Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr3
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: 42799318
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 891409 characters in sequence are not A, C, G, or T
File 135 of 141
Found at i:40463772 original size:22 final size:23
Alignment explanation
Indices: 40463719--40463809 Score: 69
Period size: 27 Copynumber: 3.7 Consensus size: 23
40463709 AAATAAAATT
*
40463719 TAAATATTAAATAATTTAATTAAAAA
1 TAAAAATTAAATAATTT-ATT--AAA
40463745 TTAAAAATTAAATAATTTATTAAA
1 -TAAAAATTAAATAATTTATTAAA
* *
40463769 -AAAAA-TAAATTATATTATTATA
1 TAAAAATTAAATAAT-TTATTAAA
40463791 TAACTAAATATAAATAATT
1 TAA--AAAT-TAAATAATT
40463810 AAATACGTAT
Statistics
Matches: 54, Mismatches: 4, Indels: 13
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.13
22 12 0.22
23 2 0.04
24 3 0.06
25 3 0.06
26 4 0.07
27 23 0.43
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAAAATTAAATAATTTATTAAA
Found at i:40463772 original size:28 final size:27
Alignment explanation
Indices: 40463712--40463770 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
40463702 ACTATTAAAA
* *
40463712 TAAAATTTAAATATTAAATAATTTAAT
1 TAAAAATTAAAAATTAAATAATTTAAT
40463739 TAAAAATTAAAAATTAAATAATTT-AT
1 TAAAAATTAAAAATTAAATAATTTAAT
40463765 TAAAAA
1 TAAAAA
40463771 AAATAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 8 0.27
27 22 0.73
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
TAAAAATTAAAAATTAAATAATTTAAT
Found at i:40463778 original size:26 final size:27
Alignment explanation
Indices: 40463724--40463780 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 27
40463714 AAATTTAAAT
*
40463724 ATTAAATAATTTAATTAAAAATTAAAA
1 ATTAAATAATTTAATTAAAAATAAAAA
40463751 ATTAAATAATTT-ATTAAAAA-AAATAA
1 ATTAAATAATTTAATTAAAAATAAA-AA
40463777 ATTA
1 ATTA
40463781 TATTATTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 2 0.07
26 14 0.50
27 12 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
ATTAAATAATTTAATTAAAAATAAAAA
Found at i:40463785 original size:19 final size:18
Alignment explanation
Indices: 40463744--40463781 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
40463734 TTAATTAAAA
40463744 ATTAAAAATTAAATAATTT
1 ATTAAAAA-TAAATAATTT
*
40463763 ATTAAAAA-AAATAAATT
1 ATTAAAAATAAATAATTT
40463780 AT
1 AT
40463782 ATTATTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 10 0.56
19 8 0.44
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTAAAAATAAATAATTT
Found at i:40466600 original size:18 final size:17
Alignment explanation
Indices: 40466570--40466605 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
40466560 TTCATGTTAT
40466570 TATTTATTTATTTTAAA
1 TATTTATTTATTTTAAA
40466587 TATTTATGTTATTTTAAA
1 TATTTAT-TTATTTTAAA
40466605 T
1 T
40466606 TAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.39
18 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTTATTTATTTTAAA
Found at i:40467309 original size:9 final size:10
Alignment explanation
Indices: 40467263--40467309 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
40467253 GAAAATTTTT
40467263 AATTTTTTA-
1 AATTTTTTAG
* *
40467272 ACTTTCTTTAT
1 AATTT-TTTAG
40467283 ACATTTTTTAG
1 A-ATTTTTTAG
40467294 AATTTTTTAG
1 AATTTTTTAG
40467304 AATTTT
1 AATTTT
40467310 ATTAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 4 0.12
10 19 0.59
11 6 0.19
12 3 0.09
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (10 bp):
AATTTTTTAG
Found at i:40476077 original size:3 final size:3
Alignment explanation
Indices: 40476069--40476156 Score: 158
Period size: 3 Copynumber: 29.3 Consensus size: 3
40476059 AAAAGATATT
*
40476069 TTC TTC TTC TTC TTC TTC TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
40476117 TTC TTC CTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
40476157 GTGTTTGATG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:40481614 original size:39 final size:39
Alignment explanation
Indices: 40481570--40481648 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
40481560 CCATTTGCCT
40481570 ATAAATACACACAGATTCAATATAGCAATCGAAAATTAA
1 ATAAATACACACAGATTCAATATAGCAATCGAAAATTAA
40481609 ATAAATACACACAGATTCAATATAGCAATCGAAAATTAA
1 ATAAATACACACAGATTCAATATAGCAATCGAAAATTAA
40481648 A
1 A
40481649 ATGGGTAACG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (39 bp):
ATAAATACACACAGATTCAATATAGCAATCGAAAATTAA
Found at i:40482765 original size:6 final size:7
Alignment explanation
Indices: 40482748--40482774 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
40482738 TTGGTAACCC
40482748 AAAAAAT
1 AAAAAAT
40482755 AAAAAAT
1 AAAAAAT
40482762 AAAAAAT
1 AAAAAAT
40482769 AAAAAA
1 AAAAAA
40482775 GAGGACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:40483491 original size:15 final size:15
Alignment explanation
Indices: 40483471--40483522 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
40483461 ACTACAAAAC
40483471 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
40483486 ATTTATAATTTTAATAAAT
1 ATTTAT--TATTAAT--AT
*
40483505 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
40483520 ATT
1 ATT
40483523 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 11 0.37
17 11 0.37
19 8 0.27
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:40483587 original size:16 final size:16
Alignment explanation
Indices: 40483556--40483592 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
40483546 ATGTGAATAA
40483556 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
40483572 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
40483588 TATTA
1 TATTA
40483593 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:40483659 original size:22 final size:22
Alignment explanation
Indices: 40483604--40483645 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
40483594 AATAAAATTG
*
40483604 AAATATTAAA-TA-ATTTATTA
1 AAATAATAAATTATATTTATTA
40483624 AAATAATAAATTATATTTATTA
1 AAATAATAAATTATATTTATTA
40483646 TATTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AAATAATAAATTATATTTATTA
Found at i:40484307 original size:14 final size:14
Alignment explanation
Indices: 40484272--40484299 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40484262 TGATAAATTA
40484272 AAAAATAAGTGTTG
1 AAAAATAAGTGTTG
40484286 AAAAATAAGTGTTG
1 AAAAATAAGTGTTG
40484300 TTATATAATA
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:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (14 bp):
AAAAATAAGTGTTG
Found at i:40493736 original size:12 final size:13
Alignment explanation
Indices: 40493718--40493759 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
40493708 AGGAAAGATT
40493718 TAATAATAATATA
1 TAATAATAATATA
40493731 -AATAATAACATATA
1 TAATAAT-A-ATATA
40493745 TACATAATAATATA
1 TA-ATAATAATATA
40493759 T
1 T
40493760 TAAAGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.24
13 1 0.04
14 11 0.44
15 2 0.08
16 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:40493751 original size:16 final size:16
Alignment explanation
Indices: 40493726--40493763 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40493716 TTTAATAATA
40493726 ATATAAATAATAACAT
1 ATATAAATAATAACAT
* *
40493742 ATATACATAATAATAT
1 ATATAAATAATAACAT
40493758 AT-TAAA
1 ATATAAA
40493764 GTTGAAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATAATAACAT
Found at i:40494012 original size:16 final size:16
Alignment explanation
Indices: 40493967--40494013 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
40493957 TTAAAATAAT
40493967 ATTATATAATAAAATA
1 ATTATATAATAAAATA
*
40493983 ATGCATATACATAAAA-A
1 AT-TATATA-ATAAAATA
40494000 ATTATATAGATAAA
1 ATTATATA-ATAAA
40494014 TATATGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 12 0.46
17 8 0.31
18 6 0.23
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (16 bp):
ATTATATAATAAAATA
Found at i:40494047 original size:3 final size:3
Alignment explanation
Indices: 40494030--40494100 Score: 88
Period size: 3 Copynumber: 23.7 Consensus size: 3
40494020 AACTAATATA
* * * * * *
40494030 AAT AAT AAC ACT AAT AAT AAT AGT AGT AGT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40494078 AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
40494101 ATTAATATTA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:40494112 original size:11 final size:11
Alignment explanation
Indices: 40494030--40494117 Score: 53
Period size: 9 Copynumber: 8.3 Consensus size: 11
40494020 AACTAATATA
*
40494030 AATAATAACACT
1 AATAATAA-AGT
40494042 AATAATAATAGT
1 AATAATAA-AGT
* *
40494054 AGTAGT--AGT
1 AATAATAAAGT
40494063 AATAAT-AA-T
1 AATAATAAAGT
40494072 AATAAT-AA-T
1 AATAATAAAGT
*
40494081 AATAATAATAAT
1 AATAATAA-AGT
*
40494093 AATAATAAATT
1 AATAATAAAGT
*
40494104 AATATTAAAGT
1 AATAATAAAGT
40494115 AAT
1 AAT
40494118 TATTTTAGTA
Statistics
Matches: 63, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
9 23 0.37
10 2 0.03
11 15 0.24
12 23 0.37
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (11 bp):
AATAATAAAGT
Found at i:40495588 original size:50 final size:49
Alignment explanation
Indices: 40495534--40495694 Score: 153
Period size: 50 Copynumber: 3.2 Consensus size: 49
40495524 ATGATGTCGA
40495534 GGAAGCAAGATTCACTGTTGTGGCTTCAATCTTTTCCACTGCACCGCCTG
1 GGAAGCAAGATTCACTGTTGTGGCTT-AATCTTTTCCACTGCACCGCCTG
* * * * ** * *
40495584 GGAAGTAAGATTCACTGTTGTAGCTTTAATCCTTTT-AACTACAATGTCAG
1 GGAAGCAAGATTCACTGTTGTGGC-TTAAT-CTTTTCCACTGCACCGCCTG
** * *
40495634 GGAAGCAAGATTCACCATTGTGGCGTTAATCTGTTCCACTGCACCGCTTG
1 GGAAGCAAGATTCACTGTTGTGGC-TTAATCTTTTCCACTGCACCGCCTG
* *
40495684 AGAAGTAAGAT
1 GGAAGCAAGAT
40495695 CTGTAATTAT
Statistics
Matches: 85, Mismatches: 23, Indels: 6
0.75 0.20 0.05
Matches are distributed among these distances:
49 4 0.05
50 74 0.87
51 7 0.08
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (49 bp):
GGAAGCAAGATTCACTGTTGTGGCTTAATCTTTTCCACTGCACCGCCTG
Found at i:40495912 original size:44 final size:44
Alignment explanation
Indices: 40495792--40495914 Score: 158
Period size: 44 Copynumber: 2.8 Consensus size: 44
40495782 CCTTTATTTT
* * *
40495792 AATCCGCTCCACTGTAATCTCAGGGAAATAGGATTACTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTC
* * * *
40495836 AATCTGCTCCGCTGTAATCTCAAGGAGGTAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTC
*
40495880 AATCTGCTCCACTGCAA-CATCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
40495915 CACCATTTTC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
43 1 0.01
44 66 0.99
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTGGCTTC
Found at i:40496531 original size:120 final size:125
Alignment explanation
Indices: 40496310--40496607 Score: 360
Period size: 120 Copynumber: 2.4 Consensus size: 125
40496300 AGATTCCATT
* ** * * *
40496310 TTCGAT-TAGCTCCACTACTGCTTAATGAGATAAGATCTGA-AA-TTCTTCAATCTATTCCACTG
1 TTCGATCT-GCTCCGCTACTGCTTAGGGAGACAAGATCT-ATAATTTC-CCAACCTATTCCACTG
* *
40496372 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACACTTGAAGAT-AA-GA-T-
63 CTGACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACACGTGAAGATAAACCACTC
*
40496431 TT-GATCTGCTCCGCTATTGCTTAGGGAGACAAGATCTATAATTTCCCAACCTATTCCACTGCTG
1 TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTATAATTTCCCAACCTATTCCACTGCTG
* *
40496495 ACCAGGGATATAGGACTTGTGGCTTAAATCTGCTTCCTTACTCGTGAAGATAAAATCCACCGTC
66 ACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACACGTGAAGAT-AAA-CCA-C-TC
* *
40496559 TTCGATCTGCTCCGTTACTGCTTAGGGAGACAAGATCTGTAATTTCCCA
1 TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTATAATTTCCCA
40496608 GATCTGTTCT
Statistics
Matches: 151, Mismatches: 14, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
119 1 0.01
120 95 0.63
121 6 0.04
122 2 0.01
124 1 0.01
127 1 0.01
128 2 0.01
129 43 0.28
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (125 bp):
TTCGATCTGCTCCGCTACTGCTTAGGGAGACAAGATCTATAATTTCCCAACCTATTCCACTGCTG
ACCAGGGATATAGGACTTGTGGCTTAAATCTACTTCCTTACACGTGAAGATAAACCACTC
Found at i:40497844 original size:8 final size:7
Alignment explanation
Indices: 40497834--40497874 Score: 57
