Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 124 of 295
Found at i:42525762 original size:7 final size:7
Alignment explanation
Indices: 42525750--42525945 Score: 86
Period size: 7 Copynumber: 29.1 Consensus size: 7
42525740 ACCTTATTTT
42525750 TATATTA
1 TATATTA
42525757 TATATTA
1 TATATTA
*
42525764 TAAAATTA
1 T-ATATTA
*
42525772 TTTTATTA
1 -TATATTA
*
42525780 TAAATTA
1 TATATTA
*
42525787 TTTA-TA
1 TATATTA
42525793 T-TATTA
1 TATATTA
*
42525799 TTTATTA
1 TATATTA
42525806 TATATTA
1 TATATTA
*
42525813 T-TTTTCA
1 TATATT-A
*
42525820 CA-AGTTA
1 TATA-TTA
42525827 T-TATTA
1 TATATTA
42525833 T-T-TTA
1 TATATTA
*
42525838 CATCA-T-
1 TAT-ATTA
42525844 TAT-TTA
1 TATATTA
42525850 TATATTA
1 TATATTA
42525857 TTATATTA
1 -TATATTA
*
42525865 TAT-GT-
1 TATATTA
42525870 T-TATTA
1 TATATTA
42525876 TATATTA
1 TATATTA
42525883 TATATTA
1 TATATTA
42525890 TATATTA
1 TATATTA
42525897 T-T-TTA
1 TATATTA
42525902 TATA-TA
1 TATATTA
*
42525908 TGCT-TT-
1 T-ATATTA
42525914 TATATTA
1 TATATTA
42525921 TATATTA
1 TATATTA
42525928 TAATTATTTA
1 T-A-TA-TTA
42525938 TATATTA
1 TATATTA
42525945 T
1 T
42525946 TAAGTCATTT
Statistics
Matches: 144, Mismatches: 18, Indels: 54
0.67 0.08 0.25
Matches are distributed among these distances:
4 1 0.01
5 13 0.09
6 30 0.21
7 71 0.49
8 21 0.15
9 4 0.03
10 4 0.03
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:42525775 original size:26 final size:25
Alignment explanation
Indices: 42525743--42525813 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
42525733 ATTTTTAACC
42525743 TTATTTTTATATTATATATTATAAAA
1 TTATTTTT-TATTATATATTATAAAA
* * *
42525769 TTA--TTTTATTATAAATTATTTATA
1 TTATTTTTTATTATATATTA-TAAAA
*
42525793 TTATTATTTATTATATATTAT
1 TTATTTTTTATTATATATTAT
42525814 TTTTCACAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
23 11 0.30
24 9 0.24
25 1 0.03
26 16 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTATTTTTTATTATATATTATAAAA
Found at i:42525780 original size:16 final size:16
Alignment explanation
Indices: 42525752--42525813 Score: 72
Period size: 16 Copynumber: 3.8 Consensus size: 16
42525742 CTTATTTTTA
42525752 TATTATATATTATAAAAT
1 TATT-TATATTAT-AAAT
42525770 TATTT-TATTATAAAT
1 TATTTATATTATAAAT
* *
42525785 TATTTATATTATTATT
1 TATTTATATTATAAAT
42525801 TATTATATATTAT
1 TATT-TATATTAT
42525814 TTTTCACAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
15 9 0.22
16 18 0.45
17 9 0.22
18 4 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTATATTATAAAT
Found at i:42525805 original size:19 final size:19
Alignment explanation
Indices: 42525743--42525967 Score: 56
Period size: 19 Copynumber: 12.0 Consensus size: 19
42525733 ATTTTTAACC
42525743 TTATT-TTTATATTA-TAT
1 TTATTATTTATATTATTAT
* * *
42525760 ATTATAAAATTATTTTATTAT
1 -TTAT-TATTTATATTATTAT
**
42525781 AAATTATTTATATTATTAT
1 TTATTATTTATATTATTAT
42525800 TTATTA--TATATTATT-T
1 TTATTATTTATATTATTAT
** *
42525816 TTCACAAGTTATTATTATT-T
1 TT-ATTATTTA-TATTATTAT
42525836 TACATCATTATTTATA-TATTA-
1 T---T-ATTATTTATATTATTAT
42525857 TTA-TA-TTATATGT-TTA-
1 TTATTATTTATAT-TATTAT
42525873 TTA-TATATTATA-TATTAT
1 TTATTAT-TTATATTATTAT
*
42525891 ATATTATTTTATATATATGCT-T
1 TTATTA-TTTATAT-TAT--TAT
*
42525913 TTA-TATTATATATTA-TAA
1 TTATTATT-TATATTATTAT
* *
42525931 TTATT-TATATATTATTAAG
1 TTATTATTTATATTATT-AT
*
42525950 TCATT-TTTATATTATTAT
1 TTATTATTTATATTATTAT
42525968 ACATTTTTAT
Statistics
Matches: 156, Mismatches: 23, Indels: 56
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.03
16 14 0.09
17 24 0.15
18 18 0.12
19 41 0.26
20 23 0.15
21 18 0.12
22 5 0.03
23 8 0.05
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATTATTTATATTATTAT
Found at i:42525874 original size:40 final size:41
Alignment explanation
Indices: 42525830--42525942 Score: 114
Period size: 40 Copynumber: 2.9 Consensus size: 41
42525820 CAAGTTATTA
*
42525830 TTATTTTACATCAT-TATTTATATATTATTATAT-TATATGT
1 TTATTATACATCATATA-TTATATATTATTATATATATATGT
* * * *
42525870 TTATTATATATTATATATTATATATTATTTTATATATATGC
1 TTATTATACATCATATATTATATATTATTATATATATATGT
*
42525911 TT-TTAT--ATTATATATTATA-ATTATT-TATATAT
1 TTATTATACATCATATATTATATATTATTATATATAT
42525943 TATTAAGTCA
Statistics
Matches: 66, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
36 7 0.11
37 6 0.09
38 13 0.20
40 30 0.45
41 10 0.15
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (41 bp):
TTATTATACATCATATATTATATATTATTATATATATATGT
Found at i:42525984 original size:14 final size:14
Alignment explanation
Indices: 42525959--42525992 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42525949 GTCATTTTTA
42525959 TATTAT-TATACAT
1 TATTATCTATACAT
*
42525972 TTTTATCTATACAT
1 TATTATCTATACAT
42525986 TATTATC
1 TATTATC
42525993 ATTAAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATCTATACAT
Found at i:42526053 original size:24 final size:24
Alignment explanation
Indices: 42526013--42526085 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
42526003 TTAAACTTGA
*
42526013 ATTATATATTTATCTTTATTTATAT
1 ATTA-ATAATTATCTTTATTTATAT
42526038 ATTAATAATTATCTTTATTTATAT
1 ATTAATAATTATCTTTATTTATAT
*
42526062 ATTAATAATTATTTTTATTTATAT
1 ATTAATAATTATCTTTATTTATAT
42526086 TCTATTATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 42 0.91
25 4 0.09
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTAATAATTATCTTTATTTATAT
Found at i:42526338 original size:26 final size:25
Alignment explanation
Indices: 42526291--42526339 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
42526281 TTATAAATAC
* * *
42526291 ATTTTTATTATATATTATATTTTAA
1 ATTTTTATTAAATATCACATTTTAA
42526316 ATTTATTATTAAATATCACATTTT
1 ATTT-TTATTAAATATCACATTTT
42526340 TATTATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTAAATATCACATTTTAA
Found at i:42530103 original size:15 final size:15
Alignment explanation
Indices: 42530067--42530116 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
42530057 CGATATCCTT
42530067 TTTGCAT-TCATGCA
1 TTTGCATCTCATGCA
42530081 TTTGCATCTCATAGCA
1 TTTGCATCTCAT-GCA
42530097 TTT-CATCAT-AT-CA
1 TTTGCATC-TCATGCA
42530110 TTTGCAT
1 TTTGCAT
42530117 TAAAAGTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
13 5 0.16
14 10 0.31
15 10 0.31
16 7 0.22
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (15 bp):
TTTGCATCTCATGCA
Found at i:42538485 original size:210 final size:209
Alignment explanation
Indices: 42538117--42538885 Score: 1086
Period size: 210 Copynumber: 3.7 Consensus size: 209
42538107 CTTCATCAGG
* * *
42538117 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCAGCGGGGAGCAGATTGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCAGATCGAAGACATAGCTG
* * * *
42538182 ATTTGGCTTTCACGTGTTTACGATAAAACAAATCTAAGATGATTTGTCGTCTCTGTATTGTTAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
* ** *
42538247 GAACAAATCGAAGTCTGGCATTTCCACTTTGATGGA-AGGCAGACACATAGCAGATCTTACCTTC
131 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGA-GCAGACACATAGCAGATCTCACCTTC
42538311 AGATGTTTACGCTGAA
195 AGATGTTTA-GCTGAA
* * *
42538327 GCAGATCTAAGATGACAGATCTTATCTCTCTATATTCGGCGGGGAGCAGATCGAAGATATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCAGATCGAAGACATAGCTG
*
42538392 GTTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
* * *
42538457 GAACAAATCAAAGTCTGGCATCTCCACTTCAATGGAGAACAGACACATAGCAGATCTCACCTTTA
131 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGACACATAGCAGATCTCACCTTCA
42538522 GATGTTTATGCTGAA
196 GATGTTTA-GCTGAA
42538537 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCAGATCGAAGACATAGCTG
1 GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCAGATCGAAGACATAGCTG
*
42538602 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGCATTGTCAGA
66 ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
* * *
42538667 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGATACACAGCAGATCTGACCTTCA
131 GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGACACATAGCAGATCTCACCTTCA
* *
42538732 GACGATTAGACTGAA
196 GATGTTTAG-CTGAA
*** * * * ** * *
42538747 GCAAGATCCAAGATGATTTAGC--ATC-CT-TGTGCTT--ACAAGGAACAAATCGAAGACATAGC
1 GC-AGATCCAAGATGACAGATCTTATCTCTCTGT-ATTCGGCGGGGAGCAGATCGAAGACATAGC
* * *
42538806 TGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGAT-AGTTTGGCATCTCTGTATTATC
64 TGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGA-TTTGTCATCTCTGTATTGTC
42538870 AGAGAACAAATCGAAG
128 AGAGAACAAATCGAAG
42538886 AAGAAGATTT
Statistics
Matches: 510, Mismatches: 44, Indels: 14
0.90 0.08 0.02
Matches are distributed among these distances:
205 1 0.00
206 94 0.18
207 3 0.01
208 4 0.01
209 4 0.01
210 388 0.76
211 16 0.03
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (209 bp):
GCAGATCCAAGATGACAGATCTTATCTCTCTGTATTCGGCGGGGAGCAGATCGAAGACATAGCTG
ATTTGGCTTTCACGTGTTTACGATGAAGCAAATCTAAGATGATTTGTCATCTCTGTATTGTCAGA
GAACAAATCGAAGTCTGGCATCTCCACTTCAATGGAGAGCAGACACATAGCAGATCTCACCTTCA
GATGTTTAGCTGAA
Found at i:42540459 original size:16 final size:16
Alignment explanation
Indices: 42540431--42540494 Score: 58
Period size: 18 Copynumber: 3.8 Consensus size: 16
42540421 CTTATTTTTA
42540431 TATTATATATTATAAAAT
1 TATT-TATATTAT-AAAT
*
42540449 TATTT-TATTATATAT
1 TATTTATATTATAAAT
*
42540464 TATTTATATTATTATTAT
1 TATTTATATTA-TA-AAT
42540482 TATTATATATTAT
1 TATT-TATATTAT
42540495 TTTTCACAAG
Statistics
Matches: 41, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
15 8 0.20
16 11 0.27
17 3 0.07
18 12 0.29
19 7 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TATTTATATTATAAAT
Found at i:42540464 original size:30 final size:30
Alignment explanation
Indices: 42540422--42540615 Score: 105
Period size: 30 Copynumber: 6.8 Consensus size: 30
42540412 ATTTTTAACC
42540422 TTATT-TT-TATATTATATATTATAAAATTA
1 TTATTATTATATATTATAT-TTATAAAATTA
**
42540451 TT-TTATTATATA-T-TATTTATATTATTA
1 TTATTATTATATATTATATTTATAAAATTA
*
42540478 TTATTATTATATATTAT-TTT-TCACAAGTTA
1 TTATTATTATATATTATATTTAT-A-AAATTA
* * * *
42540508 TTATTATTTTACATCATTATTTAT-ATATTA
1 TTATTATTATATATTA-TATTTATAAAATTA
* *
42540538 TTA-TATTATATGTT-TA-TTAT-ATATTA
1 TTATTATTATATATTATATTTATAAAATTA
* *
42540564 -TA-TATTATATATTAT-TTTATATATATGCTT
1 TTATTATTATATATTATATTTATA-AAAT--TA
*
42540594 TTA-TATTATATATTATAATTAT
