Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold220
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: 3999181
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 12171 characters in sequence are not A, C, G, or T
File 2 of 19
Found at i:219778 original size:4 final size:4
Alignment explanation
Indices: 219769--219807 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
219759 AGAAGTGAAT
219769 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
219808 TACATATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:219816 original size:8 final size:8
Alignment explanation
Indices: 219767--219830 Score: 60
Period size: 8 Copynumber: 8.2 Consensus size: 8
219757 ATAGAAGTGA
219767 ATATACAT
1 ATATACAT
*
219775 ACATACAT
1 ATATACAT
*
219783 ACATACAT
1 ATATACAT
*
219791 ACATACAT
1 ATATACAT
*
219799 ACATAC--
1 ATATACAT
219805 ATATACAT
1 ATATACAT
*
219813 ATATATAT
1 ATATACAT
*
219821 ATATATAT
1 ATATACAT
219829 AT
1 AT
219831 GTATGTATGT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
6 5 0.10
8 46 0.90
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (8 bp):
ATATACAT
Found at i:219820 original size:12 final size:12
Alignment explanation
Indices: 219767--219830 Score: 56
Period size: 12 Copynumber: 5.2 Consensus size: 12
219757 ATAGAAGTGA
*
219767 ATATACATACAT
1 ATATACATATAT
* *
219779 ACATACATACAT
1 ATATACATATAT
* *
219791 ACATACATACATAC
1 ATATACAT--ATAT
219805 ATATACATATAT
1 ATATACATATAT
*
219817 ATATATATATAT
1 ATATACATATAT
219829 AT
1 AT
219831 GTATGTATGT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
12 35 0.80
14 9 0.20
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATACATATAT
Found at i:230794 original size:3 final size:3
Alignment explanation
Indices: 230786--230813 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
230776 AAGAAAATTG
230786 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
230814 CTACAGAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:235501 original size:15 final size:15
Alignment explanation
Indices: 235481--235526 Score: 83
Period size: 15 Copynumber: 3.1 Consensus size: 15
235471 TGGTCTCTAC
*
235481 CTCTTCTCTTCTCTT
1 CTCTTCTCTTCACTT
235496 CTCTTCTCTTCACTT
1 CTCTTCTCTTCACTT
235511 CTCTTCTCTTCACTT
1 CTCTTCTCTTCACTT
235526 C
1 C
235527 ACTTGGAGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.04, C:0.41, G:0.00, T:0.54
Consensus pattern (15 bp):
CTCTTCTCTTCACTT
Found at i:235530 original size:5 final size:5
Alignment explanation
Indices: 235481--235526 Score: 74
Period size: 5 Copynumber: 9.2 Consensus size: 5
235471 TGGTCTCTAC
* *
235481 CTCTT CTCTT CTCTT CTCTT CTCTT CACTT CTCTT CTCTT CACTT C
1 CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT CTCTT C
235527 ACTTGGAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.04, C:0.41, G:0.00, T:0.54
Consensus pattern (5 bp):
CTCTT
Found at i:237551 original size:2 final size:2
Alignment explanation
Indices: 237544--237586 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
237534 GTGACTTTAA
* *
237544 AT AT AT AT AT AT AT AT AT AT AT TT AT AC 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
237586 A
1 A
237587 ATCTATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:237934 original size:12 final size:12
Alignment explanation
Indices: 237907--237958 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
237897 TATATATTTA
237907 TATTTTATTAATGT
1 TATTTT-TT-ATGT
237921 TATTTTTTATGT
1 TATTTTTTATGT
* *
237933 TATATTTTA-AT
1 TATTTTTTATGT
237944 TATTTTTTTATGT
1 TA-TTTTTTATGT
237957 TA
1 TA
237959 AGTTTATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 3 0.09
12 18 0.56
13 5 0.16
14 6 0.19
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (12 bp):
TATTTTTTATGT
Found at i:237946 original size:16 final size:15
Alignment explanation
Indices: 237890--237946 Score: 50
Period size: 14 Copynumber: 3.8 Consensus size: 15
237880 GTAAATTTTA
237890 ATATGTTTATATAT-TT
1 ATAT-TTTAT-TATGTT
237906 ATATTTTATTAATG-T
1 ATATTTTATT-ATGTT
237921 -TATTTT-TTATGTT
1 ATATTTTATTATGTT
237934 ATATTTTAATTAT
1 ATATTTT-ATTAT
237947 TTTTTTATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 3 0.09
13 3 0.09
14 13 0.37
15 8 0.23
16 8 0.23
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (15 bp):
ATATTTTATTATGTT
Found at i:238179 original size:30 final size:30
Alignment explanation
Indices: 238095--238179 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 30
238085 AAAATATTAA
* * *
238095 TTTAATTTTTTAATTT-TTTAAATATAAAT
1 TTTAATATATTAATTTATTTATATATAAAT
* * ** *
238124 TTTTATACATTAATAAATTTTTATATAAAT
1 TTTAATATATTAATTTATTTATATATAAAT
*
238154 TTTAATATGTTAATTTATTTATATAT
1 TTTAATATATTAATTTATTTATATAT
238180 TATTTATGTT
Statistics
Matches: 41, Mismatches: 14, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
29 10 0.24
30 31 0.76
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (30 bp):
TTTAATATATTAATTTATTTATATATAAAT
Found at i:240831 original size:37 final size:36
Alignment explanation
Indices: 240767--240848 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 36
240757 TTTGATTCTT
* * *
240767 AATTTATAAATAAATATCTTATTTTTATGATGTCAAAA
1 AATTT-TATATAAATATCTTATATTTATAATG-CAAAA
* *
240805 TATTTTATATAAATAT-TTATAATTTATAATGGAAAA
1 AATTTTATATAAATATCTTAT-ATTTATAATGCAAAA
240841 AATTTTAT
1 AATTTTAT
240849 TTATTTTAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
36 15 0.41
37 18 0.49
38 4 0.11
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (36 bp):
AATTTTATATAAATATCTTATATTTATAATGCAAAA
Found at i:248413 original size:2 final size:2
Alignment explanation
Indices: 248406--248431 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
248396 ACCATCATAC
248406 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
248432 ATATATATAT
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):
GT
Found at i:253315 original size:12 final size:12
Alignment explanation
Indices: 253298--253322 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
253288 CATCATCATC
253298 GTTGTTATTGTT
1 GTTGTTATTGTT
253310 GTTGTTATTGTT
1 GTTGTTATTGTT
253322 G
1 G
253323 CCGTCACAAC
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:0.08, C:0.00, G:0.28, T:0.64
Consensus pattern (12 bp):
GTTGTTATTGTT
Found at i:254651 original size:2 final size:2
Alignment explanation
Indices: 254644--254668 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
254634 GGAGGATTTC
254644 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
254669 ATGTTATGTA
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:259844 original size:30 final size:29
Alignment explanation
Indices: 259784--259845 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
259774 CATCCACTAA
*
259784 AAAAACTTATATTTTTAACTTACTTCTTT
1 AAAAACTTATATTTTTAACTTAATTCTTT
* * * *
259813 AAAAATTTATTTTTTTATATTTAATTTTTT
1 AAAAACTTATATTTTTA-ACTTAATTCTTT
259843 AAA
1 AAA
259846 CATAATTTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.56
Consensus pattern (29 bp):
AAAAACTTATATTTTTAACTTAATTCTTT
Found at i:260231 original size:6 final size:6
Alignment explanation
Indices: 260220--260253 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
260210 AAAAATGCAA
* *
260220 TATATT TATATT TATATT TATATA TATATA TATA
1 TATATT TATATT TATATT TATATT TATATT TATA
260254 GAGAGAGAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (6 bp):
TATATT
Found at i:262782 original size:29 final size:30
Alignment explanation
Indices: 262714--262789 Score: 79
Period size: 29 Copynumber: 2.7 Consensus size: 30
262704 TTAATTTATA
262714 AATATTTTTA-T-TTAAAATTAAAAAAATT
