Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold246
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: 1425817
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
File 6 of 8
Found at i:758480 original size:16 final size:16
Alignment explanation
Indices: 758459--758512 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
758449 GACTAAAAAC
758459 ATAAATTTATTATATT
1 ATAAATTTATTATATT
758475 ATAAATTCT-TTATATTT
1 ATAAATT-TATTATA-TT
**
758492 ATACTTTTA-TATATT
1 ATAAATTTATTATATT
758507 ATAAAT
1 ATAAAT
758513 AAAAAGAGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
15 6 0.19
16 17 0.55
17 8 0.26
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAAATTTATTATATT
Found at i:762400 original size:2 final size:2
Alignment explanation
Indices: 762395--762419 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
762385 TGTGTTATAT
762395 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
762420 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:762869 original size:26 final size:26
Alignment explanation
Indices: 762836--762886 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
762826 ATCAATTGAT
762836 AATGAAATTATTAA-ACTCTATAAATG
1 AATGAAATTA-TAAGACTCTATAAATG
*
762862 AATGAAATTATAAGATTCTATAAAT
1 AATGAAATTATAAGACTCTATAAAT
762887 ATGTTGCCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.35
Consensus pattern (26 bp):
AATGAAATTATAAGACTCTATAAATG
Found at i:763845 original size:2 final size:2
Alignment explanation
Indices: 763834--763870 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
763824 TGCTTTGCCT
763834 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
763871 TAGTTTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:776826 original size:19 final size:19
Alignment explanation
Indices: 776791--776830 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
776781 GTTAAAAAAA
*
776791 TTCTTAAATCATATCATAT
1 TTCTTAAATAATATCATAT
776810 TTCTTAAATAAGT-TCATAT
1 TTCTTAAATAA-TATCATAT
776829 TT
1 TT
776831 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.35, C:0.12, G:0.03, T:0.50
Consensus pattern (19 bp):
TTCTTAAATAATATCATAT
Found at i:776996 original size:30 final size:29
Alignment explanation
Indices: 776909--777041 Score: 76
Period size: 30 Copynumber: 4.5 Consensus size: 29
776899 ATCAGTTTAT
*
776909 GTTAAATATTTATTTAAGTATAAATTAAAA
1 GTTAAAAATTTA-TTAAGTATAAATTAAAA
* * * * ***
776939 GTAAAAAAATTT-TTGATTTTCTTTTAAAA
1 GT-TAAAAATTTATTAAGTATAAATTAAAA
776968 GTTAAAAATTTATCTAAGTATAAATTAAATA
1 GTTAAAAATTTAT-TAAGTATAAATTAAA-A
* * *
776999 -TTAAAGACTTATATAAATAT-AA-TAAAA
1 GTTAAAAATTTAT-TAAGTATAAATTAAAA
*
777026 ATATAAAAATTTATTA
1 GT-TAAAAATTTATTA
777042 GATAAAATAG
Statistics
Matches: 76, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
27 1 0.01
28 15 0.20
29 25 0.33
30 27 0.36
31 8 0.11
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (29 bp):
GTTAAAAATTTATTAAGTATAAATTAAAA
Found at i:777050 original size:28 final size:28
Alignment explanation
Indices: 776963--777050 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
776953 GATTTTCTTT
* * *
776963 TAAAAGTTAAAAATTTATCTAAGTATAAAT
1 TAAAAATTAAAAATTTATAT-AG-ATAAAA
* * * * *
776993 TAAATATTAAAGACTTATATAAATATAA
1 TAAAAATTAAAAATTTATATAGATAAAA
777021 TAAAAATATAAAAATTTAT-TAGATAAAA
1 TAAAAAT-TAAAAATTTATATAGATAAAA
777049 TA
1 TA
777051 GTAAAGTTTT
Statistics
Matches: 44, Mismatches: 13, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
28 19 0.43
29 10 0.23
30 15 0.34
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (28 bp):
TAAAAATTAAAAATTTATATAGATAAAA
Found at i:779048 original size:27 final size:25
Alignment explanation
Indices: 779017--779067 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
779007 AAAATGAGTG
*
779017 ATTAATGATGAAAATTTTAAAAAAAAA
1 ATTAATGA--AAAATTATAAAAAAAAA
*
779044 ATTAATGAAAAATTATATAAAAAA
1 ATTAATGAAAAATTATAAAAAAAA
779068 TTCAGTAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
27 8 0.36
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (25 bp):
ATTAATGAAAAATTATAAAAAAAAA
Found at i:780123 original size:10 final size:10
Alignment explanation
Indices: 780096--780140 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
780086 TCTCTCTCTT
*
780096 TATGTATATA
1 TATGTATATG
*
780106 TATATATATG
1 TATGTATATG
780116 TATGTATATG
1 TATGTATATG
780126 TATG-A-ATG
1 TATGTATATG
780134 TATGTAT
1 TATGTAT
780141 TTATCTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
8 7 0.23
9 2 0.07
10 21 0.70
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (10 bp):
TATGTATATG
Found at i:786158 original size:18 final size:19
Alignment explanation
Indices: 786123--786164 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
786113 TGAAACTAAG
*
786123 TTATATTTTTTATTAATTT
1 TTATATATTTTATTAATTT
786142 TTATATATTTT-TTAATTT
1 TTATATATTTTATTAATTT
*
786160 ATATA
1 TTATA
786165 AAATAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (19 bp):
TTATATATTTTATTAATTT
Found at i:786391 original size:103 final size:103
Alignment explanation
Indices: 786195--786396 Score: 239
Period size: 103 Copynumber: 2.0 Consensus size: 103
786185 ATCTAAATTT
* * * * * *
786195 ATTTAAATATGTCAAAAATAATATTAAAAAGTACATAAAACTAAAAACATTCATATTCCAAAATC
1 ATTTAAATATGTAAAAAATAATATTAAAAAGCACATAAAAATAAAAAAAATCATATTCAAAAATC
** * *
786260 AATGAATCAAATGGATCTGAACATATAAACTTTAATCA
66 AATGAATCAAATGGATCCAAACAGATAAAATTTAATCA
*
786298 ATTTAAATATGTTAAAAAATAATATTAAAAAGCACA-AGAAAATAAAAAAAAT-ATCTTCAAAAA
1 ATTTAAATATG-TAAAAAATAATATTAAAAAGCACATA-AAAATAAAAAAAATCATATTCAAAAA
* *
786361 TCAAT-ATATCAAATTGATCCAAATAGATAAAATTTA
64 TCAATGA-ATCAAATGGATCCAAACAGATAAAATTTA
786397 GATAAAATCG
Statistics
Matches: 83, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
102 1 0.01
103 49 0.59
104 33 0.40
ACGTcount: A:0.55, C:0.10, G:0.05, T:0.29
Consensus pattern (103 bp):
ATTTAAATATGTAAAAAATAATATTAAAAAGCACATAAAAATAAAAAAAATCATATTCAAAAATC
AATGAATCAAATGGATCCAAACAGATAAAATTTAATCA
Found at i:789967 original size:2 final size:2
Alignment explanation
Indices: 789956--789984 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
789946 GTAAATTAAA
789956 AT AT -T 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
789985 TGCAGGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:790624 original size:3 final size:3
Alignment explanation
Indices: 790616--790652 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
790606 TAATGAATTC
790616 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
790653 TTCAATATTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:791688 original size:20 final size:20
Alignment explanation
Indices: 791663--791703 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
791653 AAAATATATA
*
791663 TAAAAATT-ATAATTAAGATT
1 TAAAAATTGA-AATTAAAATT
791683 TAAAAATTGAAATTAAAATT
1 TAAAAATTGAAATTAAAATT
791703 T
1 T
791704 TCGTCACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (20 bp):
TAAAAATTGAAATTAAAATT
Found at i:793790 original size:26 final size:26
Alignment explanation
Indices: 793755--793814 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
793745 TTAAATTATC
*
793755 TTAAATTTTTTTTAATTGAACT-TTTTA
1 TTAAA-TTTTTTAAATTGAA-TATTTTA
*
793782 TTAAATTTTTTAAATTTAATATTTTA
1 TTAAATTTTTTAAATTGAATATTTTA
*
793808 TTCAATT
1 TTAAATT
793815 AAGTTCAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 23 0.79