1 TTATTATTATATATTATATTTAT
42540616 TTTATATATT
Statistics
Matches: 130, Mismatches: 17, Indels: 33
0.72 0.09 0.18
Matches are distributed among these distances:
25 12 0.09
26 15 0.12
27 13 0.10
28 20 0.15
29 17 0.13
30 29 0.22
31 16 0.12
32 7 0.05
33 1 0.01
ACGTcount: A:0.36, C:0.03, G:0.02, T:0.60
Consensus pattern (30 bp):
TTATTATTATATATTATATTTATAAAATTA
Found at i:42540475 original size:19 final size:19
Alignment explanation
Indices: 42540448--42540659 Score: 92
Period size: 19 Copynumber: 11.2 Consensus size: 19
42540438 TATTATAAAA
*
42540448 TTATTTTATTATATATTAT
1 TTATATTATTATATATTAT
42540467 TTATATTATTAT-TATTAT
1 TTATATTATTATATATTAT
* *
42540485 TATATATTATTTTTCACAAGTTA-
1 T-TATATTA-TTAT-A-TA-TTAT
*
42540508 TTATTATT-TTACATCATTAT
1 TTA-TATTATTATAT-ATTAT
42540528 TTATA-TATTATTATATTAT
1 TTATATTATTA-TATATTAT
* *
42540547 ATGT-TTATTATATATTA-
1 TTATATTATTATATATTAT
*
42540564 -TATATTATATATTATTTTAT
1 TTATATTAT-TA-TATATTAT
* ** *
42540584 ATATATGCTTTTATATTA-
1 TTATATTATTATATATTAT
*
42540602 -TATATTATAAT-TATT-T
1 TTATATTATTATATATTAT
42540618 TATATATTATTA-AGTCATT-T
1 T-TATATTATTATA-T-ATTAT
*
42540638 TTATATTATTATACATT-T
1 TTATATTATTATATATTAT
42540656 TTAT
1 TTAT
42540660 CTATACATTA
Statistics
Matches: 148, Mismatches: 21, Indels: 49
0.68 0.10 0.22
Matches are distributed among these distances:
16 6 0.04
17 11 0.07
18 34 0.23
19 61 0.41
20 17 0.11
21 8 0.05
22 2 0.01
23 6 0.04
24 3 0.02
ACGTcount: A:0.34, C:0.03, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATTATTATATATTAT
Found at i:42540555 original size:40 final size:41
Alignment explanation
Indices: 42540511--42540624 Score: 114
Period size: 40 Copynumber: 2.9 Consensus size: 41
42540501 CAAGTTATTA
*
42540511 TTATTTTACATCAT-TATTTATATATTATTATAT-TATATGT
1 TTATTATACATCATATA-TTATATATTATTATATATATATGT
* * * *
42540551 TTATTATATATTATATATTATATATTATTTTATATATATGC
1 TTATTATACATCATATATTATATATTATTATATATATATGT
* *
42540592 TT-TTAT--ATTATATATTATA-ATTATTTTATATAT
1 TTATTATACATCATATATTATATATTATTATATATAT
42540625 TATTAAGTCA
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
37 14 0.21
38 13 0.19
40 30 0.45
41 10 0.15
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (41 bp):
TTATTATACATCATATATTATATATTATTATATATATATGT
Found at i:42540643 original size:56 final size:53
Alignment explanation
Indices: 42540425--42540649 Score: 152
Period size: 56 Copynumber: 4.2 Consensus size: 53
42540415 TTTAACCTTA
* * *
42540425 TTTT-TATATTA-TATATTATAAAATTATT-T-TATTATATATTATTTAT-AT
1 TTTTATATATTATTATATTATATATTTATTATATATTATATATTATATATCAT
* * * *
42540473 TATTAT-TATTATTATA-TAT-TATTT-TTCACA-AGTTATTATTATTTTACATCAT
1 TTTTATATATTATTATATTATATATTTATT-ATATA-TTA-TA-TATTATATATCAT
* *
42540525 TATTTATATATTATTATATTATATGTTTATTATATATTATATATTATATATTAT
1 T-TTTATATATTATTATATTATATATTTATTATATATTATATATTATATATCAT
*
42540579 TTTATATATATGCTTTTATATTATATATTATAATTAT-T-TTATATATTAT-TAAGTCAT
1 TTT-TATATAT--TATTATATTATATATT-T-ATTATATATTATATATTATAT-A-TCAT
42540636 TTTTATATTATTAT
1 TTTTATA-TATTAT
42540650 ACATTTTTAT
Statistics
Matches: 137, Mismatches: 17, Indels: 39
0.71 0.09 0.20
Matches are distributed among these distances:
46 2 0.01
47 3 0.02
48 12 0.09
49 8 0.06
50 2 0.01
51 7 0.05
52 3 0.02
53 6 0.04
54 28 0.20
55 8 0.06
56 39 0.28
57 14 0.10
58 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.60
Consensus pattern (53 bp):
TTTTATATATTATTATATTATATATTTATTATATATTATATATTATATATCAT
Found at i:42540649 original size:3 final size:3
Alignment explanation
Indices: 42540447--42540629 Score: 84
Period size: 3 Copynumber: 60.3 Consensus size: 3
42540437 ATATTATAAA
42540447 ATT ATT -TT ATT ATAT ATT ATT -TAT ATT ATT ATT ATT ATT ATAT ATT
1 ATT ATT ATT ATT AT-T ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT
* ** * *
42540493 ATT TTT CACA AGTT ATT ATT ATT -TT A-C ATC ATT ATTT ATAT ATT ATT
1 ATT ATT -ATT A-TT ATT ATT ATT ATT ATT ATT ATT A-TT AT-T ATT ATT
42540540 A-T ATT A-T ATGT -TT ATT ATAT ATT ATAT ATT ATAT ATT ATT -TT A-T
1 ATT ATT ATT AT-T ATT ATT AT-T ATT AT-T ATT AT-T ATT ATT ATT ATT
* * *
42540584 ATAT ATG CTT -TT A-T ATT ATAT ATT ATA ATT ATT -TT ATAT ATT ATT
1 AT-T ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT AT-T ATT ATT
42540629 A
1 A
42540630 AGTCATTTTT
Statistics
Matches: 141, Mismatches: 13, Indels: 52
0.68 0.06 0.25
Matches are distributed among these distances:
2 21 0.15
3 87 0.62
4 33 0.23
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:42540666 original size:14 final size:14
Alignment explanation
Indices: 42540641--42540674 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
42540631 GTCATTTTTA
42540641 TATTAT-TATACAT
1 TATTATCTATACAT
*
42540654 TTTTATCTATACAT
1 TATTATCTATACAT
42540668 TATTATC
1 TATTATC
42540675 ATTAAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.56
Consensus pattern (14 bp):
TATTATCTATACAT
Found at i:42540736 original size:24 final size:25
Alignment explanation
Indices: 42540694--42540743 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 25
42540684 TTTAAACTTG
*
42540694 TATTATATATTTATCTTTATTTATA
1 TATTATATAATTATCTTTATTTATA
*
42540719 TATTA-ATAATTATTTTTATTTATA
1 TATTATATAATTATCTTTATTTATA
42540743 T
1 T
42540744 TCTATTATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TATTATATAATTATCTTTATTTATA
Found at i:42540995 original size:26 final size:25
Alignment explanation
Indices: 42540948--42540996 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
42540938 TTATAAATAC
* * *
42540948 ATTTTTATTATATATTATATTTTAA
1 ATTTTTATTAAATATCACATTTTAA
42540973 ATTTATTATTAAATATCACATTTT
1 ATTT-TTATTAAATATCACATTTT
42540997 TATTATTTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTTATTAAATATCACATTTTAA
Found at i:42542789 original size:18 final size:18
Alignment explanation
Indices: 42542763--42542797 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42542753 CAAGATATCC
* *
42542763 CAAATTAAAATCCAAATT
1 CAAAATAAAACCCAAATT
42542781 CAAAATAAAACCCAAAT
1 CAAAATAAAACCCAAAT
42542798 GTCTAGAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (18 bp):
CAAAATAAAACCCAAATT
Found at i:42543657 original size:29 final size:29
Alignment explanation
Indices: 42543615--42543675 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
42543605 ACACCCTATT
* *
42543615 ACAAGACCTGTTACACGGACGTGTGTCGC
1 ACAAGACCTATTACACGGACGTGTGTCAC
* *
42543644 ACAAGGCCTATTACACGGCCGTGTGTCAC
1 ACAAGACCTATTACACGGACGTGTGTCAC
42543673 ACA
1 ACA
42543676 CGACATACCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.20
Consensus pattern (29 bp):
ACAAGACCTATTACACGGACGTGTGTCAC
Found at i:42549488 original size:18 final size:18
Alignment explanation
Indices: 42549462--42549496 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42549452 CAAGATATCC
* *
42549462 CAAATTAAAATCCAAATT
1 CAAAATAAAACCCAAATT
42549480 CAAAATAAAACCCAAAT
1 CAAAATAAAACCCAAAT
42549497 GTCCAGAGAG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.60, C:0.20, G:0.00, T:0.20
Consensus pattern (18 bp):
CAAAATAAAACCCAAATT
Found at i:42554870 original size:13 final size:13
Alignment explanation
Indices: 42554852--42554891 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
42554842 ATTTCAGTCC
42554852 TTCTGTTAACTTT
1 TTCTGTTAACTTT
*
42554865 TTCTGTTAGCTTT
1 TTCTGTTAACTTT
*
42554878 TTCCTATTAACTTT
1 TT-CTGTTAACTTT
42554892 GCTAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 14 0.61
14 9 0.39
ACGTcount: A:0.15, C:0.17, G:0.07, T:0.60
Consensus pattern (13 bp):
TTCTGTTAACTTT
Found at i:42555006 original size:24 final size:23
Alignment explanation
Indices: 42554970--42555014 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
42554960 CCTTTTTTTC
42554970 TTATAAAAATTATAATTTAAAAAAA
1 TTATAAAAATTAT-A-TTAAAAAAA
42554995 TTAT-AAAATTATATTAAAAA
1 TTATAAAAATTATATTAAAAA
42555015 TTATAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 1 0.05
24 8 0.40
25 4 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTATAAAAATTATATTAAAAAAA
Found at i:42555027 original size:23 final size:21
Alignment explanation
Indices: 42554990--42555038 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 21
42554980 TATAATTTAA
42554990 AAAAATTATAAAATTA-TATT
1 AAAAATTATAAAATTATTATT
*
42555010 AAAAATTATAAGCTAATTATTTTT
1 AAAAATTATAA---AATTATTATT
42555034 AAAAA
1 AAAAA
42555039 AAAATTCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 11 0.46
23 5 0.21
24 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
AAAAATTATAAAATTATTATT
Found at i:42555328 original size:9 final size:8
Alignment explanation
Indices: 42555316--42555358 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 8
42555306 TTTTATATTT
42555316 TTTTTATA
1 TTTTTATA
42555324 GTTTTTATA
1 -TTTTTATA
*
42555333 TTTTTAAA
1 TTTTTATA
*
42555341 ATTTTATA
1 TTTTTATA
42555349 TTATTTATA
1 TT-TTTATA
42555358 T
1 T
42555359 AATATGTTCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 14 0.48
9 15 0.52
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (8 bp):
TTTTTATA
Found at i:42555534 original size:30 final size:30
Alignment explanation
Indices: 42555496--42555598 Score: 77
Period size: 30 Copynumber: 3.3 Consensus size: 30
42555486 TTTTTGGGCT
42555496 TAAA-TAATTAAAGATCAAGTAGGTCCTTC
1 TAAATTAATTAAAGATCAAGTAGGTCCTTC
* * ** *
42555525 TAAATTAATTTTAAAAAAAAT-AATTA-AACCTTTG
1 TAAATTAA--TT---AAAGATCAAGTAGGTCC-TTC
*
42555559 TAAAATAATTAAAGATCAAGTAGGTCCTTC
1 TAAATTAATTAAAGATCAAGTAGGTCCTTC
42555589 TAAATTAATT
1 TAAATTAATT
42555599 TTAAAAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 17
0.65 0.15 0.21
Matches are distributed among these distances:
29 9 0.17
30 18 0.34
31 2 0.04
32 4 0.08
33 2 0.04
34 13 0.25
35 5 0.09
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.35
Consensus pattern (30 bp):
TAAATTAATTAAAGATCAAGTAGGTCCTTC
Found at i:42555568 original size:34 final size:34
Alignment explanation
Indices: 42555525--42555632 Score: 84
Period size: 34 Copynumber: 3.3 Consensus size: 34
42555515 TAGGTCCTTC
*
42555525 TAAATTAATTTTAAAAAAAATAATTAAACCTTTG
1 TAAAATAATTTTAAAAAAAATAATTAAACCTTTG
* * ** *
42555559 TAAAATAA--TT---AAAGATCAAGTAGGTCC-TTC
1 TAAAATAATTTTAAAAAAAAT-AATTA-AACCTTTG
* *
42555589 TAAATTAATTTTAAAAAAATTAATTAAACCTTTG
