Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167904.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_17, whole genome shotgun sequence
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: 21107920
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 100000 characters in sequence are not A, C, G, or T
File 10 of 121
Found at i:1395377 original size:21 final size:21
Alignment explanation
Indices: 1395351--1395497 Score: 75
Period size: 21 Copynumber: 7.0 Consensus size: 21
1395341 TATAATTTTG
1395351 ATTTTGATAATCTTTGATAAA
1 ATTTTGATAATCTTTGATAAA
* * ** *
1395372 ATTTTGGTAACCTTCAAT-AT
1 ATTTTGATAATCTTTGATAAA
* *
1395392 ATTTTGGTAA-CTTATGATATA
1 ATTTTGATAATCTT-TGATAAA
* *
1395413 ATTTTGGTAA-CTATTGATACA
1 ATTTTGATAATCT-TTGATAAA
* * *
1395434 ATTTTAATAATTTTTTATAAA
1 ATTTTGATAATCTTTGATAAA
* * **
1395455 ATTTTAATAACCTCTTGATGTA
1 ATTTTGATAATCT-TTGATAAA
* *
1395477 ATTTTAATAAATTTTTGATAA
1 ATTTTGAT-AATCTTTGATAA
1395498 CTTATAATAT
Statistics
Matches: 96, Mismatches: 24, Indels: 11
0.73 0.18 0.08
Matches are distributed among these distances:
19 3 0.03
20 13 0.14
21 57 0.59
22 20 0.21
23 3 0.03
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.48
Consensus pattern (21 bp):
ATTTTGATAATCTTTGATAAA
Found at i:1395494 original size:22 final size:22
Alignment explanation
Indices: 1395426--1395497 Score: 74
Period size: 22 Copynumber: 3.3 Consensus size: 22
1395416 TTGGTAACTA
*
1395426 TTGATACAATTTTAAT-AATTT
1 TTGATAAAATTTTAATAAATTT
* ** *
1395447 TTTATAAAATTTTAATAACCTC
1 TTGATAAAATTTTAATAAATTT
**
1395469 TTGATGTAATTTTAATAAATTT
1 TTGATAAAATTTTAATAAATTT
1395491 TTGATAA
1 TTGATAA
1395498 CTTATAATAT
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
21 14 0.38
22 23 0.62
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (22 bp):
TTGATAAAATTTTAATAAATTT
Found at i:1395821 original size:22 final size:22
Alignment explanation
Indices: 1395795--1395948 Score: 78
Period size: 22 Copynumber: 7.0 Consensus size: 22
1395785 TTGACAGTTT
* *
1395795 AGTTATCATTAATTTATTATTA
1 AGTTATCAGTAATTTACTATTA
* *
1395817 TGTTATCAGTGATTTACTATTA
1 AGTTATCAGTAATTTACTATTA
* * * * *
1395839 AGTTATCAATGATATATTACTA
1 AGTTATCAGTAATTTACTATTA
* *
1395861 AATTATCA-TAATTTACTACTA
1 AGTTATCAGTAATTTACTATTA
* * * *
1395882 AATTA-CAATTAATTTATTACTA
1 AGTTATC-AGTAATTTACTATTA
* * * *
1395904 ATTTATAAATAATTTACTACTA
1 AGTTATCAGTAATTTACTATTA
* * * *
1395926 AATTATGACTGATTTACTATTA
1 AGTTATCAGTAATTTACTATTA
1395948 A
1 A
1395949 ATTGTTAATG
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.01
21 16 0.15
22 89 0.84
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (22 bp):
AGTTATCAGTAATTTACTATTA
Found at i:1395843 original size:44 final size:43
Alignment explanation
Indices: 1395795--1396194 Score: 137
Period size: 44 Copynumber: 8.9 Consensus size: 43
1395785 TTGACAGTTT
* ** * *
1395795 AGTTATCATTAATTTATTATTATGTTATCAGTGATTTACTATTA
1 AGTTATCATTAATTTATTACTAAATTATCA-TAATTTACTACTA
* * *
1395839 AGTTATCAATGATATATTACTAAATTATCATAATTTACTACTA
1 AGTTATCATTAATTTATTACTAAATTATCATAATTTACTACTA
* * *
1395882 AATTA-CAATTAATTTATTACTAATTTATAAATAATTTACTACTA
1 AGTTATC-ATTAATTTATTACTAAATTAT-CATAATTTACTACTA
* * * * * * * * *
1395926 AATTATGACTGATTTACTATTAAATTGTTAATGATTTACTACTA
1 AGTTATCATTAATTTATTACTAAATT-ATCATAATTTACTACTA
* * * * * * *
1395970 AATTA-CTAATGATTTATTA-TAAAGTCATAACTAATTTATTATTA
1 AGTTATC-ATTAATTTATTACTAAA-TTATCA-TAATTTACTACTA
* ** *
1396014 ATTTATCGGTAATTTATTAC-AAAGTTATCAATGATTAACTAATTTGCTACTA
1 AGTTATCATTAATTTATTACTAAA-TTATC--------A-TAATTTACTACTA
* * * * * *
1396066 AATTATCATTTATTTATCACTAAATTATTAGTGATTTATTACTA
1 AGTTATCATTAATTTATTACTAAATTATCA-TAATTTACTACTA
* * * * *
1396110 AGTTATTAATAATTTA-CATCTAAATTATCAATGATTTACTATTA
1 AGTTATCATTAATTTATTA-CTAAATTATC-ATAATTTACTACTA
* ** * *
1396154 TA-TTATTATGCATTTATTACTATATTATCATTGATTTACTA
1 -AGTTATCATTAATTTATTACTAAATTATCA-TAATTTACTA
1396195 AATAGCTTTT
Statistics
Matches: 272, Mismatches: 61, Indels: 46
0.72 0.16 0.12
Matches are distributed among these distances:
42 1 0.00
43 42 0.15
44 190 0.70
45 5 0.02
52 31 0.11
53 3 0.01
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (43 bp):
AGTTATCATTAATTTATTACTAAATTATCATAATTTACTACTA
Found at i:1395905 original size:11 final size:11
Alignment explanation
Indices: 1395853--1396125 Score: 72
Period size: 11 Copynumber: 25.2 Consensus size: 11
1395843 ATCAATGATA
*
1395853 TATTACTAAAT
1 TATTACTAATT
*
1395864 TATCA-TAATT
1 TATTACTAATT
* *
1395874 TACTACTAAAT
1 TATTACTAATT
** *
1395885 TACAATTAATT
1 TATTACTAATT
1395896 TATTACTAATT
1 TATTACTAATT
* *
1395907 TATAAATAATT
1 TATTACTAATT
* *
1395918 TACTACTAAAT
1 TATTACTAATT
* *
1395929 TATGACTGATT
1 TATTACTAATT
* * *
1395940 TACTATTAAAT
1 TATTACTAATT
* * *
1395951 TGTTAATGATT
1 TATTACTAATT
* *
1395962 TACTACTAAAT
1 TATTACTAATT
* * *
1395973 TACTAATGATT
1 TATTACTAATT
*
1395984 TATTA-TAAAGT
1 TATTACT-AATT
* *
1395995 CATAACTAATT
1 TATTACTAATT
*
1396006 TATTATTAATT
1 TATTACTAATT
***
1396017 TATCGGTAATT
1 TATTACTAATT
* *
1396028 TATTACAAAGT
1 TATTACTAATT
1396039 TA-T-C-AA-T
1 TATTACTAATT
*
1396046 GATTAACTAATT
1 TATT-ACTAATT
** *
1396058 TGCTACTAAAT
1 TATTACTAATT
* * *
1396069 TATCATTTATT
1 TATTACTAATT
* *
1396080 TATCACTAAAT
1 TATTACTAATT
* *
1396091 TATTAGTGATT
1 TATTACTAATT
*
1396102 TATTACTAAGT
1 TATTACTAATT
*
1396113 TATTAATAATT
1 TATTACTAATT
1396124 TA
1 TA
1396126 CATCTAAATT
Statistics
Matches: 175, Mismatches: 79, Indels: 16
0.65 0.29 0.06
Matches are distributed among these distances:
7 2 0.01
8 3 0.02
9 1 0.01
10 10 0.06
11 156 0.89
12 3 0.02
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (11 bp):
TATTACTAATT
Found at i:1395949 original size:22 final size:22
Alignment explanation
Indices: 1395826--1395985 Score: 135
Period size: 22 Copynumber: 7.3 Consensus size: 22
1395816 ATGTTATCAG
* * *
1395826 TGATTTACTATTAAGTTATCAA
1 TGATTTACTACTAAATTATAAA
* * *
1395848 TGATATATTACTAAATTAT-CA
1 TGATTTACTACTAAATTATAAA
* * *
1395869 TAATTTACTACTAAATTACAAT
1 TGATTTACTACTAAATTATAAA
* * *
1395891 TAATTTATTACTAATTTATAAA
1 TGATTTACTACTAAATTATAAA
* * *
1395913 TAATTTACTACTAAATTATGAC
1 TGATTTACTACTAAATTATAAA
* * *
1395935 TGATTTACTATTAAATTGTTAA
1 TGATTTACTACTAAATTATAAA
1395957 TGATTTACTACTAAATTACT-AA
1 TGATTTACTACTAAATTA-TAAA
1395979 TGATTTA
1 TGATTTA
1395986 TTATAAAGTC
Statistics
Matches: 110, Mismatches: 26, Indels: 4
0.79 0.19 0.03
Matches are distributed among these distances:
21 16 0.15
22 93 0.85
23 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (22 bp):
TGATTTACTACTAAATTATAAA
Found at i:1395963 original size:66 final size:66
Alignment explanation
Indices: 1395856--1396175 Score: 204
Period size: 66 Copynumber: 4.7 Consensus size: 66
1395846 AATGATATAT
* * * *
1395856 TACTAAATTATCA-TAATTTACTACTAAATTA-CAATTAATTTATTACTAATTTATAAATAATTT
1 TACTAAATTATCACTGATTTACTATTAAATTATTAA-TGATTTATTACTAATTTATAAATAATTT
1395919 AC
65 AC
* * * * *
1395921 TACTAAATTATGACTGATTTACTATTAAATTGTTAATGATTTACTACTAAATTACT-AATGATTT
1 TACTAAATTATCACTGATTTACTATTAAATTATTAATGATTTATTACTAATTTA-TAAATAATTT
*
1395985 AT
65 AC
* * * * * *** * *
1395987 TA-TAAAGTCATAACTAATTTATTATTAATTTATCGGTAATTTATTACAAAGTTATCAATGATTA
1 TACTAAA-TTATCACTGATTTACTATTAAATTATTAATGATTTATTACTAA-TT-T--AT-A--A
*
1396051 ACTAATTTGC
58 A-TAATTTAC
* * * * * *
1396061 TACTAAATTATCATTTATTTA-TCACTAAATTATTAGTGATTTATTACTAAGTTATTAATAATTT
1 TACTAAATTATCACTGATTTACT-ATTAAATTATTAATGATTTATTACTAATTTATAAATAATTT
1396125 AC
65 AC
* *
1396127 -ATCTAAATTATCAATGATTTACTATTATATTATT-ATGCATTTATTACTA
1 TA-CTAAATTATCACTGATTTACTATTAAATTATTAATG-ATTTATTACTA
1396176 TATTATCATT
Statistics
Matches: 193, Mismatches: 44, Indels: 35
0.71 0.16 0.13
Matches are distributed among these distances:
65 19 0.10
66 115 0.60
67 7 0.04
68 1 0.01
69 1 0.01
70 3 0.02
72 1 0.01
73 4 0.02
74 38 0.20
75 4 0.02
ACGTcount: A:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (66 bp):
TACTAAATTATCACTGATTTACTATTAAATTATTAATGATTTATTACTAATTTATAAATAATTTA
C
Found at i:1396102 original size:22 final size:22
Alignment explanation
Indices: 1396062--1396191 Score: 86
Period size: 22 Copynumber: 5.9 Consensus size: 22
1396052 CTAATTTGCT
* *
1396062 ACTAAATTATCATTTATTTATC
1 ACTAAATTATCAATGATTTATC
* * *
1396084 ACTAAATTATTAGTGATTTATT
1 ACTAAATTATCAATGATTTATC
* * *
1396106 ACTAAGTTATTAATAATTTA-C
1 ACTAAATTATCAATGATTTATC
1396127 ATCTAAATTATCAATGATTTA-C
1 A-CTAAATTATCAATGATTTATC
* * * *
1396149 TATTATATTAT-TATGCATTTATT
1 -ACTAAATTATCAATG-ATTTATC
* *
1396172 ACTATATTATCATTGATTTA
1 ACTAAATTATCAATGATTTA
1396192 CTAAATAGCT
Statistics
Matches: 85, Mismatches: 18, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
21 4 0.05
22 78 0.92
23 3 0.04
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (22 bp):
ACTAAATTATCAATGATTTATC
Found at i:1396191 original size:66 final size:66
Alignment explanation
Indices: 1396063--1396192 Score: 149
Period size: 66 Copynumber: 2.0 Consensus size: 66
1396053 TAATTTGCTA
* * *
1396063 CTAAATTATCATTTATTTATCACTAAATTATTAGTGATTTATTACTAAGTTATTAATAATTTACA
1 CTAAATTATCAATGATTTATCACTAAATTATTAGTGATTTATTACTAAGTTATCAATAATTTACA
1396128 T
66 T
* * * *
1396129 CTAAATTATCAATGATTTA-CTATTATATTATTA-TGCATTTATTACTATA-TTATCATTGATTT
1 CTAAATTATCAATGATTTATC-ACTAAATTATTAGTG-ATTTATTACTA-AGTTATCAATAATTT
1396191 AC
63 AC
1396193 TAAATAGCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
65 3 0.06
66 50 0.93
67 1 0.02
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (66 bp):
CTAAATTATCAATGATTTATCACTAAATTATTAGTGATTTATTACTAAGTTATCAATAATTTACA
T
Found at i:1396192 original size:19 final size:19
Alignment explanation
Indices: 1396157--1396194 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1396147 ACTATTATAT
*
1396157 TATTATGCATTTATTACTA
1 TATTATGCATTGATTACTA
1396176 TATTAT-CATTGATTTACTA
1 TATTATGCATTGA-TTACTA
1396195 AATAGCTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (19 bp):
TATTATGCATTGATTACTA
