensus pattern (19 bp):
GTTTTTCTTTTATTATTTT
Found at i:35602606 original size:7 final size:7
Alignment explanation
Indices: 35602594--35602623 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
35602584 ATATTTTTTG
35602594 TTGTTTA
1 TTGTTTA
35602601 TTGTTTA
1 TTGTTTA
35602608 TTGTTTA
1 TTGTTTA
35602615 TTGTTTA
1 TTGTTTA
35602622 TT
1 TT
35602624 TGGGCTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.13, C:0.00, G:0.13, T:0.73
Consensus pattern (7 bp):
TTGTTTA
Found at i:35629721 original size:2 final size:2
Alignment explanation
Indices: 35629714--35629738 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35629704 TGTATCAGCA
35629714 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
35629739 ATGGACACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:35629968 original size:4 final size:4
Alignment explanation
Indices: 35629959--35629985 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
35629949 TCAGAGAGGA
35629959 AAAG AAAG AAAG AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAAG AAAG AAAG AAA
35629986 AGGAGGCCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:35636785 original size:4 final size:4
Alignment explanation
Indices: 35636776--35636800 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
35636766 TTAATAGTGG
35636776 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
35636801 GGGAAAGGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:35637878 original size:3 final size:3
Alignment explanation
Indices: 35637870--35637903 Score: 50
Period size: 3 Copynumber: 10.7 Consensus size: 3
35637860 TCCCTTCTTT
35637870 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TATA TT
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA T-TA TT
35637904 GAAATTTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
3 23 0.79
4 6 0.21
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35645430 original size:2 final size:2
Alignment explanation
Indices: 35645425--35645450 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35645415 AAAAAAAAAA
35645425 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
35645451 TTATTGCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35650531 original size:37 final size:37
Alignment explanation
Indices: 35650506--35650578 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 37
35650496 CAAAATAATG
*
35650506 GGTGAAAAAGTTGAAGAGTATATGTTATGACAGAACAA
1 GGTGAAAAAGTTGAAGAGTATATGTTAT-ACAAAACAA
*
35650544 GGTGAAAACGTTGAAGAGTATATGTTATGACAAAA
1 GGTGAAAAAGTTGAAGAGTATATGTTAT-ACAAAA
35650579 TGTAAGCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.44, C:0.05, G:0.26, T:0.25
Consensus pattern (37 bp):
GGTGAAAAAGTTGAAGAGTATATGTTATACAAAACAA
Found at i:35656239 original size:19 final size:19
Alignment explanation
Indices: 35656191--35656245 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
35656181 TTTATTTATT
*
35656191 ATTTTAA-TATTATATAAA
1 ATTTTAATTATTATAAAAA
*
35656209 ATTATTATTTATTATAAAAA
1 ATT-TTAATTATTATAAAAA
*
35656229 ATTTTAATTATTTTAAA
1 ATTTTAATTATTATAAA
35656246 TTTAAAAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
18 3 0.10
19 15 0.48
20 13 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTTAATTATTATAAAAA
Found at i:35660236 original size:84 final size:84
Alignment explanation
Indices: 35660136--35660349 Score: 254
Period size: 84 Copynumber: 2.5 Consensus size: 84
35660126 TGATGAGAGG
* * * *
35660136 CTAGCAGAGTCGTTGCAGAAGCTTAGGAGGGTGGCTAATGGAGATGAAGATAGAGGTATTGGAGG
1 CTAGCGGAGTCATTGCAGAAGCTTAGGAGGGTGGCTAATGGAGATGAAGATAAAGGTATAGGAGG
*
35660201 AAATGTAGG-TGAAGGGACA
66 AAATGT-GGCTGAACGGACA
* * * *
35660220 CTGGCGGAGTCATTGCAAAAGCTGA-GAGGGTTGGCTAATGGAGATGAAGTTAAAGGTATAGGAG
1 CTAGCGGAGTCATTGCAGAAGCTTAGGAGGG-TGGCTAATGGAGATGAAGATAAAGGTATAGGAG
* *
35660284 GAATTGTGGCTGACCGGACA
65 GAAATGTGGCTGAACGGACA
* * *
35660304 CTAGCGGAGTCTTTGCAGAAG-TTAAGAAGGGTGGCAAATGGAGATG
1 CTAGCGGAGTCATTGCAGAAGCTT-AGGAGGGTGGCTAATGGAGATG
35660350 CAAATGGGAG
Statistics
Matches: 109, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
83 8 0.07
84 97 0.89
85 4 0.04
ACGTcount: A:0.31, C:0.10, G:0.38, T:0.21
Consensus pattern (84 bp):
CTAGCGGAGTCATTGCAGAAGCTTAGGAGGGTGGCTAATGGAGATGAAGATAAAGGTATAGGAGG
AAATGTGGCTGAACGGACA
Found at i:35672918 original size:19 final size:20
Alignment explanation
Indices: 35672881--35672918 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
35672871 TAAATATTTT
*
35672881 AATTTTATTAATAATTTAAG
1 AATTTTATTAATAAGTTAAG
*
35672901 AATTTT-TTAATCAGTTAA
1 AATTTTATTAATAAGTTAA
35672919 ATAGGAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTTATTAATAAGTTAAG
Found at i:35681127 original size:42 final size:42
Alignment explanation
Indices: 35681080--35681234 Score: 148
Period size: 42 Copynumber: 3.7 Consensus size: 42
35681070 ATCTTCTGGT
* * * * *
35681080 GAGTAGGAACGATCCCGTCTTCTGCAGTACCGTTCGTCAGGC
1 GAGTAGGAACGATCACGCCTTCTGTAGTACCGATCATCAGGC
* * * * * * *
35681122 GAGTAGGAACGATCCCACCTACGGTAGTATCGGTCATCTGGC
1 GAGTAGGAACGATCACGCCTTCTGTAGTACCGATCATCAGGC
* * *
35681164 GAGTAGCACCGATCACGCCTTCTGTAGTACCGATCATCAGGA
1 GAGTAGGAACGATCACGCCTTCTGTAGTACCGATCATCAGGC
* * *
35681206 GAGTAGGAATGGTCACGTCTTCTGTAGTA
1 GAGTAGGAACGATCACGCCTTCTGTAGTA
35681235 GCAGTCATCT
Statistics
Matches: 89, Mismatches: 24, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 89 1.00
ACGTcount: A:0.23, C:0.25, G:0.28, T:0.24
Consensus pattern (42 bp):
GAGTAGGAACGATCACGCCTTCTGTAGTACCGATCATCAGGC
Found at i:35684584 original size:28 final size:27
Alignment explanation
Indices: 35684514--35684581 Score: 82
Period size: 28 Copynumber: 2.5 Consensus size: 27
35684504 AATATAAATG
* * *
35684514 TTTTATTATAGTTATGGTGGTGGTATA
1 TTTTATTATGGTTATGATGGTGGTAGA
* *
35684541 TTTTATTATGGCTTATGATGTTTGTAGA
1 TTTTATTATGG-TTATGATGGTGGTAGA
35684569 TTTTATTATGGTT
1 TTTTATTATGGTT
35684582 TATAGATATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
27 12 0.34
28 23 0.66
ACGTcount: A:0.21, C:0.01, G:0.22, T:0.56
Consensus pattern (27 bp):
TTTTATTATGGTTATGATGGTGGTAGA
Found at i:35702232 original size:41 final size:41
Alignment explanation
Indices: 35702170--35702251 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
35702160 ATCTCATCAA
*
35702170 AGGAACAAAGAAGTACATGAGAGACTCAACTAAGCTTAGAC
1 AGGAACAAAGAAGTACATGAGAGACTCAACTAAGCTGAGAC
*
35702211 AGGACCAAAGAAGTACATGAGAGACTCAACTAAGCTGAGAC
1 AGGAACAAAGAAGTACATGAGAGACTCAACTAAGCTGAGAC
35702252 GAGGGAGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (41 bp):
AGGAACAAAGAAGTACATGAGAGACTCAACTAAGCTGAGAC