1 TAAAATAATTTTAAAAAAAATAATTAAACCTTTG
42555623 TAAAATAATT
1 TAAAATAATT
42555633 AAAGATCAAA
Statistics
Matches: 52, Mismatches: 14, Indels: 16
0.63 0.17 0.20
Matches are distributed among these distances:
29 5 0.10
30 13 0.25
31 2 0.04
32 4 0.08
33 2 0.04
34 22 0.42
35 4 0.08
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (34 bp):
TAAAATAATTTTAAAAAAAATAATTAAACCTTTG
Found at i:42555598 original size:64 final size:64
Alignment explanation
Indices: 42555497--42555641 Score: 281
Period size: 64 Copynumber: 2.3 Consensus size: 64
42555487 TTTTGGGCTT
42555497 AAATAATTAAAGATCAAGTAGGTCCTTCTAAATTAATTTTAAAAAAAATAATTAAACCTTTGTA
1 AAATAATTAAAGATCAAGTAGGTCCTTCTAAATTAATTTTAAAAAAAATAATTAAACCTTTGTA
*
42555561 AAATAATTAAAGATCAAGTAGGTCCTTCTAAATTAATTTTAAAAAAATTAATTAAACCTTTGTA
1 AAATAATTAAAGATCAAGTAGGTCCTTCTAAATTAATTTTAAAAAAAATAATTAAACCTTTGTA
42555625 AAATAATTAAAGATCAA
1 AAATAATTAAAGATCAA
42555642 ATAAATCATC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 80 1.00
ACGTcount: A:0.50, C:0.09, G:0.08, T:0.34
Consensus pattern (64 bp):
AAATAATTAAAGATCAAGTAGGTCCTTCTAAATTAATTTTAAAAAAAATAATTAAACCTTTGTA
Found at i:42567968 original size:26 final size:26
Alignment explanation
Indices: 42567841--42568135 Score: 136
Period size: 26 Copynumber: 11.7 Consensus size: 26
42567831 ATATGAACTC
42567841 TTAAAATAAATAATA-ATAATAA-AGGT
1 TTAAAATAAATAATATATAA-AATA-GT
* * *
42567867 TTACAATAAATAATA-A-AAAAGAAT
1 TTAAAATAAATAATATATAAAATAGT
* ** *
42567891 TTAAAACAGCTAACATATAAAATAGT
1 TTAAAATAAATAATATATAAAATAGT
* * * *
42567917 AT-AACTAAATAACATA-AAAA-AAT
1 TTAAAATAAATAATATATAAAATAGT
* *
42567940 TTAAAATAGATAATATATATAATAGT
1 TTAAAATAAATAATATATAAAATAGT
42567966 TTAAAATAAATAAAATATATAAAAAATA-T
1 TTAAAATAAAT--AATATAT--AAAATAGT
**
42567995 TTAAAATAAATAATAGGTAAAATAGT
1 TTAAAATAAATAATATATAAAATAGT
** *
42568021 TTAAAATAACA-AATGCA-AAAA-A-C
1 TTAAAATAA-ATAATATATAAAATAGT
* **
42568044 TTAAAATAAA-AA-ATAAAAAATAAC
1 TTAAAATAAATAATATATAAAATAGT
* * * *
42568068 TTAAAAT-AAT-GTACAATAAAACAAT
1 TTAAAATAAATAATA-TATAAAATAGT
* * * *
42568093 TTGAAATGAATACTATATAAAATAAT
1 TTAAAATAAATAATATATAAAATAGT
*
42568119 TTAAAATGAATAATATA
1 TTAAAATAAATAATATA
42568136 AGAAAAGACT
Statistics
Matches: 207, Mismatches: 42, Indels: 40
0.72 0.15 0.14
Matches are distributed among these distances:
21 1 0.00
22 7 0.03
23 15 0.07
24 38 0.18
25 40 0.19
26 74 0.36
27 8 0.04
28 7 0.03
29 12 0.06
30 5 0.02
ACGTcount: A:0.62, C:0.04, G:0.05, T:0.28
Consensus pattern (26 bp):
TTAAAATAAATAATATATAAAATAGT
Found at i:42567993 original size:20 final size:20
Alignment explanation
Indices: 42567968--42568007 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42567958 ATAATAGTTT
*
42567968 AAAATAAATAAAATATATAA
1 AAAATAAATAAAATAAATAA
**
42567988 AAAATATTTAAAATAAATAA
1 AAAATAAATAAAATAAATAA
42568008 TAGGTAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAATAAATAAAATAAATAA
Found at i:42568049 original size:23 final size:24
Alignment explanation
Indices: 42567973--42568076 Score: 86
Period size: 23 Copynumber: 4.2 Consensus size: 24
42567963 AGTTTAAAAT
*
42567973 AAATAAAATATATAAAAAAT-ATTTA
1 AAATAAAA-A-ATAAAAAATAACTTA
* * **
42567998 AAATAAATAATAGGTAAAATAGTTTA
1 AAATAAAAAATA--AAAAATAACTTA
* **
42568024 AAATAACAAATGCAAAA-AACTTA
1 AAATAAAAAATAAAAAATAACTTA
42568047 AAATAAAAAATAAAAAATAACTTA
1 AAATAAAAAATAAAAAATAACTTA
42568071 AAATAA
1 AAATAA
42568077 TGTACAATAA
Statistics
Matches: 63, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
23 21 0.33
24 17 0.27
25 12 0.19
26 13 0.21
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (24 bp):
AAATAAAAAATAAAAAATAACTTA
Found at i:42573548 original size:52 final size:52
Alignment explanation
Indices: 42573491--42573589 Score: 162
Period size: 52 Copynumber: 1.9 Consensus size: 52
42573481 ACCCACACGG
* **
42573491 GCGTGTCCTAAGCCACATGAGCGTGTGACCCCTGTTCATAGCAAAAAAATTC
1 GCGTGTCCCAAGCCACACAAGCGTGTGACCCCTGTTCATAGCAAAAAAATTC
*
42573543 GCGTGTCCCAAGCCACACAAGCGTGTGACCTCTGTTCATAGCAAAAA
1 GCGTGTCCCAAGCCACACAAGCGTGTGACCCCTGTTCATAGCAAAAA
42573590 TTTTCTAAGT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (52 bp):
GCGTGTCCCAAGCCACACAAGCGTGTGACCCCTGTTCATAGCAAAAAAATTC
Found at i:42580797 original size:84 final size:84
Alignment explanation
Indices: 42580641--42580799 Score: 189
Period size: 84 Copynumber: 1.9 Consensus size: 84
42580631 CTTTGTTTGG
* * * * *
42580641 AAACAAAACAATATCGAATAAAATCTAGTTAAAATGCAGGAATAAATTCCGAAACATATTTTTTT
1 AAACAAAACAAAATCAAATAAAATATAGTTAAAAGGCAGGAATAAATTCCGAAACATATTTTATT
42580706 TAATTTAATTCTAATTTAA
66 TAATTTAATTCTAATTTAA
* * * *
42580725 AAACAAAACAAAATTAAATAAAATATTGTTAAACGGCGGGAATAAA-TCC-AAA-ATGAATTTTA
1 AAACAAAACAAAATCAAATAAAATATAGTTAAAAGGCAGGAATAAATTCCGAAACAT--ATTTTA
42580787 TTTAATTTTAATT
64 TTTAA-TTTAATT
42580800 TCTCGTTTTT
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
81 2 0.03
82 3 0.05
83 13 0.21
84 45 0.71
ACGTcount: A:0.49, C:0.09, G:0.08, T:0.33
Consensus pattern (84 bp):
AAACAAAACAAAATCAAATAAAATATAGTTAAAAGGCAGGAATAAATTCCGAAACATATTTTATT
TAATTTAATTCTAATTTAA
Found at i:42580879 original size:88 final size:90
Alignment explanation
Indices: 42580640--42581050 Score: 289
Period size: 87 Copynumber: 4.8 Consensus size: 90
42580630 TCTTTGTTTG
* * * * * *
42580640 GAAACAAAA-CAATATC-GAATAAAATCTAGTTAAAATGCAGGAATAAAT-TCCGAAACATATTT
1 GAAACAAAATCAAAATCGGAATAAAATCCA-TTGAAAGGCGGGAATAAATCT-CGAAACAGATTT
*
42580702 T-TTTTAA-TTTAA-TTCT-A-ATTTA
64 TATTTTAATTTTAATTTCTCATTTTTA
* **
42580724 AAAACAAAA-CAAAAT-TAAATAAAAT--ATTGTTAAACGGCGGGAATAAATC-C-AAA-ATGAA
1 GAAACAAAATCAAAATCGGAATAAAATCCATTG--AAA-GGCGGGAATAAATCTCGAAACA-G-A
*
42580782 TTTTA-TTTAATTTTAATTTCTCGTTTTT-
61 TTTTATTTTAATTTTAATTTCTCATTTTTA
* * * *
42580810 GACAACAAAATCAAAAT-GTAAT-AAATCCGTTGAAAGGCGGGAGTAAATCTTGAAACAGATTTT
1 GA-AACAAAATCAAAATCGGAATAAAATCCATTGAAAGGCGGGAATAAATCTCGAAACAGATTTT
*
42580873 ATTTTAATTTTAA-TACTCATTTTTA
65 ATTTTAATTTTAATTTCTCATTTTTA
* * * * *
42580898 GAAATAAAATCAAAATCGGAATAAAATCCATTGAACGGTGGTAATAAATCTCGAAACGGATTTT-
1 GAAACAAAATCAAAATCGGAATAAAATCCATTGAAAGGCGGGAATAAATCTCGAAACAGATTTTA
* *
42580962 TTTTAACTTTAATTTC-C-TGTTTA
66 TTTTAATTTTAATTTCTCATTTTTA
* * * ** * *
42580985 GAAATAATAA--AAAAT-GGAATAAAATCCATTGAATGACATGAATAAATCCCGAAATAGATTTT
1 GAAACAA-AATCAAAATCGGAATAAAATCCATTGAAAGGCGGGAATAAATCTCGAAACAGATTTT
42581047 ATTT
65 ATTT
42581051 ACTTTGAATT
Statistics
Matches: 263, Mismatches: 38, Indels: 50
0.75 0.11 0.14
Matches are distributed among these distances:
81 3 0.01
82 4 0.02
83 14 0.05
84 37 0.14
85 42 0.16
86 22 0.08
87 57 0.22
88 44 0.17
89 40 0.15
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.34
Consensus pattern (90 bp):
GAAACAAAATCAAAATCGGAATAAAATCCATTGAAAGGCGGGAATAAATCTCGAAACAGATTTTA
TTTTAATTTTAATTTCTCATTTTTA
Found at i:42581029 original size:85 final size:86
Alignment explanation
Indices: 42580853--42581061 Score: 221
Period size: 85 Copynumber: 2.4 Consensus size: 86
42580843 AAGGCGGGAG
* * * *
42580853 TAAATCTTGAAACAGATTTTATTTTAATTTTAATACTCATTTTTAGAAATAAAATCAAAATCGGA
1 TAAATCTCGAAACAGATTTT-TTTTAACTTTAAT-TTCATGTTTAGAAATAAAA-CAAAATCGGA
*
42580918 ATAAAATCCATTGAACGGTGGTAA
63 ATAAAATCCATTGAACGATGGTAA
* *
42580942 TAAATCTCGAAACGGATTTTTTTTAACTTTAATTTCCTGTTTAGAAATAATAA-AAAAT-GGAAT
1 TAAATCTCGAAACAGATTTTTTTTAACTTTAATTTCATGTTTAGAAATAA-AACAAAATCGGAAT
*
42581005 AAAATCCATTGAATGACAT-G-AA
65 AAAATCCATTGAACG--ATGGTAA
* * *
42581027 TAAATCCCGAAATAGATTTTATTT-ACTTTGAATTT
1 TAAATCTCGAAACAGATTTTTTTTAACTTT-AATTT
42581062 AGAAAAAAAA
Statistics
Matches: 104, Mismatches: 12, Indels: 12
0.81 0.09 0.09
Matches are distributed among these distances:
84 5 0.05
85 46 0.44
86 6 0.06
87 15 0.14
88 14 0.13
89 18 0.17
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (86 bp):
TAAATCTCGAAACAGATTTTTTTTAACTTTAATTTCATGTTTAGAAATAAAACAAAATCGGAATA
AAATCCATTGAACGATGGTAA
Found at i:42582815 original size:46 final size:46
Alignment explanation
Indices: 42582748--42582914 Score: 273
Period size: 46 Copynumber: 3.6 Consensus size: 46
42582738 ATAATCTCAC
42582748 CCATAATGAACTCGGAACACAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAATGAACTCGGAACACAACTCAACGAGCTCGGGTGTTCGCAT
42582794 CCATAATGAACTCGGAACACAACTCAACGAGCTCGGGTGTTCGCAT
1 CCATAATGAACTCGGAACACAACTCAACGAGCTCGGGTGTTCGCAT
* *
42582840 CCATAATGAACTCGGAACACAACTCAACGAGTTCGGATGCTT-GCAT
1 CCATAATGAACTCGGAACACAACTCAACGAGCTCGGGTG-TTCGCAT
* *
42582886 CCATAGGTGAACTCGGAACGCAACTCAAC
1 CCATA-ATGAACTCGGAACACAACTCAAC
42582915 AAGTTTGGAT
Statistics
Matches: 115, Mismatches: 4, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
46 92 0.80
47 23 0.20
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.19
Consensus pattern (46 bp):
CCATAATGAACTCGGAACACAACTCAACGAGCTCGGGTGTTCGCAT
Found at i:42587227 original size:31 final size:31
Alignment explanation
Indices: 42587192--42587254 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
42587182 TGTGATGAAG
* *
42587192 AATGTCATATAGCATTAAATTGTCCTAATAA
1 AATGTCATATAGCACTAAATTCTCCTAATAA
42587223 AATGTCATATAGCACTAAATTCTCCTAATAA
1 AATGTCATATAGCACTAAATTCTCCTAATAA
42587254 A
1 A
42587255 CTAAAAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (31 bp):
AATGTCATATAGCACTAAATTCTCCTAATAA
Found at i:42589574 original size:12 final size:12
Alignment explanation
Indices: 42589557--42589582 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42589547 AATCGATAAT
42589557 AGTTTATGAAAA
1 AGTTTATGAAAA
42589569 AGTTTATGAAAA
1 AGTTTATGAAAA
42589581 AG
1 AG
42589583 AAAAGAAAAG
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:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (12 bp):
AGTTTATGAAAA
Found at i:42590493 original size:16 final size:16
Alignment explanation
Indices: 42590472--42590506 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42590462 AGTTCATTGG
42590472 AATGGAATAGAG-CTGT
1 AATGGAATA-AGCCTGT
42590488 AATGGAATAAGCCTGT
1 AATGGAATAAGCCTGT
42590504 AAT
1 AAT
42590507 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (16 bp):
AATGGAATAAGCCTGT
Found at i:42590552 original size:46 final size:44
Alignment explanation
Indices: 42590485--42590576 Score: 116