Found at i:1396329 original size:22 final size:22
Alignment explanation
Indices: 1396266--1396563 Score: 126
Period size: 22 Copynumber: 13.3 Consensus size: 22
1396256 CATTATCAAG
1396266 TTATCATTGATTTA-TATTAAA
1 TTATCATTGATTTACTATTAAA
*
1396287 TTATCCA-TGATTTACTCTTAAA
1 TTAT-CATTGATTTACTATTAAA
* * *
1396309 TTATCATTAATTAACTATTAAG
1 TTATCATTGATTTACTATTAAA
* *
1396331 TTATTGA-TGATTAACTATTATTAA
1 TTA-TCATTGATTTACTATTA--AA
* * *
1396355 GTTAT-GTTGATTTACTTTTAAGT
1 -TTATCATTGATTTACTATTAA-A
* * * *
1396378 TTAT-AATGATTAATTACTAAA
1 TTATCATTGATTTACTATTAAA
* * * *
1396399 CTATCATTTATTGACTATTAAG
1 TTATCATTGATTTACTATTAAA
*
1396421 TTAT--TTACGATTTACTACTAAA
1 TTATCATT--GATTTACTATTAAA
* *
1396443 TTTATTAATTAATTAATTACTATTAAA
1 -TTA-TCATTGA-T--TTACTATTAAA
*
1396470 TTATAATTGATTTACTATTAAA
1 TTATCATTGATTTACTATTAAA
* * * *
1396492 TTATAACTAATTTACTATTAAG
1 TTATCATTGATTTACTATTAAA
* * * * *
1396514 TTATTATCGATTTATTACTAAG
1 TTATCATTGATTTACTATTAAA
* *
1396536 TTATCAATTG-TTAACTACTAAA
1 TTATC-ATTGATTTACTATTAAA
1396558 TTATCA
1 TTATCA
1396564 CTTATTTTTT
Statistics
Matches: 209, Mismatches: 48, Indels: 40
0.70 0.16 0.13
Matches are distributed among these distances:
20 2 0.01
21 17 0.08
22 141 0.67
23 8 0.04
24 16 0.08
25 10 0.05
26 5 0.02
27 10 0.05
ACGTcount: A:0.37, C:0.09, G:0.06, T:0.48
Consensus pattern (22 bp):
TTATCATTGATTTACTATTAAA
Found at i:1396351 original size:90 final size:88
Alignment explanation
Indices: 1396257--1396518 Score: 224
Period size: 90 Copynumber: 2.9 Consensus size: 88
1396247 GCCATAATTC
*
1396257 ATTATCAAGTTATCATTGATTTA-TATTAAATTATCCATGATTTACTCTTAAATTATCATTAATT
1 ATTAT-AAGTTAT-ATTGATTTACTATTAAATTAT-AATGATTTACTCTTAAATTATCATTAATT
*
1396321 AACTATTAAGTTATTGATGATTAACT
63 AACTATTAAGTTATTGACGATTAACT
* * * * * * *
1396347 ATTATTAAGTTATGTTGATTTACTTTTAAGTTTATAATGATTAATTAC-TAAACTATCATTTATT
1 ATTA-TAAGTTATATTGATTTACTATTAA-ATTATAATGATTTACT-CTTAAATTATCATTAATT
* * *
1396411 GACTATTAAGTTATTTACGATTTACT
63 AACTATTAAGTTATTGACGATTAACT
* * * * * *
1396437 ACTA-AATTTATTAATTAATTAATTACTATTAAATTATAATTGATTTACTATTAAATTATAACTA
1 ATTATAAGTTA-T-ATTGA-T--TTACTATTAAATTATAA-TGATTTACTCTTAAATTATCATTA
*
1396501 ATTTACTATTAAGTTATT
60 ATTAACTATTAAGTTATT
1396519 ATCGATTTAT
Statistics
Matches: 135, Mismatches: 26, Indels: 19
0.75 0.14 0.11
Matches are distributed among these distances:
88 5 0.04
89 9 0.07
90 66 0.49
91 7 0.05
92 6 0.04
93 42 0.31
ACGTcount: A:0.37, C:0.08, G:0.06, T:0.48
Consensus pattern (88 bp):
ATTATAAGTTATATTGATTTACTATTAAATTATAATGATTTACTCTTAAATTATCATTAATTAAC
TATTAAGTTATTGACGATTAACT
Found at i:1396951 original size:22 final size:22
Alignment explanation
Indices: 1396898--1396960 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
1396888 ATGATGTATT
* *
1396898 ACTAATTTATGAATAATTTGCT
1 ACTAATTTATGAATGATTTGCC
1396920 ACTAATTTATGAATGATTTGCC
1 ACTAATTTATGAATGATTTGCC
*
1396942 A-TTATATTATGAATGATTT
1 ACTAAT-TTATGAATGATTT
1396961 ACAAATCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 3 0.08
22 34 0.92
ACGTcount: A:0.35, C:0.08, G:0.11, T:0.46
Consensus pattern (22 bp):
ACTAATTTATGAATGATTTGCC
Found at i:1397035 original size:44 final size:42
Alignment explanation
Indices: 1396987--1397094 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 42
1396977 GATTTACTAC
* *
1396987 TAAATTATTGATAATTTATTACAAAATTATTACTAATTTAAAAT
1 TAAATTATT-ATAATTTACTACAAAATTATAACT-ATTTAAAAT
* * * * *
1397031 TAAATTATCTATAATTCACTACCAAGTTATAACTATTTTATAT
1 TAAATTAT-TATAATTTACTACAAAATTATAACTATTTAAAAT
*
1397074 TAAATTATACATAATTTACTA
1 TAAATTAT-TATAATTTACTA
1397095 TTAAGTTATC
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
43 25 0.47
44 27 0.51
45 1 0.02
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (42 bp):
TAAATTATTATAATTTACTACAAAATTATAACTATTTAAAAT
Found at i:1397096 original size:22 final size:22
Alignment explanation
Indices: 1396978--1397248 Score: 73
Period size: 22 Copynumber: 12.5 Consensus size: 22
1396968 ATTGTTAGTG
**
1396978 ATTTACTACTAAATTATTGATA
1 ATTTACTACTAAATTATACATA
* *
1397000 ATTTATTACAAAATTATTAC-TA
1 ATTTACTACTAAATTA-TACATA
** *
1397022 ATTTAAAATTAAATTAT-CTATA
1 ATTTACTACTAAATTATAC-ATA
* * *
1397044 ATTCACTACCAAGTTATA-ACTA
1 ATTTACTACTAAATTATACA-TA
* *
1397066 TTTTA-TATTAAATTATACATA
1 ATTTACTACTAAATTATACATA
* * *
1397087 ATTTACTATTAAGTTAT-CAATG
1 ATTTACTACTAAATTATAC-ATA
* * ** *
1397109 ATTAACTATTATGTTAT-CAATT
1 ATTTACTACTAAATTATAC-ATA
* * *
1397131 ATTTACTACT-AGTTATA-TTG
1 ATTTACTACTAAATTATACATA
* * *
1397151 ATTTACT-CTTAAGTTTTAAATGA
1 ATTTACTAC-TAAATTATACAT-A
* *
1397174 A-TAACTACTAAATTAT-CAATT
1 ATTTACTACTAAATTATAC-ATA
* *
1397195 ATTTACTACTAATTTATA-ATTG
1 ATTTACTACTAAATTATACA-TA
** *
1397217 ATTT-CTACTAAATTATTTATT
1 ATTTACTACTAAATTATACATA
1397238 ATTTACTACTA
1 ATTTACTACTA
1397249 TCAATTAATT
Statistics
Matches: 185, Mismatches: 44, Indels: 40
0.69 0.16 0.15
Matches are distributed among these distances:
19 1 0.01
20 10 0.05
21 47 0.25
22 124 0.67
23 3 0.02
ACGTcount: A:0.39, C:0.10, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTTACTACTAAATTATACATA
Found at i:1397173 original size:64 final size:66
Alignment explanation
Indices: 1397087--1397220 Score: 182
Period size: 64 Copynumber: 2.1 Consensus size: 66
1397077 ATTATACATA
* * * **
1397087 ATTTACTATTAAGTTATCAATGATTAACTATTATGTTATCAATTATTTACTACT-AGTTAT-ATT
1 ATTTACTATTAAGTTATAAATGAATAACTACTAAATTATCAATTATTTACTACTAAGTTATAATT
1397150 G
66 G
* * *
1397151 ATTTACTCTTAAGTTTTAAATGAATAACTACTAAATTATCAATTATTTACTACTAATTTATAATT
1 ATTTACTATTAAGTTATAAATGAATAACTACTAAATTATCAATTATTTACTACTAAGTTATAATT
1397216 G
66 G
1397217 ATTT
1 ATTT
1397221 CTACTAAATT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
64 47 0.78
65 5 0.08
66 8 0.13
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (66 bp):
ATTTACTATTAAGTTATAAATGAATAACTACTAAATTATCAATTATTTACTACTAAGTTATAATT
G
Found at i:1397302 original size:22 final size:22
Alignment explanation
Indices: 1397277--1397368 Score: 103
Period size: 22 Copynumber: 4.2 Consensus size: 22
1397267 ATTGAAACTG
1397277 ATTTACTATTAAATTATCACTA
1 ATTTACTATTAAATTATCACTA
* *
1397299 ATTTACTATTAAATTATCAGTG
1 ATTTACTATTAAATTATCACTA
* * * *
1397321 ATTTATTAGTAAGTTATCAATA
1 ATTTACTATTAAATTATCACTA
* * *
1397343 ATTAACTATTAAGTTATCACTC
1 ATTTACTATTAAATTATCACTA
1397365 ATTT
1 ATTT
1397369 TTTGCTAAGT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 57 1.00
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (22 bp):
ATTTACTATTAAATTATCACTA
Found at i:1397389 original size:44 final size:44
Alignment explanation
Indices: 1397247--1397382 Score: 116
Period size: 44 Copynumber: 3.1 Consensus size: 44
1397237 TATTTACTAC
* * * * * *
1397247 TATCAATTAATTAA-TATAAAATTGA-AACTGATTTACTATTAAAT
1 TATCAA-TAATTAACTATTAAATT-ATCACTCATTTATTAGTAAGT
* * * *
1397291 TATCACTAATTTACTATTAAATTATCAGTGATTTATTAGTAAGT
1 TATCAATAATTAACTATTAAATTATCACTCATTTATTAGTAAGT
* *
1397335 TATCAATAATTAACTATTAAGTTATCACTCATTT-TTTGCTAAGT
1 TATCAATAATTAACTATTAAATTATCACTCATTTATTAG-TAAGT
1397379 TATC
1 TATC
1397383 CTTAATTTAG
Statistics
Matches: 75, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
43 10 0.13
44 65 0.87
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (44 bp):
TATCAATAATTAACTATTAAATTATCACTCATTTATTAGTAAGT
Found at i:1397397 original size:44 final size:44
Alignment explanation
Indices: 1397290--1397397 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 44
1397280 TACTATTAAA
* * *
1397290 TTATCACTAATTTACTATTAAATTATCAGTGATTTATTAGTAAG
1 TTATCAATAATTTACTATTAAATTATCACTCATTTATTAGTAAG
* * *
1397334 TTATCAATAATTAACTATTAAGTTATCACTCATTT-TTTGCTAAG
1 TTATCAATAATTTACTATTAAATTATCACTCATTTATTAG-TAAG
** *
1397378 TTATCCTTAATTTAGTATTA
1 TTATCAATAATTTACTATTA
1397398 TGTTGTTATG
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
43 3 0.06
44 50 0.94
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.47
Consensus pattern (44 bp):
TTATCAATAATTTACTATTAAATTATCACTCATTTATTAGTAAG
Found at i:1397524 original size:22 final size:20
Alignment explanation
Indices: 1397499--1397567 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 20
1397489 TCAACTAGTA
1397499 ACTATTAAATTATTATTCACTT
1 ACTATTAAATTATTATT-A-TT
* *
1397521 ACTATTAAGTTATAATTAATTT
1 ACTATTAAATTATTATT-A-TT
*
1397543 ATTATTAAATTATCTATTATT
1 ACTATTAAATTAT-TATTATT
1397564 ACTA
1 ACTA
1397568 CTAAGTTATA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
21 5 0.13
22 30 0.79
23 3 0.08
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (20 bp):
ACTATTAAATTATTATTATT
Found at i:1397633 original size:27 final size:27
Alignment explanation
Indices: 1397603--1397662 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
1397593 TTTTTAATGA
* *
1397603 TTAATTATTAAGTTATTAATTATCCAC
1 TTAACTATTAAATTATTAATTATCCAC
1397630 TTAACTATTAAATTATTAATTATCCA-
1 TTAACTATTAAATTATTAATTATCCAC
1397656 TT-ACTAT
1 TTAACTAT
1397663 GTTATCATTG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
25 5 0.16
26 2 0.06
27 24 0.77
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (27 bp):
TTAACTATTAAATTATTAATTATCCAC
Found at i:1400536 original size:17 final size:17
Alignment explanation
Indices: 1400514--1400546 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1400504 GCACTTCTTT
*
1400514 AATTTAATTATAAAAAA
1 AATTTAATAATAAAAAA
1400531 AATTTAATAATAAAAA
1 AATTTAATAATAAAAA
1400547 TTTCATTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATTTAATAATAAAAAA
Found at i:1400838 original size:16 final size:17
Alignment explanation
Indices: 1400817--1400849 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1400807 TAGATAATTT
1400817 ATATATACATAT-TAAA
1 ATATATACATATATAAA
*
1400833 ATATATATATATATAAA
1 ATATATACATATATAAA
1400850 TAAATACTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATATACATATATAAA
Found at i:1403943 original size:2 final size:2
Alignment explanation