27 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (26 bp):
TTAAATTTTTTAAATTGAATATTTTA
Found at i:799619 original size:20 final size:20
Alignment explanation
Indices: 799596--799640 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
799586 CAAATAAATT
**
799596 AATTAAAATTTTTAAATTTA
1 AATTAAAATTGATAAATTTA
799616 AATTAAAATTGATAAATTTA
1 AATTAAAATTGATAAATTTA
*
799636 TATTA
1 AATTA
799641 TAACTCTTAC
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:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
AATTAAAATTGATAAATTTA
Found at i:800166 original size:17 final size:17
Alignment explanation
Indices: 800141--800181 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
800131 TTAAAAATAA
800141 TTATATAATTTTTAATT
1 TTATATAATTTTTAATT
*
800158 TTATTTAATTTTTAATT
1 TTATATAATTTTTAATT
800175 TTA-ATAA
1 TTATATAA
800182 AATTATATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 3 0.14
17 19 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATATAATTTTTAATT
Found at i:808155 original size:2 final size:2
Alignment explanation
Indices: 808150--808177 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
808140 AAATTTCGAA
808150 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
808178 GGAGTACCTG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:809641 original size:15 final size:15
Alignment explanation
Indices: 809621--809683 Score: 56
Period size: 15 Copynumber: 4.1 Consensus size: 15
809611 AAAAATTTAA
*
809621 TTAATTTATTTAAAT
1 TTAATTAATTTAAAT
*
809636 TTAATTTAATTATAAAAA
1 TTAA-TTAATT-T-AAAT
*
809654 ATAA-TAATTTAAAT
1 TTAATTAATTTAAAT
*
809668 TTAATTAATCTAAAT
1 TTAATTAATTTAAAT
809683 T
1 T
809684 CAAAAATTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
14 6 0.16
15 15 0.39
16 10 0.26
17 1 0.03
18 6 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
TTAATTAATTTAAAT
Found at i:811902 original size:2 final size:2
Alignment explanation
Indices: 811895--811931 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
811885 ATATAAATCC
811895 TA 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 TA T
811932 GGTATTTCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:812377 original size:17 final size:18
Alignment explanation
Indices: 812349--812395 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
812339 AAATACAAAT
* *
812349 TTATAAATTTAAATTTAA
1 TTATAGATTTAAATATAA
812367 TTA-AGATTT-AATATAA
1 TTATAGATTTAAATATAA
*
812383 TTATATATTTAAA
1 TTATAGATTTAAA
812396 AGATTCACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.38
17 10 0.42
18 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTATAGATTTAAATATAA
Found at i:815881 original size:30 final size:32
Alignment explanation
Indices: 815845--815912 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 32
815835 AAAAGTTTTG
*
815845 AAGATGA-ATTT-TTTTAATACTATTAAATTA
1 AAGATGATATTTAATTTAATACTATTAAATTA
* *
815875 AAGATGATATTTAAATTTAATATTATTAAATTC
1 AAGATGATATTT-AATTTAATACTATTAAATTA
815908 AAGAT
1 AAGAT
815913 AAATATGATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 4 0.12
33 21 0.66
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (32 bp):
AAGATGATATTTAATTTAATACTATTAAATTA
Found at i:823321 original size:2 final size:2
Alignment explanation
Indices: 823314--823351 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
823304 CCAAGTTTGC
823314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
823352 GAAAAAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:826224 original size:17 final size:18
Alignment explanation
Indices: 826202--826239 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
826192 AATATATTAT
*
826202 CATATATATTA-TTTTGA
1 CATATATATAACTTTTGA
826219 CATATATATAACTTTTGA
1 CATATATATAACTTTTGA
826237 CAT
1 CAT
826240 GAATAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (18 bp):
CATATATATAACTTTTGA
Found at i:826250 original size:16 final size:15
Alignment explanation
Indices: 826212--826268 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 15
826202 CATATATATT
*
826212 ATTTTGACATATATATA
1 ATTTTGACAT-GA-ATA
826229 ACTTTTGACATGAATA
1 A-TTTTGACATGAATA
826245 ATTTTTG--ATGAATA
1 A-TTTTGACATGAATA
826259 ATTTTGACAT
1 ATTTTGACAT
826269 AAAAATATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 5 0.14
14 8 0.23
15 2 0.06
16 9 0.26
17 2 0.06
18 9 0.26
ACGTcount: A:0.37, C:0.07, G:0.11, T:0.46
Consensus pattern (15 bp):
ATTTTGACATGAATA
Found at i:826715 original size:41 final size:41
Alignment explanation
Indices: 826637--826716 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
826627 GTTGCTACCG
* **
826637 AGGAATGGATGAGCCAGAAGATGATTGAACAGTGGAGGACC
1 AGGAATAGATGAGCCAGAAGATGATTGAACAACGGAGGACC
* *
826678 AGGAATAGATGAGTC-GAAAGATGATTGCACAACGGAGGA
1 AGGAATAGATGAGCCAG-AAGATGATTGAACAACGGAGGA
826717 AGCATATGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.39, C:0.11, G:0.35, T:0.15
Consensus pattern (41 bp):
AGGAATAGATGAGCCAGAAGATGATTGAACAACGGAGGACC
Found at i:828231 original size:34 final size:35
Alignment explanation
Indices: 828185--828336 Score: 161
Period size: 34 Copynumber: 4.5 Consensus size: 35
828175 GTAAAAACCA
*
828185 TCATTTAATCAACAATGGCAACCTACCAAATCTAC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTAC
*
828220 -CATTTAGTCAACAATGGTAAGCC-ACCAAATC-AC
1 TCATTTAATCAACAATGGTAA-CCTACCAAATCTAC
* * * *
828253 CCATTTAATCAATAATGGTAAGCTACCAAAT-TTC
1 TCATTTAATCAACAATGGTAACCTACCAAATCTAC
* ** *
828287 TCATTTAATCAACAATGATAAGTTACTAAATCT-C
1 TCATTTAATCAACAATGGTAACCTACCAAATCTAC
*
828321 TCATTTAGTCAACAAT
1 TCATTTAATCAACAAT
828337 TCTTGTAAGG
Statistics
Matches: 100, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
33 3 0.03
34 94 0.94
35 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.08, T:0.30
Consensus pattern (35 bp):
TCATTTAATCAACAATGGTAACCTACCAAATCTAC
Found at i:828318 original size:68 final size:68
Alignment explanation
Indices: 828186--828336 Score: 178
Period size: 68 Copynumber: 2.2 Consensus size: 68
828176 TAAAAACCAT
* *
828186 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAGTCAACAATGGTAAGCCACCAAATC
1 CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGATAAGCCACCAAATC
828251 ACC
66 ACC
* * * * ** *
828254 CATTTAATCAATAATGGTAAGCTACCAAAT-TTCTCATTTAATCAACAATGATAAGTTACTAAAT
1 CATTTAATCAACAATGGCAACCTACCAAATCTAC-CATTTAATCAACAATGATAAGCCACCAAAT
* *
828318 CTCT
65 CACC
*
828322 CATTTAGTCAACAAT
1 CATTTAATCAACAAT
828337 TCTTGTAAGG
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
67 2 0.03
68 67 0.97
ACGTcount: A:0.40, C:0.23, G:0.08, T:0.29
Consensus pattern (68 bp):
CATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGATAAGCCACCAAATC
ACC
Found at i:832565 original size:16 final size:16
Alignment explanation
Indices: 832525--832565 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
832515 TGAGTCAAAA
*
832525 ATATTTTTAAAATATT
1 ATATTTTTAAAAAATT
* *
832541 TTATATTTAAAAAATT
1 ATATTTTTAAAAAATT
832557 ATATTTTTA
1 ATATTTTTA
832566 TATTTATATA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATTTTTAAAAAATT
Found at i:833642 original size:24 final size:24
Alignment explanation
Indices: 833588--833682 Score: 69
Period size: 24 Copynumber: 4.2 Consensus size: 24
833578 AAATATTTTT
*
833588 ATTTAAATTTAATTATAAATATTA
1 ATTTAAAATTAATTATAAATATTA
* * *
833612 ATATAAAATTAATTTTTAATATT-
1 ATTTAAAATTAATTATAAATATTA
* *