Found at i:35715605 original size:21 final size:21
Alignment explanation
Indices: 35715579--35715620 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35715569 ACTATAAACT
35715579 TTTTAAAA-ATTAAAAGCAAAA
1 TTTTAAAATATTAAAAG-AAAA
*
35715600 TTTTAAAATTTTAAAAGAAAA
1 TTTTAAAATATTAAAAGAAAA
35715621 CATAGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (21 bp):
TTTTAAAATATTAAAAGAAAA
Found at i:35718272 original size:23 final size:23
Alignment explanation
Indices: 35718210--35718272 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
35718200 TCATACGAAT
* *
35718210 ATAATA-TAAATAATTATTTTTG
1 ATAATATTTAATAATTATATTTG
*
35718232 TTAATATTTAA-AATTTATATTTG
1 ATAATATTTAATAA-TTATATTTG
35718255 A-ATATATTTAATAATTAT
1 ATA-ATATTTAATAATTAT
35718273 GTAGTACGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
22 8 0.24
23 23 0.70
24 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (23 bp):
ATAATATTTAATAATTATATTTG
Found at i:35722646 original size:22 final size:22
Alignment explanation
Indices: 35722574--35722646 Score: 103
Period size: 22 Copynumber: 3.3 Consensus size: 22
35722564 CACCTAAATG
*
35722574 TTTTAATAATAAATTATAAACA
1 TTTTAATAATAAATTATTAACA
*
35722596 TTTTAATAATAAATTATTAATA
1 TTTTAATAATAAATTATTAACA
35722618 TTTTAATAATAATATTATTAA-A
1 TTTTAATAATAA-ATTATTAACA
*
35722640 TTATAAT
1 TTTTAAT
35722647 TTTATAATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
22 39 0.83
23 8 0.17
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTAATAATAAATTATTAACA
Found at i:35722651 original size:16 final size:16
Alignment explanation
Indices: 35722605--35722651 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
35722595 ATTTTAATAA
35722605 TAAATTATTAATATT-T
1 TAAATTA-TAATATTAT
*
35722621 T-AATAATAATATTAT
1 TAAATTATAATATTAT
*
35722636 TAAATTATAATTTTAT
1 TAAATTATAATATTAT
35722652 AATAACATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 7 0.27
15 6 0.23
16 13 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTATAATATTAT
Found at i:35731432 original size:30 final size:30
Alignment explanation
Indices: 35731396--35731453 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
35731386 TCTCATATGG
*
35731396 CAAACTTTACTTCCTTTCTAGCAAATGAAC
1 CAAACTTTACTTCCTTCCTAGCAAATGAAC
*
35731426 CAAACTTTACTTCCTTCCTAGCAGATGA
1 CAAACTTTACTTCCTTCCTAGCAAATGA
35731454 GCCATTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.33
Consensus pattern (30 bp):
CAAACTTTACTTCCTTCCTAGCAAATGAAC
Found at i:35752995 original size:2 final size:2
Alignment explanation
Indices: 35752988--35753014 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35752978 CAATACATAC
35752988 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
35753015 GGCTTTCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35755753 original size:37 final size:38
Alignment explanation
Indices: 35755686--35755761 Score: 145
Period size: 37 Copynumber: 2.0 Consensus size: 38
35755676 GGGTATAGGG
35755686 TTTAGGATATGTAAACAAAGAATACATGTCTTGTGGCA
1 TTTAGGATATGTAAACAAAGAATACATGTCTTGTGGCA
35755724 TTTAGGATATGTAAAC-AAGAATACATGTCTTGTGGCA
1 TTTAGGATATGTAAACAAAGAATACATGTCTTGTGGCA
35755761 T
1 T
35755762 CCAGACATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 22 0.58
38 16 0.42
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.33
Consensus pattern (38 bp):
TTTAGGATATGTAAACAAAGAATACATGTCTTGTGGCA
Found at i:35757415 original size:20 final size:20
Alignment explanation
Indices: 35757390--35757479 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
35757380 TAGGTTTTAT
35757390 AAATATTAATATTTAACTTA
1 AAATATTAATATTTAACTTA
* ** *
35757410 AAATATTAAAAAGTAA--AA
1 AAATATTAATATTTAACTTA
* * *
35757428 AAAAATAAATATTTAATTTA
1 AAATATTAATATTTAACTTA
35757448 AAA-A--AA-ATTTAACTTA
1 AAATATTAATATTTAACTTA
35757464 AAATATTAATATTTAA
1 AAATATTAATATTTAA
35757480 ATTATTCAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
16 12 0.23
17 3 0.06
18 12 0.23
19 3 0.06
20 23 0.43
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (20 bp):
AAATATTAATATTTAACTTA
Found at i:35760680 original size:2 final size:2
Alignment explanation
Indices: 35760668--35760699 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
35760658 GAGTATTACT
35760668 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
35760700 GGACCAAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35773380 original size:17 final size:17
Alignment explanation
Indices: 35773358--35773391 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35773348 GGAATGTCAA
*
35773358 CGAGTGAACAAAGGGAT
1 CGAGTGAAAAAAGGGAT
35773375 CGAGTGAAAAAAGGGAT
1 CGAGTGAAAAAAGGGAT
35773392 GAGGACCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.35, T:0.12
Consensus pattern (17 bp):
CGAGTGAAAAAAGGGAT
Found at i:35780328 original size:30 final size:30
Alignment explanation
Indices: 35780294--35780363 Score: 140
Period size: 30 Copynumber: 2.3 Consensus size: 30
35780284 CAGGGCCATC
35780294 CTCAGCCTCAGGTTCAGCCATTTCCTCAAG
1 CTCAGCCTCAGGTTCAGCCATTTCCTCAAG
35780324 CTCAGCCTCAGGTTCAGCCATTTCCTCAAG
1 CTCAGCCTCAGGTTCAGCCATTTCCTCAAG
35780354 CTCAGCCTCA
1 CTCAGCCTCA
35780364 TCTGCAACAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.20, C:0.39, G:0.16, T:0.26
Consensus pattern (30 bp):
CTCAGCCTCAGGTTCAGCCATTTCCTCAAG
Found at i:35780515 original size:24 final size:24
Alignment explanation
Indices: 35780468--35780525 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
35780458 CATTCACAAG
* * **
35780468 CTCAGCCACAGGCCCAGCTTCAGC
1 CTCAGCCTCAGCCCCAGCCCCAGC
35780492 CTCAGCCTCAGCCCCAGCCCCAGC
1 CTCAGCCTCAGCCCCAGCCCCAGC
* *
35780516 CGCATCCTCA
1 CTCAGCCTCA
35780526 ACAAAGCCAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.19, C:0.52, G:0.17, T:0.12
Consensus pattern (24 bp):
CTCAGCCTCAGCCCCAGCCCCAGC
Found at i:35793486 original size:15 final size:15
Alignment explanation
Indices: 35793457--35793485 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
35793447 TTATGAGCAA
35793457 AATCTATTGATTTTT
1 AATCTATTGATTTTT
35793472 AATCT-TTGATTTTT
1 AATCTATTGATTTTT
35793486 TTATAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.24, C:0.07, G:0.07, T:0.62
Consensus pattern (15 bp):
AATCTATTGATTTTT
Found at i:35803040 original size:6 final size:6
Alignment explanation
Indices: 35803029--35803053 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
35803019 GATCCAAGAT
35803029 TTCTCC TTCTCC TTCTCC TTCTCC T
1 TTCTCC TTCTCC TTCTCC TTCTCC T
35803054 CCTTCTCTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCTCC
Found at i:35819030 original size:21 final size:21
Alignment explanation