Indices: 1403936--1403966 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1403926 GAATAGTGTT
*
1403936 TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1403967 TCATTAGCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1404285 original size:5 final size:5
Alignment explanation
Indices: 1404275--1404309 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
1404265 TTCAAAGTGA
1404275 AAAAT AAAAT AAAAT AAAAT ATAAAT -AAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT
1404310 TCATAGTGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.14
5 20 0.71
6 4 0.14
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:1404633 original size:134 final size:134
Alignment explanation
Indices: 1404487--1404854 Score: 641
Period size: 134 Copynumber: 2.8 Consensus size: 134
1404477 TCGGTTTATT
* * * * * *
1404487 TAAATAGTAAATTATTTGTATTCGATTTGTGCTAAATTCAATTAAGTTAAATGAGCTCGTTCATG
1 TAAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATG
1404552 AGCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTAT
66 AGCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTAT
1404617 TCGA
131 TCGA
1404621 TAAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATG
1 TAAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATG
1404686 AGCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTAT
66 AGCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTAT
1404751 TCGA
131 TCGA
1404755 TAAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATG
1 TAAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATG
* *
1404820 AGCATTAAATGAGCATGTTCA-TTAACA-TATATAAA
66 AGCATTAAATGAGAATATTCATTTAA-ATTATATAAA
1404855 CGAACATATT
Statistics
Matches: 225, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
133 12 0.05
134 213 0.95
ACGTcount: A:0.40, C:0.09, G:0.10, T:0.41
Consensus pattern (134 bp):
TAAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATG
AGCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTAT
TCGA
Found at i:1404894 original size:134 final size:133
Alignment explanation
Indices: 1404488--1404895 Score: 437
Period size: 134 Copynumber: 3.0 Consensus size: 133
1404478 CGGTTTATTT
* * * * * *
1404488 AAATAGTAAATTATTTGTATTCGATTTGTGCTAAATTCAATTAAGTTAAATGAGCTCGTTCATGA
1 AAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATGA
* * * * ** ****
1404553 GCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTATT
66 GCATTAAATGAGAATATTCATTTAAATTATATAAAAACATATACATATAACAATAAACAAATATT
*
1404618 CGAT
131 C-AC
1404622 AAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATGA
1 AAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATGA
* * * * ** ****
1404687 GCATTAAATGAGAATATTCATTTAAATTATATAAATATATATACATATATCTATTTATTCGTATT
66 GCATTAAATGAGAATATTCATTTAAATTATATAAAAACATATACATATAACAATAAACAAATATT
*
1404752 CGAT
131 C-AC
1404756 AAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATGA
1 AAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATGA
* * **
1404821 GCATTAAATGAGCATGTTCA-TTAACA-TATATAAACGAACATATTTATA-AACAATAAACAAAT
66 GCATTAAATGAGAATATTCATTTAA-ATTATATAAA--AACATATACATATAACAATAAACAAAT
1404883 CATT-ACC
128 -ATTCA-C
1404890 AAATAA
1 AAATAA
1404896 ATTCAAACAA
Statistics
Matches: 248, Mismatches: 21, Indels: 10
0.89 0.08 0.04
Matches are distributed among these distances:
133 13 0.05
134 224 0.90
135 11 0.04
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (133 bp):
AAATAATAAATTATTTGTATTCGATTTGTACTGAATTCAATTAAGTTAAATAAGCTCATTTATGA
GCATTAAATGAGAATATTCATTTAAATTATATAAAAACATATACATATAACAATAAACAAATATT
CAC
Found at i:1405040 original size:11 final size:11
Alignment explanation
Indices: 1405005--1405045 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
1404995 TAATATTATT
*
1405005 ATAAACAAACA
1 ATAAACGAACA
1405016 ATAAACGAACA
1 ATAAACGAACA
* *
1405027 ATAAATGAATA
1 ATAAACGAACA
1405038 ATAAACGA
1 ATAAACGA
1405046 TAAACAAACT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.15
Consensus pattern (11 bp):
ATAAACGAACA
Found at i:1411057 original size:15 final size:15
Alignment explanation
Indices: 1411037--1411069 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1411027 ATTTAATATT
1411037 TTTTAAAATTTTAAA
1 TTTTAAAATTTTAAA
*
1411052 TTTTAATATTTTAAA
1 TTTTAAAATTTTAAA
1411067 TTT
1 TTT
1411070 CTTTTTTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTAAAATTTTAAA
Found at i:1411848 original size:84 final size:84
Alignment explanation
Indices: 1411707--1411966 Score: 484
Period size: 84 Copynumber: 3.1 Consensus size: 84
1411697 TTGAAAATTG
* *
1411707 ACATTTTAAGTAAGATATACATGCATCTACCTCAAATCAAATGCTCTAATACCTTATTTAGATTA
1 ACATTTTAAGTAAGATATACATGCATGTACCTCAAGTCAAATGCTCTAATACCTTATTTAGATTA
1411772 CTTATAATATTATCTAATA
66 CTTATAATATTATCTAATA
1411791 ACATTTTAAGTAAGATATACATGCATGTACCTCAAGTCAAATGCTCTAATACCTTATTTAGATTA
1 ACATTTTAAGTAAGATATACATGCATGTACCTCAAGTCAAATGCTCTAATACCTTATTTAGATTA
1411856 CTTATAATATTATCTAATA
66 CTTATAATATTATCTAATA
*
1411875 ACATTTTAAGTAAGATATACATGCATGTACCTCAAGTAAAATGCTCTAATACCTTATTTAGATTA
1 ACATTTTAAGTAAGATATACATGCATGTACCTCAAGTCAAATGCTCTAATACCTTATTTAGATTA
1411940 CTTATAATATTATCTAATA
66 CTTATAATATTATCTAATA
*
1411959 AAATTTTA
1 ACATTTTA
1411967 TATTTCTTTT
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
84 172 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.38
Consensus pattern (84 bp):
ACATTTTAAGTAAGATATACATGCATGTACCTCAAGTCAAATGCTCTAATACCTTATTTAGATTA
CTTATAATATTATCTAATA
Found at i:1412363 original size:19 final size:20
Alignment explanation
Indices: 1412308--1412402 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 20
1412298 ATGCTGCAAT
*
1412308 TATTATATTAATAAAATAATA
1 TATTATATAAAT-AAATAATA
* *
1412329 T-TTTTATTATATAAATAATA
1 TATTATA-TAAATAAATAATA
*
1412349 TATTA-ATAAATAAATAATG
1 TATTATATAAATAAATAATA
* *
1412368 CATTATATAATTAATATAATA
1 TATTATATAAATAA-ATAATA
* *
1412389 TATGATATTAATAA
1 TATTATATAAATAA
1412403 TATATTATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
19 15 0.26
20 21 0.37
21 21 0.37
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (20 bp):
TATTATATAAATAAATAATA
Found at i:1412400 original size:18 final size:18
Alignment explanation
Indices: 1412369--1412467 Score: 82
Period size: 18 Copynumber: 5.4 Consensus size: 18
1412359 TAAATAATGC
1412369 ATTATATAATTAATATAAT
1 ATTATAT-ATTAATATAAT
1412388 A-TATGATATTAATA-ATAT
1 ATTAT-ATATTAATATA-AT
*
1412406 ATTATTTATTAATATATTAT
1 ATTATATATTAATATA--AT
1412426 ATTAGTAT-TT-ATATAAT
1 ATTA-TATATTAATATAAT
* *
1412443 ATTATTTATTAATATATT
1 ATTATATATTAATATAAT
1412461 ATT-TATA
1 ATTATATA
1412468 AATAATATTA
Statistics
Matches: 67, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
16 2 0.03
17 12 0.18
18 30 0.45
19 12 0.18
20 9 0.13
21 2 0.03
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (18 bp):
ATTATATATTAATATAAT
Found at i:1412420 original size:15 final size:15
Alignment explanation
Indices: 1412384--1412478 Score: 82
Period size: 15 Copynumber: 5.7 Consensus size: 15
1412374 ATAATTAATA
* *
1412384 TAATATATGATATTAA
1 TAATATATTAT-TTAT
1412400 TAATATATTATTTAT
1 TAATATATTATTTAT
1412415 TAATATATTATATTAGTATT
1 TAATATA-T-TATT--TA-T
1412435 TATATAATATTATTTAT
1 TA-AT-ATATTATTTAT
1412452 TAATATATTATTTAT
1 TAATATATTATTTAT
*
1412467 AAATAATATTAT
1 TAAT-ATATTAT
1412479 AAACATATAA
Statistics
Matches: 68, Mismatches: 3, Indels: 16
0.78 0.03 0.18
Matches are distributed among these distances:
15 24 0.35
16 20 0.29
17 7 0.10
18 2 0.03
19 2 0.03
20 7 0.10
21 3 0.04
22 3 0.04
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TAATATATTATTTAT
Found at i:1412422 original size:31 final size:30
Alignment explanation
Indices: 1412384--1412546 Score: 109
Period size: 31 Copynumber: 5.1 Consensus size: 30
1412374 ATAATTAATA
1412384 TAATATATGATATTAATAATATATTATTTAT
1 TAATATAT-ATATTAATAATATATTATTTAT
1412415 TAATATATTATATTAGTATTTATATAATATTATTTAT
1 TAATATA-TATATTA--A--TA-AT-ATATTATTTAT
* *
1412452 TAATATAT-TATTTATAA-ATAATA-TTAT
1 TAATATATATATTAATAATATATTATTTAT
* * * * *
1412479 AAACATATAAATAAATAA-ATAATATTATAT
1 TAATATATATATTAATAATATATTATT-TAT
*
1412509 TAATAGATATTATTAGATAATATTATTATATTAT
1 TAATATATA-TATTA-ATAATA-TATTAT-TTAT
1412543 TAAT
1 TAAT
1412547 CAAAAATAGA
Statistics
Matches: 104, Mismatches: 13, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
27 10 0.10
28 17 0.16
29 1 0.01
30 10 0.10
31 18 0.17
32 5 0.05
33 3 0.03
34 12 0.12
35 7 0.07
36 3 0.03
37 18 0.17
ACGTcount: A:0.48, C:0.01, G:0.02, T:0.49
Consensus pattern (30 bp):
TAATATATATATTAATAATATATTATTTAT
Found at i:1412445 original size:37 final size:36
Alignment explanation
Indices: 1412377--1412462 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
1412367 GCATTATATA
*
1412377 ATTAATATAATATATGATATTAATAATATATTATTT
1 ATTAATATATTATATGATATTAATAATATATTATTT
* *
1412413 ATTAATATATTATATTAGTATTTAT-ATAATATTATTT
1 ATTAATATATTATATGA-TATTAATAAT-ATATTATTT
1412450 ATTAATATATTAT
1 ATTAATATATTAT
1412463 TTATAAATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 17 0.38
37 28 0.62
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (36 bp):
ATTAATATATTATATGATATTAATAATATATTATTT
Found at i:1412463 original size:11 final size:13
Alignment explanation
Indices: 1412408--1412460 Score: 51
Period size: 14 Copynumber: 4.3 Consensus size: 13
1412398 AATAATATAT
1412408 TATTTATTAATA-
1 TATTTATTAATAG
*
1412420 TA-TTA-TATTAG
1 TATTTATTAATAG
*
1412431 TATTTATATAATAT
1 TATTTAT-TAATAG
1412445 TATTTATTAATA-
1 TATTTATTAATAG
1412457 TATT
1 TATT
1412461 ATTTATAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
10 4 0.12
11 5 0.15
12 9 0.26
13 5 0.15
14 11 0.32
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
TATTTATTAATAG
Found at i:1413430 original size:32 final size:30
Alignment explanation
Indices: 1413393--1413453 Score: 86
Period size: 32 Copynumber: 2.0 Consensus size: 30
1413383 TATTTAAATG
*
1413393 ATATTTAAATAATTAATTTATTAATTAATATA
1 ATATTTAAAAAATT-ATTTATT-ATTAATATA
*
1413425 ATATTTAAAAAATTATTTATTTTTAATAT