1 AATATTTTTATTATTAAAATTAAAAAAATT
* * * *
262742 AA-ATCTTAATTATTAAAATT-AAATATTT
1 AATATTTTTATTATTAAAATTAAAAAAATT
*
262770 AATATTTTTATTAATAAAAT
1 AATATTTTTATTATTAAAAT
262790 ATGAATAAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
27 5 0.13
28 11 0.29
29 22 0.58
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
AATATTTTTATTATTAAAATTAAAAAAATT
Found at i:271737 original size:12 final size:12
Alignment explanation
Indices: 271720--271758 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
271710 TGTTTAGGTT
*
271720 TATACATATACA
1 TATACATATATA
271732 TATACATATATA
1 TATACATATATA
*
271744 TATATATATATA
1 TATACATATATA
271756 TAT
1 TAT
271759 CCTCTATATG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TATACATATATA
Found at i:271744 original size:2 final size:2
Alignment explanation
Indices: 271720--271758 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
271710 TGTTTAGGTT
* * *
271720 TA TA CA TA TA CA TA TA CA 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 TA TA TA TA T
271759 CCTCTATATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:272290 original size:2 final size:2
Alignment explanation
Indices: 272285--272312 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
272275 TTTTTATAAA
272285 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
272313 GCACTAAGGT
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:287192 original size:13 final size:13
Alignment explanation
Indices: 287169--287200 Score: 55
Period size: 13 Copynumber: 2.4 Consensus size: 13
287159 CCTTGTTAAA
287169 ATTTCTATTTATCT
1 ATTT-TATTTATCT
287183 ATTTTATTTATCT
1 ATTTTATTTATCT
287196 ATTTT
1 ATTTT
287201 TCTTAAGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.78
14 4 0.22
ACGTcount: A:0.22, C:0.09, G:0.00, T:0.69
Consensus pattern (13 bp):
ATTTTATTTATCT
Found at i:297327 original size:36 final size:36
Alignment explanation
Indices: 297280--297348 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
297270 ATTACATTTG
297280 CAACTGCAATAAAGGTGACAAGATCAAAAATGTTCT
1 CAACTGCAATAAAGGTGACAAGATCAAAAATGTTCT
297316 CAACTGCAATAAAGGTGACAAGATCAAAAATGT
1 CAACTGCAATAAAGGTGACAAGATCAAAAATGT
297349 GCCCACAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.46, C:0.16, G:0.17, T:0.20
Consensus pattern (36 bp):
CAACTGCAATAAAGGTGACAAGATCAAAAATGTTCT
Found at i:298639 original size:3 final size:3
Alignment explanation
Indices: 298631--298667 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
298621 AAAAGTAACC
298631 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
298668 CTCAGTGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:305243 original size:2 final size:2
Alignment explanation
Indices: 305236--305277 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
305226 TTTCTTTATA
*
305236 TC TC TC TC TC TC TC AC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
305278 ATTTCATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.50, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:306329 original size:2 final size:2
Alignment explanation
Indices: 306322--306347 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
306312 GCATCTTCTT
306322 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
306348 AAGACAAAAA
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:306730 original size:18 final size:20
Alignment explanation
Indices: 306703--306741 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
306693 TATAAGTAAA
306703 TTAAATTTTTTTA-TATATT
1 TTAAATTTTTTTATTATATT
306722 TTAAA-TTTTTTATTATATT
1 TTAAATTTTTTTATTATATT
306741 T
1 T
306742 AAAAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTAAATTTTTTTATTATATT
Found at i:307657 original size:2 final size:2
Alignment explanation
Indices: 307650--307683 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
307640 TTCCTTCCCT
307650 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
307684 CACACCCACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:313860 original size:2 final size:2
Alignment explanation
Indices: 313853--313877 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
313843 CAGGAATCAC
313853 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
313878 CCTTGAAGCG
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:314524 original size:18 final size:19
Alignment explanation
Indices: 314501--314539 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
314491 ATAGAATGAT
*
314501 TAAAATTT-TTAATAATTA
1 TAAAATTTATAAATAATTA
314519 TAAAATTTATAAATAATTA
1 TAAAATTTATAAATAATTA
314538 TA
1 TA
314540 TTTAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAAATTTATAAATAATTA
Found at i:316061 original size:2 final size:2
Alignment explanation
Indices: 316054--316082 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
316044 AACGAAAATT
316054 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
316083 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:316087 original size:2 final size:2
Alignment explanation
Indices: 316082--316111 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
316072 TCTCTCTCTC
*
316082 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
316112 AGGCTTCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:317168 original size:2 final size:2
Alignment explanation
Indices: 317161--317188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
317151 AGCACAGGTT
317161 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
317189 ATTCTTCAAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:322011 original size:21 final size:20
Alignment explanation
Indices: 321987--322027 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
321977 AATATCGTTG
* *
321987 TTAGTATGAGTTTTTTTTTTT
1 TTAGTAAGA-TTTATTTTTTT
322008 TTAGTAAGATTTATTTTTTT
1 TTAGTAAGATTTATTTTTTT
322028 ATAATGTTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.12, T:0.68
Consensus pattern (20 bp):
TTAGTAAGATTTATTTTTTT
Found at i:325928 original size:29 final size:30
Alignment explanation
Indices: 325894--325960 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
325884 ATATAATTAT
325894 TTTTAATA-AAAAATATTA-TAAATATTAAA
1 TTTTAATATAAAAA-ATTATTAAATATTAAA
** *
325923 TTTTAA-ATTTAAAATTATTAAATATTAAT
1 TTTTAATATAAAAAATTATTAAATATTAAA
325952 TTTTAATAT
1 TTTTAATAT
325961 GATTATATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 5 0.16
29 25 0.78
30 2 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (30 bp):
TTTTAATATAAAAAATTATTAAATATTAAA
Found at i:326343 original size:13 final size:13
Alignment explanation
Indices: 326322--326368 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
326312 AATAATAATT
*
326322 ATATTTTTATATA
1 ATATTTTTATAAA
*
326335 ATTTTTTTATAAA
1 ATATTTTTATAAA
326348 ATATTTTTA-AAA
1 ATATTTTTATAAA
326360 TATATTTTT
1 -ATATTTTT
326369 TATTTAAGTG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
12 3 0.10
13 27 0.90
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATATTTTTATAAA
Found at i:326680 original size:24 final size:23
Alignment explanation
Indices: 326653--326734 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 23
326643 AATTATATGA
326653 ATTTAATTTTTTAAGATATAATTT
1 ATTTAATTTTTTAA-ATATAATTT
* *
326677 ATTTTTATTTTTTAAATTTAATTATAT
1 A-TTTAATTTTTTAAATATAA-T-T-T
326704 CAATTTAATTATTTTAAAATATAATTT
1 --ATTTAATT-TTTT-AAATATAATTT
326731 ATTT
1 ATTT
326735 TTATTTATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 15
0.71 0.06 0.23
Matches are distributed among these distances:
24 6 0.13
25 17 0.37
26 1 0.02
27 2 0.04
28 7 0.15
29 6 0.13
30 7 0.15