Indices: 35819006--35819049 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35818996 GAAGATTAGG
35819006 GCGATCGGGCATTTTCTGATT
1 GCGATCGGGCATTTTCTGATT
35819027 GCGATCGGGCATTTTCTGATT
1 GCGATCGGGCATTTTCTGATT
35819048 GC
1 GC
35819050 TCGATGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.14, C:0.20, G:0.30, T:0.36
Consensus pattern (21 bp):
GCGATCGGGCATTTTCTGATT
Found at i:35820516 original size:14 final size:15
Alignment explanation
Indices: 35820497--35820527 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
35820487 CCTTTCAAAA
35820497 TTTATTAT-TATTTT
1 TTTATTATATATTTT
35820511 TTTATTATATATTTT
1 TTTATTATATATTTT
35820526 TT
1 TT
35820528 ATACTCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTATATATTTT
Found at i:35820844 original size:17 final size:16
Alignment explanation
Indices: 35820824--35820855 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
35820814 TTCTTCTTTT
35820824 TATTTATATTATTTAAC
1 TATTTATA-TATTTAAC
35820841 TATTTATATATTTAA
1 TATTTATATATTTAA
35820856 TCATTATGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTTATATATTTAAC
Found at i:35821978 original size:21 final size:21
Alignment explanation
Indices: 35821920--35821980 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 21
35821910 TAATTAAAAA
35821920 ATAATTAATAAAATAATTTTATT
1 ATAA-TAATAAAA-AATTTTATT
* *
35821943 ATTATATATATAAAA-TTTATAT
1 ATAATA-ATAAAAAATTTTAT-T
35821965 ATAATAATAAAAAATT
1 ATAATAATAAAAAATT
35821981 AAAAAATAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
21 12 0.39
22 11 0.35
23 8 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
ATAATAATAAAAAATTTTATT
Found at i:35823001 original size:24 final size:25
Alignment explanation
Indices: 35822974--35823023 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
35822964 ACTGATCGAA
* * *
35822974 TTTTTTCTATTTGATTGA-TTTGAT
1 TTTTTTATATTTAATTAATTTTGAT
35822998 TTTTTTATATTTAATTAATTTTGAT
1 TTTTTTATATTTAATTAATTTTGAT
35823023 T
1 T
35823024 AATATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.68
Consensus pattern (25 bp):
TTTTTTATATTTAATTAATTTTGAT
Found at i:35823459 original size:362 final size:361
Alignment explanation
Indices: 35822743--35823462 Score: 1235
Period size: 361 Copynumber: 2.0 Consensus size: 361
35822733 TTTATTAATA
*
35822743 AAATATAAAATATTTAAAATTTTGTTGATATAAGGATTCGAAGTTGTATGTAGATGGAAAGTAAA
1 AAATATAAAATATTTAAAATTTTGTTGATATAAGAATTCGAAGTTGTATGTAGATGGAAAGTAAA
* *
35822808 CCAAATCTTTGCCAAGTATGAGCGAGGAAACAAATGTACGTTTTTTCTATATTTAGATTTCTTGT
66 CCAAACCTTTGCCAAATATGAGCGAGGAAACAAATGTACGTTTTTTCTATATTTAGATTTCTTGT
*
35822873 ATATTTTATAATTATGGATGAAATTTATAAATTTTAATATTATAATTTGTAAAAAAAGTGATAAA
131 ATATTTTATAATTATAGATGAAATTTATAAATTTTAATATTATAATTTGTAAAAAAAGTGATAAA
* *
35822938 ATTTTGATTCATTGATCTAAAATTGAACTGATCGAATTTTTTCTATTTGATTGATTTGATTTTTT
196 ATTTTGATTCATTGATCTAAAATTGAACCGATCGAATTTTTTCTATTTGATTGATTTAATTTTTT
*
35823003 TATATTTAATTAATTTTGATTAATATTTTAAAAATATTTAATTAATTTAGTCTTTAAATATAACA
261 TATATTTAATTAATTTTAATTAATATTTTAAAAATATTTAATTAATTTAGTCTTTAAATATAACA
35823068 AATCATCCAATTTACTCATTTACTCACCCATTTAGT
326 AATCATCCAATTTACTCATTTACTCACCCATTTAGT
*
35823104 AAATATAAAATGTTTAAAATTTTGTTGATATAAGAATTCGAAGTTGTATGTAGATGGAAAGTAAA
1 AAATATAAAATATTTAAAATTTTGTTGATATAAGAATTCGAAGTTGTATGTAGATGGAAAGTAAA
* * * * *
35823169 CCAAACCTTTTGCCAAATGTGAGTGAGGAAACAAATGTATGTTTTTTTTATATTTAGATTTTTTG
66 CCAAACC-TTTGCCAAATATGAGCGAGGAAACAAATGTACGTTTTTTCTATATTTAGATTTCTTG
* *
35823234 TATATTTTATAATTATAGATGAAGTTTATAAATTTTACTATTATAATTTGT-AAAAAAGTGATAA
130 TATATTTTATAATTATAGATGAAATTTATAAATTTTAATATTATAATTTGTAAAAAAAGTGATAA
* * * *
35823298 AATTTTGATTCATTGGTCTAAAATTGAACCGATCGAGTTTTTTTTGTTTGATTGATTTAATTTTT
195 AATTTTGATTCATTGATCTAAAATTGAACCGATCGAATTTTTTCTATTTGATTGATTTAATTTTT
*
35823363 TTATATTTAATTAATTTTAATTAATATTTTGAAATATATTTAATTAATTTAGTCTTTAAATATAA
260 TTATATTTAATTAATTTTAATTAATATTTT-AAAAATATTTAATTAATTTAGTCTTTAAATATAA
35823428 CAAATCATCCAATTTACTCATTTACTCACCCATTT
324 CAAATCATCCAATTTACTCATTTACTCACCCATTT
35823463 TAGAAGGTGG
Statistics
Matches: 337, Mismatches: 20, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
361 170 0.50
362 167 0.50
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.44
Consensus pattern (361 bp):
AAATATAAAATATTTAAAATTTTGTTGATATAAGAATTCGAAGTTGTATGTAGATGGAAAGTAAA
CCAAACCTTTGCCAAATATGAGCGAGGAAACAAATGTACGTTTTTTCTATATTTAGATTTCTTGT
ATATTTTATAATTATAGATGAAATTTATAAATTTTAATATTATAATTTGTAAAAAAAGTGATAAA
ATTTTGATTCATTGATCTAAAATTGAACCGATCGAATTTTTTCTATTTGATTGATTTAATTTTTT
TATATTTAATTAATTTTAATTAATATTTTAAAAATATTTAATTAATTTAGTCTTTAAATATAACA
AATCATCCAATTTACTCATTTACTCACCCATTTAGT
Found at i:35830449 original size:38 final size:40
Alignment explanation
Indices: 35830360--35830447 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 40
35830350 ATTATTATTA
* *
35830360 TTTAATTTTT-ATTTTATATTTTATAATTATAAATAAAAT
1 TTTAATTTTTAATATTATAATTTATAATTATAAATAAAAT
*
35830399 TTATAAAATTTTAATATTATAATTTAT-A-TA-AAATAAAAT
1 TT-T-AATTTTTAATATTATAATTTATAATTATAAATAAAAT
35830438 TTTAATTTTT
1 TTTAATTTTT
35830448 TATCCAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
37 6 0.14
38 1 0.02
39 13 0.31
40 3 0.07
41 7 0.17
42 12 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (40 bp):
TTTAATTTTTAATATTATAATTTATAATTATAAATAAAAT
Found at i:35830839 original size:14 final size:15
Alignment explanation
Indices: 35830804--35830834 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35830794 CAAAAATTAT
35830804 AACTTATAAAAAAAA
1 AACTTATAAAAAAAA
35830819 AACTTATAAAAAAAA
1 AACTTATAAAAAAAA
35830834 A
1 A
35830835 TTTATCAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.19
Consensus pattern (15 bp):
AACTTATAAAAAAAA
Found at i:35836099 original size:2 final size:2
Alignment explanation
Indices: 35836092--35836132 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35836082 ACGTTATTAA
35836092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35836133 ATTTCAAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35840693 original size:2 final size:2
Alignment explanation
Indices: 35840686--35840720 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
35840676 AAAAATATGG
*
35840686 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
35840721 TTATCAAGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35841991 original size:142 final size:139
Alignment explanation
Indices: 35841738--35842017 Score: 416
Period size: 142 Copynumber: 2.0 Consensus size: 139
35841728 TATTGATATG
* * * *
35841738 ATTTGACTAAATTAATGTAGTGTTGATCGAGTTAATATGACATTTTTTGTTGATGTGAAAAAGTA