Period size: 46 Copynumber: 2.0 Consensus size: 44
42590475 GGAATAGAGC
*
42590485 TGTAATGGAATAAGCCTGTAATCAGTAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAAGACTGTAAT-AGT-ATT-AATGTGTTTGGTTGAA
*
42590531 TGTAATGGAAT-AGAACTGTAATAGTATTATTGTGTTTGGTTGAA
1 TGTAATGGAATAAG-ACTGTAATAGTATTAATGTGTTTGGTTGAA
42590575 TG
1 TG
42590577 GAATAGATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
43 2 0.05
44 17 0.40
45 5 0.12
46 18 0.43
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.39
Consensus pattern (44 bp):
TGTAATGGAATAAGACTGTAATAGTATTAATGTGTTTGGTTGAA
Found at i:42591403 original size:40 final size:40
Alignment explanation
Indices: 42591348--42591428 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
42591338 TAATGGGAAG
42591348 ATTATTATACCACAACAGTACCTTTGAAAAACTCAACACC
1 ATTATTATACCACAACAGTACCTTTGAAAAACTCAACACC
42591388 ATTATTATACCACAACAGTACCTTTGAAAAACTCAACACC
1 ATTATTATACCACAACAGTACCTTTGAAAAACTCAACACC
42591428 A
1 A
42591429 AGGTTTTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.43, C:0.27, G:0.05, T:0.25
Consensus pattern (40 bp):
ATTATTATACCACAACAGTACCTTTGAAAAACTCAACACC
Found at i:42596009 original size:22 final size:24
Alignment explanation
Indices: 42595984--42596043 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 24
42595974 GAAGCAAAAG
42595984 AGAATAAAAAATAAAG-A-ATAAA
1 AGAATAAAAAATAAAGAACATAAA
*
42596006 AGAATAAAAATTTAAAGAACATAAA
1 AGAATAAAAA-ATAAAGAACATAAA
42596031 AG-A-AAAAAATAAA
1 AGAATAAAAAATAAA
42596044 ATTACTTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 14 0.42
23 10 0.30
24 2 0.06
25 7 0.21
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (24 bp):
AGAATAAAAAATAAAGAACATAAA
Found at i:42610895 original size:22 final size:22
Alignment explanation
Indices: 42610860--42610908 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42610850 TTTTCAATTA
*
42610860 CTTCCTCGCCCATTAGTATGAT
1 CTTCCTCGCCCATTAGTATGAC
* * *
42610882 CTTCCTTGCTCATTAGTGTGAC
1 CTTCCTCGCCCATTAGTATGAC
42610904 CTTCC
1 CTTCC
42610909 ATGTCCATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.14, C:0.33, G:0.14, T:0.39
Consensus pattern (22 bp):
CTTCCTCGCCCATTAGTATGAC
Found at i:42614018 original size:20 final size:19
Alignment explanation
Indices: 42613985--42614034 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
42613975 ATCAATCCAA
*
42613985 TATTGATACTTTTCTTAAGG
1 TATTGATA-TTTTCCTAAGG
*
42614005 TATTGATATATTTCCTATGG
1 TATTGATAT-TTTCCTAAGG
*
42614025 TATCGATATT
1 TATTGATATT
42614035 CCTACTCCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 2 0.08
20 24 0.92
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (19 bp):
TATTGATATTTTCCTAAGG
Found at i:42618650 original size:51 final size:51
Alignment explanation
Indices: 42618594--42618756 Score: 125
Period size: 51 Copynumber: 3.1 Consensus size: 51
42618584 GCCACACGGT
42618594 CGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGAC
1 CGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGAC
** * * ** * * * * **
42618645 CGTGTGTACCA-AGTTA-GTGAATTACACGGTCTGGCACACGA-CTTGCGACATGGT
1 CGTGTGT--CATTTTTATTTTAGGTGCA-GGT-T-TCACACGATC-TGAGACACGAC
* *
42618699 CGTGTGTCATTTTTATTTTAGGTGCATGTTTCACACGGTCTGAGACACGAC
1 CGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGAC
42618750 CGTGTGT
1 CGTGTGT
42618757 AGCAAGTCAA
Statistics
Matches: 77, Mismatches: 26, Indels: 18
0.64 0.21 0.15
Matches are distributed among these distances:
51 32 0.42
52 10 0.13
53 9 0.12
54 26 0.34
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (51 bp):
CGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGAC
Found at i:42618775 original size:105 final size:105
Alignment explanation
Indices: 42618591--42618797 Score: 335
Period size: 105 Copynumber: 2.0 Consensus size: 105
42618581 CTGGCCACAC
42618591 GGTCGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACCGTGTGTACCA
1 GGTCGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACCGTGTGTACCA
* * *
42618656 AGTTAGTGAATTACACGGTCTGGCACACGACTTGCGACAT
66 AGTCAATGAATTACACGGTCCGGCACACGACTTGCGACAT
* * *
42618696 GGTCGTGTGTCATTTTTATTTTAGGTGCATGTTTCACACGGTCTGAGACACGACCGTGTGTAGCA
1 GGTCGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACCGTGTGTACCA
*
42618761 AGTCAAT-AAGTTACACGGTCCGGCACACGGCTTGCGA
66 AGTCAATGAA-TTACACGGTCCGGCACACGACTTGCGA
42618798 TACAGCTGTG
Statistics
Matches: 94, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
104 2 0.02
105 92 0.98
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (105 bp):
GGTCGTGTGTCATTTTTATTTTAGGTGCAGGTTTCACACGATCTGAGACACGACCGTGTGTACCA
AGTCAATGAATTACACGGTCCGGCACACGACTTGCGACAT
Found at i:42620217 original size:39 final size:37
Alignment explanation
Indices: 42620150--42620242 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
42620140 ACCAGAATGG
* *
42620150 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
42620189 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
42620226 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
42620243 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:42620606 original size:3 final size:3
Alignment explanation
Indices: 42620598--42620645 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
42620588 ATTCCCACTC
* * * *
42620598 ATA ATA ATA ATA ATA ATA CTA ATA ATA ATA CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42620646 CTTACCTCAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:42620646 original size:18 final size:18
Alignment explanation
Indices: 42620599--42620647 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
42620589 TTCCCACTCA
*
42620599 TAATAATAATAATAATAC
1 TAATAATAATACTAATAC
42620617 TAATAATAATACTAATAC
1 TAATAATAATACTAATAC
*
42620635 TAATATTAATACT
1 TAATAATAATACT
42620648 TACCTCACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATAATAATACTAATAC
Found at i:42620647 original size:12 final size:12
Alignment explanation
Indices: 42620598--42620645 Score: 69
Period size: 12 Copynumber: 4.0 Consensus size: 12
42620588 ATTCCCACTC
*
42620598 ATAATAATAATA
1 ATAATACTAATA
42620610 ATAATACTAATA
1 ATAATACTAATA
42620622 ATAATACTAATA
1 ATAATACTAATA
* *
42620634 CTAATATTAATA
1 ATAATACTAATA
42620646 CTTACCTCAC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATACTAATA
Found at i:42621385 original size:20 final size:20
Alignment explanation
Indices: 42621351--42621390 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
42621341 TTCTATTCTG
*
42621351 TTTCTTTTCTGTTTTGTTTC
1 TTTCTTTTCTGTTTTATTTC
42621371 TTTCTTTTTCT-TTTTATTTC
1 TTTC-TTTTCTGTTTTATTTC
42621391 CTTTTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTGTTTTATTTC
Found at i:42621557 original size:31 final size:28
Alignment explanation
Indices: 42621521--42621588 Score: 73
Period size: 31 Copynumber: 2.3 Consensus size: 28
42621511 TTGTCTTTAT
**
42621521 TTAATTTATTTCTTAATATAATATTTATAA
1 TTAATTTATTTAATAATAT-A-ATTTATAA
* *
42621551 TGTAATTAATTTAATAATATACTTTATAA
1 T-TAATTTATTTAATAATATAATTTATAA
42621580 TTAATTTAT
1 TTAATTTAT
42621589 ATATTTATAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.22
29 8 0.25
30 2 0.06
31 15 0.47
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (28 bp):
TTAATTTATTTAATAATATAATTTATAA
Found at i:42621605 original size:21 final size:20
Alignment explanation
Indices: 42621567--42621605 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
42621557 TAATTTAATA
*
42621567 ATATACTTTATAATTAATTT
1 ATATACTTTATAAATAATTT
*
42621587 ATATATTTATATAAATAAT
1 ATATACTT-TATAAATAAT
42621606 AATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATATACTTTATAAATAATTT
Found at i:42623014 original size:46 final size:46
Alignment explanation
Indices: 42622960--42623178 Score: 183
Period size: 46 Copynumber: 4.7 Consensus size: 46
42622950 GGTTGAGCAT
* *
42622960 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
* * ** * * * *
42623006 TCGAACTCGTTGAGTTAAACCCGAGTT--CGT-GAGATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAA--ACGC
* * *
42623051 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
* * * * *
42623099 CCGAGCTCATTGAGTTGAGTCCGAGTTCACTCATGGATGCGAACGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
* * * *
42623145 TCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTAT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTAT
42623179 GGGCGGGTTA
Statistics
Matches: 141, Mismatches: 25, Indels: 14
0.78 0.14 0.08
Matches are distributed among these distances:
43 7 0.05
44 2 0.01
45 2 0.01
46 98 0.70
47 23 0.16
48 3 0.02
49 1 0.01
50 5 0.04
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATAGATGCAAACGC
Found at i:42634219 original size:27 final size:27
Alignment explanation
Indices: 42634181--42634235 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
42634171 TTAAAATTTT
*
42634181 ATATAATTTTAAGT-TTTAAATTATAAAA
1 ATATAATTTTAA-TCTTTAAA-AATAAAA
42634209 ATAT-ATTTTAATCTTTAAAAATAAAA
1 ATATAATTTTAATCTTTAAAAATAAAA
42634235 A
1 A
42634236 AAATTGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 13 0.52
28 4 0.16
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATAATTTTAATCTTTAAAAATAAAA
Found at i:42638997 original size:20 final size:20
Alignment explanation
Indices: 42638968--42639012 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
42638958 AGCACATGTA
* *
42638968 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
42638988 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
42639008 TTCAT
1 TTCAT
42639013 TGTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:42645621 original size:30 final size:30
Alignment explanation
Indices: 42645552--42645623 Score: 135
Period size: 30 Copynumber: 2.4 Consensus size: 30
42645542 CACATGGGTA
*
42645552 GACACACGGGCATGTGTCTAGGCCGTGTGT
1 GACACACGGTCATGTGTCTAGGCCGTGTGT
42645582 GACACACGGTCATGTGTCTAGGCCGTGTGT
1 GACACACGGTCATGTGTCTAGGCCGTGTGT
42645612 GACACACGGTCA
1 GACACACGGTCA
42645624 GCTCCCATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.19, C:0.25, G:0.33, T:0.22
Consensus pattern (30 bp):
GACACACGGTCATGTGTCTAGGCCGTGTGT
Found at i:42648568 original size:43 final size:43
Alignment explanation
Indices: 42648500--42648693 Score: 248
Period size: 43 Copynumber: 4.5 Consensus size: 43