833635 ATTTTAAA-TAA-TA-AAATA-AA
1 ATTTAAAATTAATTATAAATATTA
* *
833655 ATTTTAAATTAA-TGTAAAT-TTA
1 ATTTAAAATTAATTATAAATATTA
833677 ATTTAA
1 ATTTAA
833683 TTTAAATTTA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
20 12 0.22
21 5 0.09
22 13 0.24
23 6 0.11
24 19 0.35
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (24 bp):
ATTTAAAATTAATTATAAATATTA
Found at i:833644 original size:12 final size:13
Alignment explanation
Indices: 833589--833644 Score: 57
Period size: 12 Copynumber: 4.6 Consensus size: 13
833579 AATATTTTTA
833589 TTTAAAT-TTAAT
1 TTTAAATATTAAT
*
833601 TATAAATATTAA-
1 TTTAAATATTAAT
*
833613 TATAAA-ATTAAT
1 TTTAAATATTAAT
*
833625 TTTTAATATT-AT
1 TTTAAATATTAAT
833637 TTTAAATA
1 TTTAAATA
833645 ATAAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 25 0.68
13 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTAAATATTAAT
Found at i:833682 original size:16 final size:16
Alignment explanation
Indices: 833657--833695 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
833647 AAAATAAAAT
833657 TTTAAATTAATGTAAA
1 TTTAAATTAATGTAAA
* *
833673 TTTAATTTAATTTAAA
1 TTTAAATTAATGTAAA
833689 TTTAAAT
1 TTTAAAT
833696 AAAAAACTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (16 bp):
TTTAAATTAATGTAAA
Found at i:833690 original size:11 final size:11
Alignment explanation
Indices: 833588--833695 Score: 55
Period size: 12 Copynumber: 9.7 Consensus size: 11
833578 AAATATTTTT
833588 ATTTAAATTTA
1 ATTTAAATTTA
833599 ATTATAAATATTA
1 ATT-TAAAT-TTA
* *
833612 ATATAAAATTA
1 ATTTAAATTTA
*
833623 ATTTTTAATATTA
1 A-TTTAAAT-TTA
*
833636 TTTTAAA--TA
1 ATTTAAATTTA
* **
833645 A-TAAAATAAA
1 ATTTAAATTTA
833655 ATTTTAAA-TTA
1 A-TTTAAATTTA
*
833666 ATGTAAATTTA
1 ATTTAAATTTA
833677 ATTT-AATTTAA
1 ATTTAAATTT-A
833688 ATTTAAAT
1 ATTTAAAT
833696 AAAAAACTTT
Statistics
Matches: 71, Mismatches: 15, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
8 4 0.06
9 2 0.03
10 12 0.17
11 20 0.28
12 25 0.35
13 8 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:834807 original size:115 final size:115
Alignment explanation
Indices: 834605--834816 Score: 363
Period size: 115 Copynumber: 1.8 Consensus size: 115
834595 AGGTGAATTT
* * *
834605 TTGTGACTCCATTGACCCAAAGTTGCTGTTAAATATCATATATCGGGCTTGGACGTAAAGCCACG
1 TTGTGACTCCATTGACCCAAAGTTGCTGTTAAATATCATATATCAGACTTGGACGTAAAGCCACA
*
834670 AATGATGGCATTCATGATGTAAAAAAAGAAGATTAATATAAGAATTTATG
66 AATGATGGCACTCATGATGTAAAAAAAGAAGATTAATATAAGAATTTATG
*
834720 TTGTGAC-CTCATTGACCCAAGGTTGCTGTTAAATATCATATATCAGACTTGGACGTAAAGCCAC
1 TTGTGACTC-CATTGACCCAAAGTTGCTGTTAAATATCATATATCAGACTTGGACGTAAAGCCAC
834784 AAATGATGGCACTCATGATGTAAAAAAAGAAGA
65 AAATGATGGCACTCATGATGTAAAAAAAGAAGA
834817 AGAAGATTAA
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
114 1 0.01
115 90 0.99
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.28
Consensus pattern (115 bp):
TTGTGACTCCATTGACCCAAAGTTGCTGTTAAATATCATATATCAGACTTGGACGTAAAGCCACA
AATGATGGCACTCATGATGTAAAAAAAGAAGATTAATATAAGAATTTATG
Found at i:836647 original size:23 final size:22
Alignment explanation
Indices: 836601--836649 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
836591 CAGTTGATTC
*
836601 ATAACAAATTGCTAATAATAAA
1 ATAACAAATTGCAAATAATAAA
836623 ATAACAAATT-CAAATAAAATAAA
1 ATAACAAATTGCAAAT--AATAAA
836646 ATAA
1 ATAA
836650 GATAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 10 0.42
23 10 0.42
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAACAAATTGCAAATAATAAA
Found at i:837613 original size:6 final size:6
Alignment explanation
Indices: 837602--837711 Score: 55
Period size: 6 Copynumber: 17.7 Consensus size: 6
837592 TATTATTTTA
* * * *
837602 TAATTT TAATTT TTATAT TAATATT T-ATTAT TAATTT TAATAT TAATTA
1 TAATTT TAATTT TAATTT TAAT-TT TAATT-T TAATTT TAATTT TAATTT
* * * *
837651 TAATATAT T-ATTT TATAATT TAATTT TTATAT TAATATT T-ATTAT TAATAT
1 TAAT-T-T TAATTT TA-ATTT TAATTT TAATTT TAAT-TT TAATT-T TAATTT
*
837702 TATTTT TAAT
1 TAATTT TAAT
837712 AATATTTATT
Statistics
Matches: 76, Mismatches: 18, Indels: 20
0.67 0.16 0.18
Matches are distributed among these distances:
5 4 0.05
6 54 0.71
7 17 0.22
8 1 0.01
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (6 bp):
TAATTT
Found at i:837620 original size:25 final size:25
Alignment explanation
Indices: 837592--837665 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
837582 AACTATAACG
* *
837592 TATTATTTTATAATTTTAATTTTTA
1 TATTATTTTATAATATTAATTTTAA
837617 TATTAATATTTAT--TATTAATTTTAA
1 TATT-AT-TTTATAATATTAATTTTAA
* *
837642 TATTA-ATTATAATATATTATTTTA
1 TATTATTTTATAATAT-TAATTTTA
837666 TAATTTAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
22 4 0.10
24 4 0.10
25 25 0.62
26 2 0.05
27 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTATTTTATAATATTAATTTTAA
Found at i:837628 original size:12 final size:12
Alignment explanation
Indices: 837607--837702 Score: 81
Period size: 12 Copynumber: 7.7 Consensus size: 12
837597 TTTTATAATT
*
837607 TTAATTTTTATA
1 TTAATATTTATA
837619 TTAATATTTATTA
1 TTAATATTTA-TA
837632 TTAAT-TTTAATA
1 TTAATATTT-ATA
*
837644 TTAATTATAATATA
1 TTAA-TAT-TTATA
837658 TT-AT-TTTATAA
1 TTAATATTTAT-A
*
837669 TTTAATTTTTATA
1 -TTAATATTTATA
837682 TTAATATTTATTA
1 TTAATATTTA-TA
837695 TTAATATT
1 TTAATATT
837703 ATTTTTAATA
Statistics
Matches: 70, Mismatches: 4, Indels: 19
0.75 0.04 0.20
Matches are distributed among these distances:
10 3 0.04
11 2 0.03
12 30 0.43
13 23 0.33
14 11 0.16
15 1 0.01
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TTAATATTTATA
Found at i:837641 original size:19 final size:19
Alignment explanation
Indices: 837619--837723 Score: 64
Period size: 19 Copynumber: 5.7 Consensus size: 19
837609 AATTTTTATA
837619 TTAATATTTATTATTAATT
1 TTAATATTTATTATTAATT
*
837638 TTAATATTAATTA-TAATAT
1 TTAATATTTATTATTAAT-T
*
837657 ATT-AT-TTTATAATTTAATT
1 -TTAATATTTATTA-TTAATT
* * *
837676 TTTATA-TTAATATTTATT
1 TTAATATTTATTATTAATT
*
837694 ATTAATA-TTATTTTTAA--
1 -TTAATATTTATTATTAATT
837711 -TAATATTTATTAT
1 TTAATATTTATTAT
837724 ATTTAAAATC
Statistics
Matches: 67, Mismatches: 11, Indels: 19
0.69 0.11 0.20
Matches are distributed among these distances:
15 5 0.07
16 6 0.09
18 16 0.24
19 34 0.51
20 6 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAATATTTATTATTAATT
Found at i:837697 original size:63 final size:64
Alignment explanation
Indices: 837571--837699 Score: 215
Period size: 63 Copynumber: 2.0 Consensus size: 64
837561 TTGATGGAAC
*
837571 ATTTAAATATTAACTATAACGTATTATTTTATAATTTTAATTTTTATATTAATATTTATTATTA
1 ATTTAAATATTAACTATAACATATTATTTTATAATTTTAATTTTTATATTAATATTTATTATTA
* * *
837635 ATTTTAATATTAATTATAATATATTATTTTATAA-TTTAATTTTTATATTAATATTTATTATTA
1 ATTTAAATATTAACTATAACATATTATTTTATAATTTTAATTTTTATATTAATATTTATTATTA
837698 AT
1 AT
837700 ATTATTTTTA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 31 0.51
64 30 0.49
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (64 bp):
ATTTAAATATTAACTATAACATATTATTTTATAATTTTAATTTTTATATTAATATTTATTATTA
Found at i:837704 original size:12 final size:12
Alignment explanation
Indices: 837617--837726 Score: 64
Period size: 12 Copynumber: 8.8 Consensus size: 12
837607 TTAATTTTTA
837617 TATTAATATTTAT
1 TATTAATA-TTAT
* *
837630 TATTAATTTTAA
1 TATTAATATTAT
*
837642 TATTAATTATAAT
1 TATTAA-TATTAT
*
837655 ATATT-ATTTTAT
1 -TATTAATATTAT
* *
837667 AATTTAAT-TTTT