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.60
Consensus pattern (23 bp):
ATTTAATTTTTTAAATATAATTT
Found at i:326732 original size:54 final size:56
Alignment explanation
Indices: 326642--326812 Score: 204
Period size: 58 Copynumber: 3.0 Consensus size: 56
326632 TTATTTTTAA
* * **
326642 AAATTATATGAATTTAATT-TTTTAAGATATAATTTATTTTTATTT-TTTAAATTT
1 AAATTATATCAATTTAATTATTTTAAAATATAATTTATTTTTATTTATAAAAATTT
326696 -AATTATATCAATTTAATTATTTTAAAATATAATTTATTTTTATTTATAAAAATTT
1 AAATTATATCAATTTAATTATTTTAAAATATAATTTATTTTTATTTATAAAAATTT
* ** * *
326751 AAAATTATTTTTTATTTGATTATTTTAAAATATGATTTATTTTTATTTATAAATTAATTT
1 -AAATTA-TATCAATTTAATTATTTTAAAATATAATTTATTTTTATTTATAAA--AATTT
326811 AA
1 AA
326813 TTTTTGAGAT
Statistics
Matches: 101, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
53 17 0.17
54 25 0.25
55 7 0.07
57 5 0.05
58 40 0.40
59 2 0.02
60 5 0.05
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (56 bp):
AAATTATATCAATTTAATTATTTTAAAATATAATTTATTTTTATTTATAAAAATTT
Found at i:326741 original size:31 final size:30
Alignment explanation
Indices: 326706--326799 Score: 97
Period size: 31 Copynumber: 3.2 Consensus size: 30
326696 AATTATATCA
326706 ATTTAATTATTTTAAAATATAATTTATTTTT
1 ATTTAATTATTTTAAAATAT-ATTTATTTTT
** *
326737 ATTTATAAAAATTTAAAAT-TA--T-TTTTT
1 ATTTA-ATTATTTTAAAATATATTTATTTTT
*
326764 ATTTGATTATTTTAAAATATGATTTATTTTT
1 ATTTAATTATTTTAAAATAT-ATTTATTTTT
326795 ATTTA
1 ATTTA
326800 TAAATTAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
26 10 0.20
27 10 0.20
28 2 0.04
30 2 0.04
31 15 0.31
32 10 0.20
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (30 bp):
ATTTAATTATTTTAAAATATATTTATTTTT
Found at i:326753 original size:32 final size:31
Alignment explanation
Indices: 326716--326812 Score: 89
Period size: 27 Copynumber: 3.2 Consensus size: 31
326706 ATTTAATTAT
326716 TTTAAAATATAATTTATTTTTATTTATAAAAA
1 TTTAAAATAT-ATTTATTTTTATTTATAAAAA
* *
326748 TTTAAAAT-TA--T-TTTTTATTTGAT--TAT
1 TTTAAAATATATTTATTTTTATTT-ATAAAAA
326774 TTTAAAATATGATTTATTTTTATTTATAAATTAA
1 TTTAAAATAT-ATTTATTTTTATTTATAAA--AA
326808 TTTAA
1 TTTAA
326813 TTTTTGAGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 18
0.70 0.05 0.25
Matches are distributed among these distances:
26 9 0.18
27 10 0.20
28 4 0.08
30 4 0.08
31 10 0.20
32 8 0.16
34 6 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTAAAATATATTTATTTTTATTTATAAAAA
Found at i:327099 original size:3 final size:3
Alignment explanation
Indices: 327091--327120 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
327081 TAAAATATGA
327091 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
327121 CATATAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:336006 original size:20 final size:20
Alignment explanation
Indices: 335966--336017 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
335956 CAAATATTTT
*
335966 TAATA-TTAATATATTTTAA
1 TAATATTTAATATATTTAAA
335985 TAATATTTAATATCA-TTAAA
1 TAATATTTAATAT-ATTTAAA
*
336005 TATTATTTTAATA
1 TAATA-TTTAATA
336018 GTAAATACTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 5 0.18
20 15 0.54
21 8 0.29
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TAATATTTAATATATTTAAA
Found at i:336087 original size:33 final size:31
Alignment explanation
Indices: 336041--336119 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 31
336031 ATAAAATTAT
*
336041 TTATTATTAAAATATTAATTCTAGTAATATTTA
1 TTATTATTGAAATATTAATTCTAGTAATA--TA
* * *
336074 TTATTATTGAAATATTATTTTTATTAATATA
1 TTATTATTGAAATATTAATTCTAGTAATATA
336105 --ATTATTGAAATATTA
1 TTATTATTGAAATATTA
336120 TTATAAATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.36
31 2 0.05
33 25 0.60
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (31 bp):
TTATTATTGAAATATTAATTCTAGTAATATA
Found at i:336091 original size:14 final size:14
Alignment explanation
Indices: 336072--336123 Score: 61
Period size: 14 Copynumber: 3.6 Consensus size: 14
336062 TAGTAATATT
336072 TATTATTATTGAAA
1 TATTATTATTGAAA
*
336086 TATTATT-TTTATTAA
1 TATTATTATTGA--AA
*
336101 TATAATTATTGAAA
1 TATTATTATTGAAA
336115 TATTATTAT
1 TATTATTAT
336124 AAATAATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
13 3 0.10
14 17 0.55
15 8 0.26
16 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (14 bp):
TATTATTATTGAAA
Found at i:336130 original size:29 final size:29
Alignment explanation
Indices: 336076--336131 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
336066 AATATTTATT
* * *
336076 ATTATTGAAATATTATTTTTATTAATATA
1 ATTATTGAAATATTATTATAAATAATATA
336105 ATTATTGAAATATTATTATAAATAATA
1 ATTATTGAAATATTATTATAAATAATA
336132 ATATAACTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (29 bp):
ATTATTGAAATATTATTATAAATAATATA
Found at i:336134 original size:32 final size:29
Alignment explanation
Indices: 336043--336142 Score: 83
Period size: 29 Copynumber: 3.2 Consensus size: 29
336033 AAAATTATTT
* * *
336043 ATTATTAAAATATTAATTCTAGTAATATTTATT
1 ATTATTGAAATATT-ATT-TA-TAATA-ATATA
* *
336076 ATTATTGAAATATTATTTTTATTAATATA
1 ATTATTGAAATATTATTTATAATAATATA
336105 ATTATTGAAATATTATTATAAATAATAATATA
1 ATTATTGAAATATTATT-T--ATAATAATATA
*
336137 ACTATT
1 ATTATT
336143 AAGAGAATAT
Statistics
Matches: 56, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
29 20 0.36
30 5 0.09
31 1 0.02
32 17 0.30
33 13 0.23
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (29 bp):
ATTATTGAAATATTATTTATAATAATATA
Found at i:336808 original size:6 final size:6
Alignment explanation
Indices: 336797--336838 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
336787 AAAAAATTTT
* *
336797 ATTTAA ATTTAA ATTTAA ATTT-A ATTAAA ATTATGA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT-TAA ATTTAA
336839 TAAATAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 4 0.13
6 22 0.73
7 4 0.13
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:336814 original size:12 final size:11
Alignment explanation
Indices: 336790--336838 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
336780 TTGACCTAAA
*
336790 AAATTTTATTT
1 AAATTTAATTT
336801 AAATTTAAATTT
1 AAATTT-AATTT
*
336813 AAATTTAATTA
1 AAATTTAATTT
336824 AAATTATGAATTT
1 AAATT-T-AATTT
336837 AA
1 AA
336839 TAAATAATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
11 15 0.47
12 11 0.34
13 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:336827 original size:23 final size:24
Alignment explanation
Indices: 336790--336838 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 24
336780 TTGACCTAAA
* *
336790 AAATTTTATTTAAATT-TAAATTT
1 AAATTTAATTAAAATTATAAATTT
*
336813 AAATTTAATTAAAATTATGAATTT
1 AAATTTAATTAAAATTATAAATTT
336837 AA
1 AA
336839 TAAATAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (24 bp):
AAATTTAATTAAAATTATAAATTT
Found at i:337079 original size:13 final size:15
Alignment explanation
Indices: 337055--337087 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
337045 AAAAATATAT
337055 ATTTTAAAATTT-AA
1 ATTTTAAAATTTAAA
337069 ATTTT-AAATTTAAA
1 ATTTTAAAATTTAAA
337083 ATTTT
1 ATTTT
337088 CATTTACTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAAAATTTAAA
Found at i:337590 original size:26 final size:25
Alignment explanation
Indices: 337560--337620 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
337550 ATTTTAAATT
337560 TAAATTAATGTAA-AATATATT-TATTA
1 TAAATTAAT-TAATAA-ATATTAT-TTA
337586 TAAATTATATTAATAAATATTATTTA
1 TAAATTA-ATTAATAAATATTATTTA
337612 TAAATTAAT
1 TAAATTAAT
337621 ATTTTTATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 2 0.06
26 25 0.78
27 5 0.16
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (25 bp):
TAAATTAATTAATAAATATTATTTA