42648490 ATAGTACTAT
* *
42648500 TCGGGCCTTCGAGCCTAGCAAGCTATAATG-CTAGTGAGTTAATA
1 TCGGG-CTTCGAGCCTTGCAGGCTATAATGTC-AGTGAGTTAATA
* *
42648544 TCGGGCTTCGAGCCTTGTAGGCTATAATGTCGGTGAGTTAATA
1 TCGGGCTTCGAGCCTTGCAGGCTATAATGTCAGTGAGTTAATA
* *
42648587 TCAGGCTTCGAGCCTGGCAGGCTATAATGTCAGTGAGTTAATA
1 TCGGGCTTCGAGCCTTGCAGGCTATAATGTCAGTGAGTTAATA
* * *
42648630 TCGGGCTTTGAG-CTTAGCAGGCTATAATGCCGGTGAGTTAATA
1 TCGGGCTTCGAGCCTT-GCAGGCTATAATGTCAGTGAGTTAATA
* *
42648673 TCAGGCTTCGAGCCTAGCAGG
1 TCGGGCTTCGAGCCTTGCAGG
42648694 TGTAATGCCG
Statistics
Matches: 131, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
42 2 0.02
43 121 0.92
44 8 0.06
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.28
Consensus pattern (43 bp):
TCGGGCTTCGAGCCTTGCAGGCTATAATGTCAGTGAGTTAATA
Found at i:42648652 original size:86 final size:86
Alignment explanation
Indices: 42648506--42648701 Score: 299
Period size: 86 Copynumber: 2.3 Consensus size: 86
42648496 CTATTCGGGC
* *
42648506 CTTCGAGCCTAGCAAGCTATAATGCTAGTGAGTTAATATCGGGCTTCGAGCCTTGTAGGCTATAA
1 CTTCGAGCCTAGCAGGCTATAATGCTAGTGAGTTAATATCGGGCTTCGAGCCTTGCAGGCTATAA
*
42648571 TGTCGGTGAGTTAATATCAGG
66 TGCCGGTGAGTTAATATCAGG
* *
42648592 CTTCGAGCCTGGCAGGCTATAATG-TCAGTGAGTTAATATCGGGCTTTGAG-CTTAGCAGGCTAT
1 CTTCGAGCCTAGCAGGCTATAATGCT-AGTGAGTTAATATCGGGCTTCGAGCCTT-GCAGGCTAT
42648655 AATGCCGGTGAGTTAATATCAGG
64 AATGCCGGTGAGTTAATATCAGG
*
42648678 CTTCGAGCCTAGCAGG-TGTAATGC
1 CTTCGAGCCTAGCAGGCTATAATGC
42648702 CGGTGAATGA
Statistics
Matches: 100, Mismatches: 7, Indels: 6
0.88 0.06 0.05
Matches are distributed among these distances:
85 10 0.10
86 90 0.90
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.29
Consensus pattern (86 bp):
CTTCGAGCCTAGCAGGCTATAATGCTAGTGAGTTAATATCGGGCTTCGAGCCTTGCAGGCTATAA
TGCCGGTGAGTTAATATCAGG
Found at i:42649302 original size:16 final size:18
Alignment explanation
Indices: 42649271--42649303 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
42649261 AACTCGTCAC
42649271 ACTATCTATCGTTTTGGT
1 ACTATCTATCGTTTTGGT
42649289 ACTAT-TAT-GTTTTGG
1 ACTATCTATCGTTTTGG
42649304 AATTCGTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.18, C:0.12, G:0.18, T:0.52
Consensus pattern (18 bp):
ACTATCTATCGTTTTGGT
Found at i:42652139 original size:20 final size:20
Alignment explanation
Indices: 42652110--42652154 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
42652100 AGCACATGTA
* *
42652110 TTCATAAAATTTTAGAATTT
1 TTCATAAAATTTTACAACTT
*
42652130 TTCATCAAATTTTACAACTT
1 TTCATAAAATTTTACAACTT
42652150 TTCAT
1 TTCAT
42652155 TGTAGTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.02, T:0.49
Consensus pattern (20 bp):
TTCATAAAATTTTACAACTT
Found at i:42656064 original size:35 final size:36
Alignment explanation
Indices: 42656011--42656083 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 36
42656001 AGTAAATTAT
* * * *
42656011 ATTCAGTTTAGTAGCCTTTCGG-TCTATTCTGACTG
1 ATTCAATTTAGCAACCTTTCGGATCTATTCTAACTG
42656046 ATTCAATTTAGCAACCTTTCGGATCTATTCTAACTG
1 ATTCAATTTAGCAACCTTTCGGATCTATTCTAACTG
42656082 AT
1 AT
42656084 GTGCTCCTCT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
35 19 0.58
36 14 0.42
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (36 bp):
ATTCAATTTAGCAACCTTTCGGATCTATTCTAACTG
Found at i:42660883 original size:13 final size:13
Alignment explanation
Indices: 42660865--42660907 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
42660855 TTTAATAATA
42660865 AAATAAAGAAATG
1 AAATAAAGAAATG
42660878 AAATAAAGAAAT-
1 AAATAAAGAAATG
* *
42660890 AAATGAAATAAAAG
1 AAAT-AAAGAAATG
42660904 AAAT
1 AAAT
42660908 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAATAAAGAAATG
Found at i:42660895 original size:17 final size:18
Alignment explanation
Indices: 42660861--42660907 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
42660851 ATTGTTTAAT
* *
42660861 AATAAAATAAAGAAATGA
1 AATAAAAGAAATAAATGA
42660879 AAT-AAAGAAATAAATGA
1 AATAAAAGAAATAAATGA
42660896 AATAAAAGAAAT
1 AATAAAAGAAAT
42660908 GAAAAAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AATAAAAGAAATAAATGA
Found at i:42660899 original size:9 final size:9
Alignment explanation
Indices: 42660873--42660907 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
42660863 TAAAATAAAG
42660873 AAATGAAAT
1 AAATGAAAT
42660882 AAA-GAAAT
1 AAATGAAAT
42660890 AAATGAAAT
1 AAATGAAAT
*
42660899 AAAAGAAAT
1 AAATGAAAT
42660908 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (9 bp):
AAATGAAAT
Found at i:42660959 original size:4 final size:4
Alignment explanation
Indices: 42660950--42660980 Score: 53
Period size: 4 Copynumber: 7.5 Consensus size: 4
42660940 AGAACAGGGG
42660950 AGAA AGAA AGGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AG
42660981 GGAGAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 22 0.85
5 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:42662297 original size:5 final size:5
Alignment explanation
Indices: 42662282--42662328 Score: 67
Period size: 5 Copynumber: 9.2 Consensus size: 5
42662272 AGTGGAAAAG
* *
42662282 TGAATT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT GGAAT GGAAT T
1 TGAA-T TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT TGAAT T
42662329 ATGATTAATT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 35 0.90
6 4 0.10
ACGTcount: A:0.38, C:0.00, G:0.23, T:0.38
Consensus pattern (5 bp):
TGAAT
Found at i:42662801 original size:45 final size:45
Alignment explanation
Indices: 42662737--42662976 Score: 309
Period size: 45 Copynumber: 5.3 Consensus size: 45
42662727 CTGTTACCGC
* *
42662737 TACTGCTACTGTTACCGATTCGGCATTTTGTGTGTCGAATATTGT
1 TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* *
42662782 TACTGCTACTGTTATCGATTCGGCACTTTGTGTGTCGAATATTGT
1 TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * * * * *
42662827 TACTGTTACCATTATCGATTCAGCACTGTGTGTGTTGAATATTGT
1 TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* * *
42662872 TACTGTTACCGTTACCAATTCGACACTTTGTGTGTCGAATATTGT
1 TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
* ** * *
42662917 TACTGTTACCGTTACCGATTCAACACTTTGTGTGTTGAATACTGT
1 TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
*
42662962 TACTGCTACTGTTAC
1 TACTGCTACCGTTAC
42662977 TATTCCAGAT
Statistics
Matches: 174, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 174 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TACTGCTACCGTTACCGATTCGGCACTTTGTGTGTCGAATATTGT
Found at i:42663177 original size:18 final size:18
Alignment explanation
Indices: 42663156--42663346 Score: 135
Period size: 18 Copynumber: 10.6 Consensus size: 18
42663146 TAACTGATTA
42663156 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
* * *
42663174 TTACCGGATAATTAACTG
1 TTACTGAATAATTGACTG
* *
42663192 TTTCTGGAT-ATTAGACTG
1 TTACTGAATAATT-GACTG
* *
42663210 TTACTGAATAACTT-AATA
1 TTACTGAATAA-TTGACTG
*
42663228 TTACTGAATAATTGA-TCA
1 TTACTGAATAATTGACT-G
* *
42663246 TTACTGAATAACTGATTG
1 TTACTGAATAATTGACTG
*
42663264 TCACTGAATGAA-TGACTG
1 TTACTGAAT-AATTGACTG
* *
42663282 CTACTGAATAACTT-AATAG
1 TTACTGAATAA-TTGACT-G
*
42663301 TTACTGAAT-ATCTGA-TT
1 TTACTGAATAAT-TGACTG
42663318 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
42663336 TTACTGGATAA
1 TTACTGAATAA
42663347 CCAATCAATT
Statistics
Matches: 138, Mismatches: 21, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
17 21 0.15
18 100 0.72
19 15 0.11
20 2 0.01
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:42663424 original size:36 final size:36
Alignment explanation
Indices: 42663156--42663426 Score: 149
Period size: 36 Copynumber: 7.3 Consensus size: 36
42663146 TAACTGATTA
* * * *
42663156 TTACTGAATAATTGACTGTTACCGGATAATTAACTG
1 TTACTGAATAATTGATTGTTACTGAATAACTAACTG
* * * *
42663192 TTTCTGGAT-ATTAGACTGTTACTGAATAACTTAA-TA
1 TTACTGAATAATT-GATTGTTACTGAATAAC-TAACTG
** * *
42663228 TTACTGAATAATTGATCATTACTGAATAACTGATTG
1 TTACTGAATAATTGATTGTTACTGAATAACTAACTG
* * *
42663264 TCACTGAATGAA-TGACTGCTACTGAATAACTTAA-TAG
1 TTACTGAAT-AATTGATTGTTACTGAATAAC-TAACT-G
* *
42663301 TTACTGAAT-ATCTGATT-TTACTGAATAATTGACTG
1 TTACTGAATAAT-TGATTGTTACTGAATAACTAACTG
* * *** *
42663336 TTACTGGATAACCAATCAATTGATCGATACTGAATAACTGGTTA
1 TTACT-G------AAT-AATTGATTGTTACTGAATAACTAACTG
* *
42663380 TTATTGAATAATTGATTGTTACCGAATAACTAACTG
1 TTACTGAATAATTGATTGTTACTGAATAACTAACTG
42663416 TTACTGAATAA
1 TTACTGAATAA
42663427 ATAATTATTC
Statistics
Matches: 176, Mismatches: 39, Indels: 40
0.69 0.15 0.16
Matches are distributed among these distances:
35 14 0.08
36 109 0.62
37 26 0.15
42 3 0.02
43 5 0.03
44 19 0.11
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (36 bp):
TTACTGAATAATTGATTGTTACTGAATAACTAACTG
Found at i:42670085 original size:8 final size:8
Alignment explanation
Indices: 42670072--42670099 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
42670062 ACTTAAGTAC
42670072 ATAATATA
1 ATAATATA
42670080 ATAATATA
1 ATAATATA
42670088 ATAATATA
1 ATAATATA
42670096 ATAA
1 ATAA
42670100 AATATAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
ATAATATA
Found at i:42673721 original size:25 final size:25
Alignment explanation
Indices: 42673687--42673783 Score: 149
Period size: 25 Copynumber: 3.9 Consensus size: 25
42673677 AGATCTTCCA
42673687 AGCTGAATAATGGGAAGCTCATGCC
1 AGCTGAATAATGGGAAGCTCATGCC
42673712 AGCTGAATAATGGGAAGCTCATGCC
1 AGCTGAATAATGGGAAGCTCATGCC
* *
42673737 AGCTGAATAATGGGAAGCTCATACA
1 AGCTGAATAATGGGAAGCTCATGCC
* * *
42673762 AGCTAAACAACGGGAAGCTCAT
1 AGCTGAATAATGGGAAGCTCAT
42673784 ACGAGCTGTG
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 67 1.00
ACGTcount: A:0.36, C:0.20, G:0.26, T:0.19
Consensus pattern (25 bp):
AGCTGAATAATGGGAAGCTCATGCC
Found at i:42677382 original size:49 final size:48
Alignment explanation
Indices: 42677276--42677389 Score: 133
Period size: 49 Copynumber: 2.3 Consensus size: 48
42677266 GTCACATCTA
* * *
42677276 AGTCGATGCCATGTTCCAGATAGGTTTTACACTGGCTTCCATATATCG
1 AGTCGATGCCATGTCCCAAATAGGTATTACACTGGCTTCCATATATCG
*
42677324 AGGCTGATGCCATGTCCCAAATAGGTATTACACTGGC-TCTCACT-TATCTG
1 AGTC-GATGCCATGTCCCAAATAGGTATTACACTGGCTTC-CA-TATATC-G
*
42677374 TGTCGATGCCATGTCC
1 AGTCGATGCCATGTCC
42677390 TAGACAGATC
