Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold319
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: 745371
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.30
Warning! 60102 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:230795 original size:121 final size:120
Alignment explanation
Indices: 230589--230805 Score: 283
Period size: 121 Copynumber: 1.8 Consensus size: 120
230579 CTATCTTCAG
* * * * * * * * *
230589 TCTGCTCCGCTGTCAGTACAGGAAGGCAAGGCTGATGTCTTCAATCTGCTTCGTTGTCAGTACAG
1 TCTGCTCCACTGTCAGTACAGGAAAGCAAAGCTGATATCTTCAATCTACTTCGCTGCCAATACAA
*
230654 GAAGGCAAGATCTGCTATCTTC-AGTCTACTTTACTGCAAACTATGGTGTCTTCGA
66 GAAGACAAGATCTGCTATCTTCGA-TCTACTTTACTGCAAACTATGGTGTCTTCGA
* * * *
230709 TCTGCTTCACTGTCAGTACAGGAAAGCAATATCTGCTATCTTCGATCTACTTCGCTGCCAATACA
1 TCTGCTCCACTGTCAGTACAGGAAAGCAA-AGCTGATATCTTCAATCTACTTCGCTGCCAATACA
230774 AGAAGACAAGATCTGCTATCTTCGATCTACTT
65 AGAAGACAAGATCTGCTATCTTCGATCTACTT
230806 CGCTGCCAAT
Statistics
Matches: 81, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
120 26 0.32
121 54 0.67
122 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (120 bp):
TCTGCTCCACTGTCAGTACAGGAAAGCAAAGCTGATATCTTCAATCTACTTCGCTGCCAATACAA
GAAGACAAGATCTGCTATCTTCGATCTACTTTACTGCAAACTATGGTGTCTTCGA
Found at i:232030 original size:7 final size:7
Alignment explanation
Indices: 232013--232104 Score: 66
Period size: 7 Copynumber: 13.0 Consensus size: 7
232003 TGGCCTCTCC
232013 TTTTTCTT
1 TTTTTC-T
232021 TTTTTCT
1 TTTTTCT
232028 TTTTT-T
1 TTTTTCT
*
232034 CTTTTCT
1 TTTTTCT
232041 CTTTTTCT
1 -TTTTTCT
232049 TTCTTT-T
1 TT-TTTCT
*
232056 TTCTTC-
1 TTTTTCT
232062 TTTTTCT
1 TTTTTCT
232069 TTATTT-T
1 TT-TTTCT
* *
232076 TCTTTAT
1 TTTTTCT
*
232083 TTTTCCTT
1 TTTTTC-T
232091 TTTTTCT
1 TTTTTCT
232098 TTTTTCT
1 TTTTTCT
232105 CTATTTTTTA
Statistics
Matches: 67, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
6 15 0.22
7 28 0.42
8 24 0.36
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTCT
Found at i:232031 original size:9 final size:9
Alignment explanation
Indices: 232013--232123 Score: 90
Period size: 10 Copynumber: 12.4 Consensus size: 9
232003 TGGCCTCTCC
232013 TTTTTC-TT
1 TTTTTCTTT
232021 TTTTTC-TT
1 TTTTTCTTT
232029 TTTTTC--T
1 TTTTTCTTT
*
232036 TTTCTCTTT
1 TTTTTCTTT
232045 TTCTTTC--T
1 TT-TTTCTTT
*
232053 TTTTTCTTC
1 TTTTTCTTT
232062 TTTTTCTTT
1 TTTTTCTTT
232071 ATTTTTCTTT
1 -TTTTTCTTT
*
232081 ATTTTTCCTT
1 -TTTTTCTTT
232091 TTTTTCTTT
1 TTTTTCTTT
*
232100 TTTCTCTATT
1 TTTTTCT-TT
*
232110 TTTTATATTT
1 TTTT-TCTTT
232120 TTTT
1 TTTT
232124 ATTGAATTTG
Statistics
Matches: 86, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
7 10 0.12
8 17 0.20
9 25 0.29
10 32 0.37
11 2 0.02
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:232121 original size:26 final size:26
Alignment explanation
Indices: 232013--232112 Score: 76
Period size: 26 Copynumber: 4.2 Consensus size: 26
232003 TGGCCTCTCC
232013 TTTTT-CTTTTTTTCTTTTTT-TCT-
1 TTTTTCCTTTTTTTCTTTTTTCTCTA
* * *
232036 TTTCTCTTTTTCTTTCTTTTTTCT-TC
1 TTTTTCCTTTT-TTTCTTTTTTCTCTA
* *
232062 TTTTT-C----TTT-ATTTTTCTTTA
1 TTTTTCCTTTTTTTCTTTTTTCTCTA
232082 TTTTTCCTTTTTTTCTTTTTTCTCTA
1 TTTTTCCTTTTTTTCTTTTTTCTCTA
232108 TTTTT
1 TTTTT
232113 TATATTTTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 19
0.68 0.09 0.22
Matches are distributed among these distances:
19 7 0.12
20 9 0.16
21 1 0.02
23 4 0.07
24 4 0.07
25 14 0.24
26 19 0.33
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (26 bp):
TTTTTCCTTTTTTTCTTTTTTCTCTA
Found at i:232967 original size:22 final size:21
Alignment explanation
Indices: 232926--232967 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
232916 AAATTATGTA
*
232926 CAATATGATTATGAATGAATG
1 CAATATGATTATGAAGGAATG
232947 CAATAATGATT-TGGAAGGAAT
1 CAAT-ATGATTAT-GAAGGAAT
232968 CTAAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.43, C:0.05, G:0.21, T:0.31