Found at i:337636 original size:22 final size:22
Alignment explanation
Indices: 337603--337645 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
337593 TATTAATAAA
337603 TATTATTTATAAATTAATATTTT
1 TATTATTTATAAATTAA-ATTTT
337626 TATT-TTTATAAATTAAATTT
1 TATTATTTATAAATTAAATTT
337646 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TATTATTTATAAATTAAATTTT
Found at i:339177 original size:15 final size:14
Alignment explanation
Indices: 339150--339212 Score: 63
Period size: 15 Copynumber: 4.2 Consensus size: 14
339140 TTTTTTATTG
*
339150 ATTATAATTTTAAAT
1 ATTA-AATTTAAAAT
339165 ATATAAATATTAAAAT
1 AT-TAAAT-TTAAAAT
339181 ATTAAATTTAATAAT
1 ATTAAATTTAA-AAT
**
339196 ACAAAATTTAAAAT
1 ATTAAATTTAAAAT
339210 ATT
1 ATT
339213 TTATTCGTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
14 8 0.20
15 22 0.55
16 10 0.25
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTAAATTTAAAAT
Found at i:339522 original size:20 final size:21
Alignment explanation
Indices: 339499--339560 Score: 64
Period size: 16 Copynumber: 3.2 Consensus size: 21
339489 ATAATATAAA
*
339499 TTAATATT-TAATTTTATTAT
1 TTAATATTATAAATTTATTAT
339519 TTAATATTATAAATTTA-T-T
1 TTAATATTATAAATTTATTAT
*
339538 TT--T-TTATAAATTTATCAT
1 TTAATATTATAAATTTATTAT
339556 TTAAT
1 TTAAT
339561 TATAACATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
16 11 0.31
17 1 0.03
18 3 0.09
19 3 0.09
20 10 0.29
21 7 0.20
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTAATATTATAAATTTATTAT
Found at i:339622 original size:16 final size:16
Alignment explanation
Indices: 339603--339641 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
339593 AATATTCAAA
339603 AATTTAAATATAATAT
1 AATTTAAATATAATAT
* *
339619 AATTTAAATTTATTAT
1 AATTTAAATATAATAT
339635 AATTTAA
1 AATTTAA
339642 TACAAATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAATATAATAT
Found at i:340182 original size:20 final size:20
Alignment explanation
Indices: 340144--340182 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
340134 AAAAATAATT
* * *
340144 ATTATTACATATTATATATA
1 ATTATTAAATAATAAATATA
340164 ATTATTAAATAATAAATAT
1 ATTATTAAATAATAAATAT
340183 TTATTTTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
ATTATTAAATAATAAATATA
Found at i:340605 original size:21 final size:20
Alignment explanation
Indices: 340580--340637 Score: 53
Period size: 21 Copynumber: 2.9 Consensus size: 20
340570 AAATAATATG
340580 AATTAAATATAAATAAATTT
1 AATTAAATATAAATAAATTT
** **
340600 ATATTATTTATTTATAAATTT
1 A-ATTAAATATAAATAAATTT
* *
340621 AATCAAATAAAAATAAA
1 AATTAAATATAAATAAA
340638 AATAAAATAT
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
20 11 0.41
21 16 0.59
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTAAATATAAATAAATTT
Found at i:341487 original size:11 final size:11
Alignment explanation
Indices: 341471--341519 Score: 55
Period size: 11 Copynumber: 4.3 Consensus size: 11
341461 TTTTATTTTT
341471 AAATTTATAAA
1 AAATTTATAAA
341482 AAATTT-TAAA
1 AAATTTATAAA
341492 AATATTATATAAA
1 AA-ATT-TATAAA
*
341505 AATATTTTTAAA
1 AA-ATTTATAAA
341517 AAA
1 AAA
341520 AATTAAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
10 6 0.18
11 10 0.29
12 8 0.24
13 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTTATAAA
Found at i:341506 original size:13 final size:12
Alignment explanation
Indices: 341473--341518 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 12
341463 TTATTTTTAA
341473 ATTTATAAAAA-
1 ATTTATAAAAAT
341484 ATTT-TAAAAAT
1 ATTTATAAAAAT
341495 ATTATATAAAAAT
1 ATT-TATAAAAAT
*
341508 ATTTTTAAAAA
1 ATTTATAAAAA
341519 AAATTAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
10 6 0.19
11 7 0.23
12 8 0.26
13 10 0.32
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTTATAAAAAT
Found at i:342085 original size:15 final size:15
Alignment explanation
Indices: 342067--342137 Score: 56
Period size: 15 Copynumber: 4.7 Consensus size: 15
342057 TAAAAAATAA
342067 TAAATTTAATAAATT
1 TAAATTTAATAAATT
342082 TAAA-TTAATAAAATT
1 TAAATTTAAT-AAATT
**
342097 T-AATTTAAATTTATT
1 TAAATTT-AATAAATT
* *
342112 TAATTTTATATAATTT
1 TAAATTTA-ATAAATT
*
342128 TTAATTTAAT
1 TAAATTTAAT
342138 TTTTTAAAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
14 7 0.16
15 19 0.44
16 17 0.40
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TAAATTTAATAAATT
Found at i:342137 original size:22 final size:22
Alignment explanation
Indices: 342109--342150 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
342099 ATTTAAATTT
*
342109 ATTTAATTTTATATAATTTTTA
1 ATTTAATTTTATAAAATTTTTA
*
342131 ATTTAATTTTTTAAAATTTT
1 ATTTAATTTTATAAAATTTT
342151 AAATATTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTAATTTTATAAAATTTTTA
Found at i:342529 original size:537 final size:529
Alignment explanation
Indices: 341524--342708 Score: 1400
Period size: 537 Copynumber: 2.2 Consensus size: 529
341514 AAAAAAAATT
** *
341524 AAAAATATATAAATTAAACTAATTTAAATTTGTAAAATTTAATTCAAATCTATTTAATTTTATAT
1 AAAAATA-ATAAATTAAA-TAATTTAAATTAATAAAATTTAATTCAAATTTATTTAATTTTATAT
*
341589 AATTTTTATTTAATTTTTAAAAAATTCAAAATATTATAT-ATAAATCATAAATTTTATTTAAAAT
64 AATTTTTATTTAATTTTT-AAAAATTTAAAATATTATATAAT-AATCATAAATTTTATTTAAAAT
* ** * * *
341653 TAAATTATTATCACCTTTAAAAAATCAACTCAAGACCTCAACGTTCACCTAACTCTTTTTCTAAA
127 T-AATTATAATCACAGTTAAAAAATCAACTCAAAACCTCAACGTTCACATAACTCATTTTCTAAA
*
341718 TAAATATAATAAAATGATATATACATACTAAAAACCAATTATGATGAACTTCTGAACAATATAAT
191 TAAATATAATAAAATGATATATACATACTAAAAAACAATTATGATGAACTTCTGAACAATATAAT
* * *
341783 TTAGAGACGGTAGGGTCAGGGCCTCTGAGGGGTGGGGTTGAAAGGAAGGGGTTGCGTTGACGTTT
256 TTAGAGACCGTAGGGTCAGGGCCTCTCAGGGGTGGGGTTGAAAGGAAGGGGCTGCGTTGACGTTT
341848 ACTTCGACCCTTTTTTCTTTGAAAAAAAATATTTCTTACATTGTCATTTTTAAAAATTAAAAACA
321 ACTTCGA-CCTTTTTTCTTT-----AAAATATTTCTTACATTGTCATTTTTAAAAATTAAAAACA
* * * *
341913 AGTACTTATAAATTGGAAAAAAAAGGCACTTTTTACAGTAACATACGCTAAATGATTTTAATTTT
380 AGTACTAATAAATTGGAAAAAAAAGGCACTTTTTACAATAACATACGCTAAACGATTTCAATTTT
* * *
341978 TTTTAAAGGTAAAATAATATTATAAATTTT-AAAAAT-AAAAATTTTATGTTT-GTTTTATTTAA
445 TTTAAAAAGTAAAATAATAGTATAAATTTTAAAAAATGAAAAATTTT-T-TTTGGTTTTATTTAA
342040 ATTATATTTT-AA-T-TTTTTA
508 ATTATATTTTAAATTATTTTTA
* *
342059 AAAAATAATAAATTTAATAAATTTAAATTAATAAAATTTAATTTAAATTTATTTAATTTTATATA
1 AAAAATAATAAATTAAAT-AATTTAAATTAATAAAATTTAATTCAAATTTATTTAATTTTATATA
* * * *
342124 ATTTTTAATTTAATTTTTTAAAATTTTAAATATTACATAATAATTATAAATTTT-TTTAAAACTT
65 ATTTTT-ATTTAATTTTTAAAAATTTAAAATATTATATAATAATCATAAATTTTATTTAAAA-TT
*
342188 -ATCTA-AATCA-AGTTAAAACCAGCTCAACCTCGTAACAACCTCAACGTTCACATAACTCATTT
128 AAT-TATAATCACAGTTAAAA--A-ATCAA-CTC--AA-AACCTCAACGTTCACATAACTCATTT
* * *
342250 TCTAAATAAATGTAATAAAATTATATATATGTACATAAGTTATGAAAAACAATTATGATGAACTT
185 TCTAAATAAATATAATAAAA-T-GATATA--TACAT-A-CTA--AAAAACAATTATGATGAACTT
* ** * * *
342315 GTG-AGTA-ATAATTTGGAGTCCGTAGGGTCAGGGCCTCTCAGGGGTGGGGTTG-AAGGCAGGTG
242 CTGAACAATATAATTTAGAGACCGTAGGGTCAGGGCCTCTCAGGGGTGGGGTTGAAAGGAAGG-G
* *
342377 GCTGCGTTGACGTTTACTTCTA-CTTATTGTT-TTT-AAATATTTCTTACATTGTCATTTTTAGC
306 GCTGCGTTGACGTTTACTTCGACCTT-TT-TTCTTTAAAATATTTCTTACATTGTCATTTTTA-A
* * * *
342439 AAA-TAAAAAC-AGCTACTAATAAATTGGAAAAAAAAGGGATTTTTTACAATAATATATGCTAAA
368 AAATTAAAAACAAG-TACTAATAAATTGGAAAAAAAAGGCACTTTTTACAATAACATACGCTAAA
* ** *
342502 CGGTTTCAATTTTTTTAAAAAGTAAAATAATAGTATAGTTTTTAAAAAATGAAAACTTTTTTTTG
432 CGATTTCAATTTTTTTAAAAAGTAAAATAATAGTATAAATTTTAAAAAATGAAAAATTTTTTTTG
342567 GTTTTATTTAAATTATATTTTAAATTTATTTTTA
497 GTTTTATTTAAATTATATTTTAAA-TTATTTTTA
* * * * *
342601 AAAATTAATAAATTAAATTAATCTAATTTGATAAAATTTAATTCAAACTTATTTAATTTTATATA