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
48 5 0.09
49 47 0.84
50 4 0.07
ACGTcount: A:0.22, C:0.25, G:0.21, T:0.32
Consensus pattern (48 bp):
AGTCGATGCCATGTCCCAAATAGGTATTACACTGGCTTCCATATATCG
Found at i:42680820 original size:43 final size:43
Alignment explanation
Indices: 42680735--42680898 Score: 149
Period size: 43 Copynumber: 3.8 Consensus size: 43
42680725 CATAGGATTT
* * * **
42680735 TCGATATGTG-TTCTCGTGTAAGACCACATCTAGGACGTTGGCA
1 TCGATATGTGATT-TCATGTAAGACCACGTCTGGGACAATGGCA
*
42680778 TCGATATGTGATTTCGA-GTAAGACCATGTCTGGGACAATGGCA
1 TCGATATGTGATTTC-ATGTAAGACCACGTCTGGGACAATGGCA
* *
42680821 TTG-TAATTGTGA-TTCATGTAAGACC-CTGTCTGGGACAGTGGCA
1 TCGAT-A-TGTGATTTCATGTAAGACCAC-GTCTGGGACAATGGCA
* * *
42680864 TCGACATGTGATTACATGTAAGACCACGTTTGGGA
1 TCGATATGTGATTTCATGTAAGACCACGTCTGGGA
42680899 TGTAGGCATT
Statistics
Matches: 99, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
42 7 0.07
43 84 0.85
44 8 0.08
ACGTcount: A:0.26, C:0.18, G:0.27, T:0.30
Consensus pattern (43 bp):
TCGATATGTGATTTCATGTAAGACCACGTCTGGGACAATGGCA
Found at i:42684882 original size:11 final size:12
Alignment explanation
Indices: 42684866--42684898 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
42684856 GATTAAAATG
42684866 AAAAATAAAAC-
1 AAAAATAAAACT
42684877 AAAAATAAAACT
1 AAAAATAAAACT
*
42684889 AGAAATAAAA
1 AAAAATAAAA
42684899 TTTTTGAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.79, C:0.06, G:0.03, T:0.12
Consensus pattern (12 bp):
AAAAATAAAACT
Found at i:42689861 original size:28 final size:28
Alignment explanation
Indices: 42689829--42689883 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
42689819 ATTTATTTTA
42689829 ACATAATTTACTCAATTACTATTATAAT
1 ACATAATTTACTCAATTACTATTATAAT
42689857 ACATAATTTACTCAATTACTATTATAA
1 ACATAATTTACTCAATTACTATTATAA
42689884 CCTTTAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (28 bp):
ACATAATTTACTCAATTACTATTATAAT
Found at i:42699593 original size:42 final size:42
Alignment explanation
Indices: 42699472--42699593 Score: 140
Period size: 43 Copynumber: 2.9 Consensus size: 42
42699462 TACCGTACCA
* *
42699472 ATGCCATAT-CAGAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCCCG-GATATGGTCTTACATGTAATCTCATATCG
* * * * *
42699514 ATGCTAATAGCCCAGCTATGGTCTTACACG-AAGTCTCATATCG
1 ATGC-CATATCCCGGATATGGTCTTACATGTAA-TCTCATATCG
42699557 ATGCCATATCCCGGATATGGTCTTACATGTAATCTCA
1 ATGCCATATCCCGGATATGGTCTTACATGTAATCTCA
42699594 GTAACCCTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
42 31 0.48
43 32 0.50
44 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (42 bp):
ATGCCATATCCCGGATATGGTCTTACATGTAATCTCATATCG
Found at i:42705213 original size:138 final size:135
Alignment explanation
Indices: 42704980--42705525 Score: 466
Period size: 138 Copynumber: 4.0 Consensus size: 135
42704970 TTTTCGTCTG
* * * * * * *
42704980 CGAACCTTAATATGACAACTGGGAGTTTTGCTATCGCTAACTATTTTGGAAGTTGCGATTCTTCG
1 CGAACCTTAATATGACAACTGGGAGCTTTG-TTTCGCTAACTGTTTTAGAGGTTG-TACTCTTCG
* * * * * * * * * * *
42705045 CTTGCAAACCTTATTAAGACATTTAGGAGCTTTGCTCTCGTTAATTTTTATGGAGGTTGTGGCTC
64 CCTGCGAACCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAATTTTT-TGAAAGTTGCGGCTC
42705110 TTCACCTA
128 TTCACCTA
* * * *
42705118 CGAGCCTTAATACT-ACAATTGGGAGCTTTGTTGTCGCTAACTATTTTAAAGGTTGTAACTCTTC
1 CGAACCTTAATA-TGACAACTGGGAGCTTTGTT-TCGCTAACTGTTTTAGAGGTTGT-ACTCTTC
* * * * * * * *
42705182 ACTTGTGAACCTTAATATGATAGCTGAGAGCTTTACTCTCGCTAATTTTTTTAAAAGTTACGGCT
63 GCCTGCGAACCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAA-TTTTTTGAAAGTTGCGGCT
*
42705247 CTTCGCCTA
127 CTTCACCTA
* * * * * *
42705256 TGAACCTTAATATGATAGCTGGGAGCTTTGTTCTCACTAACTGTTTTGGAGGTTGTGACTTTTCG
1 CGAACCTTAATATGACAACTGGGAGCTTTGTT-TCGCTAACTGTTTTAGAGGTTGT-ACTCTTCG
* * * * * ****
42705321 CCTGCAAACCTTAATATAATAGTTGGGAGCTTTGC-CTTCACTAACTGTTTTGGAAGTTGTATTT
64 CCTGCGAACCTTAATATGATAGTTGGGAGCTTTGCTC-TCGCTAA-TTTTTTGAAAGTTGCGGCT
42705385 CTTCACCTA
127 CTTCACCTA
* * * * *
42705394 CGAACTTTAATATGACAACTGGGAGCTTTACTTTCGCTAATTGTTTTAGAGGTTACTGCTCTTCG
1 CGAACCTTAATATGACAACTGGGAGCTTT-GTTTCGCTAACTGTTTTAGAGGTT-GTACTCTTCG
** *
42705459 CCTGCGAGTCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCGGCTC
64 CCTGCGAACCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAATT-TTTTGAAAGTTGCGGCTC
42705524 TT
128 TT
42705526 TGCCTTTAAA
Statistics
Matches: 317, Mismatches: 81, Indels: 20
0.76 0.19 0.05
Matches are distributed among these distances:
137 4 0.01
138 303 0.96
139 10 0.03
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (135 bp):
CGAACCTTAATATGACAACTGGGAGCTTTGTTTCGCTAACTGTTTTAGAGGTTGTACTCTTCGCC
TGCGAACCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAATTTTTTGAAAGTTGCGGCTCTTC
ACCTA
Found at i:42705336 original size:207 final size:208
Alignment explanation
Indices: 42704980--42705548 Score: 504
Period size: 207 Copynumber: 2.7 Consensus size: 208
42704970 TTTTCGTCTG
* * * * * * ** * **
42704980 CGAACCTTAATATGACAACTGGGAGTTTTGCTATCGCTAACTATTTTGGAAGTTGCGATTCTTCG
1 CGAACCTTAATATGACAACTGAGAGCTTTACTCTCGCTAATTGTTTTAAAAGTTACGGCTCTTCG
* * * * * * ** * ** *
42705045 CTTGCAAACCTTATTAAGACATTTAGGAGCTTTGCTCTCGTTAA-TTTTTATGGAGGTTGTGGCT
66 CCTACGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTT-TGGAGGTTGTGGCT
* * * * * *
42705109 CTTCACCTACGAGCCTTAATACTACA-A-TTGGGAGCTTTG-TTGTCGCTAACTATTTT-AAAGG
130 TTTCGCCTACAAACCTTAATA-TACATAGTTGGGAGCTTTGCCT-TCACTAACTATTTTGAAA-G
* *
42705170 TTGTAACTCTTCACTTG
192 TTGTAACTCTTCACCTA
* * * *
42705187 TGAACCTTAATATGATAGCTGAGAGCTTTACTCTCGCTAATTTTTTTAAAAGTTACGGCTCTTCG
1 CGAACCTTAATATGACAACTGAGAGCTTTACTCTCGCTAATTGTTTTAAAAGTTACGGCTCTTCG
* * *
42705252 CCTATGAACCTTAATATGATAGCTGGGAGCTTTGTTCTCACTAACTGTTTTGGAGGTTGTGACTT
66 CCTACGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTGTGGCTT
* * *
42705317 TTCGCCTGCAAACCTTAATATA-ATAGTTGGGAGCTTTGCCTTCACTAACTGTTTTGGAAGTTGT
131 TTCGCCTACAAACCTTAATATACATAGTTGGGAGCTTTGCCTTCACTAACTATTTTGAAAGTTGT
**
42705381 ATTTCTTCACCTA
196 AACTCTTCACCTA
* * * * * *
42705394 CGAACTTTAATATGACAACTGGGAGCTTTACTTTCGCTAATTGTTTTAGAGGTTACTGCTCTTCG
1 CGAACCTTAATATGACAACTGAGAGCTTTACTCTCGCTAATTGTTTTAAAAGTTACGGCTCTTCG
* ** * * * * *
42705459 CCTGCGAGTCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCGGCTC
66 CCTACGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTGTGGCT-
**
42705524 TTT-GCCTTTAAACCTTAATAATACA
130 TTTCGCCTACAAACCTTAAT-ATACA
42705549 CGAACATTGT
Statistics
Matches: 289, Mismatches: 65, Indels: 14
0.79 0.18 0.04
Matches are distributed among these distances:
205 1 0.00
206 3 0.01
207 271 0.94
208 13 0.04
209 1 0.00
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (208 bp):
CGAACCTTAATATGACAACTGAGAGCTTTACTCTCGCTAATTGTTTTAAAAGTTACGGCTCTTCG
CCTACGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCACTAACTGTTTTGGAGGTTGTGGCTT
TTCGCCTACAAACCTTAATATACATAGTTGGGAGCTTTGCCTTCACTAACTATTTTGAAAGTTGT
AACTCTTCACCTA
Found at i:42705524 original size:69 final size:69
Alignment explanation
Indices: 42704980--42705530 Score: 342
Period size: 69 Copynumber: 8.0 Consensus size: 69
42704970 TTTTCGTCTG
* * * * * * * **
42704980 CGAACCTTAATATGACAACTGGGAGTTTTGCTATCGCTAACTATTTTGGAA-GTTGCGATTCTTC
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTT-GAAGGTTGTGGCTCTTC
* *
42705044 GCTTG
65 GCCTA
* * * * ** * * *
42705049 CAAACCTTATTAAGACATTTAGGAGCTTTGCTCTCGTTAATT-TTTATGGAGGTTGTGGCTCTTC
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTT-TGAAGGTTGTGGCTCTTC
*
42705113 ACCTA
65 GCCTA
* * ** * * * * * **
42705118 CGAGCCTTAATACT-ACAATTGGGAGCTTTGTTGTCGCTAACTATTTTAAAGGTTGTAACTCTTC
1 CGAACCTTAATA-TGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGTGGCTCTTC
* * *
42705182 ACTTG
65 GCCTA
* * * * * * **
42705187 TGAACCTTAATATGATAGCTGAGAGCTTTACTCTCGCTAATTTTTTTAAAAGTTACGGCTCTTCG
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGTGGCTCTTCG
42705252 CCTA
66 CCTA
* * * * * * *
42705256 TGAACCTTAATATGATAGCTGGGAGCTTTGTTCTCACTAACTGTTTTGGAGGTTGTGACTTTTCG
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGTGGCTCTTCG
*
42705321 CCTG
66 CCTA
* * * * * ***
42705325 CAAACCTTAATATAATAGTTGGGAGCTTTGC-CTTCACTAACTGTTTTGGAA-GTTGTATTTCTT
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTC-TCGCTAATTGTTTT-GAAGGTTGTGGCTCTT
*
42705388 CACCTA
64 CGCCTA
* * * * * *
42705394 CGAACTTTAATATGACAACTGGGAGCTTTACTTTCGCTAATTGTTTT-AGAGGTTACT-GCTCTT
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGA-AGGTT-GTGGCTCTT
*
42705457 CGCCTG
64 CGCCTA
** * * *
42705463 CGAGTCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGCGGCTCTTTG
1 CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGTGGCTCTTCG
42705528 CCT
66 CCT
42705531 TTAAACCTTA
Statistics
Matches: 365, Mismatches: 104, Indels: 26
0.74 0.21 0.05
Matches are distributed among these distances:
67 1 0.00
68 8 0.02
69 349 0.96
70 7 0.02
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (69 bp):
CGAACCTTAATATGATAGCTGGGAGCTTTGCTCTCGCTAATTGTTTTGAAGGTTGTGGCTCTTCG
CCTA
Found at i:42712533 original size:11 final size:10
Alignment explanation
Indices: 42712517--42712557 Score: 55
Period size: 11 Copynumber: 3.9 Consensus size: 10
42712507 AAATGGATTT
42712517 AATAGAAATTA
1 AATAG-AATTA
*
42712528 AATAGAATAA
1 AATAGAATTA
42712538 GAATAGAATTA
1 -AATAGAATTA
42712549 AATAGAATT
1 AATAGAATT
42712558 CTCTAATTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 13 0.48
11 14 0.52
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.27
Consensus pattern (10 bp):
AATAGAATTA
Found at i:42714051 original size:2 final size:2
Alignment explanation
Indices: 42714046--42714071 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42714036 TATGTATATA
42714046 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
42714072 GATATAGATA
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:42724773 original size:16 final size:16
Alignment explanation
Indices: 42724749--42724816 Score: 77
Period size: 16 Copynumber: 4.2 Consensus size: 16
42724739 TGGTTTACTA
*
42724749 TAATGGAATAG-GACTG
1 TAATTGAATAGAG-CTG
*
42724765 TAATTGAATAAAGCTG
1 TAATTGAATAGAGCTG
42724781 TAATTGAATAGAGCTG
1 TAATTGAATAGAGCTG
*
42724797 TAA-TGAAATAGAGTTG
1 TAATTG-AATAGAGCTG
42724813 TAAT
1 TAAT