Consensus pattern (21 bp):
CAATATGATTATGAAGGAATG
Found at i:237892 original size:12 final size:12
Alignment explanation
Indices: 237877--237920 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
237867 TATTTAAGCT
237877 AAAATTTTTTCA
1 AAAATTTTTTCA
* *
237889 AAAATTTCATTCT
1 AAAATTT-TTTCA
*
237902 ATAATTTTTTCA
1 AAAATTTTTTCA
237914 AAAATTT
1 AAAATTT
237921 CATTCTTCCC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (12 bp):
AAAATTTTTTCA
Found at i:237907 original size:25 final size:25
Alignment explanation
Indices: 237879--237926 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
237869 TTTAAGCTAA
237879 AATTTTTTCAAAAATTTCATTCTAT
1 AATTTTTTCAAAAATTTCATTCTAT
237904 AATTTTTTCAAAAATTTCATTCT
1 AATTTTTTCAAAAATTTCATTCT
237927 TCCCACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.12, G:0.00, T:0.52
Consensus pattern (25 bp):
AATTTTTTCAAAAATTTCATTCTAT
Found at i:251399 original size:15 final size:15
Alignment explanation
Indices: 251379--251428 Score: 55
Period size: 15 Copynumber: 3.2 Consensus size: 15
251369 AATAAATATA
251379 AAATATAAAATTATT
1 AAATATAAAATTATT
* *
251394 AAATATAAAAATAAT
1 AAATATAAAATTATT
*
251409 ACAATATAAATATTTTT
1 A-AATATAAA-ATTATT
251426 AAA
1 AAA
251429 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 14 0.50
16 10 0.36
17 4 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AAATATAAAATTATT
Found at i:251404 original size:16 final size:16
Alignment explanation
Indices: 251379--251428 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
251369 AATAAATATA
251379 AAATAT-AAAATTATT
1 AAATATAAAAATTATT
*
251394 AAATATAAAAA-TAAT
1 AAATATAAAAATTATT
* *
251409 ACAATATAAATATTTTT
1 A-AATATAAAAATTATT
251426 AAA
1 AAA
251429 AAAATTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 10 0.36
16 15 0.54
17 3 0.11
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATATAAAAATTATT
Found at i:251418 original size:22 final size:21
Alignment explanation
Indices: 251370--251421 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
251360 AAAAATTTCA
*
251370 ATAAATATAAAATATAAAATT
1 ATAAATATAAAATATAAAAAT
251391 ATTAAATATAAAA-ATAATACAAT
1 A-TAAATATAAAATATAA-A-AAT
251414 ATAAATAT
1 ATAAATAT
251422 TTTTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 5 0.19
22 19 0.70
23 3 0.11
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAAATATAAAATATAAAAAT
Found at i:254910 original size:18 final size:18
Alignment explanation
Indices: 254871--254930 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
254861 AAAATATAGA
**
254871 AAAATATTTAAATTTTACT
1 AAAATATTTAAAAATTA-T
*
254890 AAAA-ATTTAGAAAATTTT
1 AAAATATTTA-AAAATTAT
*
254908 AAAATTTTTAAAAATTAT
1 AAAATATTTAAAAATTAT
254926 AAAAT
1 AAAAT
254931 TACGATAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 22 0.65
19 12 0.35
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATATTTAAAAATTAT
Found at i:255063 original size:10 final size:9
Alignment explanation
Indices: 255031--255129 Score: 60
Period size: 9 Copynumber: 10.4 Consensus size: 9
255021 CACATGGTGT
*
255031 AAAATGATA
1 AAAATTATA
*
255040 AAAATTTATT
1 AAAA-TTATA
255050 AAAATTAATAA
1 AAAATT-AT-A
*
255061 AAAATCATA
1 AAAATTATA
*
255070 AAAGTTAT-
1 AAAATTATA
255078 AAAATATATTA
1 AAAAT-TA-TA
255089 CAAAA-TATA
1 -AAAATTATA
255098 AAAA-TATA
1 AAAATTATA
*
255106 GAAAATTATTT
1 -AAAATTA-TA
255117 AAAATTATA
1 AAAATTATA
255126 AAAA
1 AAAA
255130 AATATGTAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
8 12 0.17
9 26 0.37
10 23 0.32
11 6 0.08
12 4 0.06
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:255115 original size:28 final size:27
Alignment explanation
Indices: 255031--255129 Score: 83
Period size: 28 Copynumber: 3.5 Consensus size: 27
255021 CACATGGTGT
* *
255031 AAAATGATAAAAATTTATTAAAATTAATAA
1 AAAATCATAAAAA-TTA-TAAAATT-ATTA
*
255061 AAAATCATAAAAGTTATAAAATATATTA