1 AAAAATAATAAATTAAA-TAATTTAAATTAATAAAATTTAATTCAAATTTATTTAATTTTATATA
* *
342666 AATTTTATTTAATTTTTAAAAATTTAAAATATTATATATTAAT
65 ATTTTTATTTAATTTTTAAAAATTTAAAATATTATATAATAAT
342709 AATTATTTTT
Statistics
Matches: 558, Mismatches: 59, Indels: 60
0.82 0.09 0.09
Matches are distributed among these distances:
531 6 0.01
532 6 0.01
533 11 0.02
534 91 0.16
535 23 0.04
536 2 0.00
537 117 0.21
538 73 0.13
539 11 0.02
540 5 0.01
541 34 0.06
542 75 0.13
543 14 0.03
544 66 0.12
545 2 0.00
546 22 0.04
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.41
Consensus pattern (529 bp):
AAAAATAATAAATTAAATAATTTAAATTAATAAAATTTAATTCAAATTTATTTAATTTTATATAA
TTTTTATTTAATTTTTAAAAATTTAAAATATTATATAATAATCATAAATTTTATTTAAAATTAAT
TATAATCACAGTTAAAAAATCAACTCAAAACCTCAACGTTCACATAACTCATTTTCTAAATAAAT
ATAATAAAATGATATATACATACTAAAAAACAATTATGATGAACTTCTGAACAATATAATTTAGA
GACCGTAGGGTCAGGGCCTCTCAGGGGTGGGGTTGAAAGGAAGGGGCTGCGTTGACGTTTACTTC
GACCTTTTTTCTTTAAAATATTTCTTACATTGTCATTTTTAAAAATTAAAAACAAGTACTAATAA
ATTGGAAAAAAAAGGCACTTTTTACAATAACATACGCTAAACGATTTCAATTTTTTTAAAAAGTA
AAATAATAGTATAAATTTTAAAAAATGAAAAATTTTTTTTGGTTTTATTTAAATTATATTTTAAA
TTATTTTTA
Found at i:342673 original size:21 final size:20
Alignment explanation
Indices: 342649--342690 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
342639 TAATTCAAAC
*
342649 TTATTTAATTTTATATAAATT
1 TTATTTAATTTT-TAAAAATT
342670 TTATTTAATTTTTAAAAATT
1 TTATTTAATTTTTAAAAATT
342690 T
1 T
342691 AAAATATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTTAATTTTTAAAAATT
Found at i:343107 original size:13 final size:13
Alignment explanation
Indices: 343070--343109 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
343060 GAATTAATTT
343070 TTTAAAAAATAAA
1 TTTAAAAAATAAA
* * *
343083 ATTATAATATAAA
1 TTTAAAAAATAAA
343096 TTTAAAAAATAAA
1 TTTAAAAAATAAA
343109 T
1 T
343110 ATTTTATATT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
TTTAAAAAATAAA
Found at i:343124 original size:26 final size:26
Alignment explanation
Indices: 343066--343126 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
343056 AAATGAATTA
343066 ATTT-TTTAAAAAATAAAATTATAAT
1 ATTTATTTAAAAAATAAAATTATAAT
** *
343091 ATAAATTTAAAAAATAAATATT-TTAT
1 ATTTATTTAAAAAATAAA-ATTATAAT
343117 ATTTATTTAA
1 ATTTATTTAA
343127 TTCCAATTCC
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 2 0.07
26 24 0.83
27 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (26 bp):
ATTTATTTAAAAAATAAAATTATAAT
Found at i:344048 original size:39 final size:39
Alignment explanation
Indices: 343996--344664 Score: 773
Period size: 39 Copynumber: 17.0 Consensus size: 39
343986 GTTCAACCCC
* * * * *
343996 AGAGATGAGTGAAGAACCCAGTGAAGTTAATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* *
344035 AGAAATCATTGAAGAACCCAATGAAGGTGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
*
344074 AGAGAACACTGAAGAACCCAATGAAGGTGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * *
344113 GGAGATCATTGAAGAACCCAATGAAGGTAATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
*
344152 AGAGATCATTGAAGAACCCAATGAAGGTGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* *
344191 AGAGAACACTGAAGAACCTAATGAAGGTGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * **
344230 GGAGATCACCGAAGAACCCAATGAAGGCAATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* *
344269 AGAGAACACTGAAGAACCTAATGAAGGTGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * **
344308 GGAGATCACTGAAGAACCCAATAAAGGCAATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* *
344347 AGAGATCATTGAAGAACCCAATGAAGATGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * * * *
344386 AGAGACCACCGAAGAACCTAATGAAGGTCATACCAAAGC
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * * *
344425 AGAGATCATTGAAGCACCTAATGAAGCTGATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * * *
344464 AGAGATCACTGAAAAACCTAATGAAGGTAATATCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* * *
344503 AGAGATCATTGAAGAACCCAATGAACGTGACACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
* *
344542 GGAGATCACTGAAGAACCCAATGAAGGTAATGATACCCAAGA
1 AGAGATCACTGAAGAACCCAATGAAGG---TGATACCAAAGA
* * * * ** *
344584 AAATATCAGTGAAAAACAAAATGAAGGTAATAATACCAAAGA
1 AGAGATCACTGAAGAACCCAATGAAGG---TGATACCAAAGA
* * **
344626 AGATGA-CACTGAAGGACACAATGAAGGCAATACCAAAGA
1 AGA-GATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
344665 GATCAGTGAA
Statistics
Matches: 536, Mismatches: 90, Indels: 8
0.85 0.14 0.01
Matches are distributed among these distances:
39 473 0.88
42 62 0.12
43 1 0.00
ACGTcount: A:0.48, C:0.17, G:0.22, T:0.14
Consensus pattern (39 bp):
AGAGATCACTGAAGAACCCAATGAAGGTGATACCAAAGA
Found at i:344864 original size:16 final size:17
Alignment explanation
Indices: 344840--344872 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
344830 AATATATATA
*
344840 TATATTTATAA-GAAAC
1 TATAATTATAAGGAAAC
344856 TATAATTATAAGGAAAC
1 TATAATTATAAGGAAAC
344873 GAGGAAACGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (17 bp):
TATAATTATAAGGAAAC
Found at i:353760 original size:2 final size:2
Alignment explanation
Indices: 353753--353782 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
353743 CTGCTTGATA
353753 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
353783 TAATTCTCTG
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:360315 original size:19 final size:19
Alignment explanation
Indices: 360277--360315 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
360267 GTGCTAAATT
**
360277 ATTTTGTTTAGAGTTCTTA
1 ATTTTGTTTAGACATCTTA
*
360296 ATTTTGTTTAGACATGTTA
1 ATTTTGTTTAGACATCTTA
360315 A
1 A
360316 GGTTCTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.15, T:0.54
Consensus pattern (19 bp):
ATTTTGTTTAGACATCTTA
Found at i:369572 original size:2 final size:2
Alignment explanation
Indices: 369565--369593 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
369555 TTACTTCTGT
369565 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
369594 GTTGGCTTAA
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:371818 original size:51 final size:51
Alignment explanation
Indices: 371706--371818 Score: 145
Period size: 51 Copynumber: 2.2 Consensus size: 51
371696 CCCTGGTGGT
** * * **
371706 GGTGGTCCTGATGGCCCACGTGGAAACCCGAAGCCCCCCAGCCCCTGAGGA
1 GGTGGTCCTGGCGGCCCACGTGGAAACCCAAAGCCCCCAAGCCCAGGAGGA
* * *
371757 GATGGTCCTGGCGGCCCACGTGGAAACCCAAAGGCCTCAAGCCCAGGAGGA
1 GGTGGTCCTGGCGGCCCACGTGGAAACCCAAAGCCCCCAAGCCCAGGAGGA
371808 GGTGGTCCTGG
1 GGTGGTCCTGG
371819 TGGTGGGCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.20, C:0.33, G:0.35, T:0.12
Consensus pattern (51 bp):
GGTGGTCCTGGCGGCCCACGTGGAAACCCAAAGCCCCCAAGCCCAGGAGGA
Found at i:372833 original size:5 final size:5
Alignment explanation
Indices: 372823--372847 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
372813 AAGGAGGAGT
372823 TGAGG TGAGG TGAGG TGAGG TGAGG
1 TGAGG TGAGG TGAGG TGAGG TGAGG
372848 CCGGTCGGCG
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:0.20, C:0.00, G:0.60, T:0.20
Consensus pattern (5 bp):
TGAGG
Found at i:373090 original size:2 final size:2
Alignment explanation
Indices: 373083--373121 Score: 60
Period size: 2 Copynumber: 19.0 Consensus size: 2
373073 CCAAGTACTT
*
373083 TA TA TA TA TA TA TA TA TA CTT TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA
373122 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 33 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:373104 original size:21 final size:21
Alignment explanation
Indices: 373078--373121 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
373068 GTTTACCAAG
373078 TACTTTATATATATATATATA