1 TA-TTAATATTAT
837679 ATATTAATATTTAT
1 -TATTAATA-TTAT
837693 TATTAATATTAT
1 TATTAATATTAT
* *
837705 TTTTAATAATATT
1 TATTAATATTA-T
837718 TATT-ATATT
1 TATTAATATT
837727 TAAAATCATA
Statistics
Matches: 74, Mismatches: 15, Indels: 17
0.70 0.14 0.16
Matches are distributed among these distances:
11 1 0.01
12 40 0.54
13 26 0.35
14 7 0.09
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:837714 original size:15 final size:15
Alignment explanation
Indices: 837639--837717 Score: 60
Period size: 14 Copynumber: 5.5 Consensus size: 15
837629 TTATTAATTT
* *
837639 TAATATTAATTATAA
1 TAATATTATTTTTAA
837654 T-ATATTA-TTTT-A
1 TAATATTATTTTTAA
837666 TAAT-TTAATTTTT-A
1 TAATATT-ATTTTTAA
* * *
837680 TATTAATATTTATTAT
1 TAATATTATTT-TTAA
837696 TAATATTATTTTTAA
1 TAATATTATTTTTAA
837711 TAATATT
1 TAATATT
837718 TATTATATTT
Statistics
Matches: 51, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
12 4 0.08
13 6 0.12
14 18 0.35
15 14 0.27
16 9 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAATATTATTTTTAA
Found at i:837738 original size:69 final size:63
Alignment explanation
Indices: 837592--837728 Score: 204
Period size: 63 Copynumber: 2.2 Consensus size: 63
837582 AACTATAACG
* *
837592 TATTATTTTATAATTTTAATTTTTATATTAATATTTATTATTAATTTTAATATTAATTATAATA
1 TATTATTTTATAA-TTTAATTTTTATATTAATATTTATTATTAATATTAATATTAATAATAATA
* * *
837656 TATTATTTTATAATTTAATTTTTATATTAATATTTATTATTAATATTATTTTTAATAAT-ATT
1 TATTATTTTATAATTTAATTTTTATATTAATATTTATTATTAATATTAATATTAATAATAATA
837718 TATTATATTTA
1 TATTAT-TTTA
837729 AAATCATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
62 8 0.12
63 46 0.69
64 13 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (63 bp):
TATTATTTTATAATTTAATTTTTATATTAATATTTATTATTAATATTAATATTAATAATAATA
Found at i:838946 original size:17 final size:16
Alignment explanation
Indices: 838919--838951 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
838909 TATATTCCTG
838919 ATTTTTTTTAATTTTT
1 ATTTTTTTTAATTTTT
838935 ATTTTATTTTAATTTTT
1 ATTTT-TTTTAATTTTT
838952 GCTAATGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
ATTTTTTTTAATTTTT
Found at i:840362 original size:20 final size:20
Alignment explanation
Indices: 840336--840378 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 20
840326 AATTAATTAA
840336 ATTTAAT-AT-AAATTAT-T
1 ATTTAATAATAAAATTATGT
*
840353 ATTTAATAATAAAATTTTGT
1 ATTTAATAATAAAATTATGT
840373 ATTTAA
1 ATTTAA
840379 ATTTAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 6 0.27
20 7 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
ATTTAATAATAAAATTATGT
Found at i:840408 original size:52 final size:52
Alignment explanation
Indices: 840308--840408 Score: 116
Period size: 52 Copynumber: 1.9 Consensus size: 52
840298 TTGTACTTTG
* * * * *
840308 AATAAATTTTTTTATTTAAATTAATTAAATTTAATATAAATTATTATTTAAT
1 AATAAAATTTTGTATTTAAATTAATTAAATTAAATATAAATAAATATTTAAT
*
840360 AATAAAATTTTGTATTTAAATTTAATTATA-TAAATATATAA-AAATATTT
1 AATAAAATTTTGTATTTAAA-TTAATTAAATTAAATATA-AATAAATATTT
840409 TTTAATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
52 31 0.76
53 10 0.24
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (52 bp):
AATAAAATTTTGTATTTAAATTAATTAAATTAAATATAAATAAATATTTAAT
Found at i:842828 original size:20 final size:21
Alignment explanation
Indices: 842800--842849 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 21
842790 AAAGTTTTTT
842800 ATATAATTTTGATAAACATT-A
1 ATATAATTTTGATAAAC-TTCA
842821 AT-TAATTTTGATAAACTTCA
1 ATATAATTTTGATAAACTTCA
842841 ATATAATTT
1 ATATAATTT
842850 AAAAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 8 0.30
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (21 bp):
ATATAATTTTGATAAACTTCA
Found at i:845157 original size:8 final size:9
Alignment explanation
Indices: 845140--845168 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
845130 ATATATATTT
845140 AAAATAATA
1 AAAATAATA
845149 AAAAT-ATA
1 AAAATAATA
845157 AAAATAATA
1 AAAATAATA
845166 AAA
1 AAA
845169 TCATTTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
AAAATAATA
Found at i:845913 original size:2 final size:2
Alignment explanation
Indices: 845906--845945 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
845896 GCACCTTTTA
* *
845906 AT AT AT AT AT AT AT AT AT AT AT GT AT GT 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
845946 TGTTAATGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:849175 original size:19 final size:20
Alignment explanation
Indices: 849152--849206 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
849142 TTCTCTATTT
*
849152 TTAAATTTTAATAATATTAA
1 TTAAATTTTAATAATAATAA
** *
849172 -TAAAAATTAATTATAATAA
1 TTAAATTTTAATAATAATAA
849191 TTAAATTTATAATAAT
1 TTAAATTT-TAATAAT
849207 TATTTAAGAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
19 15 0.58
20 5 0.19
21 6 0.23
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAATTTTAATAATAATAA
Found at i:849863 original size:20 final size:20
Alignment explanation
Indices: 849824--849862 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
849814 TATTAAATAT
*
849824 TTAATTTTACTTATCAAAAA
1 TTAAATTTACTTATCAAAAA
849844 TTAAATTTA-TTATCAAAAA
1 TTAAATTTACTTATCAAAAA
849863 AAATGTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAATTTACTTATCAAAAA
Found at i:851796 original size:22 final size:24
Alignment explanation
Indices: 851754--851797 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
851744 AATTTAATTT
851754 AATTAATATAAATTAAATTTATCA
1 AATTAATATAAATTAAATTTATCA
*
851778 AATTAATA-AAA-TAATTTTAT
1 AATTAATATAAATTAAATTTAT
851798 TTAAATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 3 0.16
24 8 0.42
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AATTAATATAAATTAAATTTATCA
Found at i:852353 original size:23 final size:24
Alignment explanation
Indices: 852314--852358 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
852304 TATGTTTAAT
*
852314 TTTAAAATATAACA-TTTAATAAA
1 TTTAAAATATAAAATTTTAATAAA
852337 TTTAAAAT-TAAAAATTTTAATA
1 TTTAAAATAT-AAAATTTTAATA
852359 CTTACAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 11 0.58
24 7 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
TTTAAAATATAAAATTTTAATAAA
Found at i:854136 original size:20 final size:20
Alignment explanation
Indices: 854108--854148 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
854098 TTAAGAAATT
*
854108 ATTTCATTTTTCATTTTTTA
1 ATTTAATTTTTCATTTTTTA
*
854128 ATTTAATTTTTTATTTTTTA
1 ATTTAATTTTTCATTTTTTA
854148 A
1 A
854149 ATATATCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (20 bp):
ATTTAATTTTTCATTTTTTA
Found at i:856103 original size:2 final size:2
Alignment explanation
Indices: 856096--856136 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
856086 CCCTCCCTCC
856096 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
856137 GTTCACCGTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:858581 original size:2 final size:2
Alignment explanation
Indices: 858574--858598 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
858564 ACATGCAAGC
858574 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
858599 GACACACACA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:858854 original size:30 final size:31
Alignment explanation
Indices: 858820--858882 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 31
858810 CGGTTCAATT
* *
