Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold25
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: 9553305
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 6276 characters in sequence are not A, C, G, or T
File 31 of 56
Found at i:5200331 original size:17 final size:17
Alignment explanation
Indices: 5200309--5200344 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5200299 CTAAAACGTG
5200309 ATTGCTCAATTCATTAT
1 ATTGCTCAATTCATTAT
5200326 ATTGCTCAATTCATTAT
1 ATTGCTCAATTCATTAT
5200343 AT
1 AT
5200345 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTGCTCAATTCATTAT
Found at i:5202828 original size:33 final size:33
Alignment explanation
Indices: 5202786--5202851 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
5202776 TCCATCCAAA
5202786 GTCTTAAGGAATTAGGCAAGTGAATGATTCATT
1 GTCTTAAGGAATTAGGCAAGTGAATGATTCATT
5202819 GTCTTAAGGAATTAGGCAAGTGAATGATTCATT
1 GTCTTAAGGAATTAGGCAAGTGAATGATTCATT
5202852 ATCCATTCCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.33, C:0.09, G:0.24, T:0.33
Consensus pattern (33 bp):
GTCTTAAGGAATTAGGCAAGTGAATGATTCATT
Found at i:5203872 original size:26 final size:25
Alignment explanation
Indices: 5203843--5203897 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
5203833 AAAATTCAAA
*
5203843 AAAAATCCTAAAAATTTTTAAAAAAG
1 AAAAATCATAAAAA-TTTTAAAAAAG
*
5203869 AAAAATCATAAAAATTTTAAAAAAT
1 AAAAATCATAAAAATTTTAAAAAAG
5203894 AAAA
1 AAAA
5203898 TAAAATATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 14 0.52
26 13 0.48
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.25
Consensus pattern (25 bp):
AAAAATCATAAAAATTTTAAAAAAG
Found at i:5203909 original size:26 final size:25
Alignment explanation
Indices: 5203851--5203909 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
5203841 AAAAAAATCC
**
5203851 TAAAAATTTTTAAAAAAGAAAAATCA
1 TAAAAA-TTTTAAAAAAGAAAAAAAA
*
5203877 TAAAAATTTTAAAAAATAAAATAAAA
1 TAAAAATTTTAAAAAAGAAAA-AAAA
*
5203903 TATAAAT
1 TAAAAAT
5203910 AACTAATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (25 bp):
TAAAAATTTTAAAAAAGAAAAAAAA
Found at i:5208705 original size:12 final size:12
Alignment explanation
Indices: 5208673--5208710 Score: 58
Period size: 12 Copynumber: 3.0 Consensus size: 12
5208663 AACAATCAAT
5208673 TTTAATTTTGTTA
1 TTTAATTTT-TTA
5208686 TGTTAATTTTTTA
1 T-TTAATTTTTTA
5208699 TTTAATTTTTTA
1 TTTAATTTTTTA
5208711 AAAGATCATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 11 0.46
13 5 0.21
14 8 0.33
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (12 bp):
TTTAATTTTTTA
Found at i:5211684 original size:14 final size:15
Alignment explanation
Indices: 5211665--5211698 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5211655 AAAATATGTT
*
5211665 TTTTTTTATTACA-A
1 TTTTTTTAATACATA
5211679 TTTTTTTAATACATA
1 TTTTTTTAATACATA
5211694 TTTTT
1 TTTTT
5211699 AAATATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTTTTTAATACATA
Found at i:5212263 original size:23 final size:23
Alignment explanation
Indices: 5212205--5212280 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 23
5212195 ATGAGTACAA
*
5212205 AATTTATTTTTATTTGTAAAAATTT
1 AATTTATTTTTATTTAT-AAAA-TT
5212230 AAATTTA-TTTTATTT-TAAAATAT
1 -AATTTATTTTTATTTATAAAAT-T
*
5212253 AATTTATTTTTATTTATAAGATT
1 AATTTATTTTTATTTATAAAATT
5212276 AATTT
1 AATTT
5212281 GATTCAATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
22 7 0.15
23 19 0.41
24 6 0.13
25 8 0.17
26 6 0.13
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (23 bp):
AATTTATTTTTATTTATAAAATT
Found at i:5212585 original size:25 final size:26
Alignment explanation
Indices: 5212557--5212607 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
5212547 ATGAGTTTAG
*
5212557 ATTTTTAAAAG-TATAATTTATTTTT
1 ATTTGTAAAAGTTATAATTTATTTTT
*
5212582 ATTTGTAAAAGTTTTAATTTATTTTT
1 ATTTGTAAAAGTTATAATTTATTTTT
5212608 TGCTTGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (26 bp):
ATTTGTAAAAGTTATAATTTATTTTT
Found at i:5212651 original size:24 final size:24
Alignment explanation
Indices: 5212624--5212681 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
5212614 TTATATAAGT
5212624 TTATATGAGTTTGTATCCTAATAA
1 TTATATGAGTTTGTATCCTAATAA
5212648 TTATATGAGTTTGTATCCTAATAA
1 TTATATGAGTTTGTATCCTAATAA
5212672 TTATATGAGT
1 TTATATGAGT
5212682 ATAGGAGTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (24 bp):
TTATATGAGTTTGTATCCTAATAA
Found at i:5212876 original size:73 final size:73
Alignment explanation
Indices: 5212722--5213841 Score: 1075
Period size: 72 Copynumber: 15.5 Consensus size: 73
5212712 TATGAGTTTA
* *** * *
5212722 TATAATTTATTTTTATTTGT-GAAAGTTTAAATTTGTTTTCTAAATATGATTAAACAAGTTTAAA
1 TATAATTTATTTTTATTTGTAG-AAGTTTAAATTTATTTT-TTGGTATGATTATACGAGTTTAAA
* *
5212786 -TTTCAAAGT
64 TTTTTAAAGC
* * * * *
5212795 TATGATTTATTTTTATTTGTAAAAATTTAGATTTATTTTTTGGTTTGATTATACGAGTTTAAATT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATT
*
5212860 TTTAAAGG
66 TTTAAAGC
* * * * *
5212868 TATTATTTATCTCTATTTATAGAAGTTTAAATTTATTTTTTAGGTATAATTATACGAGTTTAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTT-GGTATGATTATACGAGTTTAAAT
*
5212933 TTTT-AAGT
65 TTTTAAAGC
* * * *
5212941 TATTAA-TTATTTCTATTTGTAAAAATTTAAATTTATTTTTTAGGTATGATT-T-----TAT-AA
1 TA-TAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTT-GGTATGATTATACGAGTTTAAA
*
5212998 -GTTT-AAGC
64 TTTTTAAAGC
* * * * * *
5213006 TATAATTTATTTTTATTTGTAGAAATTTAAATTTGTTTTTAAGGTATGATTTTACAAGTTCAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTT-TGGTATGATTATACGAGTTTAAAT
5213071 TTTTAAAGC
65 TTTTAAAGC
* *
5213080 TATAATTTATTTCTATTTGTAGAAGTTTAAATTTAGTTTTTTGGTATAATTATACGAGTTTAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTA-TTTTTTGGTATGATTATACGAGTTTAAAT
* **
5213145 TTTTTAATA
65 TTTTAAAGC
* * *
5213154 TATAATTTAATTTTATTTGTAGAAGTTTAAATTTATTTTTT-GTTTGATTATACGAGTTTAAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATT
*
5213218 TTT-AAGG
66 TTTAAAGC
* * * * * * *
5213225 TATTATTTATTTTTATTTCTAGAATTTTAAATTTATTTTTAGGTATAATTATACAAATTTAAATT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATT
*
5213290 TTTAAA-A
66 TTTAAAGC
* * * * *
5213297 TATAATTTATTTTTATTTGTAGTAGTGTAAATTTATTTGTTGGATATGGTTATACAAGTTTAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGG-TATGATTATACGAGTTTAAAT
5213362 TTTTAAAG-
65 TTTTAAAGC
* * * * * * *
5213370 TATAATTTATTTTTATTTGTAAAAGTTTAAAATTATTTTTTTGTTTAATTATACGAGTTCAAACT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATT
*
5213435 TTT-AAGT
66 TTTAAAGC
* * * * * *
5213442 TATTATTTATCTTTATTTGTAAAAGTTTAAATTTATTTTTGGGTATGATTTTATGAGTTTTAAA-
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAG-TTTAAAT
* *
5213506 ATTT-AAGA
65 TTTTAAAGC
* * *
5213514 TATTATTTATCTTTATTTGTAGAAGTTTAAATTTATTTTTTGAGTATGATTATACGATTTTAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTG-GTATGATTATACGAGTTTAAAT
*
5213579 TTTTTAAGC
65 TTTTAAAGC
* * * * * * * * *
5213588 TATAATTTATTTTTATTTTTAAAAATATAAATTTGTTTTTTAGCTATAATTATACAAGTTTAAAG
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTT-GGTATGATTATACGAGTTTAAAT
5213653 TTTTAATA--
65 TTTTAA-AGC
* * * * * ** *
5213661 TATGATTTATTTTTATTTATAAAACTTTAAATTTATTTTGTACTTTGATTATACGAGTTTAAATT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATT
5213726 TTTAAAG-
66 TTTAAAGC
* * * * *
5213733 TAT-TTTTATTCTTATTTGTAGAAGTTTAAATTTGTTTTTTGGGTATAATTATATGAGTTTAAAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTT-GGTATGATTATACGAGTTTAAA-
5213797 TTTTTAAA-C
64 TTTTTAAAGC
*
5213806 TATAATTTATTTTTATTTATAGAAGTTTAAATTTAT
1 TATAATTTATTTTTATTTGTAGAAGTTTAAATTTAT
5213842 ACTATAATTA
Statistics
Matches: 866, Mismatches: 149, Indels: 63
0.80 0.14 0.06
Matches are distributed among these distances:
64 3 0.00
65 48 0.06
66 3 0.00
67 2 0.00
71 73 0.08
72 264 0.30
73 258 0.30
74 208 0.24
75 7 0.01
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (73 bp):
TATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTTGGTATGATTATACGAGTTTAAATT
TTTAAAGC
Found at i:5213017 original size:65 final size:69
Alignment explanation
Indices: 5212799--5213841 Score: 380
Period size: 73 Copynumber: 14.5 Consensus size: 69
5212789 CAAAGTTATG
* * * * * *
5212799 ATTTATTTTTATTTGTAAAAATTTAGATTTATTTTTT-GGTTTGATTATACGAGTTTAAATTTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATTTTA--AG--TAAATGTTT
* *
5212863 AAAGGTATT
62 -AAGCTATA
* * * * * *
5212872 ATTTATCTCTATTTATAGAAGTTTAAATTTATTTTTTAGGTATAATTATACGAGTTTAAATTTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATTTTA--AG--TAAATGTTT
*
5212937 AAGTTATTA
62 AAGCTA-TA
*
5212946 A-TTATTTCTATTTGTAAAAATTTAAATTTATTTTTTAGGTATGATTTT-A-T-AA-GTTTAAGC
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATTTTAAGTAAATGTTTAAGC
5213006 TATA
66 TATA
* * * *
5213010 ATTTATTTTTATTTGTAGAAATTTAAATTTGTTTTTAAGGTATGATTTTACAAGTTCAAATTTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATTTT--AAG-T-AAATGTTT
5213075 AAAGCTATA
62 -AAGCTATA
* * * *
5213084 ATTTATTTCTATTTGTAGAAGTTTAAATTTAGTTTTTT-GGTATAATTATACGAGTTTAAATTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTA-TTTTTTAGGTATGATTTTA--AG--TAAA-TGT
**
5213148 TTAATATATA
60 TTAAGCTATA
* * *
5213158 ATTTAATTT-TATTTGTAGAAGTTTAAATTTATTTTTT--GTTTGATTATACGAGTTTAAAAT-T
1 ATTT-ATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATTTTA--AG--T-AAATGT
* *
5213219 TTAAGGTATT
60 TTAAGCTATA
* * * * * * *
5213229 ATTTATTTTTATTTCTAGAATTTTAAATTTA-TTTTTAGGTATAATTATACAAATTTAAATTTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATT-T--TAA-GTAAATGTTT
**
5213293 AAAATATA
62 AAGCTATA
* * * * * * * *
5213301 ATTTATTTTTATTTGTAGTAGTGTAAATTTATTTGTT-GGATATGGTTATACAAGTTTAAATTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGG-TATGATT-T-TAAG--TAAATGTT
5213365 TAAAG-TATA
61 T-AAGCTATA
* * * * * *
5213374 ATTTATTTTTATTTGTA-AAAGTTTAAAATTATTTTTT-TGTTTAATTATACGAGTTCAAACT-T
1 ATTTATTTCTATTTGTAGAAA-TTTAAATTTATTTTTTAGGTATGATTTTA--AG-T-AAA-TGT
* *
5213436 TTAAGTTATT
60 TTAAGCTATA
* *
5213446 ATTTATCTT-TATTTGTA-AAAGTTTAAATTTA-TTTTTGGGTATGATTTTATGAGTTTTAAA-A
1 ATTTAT-TTCTATTTGTAGAAA-TTTAAATTTATTTTTTAGGTATGATTTTA--AG---TAAATG
* *
5213507 TTTAAGATATT
59 TTTAAGCTATA
* * * *
5213518 ATTTATCTT-TATTTGTAGAAGTTTAAATTTATTTTTT-GAGTATGATTATACGATTTTAAATTT
1 ATTTAT-TTCTATTTGTAGAAATTTAAATTTATTTTTTAG-GTATGATTTTA--A--GTAAA-TG
5213581 TTTAAGCTATA
59 TTTAAGCTATA
* * * * * * * *
5213592 ATTTATTTTTATTTTTAAAAATATAAATTTGTTTTTTAGCTATAATTATACAAGTTTAAA-GTTT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATT-T-TAAG--TAAATG-TT
** *
5213656 TAATATATG
61 TAAGCTATA
* * * * * * *
5213665 ATTTATTTTTATTTATA-AAACTTTAAATTTATTTTGTA-CTTTGATTATACGAGTTTAAATTTT
1 ATTTATTTCTATTTGTAGAAA-TTTAAATTTATTTTTTAGGTATGATTTTA--AG--TAAATGTT
5213728 TAAAG-TAT-
61 T-AAGCTATA
* * * * * * *
5213736 TTTTA-TTCTTATTTGTAGAAGTTTAAATTTGTTTTTTGGGTATAATTATATGAGTTTAAATTTT
1 ATTTATTTC-TATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATT-T-TAAG--TAAA-TGT
*
5213800 TTAAACTATA
60 TTAAGCTATA
* * *
5213810 ATTTATTTTTATTTATAGAAGTTTAAATTTAT
1 ATTTATTTCTATTTGTAGAAATTTAAATTTAT
5213842 ACTATAATTA