1 ATTTGACTAAATTAATGTAATGTTGATCAAGTTAATATGACATTTTTTATTGATGTGAAAAACTA
35841803 AACTAAAAAGATTCTAGCTCAATGATACAATTACAAAAATACCATACCACACCTCATCATCTCAA
66 AACTAAAAAGATTCTAGCTCAATGATACAATTACAAAAATACCATACCACACCTCATCATCTCAA
*
35841868 TTATATAAA
131 CTATATAAA
* *
35841877 ATTTGACTAAATTAATGTAATGTTTTAGTCAAGTTAATATGACATTTTTCTATTGATGTGACAAA
1 ATTTGACTAAATTAATGTAATG-TTGA-TCAAGTTAATATGACATTTTT-TATTGATGTGAAAAA
** * * * *
35841942 CTAAACTATCAAGATTCTAGCTTAATGATACAATTGCAAAAATATCATACCACATCTCATCATCT
63 CTAAACTAAAAAGATTCTAGCTCAATGATACAATTACAAAAATACCATACCACACCTCATCATCT
35842007 CAACTATATAA
128 CAACTATATAA
35842018 TTTCCAAGTT
Statistics
Matches: 125, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
139 21 0.17
140 3 0.02
141 20 0.16
142 81 0.65
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (139 bp):
ATTTGACTAAATTAATGTAATGTTGATCAAGTTAATATGACATTTTTTATTGATGTGAAAAACTA
AACTAAAAAGATTCTAGCTCAATGATACAATTACAAAAATACCATACCACACCTCATCATCTCAA
CTATATAAA
Found at i:35842297 original size:455 final size:454
Alignment explanation
Indices: 35841612--35842501 Score: 1591
Period size: 455 Copynumber: 2.0 Consensus size: 454
35841602 ACGTTATTCA
* *
35841612 ATATATATATATTTCAAATTATAAATTTAGTCTTATGTTTTATGTAATTGTCGTTGAATTTTATC
1 ATATATATATATTTCAAATTATAAATTTAGTCTTATATTTTATGTAAGTGTCGTTGAATTTTATC
35841677 TTTATATAATAATTTATATTTCTAATAACGTAAAAATTCTTCTATTAAAAGTATTGATATGATTT
66 TTTATATAATAATTTATATTTCTAATAACGTAAAAATTCTTCTATTAAAAGTATTGATATGATTT
* * *
35841742 GACTAAATTAATGTAGTGTTGATCGAGTTAATATGACATTTTTTGTTGATGTGAAAAAGTAAACT
131 GACTAAATTAATGCAGTGTTGATCAAGTTAATATGACATTTTTCGTTGATGTGAAAAAGTAAACT
*
35841807 AAAAAGATTCTAGCTCAATGATACAATTACAAAAATACCATACCACACCTCATCATCTCAATTAT
196 AAAAAGATTCTAGCTCAATGATACAATTACAAAAATAACATACCACACCTCATCATCTCAATTAT
*
35841872 ATAAAATTTGACTAAATTAATGTAATGTTTTAGTCAAGTTAATATGACATTTTTCTATTGATGTG
261 ATAAAATTTGACTAAATTAATGTAATGTTTTAATCAAGTTAATATGACATTTTTCTATTGATGTG
*
35841937 ACAAACTAAACTATCAAGATTCTAGCTTAATGATACAATTGCAAAAATATCATACCACATCTCAT
326 ACAAACTAAACTATCAAGATTCTAGCTCAATGATACAATTGCAAAAATATCATACCACATCTCAT
35842002 CATCTCAACTATATAATTTCCAAGTTTAAAATAATCTCAATTCTATGAACGTTATTAAATATAT
391 CATCTCAACTATATAATTTCCAAGTTTAAAATAATCTCAATTCTATGAACGTTATTAAATATAT
*
35842066 ATATATATATATTTCAAATTATAAATTTAGTCTTATATTTTATTTAAGTGTCGTTGAATTTTATC
1 ATATATATATATTTCAAATTATAAATTTAGTCTTATATTTTATGTAAGTGTCGTTGAATTTTATC
*
35842131 TTTATATAATAATTTATATTTCTAATAACGTAAAGATTCTTCTATTAAAAAGTATTGATATGATT
66 TTTATATAATAATTTATATTTCTAATAACGTAAAAATTCTTCTATT-AAAAGTATTGATATGATT
* *
35842196 TGACTAAATTAATGCAGTGTTGATCAAGTTAATATGACATTTTTCGTTGATGTGATAAATTAAAC
130 TGACTAAATTAATGCAGTGTTGATCAAGTTAATATGACATTTTTCGTTGATGTGAAAAAGTAAAC
* * *
35842261 TAACAAGATTCTAGCTCAATGATACAATTGCAAAAATAACATACCACATCTCATCATCTCAATTA
195 TAAAAAGATTCTAGCTCAATGATACAATTACAAAAATAACATACCACACCTCATCATCTCAATTA
* * * *
35842326 TATAAAATTTGACTAAATTAATGTAGTGTTTTAATCAAGTTTATATGACATTTTTTTGTTGATGT
260 TATAAAATTTGACTAAATTAATGTAATGTTTTAATCAAGTTAATATGACATTTTTCTATTGATGT
35842391 GACAAACTAAACTATCAAGATTCTAGCTCAATGATACAATTGCAAAAATATCATACCACATCTCA
325 GACAAACTAAACTATCAAGATTCTAGCTCAATGATACAATTGCAAAAATATCATACCACATCTCA
*
35842456 TCATCTCAACTATATAATTTCTAAGTTTAAAATAATCTCAATTCTA
390 TCATCTCAACTATATAATTTCCAAGTTTAAAATAATCTCAATTCTA
35842502 ACTATTTAAT
Statistics
Matches: 415, Mismatches: 20, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
454 107 0.26
455 308 0.74
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (454 bp):
ATATATATATATTTCAAATTATAAATTTAGTCTTATATTTTATGTAAGTGTCGTTGAATTTTATC
TTTATATAATAATTTATATTTCTAATAACGTAAAAATTCTTCTATTAAAAGTATTGATATGATTT
GACTAAATTAATGCAGTGTTGATCAAGTTAATATGACATTTTTCGTTGATGTGAAAAAGTAAACT
AAAAAGATTCTAGCTCAATGATACAATTACAAAAATAACATACCACACCTCATCATCTCAATTAT
ATAAAATTTGACTAAATTAATGTAATGTTTTAATCAAGTTAATATGACATTTTTCTATTGATGTG
ACAAACTAAACTATCAAGATTCTAGCTCAATGATACAATTGCAAAAATATCATACCACATCTCAT
CATCTCAACTATATAATTTCCAAGTTTAAAATAATCTCAATTCTATGAACGTTATTAAATATAT
Found at i:35842410 original size:142 final size:139
Alignment explanation
Indices: 35842193--35842472 Score: 452
Period size: 142 Copynumber: 2.0 Consensus size: 139
35842183 TATTGATATG
* * *
35842193 ATTTGACTAAATTAATGCAGTGTTGATCAAGTTAATATGACATTTTTCGTTGATGTGATAAATTA
1 ATTTGACTAAATTAATGCAGTGTTAATCAAGTTAATATGACATTTTTCGTTGATGTGACAAACTA
35842258 AACTAACAAGATTCTAGCTCAATGATACAATTGCAAAAATAACATACCACATCTCATCATCTCAA
66 AACTAACAAGATTCTAGCTCAATGATACAATTGCAAAAATAACATACCACATCTCATCATCTCAA
*
35842323 TTATATAAA
131 CTATATAAA
* * *
35842332 ATTTGACTAAATTAATGTAGTGTTTTAATCAAGTTTATATGACATTTTTTTGTTGATGTGACAAA
1 ATTTGACTAAATTAATGCAGTG--TTAATCAAGTTAATATGACA-TTTTTCGTTGATGTGACAAA
* *
35842397 CTAAACTATCAAGATTCTAGCTCAATGATACAATTGCAAAAATATCATACCACATCTCATCATCT
63 CTAAACTAACAAGATTCTAGCTCAATGATACAATTGCAAAAATAACATACCACATCTCATCATCT
35842462 CAACTATATAA
128 CAACTATATAA
35842473 TTTCTAAGTT
Statistics
Matches: 129, Mismatches: 9, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
139 21 0.16
141 18 0.14
142 90 0.70
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (139 bp):
ATTTGACTAAATTAATGCAGTGTTAATCAAGTTAATATGACATTTTTCGTTGATGTGACAAACTA
AACTAACAAGATTCTAGCTCAATGATACAATTGCAAAAATAACATACCACATCTCATCATCTCAA
CTATATAAA
Found at i:35842995 original size:80 final size:80
Alignment explanation
Indices: 35842862--35843022 Score: 295
Period size: 80 Copynumber: 2.0 Consensus size: 80
35842852 CTTTTTCTTC
35842862 TCTTTCTTGGCTTTAGTTGCAACATTTTCTTGTGTTGAGTATAGAATATTGAAACAAAAATATAT
1 TCTTTCTTGGCTTTAGTTGCAACATTTTCTTGTGTTGAGTATAGAATATTGAAACAAAAATATAT
35842927 AAAGTGAGTATAGAA
66 AAAGTGAGTATAGAA
* * *
35842942 TCTTTCTTGGTTTTAGTTGCAACATTTTCTTTTGTTGAGTATAGAATATTGAAACAAATATATAT
1 TCTTTCTTGGCTTTAGTTGCAACATTTTCTTGTGTTGAGTATAGAATATTGAAACAAAAATATAT
35843007 AAAGTGAGTATAGAA
66 AAAGTGAGTATAGAA
35843022 T
1 T
35843023 ATTGAAAAAA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.41
Consensus pattern (80 bp):
TCTTTCTTGGCTTTAGTTGCAACATTTTCTTGTGTTGAGTATAGAATATTGAAACAAAAATATAT
AAAGTGAGTATAGAA
Found at i:35848624 original size:2 final size:2
Alignment explanation
Indices: 35848617--35848647 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35848607 TGTAATATTA
35848617 AT AT AT AT -T 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
35848648 CACTTCTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:35851519 original size:2 final size:2
Alignment explanation
Indices: 35851512--35851539 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35851502 CCCATTAAAC
35851512 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
35851540 TAAATTATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35853146 original size:35 final size:35