858820 AAATAAAAATATT-TTTTAATATAAATATTA
1 AAATAAAAATATTATTATAAAATAAATATTA
** *
858850 AAATATTAATATTATTATAAAATAAATTTTA
1 AAATAAAAATATTATTATAAAATAAATATTA
858881 AA
1 AA
858883 TACTTTTATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (31 bp):
AAATAAAAATATTATTATAAAATAAATATTA
Found at i:866320 original size:23 final size:23
Alignment explanation
Indices: 866290--866344 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
866280 TTCATTATAT
866290 TAAT-ATTTATA-ATTAAATTTAAA
1 TAATAATTTATATATT--ATTTAAA
*
866313 TAA-AATTTATATATTATTTTAA
1 TAATAATTTATATATTATTTAAA
866335 TAATAATTTA
1 TAATAATTTA
866345 GATTGAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.32
23 16 0.57
24 3 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAATTTATATATTATTTAAA
Found at i:879680 original size:3 final size:3
Alignment explanation
Indices: 879672--879699 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
879662 TTAATATAAC
879672 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
879700 ATTAATTTTA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:882876 original size:1 final size:1
Alignment explanation
Indices: 882870--882911 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
882860 AAAGTGTTTG
***
882870 AAAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
882912 TTTAAATGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 38 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:882893 original size:21 final size:21
Alignment explanation
Indices: 882867--882908 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
882857 GATAAAGTGT
882867 TTGAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAA
882888 TTGAAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAAA
882909 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.10
Consensus pattern (21 bp):
TTGAAAAAAAAAAAAAAAAAA
Found at i:882940 original size:21 final size:21
Alignment explanation
Indices: 882916--882972 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
882906 AAAAAATTTA
882916 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
882937 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
882958 AATGTATCGATACAT
1 AATGTATCGATACAT
882973 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:883052 original size:19 final size:19
Alignment explanation
Indices: 883028--883095 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
883018 AATTCAACAA
883028 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
883047 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
883062 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
883079 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
883096 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:883067 original size:13 final size:13
Alignment explanation
Indices: 883049--883073 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
883039 ACATAAGTTT
883049 TGTATCGATACAA
1 TGTATCGATACAA
883062 TGTATCGATACA
1 TGTATCGATACA
883074 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:883071 original size:32 final size:32
Alignment explanation
Indices: 883030--883092 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
883020 TTCAACAATT
*
883030 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
883062 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
883093 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:883153 original size:13 final size:13
Alignment explanation
Indices: 883135--883160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
883125 CATTTTTCTG
883135 TGTATCGATACAT
1 TGTATCGATACAT
883148 TGTATCGATACAT
1 TGTATCGATACAT
883161 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:883157 original size:33 final size:33
Alignment explanation
Indices: 883115--883181 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
883105 GCCAAGGAAA
***
883115 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
883148 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
883181 T
1 T
883182 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:885698 original size:28 final size:27
Alignment explanation
Indices: 885631--885703 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
885621 CTTCACAATC
* *
885631 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
885658 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
885686 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
885704 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:885748 original size:51 final size:51
Alignment explanation
Indices: 885686--885856 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
885676 TTATTTCTGA
* * *
885686 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
885737 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
885790 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
885842 GAGGATACTCCAACC
1 GGGGATACTCCAACC
885857 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:885875 original size:28 final size:28
Alignment explanation
Indices: 885839--885920 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
885829 ATTTTTCACA
*
885839 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
885867 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
885895 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
885921 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:898340 original size:15 final size:15
Alignment explanation
Indices: 898319--898372 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 15
898309 ACCTTCTCTT
898319 CAAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
898334 -AAAAAAAAAAAAAA
1 CAAAAAAAAAAAAAA
*
898348 CAAAAAAAAACAAAA
1 CAAAAAAAAAAAAAA
*
898363 CAAAGAAAAA
1 CAAAAAAAAA
898373 GAGAGAAAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.39
15 22 0.61
ACGTcount: A:0.91, C:0.07, G:0.02, T:0.00
Consensus pattern (15 bp):
CAAAAAAAAAAAAAA
Found at i:898388 original size:1 final size:1
Alignment explanation
Indices: 898320--898372 Score: 70
Period size: 1 Copynumber: 53.0 Consensus size: 1
898310 CCTTCTCTTC
* * * *
898320 AAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
898373 GAGAGAAAAG
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.92, C:0.06, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:899438 original size:55 final size:55
Alignment explanation
Indices: 899354--899976 Score: 941
Period size: 55 Copynumber: 11.3 Consensus size: 55
899344 TCCGCTTTTT
* *
899354 AGTCCTCAAAGAGCAGGACACGTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
899409 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
899464 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
899519 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
899574 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
899629 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
899684 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
899739 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
899794 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
899849 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
899904 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
899959 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
899977 TACAACTTAT
Statistics
Matches: 525, Mismatches: 35, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
54 13 0.02
55 499 0.95
56 13 0.02