Period size: 7 Copynumber: 5.7 Consensus size: 7
40497824 TATTTTTACT
40497834 TTTTTCA
1 TTTTTCA
40497841 TTTTTTCA
1 -TTTTTCA
40497849 TTTTTCA
1 TTTTTCA
40497856 -TTTTCA
1 TTTTTCA
40497862 TTTTTCA
1 TTTTTCA
40497869 TCTTTT
1 T-TTTT
40497875 TTTTACTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.19
7 14 0.45
8 11 0.35
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTTTCA
Found at i:40497845 original size:15 final size:15
Alignment explanation
Indices: 40497825--40497874 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
40497815 TAGCCTCTCT
*
40497825 ATTTTTACTTTTTTC
1 ATTTTTACATTTTTC
*
40497840 ATTTTTTCATTTTTC
1 ATTTTTACATTTTTC
40497855 A-TTTT-CATTTTTC
1 ATTTTTACATTTTTC
40497868 ATCTTTT
1 AT-TTTT
40497875 TTTTACTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 9 0.29
14 4 0.13
15 18 0.58
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (15 bp):
ATTTTTACATTTTTC
Found at i:40497861 original size:13 final size:13
Alignment explanation
Indices: 40497843--40497869 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40497833 TTTTTTCATT
40497843 TTTTCATTTTTCA
1 TTTTCATTTTTCA
40497856 TTTTCATTTTTCA
1 TTTTCATTTTTCA
40497869 T
1 T
40497870 CTTTTTTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTCATTTTTCA
Found at i:40497861 original size:21 final size:21
Alignment explanation
Indices: 40497835--40497874 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
40497825 ATTTTTACTT
40497835 TTTTCATTTTTTCAT-TTTTCA
1 TTTTCA-TTTTTCATCTTTTCA
40497856 TTTTCATTTTTCATCTTTT
1 TTTTCATTTTTCATCTTTT
40497875 TTTTACTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTTCATTTTTCATCTTTTCA
Found at i:40498750 original size:8 final size:8
Alignment explanation
Indices: 40498733--40498775 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
40498723 TTCATCTAGA
*
40498733 TTTTCCTC
1 TTTTCTTC
40498741 TTTTCTTC
1 TTTTCTTC
40498749 TTTTCTT-
1 TTTTCTTC
*
40498756 TTTTCTTT
1 TTTTCTTC
*
40498764 TTTTCTTA
1 TTTTCTTC
40498772 TTTT
1 TTTT
40498776 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (8 bp):
TTTTCTTC
Found at i:40498760 original size:23 final size:23
Alignment explanation
Indices: 40498733--40498780 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
40498723 TTCATCTAGA
* *
40498733 TTTTCCTCTTTTCTTCTTTTCTT
1 TTTTCCTCTTTTCTTATTTTATT
* *
40498756 TTTTCTTTTTTTCTTATTTTATT
1 TTTTCCTCTTTTCTTATTTTATT
40498779 TT
1 TT
40498781 ATTTTTTTAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTCCTCTTTTCTTATTTTATT
Found at i:40498761 original size:15 final size:16
Alignment explanation
Indices: 40498741--40498775 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
40498731 GATTTTCCTC
40498741 TTTTCTTCTTTTCTT-
1 TTTTCTTCTTTTCTTA
*
40498756 TTTTCTTTTTTTCTTA
1 TTTTCTTCTTTTCTTA
40498772 TTTT
1 TTTT
40498776 ATTTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTCTTCTTTTCTTA
Found at i:40498787 original size:23 final size:23
Alignment explanation
Indices: 40498741--40498788 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
40498731 GATTTTCCTC
* *
40498741 TTTTCTTCTTTTCTTTTTTCTTT
1 TTTTCTTATTTTATTTTTTCTTT
*
40498764 TTTTCTTATTTTATTTTAT-TTT
1 TTTTCTTATTTTATTTTTTCTTT
40498786 TTT
1 TTT
40498789 ATTTTTTTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.83
Consensus pattern (23 bp):
TTTTCTTATTTTATTTTTTCTTT
Found at i:40498796 original size:21 final size:21
Alignment explanation
Indices: 40498756--40498796 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40498746 TTCTTTTCTT
* *
40498756 TTTTCTTTTTTTCTTATTTTA
1 TTTTATTTTTTTATTATTTTA
*
40498777 TTTTATTTTTTTATTTTTTT
1 TTTTATTTTTTTATTATTTT
40498797 TGAATTGGAT
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:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTTATTTTTTTATTATTTTA
Found at i:40500887 original size:27 final size:27
Alignment explanation
Indices: 40500846--40500899 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
40500836 GGAACCAAGC
*
40500846 TCAGATCTTTTGCATCAATTCCATGGA
1 TCAGATCTTTAGCATCAATTCCATGGA
40500873 TCAGATCTTTAGCATCAATTCCATGGA
1 TCAGATCTTTAGCATCAATTCCATGGA
40500900 GACTATCGGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (27 bp):
TCAGATCTTTAGCATCAATTCCATGGA
Found at i:40503825 original size:12 final size:13
Alignment explanation
Indices: 40503807--40503848 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
40503797 AGGAAAGATT
40503807 TAATAATAATATA
1 TAATAATAATATA
40503820 -AATAATAACATATA
1 TAATAAT-A-ATATA
40503834 TACATAATAATATA
1 TA-ATAATAATATA
40503848 T
1 T
40503849 TAAAGTTGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
12 6 0.24
13 1 0.04
14 11 0.44
15 2 0.08
16 5 0.20
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATAATAATATA
Found at i:40503840 original size:16 final size:16
Alignment explanation
Indices: 40503815--40503852 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40503805 TTTAATAATA
40503815 ATATAAATAATAACAT
1 ATATAAATAATAACAT
* *
40503831 ATATACATAATAATAT
1 ATATAAATAATAACAT
40503847 AT-TAAA
1 ATATAAA
40503853 GTTGAAGTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (16 bp):
ATATAAATAATAACAT
Found at i:40504065 original size:18 final size:17
Alignment explanation
Indices: 40504042--40504186 Score: 71
Period size: 18 Copynumber: 7.8 Consensus size: 17
40504032 TGTTAACACT
40504042 TAAAATAATATTATATAA
1 TAAAATAATATTA-ATAA
40504060 TAAAATAATGCATATACATAA
1 TAAAATAAT--AT-TA-ATAA
*
40504081 -AAAATTATA-TAGATAAA
1 TAAAATAATATTA-AT-AA
*
40504098 TATATGAACTAATATAAATAA
1 TA-A--AA-TAATATTAATAA
* *
40504119 TAACACTAATAATAATAA
1 TAA-AATAATATTAATAA
*
40504137 TAATAATAATAATAATAA
1 TAA-AATAATATTAATAA
*
40504155 TAATAATAATAATAA-AGA
1 TAA-AATAATATTAATA-A
*
40504173 TAAATTAATATTAA
1 TAAAATAATATTAA
40504187 AGTAATTATT
Statistics
Matches: 103, Mismatches: 13, Indels: 23
0.74 0.09 0.17
Matches are distributed among these distances:
16 4 0.04
17 12 0.12
18 56 0.54
19 2 0.02
20 10 0.10
21 12 0.12
22 6 0.06
23 1 0.01
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.32
Consensus pattern (17 bp):
TAAAATAATATTAATAA
Found at i:40504096 original size:16 final size:16
Alignment explanation
Indices: 40504051--40504167 Score: 59
Period size: 15 Copynumber: 7.1 Consensus size: 16
40504041 TTAAAATAAT
40504051 ATTATATAATAAAATA
1 ATTATATAATAAAATA
*
40504067 ATGCATATACATAAAA-A
1 AT-TATATA-ATAAAATA
40504084 ATTATATAGAT-AAATA
1 ATTATATA-ATAAAATA
*
40504100 TATGA-ACTAATATAAATA
1 -ATTATA-TAATA-AAATA
* *
40504118 ATAACACTAATAATAATA
1 ATTATA-TAATAA-AATA
40504136 A-TA-ATAATAATAATA
1 ATTATATAATAA-AATA
40504151 A-TA-ATAATAATAATA
1 ATTATATAATAA-AATA
40504166 AT
1 AT
40504168 AAAGATAAAT
Statistics
Matches: 85, Mismatches: 6, Indels: 20
0.77 0.05 0.18
Matches are distributed among these distances:
15 30 0.35
16 14 0.16
17 18 0.21
18 23 0.27
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (16 bp):
ATTATATAATAAAATA
Found at i:40504131 original size:3 final size:3
Alignment explanation
Indices: 40504114--40504169 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
40504104 AACTAATATA
* *
40504114 AAT AAT AAC ACT 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 AAT AAT AAT
40504162 AAT AAT AA
1 AAT AAT AA
40504170 AGATAAATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:40509973 original size:38 final size:38
Alignment explanation
Indices: 40509925--40510004 Score: 133
Period size: 38 Copynumber: 2.1 Consensus size: 38
40509915 TAAGGGATTT
* *
40509925 GGATGGGAGTGGTTGGATGGTTTTAGGAGAGATTTGTG
1 GGATGGGAGTGGTTGGACGGTTTTAGGAGAGATTTGAG
*
40509963 GGATGGGAGTGGTTGTACGGTTTTAGGAGAGATTTGAG
1 GGATGGGAGTGGTTGGACGGTTTTAGGAGAGATTTGAG
40510001 GGAT
1 GGAT
40510005 TTTGGGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.20, C:0.01, G:0.46, T:0.33
Consensus pattern (38 bp):
GGATGGGAGTGGTTGGACGGTTTTAGGAGAGATTTGAG
Found at i:40511418 original size:18 final size:20
Alignment explanation
Indices: 40511381--40511422 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
40511371 GTAGGACCTG
40511381 TATACTGTATAATCTGTTAC
1 TATACTGTATAATCTGTTAC
*
40511401 TATACTG-ATTAT-TGTTAC
1 TATACTGTATAATCTGTTAC
40511419 TATA
1 TATA
40511423 ATGGGTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.48
19 4 0.19
20 7 0.33
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (20 bp):
TATACTGTATAATCTGTTAC
Found at i:40515188 original size:24 final size:24
Alignment explanation
Indices: 40515161--40515241 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 24
40515151 TCGAAAATAT
*
40515161 TTAATAAGTTCGCACACTTAGTGC
1 TTAATAAATTCGCACACTTAGTGC
40515185 TTAATAATCAATCTCGCACACTTAGTGC
1 TTAAT-A--AAT-TCGCACACTTAGTGC
*
40515213 TTTACAATTAAACTCGCACACTTAGTGC
1 -TT--AA-TAAATTCGCACACTTAGTGC
40515241 T
1 T
40515242 AATCTCATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
24 5 0.11
25 1 0.02
27 3 0.06
28 30 0.64
29 4 0.09
31 3 0.06
32 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (24 bp):
TTAATAAATTCGCACACTTAGTGC
Found at i:40515202 original size:28 final size:28
Alignment explanation
Indices: 40515170--40515241 Score: 108
Period size: 28 Copynumber: 2.6 Consensus size: 28
40515160 TTTAATAAGT
* *
40515170 TCGCACACTTAGTGCTTAATAATCAATC
1 TCGCACACTTAGTGCTTAACAATCAAAC
* *
40515198 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTAACAATCAAAC
40515226 TCGCACACTTAGTGCT
1 TCGCACACTTAGTGCT
40515242 AATCTCATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTAACAATCAAAC
Found at i:40520800 original size:30 final size:30
Alignment explanation
Indices: 40520765--40520827 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
40520755 AAGAAAATAA
40520765 TGATTGTGACGATCAAAAAGAAAGATGAGC
1 TGATTGTGACGATCAAAAAGAAAGATGAGC
*
40520795 TGATTGTGACGATTAAAAAGAAAGATGAGC
1 TGATTGTGACGATCAAAAAGAAAGATGAGC
40520825 TGA
1 TGA
40520828 ACGAAGAGGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.43, C:0.08, G:0.27, T:0.22
Consensus pattern (30 bp):
TGATTGTGACGATCAAAAAGAAAGATGAGC
Found at i:40524593 original size:19 final size:21
Alignment explanation
Indices: 40524569--40524613 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
40524559 CATTTCTCTT
*
40524569 TTTCTATTCATTC-C-ATTCA
1 TTTCTATTCAATCACAATTCA
40524588 TTTCTATTCAATCACAATTCA
1 TTTCTATTCAATCACAATTCA
40524609 TTTCT
1 TTTCT
40524614 GGTTTCAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 1 0.04
21 10 0.43
ACGTcount: A:0.24, C:0.24, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTCTATTCAATCACAATTCA
Found at i:40532757 original size:17 final size:17
Alignment explanation
Indices: 40532740--40532772 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40532730 ATAATATTAT
40532740 TTTAA-TAAATTTAATA
1 TTTAATTAAATTTAATA
*
40532756 TTTAATTTAATTTAATA
1 TTTAATTAAATTTAATA
40532773 CTTATCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAATTAAATTTAATA
Found at i:40534055 original size:18 final size:17
Alignment explanation
Indices: 40534013--40534056 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
40534003 TGTCGTTCGT
40534013 TTTCAAAACATTATTCA
1 TTTCAAAACATTATTCA
* *
40534030 TTTACAAATCATTTTTCAA
1 TTT-CAAAACATTATTC-A
40534049 TTTCAAAA
1 TTTCAAAA
40534057 TGTTTTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.14
18 15 0.68
19 4 0.18
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTCAAAACATTATTCA
Found at i:40536212 original size:13 final size:13
Alignment explanation
Indices: 40536196--40536261 Score: 96
Period size: 13 Copynumber: 5.1 Consensus size: 13
40536186 AGTTTGACAA
*
40536196 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
40536209 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
40536222 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
40536235 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
40536248 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40536261 T
1 T
40536262 TTGGTTTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 46 1.00
ACGTcount: A:0.30, C:0.08, G:0.26, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40536258 original size:26 final size:26