1 AAAATCATAAAAATTATAAAAT-TATTA
* *
255089 CAAAAT-ATAAAAATATAGAAAATTATTT
1 -AAAATCATAAAAAT-TATAAAATTATTA
*
255117 AAAATTATAAAAA
1 AAAATCATAAAAA
255130 AATATGTAGA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 5 0.08
28 27 0.46
29 16 0.27
30 11 0.19
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AAAATCATAAAAATTATAAAATTATTA
Found at i:255130 original size:10 final size:10
Alignment explanation
Indices: 255031--255130 Score: 50
Period size: 10 Copynumber: 10.4 Consensus size: 10
255021 CACATGGTGT
*
255031 AAAATGATAA
1 AAAATTATAA
* *
255041 AAATTTAT-T
1 AAAATTATAA
255050 AAAATTAATAA
1 AAAATT-ATAA
*
255061 AAAATCAT-A
1 AAAATTATAA
*
255070 AAAGTTATAA
1 AAAATTATAA
* *
255080 AATA-TATTAC
1 AAAATTA-TAA
255090 AAAA-TAT-A
1 AAAATTATAA
*
255098 AAAA-TATAG
1 AAAATTATAA
**
255107 AAAATTATTT
1 AAAATTATAA
255117 AAAATTATAA
1 AAAATTATAA
255127 AAAA
1 AAAA
255131 ATATGTAGAA
Statistics
Matches: 66, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
8 7 0.11
9 19 0.29
10 35 0.53
11 5 0.08
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (10 bp):
AAAATTATAA
Found at i:255130 original size:20 final size:20
Alignment explanation
Indices: 255096--255144 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
255086 TTACAAAATA
* * * *
255096 TAAAAATATAGAAAATTATT
1 TAAAATTATAAAAAAATATG
255116 TAAAATTATAAAAAAATATG
1 TAAAATTATAAAAAAATATG
255136 TAGAAATTA
1 TA-AAATTA
255145 GTCTTAGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (20 bp):
TAAAATTATAAAAAAATATG
Found at i:261299 original size:16 final size:16
Alignment explanation
Indices: 261278--261309 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
261268 ACTGTTATGC
261278 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
261294 CTCTATTCCATTACAG
1 CTCTATTCCATTACAG
261310 TGAACCAAAC
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:0.25, C:0.31, G:0.06, T:0.38
Consensus pattern (16 bp):
CTCTATTCCATTACAG
Found at i:264554 original size:14 final size:14
Alignment explanation
Indices: 264535--264566 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
264525 ATTATGTTAG
264535 AATTAAAAACACAT
1 AATTAAAAACACAT
264549 AATT-AAAACACAT
1 AATTAAAAACACAT
264562 -ATTAA
1 AATTAA
264567 TGATATTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:264649 original size:39 final size:39
Alignment explanation
Indices: 264545--264652 Score: 182
Period size: 39 Copynumber: 2.8 Consensus size: 39
264535 AATTAAAAAC
*
264545 ACATAATTAAA-ACACATATTAATGATATTCAAACTAAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
*
264583 ACATAATTAAAGACACATATTAATGATGTTCAAGCTAAG
1 ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
*
264622 ACATAATTAAAGACTCATATTAATGATGTTC
1 ACATAATTAAAGACACATATTAATGATGTTC
264653 GCACTAATAT
Statistics
Matches: 66, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
38 11 0.17
39 55 0.83
ACGTcount: A:0.47, C:0.13, G:0.09, T:0.31
Consensus pattern (39 bp):
ACATAATTAAAGACACATATTAATGATGTTCAAACTAAG
Found at i:264813 original size:36 final size:36
Alignment explanation
Indices: 264762--264834 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
264752 ATGGAGTGAA
* * * * *
264762 TACCCAAGCTTGATCAATTAGTCTCGTGATAGCTTC
1 TACCCAAACTCGATCAATGAGACCCGTGATAGCTTC
*
264798 TACCCAAACTCGATCAATGAGACCCGTGATGGCTTC
1 TACCCAAACTCGATCAATGAGACCCGTGATAGCTTC
264834 T
1 T
264835 TTGAACTTCT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (36 bp):
TACCCAAACTCGATCAATGAGACCCGTGATAGCTTC
Found at i:269318 original size:20 final size:22
Alignment explanation
Indices: 269293--269334 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
269283 GAAATCTATG
269293 TGTTCAC-ACT-AACATTAAAT
1 TGTTCACAACTAAACATTAAAT
*
269313 TGTTCACAATTAAACATTAAAT
1 TGTTCACAACTAAACATTAAAT
269335 ACGGTTCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 2 0.11
22 10 0.53