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:900578 original size:1 final size:1
Alignment explanation
Indices: 900572--900610 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
900562 AAAGTGTTTG
***
900572 AAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
900611 TTTAAATGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.92, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:900594 original size:20 final size:20
Alignment explanation
Indices: 900569--900608 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
900559 GATAAAGTGT
900569 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
900589 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
900609 AATTTAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (20 bp):
TTGAAAAAAAAAAAAAAAAA
Found at i:900639 original size:21 final size:21
Alignment explanation
Indices: 900615--900671 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
900605 AAAAAATTTA
900615 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
900636 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
900657 AATGTATCGATACAT
1 AATGTATCGATACAT
900672 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:900751 original size:19 final size:19
Alignment explanation
Indices: 900727--900794 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
900717 AATTCAACAA
900727 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
900746 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
900761 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
900778 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
900795 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:900766 original size:13 final size:13
Alignment explanation
Indices: 900748--900772 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
900738 ACATAAGTTT
900748 TGTATCGATACAA
1 TGTATCGATACAA
900761 TGTATCGATACA
1 TGTATCGATACA
900773 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:900770 original size:32 final size:32
Alignment explanation
Indices: 900729--900791 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
900719 TTCAACAATT
*
900729 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
900761 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
900792 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:900852 original size:13 final size:13
Alignment explanation
Indices: 900834--900859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
900824 CATTTTTCTG
900834 TGTATCGATACAT
1 TGTATCGATACAT
900847 TGTATCGATACAT
1 TGTATCGATACAT
900860 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:900856 original size:33 final size:33
Alignment explanation
Indices: 900814--900880 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
900804 GCCAAGGAAA
***
900814 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
900847 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
900880 T
1 T
900881 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:903395 original size:28 final size:27
Alignment explanation
Indices: 903328--903400 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
903318 CTTCACAATC
* *
903328 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
903355 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
903383 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
903401 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:903445 original size:51 final size:51
Alignment explanation
Indices: 903383--903553 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
903373 TTATTTCTGA
* * *
903383 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
903434 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
903487 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
903539 GAGGATACTCCAACC
1 GGGGATACTCCAACC
903554 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:903546 original size:105 final size:105
Alignment explanation
Indices: 903214--903553 Score: 273
Period size: 105 Copynumber: 3.2 Consensus size: 105
903204 CTCAATTCTC
* * * * ** *
903214 CACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTT-T-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
903277 TACTCCAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTT
66 TACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TT
* * * ** * * * * * *
903321 CACAATCGGGGACACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA---CCCCGTTATTTCT
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTCTCCTTTA-ATC-
* * * * *
903381 GAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTT
61 --GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
* * *
903427 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
903492 TACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
66 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
903532 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
903554 TCGTTATTTC
Statistics
Matches: 174, Mismatches: 44, Indels: 32
0.70 0.18 0.13
Matches are distributed among these distances:
104 25 0.14
105 44 0.25
106 24 0.14
107 36 0.21
108 19 0.11
111 26 0.15
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (105 bp):
CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
Found at i:903572 original size:28 final size:28
Alignment explanation
Indices: 903536--903617 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
903526 ATTTTTCACA
*
903536 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
903564 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
903592 --CGAGGGAACACTCCAACCTCGTTATT
1 ATCG-GGG-ATACTCCAACCTCGTTATT
903618 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.04
27 3 0.07
28 41 0.89
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:905381 original size:2 final size:2
Alignment explanation
Indices: 905369--905407 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
905359 TTCGAAGAGG
*
905369 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
905408 GGACCCGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:909544 original size:19 final size:19
Alignment explanation
Indices: 909506--909541 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
909496 TTCTCTTTAA
909506 ATTTATTATATAAAATAAT
1 ATTTATTATATAAAATAAT
*
909525 ATTT-TTATTTAAAATAA
1 ATTTATTATATAAAATAA
909542 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTATTATATAAAATAAT
Found at i:909908 original size:2 final size:2
Alignment explanation
Indices: 909901--909941 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
909891 TATTGCATTT
909901 TA TA TA 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 TA TA TA T
909942 TTGACCGAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:912605 original size:26 final size:23
Alignment explanation
Indices: 912527--912631 Score: 83
Period size: 22 Copynumber: 4.4 Consensus size: 23
912517 TTTTTAAGAT
912527 TATTAATT-TATTATATATAATAATA
1 TATTAATTAT-TTAT-TA-AATAATA
* *
912552 TATCAATTTAATATATTAAA-AATA
1 TATTAA-TT-ATTTATTAAATAATA
*
912576 -ATTAATTATTATATTCAATATAATT
1 TATTAATTATT-TATT-AA-ATAATA
912601 TATTAA-TATTTATTAAATAATA
1 TATTAATTATTTATTAAATAATA
912623 TATTAATTA
1 TATTAATTA
912632 ACTTCCAATA
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
21 2 0.03
22 17 0.26
23 10 0.15
24 9 0.14
25 14 0.22
26 9 0.14
27 3 0.05
28 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TATTAATTATTTATTAAATAATA