Alignment explanation
Indices: 40536188--40536261 Score: 96
Period size: 26 Copynumber: 2.9 Consensus size: 26
40536178 TTAGGGCAAG
* *
40536188 TTTGACAA-TGCTTTTGAAAAATGCT
1 TTTGAAAAGTGCTTTTGAAAAGTGCT
* *
40536213 TTTGAAAAGTGCTGTGGAAAAGTGCT
1 TTTGAAAAGTGCTTTTGAAAAGTGCT
*
40536239 TTTGAGAAGTGCTTTTGAAAAGT
1 TTTGAAAAGTGCTTTTGAAAAGT
40536262 TTGGTTTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 7 0.17
26 34 0.83
ACGTcount: A:0.31, C:0.08, G:0.24, T:0.36
Consensus pattern (26 bp):
TTTGAAAAGTGCTTTTGAAAAGTGCT
Found at i:40548715 original size:44 final size:44
Alignment explanation
Indices: 40548662--40549095 Score: 203
Period size: 44 Copynumber: 9.9 Consensus size: 44
40548652 AGTATAGTGT
* * *
40548662 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAG
* * * ** *
40548706 CTTCAATCTGCTTCAAC-GTAATCTCGGGGAGATAAGATCTGAAATT
1 CTTCAATCTAC-TCCACTGTAATCTCAGGGAGATAAGATCT-CTA-G
* * *
40548752 CTTCAGTCTACTCCACTGTAACCTTAGGGAGATAAGA-C-CT-G
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAG
* * * * * * * *
40548793 ATGCGATCTACTCTATTGTAACCTCAGAGAGATAAGATC-CTAAA
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCT-AG
* * ** * * *
40548837 TTTTAATCCGCTCCAGTGTAA-CTTCAGAGAGATAGGAT-TACTAG
1 CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATCT-CTAG
* * * * * **
40548881 CTTCAATCTGCTCCGCTATAATCTCAAGGAGATAAGATCTGAATTT
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT--CTAG
**
40548927 CTTCGGTCTACTCCACTGTAATCTCAGGGAGATAAGA-CT-T-G
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAG
* * * * * *
40548968 ATGT-GATCTACTCTACTGTAACCTCAGAGAGATAAGATCT-TAAA
1 CT-TCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCT-AG
* * * * * *
40549012 TTTTAATCCACTCCACTGTAA-CTTCAGAGAGATAGGAT-TACTAA
1 CTTCAATCTACTCCACTGTAATC-TCAGGGAGATAAGATCT-CTAG
* * *
40549056 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGACAAGATCT
1 CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCT
40549096 GAAATTCTTC
Statistics
Matches: 294, Mismatches: 73, Indels: 45
0.71 0.18 0.11
Matches are distributed among these distances:
41 59 0.20
42 8 0.03
43 4 0.01
44 147 0.50
45 17 0.06
46 59 0.20
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (44 bp):
CTTCAATCTACTCCACTGTAATCTCAGGGAGATAAGATCTCTAG
Found at i:40548869 original size:85 final size:85
Alignment explanation
Indices: 40548734--40549045 Score: 265
Period size: 87 Copynumber: 3.6 Consensus size: 85
40548724 TAATCTCGGG
* * *
40548734 GAGATAAGAT-CTGAAATTCTTCAGTCTACTCCACTGTAACCTT-AGGGAGATAAGACCTGATGC
1 GAGATAAGATCCT-AAATT-TT-AATCCACTCCACTGTAA-CTTCAGAGAGATAAGACCTGATGC
*
40548797 GATCTACTCTATTGTAACCTCAGA
62 GATCTACTCTACTGTAACCTCAGA
* * * * * * *
40548821 GAGATAAGATCCTAAATTTTAATCCGCTCCAGTGTAACTTCAGAGAGATAGGATTACTAGCTTCA
1 GAGATAAGATCCTAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATAAGA--CCT-GATGCG
* ** * *
40548886 ATCTGCTCCGCTATAATCTCA-A
63 ATCTACTCTACTGTAACCTCAGA
* ** * * *
40548908 GGAGATAAGAT-CTGAATTTCTTCGGTCTACTCCACTGTAA-TCTCAGGGAGATAAGACTTGATG
1 -GAGATAAGATCCT-AAATT-TT-AATCCACTCCACTGTAACT-TCAGAGAGATAAGACCTGATG
*
40548971 TGATCTACTCTACTGTAACCTCAGA
61 CGATCTACTCTACTGTAACCTCAGA
*
40548996 GAGATAAGATCTTAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATA
1 GAGATAAGATCCTAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATA
40549046 GGATTACTAA
Statistics
Matches: 171, Mismatches: 41, Indels: 28
0.71 0.17 0.12
Matches are distributed among these distances:
84 3 0.02
85 47 0.27
86 5 0.03
87 52 0.30
88 37 0.22
89 3 0.02
90 24 0.14
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (85 bp):
GAGATAAGATCCTAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATAAGACCTGATGCGATC
TACTCTACTGTAACCTCAGA
Found at i:40549093 original size:88 final size:88
Alignment explanation
Indices: 40548809--40549101 Score: 294
Period size: 88 Copynumber: 3.3 Consensus size: 88
40548799 TCTACTCTAT
* *
40548809 TGTAACCTCAGAGAGATAAGATCCT-AAATTTTAATCCGCTCCAGTGTAACTTCAGAGAGATAGG
1 TGTAACCTCAGAGAGATAAGAT-CTGAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGG
*
40548873 ATTACTAGCTTCAATCTGCTCCGC
65 ATTACTAACTTCAATCTGCTCCGC
* * * ** * *
40548897 TATAATCTCA-AGGAGATAAGATCTGAATTTCTTCGGTCTACTCCACTGTAA-TCTCAGGGAGAT
1 TGTAACCTCAGA-GAGATAAGATCTGAAATT-TT-AATCCACTCCACTGTAACT-TCAGAGAGAT
* * * * * **
40548960 AAGACT--TGA-TGT-GATCTACTCTAC
62 AGGATTACTAACT-TCAATCTGCTCCGC
*
40548984 TGTAACCTCAGAGAGATAAGATCTTAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGA
1 TGTAACCTCAGAGAGATAAGATCTGAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGA
40549049 TTACTAACTTCAATCTGCTCCGC
66 TTACTAACTTCAATCTGCTCCGC
* * *
40549072 TGTAATCTCAGGGAGACAAGATCTGAAATT
1 TGTAACCTCAGAGAGATAAGATCTGAAATT
40549102 CTTCGATCTG
Statistics
Matches: 157, Mismatches: 36, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
85 27 0.17
86 3 0.02
87 39 0.25
88 60 0.38
89 3 0.02
90 25 0.16
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (88 bp):
TGTAACCTCAGAGAGATAAGATCTGAAATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGA
TTACTAACTTCAATCTGCTCCGC
Found at i:40549106 original size:175 final size:175
Alignment explanation
Indices: 40548706--40549106 Score: 633
Period size: 175 Copynumber: 2.3 Consensus size: 175
40548696 AGATCTCTGG
** * *
40548706 CTTCAATCTGCTTCAAC-GTAATCTCGGGGAGATAAGATCTGAAATTCTTCAGTCTACTCCACTG
1 CTTCAATCTGC-TCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTG
* *
40548770 TAACCTTAGGGAGATAAGACCTGATGCGATCTACTCTATTGTAACCTCAGAGAGATAAGATCCTA
65 TAACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTA
* * *
40548835 AATTTTAATCCGCTCCAGTGTAACTTCAGAGAGATAGGATTACTAG
130 AATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGATTACTAA
* * *
40548881 CTTCAATCTGCTCCGCTATAATCTCAAGGAGATAAGATCTGAATTTCTTCGGTCTACTCCACTGT
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT
* * * *
40548946 AATCTCAGGGAGATAAGACTTGATGTGATCTACTCTACTGTAACCTCAGAGAGATAAGATCTTAA
66 AACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAA
40549011 ATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGATTACTAA
131 ATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGATTACTAA
*
40549056 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGACAAGATCTGAAATTCTTCG
1 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCG
40549107 ATCTGTTTTA
Statistics
Matches: 205, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
174 3 0.01
175 202 0.99
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (175 bp):
CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTGAAATTCTTCGGTCTACTCCACTGT
AACCTCAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACCTCAGAGAGATAAGATCCTAA
ATTTTAATCCACTCCACTGTAACTTCAGAGAGATAGGATTACTAA
Found at i:40562251 original size:169 final size:169
Alignment explanation
Indices: 40561972--40562307 Score: 672
Period size: 169 Copynumber: 2.0 Consensus size: 169
40561962 AGCAAAAAAA
40561972 CAAAAAAAAACATTCTTATTCTATAGATTTTTTTTAAAACAGAGAGCTCTCTCAGTTTTCTCCCT
1 CAAAAAAAAACATTCTTATTCTATAGATTTTTTTTAAAACAGAGAGCTCTCTCAGTTTTCTCCCT
40562037 CTTTAAGTCCGATCGTCGGTCTTCCAGGCCAAAGGTCGCCGTGACTCCACCGCAGGCGGTGGTCG
66 CTTTAAGTCCGATCGTCGGTCTTCCAGGCCAAAGGTCGCCGTGACTCCACCGCAGGCGGTGGTCG
40562102 GCGCCTTCAAAAATTGGGTTTTTAACCCCACCTTCAACC
131 GCGCCTTCAAAAATTGGGTTTTTAACCCCACCTTCAACC
40562141 CAAAAAAAAACATTCTTATTCTATAGATTTTTTTTAAAACAGAGAGCTCTCTCAGTTTTCTCCCT
1 CAAAAAAAAACATTCTTATTCTATAGATTTTTTTTAAAACAGAGAGCTCTCTCAGTTTTCTCCCT
40562206 CTTTAAGTCCGATCGTCGGTCTTCCAGGCCAAAGGTCGCCGTGACTCCACCGCAGGCGGTGGTCG
66 CTTTAAGTCCGATCGTCGGTCTTCCAGGCCAAAGGTCGCCGTGACTCCACCGCAGGCGGTGGTCG
40562271 GCGCCTTCAAAAATTGGGTTTTTAACCCCACCTTCAA
131 GCGCCTTCAAAAATTGGGTTTTTAACCCCACCTTCAA
40562308 ACCTCGCTAG
Statistics
Matches: 167, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
169 167 1.00
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (169 bp):
CAAAAAAAAACATTCTTATTCTATAGATTTTTTTTAAAACAGAGAGCTCTCTCAGTTTTCTCCCT
CTTTAAGTCCGATCGTCGGTCTTCCAGGCCAAAGGTCGCCGTGACTCCACCGCAGGCGGTGGTCG
GCGCCTTCAAAAATTGGGTTTTTAACCCCACCTTCAACC
Found at i:40583150 original size:94 final size:94
Alignment explanation
Indices: 40582947--40584645 Score: 1930
Period size: 94 Copynumber: 18.1 Consensus size: 94
40582937 TCTTATCTCT
* * * * *
40582947 CTGAAGTTGCAGTGGGTCCGATTGAAGATACCATAACAAATCTTATCTCCCTGAAGTTGCAGTGC
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
*
40583012 A-CAAGATGAAACTACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * * * * * * ** *
40583040 CTAAAGTTGTAGTGGGTCGGATTGACGTTACCATAGCAAATCTTATCTCGCTAAAGTTATAATGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
40583105 AGCAAGATGAAGCTACAAAAT-CTATACCC
66 AGCAAGATGAAGCTAC-AAATCCTATACCC
* * ** * *
40583134 CTGAAGTTACAGTGGGTCGGATTGAAGTTACCATAG-GAAATCTTA-CGTCATTGAAATTGTAGT
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCG-AATCTTATC-TCCCTGAAGTTGCAGT
*
40583197 GGAGCAAGATGAAGCTACAAATCTTATACCC
64 GGAGCAAGATGAAGCTACAAATCCTATACCC
* * * * * * *
40583228 CTAAAGTTGTAGTGGATCGGATTGAAGTTACCATAGCAAATCTAATCTCCCTAAAGTTAG-AGTG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTT-GCAGTG
* *
40583292 GAACAAGATGAAGCTACAAAACCTATACCC
65 GAGCAAGATGAAGCTACAAATCCTATACCC
* * *
40583322 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCA-AGCAAATCTTATCTCCATGAA-TTTCTAGTG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGC-AGTG
*
40583385 GAGCAAGATGAAACTACAAATCCTATACCC
65 GAGCAAGATGAAGCTACAAATCCTATACCC
* * * * * * *
40583415 CTGAAGATGTAGTGGGTCAGATTTAAGTTACCATAGTGAATCTTATCTCCCTTAAGTTGTA-AGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
* *
40583479 AGGAAGATAAAGCTACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
** * * * * * * *
40583508 CTGAA-TTAAAGTAGGTTAGATTAAAGTTGCCATAGCGAATCTCATCTCACTGAAGTTGTAGTGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
* *
40583572 AACAAGATGAAACTACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* ** *
40583601 CTGAAGTTGCAGTGGTTCAGATTGAAGTTACCATAGCGAATCTTATCTTACTGAAGTTGTAGTGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
* *
40583666 AGTAAGATGAAGCAACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
*
40583695 CTGAAGTTGCAGTGGGTTAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
*
40583760 AGCAAGATAAAGCTACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * * * * * * * * *
40583789 TTGAAGTTGGAGTGGGCCGGATTGAAGCTACAATAGCAAATCTTGTCTCTCTGAAGTTGCAATGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
* * * *
40583854 AGTAAGATAAAGCTACCAATTCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * * * * * * *
40583883 TTGAAGTTCCAGTAGGTCAGATTGAAATTA-CAGTAGCGAGTCCTATCTCCATGAAGTTACAGTG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCA-TAGCGAATCTTATCTCCCTGAAGTTGCAGTG
*
40583947 AAGCAAGATGAAGCTACAAATCCTATACCC
65 GAGCAAGATGAAGCTACAAATCCTATACCC
* * * ** * * * *
40583977 C-GAAAGTTACAATAGGTTGGATTAAAGTTACCATAGCGAATCTTATCTCCCTAAAGTTGCAATA
1 CTG-AAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTG
* *
40584041 GAGCAAGATAAAGCTACAAATCCTAAACCC
65 GAGCAAGATGAAGCTACAAATCCTATACCC
* * * *
40584071 CTGAAGTTGCAGTGGGTCAGATTGAAGCTACAATAGCAAATCTTATCTCCCTAAAGTTGCAGTGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
* *
40584136 AGCAAGATAAAGCTACAAATCCTATACTC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * * * * *
40584165 CTTAAGTTGTAGTGGGTCAGATTGAAGCTACAATAGTGAATCTTATCTCCCTGAAGTTGCAGTAG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
*
40584230 AGCAAGATGAAGCTACAAATCCTATACTC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * * * * *
40584259 CTGAATTTGCAGTGGGTCAGATTGAAGCTACAATAGCGAATATTATCTCCCTAAAGTTGCAGTAG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
40584324 AGCAAGATGAAGCTACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * * ** * *
40584353 CTGAAGTTGCAGTTGGT-TGAATTGAAATTATAATAGCGAATCTTATCTCACTGAAGTTGTAGTG
1 CTGAAGTTGCAGTGGGTCAG-ATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTG
* * * *
40584417 GAACAAGATAAAGTTATAAATCCTATACCC
65 GAGCAAGATGAAGCTACAAATCCTATACCC