1 ATATTTAAAAAATTATTTATTATTAATAT
1413454 GTCATCATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 7 0.26
31 7 0.26
32 13 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
ATATTTAAAAAATTATTTATTATTAATATA
Found at i:1413529 original size:28 final size:27
Alignment explanation
Indices: 1413497--1413563 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
1413487 TATCATATTA
* *
1413497 ATTAATAAA-TTAATAATTTAAGTATCAT
1 ATTAA-AAATTTAA-AATTGAAGTACCAT
1413525 ATTAAAAATTTTAAAATTGAAGTACCAT
1 ATTAAAAA-TTTAAAATTGAAGTACCAT
*
1413553 ATTAAATATTT
1 ATTAAAAATTT
1413564 TATTATAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 24 0.71
29 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
ATTAAAAATTTAAAATTGAAGTACCAT
Found at i:1413564 original size:28 final size:29
Alignment explanation
Indices: 1413506--1413565 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
1413496 AATTAATAAA
* *
1413506 TTAATAATTTAAGTATCATATTAAAAATT
1 TTAATAATTGAAGTACCATATTAAAAATT
*
1413535 TTAA-AATTGAAGTACCATATTAAATATT
1 TTAATAATTGAAGTACCATATTAAAAATT
1413563 TTA
1 TTA
1413566 TTATAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (29 bp):
TTAATAATTGAAGTACCATATTAAAAATT
Found at i:1419977 original size:3 final size:3
Alignment explanation
Indices: 1419969--1420008 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1419959 ATATTCTCGG
1419969 ATA 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 ATA A
1420009 AGTGGCTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1422647 original size:30 final size:30
Alignment explanation
Indices: 1422613--1422670 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
1422603 ATTTTTAAAT
* *
1422613 TTTAATTTGTATTTAAATAGAA-TCTTAACA
1 TTTAATTTATATTCAAATA-AATTCTTAACA
1422643 TTTAATTTATATTCAAATAAATTCTTAA
1 TTTAATTTATATTCAAATAAATTCTTAA
1422671 TATAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTAATTTATATTCAAATAAATTCTTAACA
Found at i:1424109 original size:30 final size:30
Alignment explanation
Indices: 1424073--1424149 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
1424063 TATTGCATCA
* *
1424073 AAATAAGTTTTTAATTTTTAATTTGTATTT
1 AAATAAGATTTTAATATTTAATTTGTATTT
* *
1424103 AAATAAGATCTTAACATTTAATTTGTATTT
1 AAATAAGATTTTAATATTTAATTTGTATTT
1424133 AAATAA-ACTTTTAATAT
1 AAATAAGA-TTTTAATAT
1424150 AAATCAATTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
29 1 0.03
30 39 0.98
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (30 bp):
AAATAAGATTTTAATATTTAATTTGTATTT
Found at i:1429674 original size:10 final size:10
Alignment explanation
Indices: 1429659--1429698 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1429649 ACATATTATT
1429659 AATAATTTTA
1 AATAATTTTA
1429669 AATAATTATT-
1 AATAATT-TTA
*
1429679 AATTATTTTA
1 AATAATTTTA
1429689 AATAATTTTA
1 AATAATTTTA
1429699 TTAAATTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
9 2 0.08
10 22 0.85
11 2 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
AATAATTTTA
Found at i:1429678 original size:20 final size:20
Alignment explanation
Indices: 1429653--1429695 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1429643 AGGAAAACAT
1429653 ATTATTAATAATTTTAAATA
1 ATTATTAATAATTTTAAATA
*
1429673 ATTATTAATTATTTTAAATA
1 ATTATTAATAATTTTAAATA
1429693 ATT
1 ATT
1429696 TTATTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATTATTAATAATTTTAAATA
Found at i:1429706 original size:30 final size:30
Alignment explanation
Indices: 1429659--1429717 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1429649 ACATATTATT
1429659 AATAATTTTAAATAATTA-TTAATTATTTTA
1 AATAATTTTAAATAATTAGTT-ATTATTTTA
*
1429689 AATAATTTT-ATTAAATTAGTTATTATTTT
1 AATAATTTTAAAT-AATTAGTTATTATTTT
1429718 GATTAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 2 0.08
30 22 0.85
31 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
AATAATTTTAAATAATTAGTTATTATTTTA
Found at i:1446056 original size:21 final size:20
Alignment explanation
Indices: 1446030--1446075 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1446020 TCACTCTCAA
*
1446030 ATTAAATTAAATAAAGGTTTG
1 ATTAAAATAAA-AAAGGTTTG
*
1446051 ATTAAAAATAAAAAAGGTTTT
1 ATT-AAAATAAAAAAGGTTTG
1446072 ATTA
1 ATTA
1446076 TTGTTGTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 1 0.05
21 14 0.64
22 7 0.32
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
ATTAAAATAAAAAAGGTTTG
Found at i:1450306 original size:20 final size:22
Alignment explanation
Indices: 1450283--1450335 Score: 67
Period size: 20 Copynumber: 2.5 Consensus size: 22
1450273 AATAATTGAT
1450283 TATATATAAATTTAT-TT-AAA
1 TATATATAAATTTATATTAAAA
1450303 TATAT-TAAAATTTATATTAAAA
1 TATATAT-AAATTTATATTAAAA
1450325 TAATATATAAA
1 T-ATATATAAA
1450336 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
19 1 0.04
20 13 0.46
21 2 0.07
22 4 0.14
23 7 0.25
24 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATATAAATTTATATTAAAA
Found at i:1450335 original size:12 final size:13
Alignment explanation
Indices: 1450301--1450340 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
1450291 AATTTATTTA
1450301 AATATATTAAAAT
1 AATATATTAAAAT
*
1450314 -TTATATTAAAAT
1 AATATATTAAAAT
1450326 AATATA-TAAAA-
1 AATATATTAAAAT
1450337 AATA
1 AATA
1450341 AAAAAATAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATATTAAAAT
Found at i:1451282 original size:14 final size:15
Alignment explanation
Indices: 1451263--1451295 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1451253 AAAATTTATC
1451263 AATATTTTAT-TAAA
1 AATATTTTATATAAA
1451277 AATA-TTTATATAAA
1 AATATTTTATATAAA
1451291 AATAT
1 AATAT
1451296 ATATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATTTTATATAAA
Found at i:1452614 original size:4 final size:4
Alignment explanation
Indices: 1452607--1452636 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1452597 TATATATATA
*
1452607 TATG TATG TATG TATG TATG CATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TA
1452637 AGTTTCATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.27, C:0.03, G:0.23, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:1452844 original size:241 final size:229
Alignment explanation
Indices: 1452411--1453066 Score: 913
Period size: 241 Copynumber: 2.8 Consensus size: 229
1452401 GCGTAATCAA
* *
1452411 CATTAGGGTATGCAGTAACTCCATAAGTGTCTGTGTCAAATACCATGGTTTTCACGTTGTGTTTT
1 CATTAGGGTATGCAGTAACTCCATAATTGTCTGTGTCAAATACCATGGTTTTCACGCTGTGTTTT
*
1452476 CTATGCATCTGCATATGTGTTGCACACACCCATTAATGACTTCAAGCTAAGATTTCCAATCAAAC
66 CTATGCATCTGCATATGTGTTGCACACACCCATTAATGACTTCAAGCTAGGATTTCCAATCAAAC
* *
1452541 TCTTAATTCTTATATTTTATGATTATTGAACGGTGTAATAATAATATTTTTTGTTATATATATAT
131 TCTTAATTCTTATATTTTATGATTATTAAACGGTGTAATAATATTATTTTTTGTTAT-T-TATAT
*
1452606 ATATGTATGTATGTATGTATGCATGTATGTAAGTTTCATCAAGAAC
194 ATA--TATGTATGTATG--T--ATGTA--T--GTCTCATCAAGAAC
* ** *
1452652 CATTAGGGTATGCAGAAACTCCATAATTGTCTGACTCAAATACCATGGTTTTTACGCTGTGTTTT
1 CATTAGGGTATGCAGTAACTCCATAATTGTCTGTGTCAAATACCATGGTTTTCACGCTGTGTTTT
* * * * *
1452717 CTATGCATCTGCACATATGTTGCACACAACCATCAATAACTTCAAGCTAGGATTTCCAATCAAAC
66 CTATGCATCTGCATATGTGTTGCACACACCCATTAATGACTTCAAGCTAGGATTTCCAATCAAAC
* * * *
1452782 TCTTAATTCTTGTGTTTTATGATTATTAAACAGTGTAATAATATTATTGTTTG-T-TTTATATAT
131 TCTTAATTCTTATATTTTATGATTATTAAACGGTGTAATAATATTATTTTTTGTTATTTATATAT
1452845 ATATGTATGTATGTATGTATGTCTCATCAAGAAC
196 ATATGTATGTATGTATGTATGTCTCATCAAGAAC
* ** * *
1452879 CATTGGGGTATATAGTAACTCCAAAATTGTCTGTGTCAAATACCATGG-TTTCATGCTGTGTTTT
1 CATTAGGGTATGCAGTAACTCCATAATTGTCTGTGTCAAATACCATGGTTTTCACGCTGTGTTTT
* *
1452943 CTCTGCATCTGCATATGTGTTGCACATACCCATTAATGACTTCAAGCTAGGATTTCCAATCAAAC
66 CTATGCATCTGCATATGTGTTGCACACACCCATTAATGACTTCAAGCTAGGATTTCCAATCAAAC
*
1453008 TCTTATTGATTCTTATATTTTATGATTATTAAACGGTGTAATACTATTATTTTTTGTTA
131 TCTTA---ATTCTTATATTTTATGATTATTAAACGGTGTAATAATATTATTTTTTGTTA
1453067 CATGTATATG
Statistics
Matches: 370, Mismatches: 40, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
226 77 0.21
227 54 0.15
229 44 0.12
230 1 0.00
231 5 0.01
233 1 0.00
235 12 0.03
237 8 0.02
238 1 0.00
239 1 0.00
240 1 0.00
241 165 0.45
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.40
Consensus pattern (229 bp):
CATTAGGGTATGCAGTAACTCCATAATTGTCTGTGTCAAATACCATGGTTTTCACGCTGTGTTTT
CTATGCATCTGCATATGTGTTGCACACACCCATTAATGACTTCAAGCTAGGATTTCCAATCAAAC
TCTTAATTCTTATATTTTATGATTATTAAACGGTGTAATAATATTATTTTTTGTTATTTATATAT
ATATGTATGTATGTATGTATGTCTCATCAAGAAC
Found at i:1457071 original size:15 final size:17
Alignment explanation
Indices: 1457039--1457072 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
1457029 CCCTACCAAG
1457039 TAAGGATCACACTTCTT
1 TAAGGATCACACTTCTT
1457056 TAAGGAT-ACA-TTCTT
1 TAAGGATCACACTTCTT
1457071 TA
1 TA
1457073 TTCTAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (17 bp):
TAAGGATCACACTTCTT
Found at i:1458977 original size:14 final size:14
Alignment explanation
Indices: 1458958--1458987 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1458948 ATACAAAACC
*
1458958 TTTTTTTCTCTCTT
1 TTTTTTTCTCTATT
1458972 TTTTTTTCTCTATT
1 TTTTTTTCTCTATT
1458986 TT
1 TT
1458988 GCCGCCACAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTTCTCTATT
Found at i:1466524 original size:23 final size:22
Alignment explanation
Indices: 1466498--1466545 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
1466488 CACATACCTC
*
1466498 TTTGAAAATTCAATTGATTATAA
1 TTTGAAAATT-AATTGATTAAAA
* *
1466521 TTTGAAGATTGATTGATTAAAA
1 TTTGAAAATTAATTGATTAAAA
1466543 TTT
1 TTT
1466546 ATCATTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (22 bp):
TTTGAAAATTAATTGATTAAAA
Found at i:1468937 original size:24 final size:24
Alignment explanation
Indices: 1468908--1468956 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1468898 ATATGAGCTA
1468908 TTAAATTAAACGT-TTATTTTATAT
1 TTAAATTAAAC-TCTTATTTTATAT
* *
1468932 TTAAATTGAACTCTTATTTTTTAT
1 TTAAATTAAACTCTTATTTTATAT
1468956 T
1 T
1468957 AATTAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