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TGTTCACAACTAAACATTAAAT
Found at i:269973 original size:14 final size:14
Alignment explanation
Indices: 269954--269985 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
269944 ATTATGTTAG
269954 AATTAAAAACACAT
1 AATTAAAAACACAT
269968 AATT-AAAACACAT
1 AATTAAAAACACAT
269981 -ATTAA
1 AATTAA
269986 TGATATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.18
13 10 0.59
14 4 0.24
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (14 bp):
AATTAAAAACACAT
Found at i:270023 original size:39 final size:38
Alignment explanation
Indices: 269964--270078 Score: 176
Period size: 39 Copynumber: 3.0 Consensus size: 38
269954 AATTAAAAAC
* *
269964 ACATAATTAAAACACATATTAATGATATTAAAACTAAG
1 ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
*
270002 ACATATTTAAAGACACATATTAATGATGTTCAAACTAAG
1 ACATAATTAAA-ACACATATTAATGATGTTCAAACTAAG
*
270041 ACATAATTAAATACTCATATTAATGATGTTCAAACTAA
1 ACATAATTAAA-ACACATATTAATGATGTTCAAACTAA
270079 AATAACTAAA
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
38 10 0.14
39 60 0.86
ACGTcount: A:0.50, C:0.12, G:0.07, T:0.31
Consensus pattern (38 bp):
ACATAATTAAAACACATATTAATGATGTTCAAACTAAG
Found at i:270087 original size:9 final size:9
Alignment explanation
Indices: 270073--270098 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
270063 ATGATGTTCA
270073 AACTAAAAT
1 AACTAAAAT
270082 AACTAAAAT
1 AACTAAAAT
270091 AACTAAAA
1 AACTAAAA
270099 ATGGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.12, G:0.00, T:0.19
Consensus pattern (9 bp):
AACTAAAAT
Found at i:273776 original size:24 final size:24
Alignment explanation
Indices: 273752--273798 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
273742 AAACTACTTC
273752 TAAAAAAAACTCAAGAGAGAATTCT
1 TAAAAAAAACTCAA-AGAGAATTCT
** *
273777 TGGAGAAAACTCAAAGAGAATT
1 TAAAAAAAACTCAAAGAGAATT
273799 TTTCACTCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (24 bp):
TAAAAAAAACTCAAAGAGAATTCT
Found at i:274129 original size:19 final size:19
Alignment explanation
Indices: 274093--274131 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
274083 ACTAAGTCTA
*
274093 GTTTGAACTTCTTGATTGG
1 GTTTGAACATCTTGATTGG
274112 GTTTGGAACATCTT-ATTGG
1 GTTT-GAACATCTTGATTGG
274131 G
1 G
274132 CCGTGTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.18, C:0.10, G:0.28, T:0.44
Consensus pattern (19 bp):
GTTTGAACATCTTGATTGG
Found at i:274979 original size:33 final size:33
Alignment explanation
Indices: 274901--274975 Score: 116
Period size: 33 Copynumber: 2.3 Consensus size: 33
274891 GTCCAGATTT
274901 AAATAAATTAATTACTAACACTTATTTAAGCTG
1 AAATAAATTAATTACTAACACTTATTTAAGCTG
*
274934 AAATACAATTAATT-CTAACACTTATTTGAGCTG
1 AAATA-AATTAATTACTAACACTTATTTAAGCTG
*
274967 AACTAAATT
1 AAATAAATT
274976 TAATAAACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
32 4 0.10
33 27 0.69
34 8 0.21
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (33 bp):
AAATAAATTAATTACTAACACTTATTTAAGCTG
Found at i:278569 original size:25 final size:24
Alignment explanation
Indices: 278541--278591 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 24
278531 TTAAAACTAC
278541 TTCTAAAAAAAAACTCAAGAGAGAA
1 TTCTAAAAAAAAACTCAA-AGAGAA
*** *
278566 TTCTTGGAGAAAACTCAAAGAGAA
1 TTCTAAAAAAAAACTCAAAGAGAA
278590 TT
1 TT
278592 TTTCATTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.22
Consensus pattern (24 bp):
TTCTAAAAAAAAACTCAAAGAGAA
Found at i:278922 original size:19 final size:19
Alignment explanation
Indices: 278886--278924 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
278876 ACTAAGTCTA
*
278886 GTTTGAACTTCTTGATTGG
1 GTTTGAACATCTTGATTGG
278905 GTTTGGAACATCTT-ATTGG
1 GTTT-GAACATCTTGATTGG
278924 G
1 G
278925 CCGTGTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.18, C:0.10, G:0.28, T:0.44
Consensus pattern (19 bp):
GTTTGAACATCTTGATTGG
Found at i:279914 original size:32 final size:32