* * ** *
40584447 CTGAAGTTGTAGTGGGTCAGATTGAAGCTAAAATAGCGAATCTTATCTCCTTGAAGTTGCAGTGG
1 CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
40584512 AGCAAGATGAAGCTACAAATCCTATACCC
66 AGCAAGATGAAGCTACAAATCCTATACCC
* * ** * * * * *
40584541 CTGAAGTTGCAGTGGGT-TGAAATGAAACTACAATGGCGAATCTTATCTCCTTGAAGTTGTAGTT
1 CTGAAGTTGCAGTGGGTCAG-ATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTG
*
40584605 GCGCAAGATGAAGCTACAAATCCTATACCC
65 GAGCAAGATGAAGCTACAAATCCTATACCC
*
40584635 TTGAAGTTGCA
1 CTGAAGTTGCA
40584646 ATGGAGCAAG
Statistics
Matches: 1369, Mismatches: 216, Indels: 41
0.84 0.13 0.03
Matches are distributed among these distances:
92 46 0.03
93 207 0.15
94 1104 0.81
95 12 0.01
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (94 bp):
CTGAAGTTGCAGTGGGTCAGATTGAAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGG
AGCAAGATGAAGCTACAAATCCTATACCC
Found at i:40583238 original size:44 final size:44
Alignment explanation
Indices: 40583185--40584660 Score: 277
Period size: 44 Copynumber: 31.6 Consensus size: 44
40583175 CTTACGTCAT
*
40583185 TGAAATTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* * * *
40583229 TAAAGTTGTAGTGGATC-GGATTGAAGTTACCATAGCAAATCTAAT-CTCCC
1 TGAAGTTGTAGTGGAGCAAGA-TGAAG----C-TA-CAAATCTTATAC-CCC
* * * *
40583279 TAAAGTTAG-AGTGGAACAAGATGAAGCTACAAAACCTATACCCC
1 TGAAGTT-GTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* * *
40583323 TGAAGTTGCAGTGG-GTC-AGATTGAAGTTACCAAGCAAATCTTAT-CTCCA
1 TGAAGTTGTAGTGGAG-CAAGA-TGAAG----CTA-CAAATCTTATAC-CCC
* * * *
40583372 TGAATTTCTAGTGGAGCAAGATGAAACTACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* * *
40583416 TGAAGATGTAGTGG-GTC-AGATTTAAGTTACCATAGTGAATCTTAT-CTCCC
1 TGAAGTTGTAGTGGAG-CAAGA-TGAAGCTA-C--A---AATCTTATAC-CCC
* * * * *
40583466 TTAAGTTGTA-AGGAGGAAGATAAAGCTACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
** * ** * * * *
40583509 TGAA-TTAAAGTAG-GTTAGATTAAAGTTGCCATAGCGAATCTCAT-CTCAC
1 TGAAGTTGTAGTGGAGCAAGA-TGAA---G-C-TA-CAAATCTTATAC-CCC
* * *
40583558 TGAAGTTGTAGTGGAACAAGATGAAACTACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* ** * **
40583602 TGAAGTTGCAGTGGTTC-AGATTGAAGTTACCATAGCGAATCTTAT-CTTAC
1 TGAAGTTGTAGTGGAGCAAGA-TGAAG----C-TA-CAAATCTTATAC-CCC
* * *
40583652 TGAAGTTGTAGTGGAGTAAGATGAAGCAACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* ** *
40583696 TGAAGTTGCAGTGG-GTTAGATTGAAGTTACCATAGCGAATCTTAT-CTCCC
1 TGAAGTTGTAGTGGAGCAAGA-TGAAG----C-TA-CAAATCTTATAC-CCC
* * * *
40583746 TGAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCTATACCCT
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* ** * *
40583790 TGAAGTTGGAGTGG-GCCGGATTGAAGCTACAATAGCAAATCTTGT-CTCTC
1 TGAAGTTGTAGTGGAGCAAGA-TGAAG---C--TA-CAAATCTTATAC-CCC
* * * * * *
40583840 TGAAGTTGCAATGGAGTAAGATAAAGCTACCAAT-TCTATACCCT
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCT-TATACCCC
** * ** * *
40583884 TGAAGTTCCAGTAGG-TC-AGATTGAAATTACAGTAGCGAGTCCTAT-CTCCA
1 TGAAGTTGTAGT-GGAGCAAGA-TGAAGCTACA--A---A-TCTTATAC-CCC
** * *
40583934 TGAAGTTACAGTGAAGCAAGATGAAGCTACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* ** * * *
40583978 -GAAAGTTACAATAGGTTGGATTAA-A-GTTACCATAGCGAATCTTAT-CTCCC
1 TG-AAGTT---GTA-G-TGGAGCAAGATG-AAGC-TA-CAAATCTTATAC-CCC
* * * * * * *
40584028 TAAAGTTGCAATAGAGCAAGATAAAGCTACAAATCCTAAACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
*
40584072 TGAAGTTGCAGTGG-GTC-AGATTGAAGCTACAATAGCAAATCTTAT-CTCCC
1 TGAAGTTGTAGTGGAG-CAAGA-TGAAG---C--TA-CAAATCTTATAC-CCC
* * * * *
40584122 TAAAGTTGCAGTGGAGCAAGATAAAGCTACAAATCCTATACTCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
*
40584166 TTAAGTTGTAGTGG-GTC-AGATTGAAGCTACAATAGTGAATCTTAT-CTCCC
1 TGAAGTTGTAGTGGAG-CAAGA-TGAAGCTAC---A---AATCTTATAC-CCC
* * * *
40584216 TGAAGTTGCAGTAGAGCAAGATGAAGCTACAAATCCTATACTCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* * * *
40584260 TGAATTTGCAGTGG-GTC-AGATTGAAGCTACAATAGCGAATATTATCTCCC
1 TGAAGTTGTAGTGGAG-CAAGA-TGAAGCTACAA-ATC--TTA-TA-C-CCC
* * * *
40584310 TAAAGTTGCAGTAGAGCAAGATGAAGCTACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* * * * * *
40584354 TGAAGTTGCAGTTGGTTG-AATTGAAATTATA-ATAGCGAATCTTAT-CTCAC
1 TGAAGTTGTAG-TGG-AGCAA--G--ATGA-AGCTA-CAAATCTTATAC-CCC
* * * * *
40584404 TGAAGTTGTAGTGGAACAAGATAAAGTTATAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* *
40584448 TGAAGTTGTAGTGG-GTC-AGATTGAAGCTAAAATAGCGAATCTTAT-CTCCT
1 TGAAGTTGTAGTGGAG-CAAGA-TGAAGC-----TA-CAAATCTTATAC-CCC
* *
40584498 TGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATACCCC
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* * * *
40584542 TGAAGTTGCAGTGG-GTTGAA-ATGAAACTACAATGGCGAATCTTAT-CTCCT
1 TGAAGTTGTAGTGGAG--CAAGATGAAGCTAC-A-----AATCTTATAC-CCC
* * * *
40584592 TGAAGTTGTAGTTGCGCAAGATGAAGCTACAAATCCTATACCCT
1 TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
* *
40584636 TGAAGTTGCAATGGAGCAAGATGAA
1 TGAAGTTGTAGTGGAGCAAGATGAA
40584661 AATGTGACAC
Statistics
Matches: 1043, Mismatches: 214, Indels: 350
0.65 0.13 0.22
Matches are distributed among these distances:
42 7 0.01
43 61 0.06
44 389 0.37
45 54 0.05
46 13 0.01
47 18 0.02
48 17 0.02
49 95 0.09
50 353 0.34
51 36 0.03
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (44 bp):
TGAAGTTGTAGTGGAGCAAGATGAAGCTACAAATCTTATACCCC
Found at i:40583677 original size:50 final size:50
Alignment explanation
Indices: 40583531--40584523 Score: 226
Period size: 50 Copynumber: 21.1 Consensus size: 50
40583521 GGTTAGATTA
* * * * **
40583531 AAGTTGCCATAGCGAATCTCATCTCACTGAAGTTGTAGTGGAACAAGATG
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * *
40583581 AA---A-C-TA-CAAATCCTATAC-CCCTGAAGTTGCAGTGG-TTCAGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
** *
40583625 AAGTTACCATAGCGAATCTTATCTTACTGAAGTTGTAGTGGAGTAAGATG
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * *
40583675 AAG----CA-A-CAAATCCTATAC-CCCTGAAGTTGCAGTGG-GTTAGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
*
40583719 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGAT-
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * * * ***
40583768 AA---AGC-TA-CAAATCCTATAC-CCTTGAAGTTGGAGTGG-GCCGGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
* * * * * * *
40583813 AAGCTACAATAGCAAATCTTGTCTCTCTGAAGTTGCAATGGAGTAAGATA
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * * * *
40583863 AAGCTACC--A---ATTC-TATAC-CCTTGAAGTTCCAGTAG-GTCAGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
* * * * * * *
40583907 AAATTA-CAGTAGCGAGTCCTATCTCCATGAAGTTACAGTGAAGCAAGATG
1 AAGTTACCA-TAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * * * ** *
40583957 AAG----C-TA-CAAATCCTATAC-CCC-GAAAGTTACAATAG-GTTGGATTA
1 AAGTTACCATAGCGAATCTTAT-CTCCCTG-AAGTTGCAGTGGAGTAAGA-TG
* * * *
40584001 AAGTTACCATAGCGAATCTTATCTCCCTAAAGTTGCAATAGAGCAAGAT-
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * * *
40584050 AA---AGC-TA-CAAATCCTAAAC-CCCTGAAGTTGCAGTGG-GTCAGATTG
1 AAGTTACCATAGCGAAT-CTTATCTCCCTGAAGTTGCAGTGGAGTAAGA-TG
* * * * *
40584095 AAGCTACAATAGCAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAAGAT-
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * * * *
40584144 AA---AGC-TA-CAAATCCTATACT-CCTTAAGTTGTAGTGG-GTCAGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
* * * * *
40584189 AAGCTACAATAGTGAATCTTATCTCCCTGAAGTTGCAGTAGAGCAAGATG
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * *
40584239 AAG----C-TA-CAAATCCTATACT-CCTGAATTTGCAGTGG-GTCAGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
* * * * * *
40584283 AAGCTACAATAGCGAATATTATCTCCCTAAAGTTGCAGTAGAGCAAGATG
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * * *
40584333 AAG----C-TA-CAAATCCTATAC-CCCTGAAGTTGCAGTTGG-TTGAA-TTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAG-TGGAGT-AAGATG
* ** * * ** *
40584377 AAATTATAATAGCGAATCTTATCTCACTGAAGTTGTAGTGGAACAAGATA
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
* * *
40584427 AAGTT---ATA---AATCCTATAC-CCCTGAAGTTGTAGTGG-GTCAGATTG
1 AAGTTACCATAGCGAATCTTAT-CTCCCTGAAGTTGCAGTGGAGTAAGA-TG
* ** * *
40584471 AAGCTAAAATAGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATG
1 AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
40584521 AAG
1 AAG
40584524 CTACAAATCC
Statistics
Matches: 674, Mismatches: 164, Indels: 210
0.64 0.16 0.20
Matches are distributed among these distances:
43 37 0.05
44 240 0.36
45 43 0.06
46 9 0.01
47 8 0.01
48 8 0.01
49 44 0.07
50 251 0.37
51 34 0.05
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (50 bp):
AAGTTACCATAGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAAGATG
Found at i:40589058 original size:17 final size:17
Alignment explanation
Indices: 40589036--40589072 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
40589026 TAATTTAAAT
*
40589036 AATTAAATATTTTTCTC
1 AATTAAATAATTTTCTC
40589053 AATTAAATAATTTTCTC
1 AATTAAATAATTTTCTC
40589070 AAT
1 AAT
40589073 CTAATTCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (17 bp):
AATTAAATAATTTTCTC
Found at i:40589355 original size:24 final size:23
Alignment explanation
Indices: 40589317--40589363 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
40589307 TTTATGTTCA
40589317 TTTGATTTAACATGCAATTCATT
1 TTTGATTTAACATGCAATTCATT
*
40589340 TTTGGTTTCAACATGCAATTCATT
1 TTTGATTT-AACATGCAATTCATT
40589364 CATTGGTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.47
Consensus pattern (23 bp):
TTTGATTTAACATGCAATTCATT
Found at i:40595954 original size:30 final size:30
Alignment explanation
Indices: 40595846--40595952 Score: 126
Period size: 30 Copynumber: 3.6 Consensus size: 30
40595836 CATTACTTGA
* * *
40595846 TGTCATCTCGGATTGCCCGGCAATGATCAC
1 TGTCATCCCGGGTTGCCCGGCAAAGATCAC
* *
40595876 TGTCATCCTGGGTTGCCCAGCAACA-ATCAC
1 TGTCATCCCGGGTTGCCCGGCAA-AGATCAC
* * *
40595906 TATCATCCCGGGTTGCCTGGTAAAGATCAC
1 TGTCATCCCGGGTTGCCCGGCAAAGATCAC
40595936 TGTCATCCCGGGTTGCC
1 TGTCATCCCGGGTTGCC
40595953 TGACAACGAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.02
30 63 0.98
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.26
Consensus pattern (30 bp):
TGTCATCCCGGGTTGCCCGGCAAAGATCAC
Found at i:40613074 original size:192 final size:192
Alignment explanation
Indices: 40612747--40613136 Score: 771
Period size: 192 Copynumber: 2.0 Consensus size: 192
40612737 TAGATTTCAT
40612747 TTTTTTCACTTAGGTACAAAAATATTGCTTTGTATTTAGATTTCTCTTTATATTCCTTAATATAT
1 TTTTTTCACTTAGGTACAAAAATATTGCTTTGTATTTAGATTTCTCTTTATATTCCTTAATATAT
*
40612812 TAAAGCTTTGTTGACTTTTAAAAATGTAAAAATCCTAACTTTAGCTGTGATTTCTTCTCCATTGT
66 TAAAGCTTTGTTGACTTCTAAAAATGTAAAAATCCTAACTTTAGCTGTGATTTCTTCTCCATTGT
40612877 TGCTATTATAATCTTCTCCAAAAAAAACTCACCAAGAGTCCCTAAGATTTTCCTAACCTTGC
131 TGCTATTATAATCTTCTCCAAAAAAAACTCACCAAGAGTCCCTAAGATTTTCCTAACCTTGC
40612939 TTTTTTCACTTAGGTACAAAAATATTGCTTTGTATTTAGATTTCTCTTTATATTCCTTAATATAT
1 TTTTTTCACTTAGGTACAAAAATATTGCTTTGTATTTAGATTTCTCTTTATATTCCTTAATATAT
40613004 TAAAGCTTTGTTGACTTCTAAAAATGTAAAAATCCTAACTTTAGCTGTGATTTCTTCTCCATTGT
66 TAAAGCTTTGTTGACTTCTAAAAATGTAAAAATCCTAACTTTAGCTGTGATTTCTTCTCCATTGT
40613069 TGCTATTATAATCTTCTCCAAAAAAAACTCACCAAGAGTCCCTAAGATTTTCCTAACCTTGC
131 TGCTATTATAATCTTCTCCAAAAAAAACTCACCAAGAGTCCCTAAGATTTTCCTAACCTTGC
40613131 TTTTTT
1 TTTTTT
40613137 ATGTTTTCTT
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
192 197 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.43
Consensus pattern (192 bp):
TTTTTTCACTTAGGTACAAAAATATTGCTTTGTATTTAGATTTCTCTTTATATTCCTTAATATAT
TAAAGCTTTGTTGACTTCTAAAAATGTAAAAATCCTAACTTTAGCTGTGATTTCTTCTCCATTGT
TGCTATTATAATCTTCTCCAAAAAAAACTCACCAAGAGTCCCTAAGATTTTCCTAACCTTGC
Found at i:40621520 original size:29 final size:29
Alignment explanation
Indices: 40621477--40621553 Score: 118
Period size: 29 Copynumber: 2.7 Consensus size: 29
40621467 TATCGACGCT
* *
40621477 CATCGAATATAAAAAGGGATGGTTACGAC
1 CATCGAATATGAAAAGGGATGGTTACAAC
* *
40621506 CATCGAATATGAAAATGGATGGTTTCAAC
1 CATCGAATATGAAAAGGGATGGTTACAAC
40621535 CATCGAATATGAAAAGGGA
1 CATCGAATATGAAAAGGGA
40621554 CGAATATGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.23, T:0.22