TTAAATTAAACTCTTATTTTATAT
Found at i:1475991 original size:16 final size:16
Alignment explanation
Indices: 1475972--1476005 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
1475962 TTTTTTTATT
1475972 ATTTTATCTAC-CAATA
1 ATTTT-TCTACACAATA
1475988 ATTTTTCTACACAATA
1 ATTTTTCTACACAATA
1476004 AT
1 AT
1476006 AATTCTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTTTTCTACACAATA
Found at i:1485843 original size:25 final size:25
Alignment explanation
Indices: 1485810--1485862 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1485800 CCATGATTAA
1485810 AAAACAAATCGAGGATCTCTAATGT
1 AAAACAAATCGAGGATCTCTAATGT
1485835 AAAACAAATCGAGGATCTCTAATGT
1 AAAACAAATCGAGGATCTCTAATGT
1485860 AAA
1 AAA
1485863 TAACTAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (25 bp):
AAAACAAATCGAGGATCTCTAATGT
Found at i:1491407 original size:15 final size:15
Alignment explanation
Indices: 1491389--1491418 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1491379 TGAATAATTT
1491389 AAATGTTAAATTTAA
1 AAATGTTAAATTTAA
*
1491404 AAATTTTAAATTTAA
1 AAATGTTAAATTTAA
1491419 TTTATATAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (15 bp):
AAATGTTAAATTTAA
Found at i:1491664 original size:24 final size:22
Alignment explanation
Indices: 1491637--1491681 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1491627 CAAAATTAAA
1491637 ATTTGAATTAATATAATATATATG
1 ATTTGAA--AATATAATATATATG
*
1491661 ATTTGAAAATTTAATATATAT
1 ATTTGAAAATATAATATATAT
1491682 ATAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 13 0.65
24 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (22 bp):
ATTTGAAAATATAATATATATG
Found at i:1491705 original size:35 final size:32
Alignment explanation
Indices: 1491634--1491706 Score: 85
Period size: 35 Copynumber: 2.2 Consensus size: 32
1491624 TAACAAAATT
*
1491634 AAAATTTGAATTAATATAATATATATGATTTG
1 AAAATTTGAATTAATATAATATATATGATTTA
*
1491666 AAAATTT-AATATATATATAAATTATATATTATTTA
1 AAAATTTGAAT-TA-ATAT-AA-TATATATGATTTA
1491701 AAAATT
1 AAAATT
1491707 CAAGATACAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 3 0.09
32 9 0.26
33 4 0.11
34 2 0.06
35 17 0.49
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (32 bp):
AAAATTTGAATTAATATAATATATATGATTTA
Found at i:1492448 original size:25 final size:27
Alignment explanation
Indices: 1492418--1492485 Score: 81
Period size: 25 Copynumber: 2.6 Consensus size: 27
1492408 TTTACATCTT
*
1492418 TATATTATATTTTATA-CAA-A-AATTA
1 TATATTATATTTTATATCAATATAA-AA
*
1492443 TATATTATAATTTATATCAATATAAAA
1 TATATTATATTTTATATCAATATAAAA
1492470 TATA-TATATTTTATAT
1 TATATTATATTTTATAT
1492486 TATTAAATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 15 0.41
26 14 0.38
27 6 0.16
28 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
TATATTATATTTTATATCAATATAAAA
Found at i:1492537 original size:11 final size:12
Alignment explanation
Indices: 1492523--1492567 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 12
1492513 AAGTTTTTAA
1492523 TTATATTAT-TT
1 TTATATTATATT
*
1492534 TTATATTATATAA
1 TTATATTATAT-T
1492547 TTATATTATATT
1 TTATATTATATT
*
1492559 TTAAATTAT
1 TTATATTAT
1492568 CATATCTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 9 0.31
12 9 0.31
13 11 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (12 bp):
TTATATTATATT
Found at i:1492551 original size:24 final size:25
Alignment explanation
Indices: 1492520--1492567 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
1492510 TAAAAGTTTT
*
1492520 TAATTATATTAT-TTTTATATTATA
1 TAATTATATTATATTTTAAATTATA
1492544 TAATTATATTATATTTTAAATTAT
1 TAATTATATTATATTTTAAATTAT
1492568 CATATCTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TAATTATATTATATTTTAAATTATA
Found at i:1493335 original size:18 final size:16
Alignment explanation
Indices: 1493289--1493336 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 16
1493279 TCATCGTTTG
1493289 AAATTAA-TTATATTA
1 AAATTAATTTATATTA
1493304 AAATTAAATATTATATTA
1 AAATT-AAT-TTATATTA
1493322 ATTAATTAATTTATA
1 A--AATTAATTTATA
1493337 ATTCAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
15 5 0.18
16 2 0.07
18 14 0.50
19 3 0.11
20 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
AAATTAATTTATATTA
Found at i:1494383 original size:29 final size:31
Alignment explanation
Indices: 1494341--1494411 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 31
1494331 TAAATAATCG
* * *
1494341 TTAAATTATAATAAAATATTTAATATGATAT
1 TTAAATTATAATAAAAAAATTAATATAATAT
*
1494372 TTAAATT-T-ATAAAAAAATTATTATAATAT
1 TTAAATTATAATAAAAAAATTAATATAATAT
*
1494401 TTAAAATATAA
1 TTAAATTATAA
1494412 ATTTATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
29 23 0.70
30 2 0.06
31 8 0.24
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
TTAAATTATAATAAAAAAATTAATATAATAT
Found at i:1501435 original size:2 final size:2
Alignment explanation
Indices: 1501430--1501455 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1501420 TCACACATAC
1501430 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
1501456 GTTCTAAACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1518579 original size:11 final size:9
Alignment explanation
Indices: 1518537--1518573 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
1518527 GTATAATAAA
1518537 TATATTATAT
1 TATATTAT-T
1518547 T-TA-TATT
1 TATATTATT
1518554 TATATTATT
1 TATATTATT
1518563 TATATTATT
1 TATATTATT
1518572 TA
1 TA
1518574 AATATTCGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
7 2 0.08
8 5 0.20
9 17 0.68
10 1 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
TATATTATT
Found at i:1520093 original size:32 final size:31
Alignment explanation
Indices: 1520035--1520111 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
1520025 TGTATTATTA
1520035 ATATATAAATTTTATATAAAATTAATAAGATG
1 ATATATAAATTTTATATAAAATTAATAA-ATG
* * *
1520067 ATATATAAAATTTATATATCAA-TAATAAATT
1 ATATATAAATTTTATATA-AAATTAATAAATG
*
1520098 AAATATAAATTTTA
1 ATATATAAATTTTA
1520112 AAAAATATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 14 0.36
32 23 0.59
33 2 0.05
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (31 bp):
ATATATAAATTTTATATAAAATTAATAAATG
Found at i:1521078 original size:2 final size:2
Alignment explanation
Indices: 1521071--1521095 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1521061 CCATCTCTTC
1521071 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 C
1521096 GAATTTAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1521277 original size:2 final size:2
Alignment explanation
Indices: 1521270--1521300 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1521260 AAATAAGTCA
1521270 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1521301 TTACAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1522734 original size:17 final size:17
Alignment explanation
Indices: 1522712--1522754 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1522702 AGGGCATGTT
1522712 AAAAAAAATAAAAAACA
1 AAAAAAAATAAAAAACA
** *
1522729 AAAAAAAGCAAAAAAGA
1 AAAAAAAATAAAAAACA
1522746 AAAAAAAAT
1 AAAAAAAAT
1522755 GGTTATTACA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.86, C:0.05, G:0.05, T:0.05
Consensus pattern (17 bp):
AAAAAAAATAAAAAACA
Found at i:1523246 original size:15 final size:15
Alignment explanation
Indices: 1523215--1523257 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1523205 GCAAAAAAAG
*
1523215 AAAAGAAAAGAAAGGA
1 AAAATAAAAG-AAGGA
*
1523231 AGAATAAAAGAAGGA
1 AAAATAAAAGAAGGA
1523246 AAAATAAAAGAA
1 AAAATAAAAGAA
1523258 ATGAATGGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (15 bp):
AAAATAAAAGAAGGA
Found at i:1523547 original size:15 final size:15
Alignment explanation
Indices: 1523527--1523570 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
1523517 ACCACTTTTG
1523527 AAAAAATTCTTTTCA
1 AAAAAATTCTTTTCA
1523542 AAAAAATTCTTTTCA
1 AAAAAATTCTTTTCA
1523557 AAAAAATTCTTTTC
1 AAAAAATTCTTTTC
1523571 CTTTTTTGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAAAATTCTTTTCA
Found at i:1523633 original size:15 final size:16
Alignment explanation
Indices: 1523613--1523646 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1523603 CATGGTGTGT
1523613 AAAAAAAAT-CAAATA
1 AAAAAAAATACAAATA
*
1523628 AAAAAAAATAGAAATA
1 AAAAAAAATACAAATA
1523644 AAA
1 AAA
1523647 GTGGCTCTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAAAATACAAATA
Found at i:1524243 original size:22 final size:22
Alignment explanation
Indices: 1524218--1524334 Score: 67
Period size: 22 Copynumber: 5.2 Consensus size: 22
1524208 AGTTAGCATG
1524218 TAAGCCTAGATTAGCTGGCACA
1 TAAGCCTAGATTAGCTGGCACA
* *
1524240 TAAGTCC-AGTTTAGCTAGCACAA
1 TAAG-CCTAGATTAGCTGGCAC-A
* * * *
1524263 TAAGCCCAAATTAGTTGGTACA
1 TAAGCCTAGATTAGCTGGCACA
* * ** *
1524285 TAA-ACTGAGTTTAATTGACACAA
1 TAAGCCT-AGATTAGCTGGCAC-A
* *
1524308 TAAGCCTAGATTAACCGGCACA
1 TAAGCCTAGATTAGCTGGCACA
1524330 TAAGC
1 TAAGC
1524335 TCAAATTAGC
Statistics
Matches: 70, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
21 1 0.01
22 37 0.53
23 30 0.43
24 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.25
Consensus pattern (22 bp):
TAAGCCTAGATTAGCTGGCACA
Found at i:1524654 original size:67 final size:65
Alignment explanation
Indices: 1524576--1524754 Score: 153
Period size: 65 Copynumber: 2.7 Consensus size: 65
1524566 AAGGGAAATC
* * * * *
1524576 TTAAGCCCAGTTTATCTAACCTCAAACGAAATTTTAAACCCAGTTTATC-TGGCATTTGAAAAAA
1 TTAAGCTCAGTTTATCTAACCCCAAA-GAAAATTTAAACCCAGTTTATCTTGCCA-TCG-AAAAA
1524640 TAT
63 TAT
* ** * * *
1524643 TTAAGCTCAGTTTATTTGGCCCCTAATAAAATTTAAGCCCAGTTTATCTTGCCATCGAAAAATAT
1 TTAAGCTCAGTTTATCTAACCCCAAAGAAAATTTAAACCCAGTTTATCTTGCCATCGAAAAATAT
* * * * * * * *
1524708 TTAAGCTCAATTTATTTGACCTCTAATAAAAGTTAAGCCCAGTTTAT
1 TTAAGCTCAGTTTATCTAACCCCAAAGAAAATTTAAACCCAGTTTAT
1524755 TTAGTCCCTA
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
65 51 0.53
66 21 0.22
67 24 0.25