1 TACTTTATATATATATATATA
373099 TACTTTATATATATATATATA
1 TACTTTATATATATATATATA
373120 TA
1 TA
373122 GAGAGAGAGA
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:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TACTTTATATATATATATATA
Found at i:373126 original size:2 final size:2
Alignment explanation
Indices: 373121--373150 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
373111 ATATATATAT
373121 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
373151 TGAATAAAGT
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):
AG
Found at i:389135 original size:20 final size:20
Alignment explanation
Indices: 389110--389157 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
389100 GAGTGGGAAC
389110 TATGAAACTAGATCCCTTTG
1 TATGAAACTAGATCCCTTTG
389130 TATGAAACTAGATCCCTTTG
1 TATGAAACTAGATCCCTTTG
*
389150 AATGAAAC
1 TATGAAAC
389158 CTGACTACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (20 bp):
TATGAAACTAGATCCCTTTG
Found at i:396459 original size:2 final size:2
Alignment explanation
Indices: 396454--396484 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
396444 GGGGAAAAAA
396454 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
396485 TGAGTTTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:405538 original size:52 final size:52
Alignment explanation
Indices: 405455--405560 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
405445 GAAAGACTAA
*
405455 TTAAGAATTTAAGATAGAGAAACCTTACAAATTGGCAAATGACAATTATGAC
1 TTAAGAATTTAAGATAGAGAAACCTTACAAATTGGCAAATGACAACTATGAC
* *
405507 TTAAGAATTTAAGATTGAGAAACCTTGCAAATTGGCAAATGACAACTATGAC
1 TTAAGAATTTAAGATAGAGAAACCTTACAAATTGGCAAATGACAACTATGAC
405559 TT
1 TT
405561 TATGACTGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.43, C:0.12, G:0.16, T:0.28
Consensus pattern (52 bp):
TTAAGAATTTAAGATAGAGAAACCTTACAAATTGGCAAATGACAACTATGAC
Found at i:406075 original size:15 final size:15
Alignment explanation
Indices: 406055--406122 Score: 66
Period size: 16 Copynumber: 4.4 Consensus size: 15
406045 TATTTTCATA
406055 TTTTTAAATTTTATT
1 TTTTTAAATTTTATT
**
406070 TTTTTAAATATAAATT
1 TTTTTAAAT-TTTATT
*
406086 TTTTTAATATTTTAAT
1 TTTTTAA-ATTTTATT
*
406102 TTTTTACAATATT-TT
1 TTTTTA-AATTTTATT
406117 TTTTTA
1 TTTTTA
406123 CATCAAGACT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
15 16 0.37
16 24 0.56
17 3 0.07
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTAAATTTTATT
Found at i:406119 original size:31 final size:30
Alignment explanation
Indices: 406055--406122 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 30
406045 TATTTTCATA
*
406055 TTTTTAAATTTTATTTTTTTAAATATAAATT
1 TTTTTAAATTTTAATTTTTTAAATAT-AATT
*
406086 TTTTTAATATTTTAATTTTTTACAATAT-TTT
1 TTTTTAA-ATTTTAATTTTTTA-AATATAATT
406117 TTTTTA
1 TTTTTA
406123 CATCAAGACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 15 0.45
32 13 0.39
33 5 0.15
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (30 bp):
TTTTTAAATTTTAATTTTTTAAATATAATT
Found at i:408555 original size:98 final size:98
Alignment explanation
Indices: 408350--408533 Score: 316
Period size: 97 Copynumber: 1.9 Consensus size: 98
408340 CTAATATGTT
408350 ACGTAATTAAATATCACCATCGAAACATAGATATTTTTTTTTATTATTTTTGTTATAAAATCATA
1 ACGTAATTAAATATCACCATCGAAACATAGATATTTTTTTTTATTATTTTTGTTATAAAATCATA
* * * * *
408415 CCGCCGTTTCTGAAGTTTTATGCCTAATATTTT
66 CCGCAGTTTCTGAAGTTTTATACCTAAGATATA
408448 ACGTAATTAAATATCACCATCGAAACATAGATA-TTTTTTTTATTATTTTTGTTATAAAATCATA
1 ACGTAATTAAATATCACCATCGAAACATAGATATTTTTTTTTATTATTTTTGTTATAAAATCATA
408512 CCGCAGTTTCTGAAGTTTTATA
66 CCGCAGTTTCTGAAGTTTTATA
408534 ACTTAGAGGA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
97 51 0.61
98 33 0.39
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (98 bp):
ACGTAATTAAATATCACCATCGAAACATAGATATTTTTTTTTATTATTTTTGTTATAAAATCATA
CCGCAGTTTCTGAAGTTTTATACCTAAGATATA
Found at i:410155 original size:10 final size:10
Alignment explanation
Indices: 410140--410177 Score: 62
Period size: 10 Copynumber: 4.0 Consensus size: 10
410130 TTGTATTTTT
410140 CATATATATA
1 CATATATATA
410150 CATATATA-A
1 CATATATATA
410159 -ATATATATA
1 CATATATATA
410168 CATATATATA
1 CATATATATA
410178 TTTGGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 7 0.27
9 2 0.08
10 17 0.65
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (10 bp):
CATATATATA
Found at i:410164 original size:18 final size:18
Alignment explanation
Indices: 410141--410175 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
410131 TGTATTTTTC
410141 ATATATATACATATATAA
1 ATATATATACATATATAA
410159 ATATATATACATATATA
1 ATATATATACATATATA
410176 TATTTGGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATATATACATATATAA
Found at i:410643 original size:16 final size:16
Alignment explanation
Indices: 410622--410652 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
410612 ATATATATTT
410622 ATTTAAATTTAAATTA
1 ATTTAAATTTAAATTA
*
410638 ATTTAATTTTAAATT
1 ATTTAAATTTAAATT
410653 TATCAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAAATTTAAATTA
Found at i:410867 original size:17 final size:17
Alignment explanation
Indices: 410856--410891 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
410846 TAAATTTACT
410856 TAATATATAAATATAAA
1 TAATATATAAATATAAA
*
410873 TAATATATATTATATAAA
1 TAATATATA-AATATAAA
410891 T
1 T
410892 GAGGAGCAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATATAAATATAAA
Found at i:423525 original size:22 final size:24
Alignment explanation
Indices: 423490--423534 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
423480 TATTATATAA
423490 TTTAATTATAAAAAATAAATAAAG
1 TTTAATTATAAAAAATAAATAAAG
*
423514 TTTAATT-T-AAAAATAATTAAA
1 TTTAATTATAAAAAATAAATAAA
423535 AATGAATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 12 0.60
23 1 0.05
24 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
TTTAATTATAAAAAATAAATAAAG
Found at i:423556 original size:2 final size:2
Alignment explanation
Indices: 423544--423578 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
423534 AAATGAATAA
423544 AT AT GAT 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
423579 TAGTAAATGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:425090 original size:3 final size:3
Alignment explanation
Indices: 425082--425131 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
425072 CTTGTTTAAA
* *
425082 ATT ATT ATT ACT CTT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
425130 AT
1 AT
425132 GTTGCACTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:427146 original size:17 final size:17
Alignment explanation
Indices: 427124--427160 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
427114 AGGAATAACA
*
427124 TTGCTCTCCTATTTGGT
1 TTGCTCTCCTATGTGGT
427141 TTGCTCTCCTATGTGGT
1 TTGCTCTCCTATGTGGT
427158 TTG
1 TTG
427161 ATATTAGCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (17 bp):
TTGCTCTCCTATGTGGT
Found at i:427202 original size:2 final size:2
Alignment explanation
Indices: 427195--427228 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
427185 AGTAATCACA
427195 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
427229 TTACTTCTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:431091 original size:34 final size:34
Alignment explanation
Indices: 431049--431158 Score: 107
Period size: 34 Copynumber: 3.2 Consensus size: 34
431039 GTGATTTGTA
431049 ATTGTTGATCAAATGAAAAATTTGATAGTTTATC
1 ATTGTTGATCAAATGAAAAATTTGATAGTTTATC
* * *****
431083 ATTATTGATTAAATGGGTGGTTTGAT-GATTTATC
1 ATTGTTGATCAAATGAAAAATTTGATAG-TTTATC
* *
431117 ATTGTTGA-CTAAATAAAAAATTTGTTAGTTTATC