Consensus pattern (29 bp):
CATCGAATATGAAAAGGGATGGTTACAAC
Found at i:40621559 original size:16 final size:16
Alignment explanation
Indices: 40621538--40621569 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40621528 TTTCAACCAT
40621538 CGAATATGAAAAGGGA
1 CGAATATGAAAAGGGA
40621554 CGAATATGAAAAGGGA
1 CGAATATGAAAAGGGA
40621570 TGGTGACGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.06, G:0.31, T:0.12
Consensus pattern (16 bp):
CGAATATGAAAAGGGA
Found at i:40621569 original size:74 final size:74
Alignment explanation
Indices: 40621480--40621627 Score: 224
Period size: 74 Copynumber: 2.0 Consensus size: 74
40621470 CGACGCTCAT
* * * * *
40621480 CGAATATAAAAAGGGATGGTTACGACCATCGAATATGAAAATGGATGGTTTCAACCATCGAATAT
1 CGAATATAAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTCAACCATCGAATAT
40621545 GAAAAGGGA
66 GAAAAGGGA
* **
40621554 CGAATATGAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTTGACCATCGAATAT
1 CGAATATAAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTCAACCATCGAATAT
40621619 GAAAAGGGA
66 GAAAAGGGA
40621628 TGGTGACGAC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.21
Consensus pattern (74 bp):
CGAATATAAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTCAACCATCGAATAT
GAAAAGGGA
Found at i:40621573 original size:45 final size:45
Alignment explanation
Indices: 40621509--40621598 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
40621499 TTACGACCAT
* ** * *
40621509 CGAATATGAAAATGGATGGTTTCAACCATCGAATATGAAAAGGGA
1 CGAATATGAAAAGGGATGGTGACAACCATAGAATATAAAAAGGGA
*
40621554 CGAATATGAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGA
1 CGAATATGAAAAGGGATGGTGACAACCATAGAATATAAAAAGGGA
40621599 TAGTTTTGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.44, C:0.10, G:0.27, T:0.19
Consensus pattern (45 bp):
CGAATATGAAAAGGGATGGTGACAACCATAGAATATAAAAAGGGA
Found at i:40621646 original size:58 final size:58
Alignment explanation
Indices: 40621554--40621671 Score: 209
Period size: 58 Copynumber: 2.0 Consensus size: 58
40621544 TGAAAAGGGA
40621554 CGAATATGAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTTGACCAT
1 CGAATATGAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTTGACCAT
* * *
40621612 CGAATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATGGTTTTGACCAT
1 CGAATATGAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTTGACCAT
40621670 CG
1 CG
40621672 TTTAGCACAC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.22
Consensus pattern (58 bp):
CGAATATGAAAAGGGATGGTGACGACCATAGAATATAAAAAGGGATAGTTTTGACCAT
Found at i:40621671 original size:29 final size:29
Alignment explanation
Indices: 40621554--40621660 Score: 160
Period size: 29 Copynumber: 3.7 Consensus size: 29
40621544 TGAAAAGGGA
40621554 CGAATATGAAAAGGGATGGTGACGACCAT
1 CGAATATGAAAAGGGATGGTGACGACCAT
* * * ***
40621583 AGAATATAAAAAGGGATAGTTTTGACCAT
1 CGAATATGAAAAGGGATGGTGACGACCAT
40621612 CGAATATGAAAAGGGATGGTGACGACCAT
1 CGAATATGAAAAGGGATGGTGACGACCAT
40621641 CGAATATGAAAAGGGATGGT
1 CGAATATGAAAAGGGATGGT
40621661 TTTGACCATC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.40, C:0.10, G:0.29, T:0.21
Consensus pattern (29 bp):
CGAATATGAAAAGGGATGGTGACGACCAT
Found at i:40629153 original size:154 final size:150
Alignment explanation
Indices: 40628876--40629158 Score: 329
Period size: 154 Copynumber: 1.8 Consensus size: 150
40628866 GAAAATAACG
* * *
40628876 TTCAGTTGGAAGCATTTTAGTACTTTTGCTAACAGTGCATCCTGCTTGGAGCATTTTTCCTTTAG
1 TTCAGTTGGAAGCATTTTAGTACTTTTGCTAACAGTACATCCTGCTTGGAGCATTTTTCCTCTAC
* *** * * **
40628941 AAACCTCATCCCGGGAATCCTGGGATATTTTTTTCAAAACTATCTCATCAAATTTATTTTCTCAG
66 AAACCTCAACCC--G-ATCCTAAAATATTTTCTTCAAAACCATCTCATCAAAAATATTTTCTCAG
40629006 AAGTAGCAGTACTGAAAAGGGCA
128 AAGTAGCAGTACTGAAAAGGGCA
* *
40629029 TTCAGTTGGAAGCGTTTTCAGTACTTTTGTTAACAGTACATCCTGCTTGGAGCATTTTTCCTCTA
1 TTCAGTTGGAAGCATTTT-AGTACTTTTGCTAACAGTACATCCTGCTTGGAGCATTTTTCCTCTA
*
40629094 CAAACCTCAACCC-ATCTCGTTAAAACTA-TTTCTTCAAAACCCATC-CTTCCAAAAATATTTTC
65 CAAACCTCAACCCGATC-C--TAAAA-TATTTTCTTCAAAA-CCATCTCAT-CAAAAATATTTTC
40629156 TCA
124 TCA
40629159 AAATCCATCC
Statistics
Matches: 109, Mismatches: 14, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
150 3 0.03
151 1 0.01
153 31 0.28
154 74 0.68
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (150 bp):
TTCAGTTGGAAGCATTTTAGTACTTTTGCTAACAGTACATCCTGCTTGGAGCATTTTTCCTCTAC
AAACCTCAACCCGATCCTAAAATATTTTCTTCAAAACCATCTCATCAAAAATATTTTCTCAGAAG
TAGCAGTACTGAAAAGGGCA
Found at i:40630393 original size:18 final size:18
Alignment explanation
Indices: 40630370--40630432 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
40630360 TTATATGATT
40630370 TAAAAAATAATTTTTATA
1 TAAAAAATAATTTTTATA
* * * *
40630388 TAAAAAATTATGTATGATT
1 TAAAAAATAAT-TTTTATA
40630407 TAAAAAATAATTTTTATA
1 TAAAAAATAATTTTTATA
40630425 TAAAAAAT
1 TAAAAAAT
40630433 TATGTTATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 22 0.61
19 14 0.39
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (18 bp):
TAAAAAATAATTTTTATA
Found at i:40630396 original size:37 final size:37
Alignment explanation
Indices: 40630350--40630435 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
40630340 ATAAATAAAA
* *
40630350 ATAATAAATTTTATATGATTTAAAAAATAATTTTTAT
1 ATAAAAAATTATATATGATTTAAAAAATAATTTTTAT
*
40630387 ATAAAAAATTATGTATGATTTAAAAAATAATTTTTAT
1 ATAAAAAATTATATATGATTTAAAAAATAATTTTTAT
40630424 ATAAAAAATTAT
1 ATAAAAAATTAT
40630436 GTTATTTTCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 46 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (37 bp):
ATAAAAAATTATATATGATTTAAAAAATAATTTTTAT
Found at i:40630436 original size:37 final size:37
Alignment explanation
Indices: 40630363--40630437 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
40630353 ATAAATTTTA
40630363 TATGATTTAAAAAATAATTTTTATATAAAAAATTATG
1 TATGATTTAAAAAATAATTTTTATATAAAAAATTATG
40630400 TATGATTTAAAAAATAATTTTTATATAAAAAATTATG
1 TATGATTTAAAAAATAATTTTTATATAAAAAATTATG
40630437 T
1 T
40630438 TATTTTCATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (37 bp):
TATGATTTAAAAAATAATTTTTATATAAAAAATTATG
Found at i:40632017 original size:99 final size:99
Alignment explanation
Indices: 40631846--40632042 Score: 376
Period size: 99 Copynumber: 2.0 Consensus size: 99
40631836 ATTATTACCA
*
40631846 CCGCCGAACCCAGCTGTCACCCCAACGGGCTCTGTCATCGTCACCGCCACCGTAGTAGTAGCACC
1 CCGCCGAACCCAGCTGTCACCCCAACGGGCCCTGTCATCGTCACCGCCACCGTAGTAGTAGCACC
40631911 AGGTATAGGTATCGTGGTGGCCGCCGCCGCTTGC
66 AGGTATAGGTATCGTGGTGGCCGCCGCCGCTTGC
*
40631945 CCGCCGAACCCAGCTGTCACCCCAACGGGCCCTGTCATCGTCGCCGCCACCGTAGTAGTAGCACC
1 CCGCCGAACCCAGCTGTCACCCCAACGGGCCCTGTCATCGTCACCGCCACCGTAGTAGTAGCACC
40632010 AGGTATAGGTATCGTGGTGGCCGCCGCCGCTTG
66 AGGTATAGGTATCGTGGTGGCCGCCGCCGCTTG
40632043 ATTCGGTTGC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
99 96 1.00
ACGTcount: A:0.17, C:0.38, G:0.28, T:0.18
Consensus pattern (99 bp):
CCGCCGAACCCAGCTGTCACCCCAACGGGCCCTGTCATCGTCACCGCCACCGTAGTAGTAGCACC
AGGTATAGGTATCGTGGTGGCCGCCGCCGCTTGC
Found at i:40632280 original size:80 final size:80
Alignment explanation
Indices: 40632188--40632347 Score: 302
Period size: 80 Copynumber: 2.0 Consensus size: 80
40632178 GTCGTAGTGG
*
40632188 GAAAAAGCGGCTCTGTTAGGGTTTTTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTT
1 GAAAAAGCGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTT
40632253 GTTGCCGACGGAAAA
66 GTTGCCGACGGAAAA
*
40632268 GAAAAAGTGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTT
1 GAAAAAGCGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTT
40632333 GTTGCCGACGGAAAA
66 GTTGCCGACGGAAAA
40632348 AGAAGGGAGC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
80 78 1.00
ACGTcount: A:0.30, C:0.12, G:0.34, T:0.24
Consensus pattern (80 bp):
GAAAAAGCGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTT
GTTGCCGACGGAAAA
Found at i:40632318 original size:42 final size:42
Alignment explanation
Indices: 40632191--40632318 Score: 97
Period size: 42 Copynumber: 3.1 Consensus size: 42
40632181 GTAGTGGGAA
* *
40632191 AAAGCGGCTCTGTTAGGGTTTTTAACGGTGACGTATTGAGAG
1 AAAGTGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAG
*** ** * ** *
40632233 AAAGTGAAGCTG--ACGGAGTTGTT---GCCGACGGA-AAAGAA
1 AAAGTGGCTCTGTTA-GG-GTTGTTAACGGTGACGTATTGAGAG
40632271 AAAGTGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAG
1 AAAGTGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAG
40632313 AAAGTG
1 AAAGTG
40632319 AAGCTGACGG
Statistics
Matches: 58, Mismatches: 20, Indels: 16
0.62 0.21 0.17
Matches are distributed among these distances:
38 18 0.31
39 8 0.14
40 2 0.03
41 8 0.14
42 22 0.38
ACGTcount: A:0.29, C:0.11, G:0.34, T:0.26
Consensus pattern (42 bp):
AAAGTGGCTCTGTTAGGGTTGTTAACGGTGACGTATTGAGAG
Found at i:40632334 original size:42 final size:42
Alignment explanation
Indices: 40632212--40632335 Score: 107
Period size: 42 Copynumber: 3.0 Consensus size: 42
40632202 GTTAGGGTTT
40632212 TTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTTG
1 TTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTTG
** * ** * ***
40632254 TT---GCCGACGGA-AAAGAAAAAGTGGCTCTGTTA-GG-GTTG
1 TTAACGGTGACGTATTGAGAGAAAGTGAAGCTG--ACGGAGTTG
40632292 TTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTTG
1 TTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTTG
40632334 TT
1 TT
40632336 GCCGACGGAA
Statistics
Matches: 56, Mismatches: 18, Indels: 16
0.62 0.20 0.18
Matches are distributed among these distances:
38 18 0.32
39 8 0.14
40 2 0.04
41 8 0.14
42 20 0.36
ACGTcount: A:0.30, C:0.10, G:0.35, T:0.25
Consensus pattern (42 bp):
TTAACGGTGACGTATTGAGAGAAAGTGAAGCTGACGGAGTTG
Found at i:40642754 original size:61 final size:61
Alignment explanation
Indices: 40642636--40642755 Score: 136
Period size: 61 Copynumber: 2.0 Consensus size: 61
40642626 TATCTACAAA
* * * * *
40642636 ATTAATTTGATAAAAATAAAGTTAAATAATTACAACATCTAAGTATAAATAGTATTTAAAC
1 ATTAATTAGATAAAAATAAACTTAAATAAGTACAACATCTAAGTACAAATAGCATTTAAAC
* * *
40642697 ATTAATTAGGTAAAAA-AAACTTAAATAAGTATAATATCTAA-TACAAATCGAGCATTTAA
1 ATTAATTAGATAAAAATAAACTTAAATAAGTACAACATCTAAGTACAAAT--AGCATTTAA
40642756 CTTATTTTGC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
59 6 0.12
60 21 0.43
61 22 0.45
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (61 bp):
ATTAATTAGATAAAAATAAACTTAAATAAGTACAACATCTAAGTACAAATAGCATTTAAAC
Found at i:40645633 original size:20 final size:21
Alignment explanation
Indices: 40645608--40645656 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
40645598 AATTATTTTT
40645608 TTATTTTAT-ATTT-TTATAAA
1 TTATTTTATAATTTATTAT-AA
*
40645628 TTATTTT-TAATTTATTGTAA
1 TTATTTTATAATTTATTATAA
40645648 TTATTTTAT
1 TTATTTTAT
40645657 TTGTTTGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 1 0.04
20 20 0.80
21 4 0.16
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
TTATTTTATAATTTATTATAA
Found at i:40646246 original size:17 final size:18
Alignment explanation
Indices: 40646211--40646263 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
40646201 AAGGGTTAAT
40646211 TTTAATTTTTTAATATTA
1 TTTAATTTTTTAATATTA
*
40646229 TTTAATTTTTTCAT-TTA
1 TTTAATTTTTTAATATTA
* *
40646246 TGTAATTTAATTAATATT
1 TTTAATTT-TTTAATATT
40646264 TTTTTATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 10 0.34
18 17 0.59
19 2 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (18 bp):
TTTAATTTTTTAATATTA
Found at i:40646775 original size:14 final size:14
Alignment explanation
Indices: 40646750--40646789 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
40646740 TAACACTAAT
40646750 CCTAAACCAT-AAC
1 CCTAAACCATAAAC
40646763 CCTAAACCCATAAAC
1 CCTAAA-CCATAAAC
*
40646778 CCTAAGCCATAA
1 CCTAAACCATAA
40646790 CATACAAGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.25
14 10 0.42
15 8 0.33
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (14 bp):
CCTAAACCATAAAC
Found at i:40649817 original size:9 final size:10
Alignment explanation