Alignment explanation
Indices: 279861--279927 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
279851 GTATTTTATC
* *
279861 TAATTTGGTACTCAAATTTGACATTTTTTTCT
1 TAATTTAGTACTCAAAGTTGACATTTTTTTCT
*
279893 TAATTTAGTA-TCTAAAGTTGACGTTTTTTTCT
1 TAATTTAGTACTC-AAAGTTGACATTTTTTTCT
279925 TAA
1 TAA
279928 GTTGATACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
31 2 0.06
32 29 0.94
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.52
Consensus pattern (32 bp):
TAATTTAGTACTCAAAGTTGACATTTTTTTCT
Found at i:294841 original size:30 final size:30
Alignment explanation
Indices: 294807--294867 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
294797 AGTGTCAGCT
*
294807 AACCTAGGGTTGAGGATAACGACAACCCTA
1 AACCTAGGGTTGAGGATAACAACAACCCTA
*
294837 AACCTAGGGTTGAGGATGACAACAACCCTA
1 AACCTAGGGTTGAGGATAACAACAACCCTA
294867 A
1 A
294868 CTCTATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (30 bp):
AACCTAGGGTTGAGGATAACAACAACCCTA
Found at i:299943 original size:524 final size:523
Alignment explanation
Indices: 298955--299999 Score: 1883
Period size: 524 Copynumber: 2.0 Consensus size: 523
298945 GAGACCGGAG
*
298955 AAAATTGTATTTGGGTCCCGAAGCTTAAGCTACATCGGTATCAAGTATGGGTAGTGTGAAGCCTA
1 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACATCGGTATCAAGTATGGGTAGTGTGAAGCCTA
299020 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTAGTTAATTAGCCGAGCT
66 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTAGTTAATTAGCCGAGCT
299085 TGTTTCAAGTGTGGATCTCGACAACATTATATTAAAGATTGCCCTGAGAAAATTGAAGAAGAAAA
131 TGTTTCAAGTGTGGATCTCGACAACATTATATTAAAGATTGCCCTGAGAAAATTGAAGAAGAAAA
299150 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
196 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
* * ** *
299215 GAGATAGTGGTAAAAGTGTAATGAAGGGTACAGTTGCAAGACCAGAACCTCGAACACCTGCCAGA
261 GAGATAGTGGTAAAAATATAATGAAGGGTACAACTGCAAGACCAGAACCTCGAACACCTGCCAAA
* **
299280 GCTTATGCCATATGTGCTCGTGAGGATGCATCATCACTTGATGTGATTACTGGTACATTCTCTCT
326 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
299345 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
391 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
*
299410 TAGTATCTAATAAAAATTTGCCTGTTGAAAACACTGAATATGTGGTAAAAGTATCAAACCCTTTA
456 TAGTATCTAA-AAAAAATTGCCTGTTGAAAACACTGAATATGTGGTAAAAGTATCAAACCCTTTA
299475 GGTA
520 GGTA
* * *
299479 AAAATTGTATTTGGGTCTCGAAGCTCAAGCTACGTCGGTATCAAGTGTGGGTAGTGTGAAGCCTA
1 AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACATCGGTATCAAGTATGGGTAGTGTGAAGCCTA
*
299544 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTGGTTAATTAGCCGAGCT
66 GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTAGTTAATTAGCCGAGCT
* * *
299609 TGTTTCAAGTGTGGCTCTTGACAACATTATATTAAAGATTGCCTTGAGAAAATTGAAGAAGAAAA
131 TGTTTCAAGTGTGGATCTCGACAACATTATATTAAAGATTGCCCTGAGAAAATTGAAGAAGAAAA
*
299674 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCTGAACTA
196 ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
*
299739 GAGATAGTGGTAAAAATATAATGAAGGGTACAACTGCAAGACCAGAACCTCGAACACCTGCTAAA
261 GAGATAGTGGTAAAAATATAATGAAGGGTACAACTGCAAGACCAGAACCTCGAACACCTGCCAAA
*
299804 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCTCCCGATGTGATTACTGGTACATTCTCTCT
326 GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
299869 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
391 CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
* *
299934 TAGTATCTAAAAAAAATTGCTTGTTGAAAACACTGAATTTGTGGTAAAAGTATCAAACCCTTTAG
456 TAGTATCTAAAAAAAATTGCCTGTTGAAAACACTGAATATGTGGTAAAAGTATCAAACCCTTTAG
299999 G
521 G
300000 CAAATATGTT
Statistics
Matches: 499, Mismatches: 22, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
523 53 0.11
524 446 0.89
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (523 bp):
AAAATTGTATTTGGGTCCCGAAGCTCAAGCTACATCGGTATCAAGTATGGGTAGTGTGAAGCCTA
GTAAACCAGAGTGTCAGCATTGTGGTAGGCAACATCCTGGTGAATGCTAGTTAATTAGCCGAGCT