42724817 CAGTAATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
15 2 0.04
16 42 0.93
17 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.24, T:0.31
Consensus pattern (16 bp):
TAATTGAATAGAGCTG
Found at i:42725065 original size:26 final size:25
Alignment explanation
Indices: 42725036--42725092 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
42725026 AATCAATAAT
* * *
42725036 TTAATCATATTTTAATATAATTATTA
1 TTAATCACAATTTAATA-AAATATTA
*
42725062 TTAATTACAATTTAATAAAATATTA
1 TTAATCACAATTTAATAAAATATTA
42725087 TATAAT
1 T-TAAT
42725093 TTAATAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 8 0.31
26 18 0.69
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (25 bp):
TTAATCACAATTTAATAAAATATTA
Found at i:42725081 original size:61 final size:58
Alignment explanation
Indices: 42725011--42725122 Score: 136
Period size: 58 Copynumber: 1.9 Consensus size: 58
42725001 TTAAATATTT
* * *
42725011 TTTAATAAAAATAAAAATCAATAATTTAATCATATT-TTAATATAATTATTATTAATTACAA
1 TTTAAT-AAAAT-AAAAT--ATAATTTAATAAAATTCTTAATATAATCATTATTAATTACAA
**
42725072 TTTAATAAAATATTATATAATTTAATAAAATTCTTAATATAATCATTATTA
1 TTTAATAAAATAAAATATAATTTAATAAAATTCTTAATATAATCATTATTA
42725123 TATGAATTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
57 14 0.31
58 17 0.38
59 3 0.07
60 5 0.11
61 6 0.13
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (58 bp):
TTTAATAAAATAAAATATAATTTAATAAAATTCTTAATATAATCATTATTAATTACAA
Found at i:42725154 original size:23 final size:21
Alignment explanation
Indices: 42725128--42725170 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
42725118 TATTATATGA
42725128 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
42725151 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
42725171 CCTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:42745244 original size:18 final size:18
Alignment explanation
Indices: 42745221--42745268 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
42745211 TAATAATATT
42745221 ATAGAATAATAAAATGAA
1 ATAGAATAATAAAATGAA
* *
42745239 ATAGAA-AAGAAAAATGGA
1 ATAGAATAA-TAAAATGAA
*
42745257 ATAAAATAATAA
1 ATAGAATAATAA
42745269 TAAAACTAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 2 0.08
18 20 0.83
19 2 0.08
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (18 bp):
ATAGAATAATAAAATGAA
Found at i:42747438 original size:42 final size:42
Alignment explanation
Indices: 42747389--42747486 Score: 151
Period size: 42 Copynumber: 2.3 Consensus size: 42
42747379 CATGGCCAGA
42747389 CACACGGGCGTGTAAAGCCATTTCAAGGGTTACACGGCCTGG
1 CACACGGGCGTGTAAAGCCATTTCAAGGGTTACACGGCCTGG
* * * *
42747431 CGCACGGGCGTGTGAGGCCATTTCAAGGGTTACATGGCCTGG
1 CACACGGGCGTGTAAAGCCATTTCAAGGGTTACACGGCCTGG
*
42747473 CACAAGGGCGTGTA
1 CACACGGGCGTGTA
42747487 TCTTGACCGT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.21, C:0.24, G:0.35, T:0.19
Consensus pattern (42 bp):
CACACGGGCGTGTAAAGCCATTTCAAGGGTTACACGGCCTGG
Found at i:42766270 original size:20 final size:18
Alignment explanation
Indices: 42766219--42766271 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 18
42766209 ATCTAGAAGA
42766219 TAATATTAAATTAA-ATT
1 TAATATTAAATTAATATT
42766236 TAATATTAAGA-TAATCACTT
1 TAATATTAA-ATTAAT-A-TT
42766256 TAATATTAAATTAATA
1 TAATATTAAATTAATA
42766272 AAATATTACA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 12 0.39
18 1 0.03
19 3 0.10
20 15 0.48
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (18 bp):
TAATATTAAATTAATATT
Found at i:42771077 original size:23 final size:24
Alignment explanation
Indices: 42771039--42771083 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
42771029 TTTTCTCTTC
*
42771039 TAGTATGAACTTGTCTTACCTTTT
1 TAGTATGAACTCGTCTTACCTTTT
42771063 TAGTAT-AACTCGTCTTACCTT
1 TAGTATGAACTCGTCTTACCTT
42771084 ACCTTACCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.22, C:0.20, G:0.11, T:0.47
Consensus pattern (24 bp):
TAGTATGAACTCGTCTTACCTTTT
Found at i:42780194 original size:26 final size:27
Alignment explanation
Indices: 42780165--42780217 Score: 90
Period size: 28 Copynumber: 2.0 Consensus size: 27
42780155 TTGATATTTT
42780165 TCACAC-TAAGTGTCATTCTCAATATC
1 TCACACGTAAGTGTCATTCTCAATATC
42780191 TCACACGTTAAGTGTCATTCTCAATAT
1 TCACACG-TAAGTGTCATTCTCAATAT
42780218 TTCGTACACT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 6 0.24
28 19 0.76
ACGTcount: A:0.30, C:0.25, G:0.09, T:0.36
Consensus pattern (27 bp):
TCACACGTAAGTGTCATTCTCAATATC
Found at i:42786567 original size:40 final size:40
Alignment explanation
Indices: 42786519--42786667 Score: 111
Period size: 40 Copynumber: 3.6 Consensus size: 40
42786509 CTTTTATCAA
* *
42786519 ATCACCGGCATTTAGCCTGCTAGGTTTTAAACCCAAATTC
1 ATCACCGGCATTTAGCCTGCTAGGCTTTAAACCCAAACTC
*** * ** **
42786559 ATCACCGGCACGAAGCCTGCTAGACTTTAAGTCTGAACTC
1 ATCACCGGCATTTAGCCTGCTAGGCTTTAAACCCAAACTC
* * * *
42786599 ATTCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCGATA-TC
1 A-TCACCGGCATTTAGCCTGCTAGGCTTTAAACCC-AAACTC
*
42786640 ATTTCACCGGCATTATAGCCTACTAGGC
1 A--TCACCGGCATT-TAGCCTGCTAGGC
42786668 CCGAAGCCCG
Statistics
Matches: 83, Mismatches: 22, Indels: 5
0.75 0.20 0.05
Matches are distributed among these distances:
40 31 0.37
41 28 0.34
42 13 0.16
43 11 0.13
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (40 bp):
ATCACCGGCATTTAGCCTGCTAGGCTTTAAACCCAAACTC
Found at i:42786618 original size:41 final size:42
Alignment explanation
Indices: 42786573--42786680 Score: 103
Period size: 43 Copynumber: 2.6 Consensus size: 42
42786563 CCGGCACGAA
* * *
42786573 GCCTGCTAGACTTTAAGTCTGA-ACTCA-TTCACCGGCATTTC
1 GCCTGCTAGACTTGAAGCCCGATA-TCATTTCACCGGCATTTC
* *
42786614 GCCTGCTAGGCTTGAAGCCCGATATCATTTCACCGGCATTATA
1 GCCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATT-TC
* * **
42786657 GCCTACTAGGCCCGAAGCCCGATA
1 GCCTGCTAGACTTGAAGCCCGATA
42786681 ATATTATTCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 21 0.38
42 13 0.23
43 22 0.39
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (42 bp):
GCCTGCTAGACTTGAAGCCCGATATCATTTCACCGGCATTTC
Found at i:42786675 original size:43 final size:42
Alignment explanation
Indices: 42786600--42786680 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
42786590 TCTGAACTCA
* * **
42786600 TTCACCGGCATTTCGCCTGCTAGGCTTGAAGCCCGATATCAT
1 TTCACCGGCATTTAGCCTACTAGGCCCGAAGCCCGATATCAT
42786642 TTCACCGGCATTATAGCCTACTAGGCCCGAAGCCCGATA
1 TTCACCGGCATT-TAGCCTACTAGGCCCGAAGCCCGATA
42786681 ATATTATTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 12 0.35
43 22 0.65
ACGTcount: A:0.22, C:0.32, G:0.21, T:0.25
Consensus pattern (42 bp):
TTCACCGGCATTTAGCCTACTAGGCCCGAAGCCCGATATCAT
Found at i:42786881 original size:28 final size:28
Alignment explanation
Indices: 42786850--42786918 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 28
42786840 ATATTTTGCT
*
42786850 CACTAAGTGTCATTCTCAATATCTCGCA
1 CACTAAGTGCCATTCTCAATATCTCGCA
* *
42786878 CACTAAGTGCCATTCTCAATATTTCGTA
1 CACTAAGTGCCATTCTCAATATCTCGCA
* *
42786906 CACTGAGTACCAT
1 CACTAAGTGCCAT
42786919 ATTTGATTGC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.29, C:0.28, G:0.12, T:0.32
Consensus pattern (28 bp):
CACTAAGTGCCATTCTCAATATCTCGCA
Found at i:42788074 original size:21 final size:21
Alignment explanation
Indices: 42788049--42788093 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
42788039 CGATACCTCA
*
42788049 TAAGGTCATACCACTTGACCT
1 TAAGGTCATACCACTTGAACT
42788070 TAAGGTCATACCACTTGAACT
1 TAAGGTCATACCACTTGAACT
42788091 TAA
1 TAA
42788094 CAAATCACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.29
Consensus pattern (21 bp):
TAAGGTCATACCACTTGAACT
Found at i:42798296 original size:12 final size:12
Alignment explanation
Indices: 42798281--42798305 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42798271 ATCCACTAGT
42798281 ACATCTGTTTCA
1 ACATCTGTTTCA
42798293 ACATCTGTTTCA
1 ACATCTGTTTCA
42798305 A
1 A
42798306 GTCACAAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (12 bp):
ACATCTGTTTCA
Found at i:42803221 original size:42 final size:41
Alignment explanation
Indices: 42803139--42803279 Score: 119
Period size: 41 Copynumber: 3.4 Consensus size: 41
42803129 GAGCTTGGTC
*
42803139 TCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGTT
1 TCGAAGGGCTTTTGAGCCACTGCTAATAACCGAACTTAGTT
* *
42803180 TCGAAGGGCTTTTTAGATCCACTG-TCATAACCGGAA-TTAGTT
1 TCGAAGGGC-TTTT-GAGCCACTGCTAATAACC-GAACTTAGTT
* * * * * * *
42803222 CCGAAGGGCCTTCGAGCCAGTAGTCTAAT--CCGAGCTTGGTC
1 TCGAAGGGCTTTTGAGCCACT-G-CTAATAACCGAACTTAGTT
42803263 TCGAAGGGCTTTTGAGC
1 TCGAAGGGCTTTTGAGC
42803280 TGATGCTAAG
Statistics
Matches: 78, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
40 8 0.10
41 32 0.41
42 25 0.32
43 13 0.17
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.28
Consensus pattern (41 bp):
TCGAAGGGCTTTTGAGCCACTGCTAATAACCGAACTTAGTT
Found at i:42808381 original size:23 final size:22
Alignment explanation
Indices: 42808351--42808430 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 22
42808341 GAGTTGATGG
*
42808351 ACAGTAAGCTAGATTGAGCTGAA
1 ACAGTAAGCTAGA-CGAGCTGAA
*
42808374 ACAGTAAGCTCTGACGAGCTGAA
1 ACAGTAAGCT-AGACGAGCTGAA
42808397 ACAGTAAGCTCTA-ACGAGCTGAAA
1 ACAGTAAG--CTAGACGAGCTG-AA
42808421 ACAGTAAGCT
1 ACAGTAAGCT
42808431 TTTATAAGCT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
22 2 0.04
23 34 0.68
24 12 0.24
25 2 0.04
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.19
Consensus pattern (22 bp):
ACAGTAAGCTAGACGAGCTGAA
Found at i:42808427 original size:24 final size:24
Alignment explanation
Indices: 42808366--42808489 Score: 130
Period size: 23 Copynumber: 5.3 Consensus size: 24
42808356 AAGCTAGATT
*
42808366 GAGCTG-AAACAGTAAGCTCTGAC
1 GAGCTGAAAACAGTAAGCTCTAAC
42808389 GAGCTG-AAACAGTAAGCTCTAAC
1 GAGCTGAAAACAGTAAGCTCTAAC
* * *
42808412 GAGCTGAAAACAGTAAGCTTTTAT
1 GAGCTGAAAACAGTAAGCTCTAAC
* * *
42808436 AAGCT-AAAATAGTAAACTGC-AAC
1 GAGCTGAAAACAGTAAGCT-CTAAC
* *
42808459 AAGCTGAAAACAGTAAGCTCTTAC
1 GAGCTGAAAACAGTAAGCTCTAAC
42808483 GAGCTGA
1 GAGCTGA
42808490 TATATCGGTA
Statistics
Matches: 83, Mismatches: 14, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
23 46 0.55
24 37 0.45