Alignment explanation
Indices: 35853119--35853374 Score: 277
Period size: 35 Copynumber: 7.3 Consensus size: 35
35853109 TTAACTGTTT
35853119 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * * *
35853154 AATTTAATTAATTAAGCCCAACAATTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
35853189 AATTTTAATCAACTAGGCCTAATGACTTAATTAAAC
1 AA-TTTAATCAATTAGGCCCAATAACTTAATTAAAC
* ****
35853225 AAATTCAATCAATTAGGCCCAATAACTTAATTGTTT
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
* * *
35853261 AATTTAATTAATTAGGGCCAATGACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
*
35853296 AATTTAATCAATTAGGCCCAATGA-TTCAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTT-AATTAAAC
* * *
35853331 AATTTAGTTAATTAGG--C-ACAACTTAATTAAAC
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
35853363 AATTTTAATCAA
1 AA-TTTAATCAA
35853375 GTGCTTGAGA
Statistics
Matches: 181, Mismatches: 35, Indels: 12
0.79 0.15 0.05
Matches are distributed among these distances:
32 12 0.07
33 10 0.06
34 2 0.01
35 104 0.57
36 51 0.28
37 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (35 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAAC
Found at i:35853246 original size:107 final size:105
Alignment explanation
Indices: 35853119--35853367 Score: 308
Period size: 107 Copynumber: 2.4 Consensus size: 105
35853109 TTAACTGTTT
*
35853119 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAATTTAAT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
*
35853184 TAAACAATTTTAATCAACTAGGCCTAATGACTT-AATTAAAC
66 TAAACAA-TTTAATCAACTAGGCCCAATGA-TTCAATTAAAC
* **** * * **
35853225 AAATTCAATCAATTAGGCCCAATAACTTAATTGTTTAATTTAATTAATTAGGGCCAATGACTTAA
1 -AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAA
*
35853290 TTAAACAATTTAATCAATTAGGCCCAATGATTCAATTAAAC
65 TTAAACAATTTAATCAACTAGGCCCAATGATTCAATTAAAC
* * *
35853331 AATTTAGTTAATTAGG--C-ACAACTTAATTAAACAATTT
1 AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTT
35853368 TAATCAAGTG
Statistics
Matches: 121, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
102 15 0.12
103 1 0.01
105 15 0.12
106 28 0.23
107 62 0.51
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (105 bp):
AATTTAATCAATTAGGCCCAATAACTTAATTAAACAATTTAATTAATTAAGCCCAACAACTTAAT
TAAACAATTTAATCAACTAGGCCCAATGATTCAATTAAAC
Found at i:35872537 original size:30 final size:31
Alignment explanation
Indices: 35872501--35872571 Score: 108
Period size: 31 Copynumber: 2.3 Consensus size: 31
35872491 ACATTTAATG
35872501 AAGTTTTTATA-TTTTTATTTTAAATCAAAT
1 AAGTTTTTATATTTTTTATTTTAAATCAAAT
* *
35872531 AAGTTTTTATATTTTTTATTTTGAGTCAAAT
1 AAGTTTTTATATTTTTTATTTTAAATCAAAT
*
35872562 AAATTTTTAT
1 AAGTTTTTAT
35872572 GATTAATGAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
30 11 0.30
31 26 0.70
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.58
Consensus pattern (31 bp):
AAGTTTTTATATTTTTTATTTTAAATCAAAT
Found at i:35872836 original size:29 final size:29
Alignment explanation
Indices: 35872804--35872860 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
35872794 TTATTTGATT
**
35872804 CAAAATAAATGAATAAAAACTTAATTAAA
1 CAAAATAAAAAAATAAAAACTTAATTAAA
* *
35872833 CAAAATAAAAAAATAAAAATTTATTTAA
1 CAAAATAAAAAAATAAAAACTTAATTAA
35872861 TTTTTTAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (29 bp):
CAAAATAAAAAAATAAAAACTTAATTAAA
Found at i:35873634 original size:30 final size:31
Alignment explanation
Indices: 35873598--35873655 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
35873588 CCTGTTACAC
35873598 ACATCAAATCA-ACCCCATTTGTGGGCATAA
1 ACATCAAATCAGACCCCATTTGTGGGCATAA
35873628 ACATCAAATCAGACCCCATTTGTGGGCA
1 ACATCAAATCAGACCCCATTTGTGGGCA
35873656 ATTGGTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (31 bp):
ACATCAAATCAGACCCCATTTGTGGGCATAA
Found at i:35876913 original size:13 final size:13
Alignment explanation
Indices: 35876895--35876919 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35876885 TACAAGATAA
35876895 TTAGAGAGAGAAT
1 TTAGAGAGAGAAT
35876908 TTAGAGAGAGAA
1 TTAGAGAGAGAA
35876920 GCTCTCAAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (13 bp):
TTAGAGAGAGAAT
Found at i:35877176 original size:29 final size:29
Alignment explanation
Indices: 35877138--35877207 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
35877128 AGAAAAAAGG
*
35877138 TGTACAAGAATAGGTACAAGAGAATAAGT
1 TGTACAAGAATAGGTACAAGAGAATAAGC
* *
35877167 TGTACGAGAATAGGTATAAGAGAATAAGC
1 TGTACAAGAATAGGTACAAGAGAATAAGC
*
35877196 TGTACATGAATA
1 TGTACAAGAATA
35877208 AGTATACGAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.23
Consensus pattern (29 bp):
TGTACAAGAATAGGTACAAGAGAATAAGC
Found at i:35877177 original size:15 final size:14
Alignment explanation
Indices: 35877157--35877219 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
35877147 ATAGGTACAA
*
35877157 GAGAATAAGTTGTAC
1 GAGAATAAG-TATAC
* *
35877172 GAGAATAGGTATAA
1 GAGAATAAGTATAC
*
35877186 GAGAATAAGCTGTAC
1 GAGAATAAG-TATAC
35877201 -ATGAATAAGTATAC
1 GA-GAATAAGTATAC
35877215 GAGAA
1 GAGAA
35877220 CAAGGCAAGA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
14 19 0.50
15 19 0.50
ACGTcount: A:0.46, C:0.06, G:0.25, T:0.22
Consensus pattern (14 bp):
GAGAATAAGTATAC
Found at i:35877212 original size:29 final size:28
Alignment explanation
Indices: 35877138--35877219 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 28
35877128 AGAAAAAAGG
* *
35877138 TGTACAAGAATAGGTACAAGAGAATAAGT
1 TGTAC-AGAATAGGTATAAGAGAATAAGC
35877167 TGTACGAGAATAGGTATAAGAGAATAAGC
1 TGTAC-AGAATAGGTATAAGAGAATAAGC
* *
35877196 TGTACATGAATAAGTATACGAGAA
1 TGTACA-GAATAGGTATAAGAGAA
35877220 CAAGGCAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 1 0.02
29 46 0.98
ACGTcount: A:0.46, C:0.07, G:0.24, T:0.22
Consensus pattern (28 bp):
TGTACAGAATAGGTATAAGAGAATAAGC
Found at i:35877516 original size:26 final size:26
Alignment explanation
Indices: 35877487--35877561 Score: 141
Period size: 26 Copynumber: 2.9 Consensus size: 26
35877477 AAGTAATACT
35877487 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
35877513 TGAAGTAGCGCTTCACTTGTTCTGCG
1 TGAAGTAGCGCTTCACTTGTTCTGCG
*
35877539 TGAAGTAACGCTTCACTTGTTCT
1 TGAAGTAGCGCTTCACTTGTTCT
35877562 AGTTATTCTG
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (26 bp):
TGAAGTAGCGCTTCACTTGTTCTGCG
Found at i:35877578 original size:35 final size:35
Alignment explanation
Indices: 35877532--35877605 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
35877522 GCTTCACTTG
*
35877532 TTCTGCGTGAAGTAACGCTTCACTTGTTCTAGTTA
1 TTCTGCGTGAAGTAACACTTCACTTGTTCTAGTTA