Indices: 40649797--40649826 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
40649787 AATTATTTTG
40649797 TATTTGGTTT
1 TATTTGGTTT
40649807 TATTT-GTTT
1 TATTTGGTTT
40649816 TATTTGGTTT
1 TATTTGGTTT
40649826 T
1 T
40649827 GGCATTGAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.10, C:0.00, G:0.17, T:0.73
Consensus pattern (10 bp):
TATTTGGTTT
Found at i:40650282 original size:44 final size:45
Alignment explanation
Indices: 40650234--40650436 Score: 200
Period size: 44 Copynumber: 4.6 Consensus size: 45
40650224 TTTAATCCGT
* * *
40650234 TCCACTGTAACTTCAGGAAGA-AAGGA-TTAGTAGCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAA-GACTTAGTAGCTTCAATCTGC
* * * * * *
40650278 TCCACTACAACATCAGGGAGATAAGACTCACTATCTTCAGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTAGTAGCTTCAATCTGC
* * *
40650323 TCCACTGTAACTTCAGGGAGATAAGACTTA-TATCTTCAATTTGC
1 TCCACTGCAACTTCAGGGAGATAAGACTTAGTAGCTTCAATCTGC
* *
40650367 CCCACTGCAACTTCAAGGG-GATAAGA-TTAGTGGCTTCAATCTGC
1 TCCACTGCAACTTC-AGGGAGATAAGACTTAGTAGCTTCAATCTGC
* * *
40650411 TCTACTACAACTTTAGGGAGATAAGA
1 TCCACTGCAACTTCAGGGAGATAAGA
40650437 TTCATCATTG
Statistics
Matches: 132, Mismatches: 22, Indels: 10
0.80 0.13 0.06
Matches are distributed among these distances:
43 7 0.05
44 78 0.59
45 47 0.36
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (45 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTAGTAGCTTCAATCTGC
Found at i:40650391 original size:89 final size:88
Alignment explanation
Indices: 40650234--40650438 Score: 209
Period size: 89 Copynumber: 2.3 Consensus size: 88
40650224 TTTAATCCGT
* * *
40650234 TCCACTGTAACTTCAGGAAGA-AAGGATTAGTAGCTTCAGTCTGCTCCACTACAACATCAGGGAG
1 TCCACTGTAACTTCAGGGAGATAA-GATTAGTAGCTTCAATCTGCCCCACTACAACATCAGGGAG
* *
40650298 ATAAGACTCACTATCTTCAGTCTGC
65 ATAAGA-TCACTAGCTTCAATCTGC
* * * *
40650323 TCCACTGTAACTTCAGGGAGATAAGACTTA-TATCTTCAATTTGCCCCACTGCAACTTCAAGGG-
1 TCCACTGTAACTTCAGGGAGATAAGA-TTAGTAGCTTCAATCTGCCCCACTACAACATC-AGGGA
* * *
40650386 GATAAGATTAGTGGCTTCAATCTGC
64 GATAAGATCACTAGCTTCAATCTGC
* ** *
40650411 TCTACTACAACTTTAGGGAGATAAGATT
1 TCCACTGTAACTTCAGGGAGATAAGATT
40650439 CATCATTGTA
Statistics
Matches: 97, Mismatches: 16, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
87 2 0.02
88 35 0.36
89 51 0.53
90 9 0.09
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.28
Consensus pattern (88 bp):
TCCACTGTAACTTCAGGGAGATAAGATTAGTAGCTTCAATCTGCCCCACTACAACATCAGGGAGA
TAAGATCACTAGCTTCAATCTGC
Found at i:40650537 original size:50 final size:49
Alignment explanation
Indices: 40650477--40650917 Score: 357
Period size: 50 Copynumber: 8.8 Consensus size: 49
40650467 GCACTGTCAG
* * *
40650477 GGAAATAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCATTGTCGA
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCACTG-CGA
* * ** * * *
40650527 GGAAGGAAGATTCGCCGTTGTAGCTTCAATCTGTCCT-ACTGCACCGCCA
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTTAATTGCACTGCGA
* * * * *
40650576 GGAAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGTAATGTCGG
1 GG-AAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCACTG-CGA
** * * * ** * *
40650627 GGAAACAAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACTGCTA
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCACTGCGA
* *
40650676 GGGAATTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGA
1 -GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCACTG-CGA
* * * * * * * *
40650727 GGAAGCAAGATTCACCGTTGTAGCTTCAATATGTTCT-ACTGCACAGCCA
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCT-TTTTAATTGCACTGCGA
* * *
40650776 GAGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGG
1 G-GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCACTG-CGA
* * *** * * *
40650827 GGAAGCAAGATTCGCCGTTGTAGCTTCAAT-TTGTCCCACTGCACCGCCA
1 GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTT-TTTAATTGCACTGCGA
40650876 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTG
1 -GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTG
40650918 TAACCTCAGG
Statistics
Matches: 294, Mismatches: 84, Indels: 26
0.73 0.21 0.06
Matches are distributed among these distances:
49 16 0.05
50 264 0.90
51 14 0.05
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (49 bp):
GGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTAATTGCACTGCGA
Found at i:40650548 original size:100 final size:100
Alignment explanation
Indices: 40650444--40650917 Score: 652
Period size: 100 Copynumber: 4.7 Consensus size: 100
40650434 AGATTCATCA
* * *
40650444 TTGTAGCTTCAATTCGTTCCACTGCACTGTCAGGGAAATAAGATTCACCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATTCGTTCCACTGCACCGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCT
* *
40650509 TTTTAATTGCATTGTCGAGGAAGGAAGATTCGCCG
66 TTTTAATTGCAATGTCGAGGAAGCAAGATTCGCCG
* *
40650544 TTGTAGCTTCAA-TC-TGTCCTACTGCACCGCCA-GGAAAGTAAGATTCACTGTTGTGGCTTCAA
1 TTGTAGCTTCAATTCGT-TCC-ACTGCACCGCCAGGGAAA-TAAGATTCGCCGTTGTGGCTTCAA
* * * *
40650606 TCTTTTTAATTGTAATGTCGGGGAAACAAGATTCGCCA
63 TCTTTTTAATTGCAATGTCGAGGAAGCAAGATTCGCCG
* * *
40650644 TTGTAGCTTCAA-TCTGTTCCACTGCACTGCTAGGGAATTAAGATTCGCCGTTGTGGCTTCAATC
1 TTGTAGCTTCAATTC-GTTCCACTGCACCGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATC
*
40650708 TTTTTAATTGCAATGTCGAGGAAGCAAGATTCACCG
65 TTTTTAATTGCAATGTCGAGGAAGCAAGATTCGCCG
* * * * *
40650744 TTGTAGCTTCAATAT-GTTCTACTGCACAGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTTAATC
1 TTGTAGCTTCAAT-TCGTTCCACTGCACCGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATC
*
40650808 TTTTTAATTGCAATGTCGGGGAAGCAAGATTCGCCG
65 TTTTTAATTGCAATGTCGAGGAAGCAAGATTCGCCG
* * *
40650844 TTGTAGCTTCAATTTGTCCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGTGGCTTCAATCT
1 TTGTAGCTTCAATTCGTTCCACTGCACCGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCT
40650909 TTTTAATTG
66 TTTTAATTG
40650918 TAACCTCAGG
Statistics
Matches: 333, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
98 1 0.00
99 11 0.03
100 312 0.94
101 7 0.02
102 2 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (100 bp):
TTGTAGCTTCAATTCGTTCCACTGCACCGCCAGGGAAATAAGATTCGCCGTTGTGGCTTCAATCT
TTTTAATTGCAATGTCGAGGAAGCAAGATTCGCCG
Found at i:40650739 original size:200 final size:199
Alignment explanation
Indices: 40650433--40650917 Score: 731
Period size: 200 Copynumber: 2.4 Consensus size: 199
40650423 TTAGGGAGAT
** *
40650433 AAGATTCATCATTGTAGCTTCAATTCGTTCCACTGCACTG-TCAGGGAAATAAGATTCACCGTTG
1 AAGATTCGCCATTGTAGCTTCAATT-GTTCCACTGCACTGCT-AGGGAAATAAGATTCGCCGTTG
* * * *
40650497 TGGCTTCAATCTTTTTAATTGCATTGTCGAGGAAGGAAGATTCGCCGTTGTAGCTTCAATCTGTC
64 TGGCTTCAATCTTTTTAATTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATATGTC
* * *
40650562 CTACTGCACCGCCAG-GAAAGTAAGATTCACTGTTGTGGCTTCAATCTTTTTAATTGTAATGTCG
129 CTACTGCACAGCCAGAG-AAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCG
40650626 GGGAAAC
193 GGGAAAC
*
40650633 AAGATTCGCCATTGTAGCTTCAATCTGTTCCACTGCACTGCTAGGGAATTAAGATTCGCCGTTGT
1 AAGATTCGCCATTGTAGCTTCAAT-TGTTCCACTGCACTGCTAGGGAAATAAGATTCGCCGTTGT
*
40650698 GGCTTCAATCTTTTTAATTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATATGTTC
65 GGCTTCAATCTTTTTAATTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATATGTCC
* *
40650763 TACTGCACAGCCAGAGAAGTAAGATTCGCCGTTGTGGCTTTAATCTTTTTAATTGCAATGTCGGG
130 TACTGCACAGCCAGAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGG
*
40650828 GAAGC
195 GAAAC
* * * * *
40650833 AAGATTCGCCGTTGTAGCTTCAATTTGTCCCACTGCACCGCCAGGGAAGTAAGATTCGCCGTTGT
1 AAGATTCGCCATTGTAGCTTCAA-TTGTTCCACTGCACTGCTAGGGAAATAAGATTCGCCGTTGT
40650898 GGCTTCAATCTTTTTAATTG
65 GGCTTCAATCTTTTTAATTG
40650918 TAACCTCAGG
Statistics
Matches: 261, Mismatches: 20, Indels: 8
0.90 0.07 0.03
Matches are distributed among these distances:
200 257 0.98
201 4 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.33
Consensus pattern (199 bp):
AAGATTCGCCATTGTAGCTTCAATTGTTCCACTGCACTGCTAGGGAAATAAGATTCGCCGTTGTG
GCTTCAATCTTTTTAATTGCAATGTCGAGGAAGCAAGATTCACCGTTGTAGCTTCAATATGTCCT
ACTGCACAGCCAGAGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGTCGGGG
AAAC
Found at i:40651747 original size:16 final size:16
Alignment explanation
Indices: 40651697--40651750 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
40651687 TGGCCTCTCC
* *
40651697 TTTTTCTTTTTCTTAT
1 TTTTTATTTTTTTTAT
*
40651713 TTTCTT-TTTTTTGTA-
1 TTT-TTATTTTTTTTAT
40651728 TTTTTATTTTTTTTAT
1 TTTTTATTTTTTTTAT
40651744 TTTTTAT
1 TTTTTAT
40651751 GAAACATTTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 2 0.06
15 11 0.34
16 17 0.53
17 2 0.06
ACGTcount: A:0.09, C:0.06, G:0.02, T:0.83
Consensus pattern (16 bp):
TTTTTATTTTTTTTAT
Found at i:40651748 original size:17 final size:17
Alignment explanation
Indices: 40651712--40651750 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
40651702 CTTTTTCTTA
* *
40651712 TTTTCTTTTTTTTGTAT
1 TTTTATTTTTTTTATAT
40651729 TTTTATTTTTTTTAT-T
1 TTTTATTTTTTTTATAT
40651745 TTTTAT
1 TTTTAT
40651751 GAAACATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTATTTTTTTTATAT
Found at i:40654959 original size:20 final size:19
Alignment explanation
Indices: 40654934--40654972 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40654924 ATTAGAACAA
40654934 CTTTACTAGAAAACAAATAT
1 CTTTAC-AGAAAACAAATAT
* *
40654954 CTTTACATAAAACGAATAT
1 CTTTACAGAAAACAAATAT
40654973 ATATACGACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.31
Consensus pattern (19 bp):
CTTTACAGAAAACAAATAT
Found at i:40659355 original size:10 final size:10
Alignment explanation
Indices: 40659332--40659365 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
40659322 TAAATGTATT
40659332 ATTTTT-AT-
1 ATTTTTAATA
40659340 ATTTTTAATA
1 ATTTTTAATA
40659350 ATTTTTAATA
1 ATTTTTAATA
40659360 ATTTTT
1 ATTTTT
40659366 CAAATATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 6 0.25
9 2 0.08
10 16 0.67
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:40662257 original size:4 final size:4
Alignment explanation
Indices: 40662248--40662290 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
40662238 TTAGAAATCT
40662248 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
40662291 TTTGCATGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:40665468 original size:2 final size:2
Alignment explanation
Indices: 40665461--40665488 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40665451 TTTGATTGAC
40665461 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
40665489 TGTATTAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:40669227 original size:6 final size:7
Alignment explanation
Indices: 40669210--40669257 Score: 69
Period size: 7 Copynumber: 6.9 Consensus size: 7
40669200 AATTAAACAA
40669210 AAAAATC
1 AAAAATC
40669217 AAAAATC
1 AAAAATC
40669224 AAAAATC
1 AAAAATC
*
40669231 AAAAATG
1 AAAAATC
*
40669238 AAAAATG
1 AAAAATC
*
40669245 AAAAATG
1 AAAAATC
40669252 AAAAAT
1 AAAAAT
40669258 ATTTTTGGAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (7 bp):
AAAAATC
Found at i:40669229 original size:14 final size:14
Alignment explanation
Indices: 40669210--40669257 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
40669200 AATTAAACAA
*
40669210 AAAAATCAAAAATC
1 AAAAATCAAAAATG
40669224 AAAAATCAAAAATG
1 AAAAATCAAAAATG
*
40669238 AAAAATGAAAAATG
1 AAAAATCAAAAATG
40669252 AAAAAT
1 AAAAAT
40669258 ATTTTTGGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.73, C:0.06, G:0.06, T:0.15
Consensus pattern (14 bp):
AAAAATCAAAAATG
Found at i:40680462 original size:20 final size:18
Alignment explanation
Indices: 40680415--40680521 Score: 60
Period size: 19 Copynumber: 5.8 Consensus size: 18
40680405 TAAGATAAAC
40680415 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATATTTAAT
40680432 ATTAAGA-TAATCACTTTAAT
1 ATTAA-ATTAAT-A-TTTAAT
** *
40680452 ATTAAATTAATAAAATACT
1 ATTAAATTAAT-ATTTAAT
*
40680471 ATTAAGA-TAAGTATTAAAT
1 ATTAA-ATTAA-TATTTAAT
* *
40680490 -TTAATTTAATATTAAACT
1 ATTAAATTAATATTTAA-T
*
40680508 ATTAAAATAATATT
1 ATTAAATTAATATT
40680522 ATATTTGGAA
Statistics
Matches: 69, Mismatches: 11, Indels: 18