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.20
Consensus pattern (24 bp):
GAGCTGAAAACAGTAAGCTCTAAC
Found at i:42808450 original size:47 final size:47
Alignment explanation
Indices: 42808366--42808479 Score: 133
Period size: 47 Copynumber: 2.4 Consensus size: 47
42808356 AAGCTAGATT
* * *
42808366 GAGCTG-AAACAGTAAGCTCTGACGAGCTGAAACAGTAAGCT-CTAAC
1 GAGCTGAAAACAGTAAGCTCTGACAAGCTAAAACAGTAAACTGC-AAC
* * * *
42808412 GAGCTGAAAACAGTAAGCTTTTATAAGCTAAAATAGTAAACTGCAAC
1 GAGCTGAAAACAGTAAGCTCTGACAAGCTAAAACAGTAAACTGCAAC
*
42808459 AAGCTGAAAACAGTAAGCTCT
1 GAGCTGAAAACAGTAAGCTCT
42808480 TACGAGCTGA
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
46 6 0.11
47 50 0.88
48 1 0.02
ACGTcount: A:0.41, C:0.18, G:0.20, T:0.20
Consensus pattern (47 bp):
GAGCTGAAAACAGTAAGCTCTGACAAGCTAAAACAGTAAACTGCAAC
Found at i:42814846 original size:19 final size:19
Alignment explanation
Indices: 42814811--42814860 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
42814801 TACAAAATAA
*
42814811 TCAAAATAATTTTTAAAAAT
1 TCAAAAT-ATTTATAAAAAT
42814831 TCAAAATATTTATAAAAAT
1 TCAAAATATTTATAAAAAT
*
42814850 TCCAAAT-TTTA
1 TCAAAATATTTA
42814861 ATTATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 4 0.14
19 17 0.61
20 7 0.25
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (19 bp):
TCAAAATATTTATAAAAAT
Found at i:42821058 original size:20 final size:20
Alignment explanation
Indices: 42821030--42821072 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
42821020 CAAATGTTAC
*
42821030 AATAATTTATATAATTGAAT
1 AATAATTTATAAAATTGAAT
* *
42821050 AATATTTTATAAAATTGTAT
1 AATAATTTATAAAATTGAAT
42821070 AAT
1 AAT
42821073 TATATAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AATAATTTATAAAATTGAAT
Found at i:42825258 original size:21 final size:21
Alignment explanation
Indices: 42825232--42825272 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
42825222 AAAATACTTC
42825232 AAAAACTAGAGCTAACAATTG
1 AAAAACTAGAGCTAACAATTG
*
42825253 AAAAACTAGAGCTAATAATT
1 AAAAACTAGAGCTAACAATT
42825273 TCCGCCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.22
Consensus pattern (21 bp):
AAAAACTAGAGCTAACAATTG
Found at i:42836130 original size:35 final size:35
Alignment explanation
Indices: 42836091--42836161 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
42836081 CTGCACCAAC
*
42836091 TTACATCCAGTTACCAACCAATCCAAGCATTGAAT
1 TTACATCCAATTACCAACCAATCCAAGCATTGAAT
42836126 TTACATCCAATTACCAACCAATCCAAGCATTGAAT
1 TTACATCCAATTACCAACCAATCCAAGCATTGAAT
42836161 T
1 T
42836162 CAAGCAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.27
Consensus pattern (35 bp):
TTACATCCAATTACCAACCAATCCAAGCATTGAAT
Found at i:42842726 original size:16 final size:16
Alignment explanation
Indices: 42842702--42842736 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
42842692 TTATTATATA
*
42842702 ATAATGGCTTAATTGG
1 ATAAGGGCTTAATTGG
*
42842718 ATAAGGGCTTATTTGG
1 ATAAGGGCTTAATTGG
42842734 ATA
1 ATA
42842737 TAAGTTACAA
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:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (16 bp):
ATAAGGGCTTAATTGG
Found at i:42843825 original size:24 final size:25
Alignment explanation
Indices: 42843781--42843836 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
42843771 ATTATTTTAG
42843781 ATTAAAAAGTAAATTAGTTTTT-CT
1 ATTAAAAAGTAAATTAGTTTTTACT
* *
42843805 ATTAAAAATTTAATCTA-TTTTTACT
1 ATTAAAAAGTAAAT-TAGTTTTTACT
*
42843830 GTTAAAA
1 ATTAAAA
42843837 CTAGCTCATG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.46
Consensus pattern (25 bp):
ATTAAAAAGTAAATTAGTTTTTACT
Found at i:42843826 original size:25 final size:24
Alignment explanation
Indices: 42843768--42843836 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 24
42843758 AAAAAATGAA
*
42843768 TAAATTA-TTTTA-GATTAAAAAG
1 TAAATTAGTTTTACTATTAAAAAG
* *
42843790 TAAATTAGTTTTTCTATTAAAAAT
1 TAAATTAGTTTTACTATTAAAAAG
* * *
42843814 TTAATCTATTTTTACTGTTAAAA
1 TAAAT-TAGTTTTACTATTAAAA
42843837 CTAGCTCATG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
22 7 0.19
23 4 0.11
24 12 0.32
25 14 0.38
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (24 bp):
TAAATTAGTTTTACTATTAAAAAG
Found at i:42849721 original size:24 final size:22
Alignment explanation
Indices: 42849686--42849730 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
42849676 AAAAAATTGA
42849686 AATAAAATGAAGGAAATTCAAAAG
1 AATAAAATGAA-GAAA-TCAAAAG
42849710 AATAACAA-GAAGAAATCAAAA
1 AATAA-AATGAAGAAATCAAAA
42849731 CAAAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
23 4 0.20
24 8 0.40
25 2 0.10
ACGTcount: A:0.67, C:0.07, G:0.13, T:0.13
Consensus pattern (22 bp):
AATAAAATGAAGAAATCAAAAG
Found at i:42852757 original size:18 final size:18
Alignment explanation
Indices: 42852736--42852770 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
42852726 ATTTATTCTT
42852736 TGTTTTCAATTTTTTTAC
1 TGTTTTCAATTTTTTTAC
* *
42852754 TGTTTTTATTTTTTTTA
1 TGTTTTCAATTTTTTTA
42852771 TTTCTAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.06, G:0.06, T:0.74
Consensus pattern (18 bp):
TGTTTTCAATTTTTTTAC
Found at i:42861644 original size:42 final size:43
Alignment explanation
Indices: 42861562--42861660 Score: 123
Period size: 42 Copynumber: 2.3 Consensus size: 43
42861552 CGCCCCAAAC
* *
42861562 GTGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAGATA
1 GTGGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGA-A
* *
42861606 G-GGTCTTACACGAAATCAAGTA-CGATGCCAAC-GTCCCAGAC
1 GTGGTCTTACACGAAATCAAATATCGATGCC-ACTGTCCCAGAA
42861647 GTGGTCTTACACGA
1 GTGGTCTTACACGA
42861661 TAATACATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 1 0.02
42 27 0.55
43 20 0.41
44 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (43 bp):
GTGGTCTTACACGAAATCAAATATCGATGCCACTGTCCCAGAA
Found at i:42865560 original size:50 final size:49
Alignment explanation
Indices: 42865437--42865573 Score: 141
Period size: 49 Copynumber: 2.8 Consensus size: 49
42865427 ATAGGGTGTA
* * *
42865437 ATGCCGATGCCATGCCCCAGACATGGTCTTACACTGACTATCGAAATCG
1 ATGCCGAAGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCC
* * * * * * *
42865486 AGGCCGACGCCATGTCTCAAACATGGTCTTACACTGGCTCTC-ACATCTCC
1 ATGCCGAAGCCATGTCCCAGACATGGTCTTACACTGACTATCGA-A-ATCC
* *
42865536 TTGCCGAAGCCATGTCCCAGACATGGTCTTATACTGAC
1 ATGCCGAAGCCATGTCCCAGACATGGTCTTACACTGAC
42865574 ACCTTTATAC
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
48 1 0.01
49 36 0.51
50 33 0.47
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (49 bp):
ATGCCGAAGCCATGTCCCAGACATGGTCTTACACTGACTATCGAAATCC
Found at i:42868312 original size:54 final size:54
Alignment explanation
Indices: 42868130--42868290 Score: 252
Period size: 54 Copynumber: 3.0 Consensus size: 54
42868120 GTAAGCGAAT
* * * *
42868130 ACCATATAGTGTAAGGCTTAGCCATTTGCTAT-GAATTTATATGGGGAAAGGAAG
1 ACCATATAGTGTAAGGCCTAGCCGTTTGCTATGGCA-TTATATGGGGAAATGAAG
* *
42868184 ACCATATAGTGTAAGGCCTAGTCGTTTGCTATGGCATCATATGGGGAAATGAAG
1 ACCATATAGTGTAAGGCCTAGCCGTTTGCTATGGCATTATATGGGGAAATGAAG
42868238 ACCATATAGTGTAAGGCCTAGCCGTTTGCTATGGCATTATATGGGGAAATGAA
1 ACCATATAGTGTAAGGCCTAGCCGTTTGCTATGGCATTATATGGGGAAATGAA
42868291 TAATACATAG
Statistics
Matches: 98, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
54 96 0.98
55 2 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.29
Consensus pattern (54 bp):
ACCATATAGTGTAAGGCCTAGCCGTTTGCTATGGCATTATATGGGGAAATGAAG
Found at i:42870645 original size:14 final size:16
Alignment explanation
Indices: 42870626--42870657 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
42870616 GGATAAATTT
42870626 ATTGGCA-AATC-AAA
1 ATTGGCATAATCTAAA
42870640 ATTGGCATAATCTAAA
1 ATTGGCATAATCTAAA
42870656 AT
1 AT
42870658 CCTGGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 4 0.25
16 5 0.31
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (16 bp):
ATTGGCATAATCTAAA
Found at i:42871293 original size:12 final size:13
Alignment explanation
Indices: 42871263--42871292 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
42871253 TATAAGGGCT
*
42871263 TTTTTATTTAATA
1 TTTTTATATAATA
42871276 TTTTTATATAATA
1 TTTTTATATAATA
42871289 TTTT
1 TTTT
42871293 AAATAAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTATATAATA
Found at i:42874729 original size:14 final size:15
Alignment explanation
Indices: 42874712--42874740 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42874702 GAATATGGTA
42874712 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
42874726 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
42874741 TACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:42875160 original size:12 final size:12
Alignment explanation
Indices: 42875143--42875167 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42875133 CATTCATAAT
42875143 ATAAAATAAAAA
1 ATAAAATAAAAA
42875155 ATAAAATAAAAA
1 ATAAAATAAAAA
42875167 A
1 A
42875168 ATTAAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:42876232 original size:37 final size:37
Alignment explanation
Indices: 42876168--42876243 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
42876158 TTACAAGCCA
42876168 AAATCATTATAAGCCACATCTCATGGCTACAT-ACAAC
1 AAATCATTATAAGCCACATCTCATGGCTA-ATCACAAC
*
42876205 AAATCATTATAAGCCA-ATACAT-TTGGCTAATCACAAC
1 AAATCATTATAAGCCACAT-C-TCATGGCTAATCACAAC
42876242 AA
1 AA
42876244 CATCGATCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
36 4 0.11
37 30 0.86
38 1 0.03
ACGTcount: A:0.43, C:0.24, G:0.08, T:0.25
Consensus pattern (37 bp):
AAATCATTATAAGCCACATCTCATGGCTAATCACAAC
Found at i:42882024 original size:55 final size:55
Alignment explanation
Indices: 42881924--42882029 Score: 131
Period size: 55 Copynumber: 1.9 Consensus size: 55
42881914 TGACTTTTAA
* * * *
42881924 ACATGGCCATGGCACACGCCCGTGTGGACTGCCCATGTTCAATACTGACTTTGGG
1 ACATGGCCATGGCACACGCCAGTGTGGACTACCCATGTCCAATACTAACTTTGGG
* * * * *
42881979 ACATGGCTATGGGACACGCCAGTGTGGCCTACCCGTGTCCTATACTAACTT
1 ACATGGCCATGGCACACGCCAGTGTGGACTACCCATGTCCAATACTAACTT
42882030 ATAAATTAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 42 1.00
ACGTcount: A:0.21, C:0.29, G:0.25, T:0.25
Consensus pattern (55 bp):
ACATGGCCATGGCACACGCCAGTGTGGACTACCCATGTCCAATACTAACTTTGGG
Done.