Statistics
Matches: 775, Mismatches: 124, Indels: 141
0.75 0.12 0.14
Matches are distributed among these distances:
64 3 0.00
65 51 0.07
66 2 0.00
67 1 0.00
68 1 0.00
70 15 0.02
71 71 0.09
72 202 0.26
73 220 0.28
74 188 0.24
75 20 0.03
76 1 0.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (69 bp):
ATTTATTTCTATTTGTAGAAATTTAAATTTATTTTTTAGGTATGATTTTAAGTAAATGTTTAAGC
TATA
Found at i:5213357 original size:145 final size:143
Alignment explanation
Indices: 5212721--5213841 Score: 1037
Period size: 145 Copynumber: 7.8 Consensus size: 143
5212711 ATATGAGTTT
* ** *
5212721 ATATAATTTATTTTTATTTGT-GAAAGTTTAAATTTGTTTTCTAAATATGATTAAACAAGTTTAA
1 ATATAATTTATTTTTATTTGTAG-AAGTTTAAATTTATTTT-T-GGTATGATTATACAAGTTTAA
** * * * * *
5212785 ATTTCAAAGTTATGATTTATTTTTATTTGTAAAAATTTAGATTTATTTTTTGGTTTGATTATACG
63 ATTTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACG
5212850 AGTTTAAATTTTTAAA
128 AGTTTAAATTTTTAAA
* * * * * * *
5212866 GGTATTATTTATCTCTATTTATAGAAGTTTAAATTTATTTTTTAGGTATAATTATACGAGTTTAA
1 -ATATAATTTATTTTTATTTGTAGAAGTTTAAATTTA-TTTTT-GGTATGATTATACAAGTTTAA
* * *
5212931 ATTTTTAAGTTATTAA-TTATTTCTATTTGTAAAAATTTAAATTTATTTTTTAGGTATGATT-T-
63 ATTTTTAAGATA-TAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTT-GGTATGATTATA
* * *
5212993 ----TAT-AA-GTTTAAG
126 CGAGTTTAAATTTTTAAA
* * * * *
5213005 CTATAATTTATTTTTATTTGTAGAAATTTAAATTTGTTTTTAAGGTATGATTTTACAAGTTCAAA
1 ATATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTT--GGTATGATTATACAAGTTTAAA
* * * *
5213070 TTTTTAAAGCTATAATTTATTTCTATTTGTAGAAGTTTAAATTTAGTTTTTTGGTATAATTATAC
64 TTTTT-AAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTA-TTTTTTGGTATGATTATAC
*
5213135 GAGTTTAAATTTTTTAAT
127 GAGTTTAAA-TTTTTAAA
* * * * *
5213153 ATATAATTTAATTTTATTTGTAGAAGTTTAAATTTATTTTTTGTTTGATTATACGAGTTTAAAAT
1 ATATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTGGTATGATTATACAAGTTTAAATT
* * * * * * * * *
5213218 TTTAAGGTATTATTTATTTTTATTTCTAGAATTTTAAATTTATTTTTAGGTATAATTATACAAAT
66 TTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACGAGT
5213283 TTAAATTTTTAAA
131 TTAAATTTTTAAA
* * *
5213296 ATATAATTTATTTTTATTTGTAGTAGTGTAAATTTATTTGTTGGATATGGTTATACAAGTTTAAA
1 ATATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTT-TTGG-TATGATTATACAAGTTTAAA
* * * *
5213361 TTTTTAA-AGTATAATTTATTTTTATTTGTAAAAGTTTAAAATTATTTTTTTGTTTAATTATACG
64 TTTTTAAGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACG
* * *
5213425 AGTTCAAACTTTTAAG
128 AGTTTAAATTTTTAAA
* * * * * **
5213441 TTATTATTTATCTTTATTTGTAAAAGTTTAAATTTATTTTTGGGTATGATTTTATGAGTTTTAAA
1 ATATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTT-GGTATGATTATACAAG-TTTAAA
* * * *
5213506 -ATTTAAGATATTATTTATCTTTATTTGTAGAAGTTTAAATTTATTTTTTGAGTATGATTATACG
64 TTTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTG-GTATGATTATACG
* *
5213570 ATTTTAAATTTTTTAAG
128 AGTTTAAA-TTTTTAAA
* * * * * * * *
5213587 CTATAATTTATTTTTATTTTTAAAAATATAAATTTGTTTTTTAGCTATAATTATACAAGTTTAAA
1 ATATAATTTATTTTTATTTGTAGAAGTTTAAATTT-ATTTTT-GGTATGATTATACAAGTTTAAA
* * * * * * ** *
5213652 GTTTTAATATATGATTTATTTTTATTTATAAAACTTTAAATTTATTTTGTACTTTGATTATACGA
64 TTTTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACGA
5213717 GTTTAAATTTTTAAA
129 GTTTAAATTTTTAAA
* * * * * **
5213732 GTAT-TTTTATTCTTATTTGTAGAAGTTTAAATTTGTTTTTTGGGTATAATTATATGAGTTTAAA
1 ATATAATTTATTTTTATTTGTAGAAGTTTAAATTT-ATTTTT-GGTATGATTATACAAGTTTAAA
* *
5213796 TTTTTTAA-ACTATAATTTATTTTTATTTATAGAAGTTTAAATTTAT
64 -TTTTTAAGA-TATAATTTATTTTTATTTGTAAAAGTTTAAATTTAT
5213842 ACTATAATTA
Statistics
Matches: 805, Mismatches: 141, Indels: 59
0.80 0.14 0.06
Matches are distributed among these distances:
137 5 0.01
138 56 0.07
139 45 0.06
140 9 0.01
141 2 0.00
143 43 0.05
144 133 0.17
145 225 0.28
146 173 0.21
147 72 0.09
148 42 0.05
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (143 bp):
ATATAATTTATTTTTATTTGTAGAAGTTTAAATTTATTTTTGGTATGATTATACAAGTTTAAATT
TTTAAGATATAATTTATTTTTATTTGTAAAAGTTTAAATTTATTTTTTGGTATGATTATACGAGT
TTAAATTTTTAAA
Found at i:5213478 original size:33 final size:33
Alignment explanation
Indices: 5213441--5213550 Score: 82
Period size: 33 Copynumber: 3.2 Consensus size: 33
5213431 AACTTTTAAG
5213441 TTATTATTTATCTTTATTTGTAAAAGTTTAAAT
1 TTATTATTTATCTTTATTTGTAAAAGTTTAAAT
* * *
5213474 TTATTTTTGGGTATGATTTTATGAGTTTTAAAA-TTTAAGA-
1 TTATTATT---TAT--CTTTAT---TTGTAAAAGTTTAA-AT
*
5213514 -TATTATTTATCTTTATTTGTAGAAGTTTAAAT
1 TTATTATTTATCTTTATTTGTAAAAGTTTAAAT
5213546 TTATT
1 TTATT
5213551 TTTTGAGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 24
0.65 0.08 0.27
Matches are distributed among these distances:
31 7 0.12
32 5 0.09
33 11 0.19
34 5 0.09
36 6 0.10
38 5 0.09
39 6 0.10
40 5 0.09
41 8 0.14
ACGTcount: A:0.31, C:0.02, G:0.11, T:0.56
Consensus pattern (33 bp):
TTATTATTTATCTTTATTTGTAAAAGTTTAAAT
Found at i:5215267 original size:16 final size:15
Alignment explanation
Indices: 5215236--5215271 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5215226 ATAATTTTTT
5215236 AATATAATTGTAAAA
1 AATATAATTGTAAAA
*
5215251 AATATATATTTTAAAA
1 AATATA-ATTGTAAAA
5215267 AATAT
1 AATAT
5215272 TTATGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AATATAATTGTAAAA
Found at i:5230314 original size:42 final size:42
Alignment explanation
Indices: 5230253--5230337 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
5230243 CAGGATCGAA
* * *
5230253 AATGGGTTCAGATTTTGGAGATTCAGGTTCGGACACATGGTC
1 AATGGGTTCAAATTCTGGAGATTCAAGTTCGGACACATGGTC
5230295 AATGGGTTCAAATTCTGGAGATTCAAGTTCGGACACATGGTC
1 AATGGGTTCAAATTCTGGAGATTCAAGTTCGGACACATGGTC
5230337 A
1 A
5230338 GGTTTGGACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (42 bp):
AATGGGTTCAAATTCTGGAGATTCAAGTTCGGACACATGGTC
Found at i:5232261 original size:31 final size:31
Alignment explanation
Indices: 5232219--5232321 Score: 111
Period size: 31 Copynumber: 3.3 Consensus size: 31
5232209 CTATCAAACA
*
5232219 AAATCAATCAGCAATGAAAGCTGACTGAATG
1 AAATAAATCAGCAATGAAAGCTGACTGAATG
* * **
5232250 AAATAAATCAGCGATAAAAGCTGATCT-AACA
1 AAATAAATCAGCAATGAAAGCTGA-CTGAATG
* *
5232281 AAATCAATCAGCATTG-AAGACTGACTGAATG
1 AAATAAATCAGCAATGAAAG-CTGACTGAATG
5232312 AAATAAATCA
1 AAATAAATCA
5232322 ACGATAAAAA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
30 5 0.09
31 50 0.88
32 2 0.04
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.20
Consensus pattern (31 bp):
AAATAAATCAGCAATGAAAGCTGACTGAATG
Found at i:5232312 original size:62 final size:62
Alignment explanation
Indices: 5232207--5232336 Score: 201
Period size: 62 Copynumber: 2.1 Consensus size: 62
5232197 ATGTGCAGCC
* *
5232207 AACT-ATCAAACAAAATCAATCAGCAATGAAAGCTGACTGAATGAAATAAATCAGCGATAAA
1 AACTGATCTAACAAAATCAATCAGCAATGAAAGCTGACTGAATGAAATAAATCAACGATAAA
* *
5232268 AGCTGATCTAACAAAATCAATCAGCATTG-AAGACTGACTGAATGAAATAAATCAACGATAAA
1 AACTGATCTAACAAAATCAATCAGCAATGAAAG-CTGACTGAATGAAATAAATCAACGATAAA
5232330 AACTGAT
1 AACTGAT
5232337 TCGAACCTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
61 6 0.10
62 56 0.90
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (62 bp):
AACTGATCTAACAAAATCAATCAGCAATGAAAGCTGACTGAATGAAATAAATCAACGATAAA
Found at i:5232335 original size:31 final size:31
Alignment explanation
Indices: 5232219--5232335 Score: 103
Period size: 31 Copynumber: 3.8 Consensus size: 31
5232209 CTATCAAACA
* * * *
5232219 AAATCAATCAGCAATGAAAGCTGACTGAATG
1 AAATAAATCAGCGATAAAAACTGACTGAATG
* **
5232250 AAATAAATCAGCGATAAAAGCTGATCT-AACA
1 AAATAAATCAGCGATAAAAACTGA-CTGAATG
* * *
5232281 AAATCAATCAGC-ATTGAAGACTGACTGAATG
1 AAATAAATCAGCGA-TAAAAACTGACTGAATG
*
5232312 AAATAAATCAACGATAAAAACTGA
1 AAATAAATCAGCGATAAAAACTGA
5232336 TTCGAACCTA
Statistics
Matches: 67, Mismatches: 15, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
30 3 0.04
31 61 0.91
32 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.20
Consensus pattern (31 bp):
AAATAAATCAGCGATAAAAACTGACTGAATG
Found at i:5243387 original size:2 final size:2
Alignment explanation
Indices: 5243380--5243407 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5243370 TGAATTTAAG
5243380 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5243408 ACATAATAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5244761 original size:2 final size:2
Alignment explanation
Indices: 5244754--5244786 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5244744 ATTTTTATTT
5244754 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 T
5244787 GTGTGTGTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5245576 original size:117 final size:118
Alignment explanation
Indices: 5245247--5245606 Score: 609
Period size: 121 Copynumber: 3.0 Consensus size: 118
5245237 CGGATATAAG
5245247 TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAAGATGGTTAATCTGACACTACATATGCACA
1 TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAAGATGGTTAATCTGACACTACATATGCACA
*
5245312 TTGGACTCACTGGGACAATGAAAAAAAAAAAAAAGTTGATTAACCAACAAAGTA
66 TTGGACTCACTGGGACAATG-AAAAAAAAAAAAAGTTGATTAACCAACAGAGTA
5245366 TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAAGATGGTTAATCTG--ACTACATATGCACA
1 TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAAGATGGTTAATCTGACACTACATATGCACA
*
5245429 TTGGACTCACTGGGACAATGAAAAAAAAAAAAAAAAAAGTTGATTAACCAACAGAGTT
66 TTGGACTCACTGGGACAATG-----AAAAAAAAAAAAAGTTGATTAACCAACAGAGTA
*
5245487 TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAACATGGTTAATCTGACACTACATATGCACA
1 TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAAGATGGTTAATCTGACACTACATATGCACA
*
5245552 TTGGACTCACTGGGACAATG-AAAAAAAAAAAATTTGATTAACCAACAGAGTA
66 TTGGACTCACTGGGACAATGAAAAAAAAAAAAAGTTGATTAACCAACAGAGTA
5245604 TTA
1 TTA
5245607 GATAACCCAA
Statistics
Matches: 230, Mismatches: 5, Indels: 14
0.92 0.02 0.06
Matches are distributed among these distances:
117 67 0.29
119 49 0.21
121 80 0.35
123 34 0.15
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.21
Consensus pattern (118 bp):
TTAACTAAAAATCAGGGCCAAGCCTTGAACAGAAAAGATGGTTAATCTGACACTACATATGCACA
TTGGACTCACTGGGACAATGAAAAAAAAAAAAAGTTGATTAACCAACAGAGTA
Found at i:5249759 original size:2 final size:2
Alignment explanation
Indices: 5249752--5249781 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5249742 AAAGAAAATA
*
5249752 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5249782 GTAGAAAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5253496 original size:10 final size:10
Alignment explanation
Indices: 5253481--5253510 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
5253471 AGATGATGGG
5253481 TAGCTTTCCA
1 TAGCTTTCCA
5253491 TAGCTTTCCA
1 TAGCTTTCCA
5253501 TAGCTTTCCA
1 TAGCTTTCCA
5253511 AGTCAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (10 bp):
TAGCTTTCCA
Found at i:5255181 original size:33 final size:32
Alignment explanation
Indices: 5255142--5255203 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
5255132 CAAAATTAAT
* *
5255142 TATTTTATCTTATATATATAAATATTATAATTA
1 TATTTTATATAATATATATAAATA-TATAATTA
*
5255175 TATTTTATATAATATATATATATATATAA
1 TATTTTATATAATATATATAAATATATAA