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (65 bp):
TTAAGCTCAGTTTATCTAACCCCAAAGAAAATTTAAACCCAGTTTATCTTGCCATCGAAAAATAT
Found at i:1524686 original size:32 final size:31
Alignment explanation
Indices: 1524635--1524814 Score: 146
Period size: 33 Copynumber: 5.5 Consensus size: 31
1524625 TGGCATTTGA
*
1524635 AAAAATATTTAAGCTCAGTTTATTTGGCCCCT
1 AAAAA-ATTTAAGCCCAGTTTATTTGGCCCCT
* *
1524667 AATAAAATTTAAGCCCAGTTTATCTT-GCCATCG
1 AA-AAAATTTAAGCCCAGTTTAT-TTGGCC-CCT
* * * *
1524700 AAAAATATTTAAGCTCAATTTATTTGACCTCT
1 AAAAA-ATTTAAGCCCAGTTTATTTGGCCCCT
* * *
1524732 AATAAAAGTTAAGCCCAGTTTATTTAGTCCCT
1 AA-AAAATTTAAGCCCAGTTTATTTGGCCCCT
* *
1524764 AAAGAAATCTTAAGCCCAGTTTATCTGGCTCCT
1 AAA-AAAT-TTAAGCCCAGTTTATTTGGCCCCT
*
1524797 AAGAAAATCTTAAACCCA
1 AA-AAAAT-TTAAGCCCA
1524815 AATTAGCTAG
Statistics
Matches: 119, Mismatches: 20, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
31 1 0.01
32 54 0.45
33 63 0.53
34 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (31 bp):
AAAAAATTTAAGCCCAGTTTATTTGGCCCCT
Found at i:1524713 original size:33 final size:33
Alignment explanation
Indices: 1524576--1524754 Score: 127
Period size: 33 Copynumber: 5.5 Consensus size: 33
1524566 AAGGGAAATC
** * *
1524576 TTAAGCCCAGTTTATCTAACCTCAAACGAAAT-T
1 TTAAGCCCAGTTTATCTTGCCTCGAA-TAAATAT
* * * * *
1524609 TTAAACCCAGTTTATCTGGCATTTGAAAAAATAT
1 TTAAGCCCAGTTTATCTTGC-CTCGAATAAATAT
* * *
1524643 TTAAGCTCAGTTTAT-TTGGCCCCTAATAAA-AT
1 TTAAGCCCAGTTTATCTT-GCCTCGAATAAATAT
1524675 TTAAGCCCAGTTTATCTTGCCATCGAA-AAATAT
1 TTAAGCCCAGTTTATCTTGCC-TCGAATAAATAT
* * * *
1524708 TTAAGCTCAATTTAT-TTGACCTCTAATAAA-AG
1 TTAAGCCCAGTTTATCTTG-CCTCGAATAAATAT
1524740 TTAAGCCCAGTTTAT
1 TTAAGCCCAGTTTAT
1524755 TTAGTCCCTA
Statistics
Matches: 114, Mismatches: 24, Indels: 17
0.74 0.15 0.11
Matches are distributed among these distances:
32 43 0.38
33 52 0.46
34 19 0.17
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (33 bp):
TTAAGCCCAGTTTATCTTGCCTCGAATAAATAT
Found at i:1524723 original size:65 final size:66
Alignment explanation
Indices: 1524608--1524754 Score: 208
Period size: 65 Copynumber: 2.2 Consensus size: 66
1524598 CAAACGAAAT
* * * * *
1524608 TTTAAACCCAGTTTATCTGGCATTTGAAAAAATATTTAAGCTCAGTTTATTTGGCCCCTAATAAA
1 TTTAAGCCCAGTTTATCTGCCATTCGAAAAAATATTTAAGCTCAATTTATTTGACCCCTAATAAA
1524673 A
66 A
*
1524674 TTTAAGCCCAGTTTATCTTGCCA-TCG-AAAAATATTTAAGCTCAATTTATTTGACCTCTAATAA
1 TTTAAGCCCAGTTTATC-TGCCATTCGAAAAAATATTTAAGCTCAATTTATTTGACCCCTAATAA
1524737 AA
65 AA
*
1524739 GTTAAGCCCAGTTTAT
1 TTTAAGCCCAGTTTAT
1524755 TTAGTCCCTA
Statistics
Matches: 73, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
65 51 0.70
66 18 0.25
67 4 0.05
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.37
Consensus pattern (66 bp):
TTTAAGCCCAGTTTATCTGCCATTCGAAAAAATATTTAAGCTCAATTTATTTGACCCCTAATAAA
A
Found at i:1524798 original size:33 final size:32
Alignment explanation
Indices: 1524571--1524814 Score: 119
Period size: 33 Copynumber: 7.4 Consensus size: 32
1524561 GCCCCAAGGG
**
1524571 AAATCTTAAGCCCAGTTTATCT--AACCTCAAA
1 AAATCTTAAGCCCAGTTTATCTGGCTCCT-AAA
* * *
1524602 CGAAATTTTAAACCCAGTTTATCTGGCAT-TTGAAA
1 --AAATCTTAAGCCCAGTTTATCTGGC-TCCT-AAA
* * * *
1524637 AAATATTTAAGCTCAGTTTATTTGGCCCCTAATA
1 AAAT-CTTAAGCCCAGTTTATCTGGCTCCTAA-A
* *
1524671 AAAT-TTAAGCCCAGTTTATCTTGC-CATCGAAA
1 AAATCTTAAGCCCAGTTTATCTGGCTC--CTAAA
* * * *
1524703 AATAT-TTAAGCTCAATTTATTTGAC-CTCTAATA
1 AA-ATCTTAAGCCCAGTTTATCTGGCTC-CTAA-A
* * *
1524736 AAA-GTTAAGCCCAGTTTATTTAG-TCCCTAAA
1 AAATCTTAAGCCCAGTTTATCTGGCT-CCTAAA
1524767 GAAATCTTAAGCCCAGTTTATCTGGCTCCTAAGA
1 -AAATCTTAAGCCCAGTTTATCTGGCTCCTAA-A
*
1524801 AAATCTTAAACCCA
1 AAATCTTAAGCCCA
1524815 AATTAGCTAG
Statistics
Matches: 165, Mismatches: 29, Indels: 34
0.72 0.13 0.15
Matches are distributed among these distances:
31 2 0.01
32 47 0.28
33 86 0.52
34 26 0.16
35 4 0.02
ACGTcount: A:0.35, C:0.20, G:0.11, T:0.33
Consensus pattern (32 bp):
AAATCTTAAGCCCAGTTTATCTGGCTCCTAAA
Found at i:1525028 original size:103 final size:103
Alignment explanation
Indices: 1524849--1525054 Score: 394
Period size: 103 Copynumber: 2.0 Consensus size: 103
1524839 TTAAGCCTAA
1524849 TTTTTCTGGCACCAAAGAAAGATTTAAGTCTAGATTAATTGGTACTAATAAATGTTAAGCTTAGT
1 TTTTTCTGGCACCAAAGAAAGATTTAAGTCTAGATTAATTGGTACTAATAAATGTTAAGCTTAGT
1524914 TTATCTAGCCTTCAAACAAAGATTTAAGCCTAGTTTAG
66 TTATCTAGCCTTCAAACAAAGATTTAAGCCTAGTTTAG
*
1524952 TTTTTCTGGCACCAGAGAAAGATTTAAGTCTAGATTAATTGGTACTAATAAATGTTAAGCTTAGT
1 TTTTTCTGGCACCAAAGAAAGATTTAAGTCTAGATTAATTGGTACTAATAAATGTTAAGCTTAGT
*
1525017 TTATCTAGCCTTCGAACAAAGATTTAAGCCTAGTTTAG
66 TTATCTAGCCTTCAAACAAAGATTTAAGCCTAGTTTAG
1525055 CTGGCCTAAT
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.36
Consensus pattern (103 bp):
TTTTTCTGGCACCAAAGAAAGATTTAAGTCTAGATTAATTGGTACTAATAAATGTTAAGCTTAGT
TTATCTAGCCTTCAAACAAAGATTTAAGCCTAGTTTAG
Found at i:1525051 original size:34 final size:32
Alignment explanation
Indices: 1525006--1525117 Score: 111
Period size: 31 Copynumber: 3.4 Consensus size: 32
1524996 CTAATAAATG
* * *
1525006 TTAAGCTTAGTTTATCTAGCCTTCGAACAAAGAT
1 TTAAGCCTAGTTTATCTAGCC-TC-AAGAAAGTT
* *
1525040 TTAAGCCTAGTTTAGCTGGCCT-AATGAAA-TT
1 TTAAGCCTAGTTTATCTAGCCTCAA-GAAAGTT
* *
1525071 TTAAGCCTTGTTTATCTAGCATCAAAGAAAGTT
1 TTAAGCCTAGTTTATCTAGCCTC-AAGAAAGTT
1525104 TTAAGCCTAGTTTA
1 TTAAGCCTAGTTTA
1525118 GTTGGCATGC
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
31 21 0.33
32 7 0.11
33 18 0.28
34 18 0.28
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.37
Consensus pattern (32 bp):
TTAAGCCTAGTTTATCTAGCCTCAAGAAAGTT
Found at i:1525075 original size:65 final size:63
Alignment explanation
Indices: 1524969--1525123 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 63
1524959 GGCACCAGAG
* * * * * *
1524969 AAAGATTTAAGTCTAGATTAATTGGTACTAATAAATGTTAAG-CTTAGTTTATCTAGCCTTCGAA
1 AAAGATTTAAGCCTAGTTTAGTTGG-CCTAATAAATGTTAAGCCTT-GTTTATCTAG-CATCAAA
1525033 C
63 C
* * *
1525034 AAAGATTTAAGCCTAGTTTAGCTGGCCTAATGAAATTTTAAGCCTTGTTTATCTAGCATCAAAG
1 AAAGATTTAAGCCTAGTTTAGTTGGCCTAAT-AAATGTTAAGCCTTGTTTATCTAGCATCAAAC
*
1525098 AAAGTTTTAAGCCTAGTTTAGTTGGC
1 AAAGATTTAAGCCTAGTTTAGTTGGC
1525124 ATGCAAACCT
Statistics
Matches: 77, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
64 34 0.44
65 40 0.52
66 3 0.04
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (63 bp):
AAAGATTTAAGCCTAGTTTAGTTGGCCTAATAAATGTTAAGCCTTGTTTATCTAGCATCAAAC
Found at i:1525077 original size:31 final size:33
Alignment explanation
Indices: 1525034--1525130 Score: 108
Period size: 33 Copynumber: 3.0 Consensus size: 33
1525024 GCCTTCGAAC
* * *
1525034 AAAGATTTAAGCCTAGTTTAGCTGGCCT-AATG
1 AAAGTTTTAAGCCTAGTTTAGCTGGCATCAAAG
* * *
1525066 AAA-TTTTAAGCCTTGTTTATCTAGCATCAAAG
1 AAAGTTTTAAGCCTAGTTTAGCTGGCATCAAAG
*
1525098 AAAGTTTTAAGCCTAGTTTAGTTGGCATGCAAA
1 AAAGTTTTAAGCCTAGTTTAGCTGGCAT-CAAA
1525131 CCTAGATTAA
Statistics
Matches: 52, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
31 19 0.37
32 9 0.17
33 20 0.38
34 4 0.08
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (33 bp):
AAAGTTTTAAGCCTAGTTTAGCTGGCATCAAAG
Found at i:1525313 original size:35 final size:34
Alignment explanation
Indices: 1525263--1525377 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 34
1525253 TTTTTTATAT
*
1525263 TTTGACTTGCAGTGTTGTCCCGATTGTTTTTCTTTA
1 TTTGACTTGCGGTGTTGTCCC-A-TGTTTTTCTTTA
**
1525299 TTTGACTTG-GGTGTTGTCCCA-GTCGATTCTTTA
1 TTTGACTTGCGGTGTTGTCCCATGT-TTTTCTTTA
* *
1525332 TTTCTGACTTGTGATGTTGTCCCAATCGTTTTTCTTTA
1 -TT-TGACTTGCGGTGTTGTCCC-AT-GTTTTTCTTTA
*
1525370 TTTAACTT
1 TTTGACTT
1525378 ACAGTGCTAT
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
32 2 0.03
33 7 0.11
34 3 0.05
35 17 0.26
36 24 0.37
37 3 0.05
38 7 0.11
39 2 0.03
ACGTcount: A:0.13, C:0.17, G:0.18, T:0.51
Consensus pattern (34 bp):
TTTGACTTGCGGTGTTGTCCCATGTTTTTCTTTA
Found at i:1526979 original size:17 final size:17
Alignment explanation
Indices: 1526927--1526980 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
1526917 TAATTATTAT
*
1526927 TAATAATAAC-AAAATA
1 TAATAATAACTAAAAGA
* *
1526943 AAATAATAAATAAAAGA
1 TAATAATAACTAAAAGA
1526960 TAATAATAACTGAAAA-A
1 TAATAATAACT-AAAAGA
1526977 TAAT
1 TAAT
1526981 TATCTAAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 8 0.26
17 19 0.61
18 4 0.13
ACGTcount: A:0.69, C:0.04, G:0.04, T:0.24
Consensus pattern (17 bp):
TAATAATAACTAAAAGA
Found at i:1527123 original size:12 final size:13
Alignment explanation
Indices: 1527092--1527132 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
1527082 AATGTTAGAG
*
1527092 AATTATTAAAAAAT
1 AATTATT-AATAAT
1527106 AATTATTAATAA-
1 AATTATTAATAAT
1527118 AATTATTAATAAT
1 AATTATTAATAAT
1527131 AA
1 AA
1527133 ATTGTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 12 0.48
13 6 0.24
14 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
AATTATTAATAAT
Found at i:1527125 original size:15 final size:15
Alignment explanation
Indices: 1527092--1527133 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1527082 AATGTTAGAG
1527092 AATTATTAA-AAAAT
1 AATTATTAATAAAAT
1527106 AATTATTAATAAAAT
1 AATTATTAATAAAAT
* *
1527121 TATTAATAATAAA
1 AATTATTAATAAA
1527134 TTGTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATTATTAATAAAAT
Found at i:1527135 original size:26 final size:25
Alignment explanation
Indices: 1527092--1527145 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1527082 AATGTTAGAG
1527092 AATTATTAAAAAATAATTATTAATAA
1 AATTATTAAAAAATAATTATT-ATAA
* *
1527118 AATTATT-AATAATAAATTGTTATAA
1 AATTATTAAAAAAT-AATTATTATAA
1527143 AAT
1 AAT
1527146 AAAAATACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
AATTATTAAAAAATAATTATTATAA
Found at i:1527328 original size:21 final size:21
Alignment explanation
Indices: 1527289--1527457 Score: 101
Period size: 21 Copynumber: 7.7 Consensus size: 21
1527279 TTAAAACTTT
*
1527289 AAACCCTTCAAACCTTAAAATCA
1 AAACCC-T-AAACCCTAAAATCA