* *
35877567 TTCTGCGTGAAGTAACACTTCACTTGTTCTGGTTG
1 TTCTGCGTGAAGTAACACTTCACTTGTTCTAGTTA
35877602 TTCT
1 TTCT
35877606 CTATATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (35 bp):
TTCTGCGTGAAGTAACACTTCACTTGTTCTAGTTA
Found at i:35908726 original size:20 final size:20
Alignment explanation
Indices: 35908691--35908728 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35908681 TATGTTTTTT
**
35908691 AAATACCATAGTTGATACTA
1 AAATACCATAAATGATACTA
35908711 AAATACCATAAATGATAC
1 AAATACCATAAATGATAC
35908729 CATTTAGATA
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:0.50, C:0.16, G:0.08, T:0.26
Consensus pattern (20 bp):
AAATACCATAAATGATACTA
Found at i:35912229 original size:23 final size:23
Alignment explanation
Indices: 35912195--35912256 Score: 60
Period size: 23 Copynumber: 2.8 Consensus size: 23
35912185 TAGGGCATTC
35912195 AAATATGT-ATATTAATAATTA-AA
1 AAATAT-TAATATTAA-AATTACAA
*
35912218 AAATATTAATATTTAAATTACAA
1 AAATATTAATATTAAAATTACAA
*
35912241 AAA-A-TAATATTTAAAT
1 AAATATTAATATTAAAAT
35912257 GTTAATATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
21 12 0.33
22 7 0.19
23 17 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATATTAATATTAAAATTACAA
Found at i:35912250 original size:21 final size:22
Alignment explanation
Indices: 35912211--35912256 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 22
35912201 GTATATTAAT
35912211 AATTAAAAAATATTAATATTTA
1 AATTAAAAAATATTAATATTTA
35912233 AATTACAAAAA-A-TAATATTTA
1 AATTA-AAAAATATTAATATTTA
35912254 AAT
1 AAT
35912257 GTTAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 12 0.52
22 6 0.26
23 5 0.22
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
AATTAAAAAATATTAATATTTA
Found at i:35920258 original size:17 final size:17
Alignment explanation
Indices: 35920236--35920269 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
35920226 ATACTTAATC
35920236 ATTTA-TTAATTATAAAA
1 ATTTATTTAATT-TAAAA
35920253 ATTTATTTAATTTAAAA
1 ATTTATTTAATTTAAAA
35920270 TTAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
ATTTATTTAATTTAAAA
Found at i:35921113 original size:2 final size:2
Alignment explanation
Indices: 35921106--35921135 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35921096 TTGCAGGTTT
35921106 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
35921136 AATGGCGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:35926151 original size:20 final size:20
Alignment explanation
Indices: 35926106--35926159 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 20
35926096 TATTTCAAAT
35926106 ATAAAATATATTATGAATTA
1 ATAAAATATATTATGAATTA
*
35926126 AAAAAATAT-TTATCG-ATTA
1 ATAAAATATATTAT-GAATTA
*
35926145 AGTAAAATATCTTAT
1 A-TAAAATATATTAT
35926160 ATCATTTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 9 0.31
20 16 0.55
21 4 0.14
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.39
Consensus pattern (20 bp):
ATAAAATATATTATGAATTA
Found at i:35928070 original size:3 final size:3
Alignment explanation
Indices: 35928062--35928099 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
35928052 GTGGTAAGCT
35928062 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35928100 TTGTTTTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:35933846 original size:21 final size:21
Alignment explanation
Indices: 35933797--35933838 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
35933787 ATAGGTATTT
*
35933797 ACCACCAATTCAAGGTCATCC
1 ACCACCTATTCAAGGTCATCC
35933818 ACCACCTATTCACAGG-CATCC
1 ACCACCTATTCA-AGGTCATCC
35933839 TCCTCCTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.31, C:0.40, G:0.10, T:0.19
Consensus pattern (21 bp):
ACCACCTATTCAAGGTCATCC
Found at i:35934769 original size:3 final size:3
Alignment explanation
Indices: 35934763--35934787 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
35934753 AAAAAATATA
35934763 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
35934788 TAAATAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35935073 original size:96 final size:96
Alignment explanation
Indices: 35934904--35935493 Score: 849
Period size: 96 Copynumber: 6.1 Consensus size: 96
35934894 CTCCGCCCCT
* * * * *
35934904 GGTCATCCACCACCTAGGTAATACCTGCCACCCACTCAAGGCTACTCGCCACCTCAAAAGCATCC
1 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
* *
35934969 ACCACCATCTAGATACCTTCCTCCCACTTAA
66 ACCACCATCTAGATACCCTCCTCCCACTCAA
* ** *
35935000 GGTCATCCACCACCAAGGTAATACTTGCCACCCACTCAAGGCTACTCGCCACCTCAAAAGTATCC
1 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
* * *
35935065 ATCGCCATCTAAATACCCTCCTCCCACTCAA
66 ACCACCATCTAGATACCCTCCTCCCACTCAA
35935096 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
1 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
* * *
35935161 ATCGCCATCTAAATACCCTCCTCCCACTCAA
66 ACCACCATCTAGATACCCTCCTCCCACTCAA
35935192 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
1 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
* * *
35935257 ACCGCCATCTAGATACCCTCATCCCACTGAA
66 ACCACCATCTAGATACCCTCCTCCCACTCAA
* ** * * *
35935288 GTTCATCCAATACCAAGGCAATACTCGCCACCTACTCAAGGCCACTCGCCACCTCAAAGGTATCC
1 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
* *
35935353 ACCACCATCTAGATACCCT-CTATCTACTCAA
66 ACCACCATCTAGATACCCTCCT-CCCACTCAA
* * * *
35935384 GGTCATCCAACACCAAGGCAATACTCGCCACCTACTCAAGGCCACTCGCCACCTCAAAGGTATCC
1 GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
* * *
35935449 ACCACCATTTAGATACCCTCCACCTACTCAA
66 ACCACCATCTAGATACCCTCCTCCCACTCAA
35935480 GGTCATCCACCACC
1 GGTCATCCACCACC
35935494 CACTCAAGGC
Statistics
Matches: 459, Mismatches: 33, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
95 1 0.00
96 457 1.00
97 1 0.00
ACGTcount: A:0.29, C:0.42, G:0.11, T:0.18
Consensus pattern (96 bp):
GGTCATCCACCACCAAGGCAATACCCGCCACCCACTCAAGGCCACTCGCCACCTCAAAAGTATCC
ACCACCATCTAGATACCCTCCTCCCACTCAA
Found at i:35935493 original size:78 final size:79
Alignment explanation
Indices: 35935411--35935787 Score: 361
Period size: 78 Copynumber: 4.8 Consensus size: 79
35935401 GCAATACTCG
* *
35935411 CCACCTACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATTTAGATACCCTCCACCTAC
1 CCACCCACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTAC
35935476 TCAAGGTC-ATCCA
66 TCAAGGTCAATCCA
* * * * *
35935489 CCACCCACTCAAGGCCACTCACCACCATC-TAGATATCCTCCACC-TACTCATGAT--CATCCAC
1 CCACCCACTCAAGGCCACTCGCCACC-TCAAAGGTATCCACCACCAT-CT-A-GATACCCTCCAC
*
35935550 C-AC-CAAGG-CAATACCCG
62 CTACTCAAGGTCAAT--CCA
* *
35935567 CCACCCACTTAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCGCCTAC
1 CCACCCACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTAC
*
35935632 TTAAGGTC-ATCCA
66 TCAAGGTCAATCCA
* * * * * * *
35935645 CCACCCACTCAAGGCCACTCACCACCATC-TAGATATCCTCCACCTACTCAAGGT--CATCCACC
1 CCACCCACTCAAGGCCACTCGCCACC-TCAAAGGTATCCACCACC-A-TCTAGATACCCTCCACC
* *
35935707 -A-TCAA-GTCAATATTCG
63 TACTCAAGGTC-A-ATCCA
*
35935723 CCACCCACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCTACCTAC
1 CCACCCACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTAC
35935788 CACTCAAGTT
Statistics
Matches: 237, Mismatches: 37, Indels: 48
0.74 0.11 0.15
Matches are distributed among these distances:
75 4 0.02
76 18 0.08
77 10 0.04
78 180 0.76
79 10 0.04
80 14 0.06
81 1 0.00
ACGTcount: A:0.28, C:0.43, G:0.10, T:0.19
Consensus pattern (79 bp):
CCACCCACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTAC
TCAAGGTCAATCCA
Found at i:35935546 original size:156 final size:156
Alignment explanation
Indices: 35935352--35935787 Score: 728
Period size: 156 Copynumber: 2.8 Consensus size: 156
35935342 CAAAGGTATC
* * * * *
35935352 CACCACCATCTAGATACCCTCTATCTACTCAAGGTCATCCAACACCAAGGCAATACTCGCCACCT
1 CACCACCATCTAGATATCCTCCACCTACTCAAGGTCATCCACCACCAAGGCAATACTCGCCACCC
*
35935417 ACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATTTAGATACCCTCCACCTACTCAAGG
66 ACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTACTCAAGG
35935482 TCATCCACCACCCACTCAAGGCCACT
131 TCATCCACCACCCACTCAAGGCCACT
* * *
35935508 CACCACCATCTAGATATCCTCCACCTACTCATGATCATCCACCACCAAGGCAATACCCGCCACCC
1 CACCACCATCTAGATATCCTCCACCTACTCAAGGTCATCCACCACCAAGGCAATACTCGCCACCC
* * *
35935573 ACTTAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCGCCTACTTAAGG
66 ACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTACTCAAGG
35935638 TCATCCACCACCCACTCAAGGCCACT
131 TCATCCACCACCCACTCAAGGCCACT
* * *
35935664 CACCACCATCTAGATATCCTCCACCTACTCAAGGTCATCCACCATCAAGTCAATATTCGCCACCC
1 CACCACCATCTAGATATCCTCCACCTACTCAAGGTCATCCACCACCAAGGCAATACTCGCCACCC
*
35935729 ACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCTACCTAC
66 ACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTAC
35935788 CACTCAAGTT
Statistics
Matches: 259, Mismatches: 21, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
156 259 1.00
ACGTcount: A:0.29, C:0.42, G:0.10, T:0.19
Consensus pattern (156 bp):
CACCACCATCTAGATATCCTCCACCTACTCAAGGTCATCCACCACCAAGGCAATACTCGCCACCC
ACTCAAGGCCACTCGCCACCTCAAAGGTATCCACCACCATCTAGATACCCTCCACCTACTCAAGG
TCATCCACCACCCACTCAAGGCCACT
Found at i:35936374 original size:19 final size:19
Alignment explanation
Indices: 35936350--35936390 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35936340 GCTTTTAAAA
*
35936350 TTTAATTTTTTGAA-TTAAT
1 TTTAATTTATT-AATTTAAT
35936369 TTTAATTTATTAATTTAAT
1 TTTAATTTATTAATTTAAT
35936388 TTT
1 TTT
35936391 CATTAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 2 0.10
19 18 0.90
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTAATTTATTAATTTAAT
Found at i:35946136 original size:19 final size:19
Alignment explanation
Indices: 35946109--35946147 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
35946099 ACAAAAACAA
*
35946109 TAATCAATATTATCAAAAT
1 TAATAAATATTATCAAAAT
35946128 TAATAAATATTATCAAAAT
1 TAATAAATATTATCAAAAT
35946147 T
1 T
35946148 TGGACTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (19 bp):
TAATAAATATTATCAAAAT
Found at i:35953333 original size:16 final size:16
Alignment explanation
Indices: 35953314--35953348 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
35953304 TAATTATTAA
* *
35953314 TTATTTTTATATTTTT
1 TTATATTTATATATTT
35953330 TTATATTTATATATTT
1 TTATATTTATATATTT
35953346 TTA
1 TTA
35953349 ATATAATAAA
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:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATATTTATATATTT
Found at i:35955184 original size:340 final size:341
Alignment explanation
Indices: 35954550--35955234 Score: 1174
Period size: 340 Copynumber: 2.0 Consensus size: 341
35954540 TGTAAGAAAA
*
35954550 GCAATATTTTAACTTTATTTATGATTCAAAGTTATATTGCTCTCAAGAAATAACTTGTTATTAAA
1 GCAATAGTTTAACTTTATTTATGATTCAAAGTTATATTGCTCTCAAGAAATAACTTGTTATTAAA
* *
35954615 AAAATATTAATCACAACAATTTGCATCTAATAATTACTAATGAACCTAATTACTCTTTGACCAAA
66 AAAATATTAATCACAACAATTTGCATCTAATAATCACTAATGAACCTAATTAATCTTTGACCAAA
* *
35954680 TATAAAAGATAACTTAATTTAGTTGTTACCTGGATGAAAAGACAAAATATCTTCTCAAATTTAAA
131 TATAAAAGATAACATAATTTAGTTGTTACCTGGATGAAAAGACAAAATATCTTCTCAAATTAAAA
*
35954745 AAATATTAAACACTACTATTAATGAAGATTTATCAAAGATTGTTGTCCTCATCTATGAAATTCTT
196 AAATATTAAACACTACTATTAATGAAGATTTATCAAAGATTGTTGTCCTCATCCATGAAATTCTT
* *
35954810 CAAAACCCACAAATTTGACTTGAAAAAATGGGCTATATAGAGTATTTATTTTTGGTCTAATTTTT
261 CAAAACCCACAAATTTGACTTGAAAAAATGGGCTATATAGAGTATTTATTTTTGGCCTAATTTTC
*
35954875 GTGGATCACCTTAAAT
326 GTGAATCACCTTAAAT
* *
35954891 GCAATAGTTTAATTTTATTTATGATTCAAAGTTATATTGCTTTCAAGAAATAACTTGTTATTAAA
1 GCAATAGTTTAACTTTATTTATGATTCAAAGTTATATTGCTCTCAAGAAATAACTTGTTATTAAA
* *
35954956 AAAATATTAATCACAAC-ATTTGCATCTAATAATCACTAATGAACTTAGTTAATCTTTGACCAAA
66 AAAATATTAATCACAACAATTTGCATCTAATAATCACTAATGAACCTAATTAATCTTTGACCAAA
**
35955020 TATAAAAGATAACATAATTTAGTTGTTATGTGGATGAAAAGACAAAATATCTTCTCAAATTAAAA
131 TATAAAAGATAACATAATTTAGTTGTTACCTGGATGAAAAGACAAAATATCTTCTCAAATTAAAA
* * * * *
35955085 AAATGTTAAACACTACTATTTATGAAGATTTATTAGAGATTGTTGTCCTCATCCATGGAATTCTT
196 AAATATTAAACACTACTATTAATGAAGATTTATCAAAGATTGTTGTCCTCATCCATGAAATTCTT
35955150 CAAAACCCACAAATTTGACTTGAAAAAATGGGCTATATAGAGTATTTATTTTTGGCCTAATTTTC
261 CAAAACCCACAAATTTGACTTGAAAAAATGGGCTATATAGAGTATTTATTTTTGGCCTAATTTTC
*
35955215 GTGAATCTCCTTAAAT
326 GTGAATCACCTTAAAT
35955231 GCAA
1 GCAA
35955235 CAAGGAAAGA
Statistics
Matches: 323, Mismatches: 21, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
340 244 0.76
341 79 0.24
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (341 bp):
GCAATAGTTTAACTTTATTTATGATTCAAAGTTATATTGCTCTCAAGAAATAACTTGTTATTAAA
AAAATATTAATCACAACAATTTGCATCTAATAATCACTAATGAACCTAATTAATCTTTGACCAAA
TATAAAAGATAACATAATTTAGTTGTTACCTGGATGAAAAGACAAAATATCTTCTCAAATTAAAA
AAATATTAAACACTACTATTAATGAAGATTTATCAAAGATTGTTGTCCTCATCCATGAAATTCTT
CAAAACCCACAAATTTGACTTGAAAAAATGGGCTATATAGAGTATTTATTTTTGGCCTAATTTTC
GTGAATCACCTTAAAT
Found at i:35960270 original size:19 final size:19
Alignment explanation
Indices: 35960233--35960271 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35960223 AATATTTTAA
*
35960233 AAAAATCTTTAAATTATTT
1 AAAAATCTTTAAATAATTT
35960252 AAAAAT-TTTAAATAAATTT
1 AAAAATCTTTAAAT-AATTT
35960271 A
1 A
35960272 TATATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