5255204 CCATCAGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 5 0.19
33 21 0.81
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (32 bp):
TATTTTATATAATATATATAAATATATAATTA
Found at i:5255291 original size:15 final size:16
Alignment explanation
Indices: 5255250--5255303 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
5255240 TTTTTATTTT
5255250 TTTAAATAAATATAAA
1 TTTAAATAAATATAAA
*
5255266 TGATGAAATAAATAT-AA
1 T--TTAAATAAATATAAA
5255283 TTTAAATAAAT-TAAA
1 TTTAAATAAATATAAA
5255298 TTTAAA
1 TTTAAA
5255304 ATCAATCTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
14 1 0.03
15 17 0.52
16 1 0.03
17 3 0.09
18 11 0.33
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (16 bp):
TTTAAATAAATATAAA
Found at i:5255366 original size:6 final size:6
Alignment explanation
Indices: 5255355--5255396 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
5255345 TATATTTAAA
*
5255355 TATATT TATATT CATATT TATA-- T-TATT TATATT TATATT TAT
1 TATATT TATATT TATATT TATATT TATATT TATATT TATATT TAT
5255397 TTAAAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
3 2 0.06
4 1 0.03
5 1 0.03
6 27 0.87
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:5255373 original size:12 final size:11
Alignment explanation
Indices: 5255343--5255396 Score: 60
Period size: 12 Copynumber: 5.0 Consensus size: 11
5255333 CATACCATAA
5255343 ATTATATTTA-
1 ATTATATTTAT
*
5255353 AATATATTTAT
1 ATTATATTTAT
5255364 ATTCATATTTAT
1 ATT-ATATTTAT
5255376 A-T-TATTTAT
1 ATTATATTTAT
5255385 ATTTATATTTAT
1 A-TTATATTTAT
5255397 TTAAAAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 8 0.22
10 9 0.24
11 4 0.11
12 16 0.43
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
ATTATATTTAT
Found at i:5255383 original size:21 final size:22
Alignment explanation
Indices: 5255346--5255396 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 22
5255336 ACCATAAATT
*
5255346 ATATTTAAATATATTTATATTC
1 ATATTTATATATATTTATATTC
*
5255368 ATATTTATAT-TATTTATATTT
1 ATATTTATATATATTTATATTC
5255389 ATATTTAT
1 ATATTTAT
5255397 TTAAAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATTTATATATATTTATATTC
Found at i:5255386 original size:15 final size:16
Alignment explanation
Indices: 5255355--5255399 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
5255345 TATATTTAAA
5255355 TATATTTATATTCATATT
1 TATATTTAT-TT-ATATT
5255373 TATA-TTATTTATATT
1 TATATTTATTTATATT
5255388 TATATTTATTTA
1 TATATTTATTTA
5255400 AAAAATATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 9 0.35
16 9 0.35
17 4 0.15
18 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTATTTATATT
Found at i:5255433 original size:23 final size:22
Alignment explanation
Indices: 5255379--5255479 Score: 73
Period size: 23 Copynumber: 4.5 Consensus size: 22
5255369 TATTTATATT
*
5255379 ATTTATATTTATATTTATTTAA-A
1 ATTTAT-TTTA-ATTTATATAATA
**
5255402 AAATATTTTAATTTATCATAATA
1 ATTTATTTTAATTTAT-ATAATA
*
5255425 ATTTATTTTTAACTT-TA-AATA
1 ATTTA-TTTTAATTTATATAATA
* * *
5255446 ATTTATATTATTTTATATTTATA
1 ATTTATTTTAATTTATA-TAATA
5255469 ATTTATTTTAA
1 ATTTATTTTAA
5255480 AAGATATTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
20 6 0.10
21 17 0.28
22 8 0.13
23 21 0.35
24 8 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTATTTTAATTTATATAATA
Found at i:5258048 original size:228 final size:226
Alignment explanation
Indices: 5257598--5258277 Score: 714
Period size: 228 Copynumber: 3.0 Consensus size: 226
5257588 CTACATCCCT
* * * *
5257598 CCACGGAGCCTGAGCACAAGGTGAAGGGTAGACTCTTTCTGGATATTGTAATCCGCAAGGGTCCT
1 CCACGGAGCCTGAGCACAAGGTGAAGAGTCGATTCTTTCTGGATATTGTAATCCGCAAGGGTAC-
* * * * * * *
5257663 GCCATCTTCCAGCTGCTTCCCAGCGAAAATCAACCTCTGCTGATCTGGAGGGATCCCTTCCTTAT
65 GCCATCTTCGAGTTGCTTCCCAGCGAAAATCAATCGCTGTTGATCCGGAGGGATGCCTTCCTTAT
* * * * * * * * * * *
5257728 CCTGGATTTTCGCCTTCACATTGTCTATCGTATCCGAGCTCTCTACCTCCAAGGTAATTGTTTTT
130 CTTGGATCTTGGCCTTGACATTGTCTATAGTGTCAGAGCTCTCCA-CTTCAAGGTGATAGTTTTT
* * * *
5257793 CCGGTCAAGGTTTTAACAAAAATCTGCATGCCC
194 CCGGTCAGGGTTTTGACAAAGATCTGCATGCCA
* * *
5257826 CCACGTAGCCTGAGCACAAGGTGAAGAGTCGATTCCTTT-TGGATATTGTAATCCGCCAGGGTGC
1 CCACGGAGCCTGAGCACAAGGTGAAGAGTCGATT-CTTTCTGGATATTGTAATCCGCAAGGGTAC
* * *
5257890 GCCCATCCTCGAGTTGCTTGCCAGCGAAAATCAATCGCTGTTGGTCCGGAGGGATGCCTTCCTTA
65 G-CCATCTTCGAGTTGCTTCCCAGCGAAAATCAATCGCTGTTGATCCGGAGGGATGCCTTCCTTA
* * * * *
5257955 TCTTGAATCTTGGCCTTGACATTGTCTATGGTGTCAGAGCTTTCGACTTCAAGAGTGATAGTCTT
129 TCTTGGATCTTGGCCTTGACATTGTCTATAGTGTCAGAGCTCTCCACTTCAAG-GTGATAGTTTT
* * *
5258020 GCCGGTTAGGGTTTTGACGAAGATCTGCATGCCA
193 TCCGGTCAGGGTTTTGACAAAGATCTGCATGCCA
* * * * * * * * * *
5258054 CCACGGAGACGGAGGACCAGATGGAGAGTCGATTCTTTCTGGATGTTATAATCGGCGAGGGTACG
1 CCACGGAGCCTGAGCACAAGGTGAAGAGTCGATTCTTTCTGGATATTGTAATCCGCAAGGGTAC-
* * * * *
5258119 GCCGTCTTCGAGTTGCTTCCCGGCGAAGATCAATCGCTGTTGATCGGGAGGGATGCCTTCCTTGT
65 GCCATCTTCGAGTTGCTTCCCAGCGAAAATCAATCGCTGTTGATCCGGAGGGATGCCTTCCTTAT
* * * * * * *
5258184 CTTGGATCTTGGCCTTGACGTTATCGATAGTGTCGGAGCTCTCCACCTCGAGGGTGATGGTTTTT
130 CTTGGATCTTGGCCTTGACATTGTCTATAGTGTCAGAGCTCTCCACTTC-AAGGTGATAGTTTTT
* *
5258249 CCGGTGAGGGTCTTGACAAAGATCTGCAT
194 CCGGTCAGGGTTTTGACAAAGATCTGCAT
5258278 CTTCGACTAC
Statistics
Matches: 373, Mismatches: 73, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
227 11 0.03
228 355 0.95
229 7 0.02
ACGTcount: A:0.20, C:0.24, G:0.26, T:0.29
Consensus pattern (226 bp):
CCACGGAGCCTGAGCACAAGGTGAAGAGTCGATTCTTTCTGGATATTGTAATCCGCAAGGGTACG
CCATCTTCGAGTTGCTTCCCAGCGAAAATCAATCGCTGTTGATCCGGAGGGATGCCTTCCTTATC
TTGGATCTTGGCCTTGACATTGTCTATAGTGTCAGAGCTCTCCACTTCAAGGTGATAGTTTTTCC
GGTCAGGGTTTTGACAAAGATCTGCATGCCA
Found at i:5258736 original size:15 final size:15
Alignment explanation
Indices: 5258716--5258746 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5258706 GTAATTTAAA
5258716 ATTTTTAAAATTAATT
1 ATTTTTAAAA-TAATT
5258732 ATTTTTAAAATAATT
1 ATTTTTAAAATAATT
5258747 TTTAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTAAAATAATT
Found at i:5260342 original size:17 final size:16
Alignment explanation
Indices: 5260322--5260362 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
5260312 TATTATGTTT
5260322 TATAATAAATTATAAAA
1 TATAATAAATTAT-AAA
* *
5260339 TATAAAAAATTATAAT
1 TATAATAAATTATAAA
5260355 TATAATAA
1 TATAATAA
5260363 TATTTGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TATAATAAATTATAAA
Found at i:5262085 original size:26 final size:22
Alignment explanation
Indices: 5262032--5262077 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
5262022 TATGTTAGTA
5262032 AAATTTATAAATAAAATTTGTT
1 AAATTTATAAATAAAATTTGTT
5262054 AAATTTATAAATAAAATTTGTT
1 AAATTTATAAATAAAATTTGTT
5262076 AA
1 AA
5262078 GTATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
AAATTTATAAATAAAATTTGTT
Found at i:5262576 original size:19 final size:20
Alignment explanation
Indices: 5262552--5262592 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5262542 AGTTTAAAAA
* *
5262552 TTTAATAGAT-TTTTTTATT
1 TTTAATAAATATTTATTATT
5262571 TTTAATAAATATTTATTATT
1 TTTAATAAATATTTATTATT
5262591 TT
1 TT
5262593 AATTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTAATAAATATTTATTATT
Found at i:5262593 original size:19 final size:19
Alignment explanation
Indices: 5262552--5262603 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
5262542 AGTTTAAAAA
* *
5262552 TTTAATAGATTTTTTTATT
1 TTTAATAAATTTTATTATT
5262571 TTTAATAAATATTTATTA-T
1 TTTAATAAAT-TTTATTATT
*
5262590 TTTAATTAATTTTA
1 TTTAATAAATTTTA
5262604 AAAAATCACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 19 0.66
20 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTAATAAATTTTATTATT
Found at i:5262637 original size:27 final size:27
Alignment explanation
Indices: 5262593--5262653 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
5262583 TTATTATTTT
* *
5262593 AATTAATTTTAAAAAATCACAAT-TAAA
1 AATTAAATATAAAAAATCA-AATATAAA
* *
5262620 ACTTAAATATAAATAATCAAATATAAA
1 AATTAAATATAAAAAATCAAATATAAA
5262647 AATTAAA
1 AATTAAA
5262654 ATTTTTTTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (27 bp):
AATTAAATATAAAAAATCAAATATAAA
Found at i:5265758 original size:2 final size:2
Alignment explanation
Indices: 5265745--5265781 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5265735 GCTTTCAATG
* *
5265745 AT AT AT AC AT AT AT AC 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 A
5265782 AATAGAAATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:5267150 original size:21 final size:21
Alignment explanation
Indices: 5267109--5267151 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
5267099 TCCTCTCTCC
5267109 TGCATTCCTTTTCTCTGCATT
1 TGCATTCCTTTTCTCTGCATT
5267130 TGCATTCCTTTTCTCTGCATT
1 TGCATTCCTTTTCTCTGCATT
5267151 T
1 T
5267152 TTTGTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.09, C:0.28, G:0.09, T:0.53
Consensus pattern (21 bp):
TGCATTCCTTTTCTCTGCATT
Found at i:5269208 original size:64 final size:64
Alignment explanation
Indices: 5269132--5269262 Score: 253
Period size: 64 Copynumber: 2.0 Consensus size: 64
5269122 TTGAGCCTTT
*
5269132 TAAAAGAGAATAAATTGATAGAGGGTGTAAATTGGTTTCTTAATTGTTCTTTATTCTGAGGTTA
1 TAAAAGAGAATAAATTGATAGAGGGTGTAAATTAGTTTCTTAATTGTTCTTTATTCTGAGGTTA
5269196 TAAAAGAGAATAAATTGATAGAGGGTGTAAATTAGTTTCTTAATTGTTCTTTATTCTGAGGTTA
1 TAAAAGAGAATAAATTGATAGAGGGTGTAAATTAGTTTCTTAATTGTTCTTTATTCTGAGGTTA
5269260 TAA
1 TAA
5269263 GGGCAGAAAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (64 bp):
TAAAAGAGAATAAATTGATAGAGGGTGTAAATTAGTTTCTTAATTGTTCTTTATTCTGAGGTTA
Found at i:5273113 original size:2 final size:2
Alignment explanation
Indices: 5273106--5273140 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5273096 GTGGAAAAGT
5273106 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
5273141 GTGGAAAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5277572 original size:17 final size:16
Alignment explanation
Indices: 5277539--5277591 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
5277529 GATATGATTT
*
5277539 TTTTAGATTTAAATTA
1 TTTTAAATTTAAATTA
5277555 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAA-TTA
* *
5277572 TTTTTAATTTGAATTA
1 TTTTAAATTTAAATTA
5277588 TTTT
1 TTTT
5277592 GAGTTGAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 19 0.58
17 14 0.42
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:5277855 original size:16 final size:16
Alignment explanation
Indices: 5277795--5277872 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 16
5277785 TTACATAATG
5277795 ATAAAATTAGTA-AAAT
1 ATAAAATTA-TATAAAT
* *
5277811 -TAAAATTTTAAAAATT
1 ATAAAATTATATAAA-T
5277827 AATAAATATTTATATAAAT
1 -ATAAA-A-TTATATAAAT
5277846 ATAAAATTATAT-AAT
1 ATAAAATTATATAAAT
*
5277861 A-ATAATTATATA
1 ATAAAATTATATA
5277873 TTGAGAATAA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
14 11 0.22
15 14 0.27
16 7 0.14
17 1 0.02
18 9 0.18
19 2 0.04
20 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (16 bp):
ATAAAATTATATAAAT
Found at i:5278019 original size:17 final size:18
Alignment explanation