1527312 AAACCCTAAACCCTAAAATCA
1 AAACCCTAAACCCTAAAATCA
* * *
1527333 AAA-CCTAAACCTTTTAAACTCC
1 AAACCCTAAACC--CTAAAATCA
* *
1527355 AAACACTAAACCCT-AAATCTTTT
1 AAACCCTAAACCCTAAAATC---A
*
1527378 AAACCCTAAACCCTAAAATTA
1 AAACCCTAAACCCTAAAATCA
* * *
1527399 AAACCATAAGCCTTAAAATCTA
1 AAACCCTAAACCCTAAAATC-A
* *
1527421 AAA-TCAAAACCCTAAAAATCGA
1 AAACCCTAAACCCT-AAAATC-A
*
1527443 AAACCGTAAAACCCT
1 AAACCCT-AAACCCT
1527458 CTAAATCCTA
Statistics
Matches: 111, Mismatches: 24, Indels: 21
0.71 0.15 0.13
Matches are distributed among these distances:
20 12 0.11
21 38 0.34
22 24 0.22
23 26 0.23
24 11 0.10
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.21
Consensus pattern (21 bp):
AAACCCTAAACCCTAAAATCA
Found at i:1527377 original size:30 final size:30
Alignment explanation
Indices: 1527257--1527394 Score: 92
Period size: 30 Copynumber: 4.7 Consensus size: 30
1527247 ATAAAAATCA
** *
1527257 TTTAAACCCTAAACACTAAACATTAAAAC-
1 TTTAAACCCTAAACACTAAACCCTAAACCT
** *
1527286 TTTAAACCCTTCAAAC-CTTAAAATCAAAACC-
1 TTTAAACCC-T-AAACAC-TAAACCCTAAACCT
* *
1527317 -CTAAACCCTAAA-A-TCAAAACCTAAACCT
1 TTTAAACCCTAAACACT-AAACCCTAAACCT
*
1527345 TTTAAACTCC-AAACACTAAACCCTAAATCT
1 TTTAAAC-CCTAAACACTAAACCCTAAACCT
*
1527375 TTTAAACCCTAAACCCTAAA
1 TTTAAACCCTAAACACTAAA
1527395 ATTAAAACCA
Statistics
Matches: 86, Mismatches: 12, Indels: 21
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.01
27 10 0.12
28 3 0.03
29 20 0.23
30 39 0.45
31 13 0.15
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (30 bp):
TTTAAACCCTAAACACTAAACCCTAAACCT
Found at i:1527447 original size:16 final size:15
Alignment explanation
Indices: 1527420--1527484 Score: 51
Period size: 16 Copynumber: 4.2 Consensus size: 15
1527410 CTTAAAATCT
1527420 AAAATCAAAACCCTA
1 AAAATCAAAACCCTA
*
1527435 AAAATCGAAAACCGTA
1 AAAATC-AAAACCCTA
* * *
1527451 AAACCCTCTAAATCCT-
1 AAA--ATCAAAACCCTA
*
1527467 AAAATTAAAACCCTA
1 AAAATCAAAACCCTA
1527482 AAA
1 AAA
1527485 CCCTAAACTC
Statistics
Matches: 37, Mismatches: 9, Indels: 8
0.69 0.17 0.15
Matches are distributed among these distances:
14 7 0.19
15 9 0.24
16 14 0.38
17 5 0.14
18 2 0.05
ACGTcount: A:0.55, C:0.25, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAATCAAAACCCTA
Found at i:1531286 original size:15 final size:14
Alignment explanation
Indices: 1531266--1531303 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
1531256 AATTAATTTG
1531266 ATAATTATTTTTAA
1 ATAATTATTTTTAA
*
1531280 TATAATTAATTTTAA
1 -ATAATTATTTTTAA
1531295 ATAATTATT
1 ATAATTATT
1531304 CGTGATAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATTATTTTTAA
Found at i:1534287 original size:3 final size:3
Alignment explanation
Indices: 1534281--1534334 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
1534271 TTGTTGTCTC
1534281 ATA ATA ATA ATTA ATA ATA ATA ATA ATA A-A ATA ATAA ATA A-A AT-
1 ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA
1534325 ATA ATA ATA A
1 ATA ATA ATA A
1534335 CTAAAAAGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.13
3 34 0.74
4 6 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:1534315 original size:17 final size:16
Alignment explanation
Indices: 1534281--1534380 Score: 71
Period size: 17 Copynumber: 6.2 Consensus size: 16
1534271 TTGTTGTCTC
**
1534281 ATAATAATAATTAATA
1 ATAATAATAAAAAATA
1534297 ATAATAATAATAAAATA
1 ATAATAATAA-AAAATA
*
1534314 AT-A-AATAAAATATA
1 ATAATAATAAAAAATA
*
1534328 ATAATAACTAAAAAGTA
1 ATAATAA-TAAAAAATA
* * *
1534345 ATTAT-CTAAAAAATG
1 ATAATAATAAAAAATA
* *
1534360 ATAATAAGAATAAAGTA
1 ATAATAATAA-AAAATA
1534377 ATAA
1 ATAA
1534381 GGAAAATTTT
Statistics
Matches: 64, Mismatches: 14, Indels: 11
0.72 0.16 0.12
Matches are distributed among these distances:
14 7 0.11
15 17 0.27
16 15 0.23
17 25 0.39
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (16 bp):
ATAATAATAAAAAATA
Found at i:1535222 original size:10 final size:10
Alignment explanation
Indices: 1535194--1535245 Score: 70
Period size: 10 Copynumber: 5.2 Consensus size: 10
1535184 TCGGCTTAAA
1535194 TGCATTTGTT
1 TGCATTTGTT
*
1535204 TG-TTATTGTT
1 TGCAT-TTGTT
1535214 TGCATTTGTT
1 TGCATTTGTT
*
1535224 TACATTTGTT
1 TGCATTTGTT
1535234 TGCATTTGTT
1 TGCATTTGTT
1535244 TG
1 TG
1535246 TCTTTAATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
9 1 0.03
10 34 0.94
11 1 0.03
ACGTcount: A:0.12, C:0.08, G:0.19, T:0.62
Consensus pattern (10 bp):
TGCATTTGTT
Found at i:1536176 original size:26 final size:25
Alignment explanation
Indices: 1536125--1536179 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
1536115 AAATAATAAT
* *
1536125 AAAAATTATTGTAATTGTGATTAAA
1 AAAAATTACTGTAATTGCGATTAAA
1536150 AAAAATTACTGTAATTGCGATTAAA
1 AAAAATTACTGTAATTGCGATTAAA
1536175 AAAAA
1 AAAAA
1536180 ATTTAATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.33
Consensus pattern (25 bp):
AAAAATTACTGTAATTGCGATTAAA
Found at i:1536705 original size:20 final size:22
Alignment explanation
Indices: 1536662--1536707 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1536652 AAAATATAAA
*
1536662 ATATAAAAAAATAATTTTTAAG
1 ATATAAAAAAATAAGTTTTAAG
*
1536684 ATATAAAAAAA-GAGTTTT-AG
1 ATATAAAAAAATAAGTTTTAAG
1536704 ATAT
1 ATAT
1536708 TAAATAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.35
Consensus pattern (22 bp):
ATATAAAAAAATAAGTTTTAAG
Found at i:1542583 original size:27 final size:25
Alignment explanation
Indices: 1542554--1542620 Score: 80
Period size: 27 Copynumber: 2.6 Consensus size: 25
1542544 GAATCAATTT
*
1542554 TTTTTAAAATTAATTATATTATATTA
1 TTTTTAAAATTAATTAAATT-TATTA
*
1542580 TTTTTATTAATTAAATTAAATTTATTA
1 TTTTTA-AAATT-AATTAAATTTATTA
*
1542607 ATTTTAAAATTAAT
1 TTTTTAAAATTAAT
1542621 CAATTAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 3 0.09
26 10 0.29
27 14 0.40
28 8 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TTTTTAAAATTAATTAAATTTATTA
Found at i:1562830 original size:11 final size:11
Alignment explanation
Indices: 1562814--1562847 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
1562804 AAATTTTTAA
*
1562814 TTATATTATTT
1 TTATATTATAT
1562825 TTATATTATAT
1 TTATATTATAT
*
1562836 TTATATCATAT
1 TTATATTATAT
1562847 T
1 T
1562848 ATTATATCGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (11 bp):
TTATATTATAT
Found at i:1562832 original size:16 final size:15
Alignment explanation
Indices: 1562806--1562836 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1562796 AACTATTAAA
1562806 ATTTTTAATTATATT
1 ATTTTTAATTATATT
1562821 ATTTTTATATTATATT
1 ATTTTTA-ATTATATT
1562837 TATATCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTAATTATATT
Found at i:1563361 original size:29 final size:29
Alignment explanation
Indices: 1563307--1563363 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
1563297 TAAATACAAT
**
1563307 ATAAATAAATATAAATAATATGGATATAC
1 ATAAATAAATATAAATAATACAGATATAC
* *
1563336 ATAAATAAATATGACTAATACAGATATA
1 ATAAATAAATATAAATAATACAGATATA
1563364 TCCGAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.30
Consensus pattern (29 bp):
ATAAATAAATATAAATAATACAGATATAC
Found at i:1564390 original size:12 final size:12
Alignment explanation
Indices: 1564373--1564403 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1564363 AAATATCATG
1564373 ATAAAATAAAAA
1 ATAAAATAAAAA
1564385 ATAAAATAAAAA
1 ATAAAATAAAAA
*
1564397 GTAAAAT
1 ATAAAAT
1564404 TTTGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (12 bp):
ATAAAATAAAAA
Found at i:1570227 original size:18 final size:17
Alignment explanation
Indices: 1570201--1570234 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1570191 AGCTCAATAT
1570201 CTTCATTTAATTTTAGAA
1 CTTCATTT-ATTTTAGAA
*
1570219 CTTCTTTTATTTTAGA
1 CTTCATTTATTTTAGA
1570235 GATACCAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.26, C:0.12, G:0.06, T:0.56
Consensus pattern (17 bp):
CTTCATTTATTTTAGAA
Found at i:1576372 original size:16 final size:16
Alignment explanation
Indices: 1576332--1576391 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
1576322 CTTTCAAATA
*
1576332 TAAAAATTCAAAACTTTT
1 TAAAAATT-AAAA-ATTT
* *
1576350 TACAAATTTAAAATTT
1 TAAAAATTAAAAATTT
* *
1576366 TAAAAATAAAAAATAT
1 TAAAAATTAAAAATTT
1576382 TAAAAATTAA
1 TAAAAATTAA
1576392 TTAATTAACT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
16 24 0.71
17 3 0.09
18 7 0.21
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAAATTAAAAATTT
Found at i:1577342 original size:23 final size:22
Alignment explanation
Indices: 1577290--1577348 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 22
1577280 AATATATAAA
*
1577290 ATTTGAATTTA-ATTTGATTCG
1 ATTTGATTTTATATTTGATTCG
*
1577311 ATAAT-ATTTTATATTTGAATTCG
1 AT-TTGATTTTATATTTG-ATTCG
*
1577334 ATTTGATTTAATATT
1 ATTTGATTTTATATT
1577349 ATATAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
21 7 0.23
22 7 0.23
23 16 0.53
ACGTcount: A:0.32, C:0.03, G:0.10, T:0.54
Consensus pattern (22 bp):
ATTTGATTTTATATTTGATTCG
Found at i:1577398 original size:38 final size:38
Alignment explanation
Indices: 1577319--1577398 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
1577309 CGATAATATT
* * * *
1577319 TTATATTTGAATTCGATTTGATTTAATATTATATAAAA
1 TTATATTCGAATTCAATTTGATTTAAAATAATATAAAA
1577357 TTATATTCG-ATTCAATTTGATTTGAAAATAATA-AAATA
1 TTATATTCGAATTCAATTTGATTT-AAAATAATATAAA-A
1577395 TTAT
1 TTAT
1577399 TTTTAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 16 0.44
38 20 0.56
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (38 bp):
TTATATTCGAATTCAATTTGATTTAAAATAATATAAAA
Found at i:1577428 original size:20 final size:19
Alignment explanation
Indices: 1577406--1577478 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
1577396 TATTTTTAAT
*
1577406 ATAAATATAAAATT-AAAA
1 ATAATTATAAAATTAAAAA
*
1577424 ATATATTA-AAAAATATAAAA
1 ATA-ATTATAAAATTA-AAAA
1577444 ATAATTATAAAATTAAATAA
1 ATAATTATAAAATTAAA-AA
*
1577464 ATAATTAAAAAATTA
1 ATAATTATAAAATTA