0.70 0.11 0.18
Matches are distributed among these distances:
17 15 0.22
18 9 0.13
19 27 0.39
20 18 0.26
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATATTTAAT
Found at i:40689358 original size:20 final size:20
Alignment explanation
Indices: 40689341--40689378 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40689331 GACGTTCATC
*
40689341 TATCATATATTCATTTCACA
1 TATCACATATTCATTTCACA
*
40689361 TATCACATTTTCATTTCA
1 TATCACATATTCATTTCA
40689379 AATGTCTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (20 bp):
TATCACATATTCATTTCACA
Found at i:40689419 original size:14 final size:13
Alignment explanation
Indices: 40689399--40689463 Score: 69
Period size: 13 Copynumber: 4.8 Consensus size: 13
40689389 CCAATGTTCC
*
40689399 ATTTCATATATCT
1 ATTTCATATAACT
*
40689412 ATTTTCATATATCT
1 A-TTTCATATAACT
*
40689426 GA-TTCATATAACC
1 -ATTTCATATAACT
40689439 ATTTCATATAACT
1 ATTTCATATAACT
40689452 ATTTCCATATAA
1 ATTT-CATATAA
40689464 AAAATTTGTA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
12 1 0.02
13 24 0.53
14 19 0.42
15 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (13 bp):
ATTTCATATAACT
Found at i:40695691 original size:15 final size:16
Alignment explanation
Indices: 40695662--40695703 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
40695652 CATAAGATCC
*
40695662 TTTTTGCATTCATTGT
1 TTTTTGCATTAATTGT
*
40695678 TTTTTGC-TTAATTGA
1 TTTTTGCATTAATTGT
*
40695693 TCTTTGCATTA
1 TTTTTGCATTA
40695704 TACATTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.17, C:0.12, G:0.12, T:0.60
Consensus pattern (16 bp):
TTTTTGCATTAATTGT
Found at i:40706687 original size:133 final size:133
Alignment explanation
Indices: 40706485--40707307 Score: 1282
Period size: 133 Copynumber: 6.2 Consensus size: 133
40706475 CATGTTTCAC
*
40706485 AGATAACAGATCCTGTCTTCATATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
40706549 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
40706614 CGA
131 CGA
* * * * * *
40706617 AGATAGCAGATCCTGTCTTCCTATATCGGTAGCTAAGTGGATCGAACATGTAGTTCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * * * *
40706682 CATACTGGTGGCGAAGTAGATCGAAAAAAACAGATCTTGGCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
40706747 CGA
131 CGA
* * *
40706750 AGATAGCAGATCCTGTCTTCCTATATTTGTAGCGAA---GATCGAATATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
40706812 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
40706877 CGA
131 CGA
* *
40706880 AGATAACAGATCCTGTCTTCCTATATTTGTAGCGAA---GATCGAATATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
40706942 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
40707007 CGA
131 CGA
*
40707010 AGATAACAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * *
40707075 CATACTGGTGGTGAAGTGGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
*
40707140 TGA
131 CGA
* *
40707143 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAATTGGATTGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * * *
40707208 CATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTGGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
*
40707273 CAA
131 CGA
* * *
40707276 AAATAGCAGATCCTGTCTTCTTATATTGGTAG
1 AGATAACAGATCCTGTCTTCCTATATTGGTAG
40707308 TGAGGCAGAC
Statistics
Matches: 640, Mismatches: 47, Indels: 7
0.92 0.07 0.01
Matches are distributed among these distances:
130 248 0.39
132 29 0.05
133 363 0.57
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (133 bp):
AGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
CGA
Found at i:40707055 original size:263 final size:264
Alignment explanation
Indices: 40706485--40707310 Score: 1302
Period size: 263 Copynumber: 3.1 Consensus size: 264
40706475 CATGTTTCAC
*
40706485 AGATAACAGATCCTGTCTTCATATATTGGTAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
40706549 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
* * * * *
40706614 CGAAGATAGCAGATCCTGTCTTCCTATATCGGTAGCTAAGTGGATCGAACATGTAGTTCTTGTCT
131 CGAAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAA--GGATCGAACATGCAGATCTTGTCT
* * *
40706679 TCCCATACTGGTGGCGAAGTAGATCGAAAAAAACAGATCTTGGCTTCATGTATTGGCGTGAAGTA
194 TCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
40706744 GATCGA
259 GATCGA
* * * *
40706750 AGATAGCAGATCCTGTCTTCCTATATTTGTAGCGAA---GATCGAATATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
40706812 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
* *
40706877 CGAAGATAACAGATCCTGTCTTCCTATATTTGTAGCGAA-GATCGAATATGCAGATCTTGTCTTC
131 CGAAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGGATCGAACATGCAGATCTTGTCTTC
* * *
40706941 CCATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGA
196 CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
40707006 TCGA
261 TCGA
40707010 AGATAACAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
* * * *
40707075 CATACTGGTGGTGAAGTGGATCGAAGAAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGAT
66 CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
* * *
40707140 TGAAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAATTGGATTGAAGATGCAGATCTTGTCT
131 CGAAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAA--GGATCGAACATGCAGATCTTGTCT
* *
40707205 TCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTG
194 TCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTA
*
40707270 GATCAA
259 GATCGA
* * *
40707276 AAATAGCAGATCCTGTCTTCTTATATTGGTAGTGA
1 AGATAACAGATCCTGTCTTCCTATATTGGTAGTGA
40707311 GGCAGACTTA
Statistics
Matches: 516, Mismatches: 38, Indels: 13
0.91 0.07 0.02
Matches are distributed among these distances:
260 118 0.23
263 248 0.48
265 29 0.06
266 121 0.23
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (264 bp):
AGATAACAGATCCTGTCTTCCTATATTGGTAGTGAAGTGGATCGAAGATGCAGATCTTGTCTTCC
CATACTGGTGGTGAAATAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCATGAAGTAGAT
CGAAGATAACAGATCCTGTCTTCCTATATTGGTAGCGAAGGATCGAACATGCAGATCTTGTCTTC
CCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGA
TCGA
Found at i:40716314 original size:21 final size:21
Alignment explanation
Indices: 40716266--40716319 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
40716256 TTAAAAACCC
*
40716266 AATGGTACCGATATTTTTATA
1 AATGGTATCGATATTTTTATA
* * *
40716287 AA-AGTATTGATATTTTTTTA
1 AATGGTATCGATATTTTTATA
40716307 AATGGTATCGATA
1 AATGGTATCGATA
40716320 CCTAATTACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (21 bp):
AATGGTATCGATATTTTTATA
Found at i:40723655 original size:14 final size:15
Alignment explanation
Indices: 40723638--40723666 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40723628 GAGTATAGTA
40723638 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
40723652 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
40723667 TACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:40723982 original size:15 final size:16
Alignment explanation
Indices: 40723955--40723984 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
40723945 ATGAGTATTG
40723955 TAAATATTTTAAAAAA
1 TAAATATTTTAAAAAA
40723971 TAAATA-TTTAAAAA
1 TAAATATTTTAAAAA
40723985 GAGAGATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATATTTTAAAAAA
Found at i:40731179 original size:36 final size:36
Alignment explanation
Indices: 40731132--40731209 Score: 129
Period size: 36 Copynumber: 2.2 Consensus size: 36
40731122 TTTGTATGAA
* *
40731132 CTTACTAAGCCTTTGATATGATTACTGTTGTCTTCC
1 CTTACTAAGCCTTTGATATGATTACCGTTGTCCTCC
*
40731168 CTTACTAAGCCTTTGATATGCTTACCGTTGTCCTCC
1 CTTACTAAGCCTTTGATATGATTACCGTTGTCCTCC
40731204 CTTACT
1 CTTACT
40731210 TGTAGATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.18, C:0.27, G:0.13, T:0.42
Consensus pattern (36 bp):
CTTACTAAGCCTTTGATATGATTACCGTTGTCCTCC
Found at i:40733071 original size:11 final size:13
Alignment explanation
Indices: 40733055--40733088 Score: 54
Period size: 11 Copynumber: 2.8 Consensus size: 13
40733045 AATTTCACAG
40733055 AAAAATTTCG-T-
1 AAAAATTTCGTTC
40733066 AAAAATTTCGTTC
1 AAAAATTTCGTTC
40733079 AAAAATTTCG
1 AAAAATTTCG
40733089 ACGTTTGGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 10 0.48
12 1 0.05
13 10 0.48
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (13 bp):
AAAAATTTCGTTC
Found at i:40734221 original size:33 final size:33
Alignment explanation
Indices: 40734157--40734493 Score: 157
Period size: 42 Copynumber: 9.8 Consensus size: 33
40734147 ATATAAAGGG
*
40734157 GGTTGCTAAGTGCTGATTCCCC----CA-AGG-
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
*
40734184 GGTTGCTAAGTGCTGATTCCTCGATTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
40734217 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-TG---GT
*
40734259 GGTTGCTAAGTGCTGATTCCCCGACTCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* *
40734292 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCC-CCG-A--TT-CAT-T---GGT
*
40734334 GGTTGCTAAGTGTTGATTCCCC----CGA--GG-
1 GGTTGCTAAGTGCTGATTCCCCGATTC-ATTGGT
*
40734361 GGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
* * *
40734394 GGTTGCTAAGTACTGA-TCCCACCATATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCC-CGAT-TC----AT-TG---GT
*
40734436 GGTTGCTAAGTGCTGATAT--CCGACTCATTGGT
1 GGTTGCTAAGTGCTGAT-TCCCCGATTCATTGGT
*
40734468 GGTTGCTAAGTGCTGAATCCACCGAT
1 GGTTGCTAAGTGCTGATTCC-CCGAT
40734494 AACGGATAAC
Statistics
Matches: 239, Mismatches: 24, Indels: 87
0.68 0.07 0.25
Matches are distributed among these distances:
27 42 0.18
28 2 0.01
30 1 0.00
31 4 0.02
32 25 0.10
33 58 0.24
34 12 0.05
35 4 0.02
36 4 0.02
37 5 0.02
38 7 0.03
39 5 0.02
40 3 0.01
41 7 0.03
42 59 0.25
44 1 0.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.31
Consensus pattern (33 bp):
GGTTGCTAAGTGCTGATTCCCCGATTCATTGGT
Found at i:40734276 original size:42 final size:41
Alignment explanation
Indices: 40734217--40734353 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 41
40734207 ATTCATTGGT
40734217 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG-AAGG
* *
40734259 GGTTGCTAAGTGCTGATTCC-CCG-A-C-T-CAT-TG--GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
40734292 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAA-GG
*
40734334 GGTTGCTAAGTGTTGATTCC
1 GGTTGCTAAGTGCTGATTCC
40734354 CCCGAGGGGT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 21 0.26
34 3 0.04
35 1 0.01
36 3 0.04
37 3 0.04
38 3 0.04
39 3 0.04
40 1 0.01
41 3 0.04
42 40 0.49
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGG
Found at i:40734303 original size:75 final size:75
Alignment explanation
Indices: 40734180--40734355 Score: 316
Period size: 75 Copynumber: 2.3 Consensus size: 75
40734170 TGATTCCCCC
* *
40734180 AAGGGGTTGCTAAGTGCTGATTCCTCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
40734245 TTAAATGTGA
66 TTAAATGTGA
40734255 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
40734320 TTAAATGTGA
66 TTAAATGTGA
* *
40734330 AGGGGGTTGCTAAGTGTTGATTCCCC
1 AAGGGGTTGCTAAGTGCTGATTCCCC
40734356 CGAGGGGTTG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
75 97 1.00
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:40734362 original size:102 final size:102
Alignment explanation
Indices: 40734256--40734452 Score: 340
Period size: 102 Copynumber: 1.9 Consensus size: 102
40734246 TAAATGTGAA
* * * *
40734256 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGATCCCACCATATCT
* *
40734321 TAAATGTGAAGGGGGTTGCTAAGTGTTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
40734358 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGATCCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGATCCCACCATATCT
40734423 TAAATGTGAAAGGGGTTGCTAAGTGCTGAT
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGAT
40734453 ATCCGACTCA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.31
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTACTGATCCCACCATATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:40734448 original size:177 final size:176
Alignment explanation
Indices: 40734152--40734491 Score: 583