Indices: 5277997--5278030 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5277987 TAACTAAAAA
*
5277997 ATAATTGTTA-TATTTTC
1 ATAATTCTTATTATTTTC
5278014 ATAATTCTTATTATTTT
1 ATAATTCTTATTATTTT
5278031 ACAATGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.06, G:0.03, T:0.62
Consensus pattern (18 bp):
ATAATTCTTATTATTTTC
Found at i:5278225 original size:195 final size:193
Alignment explanation
Indices: 5277991--5278385 Score: 610
Period size: 195 Copynumber: 2.0 Consensus size: 193
5277981 TTATAATAAC
5277991 TAAAAAATAATTGTTATATTTTCATAATTCTTATTATTTTACAATGATTATATATTTATATTTTG
1 TAAAAAATAATTGTTATATTTTCATAATTCTTATTATTTTACAATGATTATATATTTATATTTTG
* * *
5278056 GTTAAATTTTATGATATTTAATATTGATATAATTAATGATTATATAAAAATTTTTTGTTTTATAA
66 GTTAAATTTTATAATATTTAATATTAATATAATTAATGATCATAT-AAAATTTTTTG-TTTATAA
* * * * * *
5278121 TTGAGCTAAAATAAATATAAAATGATACTAGATAAAGTGAATGTCAAAAATCATTAGATTACAAT
129 TTGAGCTAAAACAAATATAAAATAATACTAGATAAAATAAATATAAAAAATCATTAGATTACAAT
* * * * *
5278186 TAAAAAATAATTTTTATATTTTGATACTTCTTGTTATTTTACAATGATTATATATTTATATTTTT
1 TAAAAAATAATTGTTATATTTTCATAATTCTTATTATTTTACAATGATTATATATTTATATTTTG
*
5278251 GTTAGATTTTATAATATTTAATATTAATATAATTAATGATCATATAAAATTTTTTGTTTATAATT
66 GTTAAATTTTATAATATTTAATATTAATATAATTAATGATCATATAAAATTTTTTGTTTATAATT
* *
5278316 GAGCTAAAACAAATATAAAATAATACTAGATAAAATAAATATAAAAAATTATTAGATTACATT
131 GAGCTAAAACAAATATAAAATAATACTAGATAAAATAAATATAAAAAATCATTAGATTACAAT
*
5278379 TTAAAAA
1 TAAAAAA
5278386 GTTATTAGAA
Statistics
Matches: 182, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
193 70 0.38
194 11 0.06
195 101 0.55
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (193 bp):
TAAAAAATAATTGTTATATTTTCATAATTCTTATTATTTTACAATGATTATATATTTATATTTTG
GTTAAATTTTATAATATTTAATATTAATATAATTAATGATCATATAAAATTTTTTGTTTATAATT
GAGCTAAAACAAATATAAAATAATACTAGATAAAATAAATATAAAAAATCATTAGATTACAAT
Found at i:5278338 original size:25 final size:24
Alignment explanation
Indices: 5278310--5278366 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
5278300 TTTTTTGTTT
*
5278310 ATAATTGAGCTAAAACAAATATAAA
1 ATAATT-AGATAAAACAAATATAAA
*
5278335 ATAATACTAGATAAAATAAATATAAA
1 ATAAT--TAGATAAAACAAATATAAA
5278361 A-AATTA
1 ATAATTA
5278367 TTAGATTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
23 2 0.07
25 8 0.29
26 17 0.61
27 1 0.04
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (24 bp):
ATAATTAGATAAAACAAATATAAA
Found at i:5278435 original size:195 final size:195
Alignment explanation
Indices: 5278033--5278439 Score: 475
Period size: 193 Copynumber: 2.1 Consensus size: 195
5278023 ATTATTTTAC
* * *
5278033 AATGATTATATATTTATATTTTGGTTAAATTTTATGATATTTAATATTGATATAATTAATGATTA
1 AATGATTATATATTTATATTTTGGTTAAATTTTATAATATTTAATATTAATATAATTAATGATCA
* * * *
5278098 TATAAAAATTTTTTGTTTTATAATTGAGCTAAAATAAATATAAAATGATACTAGATAAAGTGAAT
66 TATAAAAATTTTTTGTTTTATAATTGAGCTAAAACAAATATAAAATAATACTAGATAAAATAAAT
* * *** *** * ** * ** *
5278163 GTCAAAAATCATTAGATTACAATTAAAAAATAATTTTTATATTTTGATACTTCTTGTTATTTTAC
131 ATAAAAAATCATTAGATTACAATTAAAAAATAATTAGAATAAAATGATACTTATAATAATTAAAA
* *
5278228 AATGATTATATATTTATATTTTTGTTAGATTTTATAATATTTAATATTAATATAATTAATGATCA
1 AATGATTATATATTTATATTTTGGTTAAATTTTATAATATTTAATATTAATATAATTAATGATCA
5278293 TAT-AAAATTTTTTG-TTTATAATTGAGCTAAAACAAATATAAAATAATACTAGATAAAATAAAT
66 TATAAAAATTTTTTGTTTTATAATTGAGCTAAAACAAATATAAAATAATACTAGATAAAATAAAT
* * * *
5278356 ATAAAAAATTATTAGATTACATTTTAAAAAGTTATTAGAATAAAAT-A-ACTTATAAATAAATTC
131 ATAAAAAATCATTAGATTACA-ATTAAAAAATAATTAGAATAAAATGATACTTAT-AAT-AATT-
5278419 AAAA
192 AAAA
*
5278423 AAT--TTATATATATATAT
1 AATGATTATATATTTATAT
5278440 ATATATTTAA
Statistics
Matches: 179, Mismatches: 29, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
192 5 0.03
193 78 0.44
194 29 0.16
195 67 0.37
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.44
Consensus pattern (195 bp):
AATGATTATATATTTATATTTTGGTTAAATTTTATAATATTTAATATTAATATAATTAATGATCA
TATAAAAATTTTTTGTTTTATAATTGAGCTAAAACAAATATAAAATAATACTAGATAAAATAAAT
ATAAAAAATCATTAGATTACAATTAAAAAATAATTAGAATAAAATGATACTTATAATAATTAAAA
Found at i:5280004 original size:16 final size:15
Alignment explanation
Indices: 5279981--5280030 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
5279971 ATTATGTGGA
5279981 TTTTAAATTTAATTT
1 TTTTAAATTTAATTT
5279996 TTTTAAAATTTAATTTAT
1 TTTT-AAATTTAA-TT-T
*
5280014 TTTTATATTTAAATTT
1 TTTTAAATTT-AATTT
5280030 T
1 T
5280031 AAATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 9 0.30
18 7 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTAAATTTAATTT
Found at i:5280567 original size:2 final size:2
Alignment explanation
Indices: 5280560--5280586 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5280550 ATGTTTAATC
5280560 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
5280587 AATGCCCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5285186 original size:3 final size:3
Alignment explanation
Indices: 5285178--5285215 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
5285168 CTCTTCATAA
5285178 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5285216 AAGTAACATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5285955 original size:2 final size:2
Alignment explanation
Indices: 5285948--5285982 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5285938 GTATGATTTT
*
5285948 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5285983 TATTTTGGGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5286788 original size:16 final size:16
Alignment explanation
Indices: 5286769--5286848 Score: 76
Period size: 16 Copynumber: 5.1 Consensus size: 16
5286759 TAAAATAAAA
*
5286769 AAATTTAAATCATTTT
1 AAATTTAAATTATTTT
5286785 AAATTTAAATTA-TTT
1 AAATTTAAATTATTTT
* *
5286800 AGTATTCAAATTATTTT
1 A-AATTTAAATTATTTT
* *
5286817 AGATTTATA-TATTTT
1 AAATTTAAATTATTTT
*
5286832 AAGTTTAAATT-TTTT
1 AAATTTAAATTATTTT
5286847 AA
1 AA
5286849 TATAAAAAAA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
15 22 0.42
16 26 0.50
17 4 0.08
ACGTcount: A:0.40, C:0.03, G:0.04, T:0.54
Consensus pattern (16 bp):
AAATTTAAATTATTTT
Found at i:5286838 original size:15 final size:16
Alignment explanation
Indices: 5286771--5286848 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 16
5286761 AAATAAAAAA
5286771 ATTTAAATCATTTTAA-
1 ATTTAAAT-ATTTTAAG
5286787 ATTTAAAT-TATTT-AG
1 ATTTAAATAT-TTTAAG
*
5286802 TATTCAAATTATTTT-AG
1 -ATTTAAA-TATTTTAAG
*
5286819 ATTTATATATTTTAAG
1 ATTTAAATATTTTAAG
*
5286835 -TTTAAATTTTTTAA
1 ATTTAAATATTTTAA
5286849 TATAAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 2 0.04
15 21 0.41
16 21 0.41
17 6 0.12
18 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTTAAATATTTTAAG
Found at i:5289388 original size:147 final size:147
Alignment explanation
Indices: 5289098--5289391 Score: 475
Period size: 147 Copynumber: 2.0 Consensus size: 147
5289088 AATTAGTTTT
* *
5289098 ACTTGACTTATTACATCAAATTTTATTATAAACTTTATTATTAATTAAATTTGACATATTTATTT
1 ACTTGACTTATGACATCAAATTATATTATAAACTTTATTATTAATTAAATTTGACATATTTATTT
5289163 TGTAAATGACAAAGTAAATTAAAAATGTGAAAAAATAAAGGAAAATAATAACTAGACATAGTGAA
66 TGTAAATGACAAAGTAAATTAAAAATGTGAAAAAATAAAGGAAAATAATAACTAGACATAGTGAA
*
5289228 TTTTTAAGTTAAAAATA
131 TTTTTAAGATAAAAATA
*
5289245 ACTTGATTTATGACATCAAATTATATTATAAACTTTATTATTAATTAAATTTGACATATTTATTT
1 ACTTGACTTATGACATCAAATTATATTATAAACTTTATTATTAATTAAATTTGACATATTTATTT
** * * *
5289310 TGTAAATGATGAAGTATATTAAAAATGTGAAAAAAATGAAGGAAAATAATAACTAGACGTAGTG-
66 TGTAAATGACAAAGTAAATTAAAAATGTG-AAAAAATAAAGGAAAATAATAACTAGACATAGTGA
5289374 ATTTCTTAA-ATAAAAATA
130 ATTT-TTAAGATAAAAATA
5289392 GGCAAAAATA
Statistics
Matches: 136, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
147 100 0.74
148 36 0.26
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (147 bp):
ACTTGACTTATGACATCAAATTATATTATAAACTTTATTATTAATTAAATTTGACATATTTATTT
TGTAAATGACAAAGTAAATTAAAAATGTGAAAAAATAAAGGAAAATAATAACTAGACATAGTGAA
TTTTTAAGATAAAAATA
Found at i:5290437 original size:119 final size:119
Alignment explanation
Indices: 5290189--5290473 Score: 287
Period size: 119 Copynumber: 2.4 Consensus size: 119
5290179 GAATACCAAA
* * * *
5290189 TTTTTAAATAAATTATTTAAAATTAAAATCAAGATAA-TAATAAAATAATTTTTATTTTAATTTT
1 TTTTTAAATATATTATTTAAAAATAAAATAAAAATAATTAATAAAATAA--TTTATTTTAATTTT
* * ** * *
5290253 TTAAATAAATTTAATATAAATTTTAATTTGATATGTCAATTAATATATAAATTAAT
64 TTAAATAAATTTAATAGAAATTTTAAATCAATATATAAATTAATATATAAATTAAT
* * * *
5290309 CTCTTAAATATATCATTTAAAAATAAAATAAATATAATTAATAAAATAA-TT-TTTTAATTTTTT
1 TTTTTAAATATATTATTTAAAAATAAAATAAAAATAATTAATAAAATAATTTATTTTAATTTTTT
* *
5290372 AAAAATAAATTTGATACGAAA-TTTAAATCAATTTATAAATTAACT-TATAAATT-AT
66 --AAATAAATTTAATA-GAAATTTTAAATCAATATATAAATTAA-TATATAAATTAAT
* *
5290427 TTTTTAAAATATATTATCTAAAAAT-TAATAAAAATCAATTAATAAAA
1 TTTTT-AAATATATTATTTAAAAATAAAATAAAAAT-AATTAATAAAA
5290474 AAATATTAAA
Statistics
Matches: 137, Mismatches: 21, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
117 12 0.09
118 15 0.11
119 65 0.47
120 34 0.25
121 11 0.08
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.44
Consensus pattern (119 bp):
TTTTTAAATATATTATTTAAAAATAAAATAAAAATAATTAATAAAATAATTTATTTTAATTTTTT
AAATAAATTTAATAGAAATTTTAAATCAATATATAAATTAATATATAAATTAAT
Found at i:5291093 original size:18 final size:19
Alignment explanation
Indices: 5291049--5291099 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
5291039 GATCCATCTC
5291049 TTAATAAAA-AAAATAAAT
1 TTAATAAAATAAAATAAAT
* * *
5291067 GTAAAAAAATAAAA-ATAT
1 TTAATAAAATAAAATAAAT
5291085 TTAATAAAATAAAAT
1 TTAATAAAATAAAAT
5291100 TTTAAAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (19 bp):
TTAATAAAATAAAATAAAT
Found at i:5292602 original size:2 final size:2
Alignment explanation
Indices: 5292595--5292623 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5292585 TATCATACTT
5292595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5292624 TCTTGGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5293087 original size:19 final size:18
Alignment explanation
Indices: 5293060--5293099 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5293050 AGTTTGACTC
5293060 AAAACAATAATTTTTAATT
1 AAAACAAT-ATTTTTAATT
* *
5293079 AAAATAATATTTTTATTT
1 AAAACAATATTTTTAATT
5293097 AAA
1 AAA
5293100 TTTAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (18 bp):
AAAACAATATTTTTAATT
Found at i:5295670 original size:16 final size:16
Alignment explanation
Indices: 5295620--5295715 Score: 81
Period size: 16 Copynumber: 6.0 Consensus size: 16
5295610 GATTTAAACC
5295620 CGAAATGATCC-GAACT
1 CGAAATGA-CCTGAACT
* * * *
5295636 CAAAATGATCGGAATT
1 CGAAATGACCTGAACT
5295652 CGAAATGACCTGAACT
1 CGAAATGACCTGAACT
*
5295668 CGAAAGGA-CTCGAA-T
1 CGAAATGACCT-GAACT
* *
5295683 CCGAAATAACTTGAACT
1 -CGAAATGACCTGAACT
5295700 CGAAATGACCTGAACT
1 CGAAATGACCTGAACT
5295716 TAAATTAAGT
Statistics
Matches: 62, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
15 4 0.06
16 56 0.90
17 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.19, T:0.20
Consensus pattern (16 bp):
CGAAATGACCTGAACT