1 ATTGTTGATC-AAATGAAAAATTTGATAGTTTATC
431151 ATTGTTGA
1 ATTGTTGA
431159 ATTAAATAGA
Statistics
Matches: 57, Mismatches: 16, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
33 1 0.02
34 55 0.96
35 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.45
Consensus pattern (34 bp):
ATTGTTGATCAAATGAAAAATTTGATAGTTTATC
Found at i:431149 original size:68 final size:69
Alignment explanation
Indices: 431035--431165 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 69
431025 TCATTATTAA
* * *
431035 TTTGGTGATTTGTAATTGTTGATCAAATGAAAAATTTGATAGTTTATCATTATTG-ATTAAATGG
1 TTTGATGATTTATAATTGTTGATCAAATAAAAAATTTGATAGTTTATCATTATTGAATTAAATGG
431099 GTGG
66 GTGG
* * *
431103 TTTGATGATTTATCATTGTTGA-CTAAATAAAAAATTTGTTAGTTTATCATTGTTGAATTAAAT
1 TTTGATGATTTATAATTGTTGATC-AAATAAAAAATTTGATAGTTTATCATTATTGAATTAAAT
431166 AGATGATTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
67 1 0.02
68 47 0.85
69 7 0.13
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.46
Consensus pattern (69 bp):
TTTGATGATTTATAATTGTTGATCAAATAAAAAATTTGATAGTTTATCATTATTGAATTAAATGG
GTGG
Found at i:432462 original size:28 final size:28
Alignment explanation
Indices: 432426--432482 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
432416 CCTAGTTTGA
*
432426 TATATTTGGTGAAAAATCTGGCGATGAT
1 TATATTTGGTCAAAAATCTGGCGATGAT
* *
432454 TATATTTGGTCAAAAATCTGTCTATGAT
1 TATATTTGGTCAAAAATCTGGCGATGAT
432482 T
1 T
432483 TCTCTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (28 bp):
TATATTTGGTCAAAAATCTGGCGATGAT
Found at i:433937 original size:21 final size:21
Alignment explanation
Indices: 433913--433955 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
433903 GTTCTATTCG
*
433913 CTGCTGCTCCTTCTCCTGCCT
1 CTGCTGCTCCTCCTCCTGCCT
*
433934 CTGCTGCTCCTCCTTCTGCCT
1 CTGCTGCTCCTCCTCCTGCCT
433955 C
1 C
433956 CACTTCTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.49, G:0.14, T:0.37
Consensus pattern (21 bp):
CTGCTGCTCCTCCTCCTGCCT
Found at i:437551 original size:54 final size:54
Alignment explanation
Indices: 437469--437590 Score: 208
Period size: 54 Copynumber: 2.3 Consensus size: 54
437459 CCTCGTGAAC
437469 TAGGCTTGATAAAACAACAGATTTTTTTCTTAATATTGATCATAAAATCTTTGA
1 TAGGCTTGATAAAACAACAGATTTTTTTCTTAATATTGATCATAAAATCTTTGA
* * *
437523 TAGGCTTGATAAAACAACATATTTTTTTCTTGATCTTGATCATAAAATCTTTGA
1 TAGGCTTGATAAAACAACAGATTTTTTTCTTAATATTGATCATAAAATCTTTGA
*
437577 TAGGCTGGATAAAA
1 TAGGCTTGATAAAA
437591 TCTTTAACTT
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 64 1.00
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.39
Consensus pattern (54 bp):
TAGGCTTGATAAAACAACAGATTTTTTTCTTAATATTGATCATAAAATCTTTGA
Found at i:440420 original size:19 final size:19
Alignment explanation
Indices: 440396--440434 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
440386 ATTAATTACA
* *
440396 CATAAGATGTAAGTATATT
1 CATAAGACGTAAATATATT
440415 CATAAGACGTAAATATATT
1 CATAAGACGTAAATATATT
440434 C
1 C
440435 TTATATTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.33
Consensus pattern (19 bp):
CATAAGACGTAAATATATT
Found at i:448873 original size:18 final size:19
Alignment explanation
Indices: 448844--448879 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
448834 TAAAGTGATA
448844 TGAAAGATAAAAGCAAAGG
1 TGAAAGATAAAAGCAAAGG
*
448863 TGAAAGA-AAAAGGAAAG
1 TGAAAGATAAAAGCAAAG
448880 TCGAGAGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.61, C:0.03, G:0.28, T:0.08
Consensus pattern (19 bp):
TGAAAGATAAAAGCAAAGG
Found at i:449787 original size:8 final size:8
Alignment explanation
Indices: 449771--449831 Score: 58
Period size: 8 Copynumber: 8.0 Consensus size: 8
449761 TGATATAATA
*
449771 ATTTTTAT
1 ATTTATAT
449779 ATTTATAT
1 ATTTATAT
*
449787 AATTTTTAT
1 -ATTTATAT
449796 A-TTATA-
1 ATTTATAT
449802 ATTT-TAT
1 ATTTATAT
*
449809 -TTAATAT
1 ATTTATAT
449816 ATTTATAT
1 ATTTATAT
449824 ATTTATAT
1 ATTTATAT
449832 CATATTTATT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
6 5 0.12
7 9 0.21
8 22 0.51
9 7 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
ATTTATAT
Found at i:449790 original size:17 final size:17
Alignment explanation
Indices: 449768--449831 Score: 68
Period size: 17 Copynumber: 4.1 Consensus size: 17
449758 GTTTGATATA
449768 ATAATTTTTATATTTAT
1 ATAATTTTTATATTTAT
449785 ATAATTTTTATA--T-T
1 ATAATTTTTATATTTAT
*
449799 ATAA-TTTTAT-TTAAT
1 ATAATTTTTATATTTAT
*
449814 AT-ATTTATATATTTAT
1 ATAATTTTTATATTTAT
449830 AT
1 AT
449832 CATATTTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
13 6 0.15
14 6 0.15
15 9 0.23
16 6 0.15
17 12 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATAATTTTTATATTTAT
Found at i:449803 original size:14 final size:14
Alignment explanation
Indices: 449763--449806 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
449753 ATGTTGTTTG
*
449763 ATATAATAATTTTT
1 ATATTATAATTTTT
449777 ATATTTATATAATTTTT
1 ATA--T-TATAATTTTT
449794 ATATTATAATTTT
1 ATATTATAATTTT
449807 ATTTAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.46
15 1 0.04
16 1 0.04
17 12 0.46
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
ATATTATAATTTTT
Found at i:449819 original size:28 final size:31
Alignment explanation
Indices: 449763--449826 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 31
449753 ATGTTGTTTG
* * *
449763 ATATAATAATTTTTATATTTATATAATTTTT
1 ATATTATAATTTTTATATTAATATAATTTAT
449794 ATATTATAA-TTTTAT-TTAATAT-ATTTAT
1 ATATTATAATTTTTATATTAATATAATTTAT
449822 ATATT
1 ATATT
449827 TATATCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 10 0.33
29 6 0.20
30 6 0.20
31 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
ATATTATAATTTTTATATTAATATAATTTAT
Found at i:449838 original size:19 final size:17
Alignment explanation
Indices: 449806--449840 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
449796 ATTATAATTT
449806 TATTTAATATATTTATA
1 TATTTAATATATTTATA
449823 TATTTATATCATATTTAT
1 TATTTA-AT-ATATTTAT
449841 TTCTCATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 2 0.12
19 8 0.50
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTTAATATATTTATA
Found at i:465747 original size:21 final size:22
Alignment explanation
Indices: 465723--465772 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
465713 TTTTTAATTA
* *
465723 ATATTATTTTGATAAATTTTT-
1 ATATAATTTTAATAAATTTTTG
*
465744 ATATAATTTTAATAATTTTTTG
1 ATATAATTTTAATAAATTTTTG
465766 ATATAAT
1 ATATAAT
465773 ACTTGTAAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (22 bp):
ATATAATTTTAATAAATTTTTG
Found at i:465836 original size:10 final size:10
Alignment explanation
Indices: 465809--465860 Score: 61
Period size: 10 Copynumber: 5.2 Consensus size: 10
465799 ATATTTGATT
465809 TAATTTTTAA
1 TAATTTTTAA
*
465819 TAAATTTTAA
1 TAATTTTTAA
*
465829 TATTTTTTAA
1 TAATTTTTAA
*
465839 -ATATTTTTAT
1 TA-ATTTTTAA
465849 TAATTTTTAA
1 TAATTTTTAA
465859 TA
1 TA
465861 CTTAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 1 0.03
10 32 0.94
11 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:466099 original size:8 final size:8
Alignment explanation
Indices: 466086--466136 Score: 50
Period size: 8 Copynumber: 6.0 Consensus size: 8
466076 AAAACTTTAA
466086 ATTTTATT
1 ATTTTATT
466094 ATTTTATT
1 ATTTTATT
*
466102 ATATTTAAATAA
1 AT-TTT--AT-T
466114 ATTTTATT
1 ATTTTATT
466122 -TTTTATT
1 ATTTTATT
466129 ATTTTATT
1 ATTTTATT
466137 TATATTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
7 7 0.19
8 17 0.47
9 5 0.14
11 5 0.14
12 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (8 bp):
ATTTTATT
Found at i:466115 original size:28 final size:26
Alignment explanation