1577479 TTTTTATATA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 8 0.17
19 9 0.20
20 29 0.63
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAATTATAAAATTAAAAA
Found at i:1577433 original size:11 final size:11
Alignment explanation
Indices: 1577417--1577456 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
1577407 TAAATATAAA
1577417 ATTAAAAATAT
1 ATTAAAAATAT
1577428 ATTAAAAA-AT
1 ATTAAAAATAT
1577438 A-TAAAAATA-
1 ATTAAAAATAT
1577447 ATTATAAAAT
1 ATTA-AAAAT
1577457 TAAATAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 7 0.27
10 6 0.23
11 13 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
ATTAAAAATAT
Found at i:1578922 original size:18 final size:17
Alignment explanation
Indices: 1578901--1578948 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1578891 TTATTATATA
1578901 AATTTATTAAAAAATTTT
1 AATTTATTAAAAAA-TTT
*
1578919 AATTTTTTAATTAAAATTT
1 AATTTATTAA--AAAATTT
1578938 AA-TTATTAAAA
1 AATTTATTAAAA
1578949 TTAAAATCTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 2 0.08
18 15 0.58
19 5 0.19
20 4 0.15
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTATTAAAAAATTT
Found at i:1578936 original size:20 final size:21
Alignment explanation
Indices: 1578911--1578955 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1578901 AATTTATTAA
**
1578911 AAAATTTTAATT-TTTTAATT
1 AAAATTTTAATTATTAAAATT
1578931 AAAA-TTTAATTATTAAAATT
1 AAAATTTTAATTATTAAAATT
1578951 AAAAT
1 AAAAT
1578956 CTAACACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
AAAATTTTAATTATTAAAATT
Found at i:1586167 original size:13 final size:13
Alignment explanation
Indices: 1586149--1586178 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1586139 AATTTCTCAT
1586149 ATATATATATTAC
1 ATATATATATTAC
1586162 ATATATATATTAC
1 ATATATATATTAC
1586175 -TATA
1 ATATA
1586179 ATAACATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (13 bp):
ATATATATATTAC
Found at i:1592170 original size:8 final size:8
Alignment explanation
Indices: 1592169--1592272 Score: 141
Period size: 8 Copynumber: 13.8 Consensus size: 8
1592159 AAAATGAAAA
1592169 AAAAAATG
1 AAAAAATG
1592177 -AAAAATG
1 AAAAAATG
1592184 -AAAAATG
1 AAAAAATG
1592191 --AAAATG
1 AAAAAATG
1592197 -AAAAATG
1 AAAAAATG
1592204 AAAAAATG
1 AAAAAATG
1592212 -AAAAATG
1 AAAAAATG
1592219 AAAAAATG
1 AAAAAATG
1592227 AAAAAATG
1 AAAAAATG
1592235 AAAAAATG
1 AAAAAATG
1592243 -AAAAATG
1 AAAAAATG
1592250 AAAAAATG
1 AAAAAATG
*
1592258 AAAATGATG
1 AAAA-AATG
1592267 AAAAAA
1 AAAAAA
1592273 AGTGAACAAG
Statistics
Matches: 89, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
6 6 0.07
7 34 0.38
8 42 0.47
9 7 0.08
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAAAAATG
Found at i:1592180 original size:7 final size:7
Alignment explanation
Indices: 1592158--1592271 Score: 144
Period size: 7 Copynumber: 15.7 Consensus size: 7
1592148 TATGCTTGAA
1592158 AAAAATG
1 AAAAATG
1592165 AAAAA--
1 AAAAATG
1592170 AAAAATG
1 AAAAATG
1592177 AAAAATG
1 AAAAATG
1592184 AAAAATG
1 AAAAATG
1592191 -AAAATG
1 AAAAATG
1592197 AAAAATG
1 AAAAATG
1592204 AAAAAATG
1 -AAAAATG
1592212 AAAAATG
1 AAAAATG
1592219 AAAAAATG
1 -AAAAATG
1592227 AAAAAATG
1 -AAAAATG
1592235 AAAAAATG
1 -AAAAATG
1592243 AAAAATG
1 AAAAATG
1592250 AAAAAATG
1 -AAAAATG
1592258 AAAATGATG
1 AAAA--ATG
1592267 AAAAA
1 AAAAA
1592272 AAGTGAACAA
Statistics
Matches: 99, Mismatches: 0, Indels: 16
0.86 0.00 0.14
Matches are distributed among these distances:
5 5 0.05
6 6 0.06
7 44 0.44
8 37 0.37
9 7 0.07
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:1592187 original size:15 final size:15
Alignment explanation
Indices: 1592158--1592272 Score: 161
Period size: 15 Copynumber: 7.9 Consensus size: 15
1592148 TATGCTTGAA
1592158 AAAAATG-AAAAA--
1 AAAAATGAAAAAATG
1592170 AAAAATG-AAAAATG
1 AAAAATGAAAAAATG
1592184 AAAAATG--AAAATG
1 AAAAATGAAAAAATG
1592197 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
1592212 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
1592227 AAAAAATGAAAAAATG
1 -AAAAATGAAAAAATG
1592243 AAAAATGAAAAAATG
1 AAAAATGAAAAAATG
1592258 AAAATGATGAAAAAA
1 AAAA--ATGAAAAAA
1592273 AGTGAACAAG
Statistics
Matches: 96, Mismatches: 0, Indels: 9
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.12
13 13 0.14
14 7 0.07
15 40 0.42
16 15 0.16
17 9 0.09
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAATGAAAAAATG
Found at i:1593332 original size:41 final size:40
Alignment explanation
Indices: 1593287--1593821 Score: 670
Period size: 41 Copynumber: 13.0 Consensus size: 40
1593277 GTCTAGGAGT
*
1593287 ATTTACTTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTCCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
* * **
1593328 ATTTACTTTTTCAAAGTCGTGGTGCCTCTGTTTAAAAAAGCA
1 ATTTAC-TTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
1593370 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* * *
1593412 ATTTACTTTCCAAAGTTGTGGTACCTTTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
1593453 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* *
1593494 ATTTACTGT-CAAAGTTCCGT-TGCCTCTGTTTAGAGAAGCA
1 ATTTACTTTCCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCA
1593534 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
1593575 ATTTACTTT-CAAAGTTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG--TCGTGTGCCTCTGTTTAGAGGAGCA
1593615 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTAC-TTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
1593657 ATTTACTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
1593698 ATTTACTGT-CAAAGTTCCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCA
1593738 ATTTACTTTCCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTCC-AAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
* * *
1593780 ATTTATGTTTCTCAAAATCGTTGAGCCTCTGTTTAGAGGAGC
1 ATTTA-CTTTC-CAAAGTCG-TGTGCCTCTGTTTAGAGGAGC
1593822 TTTGGTAAAA
Statistics
Matches: 448, Mismatches: 24, Indels: 42
0.87 0.05 0.08
Matches are distributed among these distances:
39 3 0.01
40 107 0.24
41 177 0.40
42 130 0.29
43 29 0.06
44 2 0.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (40 bp):
ATTTACTTTCCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:1593554 original size:81 final size:81
Alignment explanation
Indices: 1593287--1593821 Score: 692
Period size: 81 Copynumber: 6.5 Consensus size: 81
1593277 GTCTAGGAGT
* *
1593287 ATTTACTTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTTCAAAGTCGTGG
1 ATTTAC-TTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCCAAAGTCGT-G
* **
1593350 TGCCTCTGTTTAAAAAAGCA
62 TGCCTCTGTTTAGAGGAGCA
* * *
1593370 ATTTACTTTTCCAAAGTCGTGGTACCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTTGTGGTA
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT-GTG
*
1593435 CCTTTGTTTAGAGGAGCA
64 CCTCTGTTTAGAGGAGCA
*
1593453 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTGT-CAAAGTTCCGT-TG
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG-T-CGTGTG
*
1593516 CCTCTGTTTAGAGAAGCA
64 CCTCTGTTTAGAGGAGCA
1593534 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTT-CAAAGTTTCGT-TG
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAG--TCGTGTG
1593597 CCTCTGTTTAGAGGAGCA
64 CCTCTGTTTAGAGGAGCA
*
1593615 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGGTA
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGT-GTG
1593680 CCTCTGTTTAGAGGAGCA
64 CCTCTGTTTAGAGGAGCA
*
1593698 ATTTACTGT-CAAAGTTCCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAAGTCGTGG
1 ATTTACTTTCCAAAG-T-CGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCC-AAAGTCGT-G
1593760 TGCCTCTGTTTAGAGGAGCA
62 TGCCTCTGTTTAGAGGAGCA
* * * *
1593780 ATTTATGTTTCTCAAAATCGTTGAGCCTCTGTTTAGAGGAGC
1 ATTTA-CTTTC-CAAAGTCGTGGTGCCTCTGTTTAGAGGAGC
1593822 TTTGGTAAAA
Statistics
Matches: 411, Mismatches: 24, Indels: 32
0.88 0.05 0.07
Matches are distributed among these distances:
81 144 0.35
82 130 0.32
83 89 0.22
84 26 0.06
85 22 0.05
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (81 bp):
ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTCCAAAGTCGTGTGCC
TCTGTTTAGAGGAGCA
Found at i:1594068 original size:16 final size:19
Alignment explanation
Indices: 1594047--1594095 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 19
1594037 TTTTATGTAT
1594047 TGTATTATTTATT-AT-TA
1 TGTATTATTTATTAATATA
*
1594064 T-TATTATGTATTAATATA
1 TGTATTATTTATTAATATA
1594082 TGTATATATTTATT
1 TGTAT-TATTTATT
1594096 TATTTTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.38
17 3 0.12
18 3 0.12
19 3 0.12
20 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
TGTATTATTTATTAATATA
Found at i:1594138 original size:16 final size:16
Alignment explanation
Indices: 1594033--1594138 Score: 51
Period size: 16 Copynumber: 6.4 Consensus size: 16
1594023 CTTCTTCTTT
1594033 TGTATTTTATGTATTGTA
1 TGTATTTTAT-TATT-TA
1594051 T-TA-TTTATTA-TTA
1 TGTATTTTATTATTTA
*
1594064 T-TATTATGTATTAATATA
1 TGTATT-T-TATT-ATTTA
*
1594082 TGTA-TATATTTATTTA
1 TGTATTTTA-TTATTTA
* * *
1594098 TTTTTTGTTAATATTTA
1 TGTATT-TTATTATTTA
1594115 TGTGTATTTTATTATTTA
1 --TGTATTTTATTATTTA
1594133 TGTATT
1 TGTATT
1594139 ATTACTAATA
Statistics
Matches: 67, Mismatches: 10, Indels: 24
0.66 0.10 0.24
Matches are distributed among these distances:
13 5 0.07
14 2 0.03
15 3 0.04
16 23 0.34
17 12 0.18
18 16 0.24
19 6 0.09
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.64
Consensus pattern (16 bp):
TGTATTTTATTATTTA
Found at i:1594175 original size:9 final size:8
Alignment explanation
Indices: 1594160--1594198 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
1594150 GTATATATAT
1594160 TTTTTTTA
1 TTTTTTTA
1594168 TCTTTTTTA
1 T-TTTTTTA
1594177 TTTTATTTA
1 TTTT-TTTA
*
1594186 TTTTTGTA
1 TTTTTTTA
1594194 TTTTT
1 TTTTT
1594199 ACTTATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
8 12 0.43
9 16 0.57
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.82
Consensus pattern (8 bp):
TTTTTTTA
Done.