Found at i:5295688 original size:32 final size:32
Alignment explanation
Indices: 5295619--5295704 Score: 95
Period size: 32 Copynumber: 2.7 Consensus size: 32
5295609 TGATTTAAAC
* *
5295619 CCGAAATGATCC-GAACTCAAAATGATCGGAAT
1 CCGAAATGA-CCTGAACTCGAAAGGATCGGAAT
*
5295651 TCGAAATGACCTGAACTCGAAAGGACTC-GAAT
1 CCGAAATGACCTGAACTCGAAAGGA-TCGGAAT
* *
5295683 CCGAAATAACTTGAACTCGAAA
1 CCGAAATGACCTGAACTCGAAA
5295705 TGACCTGAAC
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 2 0.04
32 42 0.91
33 2 0.04
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (32 bp):
CCGAAATGACCTGAACTCGAAAGGATCGGAAT
Found at i:5295783 original size:21 final size:22
Alignment explanation
Indices: 5295747--5295788 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5295737 TAAAAAATAT
*
5295747 TAAGTTAATAAAATAATATTTA
1 TAAGTTAATAAAATAAAATTTA
*
5295769 TAAGTT-ATAATATAAAATTT
1 TAAGTTAATAAAATAAAATTT
5295789 TGAATTAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (22 bp):
TAAGTTAATAAAATAAAATTTA
Found at i:5296642 original size:21 final size:22
Alignment explanation
Indices: 5296595--5296643 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
5296585 TTAAAATGGC
* *
5296595 TTAAACTTGATGAATTCAAATT
1 TTAAACATGATGAACTCAAATT
*
5296617 TTAAACATGATTAACTCAAA-T
1 TTAAACATGATGAACTCAAATT
5296638 TTAAAC
1 TTAAAC
5296644 TTAAAATGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (22 bp):
TTAAACATGATGAACTCAAATT
Found at i:5296947 original size:2 final size:2
Alignment explanation
Indices: 5296940--5296980 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
5296930 AACAAGTCTA
5296940 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5296981 AAAGCATGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5297235 original size:23 final size:22
Alignment explanation
Indices: 5297190--5297239 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
5297180 TTTAATTTTT
*
5297190 AAAATTTTATTTAAATAAATAA
1 AAAATTTAATTTAAATAAATAA
** *
5297212 ATAAATTTAATTTATTTAATTAA
1 A-AAATTTAATTTAAATAAATAA
5297235 AAAAT
1 AAAAT
5297240 AAAAATCACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAATTTAATTTAAATAAATAA
Found at i:5297335 original size:16 final size:16
Alignment explanation
Indices: 5297314--5297349 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5297304 AATTTTTTTA
5297314 ATATATGTAT-ATATAT
1 ATATATGTATGA-ATAT
5297330 ATATATGTATGAATAT
1 ATATATGTATGAATAT
5297346 ATAT
1 ATAT
5297350 TTTATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.47
Consensus pattern (16 bp):
ATATATGTATGAATAT
Found at i:5297949 original size:3 final size:3
Alignment explanation
Indices: 5297943--5297970 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5297933 AAAGAAAGCT
5297943 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5297971 AAATCTTGGA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5298938 original size:23 final size:23
Alignment explanation
Indices: 5298894--5298939 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5298884 TTAAAATTTC
***
5298894 TATTGACTTTTTATTTTCTTAAA
1 TATTGACTTTTTATTAAATTAAA
*
5298917 TATTGATTTTTTATTAAATTAAA
1 TATTGACTTTTTATTAAATTAAA
5298940 AATAATAACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (23 bp):
TATTGACTTTTTATTAAATTAAA
Found at i:5299375 original size:3 final size:3
Alignment explanation
Indices: 5299367--5299405 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
5299357 GATTTAGCAA
5299367 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5299406 GTGACTGTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5309324 original size:119 final size:120
Alignment explanation
Indices: 5309111--5309354 Score: 445
Period size: 119 Copynumber: 2.0 Consensus size: 120
5309101 TTGCACATCG
*
5309111 AAGAATAGAACAATAAGACTAATATTCCAATCATATAATGCAAAATCTGATTATTCTAGCTATGT
1 AAGAATAGAACAATAAGACTAATATTCCAATCATATAATGAAAAATCTGATTATTCTAGCTATGT
*
5309176 ACTACAACAGGTTTAAGATGCATCATCTGTCTTTCTTCCCTTGCATTCAAGAAAA
66 ACTACAACAGGTTTAAGATGCATCATCTGTCTCTCTTCCCTTGCATTCAAGAAAA
*
5309231 AAGAATAGAACAATAAGACTAATATTCCAATCGTAT-ATGAAAAATCTGATTATTCTAGCTATGT
1 AAGAATAGAACAATAAGACTAATATTCCAATCATATAATGAAAAATCTGATTATTCTAGCTATGT
*
5309295 ACTACAACAGGTTTAAGATGCATCGTCTGTCTCTCTTCCCTTGCATTCAAGAAAA
66 ACTACAACAGGTTTAAGATGCATCATCTGTCTCTCTTCCCTTGCATTCAAGAAAA
5309350 AAGAA
1 AAGAA
5309355 AAGGGGTAGG
Statistics
Matches: 120, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
119 85 0.71
120 35 0.29
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (120 bp):
AAGAATAGAACAATAAGACTAATATTCCAATCATATAATGAAAAATCTGATTATTCTAGCTATGT
ACTACAACAGGTTTAAGATGCATCATCTGTCTCTCTTCCCTTGCATTCAAGAAAA
Found at i:5311257 original size:21 final size:18
Alignment explanation
Indices: 5311242--5311297 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 18
5311232 CAATTGTTTA
5311242 TTTTTATAAAATAATTTATT
1 TTTTTA-AAAATAATTT-TT
*
5311262 TTTTTAAAAAATTAATATATT
1 TTTTT-AAAAA-TAAT-TTTT
5311283 TTTTTAAAAATAATT
1 TTTTTAAAAATAATT
5311298 GATATTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
18 1 0.03
19 4 0.12
20 14 0.44
21 12 0.38
22 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTTTTAAAAATAATTTTT
Found at i:5311261 original size:18 final size:17
Alignment explanation
Indices: 5311238--5311274 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
5311228 ATATCAATTG
5311238 TTTATTTTTATAAAATAA
1 TTTATTTTTATAAAA-AA
*
5311256 TTTATTTTTTTAAAAAA
1 TTTATTTTTATAAAAAA
5311273 TT
1 TT
5311275 AATATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTATTTTTATAAAAAA
Found at i:5311267 original size:20 final size:20
Alignment explanation
Indices: 5311242--5311318 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 20
5311232 CAATTGTTTA
5311242 TTTTTATAAAATAATTTATT
1 TTTTTATAAAATAATTTATT
* *
5311262 TTTTTAAAAAATTAATATATT
1 TTTTTATAAAA-TAATTTATT
5311283 TTTTTA-AAAATAATTGATATT
1 TTTTTATAAAATAATT--TATT
*
5311304 TTTTTTTAAGAATAA
1 TTTTTATAA-AATAA
5311319 CCTATGTCCT
Statistics
Matches: 48, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 4 0.08
20 14 0.29
21 23 0.48
22 2 0.04
23 5 0.10
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTTATAAAATAATTTATT
Found at i:5311297 original size:23 final size:23
Alignment explanation
Indices: 5311253--5311318 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
5311243 TTTTATAAAA
*
5311253 TAATTTATTTTTTT-AAAA-AAT
1 TAATATATTTTTTTAAAAATAAT
5311274 TAATATATTTTTTTAAAAATAAT
1 TAATATATTTTTTTAAAAATAAT
* * *
5311297 TGATATTTTTTTTTAAGAATAA
1 TAATATATTTTTTTAAAAATAA
5311319 CCTATGTCCT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.33
22 4 0.10
23 22 0.56
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
TAATATATTTTTTTAAAAATAAT
Found at i:5315496 original size:2 final size:2
Alignment explanation
Indices: 5315491--5315528 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5315481 AGACCGATTA
5315491 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5315529 CATACTCAGG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5322209 original size:16 final size:16
Alignment explanation
Indices: 5322166--5322215 Score: 50
Period size: 18 Copynumber: 3.0 Consensus size: 16
5322156 ATTAAAAAAG
5322166 AATTTAACTATAAAATA
1 AATTTAA-TATAAAATA
5322183 AATATTAAATATAATAA-A
1 AAT-TT-AATATAA-AATA
5322201 AATTTAATA-AAAATA
1 AATTTAATATAAAATA
5322216 TGTACTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
14 2 0.07
15 3 0.10
16 4 0.14
17 5 0.17
18 11 0.38
19 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (16 bp):
AATTTAATATAAAATA
Found at i:5329362 original size:12 final size:12
Alignment explanation
Indices: 5329345--5329369 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5329335 TAATATTGTA
5329345 ATATTTTTAAAT
1 ATATTTTTAAAT
5329357 ATATTTTTAAAT
1 ATATTTTTAAAT
5329369 A
1 A
5329370 AAAATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTTTAAAT
Found at i:5329413 original size:16 final size:16
Alignment explanation
Indices: 5329372--5329413 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
5329362 TTTAAATAAA
5329372 AATA-ATAAAA-AATT
1 AATATATAAAATAATT
*
5329386 AATTTATAAAATAATT
1 AATATATAAAATAATT
*
5329402 AATATATCAAAT
1 AATATATAAAAT
5329414 TATATTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 3 0.13
15 6 0.26
16 14 0.61
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AATATATAAAATAATT
Found at i:5337107 original size:22 final size:22
Alignment explanation
Indices: 5337079--5337127 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
5337069 TGTTGTAATC
* *
5337079 TCCTTAATTATTGTTATCTCTA
1 TCCTTAATTATAGTGATCTCTA
5337101 TCCTTAATTATAGTGATCTCTA
1 TCCTTAATTATAGTGATCTCTA
5337123 TCCTT
1 TCCTT
5337128 GTATATTAGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.51
Consensus pattern (22 bp):
TCCTTAATTATAGTGATCTCTA
Found at i:5340751 original size:26 final size:26
Alignment explanation
Indices: 5340700--5340752 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5340690 TCTCTCAATC
*
5340700 TTTTTTCAACCACACTTTCAACCATA
1 TTTTTTCAACCACACTTACAACCATA
*
5340726 TTTTTTCAACCACA-TTACCACTCATA
1 TTTTTTCAACCACACTTACAAC-CATA
5340752 T
1 T
5340753 CTCAGCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTTTTCAACCACACTTACAACCATA
Found at i:5350701 original size:11 final size:11
Alignment explanation
Indices: 5350669--5350707 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
5350659 GTCATAAACT
*
5350669 AACAAAAAAAA
1 AACAAAAAAAG
5350680 AACAAAAAAAG
1 AACAAAAAAAG
5350691 AACAAAAAAAG
1 AACAAAAAAAG
5350702 AA-AAAA
1 AACAAAA
5350708 GGTGAAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
10 4 0.15
11 23 0.85
ACGTcount: A:0.87, C:0.08, G:0.05, T:0.00
Consensus pattern (11 bp):
AACAAAAAAAG
Found at i:5350842 original size:20 final size:21
Alignment explanation
Indices: 5350802--5350843 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5350792 TTAAAATTAC
*
5350802 AAAAATAAAAAAAAGTTATAA
1 AAAAATAAAAAAAAGTAATAA
*
5350823 AAAAATGAAAAAAA-TAATAA
1 AAAAATAAAAAAAAGTAATAA
5350843 A
1 A
5350844 CACAAAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (21 bp):
AAAAATAAAAAAAAGTAATAA
Found at i:5351669 original size:28 final size:28
Alignment explanation
Indices: 5351629--5351998 Score: 339
Period size: 28 Copynumber: 13.4 Consensus size: 28
5351619 TACTAGAAAA
* *
5351629 AAAGCTCACAAGTTAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
5351657 AAAGCCCACAAGTCAGTAGCATCCTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
5351685 AAAGCCCACAAGTCAGTGGCAACCCTTTTC
1 AAAGCCCACAAGTCAGTGGC-ATCC-TTTC
*
5351715 AAAGCCCACAAGTCAGTGACA-CCTTCTC
1 AAAGCCCACAAGTCAGTGGCATCCTT-TC
* * * * *
5351743 AAAGGCCATAAGTCGGTGGTATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
5351771 AAAGCCCACAAGTCAGTGGCAACCCTTTTT
1 AAAGCCCACAAGTCAGTGGC-ATCC-TTTC
* *
5351801 AAAGCCCACAAGTCAATGGCA-CATTCTC
1 AAAGCCCACAAGTCAGTGGCATCCTT-TC
** *
5351829 AAAGCCCACAAGTTTGTGCCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
** *
5351857 AAAATCCACAAGT---T---AT--TTTG
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