Indices: 466083--466134 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
466073 AAAAAAACTT
466083 TAAATTTTATTATTTTATTATATTTAAA
1 TAAATTTTATT-TTTTATTAT-TTTAAA
466111 TAAATTTTATTTTTTATTATTTTA
1 TAAATTTTATTTTTTATTATTTTA
466135 TTTATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 11 0.46
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TAAATTTTATTTTTTATTATTTTAAA
Found at i:466126 original size:35 final size:37
Alignment explanation
Indices: 466087--466160 Score: 134
Period size: 36 Copynumber: 2.1 Consensus size: 37
466077 AAACTTTAAA
466087 TTTTATTATTTTA-TTATATTTAAATAAA-TTTTATT
1 TTTTATTATTTTATTTATATTTAAATAAATTTTTATT
466122 TTTTATTATTTTATTTATATTTAAATAAATTTTTATT
1 TTTTATTATTTTATTTATATTTAAATAAATTTTTATT
466159 TT
1 TT
466161 AAATAAAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
35 13 0.35
36 15 0.41
37 9 0.24
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (37 bp):
TTTTATTATTTTATTTATATTTAAATAAATTTTTATT
Found at i:466161 original size:35 final size:35
Alignment explanation
Indices: 466067--466161 Score: 129
Period size: 35 Copynumber: 2.7 Consensus size: 35
466057 TTAGGCTAAA
* * * *
466067 ATATTAAAAAAAACTTTAAATTTTATTATTTTATT
1 ATATTTAAATAAATTTTATATTTTATTATTTTATT
*
466102 ATATTTAAATAAATTTTATTTTTTATTATTTTATTT
1 ATATTTAAATAAATTTTATATTTTATTATTTTA-TT
466138 ATATTTAAATAAATTTT-TATTTTA
1 ATATTTAAATAAATTTTATATTTTA
466162 AATAAAATAT
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
35 34 0.64
36 19 0.36
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (35 bp):
ATATTTAAATAAATTTTATATTTTATTATTTTATT
Found at i:466169 original size:18 final size:18
Alignment explanation
Indices: 466100--466167 Score: 68
Period size: 17 Copynumber: 3.8 Consensus size: 18
466090 TATTATTTTA
466100 TTATATTTAAATAAA-TT
1 TTATATTTAAATAAATTT
* * * **
466117 TTATTTTTTATTATTTTAT
1 TTATATTTAAATAAATT-T
466136 TTATATTTAAATAAATTT
1 TTATATTTAAATAAATTT
466154 TTAT-TTTAAATAAA
1 TTATATTTAAATAAA
466168 ATATTAATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
17 20 0.51
18 6 0.15
19 13 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTATATTTAAATAAATTT
Found at i:466178 original size:17 final size:17
Alignment explanation
Indices: 466140--466178 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
466130 TTTTATTTAT
* *
466140 ATTTAAATAAATTTTTA
1 ATTTAAATAAAATATTA
*
466157 TTTTAAATAAAATATTA
1 ATTTAAATAAAATATTA
466174 ATTTA
1 ATTTA
466179 CGCTTAGACT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATAAAATATTA
Found at i:466527 original size:29 final size:28
Alignment explanation
Indices: 466482--466566 Score: 82
Period size: 29 Copynumber: 2.9 Consensus size: 28
466472 GTTTAAAAAC
*
466482 ATAAATTAAAAATTAAAAACTTCTTTAA
1 ATAAAATAAAAATTAAAAACTTCTTTAA
** * *
466510 ATCTAATAAAAATATAAAAATTTATTTAA
1 ATAAAATAAAAAT-TAAAAACTTCTTTAA
466539 ATAAAATAATAAAATTTAAAAAC-TCTTT
1 ATAAAAT-A-AAAA-TTAAAAACTTCTTT
466567 TAATTTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
28 10 0.23
29 18 0.41
30 5 0.11
31 10 0.23
32 1 0.02
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (28 bp):
ATAAAATAAAAATTAAAAACTTCTTTAA
Found at i:466528 original size:49 final size:49
Alignment explanation
Indices: 466434--466529 Score: 115
Period size: 49 Copynumber: 2.0 Consensus size: 49
466424 TATTTAAATT
* * * *
466434 TAAATTAAAAATTAAGAAATTTTTAAGTATAATTTAAAGTTTAAAAACA
1 TAAATTAAAAATTAAGAAATTTTTAAATATAATTAAAAATATAAAAACA
*
466483 TAAATTAAAAATTAA-AAACTTCTTTAAATCTAA-TAAAAATATAAAAA
1 TAAATTAAAAATTAAGAAA-TT-TTTAAATATAATTAAAAATATAAAAA
466530 TTTATTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 3 0.08
49 28 0.70
50 9 0.22
ACGTcount: A:0.58, C:0.04, G:0.03, T:0.34
Consensus pattern (49 bp):
TAAATTAAAAATTAAGAAATTTTTAAATATAATTAAAAATATAAAAACA
Found at i:469947 original size:2 final size:2
Alignment explanation
Indices: 469940--470000 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
469930 ACTAGGGTGT
469940 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
469982 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
470001 GTGAAAGGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:473262 original size:2 final size:2
Alignment explanation
Indices: 473255--473289 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
473245 ACTATGTATT
473255 TA TA TA 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 TA TA TA T
473290 GCACACACAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:473665 original size:18 final size:18
Alignment explanation
Indices: 473642--473683 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
473632 GTCAACTCCT
473642 TTCTTCTC-TGTCTTCTTC
1 TTCTTCTCTTG-CTTCTTC
473660 TTCTTCTCTTGCTTCTTC
1 TTCTTCTCTTGCTTCTTC
*
473678 TGCTTC
1 TTCTTC
473684 ACTACTGCAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.91
19 2 0.09
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (18 bp):
TTCTTCTCTTGCTTCTTC
Found at i:474536 original size:2 final size:2
Alignment explanation
Indices: 474529--474553 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
474519 AGTGTGCGTG
474529 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 T
474554 GCTGTGCCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:476645 original size:16 final size:17
Alignment explanation
Indices: 476624--476657 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
476614 AAATAACATC
*
476624 TAATATAT-TTAAATTT
1 TAATATATATAAAATTT
476640 TAATATATATAAAATTT
1 TAATATATATAAAATTT
476657 T
1 T
476658 TTCACTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATATATATAAAATTT
Found at i:485989 original size:16 final size:15
Alignment explanation
Indices: 485931--485990 Score: 54
Period size: 16 Copynumber: 4.0 Consensus size: 15
485921 ATTTTTATTA
485931 AATATATTAA-AAAT
1 AATATATTAATAAAT
* *
485945 AAAAT-TTAATAAAA
1 AATATATTAATAAAT
485959 AAT-TATTATTATAAAT
1 AATATATTA--ATAAAT
485975 AATATATTAATTAAAT
1 AATATATTAA-TAAAT
485991 TAAAATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
13 5 0.14
14 12 0.33
15 1 0.03
16 13 0.36
17 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATATTAATAAAT
Found at i:485998 original size:17 final size:15
Alignment explanation
Indices: 485929--485999 Score: 58
Period size: 17 Copynumber: 4.6 Consensus size: 15
485919 ATATTTTTAT
485929 TAAATATATTAA-AAA
1 TAAA-ATATTAATAAA
485944 TAAAAT-TTAATAAA
1 TAAAATATTAATAAA
*
485958 -AAATTATTATTATAAA
1 TAAAATATTA--ATAAA
*
485974 TAATATATTAATTAAA
1 TAAAATATTAA-TAAA
485990 TTAAAATATT
1 -TAAAATATT
486000 TTAAAGATAT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
13 8 0.18
14 8 0.18
15 5 0.11
16 9 0.20
17 15 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TAAAATATTAATAAA
Found at i:486571 original size:18 final size:18
Alignment explanation
Indices: 486548--486625 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
486538 TATATTTTAT
486548 ATTTAAATTTAAATAATA
1 ATTTAAATTTAAATAATA
*
486566 ATTT-AAGTTAAATAATA
1 ATTTAAATTTAAATAATA
* * **
486583 TTATTAAATTT-TATTTTA
1 AT-TTAAATTTAAATAATA
486601 TATTTAAA-TTAAATTAATA
1 -ATTTAAATTTAAA-TAATA
486620 ATTTAA
1 ATTTAA
486626 TAAATTTAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
17 15 0.33
18 22 0.49
19 8 0.18
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (18 bp):
ATTTAAATTTAAATAATA
Found at i:488470 original size:2 final size:2
Alignment explanation
Indices: 488463--488491 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
488453 TGTAAACTTT
488463 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
488492 CACTGGGTGT
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
Done.