TGTTTCAAGTGTGGATCTCGACAACATTATATTAAAGATTGCCCTGAGAAAATTGAAGAAGAAAA
ATTTCAGAATGTTAGATCGAGTGATACTGTCAGCAGAGGTAGACCACCGAGAAACACCGGAACTA
GAGATAGTGGTAAAAATATAATGAAGGGTACAACTGCAAGACCAGAACCTCGAACACCTGCCAAA
GCTTATGCCATACGTGCTCGTGAGGATGCATCATCACCCGATGTGATTACTGGTACATTCTCTCT
CTATGATATTGATGTTGTTGCTTTGATTGACCCTGGGTCTACTCATTCATATGTATGTGTGAATT
TAGTATCTAAAAAAAATTGCCTGTTGAAAACACTGAATATGTGGTAAAAGTATCAAACCCTTTAG
GTA
Found at i:304558 original size:51 final size:50
Alignment explanation
Indices: 304493--304617 Score: 144
Period size: 51 Copynumber: 2.5 Consensus size: 50
304483 GAACACGTGT
* *
304493 GTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATG-ATGGTCACATGC
1 GTAGTACTATGTGAAGGCTACTACGTGAACCGA-AAA-GCATGGTCACATGC
* * * * * *
304544 GTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGTCACGTGT
1 GTAGTACTATGTGAAGGCTACTACGTGAACCGAAAAGC-ATGGTCACATGC
304595 GTAGTACTATGTGAAGGCTACTA
1 GTAGTACTATGTGAAGGCTACTA
304618 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
49 1 0.02
50 3 0.05
51 59 0.94
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (50 bp):
GTAGTACTATGTGAAGGCTACTACGTGAACCGAAAAGCATGGTCACATGC
Found at i:304743 original size:51 final size:50
Alignment explanation
Indices: 304679--304842 Score: 188
Period size: 51 Copynumber: 3.2 Consensus size: 50
304669 AGAAGCTTTA
* *
304679 GTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATG-ATG
1 GTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGA-AAA-GCATG
* * * * * *
304730 GTCACATGCGTAGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTG
1 GTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAAAAGC-ATG
*
304781 GTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAA-CTTG
1 GTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-AAAAGCATG
*
304831 ATCACGTGTGTA
1 GTCACGTGTGTA
304843 CTGTGTCAGA
Statistics
Matches: 96, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
49 1 0.01
50 17 0.18
51 74 0.77
52 4 0.04
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (50 bp):
GTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGAAAAGCATG
Found at i:317091 original size:13 final size:13
Alignment explanation
Indices: 317073--317119 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
317063 CCGTATGCAA
*
317073 TTTTTTTTCAATT
1 TTTTTTTTCGATT
317086 TTTTTTTTCGATT
1 TTTTTTTTCGATT
*
317099 TTTTTTTCTTGATT
1 TTTTTTT-TCGATT
317113 TTTTTTT
1 TTTTTTT
317120 CGAAACTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (13 bp):
TTTTTTTTCGATT
Found at i:317092 original size:14 final size:14
Alignment explanation
Indices: 317073--317119 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
317063 CCGTATGCAA
*
317073 TTTTTTTTC-AATT
1 TTTTTTTTCGATTT
317086 TTTTTTTTCGATTT
1 TTTTTTTTCGATTT
317100 TTTTTTCTT-GATTT
1 TTTTTT-TTCGATTT
317114 TTTTTT
1 TTTTTT
317120 CGAAACTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 9 0.29
14 20 0.65
15 2 0.06
ACGTcount: A:0.09, C:0.06, G:0.04, T:0.81
Consensus pattern (14 bp):
TTTTTTTTCGATTT
Found at i:325913 original size:19 final size:19
Alignment explanation
Indices: 325877--325912 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
325867 CGACGGTTGG
325877 CTAAAAAAAATGGTTTTTA
1 CTAAAAAAAATGGTTTTTA
*
325896 CTAAAACAAA-GGTTTTT
1 CTAAAAAAAATGGTTTTT
325913 TTTTCTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (19 bp):
CTAAAAAAAATGGTTTTTA
Found at i:329230 original size:54 final size:50
Alignment explanation
Indices: 329166--329347 Score: 181
Period size: 54 Copynumber: 3.6 Consensus size: 50
329156 GGTAAAGAGA
* * **
329166 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTGAGATTATGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA-C--CGAGATGA-GAAC
* *
329220 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAAC
* * * * *