AAAAATCTTTAAATAATTT
Found at i:35960291 original size:29 final size:30
Alignment explanation
Indices: 35960259--35960315 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
35960249 TTTAAAAATT
35960259 TTAAATAAATTTATATATTTTT-ATTAAGA
1 TTAAATAAATTTATATATTTTTAATTAAGA
* * *
35960288 TTAATTAAGTTTTTATATTTTTAATTAA
1 TTAAATAAATTTATATATTTTTAATTAA
35960316 AATATTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (30 bp):
TTAAATAAATTTATATATTTTTAATTAAGA
Found at i:35968402 original size:31 final size:31
Alignment explanation
Indices: 35968362--35968420 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
35968352 TTCATTGATC
* *
35968362 AAAACTAAATATAAACATCTAAA-AATCACAT
1 AAAACTAAATAAAAAAATC-AAATAATCACAT
*
35968393 AAAATTAAATAAAAAAATCAAATAATCA
1 AAAACTAAATAAAAAAATCAAATAATCA
35968421 ATATCTACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.66, C:0.12, G:0.00, T:0.22
Consensus pattern (31 bp):
AAAACTAAATAAAAAAATCAAATAATCACAT
Found at i:35968837 original size:17 final size:16
Alignment explanation
Indices: 35968812--35968854 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
35968802 AAATTTATTT
* *
35968812 TTTAATAATATTTAAA
1 TTTATTAATATATAAA
35968828 TATTATTAATATATAAA
1 T-TTATTAATATATAAA
*
35968845 TTTTTTAATA
1 TTTATTAATA
35968855 AAATTCAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.39
17 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTATTAATATATAAA
Found at i:35971558 original size:2 final size:2
Alignment explanation
Indices: 35971553--35971601 Score: 50
Period size: 2 Copynumber: 26.0 Consensus size: 2
35971543 ATACGCTAAT
* * *
35971553 TA TA TA TA TA TA T- TA -A TA TA TA -A AA TA TA TT TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35971592 TA TA TA TA TA
1 TA TA TA TA TA
35971602 AAAAANATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35971580 original size:21 final size:21
Alignment explanation
Indices: 35971556--35971595 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35971546 CGCTAATTAT
35971556 ATATATATATTA-ATATATAAA
1 ATATAT-TATTATATATATAAA
*
35971577 ATATATTTTTATATATATA
1 ATATATTATTATATATATA
35971596 TATATAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATATTATTATATATATAAA
Found at i:35971661 original size:49 final size:52
Alignment explanation
Indices: 35971562--35971663 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 52
35971552 TTATATATAT
* * *
35971562 ATATTAATATATAAAATATATTTTTATATATATATATATAAAAAANATAATA
1 ATATAAATATATAAAATATATTTTTATATATATATATAGAAAAAAGATAATA
**
35971614 ATATAAATA-ATAAAATATATTTTTATATATAT-TA-AGAAAATGGATAATA
1 ATATAAATATATAAAATATATTTTTATATATATATATAGAAAAAAGATAATA
35971663 A
1 A
35971664 ACTTAATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
49 12 0.27
50 2 0.04
51 23 0.51
52 8 0.18
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.40
Consensus pattern (52 bp):
ATATAAATATATAAAATATATTTTTATATATATATATAGAAAAAAGATAATA
Found at i:35973770 original size:2 final size:2
Alignment explanation
Indices: 35973765--35973800 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
35973755 TCACACTAAT
35973765 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35973801 AAATATTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35974512 original size:139 final size:139
Alignment explanation
Indices: 35974261--35974535 Score: 435
Period size: 139 Copynumber: 2.0 Consensus size: 139
35974251 GCACTGGCTC
* * **
35974261 TTTACCTGTAGAGGAGAGGGACTCTTACGCTAGTTCGGGTCTACCTTGATCCTTGTATCTCTCAT
1 TTTACCCGTAGAGGAGAAGGACTCTTACAATAGTTCGGGTCTACCTTGATCCTTGTATCTCTCAT
* * * *
35974326 GGGAGCCCACATTAATGAATATTTGAGTTTGCTTTGATACCACTTGTCACAAGCCGAAACTTAAG
66 GGGAGCCCACATTAATGAATATCTGAGTTTACTTTGATACAAATTGTCACAAGCCGAAACTTAAG
35974391 CCCAACTTT
131 CCCAACTTT
*
35974400 TTTACCCGTAGAGGAGAAGGACTCTTACAATAGTTTGGGTCTACCTTGATCCTTGTATCTCTCAT
1 TTTACCCGTAGAGGAGAAGGACTCTTACAATAGTTCGGGTCTACCTTGATCCTTGTATCTCTCAT
* *
35974465 GGG-GCCCTACATTAGTGAATATCTGAGTTTACTTTGATACAAATTGTCACAAGCTGAAACTTAA
66 GGGAGCCC-ACATTAATGAATATCTGAGTTTACTTTGATACAAATTGTCACAAGCCGAAACTTAA
35974529 GCCCAAC
130 GCCCAAC
35974536 CCCATACGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
138 4 0.03
139 120 0.97
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (139 bp):
TTTACCCGTAGAGGAGAAGGACTCTTACAATAGTTCGGGTCTACCTTGATCCTTGTATCTCTCAT
GGGAGCCCACATTAATGAATATCTGAGTTTACTTTGATACAAATTGTCACAAGCCGAAACTTAAG
CCCAACTTT
Found at i:35978167 original size:29 final size:29
Alignment explanation
Indices: 35978129--35978198 Score: 104
Period size: 29 Copynumber: 2.4 Consensus size: 29
35978119 AGAAAAGAGG
*
35978129 TGTACAAGAATAGGTACAAGAGCAGAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
* *
35978158 TGTACGAGAATAGGTACAAGAGAATAAGC
1 TGTACAAGAATAGGTACAAGAGAAGAAGC
*
35978187 TGTACATGAATA
1 TGTACAAGAATA
35978199 AGTATACAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (29 bp):
TGTACAAGAATAGGTACAAGAGAAGAAGC
Found at i:35978489 original size:35 final size:35
Alignment explanation
Indices: 35978450--35978602 Score: 207
Period size: 35 Copynumber: 4.4 Consensus size: 35
35978440 GTTCTATTTA
*
35978450 TTCTAGTTATTCTGCGTTAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* * **
35978485 TTCTAGTTGTTTTGCGTGAAGTAGTGCTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
35978520 TTCTACTTATTCTACGTGAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
35978555 TTTTACTTATTCTGCGTGAAGTAGCACTTCACTTG
1 TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
* *
35978590 TTCTGGTTGTTCT
1 TTCTAGTTATTCT
35978603 CTGTACAACA
Statistics
Matches: 101, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 101 1.00
ACGTcount: A:0.18, C:0.19, G:0.19, T:0.44
Consensus pattern (35 bp):
TTCTAGTTATTCTGCGTGAAGTAGCACTTCACTTG
Found at i:35979854 original size:2 final size:2
Alignment explanation
Indices: 35979847--35979872 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35979837 TGCAGTAGTT
35979847 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
35979873 GAAAGGGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35980655 original size:35 final size:35
Alignment explanation
Indices: 35980615--35980698 Score: 96
Period size: 35 Copynumber: 2.4 Consensus size: 35
35980605 CCTCGCGATT
*
35980615 TACCGCAAGTTATTTCTATTGAAGCTCGCGGCATA
1 TACCGCAAGTTATTTCTATTAAAGCTCGCGGCATA
* * * **
35980650 TACCGCGAGCTATTTCTTTTAAAGCTCGCGGTTTA
1 TACCGCAAGTTATTTCTATTAAAGCTCGCGGCATA
* *
35980685 TGCCGTAAGTTATT
1 TACCGCAAGTTATT
35980699 ATTATTGTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (35 bp):
TACCGCAAGTTATTTCTATTAAAGCTCGCGGCATA
Done.