5351877 AAAGCCCACAAGTCAGTGGCATCTTTTT
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
* *
5351905 AAAGCCCACAAGTAAGTGGCA-CCTTTTT
1 AAAGCCCACAAGTCAGTGGCATCC-TTTC
* * *
5351933 AAAGCCCACAAGTAAGTAGCATCTTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
*
5351961 AAAGCCCACAAGTGAGTGGCATCCTTTC
1 AAAGCCCACAAGTCAGTGGCATCCTTTC
5351989 AAAGCCCACA
1 AAAGCCCACA
5351999 CAAGTCATTG
Statistics
Matches: 281, Mismatches: 43, Indels: 36
0.78 0.12 0.10
Matches are distributed among these distances:
20 14 0.05
22 2 0.01
23 1 0.00
25 1 0.00
26 2 0.01
27 5 0.02
28 198 0.70
29 14 0.05
30 44 0.16
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCATCCTTTC
Found at i:5351775 original size:86 final size:86
Alignment explanation
Indices: 5351629--5351998 Score: 342
Period size: 86 Copynumber: 4.4 Consensus size: 86
5351619 TACTAGAAAA
* *
5351629 AAAGCTCACAAGTTAGTGGCATCCTT-TCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCA-CCTTCTCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCA
5351693 CAAGTCAGTGGCAACCCTTTTC
65 CAAGTCAGTGGCAACCCTTTTC
* * * * * *
5351715 AAAGCCCACAAGTCAGTGACACCTTCTCAAAGGCCATAAGTCGGTGGTAT-CTTTTCAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTAGCATCCTTTT-AAAGCCCA
*
5351779 CAAGTCAGTGGCAACCCTTTTT
65 CAAGTCAGTGGCAACCCTTTTC
* * ** * **
5351801 AAAGCCCACAAGTCAATGGCACATTCTCAAAGCCCACAAGTTTGT-GCCATCCTTTCAAAATCCA
1 AAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTAG-CATCCTTTTAAAGCCCA
*
5351865 CAAGT---T----A---TTTTG
65 CAAGTCAGTGGCAACCCTTTTC
* * * * *
5351877 AAAGCCCACAAGTCAGTGGCATCTTTTTAAAGCCCACAAGTAAGTGGCA-CCTTTTTAAAGCCCA
1 AAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTAGCATCC-TTTTAAAGCCCA
* * *
5351941 CAAGTAAGTAGC-A-TCTTTTC
65 CAAGTCAGTGGCAACCCTTTTC
*
5351961 AAAGCCCACAAGTGAGTGGCATCCTT-TCAAAGCCCACA
1 AAAGCCCACAAGTCAGTGGCA-CCTTCTCAAAGCCCACA
5351999 CAAGTCATTG
Statistics
Matches: 234, Mismatches: 35, Indels: 32
0.78 0.12 0.11
Matches are distributed among these distances:
75 2 0.01
76 58 0.25
77 1 0.00
79 2 0.01
82 1 0.00
83 1 0.00
84 35 0.15
85 13 0.06
86 117 0.50
87 4 0.02
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.24
Consensus pattern (86 bp):
AAAGCCCACAAGTCAGTGGCACCTTCTCAAAGCCCACAAGTCAGTAGCATCCTTTTAAAGCCCAC
AAGTCAGTGGCAACCCTTTTC
Found at i:5351942 original size:76 final size:76
Alignment explanation
Indices: 5351796--5351945 Score: 178
Period size: 76 Copynumber: 2.0 Consensus size: 76
5351786 GTGGCAACCC
* **
5351796 TTTTTAAAGCCCACAAGTCAATGGCACATTCTCAAAGCCCACAAGTTTGTGCCATCCTTTCAAAA
1 TTTTGAAAGCCCACAAGTCAATGGCACATTCTCAAAGCCCACAAGTAAGTGCCATCCTTTCAAAA
*
5351861 TCCACAAGTTA
66 CCCACAAGTTA
* * * * *
5351872 TTTTGAAAGCCCACAAGTCAGTGGCATC-TTTTTAAAGCCCACAAGTAAGTGGCA-CCTTTTTAA
1 TTTTGAAAGCCCACAAGTCAATGGCA-CATTCTCAAAGCCCACAAGTAAGTGCCATCC-TTTCAA
*
5351935 AGCCCACAAGT
64 AACCCACAAGT
5351946 AAGTAGCATC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
75 2 0.03
76 59 0.95
77 1 0.02
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.27
Consensus pattern (76 bp):
TTTTGAAAGCCCACAAGTCAATGGCACATTCTCAAAGCCCACAAGTAAGTGCCATCCTTTCAAAA
CCCACAAGTTA
Found at i:5351961 original size:104 final size:106
Alignment explanation
Indices: 5351766--5351973 Score: 280
Period size: 104 Copynumber: 2.0 Consensus size: 106
5351756 CGGTGGTATC
5351766 TTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTTTAAAGCCCACAAGTCAATGGCACATTCTCAA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTTTAAAGCCCACAAGTCAATGGCACATTCTCAA
** *
5351831 AGCCCACAAGTTTGTGCCATCCTTTCAAAATCCACAAGTTA
66 AGCCCACAAGTAAGTGCCATCCTTTCAAAACCCACAAGTTA
* * * * *
5351872 TTTTGAAAGCCCACAAGTCAGTGGC-A-TCTTTTTAAAGCCCACAAGT-AAGTGGCACCTTTTTA
1 TTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTTTAAAGCCCACAAGTCAA-TGGCACATTCTCA
* *
5351934 AAGCCCACAAGTAAGTAG-CATCTTTTCAAAGCCCACAAGT
65 AAGCCCACAAGTAAGT-GCCATCCTTTCAAAACCCACAAGT
5351974 GAGTGGCATC
Statistics
Matches: 90, Mismatches: 10, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
103 2 0.02
104 62 0.69
105 2 0.02
106 24 0.27
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (106 bp):
TTTTCAAAGCCCACAAGTCAGTGGCAACCCTTTTTAAAGCCCACAAGTCAATGGCACATTCTCAA
AGCCCACAAGTAAGTGCCATCCTTTCAAAACCCACAAGTTA
Found at i:5353403 original size:14 final size:14
Alignment explanation
Indices: 5353384--5353411 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5353374 AGTAGCACCC
5353384 AACCACTCTGCCAT
1 AACCACTCTGCCAT
5353398 AACCACTCTGCCAT
1 AACCACTCTGCCAT
5353412 GCTCATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.43, G:0.07, T:0.21
Consensus pattern (14 bp):
AACCACTCTGCCAT
Found at i:5354784 original size:27 final size:27
Alignment explanation
Indices: 5354754--5354823 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
5354744 TTTATTTATT
*
5354754 GGGGATACTCCAATCCTATTCCTCCGA
1 GGGGATACTCCAACCCTATTCCTCCGA
5354781 GGGGATACTCCAACCCTATTCCTCCGA
1 GGGGATACTCCAACCCTATTCCTCCGA
* *
5354808 GAGGATACTCGAACCC
1 GGGGATACTCCAACCC
5354824 CGCTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCTATTCCTCCGA
Found at i:5358777 original size:262 final size:265
Alignment explanation
Indices: 5358304--5358826 Score: 845
Period size: 262 Copynumber: 2.0 Consensus size: 265
5358294 GGTGCTGCTT
*
5358304 AGATGCGTCGATGCTCTTGAAGCCAAAAGGATCCTAGAAGAAGTTCATGATGGGATTTGCGGCAC
1 AGATGCGTCGATGCTCTTGAAGCCAAAAGGATCCTAGAAGAAGTTCA--ATGGGATTTACGGCAC
* *
5358369 ACATGCTAATGGGCATCAGATAGCCAAGCAAATTATGAGAGCAGGTTATTACTGGTTGACCCTCT
64 ACATGCTAATGGGCATCAGATAGCCAAGCAAATTATGAGAGCAAGTTATTACTGGTTGACCCTCG
* * *
5358434 AGAGAGACTACATTGATTATGCCAAAAAATGCCATAAATGTCAAATCTATGTAGACAAGATCAAT
129 AGAGAAACTACATTGATTATGCCAAAAAATGCCATAAATGTCAAATCTATGCAGAAAAGATCAAT
* *
5358499 ATCCCTCCAGCACCACTTCACGTCATGACGACCTCGTGGCCC-TCTCTATGTGGGGCATGGATGT
194 ATCCCTCCACCACCACTTCACGTCATGACGACCTCGTAGCCCTTCTCTATGTGGGGCATGGATGT
5358563 GCTATTC
259 GCTATTC
* *
5358570 AGATGCGTCGATGCTCTTGAAGCCAAAAGGATCCTAGAAGAAGTTC-AT-GGATTTACGGCATAT
1 AGATGCGTCGATGCTCTTGAAGCCAAAAGGATCCTAGAAGAAGTTCAATGGGATTTACGGCACAC
* *
5358633 ATGCTAATGGGTATCGGATAGCCAAGCAAATTATGAGAGCAAGTTATTACTGGTTGACCCTCGAG
66 ATGCTAATGGGCATCAGATAGCCAAGCAAATTATGAGAGCAAGTTATTACTGGTTGACCCTCGAG
* * *
5358698 AGAAATTGCATTGATTATGCCAAAAAATGCCATAAATGTCAAATCTATGCAGAAAAGATCAATGT
131 AGAAACTACATTGATTATGCCAAAAAATGCCATAAATGTCAAATCTATGCAGAAAAGATCAATAT
* * *
5358763 CCCTCCACCACCACTTCATGTCATGATGGCCTCGTAGCCCTTCTCTATGTGGGGCATGGATGTG
196 CCCTCCACCACCACTTCACGTCATGACGACCTCGTAGCCCTTCTCTATGTGGGGCATGGATGTG
5358827 ATCGGCCCAA
Statistics
Matches: 238, Mismatches: 18, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
262 167 0.70
263 25 0.11
266 46 0.19
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (265 bp):
AGATGCGTCGATGCTCTTGAAGCCAAAAGGATCCTAGAAGAAGTTCAATGGGATTTACGGCACAC
ATGCTAATGGGCATCAGATAGCCAAGCAAATTATGAGAGCAAGTTATTACTGGTTGACCCTCGAG
AGAAACTACATTGATTATGCCAAAAAATGCCATAAATGTCAAATCTATGCAGAAAAGATCAATAT
CCCTCCACCACCACTTCACGTCATGACGACCTCGTAGCCCTTCTCTATGTGGGGCATGGATGTGC
TATTC
Found at i:5361004 original size:26 final size:27
Alignment explanation
Indices: 5360929--5361005 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
5360919 TTTGCCATTT
*
5360929 GTCAAGAAATCGTTGTCAAGAAATTATC
1 GTCAAGAAA-CTTTGTCAAGAAATTATC
**
5360957 GTCAAG-AACTTTTGTTGA-AAATGT-TC
1 GTCAAGAAAC-TTTGTCAAGAAAT-TATC
5360983 GT-AAGAAACTTTGTCAAGAAATT
1 GTCAAGAAACTTTGTCAAGAAATT
5361006 TTTGTCAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
25 10 0.25
26 16 0.40
27 8 0.20
28 6 0.15
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (27 bp):
GTCAAGAAACTTTGTCAAGAAATTATC
Found at i:5361009 original size:14 final size:14
Alignment explanation
Indices: 5360926--5361013 Score: 58
Period size: 14 Copynumber: 6.6 Consensus size: 14
5360916 CAATTTGCCA
*
5360926 TTTGTCAAGAAATC
1 TTTGTCAAGAAATT
*
5360940 GTTGTCAAGAAATT
1 TTTGTCAAGAAATT
* * *
5360954 ATCGTCAAG-AACT
1 TTTGTCAAGAAATT
** *
5360967 TTTGTTGA-AAATG
1 TTTGTCAAGAAATT
* *
5360980 TTCGT-AAGAAA-C
1 TTTGTCAAGAAATT
5360992 TTTGTCAAGAAATT
1 TTTGTCAAGAAATT
5361006 TTTGTCAA
1 TTTGTCAA
5361014 TACGACCTCT
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
12 5 0.09
13 22 0.41
14 27 0.50
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (14 bp):
TTTGTCAAGAAATT
Found at i:5361096 original size:28 final size:27
Alignment explanation
Indices: 5361024--5361615 Score: 483
Period size: 28 Copynumber: 21.1 Consensus size: 27
5361014 TACGACCTCT
* * *
5361024 TTTCAAAGCCCACAAGTCAATGACAACATT
1 TTTCAAAGCCCACAAGTCAGTGGC-AC--C
* * *
5361054 TTTCAAAGCCTACAAGTCAATGGTATCC
1 TTTCAAAGCCCACAAGTCAGTGGCA-CC
*
5361082 TTTCAAAGCCCACAAGTCAGTAGCACC
1 TTTCAAAGCCCACAAGTCAGTGGCACC
5361109 ATTTTCAAAGCCCACAAGTCAGTGGCATCC
1 --TTTCAAAGCCCACAAGTCAGTGGCA-CC
* ** *
5361139 TTTCAAAGCCCTC-TTTCTAGTGCCACC
1 TTTCAAAGCCCACAAGTC-AGTGGCACC
*
5361166 TTTTCAAAGCCCACAAGTCAGTGGCATCT
1 -TTTCAAAGCCCACAAGTCAGTGGCA-CC
* * * *
5361195 TTTTAAAGCCCACAAGTTAGTAGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-C
* * * *
5361223 TTTCAAAACCCACAAGTCTGTGACACAT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-C
*
5361251 TTTCAAAACCCACAAGTCAGTGGCACC
1 TTTCAAAGCCCACAAGTCAGTGGCACC
5361278 TTTTCAAAGCCCACAAGTCAGTGGCATCC
1 -TTTCAAAGCCCACAAGTCAGTGGCA-CC
* *
5361307 GTTT-AAAGCCTACAAGTCAGTGGCACAT
1 -TTTCAAAGCCCACAAGTCAGTGGCAC-C
*
5361335 TTTCAAAGCCCACAAGTCAGTGGCATC
1 TTTCAAAGCCCACAAGTCAGTGGCACC
* * *
5361362 TTTCAAAGCCCATAAGTTAGTGGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-C
* *
5361390 TTTTAAAGCCCACAAGTTAGTGGCACC
1 TTTCAAAGCCCACAAGTCAGTGGCACC
* *
5361417 TTTCTCAAAGCTCATAAGTCAGTGGCATCC
1 -TT-TCAAAGCCCACAAGTCAGTGGCA-CC
*
5361447 TTTC-AAGGCCACAAGTCAGTGGCACC
1 TTTCAAAGCCCACAAGTCAGTGGCACC
* *
5361473 TACTCAAAGCCCACAAGTCAGTGGTATCC
1 T-TTCAAAGCCCACAAGTCAGTGGCA-CC
* * *
5361502 TTTCAAAACCTACAAGTTAGTGGCA-C
1 TTTCAAAGCCCACAAGTCAGTGGCACC
* * *
5361528 TTTCTTAAAGCTCATAAGTCAGTAGCATCC
1 TTTC--AAAGCCCACAAGTCAGTGGCA-CC
*** * * *
5361558 TTTCAAAGTTTA-AAGTCAATAGCACAT
1 TTTCAAAGCCCACAAGTCAGTGGCAC-C
*
5361585 TTTCAAAGCCCACAAGTCAATGGCAACC
1 TTTCAAAGCCCACAAGTCAGTGGC-ACC
5361613 TTT
1 TTT
5361616 TTCAAAGCTT
Statistics
Matches: 461, Mismatches: 74, Indels: 56
0.78 0.13 0.09
Matches are distributed among these distances:
26 9 0.02
27 73 0.16
28 289 0.63
29 59 0.13
30 31 0.07
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (27 bp):
TTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:5362107 original size:11 final size:12
Alignment explanation
Indices: 5362078--5362107 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
5362068 GACTTATTTG
5362078 AAAAAAATACAA
1 AAAAAAATACAA
5362090 AAAAAAATA-AA
1 AAAAAAATACAA
5362101 AAAAAAA
1 AAAAAAA
5362108 GAAGGGGTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAATACAA
Found at i:5362671 original size:20 final size:20
Alignment explanation
Indices: 5362618--5362675 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
5362608 TATTGCTACC
5362618 TTTTTCAATGTATCGATACA
1 TTTTTCAATGTATCGATACA
* * *
5362638 TGTATGAATGTATCGATACA