329270 TCCCATGTAAGACCATATCTAGGATATGTCATTGGCA--GTACAAGA-AAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCG-AGATGAGAAC
*
329318 ATCCCATGTAAGACCATGTCTGGGACATGG
1 -TCCCATGTAAGACCATGTCTGGGATATGG
329348 TTTTGGCATG
Statistics
Matches: 109, Mismatches: 17, Indels: 9
0.81 0.13 0.07
Matches are distributed among these distances:
48 4 0.04
49 29 0.27
50 34 0.31
51 6 0.06
53 1 0.01
54 35 0.32
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATGAGAAC
Found at i:329305 original size:50 final size:53
Alignment explanation
Indices: 329166--329356 Score: 184
Period size: 50 Copynumber: 3.7 Consensus size: 53
329156 GGTAAAGAGA
* * **
329166 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCATTGAGATTATGAGG
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCA-CGAGATGATGAAC
* *
329220 TCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGAGATGA-GAAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCACGAGATGATGAAC
* * *
329270 TCCCATGTAAGACCATATCTAGGATATGTCATTGGCAGT-AC-A-A-GA--AAC
1 TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCA-TCACGAGATGATGAAC
* **
329318 ATCCCATGTAAGACCATGTCTGGGACATGGTTTTGGCAT
1 -TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCAT
329357 GTTATTATCA
Statistics
Matches: 116, Mismatches: 17, Indels: 14
0.79 0.12 0.10
Matches are distributed among these distances:
48 4 0.03
49 33 0.28
50 35 0.30
51 7 0.06
52 1 0.01
53 1 0.01
54 35 0.30
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (53 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCATTGGCATCACGAGATGATGAAC
Found at i:341470 original size:50 final size:49
Alignment explanation
Indices: 341402--341498 Score: 158
Period size: 50 Copynumber: 2.0 Consensus size: 49
341392 TTAACTATTA
* *
341402 TCATTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCTT
1 TCATTCGATACACATAGTAGCCTACACATAGTACTACACACGTGACCTT
*
341451 TCATTCCGGTACACATAGTAGCCTACACATAGTACTACACACGTGACC
1 TCATT-CGATACACATAGTAGCCTACACATAGTACTACACACGTGACC
341499 ATCACTTTCA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
49 5 0.11
50 39 0.89
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (49 bp):
TCATTCGATACACATAGTAGCCTACACATAGTACTACACACGTGACCTT
Found at i:358393 original size:24 final size:24
Alignment explanation
Indices: 358365--358425 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
358355 AATTTGGTTT
**
358365 ATTTCGTACCAAAAATTCCATACC
1 ATTTCGTACCAAAAACCCCATACC
*
358389 ATTTCGTA-CTAAAACCCCATACC
1 ATTTCGTACCAAAAACCCCATACC
358412 ATTTCGTACCAAAA
1 ATTTCGTACCAAAA
358426 CCAACTCCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.38, C:0.30, G:0.05, T:0.28
Consensus pattern (24 bp):
ATTTCGTACCAAAAACCCCATACC
Found at i:363151 original size:208 final size:210
Alignment explanation
Indices: 362778--363202 Score: 710
Period size: 208 Copynumber: 2.0 Consensus size: 210
362768 GCGCCTAACT
*
362778 CGTTGTCAAATTTATCCTTACTTCAAATATTTCCCTTCACATTCTAAAAAAAAGTCTCTCTCTAC
1 CGTTCTCAAATTTATCCTTACTTCAAATATTTCCCTTCACATTCT-AAAAAAAGTCTCTCTCTAC
* *
362843 CATAAATCAAGGTTTCCCTAAAAATTTTGTATAAAGAACAAAGCAATAGCATAACAATATCATAG
65 CATAAATCAAGGTTTCCCTAAAAATTTTGTATAAAGAACAAAGCAATAACATAACAATAACATAG
* *
362908 TCTCTTTCTATGATGGCCTCAACATTCGTTAGATCATTGAGAAGAGTGAAATATTCACTAATATG
130 TCTCTTTCTATAATGGCCTCAACATTCGATAGATCATTGAGAAGAGTGAAATATTCACTAATATG
362973 GGCCCTAATAGACTCA
195 GGCCCTAATAGACTCA
* * *
362989 CGTTCTCAAATTTATCCTTACTTCAAATATTTCCCTTCACGTTCT-CAAAAAG-GTCTCTCTACC
1 CGTTCTCAAATTTATCCTTACTTCAAATATTTCCCTTCACATTCTAAAAAAAGTCTCTCTCTACC
* *
363052 ATAAATCATGGTTTCCCTAAAAATTTTGTATGAAGAACAAAGCAATAACATAACAATAACATAGT
66 ATAAATCAAGGTTTCCCTAAAAATTTTGTATAAAGAACAAAGCAATAACATAACAATAACATAGT
* *
363117 CTCTTTCTGTAATGGCCTCAACATTTGATAGATCATTGAGAAGAGTGAAATATTCACTAATATGG
131 CTCTTTCTATAATGGCCTCAACATTCGATAGATCATTGAGAAGAGTGAAATATTCACTAATATGG
363182 GCCCTAATAGACTCA
196 GCCCTAATAGACTCA
*
363197 CCTTCT
1 CGTTCT
363203 TCCATATGAA
Statistics