Period size: 177 Copynumber: 1.9 Consensus size: 176
40734142 ATTGAATATA
* *
40734152 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCTCGATTCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
* * *
40734217 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGAT-TCCCC
66 GGTTGCTAAGTACTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATAT--CC
*
40734281 GACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTG
129 GACTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTTAAATGTG
* *
40734329 AAGGGGGTTGCTAAGTGTTGATTCCCCCGAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
1 AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
40734394 GGTTGCTAAGTACTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATATCCGA
66 GGTTGCTAAGTACTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATATCCGA
40734459 CTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
131 CTCATTGGTGGTTGCTAAGTGCTGAATCCACCG
40734492 ATAACGGATA
Statistics
Matches: 154, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
176 36 0.23
177 117 0.76
178 1 0.01
ACGTcount: A:0.21, C:0.20, G:0.28, T:0.31
Consensus pattern (176 bp):
AAGGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGT
GGTTGCTAAGTACTGATCCCACCATATCTTAAATGTGAAAGGGGTTGCTAAGTGCTGATATCCGA
CTCATTGGTGGTTGCTAAGTGCTGAATCCACCGTATCTTAAATGTG
Found at i:40740139 original size:42 final size:42
Alignment explanation
Indices: 40740053--40740172 Score: 134
Period size: 42 Copynumber: 2.8 Consensus size: 42
40740043 AGCTCGTACA
* * ** *
40740053 ATGCCATATCCCAGATAAGGTCTTACATGTTATAATATACCG
1 ATGCCATGTCCCAGATAAGGTCTTACACGAAATCATATACCG
*
40740095 ATGCCACTGTCCCAGATAGGGTCTTACACGAAATCATATA-CG
1 ATGCCA-TGTCCCAGATAAGGTCTTACACGAAATCATATACCG
* * *
40740137 ATGCCAATGTCCCAGACATGGTCTTACACAAAATCA
1 ATGCC-ATGTCCCAGATAAGGTCTTACACGAAATCA
40740173 CACCTCGGAA
Statistics
Matches: 67, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
42 39 0.58
43 28 0.42
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (42 bp):
ATGCCATGTCCCAGATAAGGTCTTACACGAAATCATATACCG
Found at i:40747018 original size:98 final size:97
Alignment explanation
Indices: 40746824--40747031 Score: 371
Period size: 100 Copynumber: 2.1 Consensus size: 97
40746814 ATTGCGTGTT
40746824 TTGGACTTAGGGACTAAATTGCATAGAAGTGAAATATTGGGCTAATTTGTAAAAAATTATAAAAG
1 TTGGACTTAGGGACTAAATTGCATAGAAGTGAAATATTGGGCTAATTTGTAAAAAATTATAAAAG
40746889 GACTTAAATGCATAAAATGAGTTAATTTTTTTG
66 GACTTAAATGCATAAAATGAGTTAA-TTTTTTG
40746922 TTGGACTTAGGGACTAAATTGCATAGAAGTGAAATATTGGGCTAATTTTGTAAAAAAATTATAAA
1 TTGGACTTAGGGACTAAATTGCATAGAAGTGAAATATTGGGCTAA-TTTGT-AAAAAATTATAAA
40746987 AGGACTTAAATGCATAAAATGAGTTAATTTTTTTG
64 AGGACTTAAATGCATAAAATGAGTTAA-TTTTTTG
*
40747022 TTGGAATTAG
1 TTGGACTTAG
40747032 TTAATTGAAT
Statistics
Matches: 107, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
98 45 0.42
99 5 0.05
100 57 0.53
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (97 bp):
TTGGACTTAGGGACTAAATTGCATAGAAGTGAAATATTGGGCTAATTTGTAAAAAATTATAAAAG
GACTTAAATGCATAAAATGAGTTAATTTTTTG
Found at i:40750065 original size:21 final size:21
Alignment explanation
Indices: 40750032--40750093 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
40750022 ATGGTCTACA
* *
40750032 TACATGGGTATGTGAAGTAGT
1 TACACGGGCATGTGAAGTAGT
40750053 TACACGGGCATGTGAAGTAGT
1 TACACGGGCATGTGAAGTAGT
* *
40750074 TACGCGGGCATGTGGAGTAG
1 TACACGGGCATGTGAAGTAG
40750094 CCATACGGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.26, C:0.11, G:0.37, T:0.26
Consensus pattern (21 bp):
TACACGGGCATGTGAAGTAGT
Found at i:40752182 original size:41 final size:41
Alignment explanation
Indices: 40752127--40752208 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
40752117 TCAGCAGATA
*
40752127 AAAGCTGAACATCAAGTACCATTAGGATTGTTACAACCTAT
1 AAAGCTGAACATCAAGTACCATCAGGATTGTTACAACCTAT
40752168 AAAGCTGAACATCAAGTACCATCAGGATTGTTACAACCTAT
1 AAAGCTGAACATCAAGTACCATCAGGATTGTTACAACCTAT
40752209 CACGATTCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.26
Consensus pattern (41 bp):
AAAGCTGAACATCAAGTACCATCAGGATTGTTACAACCTAT
Found at i:40753946 original size:6 final size:6
Alignment explanation
Indices: 40753935--40753967 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40753925 GTATTGCAAT
*
40753935 TTTCCA TTTCCA TTTCCA TTTCCA TTTCTA TTT
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTT
40753968 TTGAAAACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.27, G:0.00, T:0.58
Consensus pattern (6 bp):
TTTCCA
Found at i:40755285 original size:25 final size:25
Alignment explanation
Indices: 40755251--40755322 Score: 108
Period size: 25 Copynumber: 2.9 Consensus size: 25
40755241 AACCAAGCCA
*
40755251 AGCCTTTGTGACGAATTATCTAAAG
1 AGCCTTTGTGATGAATTATCTAAAG
* *
40755276 AGCCTTTGTGGTGAATTATCTGAAG
1 AGCCTTTGTGATGAATTATCTAAAG
*
40755301 AGCCTTTGTGATGTATTATCTA
1 AGCCTTTGTGATGAATTATCTA
40755323 GAACGTTTGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.14, G:0.22, T:0.38
Consensus pattern (25 bp):
AGCCTTTGTGATGAATTATCTAAAG
Found at i:40776382 original size:66 final size:66
Alignment explanation
Indices: 40776276--40776399 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 66
40776266 TTTCTGCACG
* *
40776276 AATGTCACTGCATGAATTAATTCTACACTACGTCCAGAATTGTCACCGCAGTTGACAGATATTTG
1 AATGTCACTACATGAATTAATTCCACACTACGTCCAGAATTGTCACCGCAGTTGACAGATATTTG
40776341 C
66 C
* * * * **
40776342 AATGTCGCTACATGAGTTAATTCCAGATTACGTCCAGAATTGTTGCCGCAGTTGACAG
1 AATGTCACTACATGAATTAATTCCACACTACGTCCAGAATTGTCACCGCAGTTGACAG
40776400 CTGTCTGATA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 50 1.00
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (66 bp):
AATGTCACTACATGAATTAATTCCACACTACGTCCAGAATTGTCACCGCAGTTGACAGATATTTG
C
Found at i:40778875 original size:50 final size:50
Alignment explanation
Indices: 40778755--40779046 Score: 300
Period size: 50 Copynumber: 5.7 Consensus size: 50
40778745 GAGGATGAAA
*
40778755 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATGAGAGG
* *
40778811 TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
*
40778861 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
** * * * **
40778911 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCTATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * * * **
40778961 TCTCATGTAAGACCATATCTGGGATATGACATTGGCA--GTACAAGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* * *
40779010 TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40779047 TGTTATATTC
Statistics
Matches: 203, Mismatches: 32, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
49 35 0.17
50 129 0.64
53 3 0.01
55 1 0.00
56 35 0.17
ACGTcount: A:0.27, C:0.22, G:0.28, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:40778996 original size:150 final size:153
Alignment explanation
Indices: 40778761--40779046 Score: 339
Period size: 149 Copynumber: 1.9 Consensus size: 153
40778751 GAAATCCCAT
* * **
40778761 GTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATATAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCACT--GATTATGAGAACTCCCATATAAGACCA
* * * * * * ** *
40778826 TGTCTGGGACATGGCGTTGGCACCG-AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG
64 TATCTGGGACATGACATTGGCA--GTACAAGAAACATCCCATGTAAGACCATGTCTGGGACATAG
40778890 CGTTGGCACCGAGATGAGAGGTCCCCC
127 CGTTGGCACCGAGATGAGAGGTCCCCC
* *
40778917 GTAAGACCATGTCTGGGACATGGCATGGGCA-C-CT-A-TATGAGAACTCTCATGTAAGACCATA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCACTGATTATGAGAACTCCCATATAAGACCATA
* * *
40778978 TCTGGGATATGACATTGGCAGTACAAGAAACATCCCATGTAAGACTATGTCTGGGACATAGCTTT
66 TCTGGGACATGACATTGGCAGTACAAGAAACATCCCATGTAAGACCATGTCTGGGACATAGCGTT
40779043 GGCA
131 GGCA
40779047 TGTTATATTC
Statistics
Matches: 111, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
148 1 0.01
149 39 0.35
150 38 0.34
151 1 0.01
154 1 0.01
155 1 0.01
156 30 0.27
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (153 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCACTGATTATGAGAACTCCCATATAAGACCATA
TCTGGGACATGACATTGGCAGTACAAGAAACATCCCATGTAAGACCATGTCTGGGACATAGCGTT
GGCACCGAGATGAGAGGTCCCCC
Found at i:40783644 original size:6 final size:6
Alignment explanation
Indices: 40783633--40783665 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
40783623 TTCTTAGAAA
*
40783633 TTTTAT TTTTAT TTTTAT TTTTAT TTTTCT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
40783666 CAAAAGTCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:40788050 original size:20 final size:19
Alignment explanation
Indices: 40788025--40788076 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
40788015 ACATATAATT
40788025 ATTATATTTTAATAAATATA
1 ATTATA-TTTAATAAATATA
*
40788045 ATTATA-TTAATTAATATA
1 ATTATATTTAATAAATATA
*
40788063 TTTATAATTTAATA
1 ATTAT-ATTTAATA
40788077 CATTTGGGTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.56
19 1 0.04
20 11 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATATTTAATAAATATA
Found at i:40795430 original size:95 final size:95
Alignment explanation
Indices: 40795320--40795508 Score: 283
Period size: 95 Copynumber: 2.0 Consensus size: 95
40795310 AATTCTCAAG
* *
40795320 TTATATTATGATTTTAGTAAATTCATATAAGAACATTTATTATTAAGAATTATATGAAATTATAT
1 TTATATTATGATTTTAGTAAATTCATATAAAAACATTGATTATTAAGAATTATATGAAATTATAT
*
40795385 ATCATT-ATTA-AATTATATTTAATATTTATC
66 AT-ATTAATTATAA-TATATTTAATAATTATC
* * *
40795415 TTATATTATGATTTTAGTAAATTCATATAAAAATATTGATTATTAAGAATTTTATTAAATTATAT
1 TTATATTATGATTTTAGTAAATTCATATAAAAACATTGATTATTAAGAATTATATGAAATTATAT
*
40795480 ATTTTAATTATAATATATTTAATAATTAT
66 ATATTAATTATAATATATTTAATAATTAT
40795509 TATGTTAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
94 2 0.02
95 81 0.95
96 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.05, T:0.50
Consensus pattern (95 bp):
TTATATTATGATTTTAGTAAATTCATATAAAAACATTGATTATTAAGAATTATATGAAATTATAT
ATATTAATTATAATATATTTAATAATTATC
Found at i:40795740 original size:45 final size:44
Alignment explanation
Indices: 40795657--40795744 Score: 124
Period size: 44 Copynumber: 2.0 Consensus size: 44
40795647 ATTACACATC
*
40795657 TATTCCATTCAACCAAACACAAGAATACTATTACGCCTCTATTT
1 TATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTT
* *
40795701 TATTACATTCAACCAAACA-ATTGATTTACTATTACGCCTCTATT
1 TATTACATTCAACCAAACACA-AGA-ATACTATTACGCCTCTATT
40795745 CCAATACAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
43 1 0.03
44 20 0.51
45 18 0.46
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (44 bp):
TATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTT
Found at i:40800636 original size:97 final size:97
Alignment explanation
Indices: 40800521--40800963 Score: 663
Period size: 97 Copynumber: 4.5 Consensus size: 97
40800511 TTTTATGTTG
40800521 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
40800586 TTTGTTAGGTTATGAATGTAAATTTTTATTAA
66 TTTGTTAGGTTATGAATGTAAATTTTTATTAA
40800618 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
40800683 TTTGTTAGGTTATGAATGTAAATTTTTATTAA
66 TTTGTTAGGTTATGAATGTAAATTTTTATTAA
40800715 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
40800780 TTTGTTAGGTTATGAATGTAAATTTTTATTAA
66 TTTGTTAGGTTATGAATGTAAATTTTTATTAA
** * * *
40800812 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTAAGTTTTGTGATTAGGTTAATTGTTTGTTTAGG
1 TTTTTAATTTATTTTAAAGTTATTTTG-T--T-AG-TTACT-ATTA--TAAAATATTTGTTTA--
* * **
40800877 GTTTATTGTGATTTGTTAGGTTATGAATGT-AATCTTTTAATCT
56 G-TTATTGTAATTTGTTAGGTTATGAATGTAAAT-TTTTATTAA
* * *
40800920 TTTTTAATTTATTTGAAAGTTATTTTGTTAGTAAGTATTATAAA
1 TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAA
40800964 TTAATTATTA
Statistics
Matches: 321, Mismatches: 13, Indels: 21
0.90 0.04 0.06
Matches are distributed among these distances:
97 221 0.69
98 1 0.00
100 4 0.01
101 2 0.01
102 7 0.02
103 7 0.02
104 2 0.01
105 13 0.04
107 5 0.02
108 59 0.18
ACGTcount: A:0.29, C:0.01, G:0.13, T:0.56
Consensus pattern (97 bp):
TTTTTAATTTATTTTAAAGTTATTTTGTTAGTTACTATTATAAAATATTTGTTTAGTTATTGTAA
TTTGTTAGGTTATGAATGTAAATTTTTATTAA
Done.