1 TTTTTCAATGTATCGATACA
*
5362658 TTTTTCAATATATCGATA
1 TTTTTCAATGTATCGATA
5362676 TATTCTGTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.43
Consensus pattern (20 bp):
TTTTTCAATGTATCGATACA
Found at i:5362703 original size:31 final size:32
Alignment explanation
Indices: 5362665--5362741 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
5362655 ACATTTTTCA
*
5362665 ATATATCGATATATTCTG-TTTTTTTACCCAG
1 ATATATCGATACATTCTGTTTTTTTTACCCAG
* *
5362696 ATGTATCGATACATTCTGTTTTTTTTACCTAG
1 ATATATCGATACATTCTGTTTTTTTTACCCAG
5362728 ATATATCGATACAT
1 ATATATCGATACAT
5362742 CAAAAAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
31 16 0.39
32 25 0.61
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (32 bp):
ATATATCGATACATTCTGTTTTTTTTACCCAG
Found at i:5368586 original size:39 final size:38
Alignment explanation
Indices: 5368520--5368603 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 38
5368510 CCGACAATTT
* *
5368520 TAAATATAATATAAAAATAATAAAAATATATTACAATATAA
1 TAAA-ATAATATAAAAACAATAAAAATACA-TA-AATATAA
*
5368561 -AAAATAATACT-AAAACAATATAAATACATAAATATAA
1 TAAAATAATA-TAAAAACAATAAAAATACATAAATATAA
5368598 TAAAAT
1 TAAAAT
5368604 CTACATAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
37 7 0.18
38 7 0.18
39 20 0.53
40 4 0.11
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (38 bp):
TAAAATAATATAAAAACAATAAAAATACATAAATATAA
Found at i:5368806 original size:2 final size:2
Alignment explanation
Indices: 5368799--5368833 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5368789 AAACAAAAAC
*
5368799 AT AT AT AT AT AT AT AT AA 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 A
5368834 AATTATTGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5369323 original size:40 final size:40
Alignment explanation
Indices: 5369300--5369386 Score: 174
Period size: 40 Copynumber: 2.2 Consensus size: 40
5369290 TTTTTATTAT
5369300 ATATTATGTAATTATATCATATAAAATTATATATAATTTA
1 ATATTATGTAATTATATCATATAAAATTATATATAATTTA
5369340 ATATTATGTAATTATATCATATAAAATTATATATAATTTA
1 ATATTATGTAATTATATCATATAAAATTATATATAATTTA
5369380 ATATTAT
1 ATATTAT
5369387 ATAACATTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (40 bp):
ATATTATGTAATTATATCATATAAAATTATATATAATTTA
Found at i:5369387 original size:15 final size:14
Alignment explanation
Indices: 5369295--5369390 Score: 55
Period size: 15 Copynumber: 7.1 Consensus size: 14
5369285 ATTTATTTTT
*
5369295 ATTATATATTATGTA
1 ATTA-ATATTATATA
*
5369310 ATT-ATATCATATA
1 ATTAATATTATATA
5369323 A--AAT-TATATATA
1 ATTAATAT-TATATA
*
5369335 ATTTAATATTATGTA
1 A-TTAATATTATATA
*
5369350 ATT-ATATCATATA
1 ATTAATATTATATA
5369363 A--AAT-TATATATA
1 ATTAATAT-TATATA
5369375 ATTTAATATTATATA
1 A-TTAATATTATATA
5369390 A
1 A
5369391 CATTAAAAAT
Statistics
Matches: 62, Mismatches: 7, Indels: 24
0.67 0.08 0.26
Matches are distributed among these distances:
11 2 0.03
12 16 0.26
13 18 0.29
14 2 0.03
15 22 0.35
16 2 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTAATATTATATA
Found at i:5369581 original size:16 final size:16
Alignment explanation
Indices: 5369538--5369592 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5369528 TTATTTATTA
*
5369538 ATAAATATAAATAAAT
1 ATAAATTTAAATAAAT
* *
5369554 TTATATTTTAAATTAAAT
1 ATA-AATTTAAA-TAAAT
5369572 -TAAATTTAAATAAAT
1 ATAAATTTAAATAAAT
5369587 ATAAAT
1 ATAAAT
5369593 AATATTAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
15 5 0.16
16 14 0.44
17 8 0.25
18 5 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAATTTAAATAAAT
Found at i:5369950 original size:4 final size:4
Alignment explanation
Indices: 5369807--5369996 Score: 200
Period size: 4 Copynumber: 47.5 Consensus size: 4
5369797 ACATACATAC
* * * * *
5369807 ATAT ATAT ATAT ATAT ACAT ACAT ACAT ATAT ATAT ATAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * * * *
5369855 ACAT ACAT ATAT ACAT ATAT ATAT ATAT ATAC ATAC ATAT ACAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * * * *
5369903 ACAT ATAT ATAC ATAC ATAT ATAT ATAT ATAC ATAT ATAC ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
5369951 AGAT ACAT ATAT ATAT ATAT ATAT GTAT ATAT ATAT ATAT ATAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
5369997 CTTCACATAC
Statistics
Matches: 165, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 165 1.00
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.40
Consensus pattern (4 bp):
ATAT
Found at i:5369994 original size:28 final size:28
Alignment explanation
Indices: 5369807--5369996 Score: 227
Period size: 28 Copynumber: 6.7 Consensus size: 28
5369797 ACATACATAC
* *
5369807 ATATATATATATATATACATACATACAT
1 ATATATATATATATATATATACATATAT
* *
5369835 ATATATATATATACATACATACATACATAT
1 ATATATATATATATATATATACAT--ATAT
* *
5369865 ATACATATATATATATATATACATACAT
1 ATATATATATATATATATATACATATAT
* * * *
5369893 ATACATACATACATATATATACATACAT
1 ATATATATATATATATATATACATATAT
*
5369921 ATATATATATATACATATATACATATAT
1 ATATATATATATATATATATACATATAT
* * * *
5369949 ATAGATACATATATATATATATATATGT
1 ATATATATATATATATATATACATATAT
5369977 ATATATATATATATATATAT
1 ATATATATATATATATATAT
5369997 CTTCACATAC
Statistics
Matches: 140, Mismatches: 20, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
28 116 0.83
30 24 0.17
ACGTcount: A:0.49, C:0.09, G:0.01, T:0.40
Consensus pattern (28 bp):
ATATATATATATATATATATACATATAT
Found at i:5371321 original size:167 final size:168
Alignment explanation
Indices: 5371030--5371350 Score: 536
Period size: 167 Copynumber: 1.9 Consensus size: 168
5371020 TCTTTCAAAA
* * *
5371030 AATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAAACTGTTCATTCATAATTCTTTGTCA
1 AATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAAACTGTTCATTCAGAATTCCTTCTCA
*
5371095 AATGTCAACACCAAATTTAGTAAAGTCTTGAATTGTTCATTACTCTTCCATTCCAAATAAAGATA
66 AATGTCAACACCAAATTTAGTAAAGCCTTGAATTGTTCATTACTCTTCCATTCCAAATAAAGATA
5371160 AAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
131 AAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
* * * * *
5371198 AATTAAAACTGACA-AAGTTAATGTTAAACTTTTTGTGAAACTGTTCATTTAGAATTCCTTCTCA
1 AATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAAACTGTTCATTCAGAATTCCTTCTCA
* *
5371262 AATGTCAACACCAAGTTTAGTAAAGCCTTGAATTGTTCATTACTCTTTCATTCCAAATAAAGATA
66 AATGTCAACACCAAATTTAGTAAAGCCTTGAATTGTTCATTACTCTTCCATTCCAAATAAAGATA
5371327 AAATATTTTGTTTTTGGTTTTTTA
131 AAATATTTTGTTTTTGGTTTTTTA
5371351 TATTAATCAG
Statistics
Matches: 142, Mismatches: 11, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
167 129 0.91
168 13 0.09
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (168 bp):
AATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAAACTGTTCATTCAGAATTCCTTCTCA
AATGTCAACACCAAATTTAGTAAAGCCTTGAATTGTTCATTACTCTTCCATTCCAAATAAAGATA
AAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
Found at i:5371620 original size:449 final size:451
Alignment explanation
Indices: 5370745--5371648 Score: 1294
Period size: 449 Copynumber: 2.0 Consensus size: 451
5370735 TCTTTTAAAA
* * * *
5370745 AATTAAAATTGACATAAATTAATTTTAAATTCTCTGTGAAAATGTTCATTTAGAATTTCTTGTCA
1 AATTAAAACTGACATAAATTAATGTTAAATTCTCTGTGAAAATGTTCATTTAGAATTCCTTCTCA
* *
5370810 AATGTAAACACCAACTTTTGTAAAGTCTTGAATTATTCATTACTCTTTCACTCCAAATAAAGATA
66 AATGTAAACACCAACTTTAGTAAAGCCTTGAATTATTCATTACTCTTTCACTCCAAATAAAGATA
*
5370875 AAATATTTTATATTTGGTTTTTGATATTAGTTATCAACAAAGCAAATCAAGTCTTAAACTTTATA
131 AAATATTTTATATTTGGTTTTTGATATTA--TATCAACAAAGCAAATCAAGTCTTAAACTCTATA
* * * *
5370940 AAAAAGATATCAAATTCGATCATTTTTTAAGCCTTGAAAAAAATTGTCAAACCTTTTAAGAGTAT
194 AAAAAGATATCAAATTCAATCACTTTTTAAGCCTTGAAAAAAATTGCCAAACCTTTTAAGAGCAT
*
5371005 TTGTCTATCATTAGTTCTTTCAAAAAATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAA
259 TTGTCTATCATTAGTCCTTTCAAAAAATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAA
* * * *
5371070 ACTGTTCATTCATAATTCTTTGTCAAATGTCAACACCAAATTTAGTAAAGTCTTGAATTGTTCAT
324 ACTGTTCATTCAGAATTCTTTGTCAAATGTCAACACCAAATTTAGTAAAGCCATAAATTGTTCAT
5371135 TACTCTTCCATTCCAAATAAAGATAAAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
389 TACTCTTCCATTCCAAATAAAGATAAAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
* * *
5371198 AATTAAAACTGACA-AAGTTAATGTTAAACTT-TTTGTGAAACTGTTCATTTAGAATTCCTTCTC
1 AATTAAAACTGACATAAATTAATGTTAAA-TTCTCTGTGAAAATGTTCATTTAGAATTCCTTCTC
* * * *
5371261 AAATGTCAACACCAAGTTTAGTAAAGCCTTGAATTGTTCATTACTCTTTCATTCCAAATAAAGAT
65 AAATGTAAACACCAACTTTAGTAAAGCCTTGAATTATTCATTACTCTTTCACTCCAAATAAAGAT
* * * * * * *
5371326 AAAATATTTTGTTTTTGGTTTTTTATATTA-ATCAGCAAAGCAAATTAGGTCTTAAACTCTATGA
130 AAAATATTTTATATTTGGTTTTTGATATTATATCAACAAAGCAAATCAAGTCTTAAACTCTATAA
* * * *
5371390 AAAAGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAATTGCCAAACCTTTTAAGAGCGTT
195 AAAAGATATCAAATTCAATCACTTTTTAAGCCTTGAAAAAAATTGCCAAACCTTTTAAGAGCATT
* * * * * * * *
5371455 TGTCTGTCGTTAGTCCTTT-AAAGAAATTAAAATTGACACAAGTTAATATTAGATTTTTTGTGAA
260 TGTCTATCATTAGTCCTTTCAAA-AAATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAA
* * * *
5371519 ATTGTTTATTTAGAATTCTTTGTCAAATGTCAACACCAATTTTAGTAAAGCCATAAATTGTTCAT
324 ACTGTTCATTCAGAATTCTTTGTCAAATGTCAACACCAAATTTAGTAAAGCCATAAATTGTTCAT
* * * *
5371584 TACTCTTCCATTTCAAATAAAGATAAAATATTTTGTTTTTGGTTTTTTATATTAGTTATTAGC
389 TACTCTTCCATTCCAAATAAAGATAAAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
5371647 AA
1 AA
5371649 AGCAAATTAG
Statistics
Matches: 399, Mismatches: 50, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
448 3 0.01
449 255 0.64
452 126 0.32
453 15 0.04
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.40
Consensus pattern (451 bp):
AATTAAAACTGACATAAATTAATGTTAAATTCTCTGTGAAAATGTTCATTTAGAATTCCTTCTCA
AATGTAAACACCAACTTTAGTAAAGCCTTGAATTATTCATTACTCTTTCACTCCAAATAAAGATA
AAATATTTTATATTTGGTTTTTGATATTATATCAACAAAGCAAATCAAGTCTTAAACTCTATAAA
AAAGATATCAAATTCAATCACTTTTTAAGCCTTGAAAAAAATTGCCAAACCTTTTAAGAGCATTT
GTCTATCATTAGTCCTTTCAAAAAATTAAAACTAACACAAGTTAATATTAAACTTCTTGTAAAAC
TGTTCATTCAGAATTCTTTGTCAAATGTCAACACCAAATTTAGTAAAGCCATAAATTGTTCATTA
CTCTTCCATTCCAAATAAAGATAAAATATTTTGTTTTTGGTTTTTTAGACTAGTTATCAGC
Found at i:5371823 original size:285 final size:283
Alignment explanation
Indices: 5371202--5371930 Score: 1079
Period size: 285 Copynumber: 2.6 Consensus size: 283
5371192 ATCAGCAATT
* * *
5371202 AAAACTG-ACAAAGTTAATGTTAAACTTTTTGTGAAACTGTTCATTTAGAATTCCTTCTCAAATG
1 AAAACTGCACAAA-TTAATGTTAGACTTTTTGTGAAACTGTTCATTTAGAATTCTTTGTCAAATG
* *
5371266 TCAACACCAAGTTTAGTAAAGCCTTGAATTGTTCATTACTCTTTCATTCCAAATAAAGATAAAAT
65 TCAACACCAACTTTAGTAAAGCC-TGAATTGTTCATTACTCTTCCATTCCAAATAAAGATAAAAT
5371331 ATTTTGTTTTTGGTTTTTTATATTA---ATCAGCAAAGCAAATTAGGTCTTAAACTCTATGAAAA
129 ATTTTGTTTTTGGTTTTTTATATTAGTTATCAGCAAAGCAAATTAGGTCTTAAACTCTATGAAAA
5371393 AGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAATTGCCAAACCTTTTAAGAGCGTTTGT
194 AGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAATTGCCAAACCTTTTAAGAGCGTTTGT
* * * *
5371458 CTGTCGTTAGTCCTTTAAAGAAATT
259 CTATCATTAGTCATTTAAAGAAATA
* * * * * *
5371483 AAAATTGACACAAGTTAATATTAGATTTTTTGTGAAATTGTTTATTTAGAATTCTTTGTCAAATG