Found at i:912616 original size:36 final size:36
Alignment explanation
Indices: 912545--912626 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
912535 TATTATATAT
*
912545 AATAATATA-TCAATTTAATATATTAAAAATAATTA
1 AATAATATATTCAATATAATATATTAAAAATAATTA
* * * * * *
912580 ATTATTATATTCAATATAATTTATTAATATTTATTA
1 AATAATATATTCAATATAATATATTAAAAATAATTA
912616 AATAATATATT
1 AATAATATATT
912627 AATTAACTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
35 7 0.19
36 30 0.81
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (36 bp):
AATAATATATTCAATATAATATATTAAAAATAATTA
Found at i:912644 original size:2 final size:2
Alignment explanation
Indices: 912639--912663 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
912629 TTAACTTCCA
912639 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
912664 AAGACTATTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:916068 original size:3 final size:3
Alignment explanation
Indices: 916062--916092 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
916052 AAAATTATAG
*
916062 TAA TAA TAA TAA TAA TAA TAA TAA CAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
916093 TTATTTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:922706 original size:18 final size:18
Alignment explanation
Indices: 922671--922725 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
922661 ATGTACTTAC
*
922671 TTTATATT-TATAATATT
1 TTTATATTATATCATATT
922688 TTTATATTATATCATATT
1 TTTATATTATATCATATT
*
922706 TATATATTATAATCATATT
1 TTTATATTAT-ATCATATT
922725 T
1 T
922726 AATCTAAAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.24
18 17 0.50
19 9 0.26
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTATATTATATCATATT
Found at i:923555 original size:3 final size:3
Alignment explanation
Indices: 923536--923574 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
923526 AATGAAAAAC
* *
923536 AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
923575 GAAAGAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:924075 original size:25 final size:25
Alignment explanation
Indices: 924026--924076 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
924016 GATTTTTGTA
*
924026 TGATTTAATTATAATTTAAGTAATT
1 TGATTTAATTATAATTTAAGAAATT
924051 TGATTTAATT-TAAATTATAA-AAATT
1 TGATTTAATTAT-AATT-TAAGAAATT
924076 T
1 T
924077 ATAAATAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 1 0.04
25 19 0.83
26 3 0.13
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (25 bp):
TGATTTAATTATAATTTAAGAAATT
Found at i:924463 original size:30 final size:30
Alignment explanation
Indices: 924393--924499 Score: 97
Period size: 30 Copynumber: 3.7 Consensus size: 30
924383 GATATCGATT
924393 ATATTT-T-TATATTGTATAATTAAATTTA-A
1 ATATTTATATATATT-TAT-ATTAAATTTATA
*
924422 A-ATAT-TATATATTTAT-TTAAATTT-TA
1 ATATTTATATATATTTATATTAAATTTATA
*
924448 ATATATTAATATATATTTATATTAGATTTATA
1 ATAT-TT-ATATATATTTATATTAAATTTATA
924480 ATATTTATA-ATATTT-TATTA
1 ATATTTATATATATTTATATTA
924500 TATATATATA
Statistics
Matches: 67, Mismatches: 3, Indels: 17
0.77 0.03 0.20
Matches are distributed among these distances:
26 10 0.15
27 2 0.03
28 13 0.19
29 13 0.19
30 14 0.21
31 9 0.13
32 6 0.09
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
ATATTTATATATATTTATATTAAATTTATA
Found at i:924465 original size:20 final size:21
Alignment explanation
Indices: 924428--924515 Score: 74
Period size: 20 Copynumber: 4.3 Consensus size: 21
924418 TTAAAATATT
* * *
924428 ATATATTTATTTAAATTT-TA
1 ATATATTAATATATATTTATA
924448 ATATATTAATATATATTTATA
1 ATATATTAATATATATTTATA
* * *
924469 TTAGATTTATA-ATATTTATA
1 ATATATTAATATATATTTATA
* * *
924489 ATATTTTATTATATATATAT-
1 ATATATTAATATATATTTATA
924509 ATATATT
1 ATATATT
924516 TTAAATATTA
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
20 36 0.68
21 17 0.32
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
ATATATTAATATATATTTATA
Found at i:924500 original size:22 final size:22
Alignment explanation
Indices: 924451--924518 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
924441 AATTTTAATA
* *
924451 TATTA-ATATATATTTATATTA
1 TATTATATATATATATATATTT
* *
924472 GATT-TATAATATTTATAATATTT
1 TATTATAT-ATATATAT-ATATTT
924495 TATTATATATATATATATATTT
1 TATTATATATATATATATATTT
924517 TA
1 TA
924519 AATATTATGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 5 0.14
22 14 0.38
23 15 0.41
24 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (22 bp):
TATTATATATATATATATATTT
Found at i:924845 original size:31 final size:34
Alignment explanation
Indices: 924776--924847 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 34
924766 TTAAAAATTT
* *
924776 TTTAATTTATTTTTTTATATTTAAAATTATCAAAA
1 TTTAATTTAATTTTATATATTTAAAATTA-CAAAA
924811 TTTAATTTAATTTTAT-TA-TTAAAATTA-AAAA
1 TTTAATTTAATTTTATATATTTAAAATTACAAAA
924842 TTTAAT
1 TTTAAT
924848 ATTCTATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 10 0.29
33 9 0.26
34 2 0.06
35 14 0.40
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTAATTTAATTTTATATATTTAAAATTACAAAA
Found at i:926221 original size:28 final size:27
Alignment explanation
Indices: 926187--926271 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 27
926177 AATTTAATAA
926187 TAAAATTAAGTTTTAAAATTTAAATTAT
1 TAAAATTAA-TTTTAAAATTTAAATTAT
* **
926215 TAAAATTATTTTTTAAAAGAT-AATTA-
1 TAAAATTA-ATTTTAAAATTTAAATTAT
926241 TATAAATTAA--TTAAAATTTAAATTAT
1 TA-AAATTAATTTTAAAATTTAAATTAT
*
926267 CAAAA
1 TAAAA
926272 GTTATTATAG
Statistics
Matches: 46, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
24 7 0.15
25 8 0.17
26 3 0.07
27 11 0.24
28 17 0.37
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (27 bp):
TAAAATTAATTTTAAAATTTAAATTAT
Found at i:927625 original size:2 final size:2
Alignment explanation
Indices: 927618--927650 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
927608 CGCTGTTGGT
927618 AG 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 AG A
927651 TGACTTCAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:934256 original size:14 final size:14
Alignment explanation
Indices: 934226--934266 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
934216 TTTACTTTCC
934226 TTTCTTTTCTTTCTT
1 TTTCTTTT-TTTCTT
*
934241 TTTCTTTTTTTTTT
1 TTTCTTTTTTTCTT
934255 TTTCTTGTTTTT
1 TTTCTT-TTTTT
934267 AGGTCTGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.85
Consensus pattern (14 bp):
TTTCTTTTTTTCTT
Found at i:937535 original size:2 final size:2
Alignment explanation
Indices: 937528--937565 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
937518 GGACTTACCG
937528 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
937566 GGAAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:946435 original size:24 final size:26
Alignment explanation
Indices: 946388--946441 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
946378 AATTATAATT
* *
946388 TATAACAAAATAATTAATATAATATGA
1 TATAAAAAAATAATT-ATATAATACGA
946415 TATAAAAAAATAATT-TA-AATACGA
1 TATAAAAAAATAATTATATAATACGA
946439 TAT
1 TAT
946442 TAAATTTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.36
25 2 0.08
27 14 0.56
ACGTcount: A:0.59, C:0.04, G:0.04, T:0.33
Consensus pattern (26 bp):
TATAAAAAAATAATTATATAATACGA
Found at i:946547 original size:43 final size:43
Alignment explanation
Indices: 946486--946600 Score: 205
Period size: 43 Copynumber: 2.7 Consensus size: 43
946476 GTCTGAACTT
*
946486 TGAAGCTAACAACAAAGGCAATGGCATACAC-TTCAACAATGTC
1 TGAAGCTAACAACCAAGGCAATGGCATACACATT-AACAATGTC
946529 TGAAGCTAACAACCAAGGCAATGGCATACACATTAACAATGTC
1 TGAAGCTAACAACCAAGGCAATGGCATACACATTAACAATGTC
946572 TGAAGCTAACAACCAAGGCAATGGCATAC
1 TGAAGCTAACAACCAAGGCAATGGCATAC
946601 TCACTCACAC
Statistics
Matches: 70, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
43 68 0.97
44 2 0.03
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (43 bp):
TGAAGCTAACAACCAAGGCAATGGCATACACATTAACAATGTC
Found at i:951991 original size:2 final size:2
Alignment explanation
Indices: 951984--952017 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
951974 ACTTGCAGAA
951984 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
952018 CAATATTGTC
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:968629 original size:108 final size:108
Alignment explanation
Indices: 968489--968707 Score: 393
Period size: 108 Copynumber: 2.0 Consensus size: 108
968479 CTATCTGACC
968489 GCTGGCTATTGCTCCAACCATGGCACCAACATTTGATAAAGAACCAAATAAAGAATACTGTCACA
1 GCTGGCTATTGCTCCAACCATGGCACCAACATTTGATAAAGAACCAAATAAAGAATACTGTCACA
* *
968554 AAAATAAGACTTATTAACTGAGTTAAGTCAAAGAGAAAAACCA
66 AAAATAAGACTTATTAACCGAGTCAAGTCAAAGAGAAAAACCA
* *
968597 GCTGGCTATTGCTCCAACCATGGCACCAACATTTGATAAAGAATCATATAAAGAATACTGTCACA
1 GCTGGCTATTGCTCCAACCATGGCACCAACATTTGATAAAGAACCAAATAAAGAATACTGTCACA
*
968662 AAAATAAGACTTATTAGCCGAGTCAAGTCAAAGAGAAAAACCA
66 AAAATAAGACTTATTAACCGAGTCAAGTCAAAGAGAAAAACCA
968705 GCT
1 GCT
968708 AACCAAACCA
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (108 bp):
GCTGGCTATTGCTCCAACCATGGCACCAACATTTGATAAAGAACCAAATAAAGAATACTGTCACA
AAAATAAGACTTATTAACCGAGTCAAGTCAAAGAGAAAAACCA
Found at i:969896 original size:21 final size:20
Alignment explanation
Indices: 969857--969897 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
969847 TATAATTCGC
**
969857 ATATTTTTTTTATTTTTATA
1 ATATTTTTTTTATAATTATA
969877 ATATTTTTTATTATAATTATA
1 ATATTTTTT-TTATAATTATA
969898 TTTAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
ATATTTTTTTTATAATTATA
Found at i:969898 original size:18 final size:18
Alignment explanation
Indices: 969862--969900 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
969852 TTCGCATATT
* *
969862 TTTTTTATTTTTATAATA
1 TTTTTTATTATAATAATA
*
969880 TTTTTTATTATAATTATA
1 TTTTTTATTATAATAATA
969898 TTT
1 TTT
969901 AAATATTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATTATAATAATA
Found at i:969909 original size:19 final size:19
Alignment explanation
Indices: 969885--969923 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
969875 TAATATTTTT
*
969885 TATTATA-ATTATATTTAAA
1 TATTATATATT-TATATAAA
969904 TATTATATATTTATATAAA
1 TATTATATATTTATATAAA
969923 T
1 T
969924 TTTAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATATTTATATAAA
Found at i:974529 original size:18 final size:18
Alignment explanation
Indices: 974508--974557 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
974498 TTATAACAAA
974508 TAAAAAA-ATTAACAATAT
1 TAAAAAATATTAA-AATAT
*
974526 TAAAAATATATTTAAATAT
1 TAAAAA-ATATTAAAATAT
974545 TAAAAAATATTAA
1 TAAAAAATATTAA
974558 TGTAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.43
19 12 0.43
20 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
TAAAAAATATTAAAATAT
Found at i:974768 original size:15 final size:14
Alignment explanation
Indices: 974724--974774 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 14
974714 TTTTATTTGT
*
974724 TATAATTTTTAAAA
1 TATAAATTTTAAAA
*
974738 CATAAAATTTT-AAA
1 TAT-AAATTTTAAAA
974752 TATAAATTTTAATAA
1 TATAAATTTTAA-AA
974767 TATAAATT
1 TATAAATT
974775 AAAAATTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 7 0.23
14 8 0.26
15 16 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAAATTTTAAAA
Found at i:981039 original size:63 final size:63
Alignment explanation
Indices: 980935--981084 Score: 273
Period size: 63 Copynumber: 2.4 Consensus size: 63
980925 CACTTCCCTT
*
980935 ATCACGATTCTGGTTTGTGGCATTACCAGGAGTATGACAGTCTTCCTTATAACCTTGCCGCTC
1 ATCATGATTCTGGTTTGTGGCATTACCAGGAGTATGACAGTCTTCCTTATAACCTTGCCGCTC
*
980998 ATCATGATTCTGGTTTATGGCATTACCAGGAGTATGACAGTCTTCCTTATAACCTTGCCGCTC
1 ATCATGATTCTGGTTTGTGGCATTACCAGGAGTATGACAGTCTTCCTTATAACCTTGCCGCTC
*
981061 ATCATGATTCTGGTCTGTGGCATT
1 ATCATGATTCTGGTTTGTGGCATT
981085 GGTAGTAAGA
Statistics
Matches: 83, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 83 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (63 bp):
ATCATGATTCTGGTTTGTGGCATTACCAGGAGTATGACAGTCTTCCTTATAACCTTGCCGCTC
Found at i:982693 original size:18 final size:18
Alignment explanation
Indices: 982651--982693 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
982641 GCTGTCGGCA
982651 GCTGCTGCTCCCCGTCCT
1 GCTGCTGCTCCCCGTCCT
*
982669 G-TAGCTGCTCCTCGTCCT
1 GCT-GCTGCTCCCCGTCCT
982687 GCTGCTG
1 GCTGCTG
982694 AACCGCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.02, C:0.42, G:0.26, T:0.30
Consensus pattern (18 bp):
GCTGCTGCTCCCCGTCCT
Found at i:989744 original size:17 final size:16
Alignment explanation
Indices: 989708--989740 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
989698 ATTTTACATA
989708 TATTAATAAATATAAT
1 TATTAATAAATATAAT
989724 TATTAAATAAA-ATAAT
1 TATT-AATAAATATAAT
989740 T
1 T
989741 TATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATTAATAAATATAAT
Found at i:993305 original size:10 final size:10
Alignment explanation
Indices: 993292--993325 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
993282 TTTATATAAA
993292 TAAAAAAATT
1 TAAAAAAATT
993302 TAAAAAAATTT
1 TAAAAAAA-TT
993313 TAAAAAATATT
1 TAAAAAA-ATT
993324 TA
1 TA
993326 TATTTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.36
11 13 0.59
12 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
TAAAAAAATT
Found at i:993334 original size:13 final size:13
Alignment explanation
Indices: 993318--993349 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
993308 AATTTTAAAA
993318 AATATTTATATTT
1 AATATTTATATTT
993331 AATATTTATATTT
1 AATATTTATATTT
993344 AA-ATTT
1 AATATTT
993350 GAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:994575 original size:2 final size:2
Alignment explanation
Indices: 994568--994605 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
994558 TCTGTCTGTA
994568 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
994606 ACTATCAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1001127 original size:29 final size:29
Alignment explanation
Indices: 1001085--1001144 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
1001075 CTTTTGGGTG
1001085 ACTACAGAGAGGATAACTTGCAAGTTGCA
1 ACTACAGAGAGGATAACTTGCAAGTTGCA
1001114 ACTACAGAGAGGATAACTTGCAAGTTGCA
1 ACTACAGAGAGGATAACTTGCAAGTTGCA
1001143 AC
1 AC
1001145 GGGAAACTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.38, C:0.18, G:0.23, T:0.20
Consensus pattern (29 bp):
ACTACAGAGAGGATAACTTGCAAGTTGCA
Found at i:1003623 original size:29 final size:30
Alignment explanation
Indices: 1003578--1003636 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
1003568 TATCGTAATT
*
1003578 TTAAATATAAAATTAAAAT-ATTATTATAA
1 TTAAATATAAAATTAAAATAATAATTATAA
*
1003607 TTAATTATAATAA-TAAAATAATAATTATAA
1 TTAAATATAA-AATTAAAATAATAATTATAA
1003637 CAACATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAAATATAAAATTAAAATAATAATTATAA
Done.