1 AAAACTG-CACAAATTAATGTTAGACTTTTTGTGAAACTGTTCATTTAGAATTCTTTGTCAAATG
* * *
5371548 TCAACACCAATTTTAGTAAAGCCATAAATTGTTCATTACTCTTCCATTTCAAATAAAGATAAAAT
65 TCAACACCAACTTTAGTAAAGCC-TGAATTGTTCATTACTCTTCCATTCCAAATAAAGATAAAAT
*
5371613 ATTTTGTTTTTGGTTTTTTATATTAGTTATTAGCAAAGCAAATTAGGTCTTAAACTCTATGAAAA
129 ATTTTGTTTTTGGTTTTTTATATTAGTTATCAGCAAAGCAAATTAGGTCTTAAACTCTATGAAAA
* * *
5371678 AGATATCAAGTTCAATCACTTTTTAGGCTTTGGAAACAATTGCCAAACCTTTTAAGAGTGTTTGT
194 AGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAATTGCCAAACCTTTTAAGAGCGTTTGT
* *
5371743 CTATCATTAGTTATTTCAAGAAATA
259 CTATCATTAGTCATTTAAAGAAATA
* * * * *
5371768 AAAACTAGCACAAATTAATGTTAGACTTGTTGTAAAACTATTCATTCAAAATTCTTTGTCAAATG
1 AAAACT-GCACAAATTAATGTTAGACTTTTTGTGAAACTGTTCATTTAGAATTCTTTGTCAAATG
* * *
5371833 TCAACACCAACTTTAGTAAAGCCTGAATTATTCATTACTTTTCCATTCCAAATAAAGGTAAAATA
65 TCAACACCAACTTTAGTAAAGCCTGAATTGTTCATTACTCTTCCATTCCAAATAAAGATAAAATA
* *
5371898 TTTTATTTTTAGTTTTTTATATTAGTTATCAGC
130 TTTTGTTTTTGGTTTTTTATATTAGTTATCAGC
5371931 CATTAAAATT
Statistics
Matches: 398, Mismatches: 44, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
281 6 0.02
282 129 0.32
283 4 0.01
284 67 0.17
285 191 0.48
286 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (283 bp):
AAAACTGCACAAATTAATGTTAGACTTTTTGTGAAACTGTTCATTTAGAATTCTTTGTCAAATGT
CAACACCAACTTTAGTAAAGCCTGAATTGTTCATTACTCTTCCATTCCAAATAAAGATAAAATAT
TTTGTTTTTGGTTTTTTATATTAGTTATCAGCAAAGCAAATTAGGTCTTAAACTCTATGAAAAAG
ATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAATTGCCAAACCTTTTAAGAGCGTTTGTCT
ATCATTAGTCATTTAAAGAAATA
Found at i:5372072 original size:451 final size:445
Alignment explanation
Indices: 5371480--5372296 Score: 1186
Period size: 451 Copynumber: 1.8 Consensus size: 445
5371470 CTTTAAAGAA
* * * * * *
5371480 ATTAAAATTGACACAAGTTAATATTAGATTTTTTGTGAAATTGTTTATTTAGAATTCTTTGTCAA
1 ATTAAAATTGACACAAGTTAATATTAGACTTGTTGTAAAACTGTTCATTTAGAATTCCTTGTCAA
* * *
5371545 ATGTCAACACCAATTTTAGTAAAGCCATAAATTGTTCATTACTCTTCCATTTCAAATAAAGATAA
66 ATATCAACACCAACTTTAGTAAAGCCATAAATTGTTCATTACTCTTCCATTCCAAATAAAGATAA
** * *
5371610 AATATTTTGTTTTTGGTTTTTTATATTAGTTATTAGCAAAGCAAATTAGGTCTTAAACTCTATGA
131 AATATTTTGTTTTTAATTTTTTATATTAATTATTAGCAAAGCAAATTAAGTCTTAAACTCTATGA
* * * ** **
5371675 AAAAGATATCAAGTTCAATCACTTTTTAGGCTTTGGAAACAATTGCCAAACCTTTTAAGAGTGTT
196 AAAAGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAAGTG-------TTAAAAGAACGTT
* * * * *
5371740 TGTCTATCATTAGTTATTTCAAGAAATAAAAACTAGCACAAATTAATGTTAGACTTGTTGTAAAA
254 TGTCTAACATTAGTTATTTAAAAAAATAAAAACTAACACAAATTAATATTAGACTTGTTGTAAAA
*
5371805 CTATTCATTCAAAATTCTTTGTCAAATGTCAACACCAACTTTAGTAAAGCCTGAATTATTCATTA
319 CTATTCATTCAAAATTCCTTGTCAAATGTCAACACCAACTTTAGTAAAGCCTGAATTATTCATTA
5371870 CTTTTCCATTCCAAATAAAGGTAAAATATTTTATTTTTAGTTTTTTATATTAGTTATCAGCC
384 CTTTTCCATTCCAAATAAAGGTAAAATATTTTATTTTTAGTTTTTTATATTAGTTATCAGCC
*
5371932 ATTAAAATTGACA-AAGTTAATGTTAGACTTGTTGTAAAACTGTTCATTTAGAATTCCTTGTCAA
1 ATTAAAATTGACACAAGTTAATATTAGACTTGTTGTAAAACTGTTCATTTAGAATTCCTTGTCAA
* * * * *
5371996 ATATCAACACCAACTTTAGTAAAGTCTTGAATTGTTTATTACTTTTCCATTCCAAATAAAGATAA
66 ATATCAACACCAACTTTAGTAAAGCCATAAATTGTTCATTACTCTTCCATTCCAAATAAAGATAA
5372061 AATATTTTGTTTTTAATTTTTTATATTAATTATTAGCAAAGCAAATTAAGTCTTAAACTCTATGA
131 AATATTTTGTTTTTAATTTTTTATATTAATTATTAGCAAAGCAAATTAAGTCTTAAACTCTATGA
5372126 AAAAGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAAGTGTTAAAAGAACGTTTGTCTAA
196 AAAAGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAAGTGTTAAAAGAACGTTTGTCTAA
* * * * * * *
5372191 CGTTAGTTATTTAAAAAAATTAAAATTAACACAAGTTAATATTAGATTTTTTGTAAAATTATTCA
261 CATTAGTTATTTAAAAAAATAAAAACTAACACAAATTAATATTAGACTTGTTGTAAAACTATTCA
* * *
5372256 TTCAGAATTCCTTGTTAAATGTTAACACCAACTTTAGTAAA
326 TTCAAAATTCCTTGTCAAATGTCAACACCAACTTTAGTAAA
5372297 ACCATAAATT
Statistics
Matches: 323, Mismatches: 42, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
444 106 0.33
451 204 0.63
452 13 0.04
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (445 bp):
ATTAAAATTGACACAAGTTAATATTAGACTTGTTGTAAAACTGTTCATTTAGAATTCCTTGTCAA
ATATCAACACCAACTTTAGTAAAGCCATAAATTGTTCATTACTCTTCCATTCCAAATAAAGATAA
AATATTTTGTTTTTAATTTTTTATATTAATTATTAGCAAAGCAAATTAAGTCTTAAACTCTATGA
AAAAGATATCAAGTTCAATCACTTTTTAAGCCTTGGAAACAAGTGTTAAAAGAACGTTTGTCTAA
CATTAGTTATTTAAAAAAATAAAAACTAACACAAATTAATATTAGACTTGTTGTAAAACTATTCA
TTCAAAATTCCTTGTCAAATGTCAACACCAACTTTAGTAAAGCCTGAATTATTCATTACTTTTCC
ATTCCAAATAAAGGTAAAATATTTTATTTTTAGTTTTTTATATTAGTTATCAGCC
Found at i:5376169 original size:26 final size:26
Alignment explanation
Indices: 5376123--5376185 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
5376113 TCGGAAATAT
*
5376123 AATATAAAAAAATTAACATATAAAAA
1 AATATAAAATAATTAACATATAAAAA
*
5376149 AATATAAAATAATATAA-ATATATAAA
1 AATATAAAATAAT-TAACATATAAAAA
*
5376175 TATATCAAAAT
1 AATAT-AAAAT
5376186 TTATATAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 24 0.75
27 8 0.25
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (26 bp):
AATATAAAATAATTAACATATAAAAA
Found at i:5378638 original size:2 final size:2
Alignment explanation
Indices: 5378633--5378661 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5378623 TGTGTGTGTC
5378633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5378662 CCACATGTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5381935 original size:2 final size:2
Alignment explanation
Indices: 5381930--5381959 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5381920 ACAAAGAGGA
*
5381930 AG AG AG AG AG AG AG AG AG AG AA AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5381960 GGAGCTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5381939 original size:12 final size:12
Alignment explanation
Indices: 5381901--5381959 Score: 52
Period size: 12 Copynumber: 5.1 Consensus size: 12
5381891 AACATAACAT
*
5381901 GAGGAAGAGTGA
1 GAGGAAGAGAGA
* *
5381913 GA-GACAGACAAA
1 GAGGA-AGAGAGA
5381925 GAGGAAGAGAGA
1 GAGGAAGAGAGA
5381937 GA-G-AGAGAGA
1 GAGGAAGAGAGA
*
5381947 GAGAAAGAGAGA
1 GAGGAAGAGAGA
5381959 G
1 G
5381960 GGAGCTTAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 8
0.73 0.12 0.16
Matches are distributed among these distances:
10 9 0.24
11 3 0.08
12 23 0.62
13 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.44, T:0.02
Consensus pattern (12 bp):
GAGGAAGAGAGA
Found at i:5382365 original size:18 final size:18
Alignment explanation
Indices: 5382331--5382365 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5382321 AATTAAAAAG
* *
5382331 TTAAAAATAATTTTTTAT
1 TTAAAAATAAGTATTTAT
5382349 TTAAAAATAAGTATTTA
1 TTAAAAATAAGTATTTA
5382366 AATTCTCAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (18 bp):
TTAAAAATAAGTATTTAT
Found at i:5383453 original size:5 final size:5
Alignment explanation
Indices: 5383439--5383468 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
5383429 TTAATCATGC
5383439 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
5383469 AATCTTCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:5384288 original size:2 final size:2
Alignment explanation
Indices: 5384283--5384312 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5384273 AAAATGTAGA
5384283 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
5384313 TTGTAAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5384876 original size:21 final size:21
Alignment explanation
Indices: 5384836--5384876 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5384826 CAATCGATTA
* *
5384836 AAATTAAATTAACAAGAAATC
1 AAATTAAATCAACAAAAAATC
*
5384857 AAATTAAATCAATAAAAAAT
1 AAATTAAATCAACAAAAAAT
5384877 TAATTTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.66, C:0.07, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATTAAATCAACAAAAAATC
Found at i:5387362 original size:23 final size:23
Alignment explanation
Indices: 5387305--5387362 Score: 64
Period size: 28 Copynumber: 2.3 Consensus size: 23
5387295 TTGATTACAT
5387305 ATTAA-AATAATATCTTAAATAA
1 ATTAATAATAATATCTTAAATAA
5387327 ATTAAATATATAATAATATCTTAAATAA
1 A-T---TA-ATAATAATATCTTAAATAA
5387355 ATTAATAA
1 ATTAATAA
5387363 AATGTTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
22 1 0.03
23 5 0.17
24 2 0.07
26 2 0.07
27 2 0.07
28 18 0.60
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (23 bp):
ATTAATAATAATATCTTAAATAA
Found at i:5388480 original size:17 final size:18
Alignment explanation
Indices: 5388448--5388482 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
5388438 AGTCATTATT
5388448 TTAAAAGCATATTTTTGAA
1 TTAAAAGCA-ATTTTTGAA
5388467 TTAAAAGC-ATTTTTGA
1 TTAAAAGCAATTTTTGA
5388483 GATCTTCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (18 bp):
TTAAAAGCAATTTTTGAA
Found at i:5393217 original size:28 final size:28
Alignment explanation
Indices: 5393162--5393219 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
5393152 CTTTCGGTAT
* *
5393162 ATTTTTTTTCTTTTCTTTTCTTTTTTGA
1 ATTTTTTTTCTTTTCTTTACTTTCTTGA
*
5393190 ATTTATTTTTCTTTT-TTTAGTTTCTTGA
1 ATTT-TTTTTCTTTTCTTTACTTTCTTGA
5393218 AT
1 AT
5393220 ATTGTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 16 0.62
29 10 0.38
ACGTcount: A:0.12, C:0.09, G:0.05, T:0.74
Consensus pattern (28 bp):
ATTTTTTTTCTTTTCTTTACTTTCTTGA
Found at i:5402654 original size:19 final size:22
Alignment explanation
Indices: 5402613--5402659 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 22
5402603 TTAATTTTAA
5402613 AAAATAAATTTAAATAAATTTTT
1 AAAATAAA-TTAAATAAATTTTT
5402636 AAAATAAA-TAAA-AAA-TTTT
1 AAAATAAATTAAATAAATTTTT
5402655 AAAAT
1 AAAAT
5402660 CGAATCAGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 4 0.17
23 8 0.33
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAATAAATTAAATAAATTTTT
Found at i:5406976 original size:35 final size:35
Alignment explanation
Indices: 5406908--5406979 Score: 90
Period size: 35 Copynumber: 2.1 Consensus size: 35
5406898 TTTATTTTTT
* ** * *
5406908 GAAAAAATGAATTTATATTTGATGTATTGACAGTA
1 GAAAAAATGAATTTATATTTAACATACTAACAGTA
*
5406943 GAAAAAATGGATTTATATTTAACATACTAACAGTA
1 GAAAAAATGAATTTATATTTAACATACTAACAGTA
5406978 GA
1 GA
5406980 CCTGTTCATG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.46, C:0.06, G:0.15, T:0.33
Consensus pattern (35 bp):
GAAAAAATGAATTTATATTTAACATACTAACAGTA
Found at i:5408559 original size:38 final size:38
Alignment explanation
Indices: 5408508--5408585 Score: 156
Period size: 38 Copynumber: 2.1 Consensus size: 38
5408498 TTTCAAACAG
5408508 GCGGGACTACAGCATATACGACATAGTTTCGCTCTTAA
1 GCGGGACTACAGCATATACGACATAGTTTCGCTCTTAA
5408546 GCGGGACTACAGCATATACGACATAGTTTCGCTCTTAA
1 GCGGGACTACAGCATATACGACATAGTTTCGCTCTTAA
5408584 GC
1 GC
5408586 CTGCCTCACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (38 bp):
GCGGGACTACAGCATATACGACATAGTTTCGCTCTTAA
Found at i:5414723 original size:13 final size:13
Alignment explanation
Indices: 5414705--5414729 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5414695 CATAAAGTGT
5414705 TGTATCGATACAA
1 TGTATCGATACAA
5414718 TGTATCGATACA
1 TGTATCGATACA
5414730 TATTTTTTTA
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
Done.