Matches: 201, Mismatches: 13, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
208 152 0.76
209 6 0.03
211 43 0.21
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (210 bp):
CGTTCTCAAATTTATCCTTACTTCAAATATTTCCCTTCACATTCTAAAAAAAGTCTCTCTCTACC
ATAAATCAAGGTTTCCCTAAAAATTTTGTATAAAGAACAAAGCAATAACATAACAATAACATAGT
CTCTTTCTATAATGGCCTCAACATTCGATAGATCATTGAGAAGAGTGAAATATTCACTAATATGG
GCCCTAATAGACTCA
Found at i:364748 original size:16 final size:16
Alignment explanation
Indices: 364727--364783 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
364717 TTTGGTTCGC
*
364727 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
364743 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
364759 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
364775 TGTAATGGA
1 TGTAATGGA
364784 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:365050 original size:18 final size:17
Alignment explanation
Indices: 365029--365063 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
365019 TTATTATTAA
*
365029 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
365047 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
365064 TCTTAANNNN
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:384220 original size:30 final size:30
Alignment explanation
Indices: 384184--384245 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
384174 TCCAGAATTA
*
384184 TGCATGGTACATTTCC-TTTGTAAGAGGCCT
1 TGCATGGTACA-TTCCGTTTGCAAGAGGCCT
*
384214 TGCATGGTACATTCCGTTTGCAAGAGGTCT
1 TGCATGGTACATTCCGTTTGCAAGAGGCCT
384244 TG
1 TG
384246 GTAGACAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.14
30 25 0.86
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (30 bp):
TGCATGGTACATTCCGTTTGCAAGAGGCCT
Found at i:384415 original size:37 final size:37
Alignment explanation
Indices: 384360--384431 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
384350 CACATCACGG
*
384360 GTGTACTATAATTCTAGTACAGTATATATATGGATGA
1 GTGTACTATAAATCTAGTACAGTATATATATGGATGA
* **
384397 GTGTGCTATAAATCTAGTATGGTATATATATGGAT
1 GTGTACTATAAATCTAGTACAGTATATATATGGAT
384432 AGAATTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (37 bp):
GTGTACTATAAATCTAGTACAGTATATATATGGATGA
Found at i:386369 original size:32 final size:33
Alignment explanation
Indices: 386299--386369 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
386289 TATGAATCGT
* *
386299 AAAATGAATATGAATATATATTGGTTCTACTAA
1 AAAATAAATATGAATATATATTGATTCTACTAA
* *
386332 TAAATAAATATGAATTATATATTTATT-T-CTAA
1 AAAATAAATATGAA-TATATATTGATTCTACTAA
386364 AAAATA
1 AAAATA
386370 TTTATTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
32 9 0.28
33 13 0.41
34 10 0.31
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.39
Consensus pattern (33 bp):
AAAATAAATATGAATATATATTGATTCTACTAA
Found at i:387128 original size:65 final size:65
Alignment explanation
Indices: 387046--387173 Score: 188
Period size: 65 Copynumber: 2.0 Consensus size: 65
387036 ATAGTTACAA
*
387046 GTGAAATATTATAATAAATCTAAAA-TTATAATTTAAAAAATGATAAATAATGCCTCCTTAATTA
1 GTGAAATATTATAATAAATCCAAAAGTTATAA-TTAAAAAATGATAAATAATGCCT-CTTAATTA
387110 TT
64 TT
* * *
387112 GTGAAAT-TTATAATAAATCCAAAAGTTATAATTGAAAAATGATACATTATGCCTCTTAATTA
1 GTGAAATATTATAATAAATCCAAAAGTTATAATTAAAAAATGATAAATAATGCCTCTTAATTA
387174 AGGAGACTTG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
64 8 0.14
65 36 0.63
66 13 0.23
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.37
Consensus pattern (65 bp):
GTGAAATATTATAATAAATCCAAAAGTTATAATTAAAAAATGATAAATAATGCCTCTTAATTATT
Found at i:389411 original size:50 final size:50
Alignment explanation
Indices: 389302--389549 Score: 293
Period size: 50 Copynumber: 4.8 Consensus size: 50
389292 ATTTGGATAA
*
389302 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--AAGA-C--G
*
389358 AGAGGTCCCATGTAAGA-CATGGTCTGGGACATGGCATTGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCACCAAGACG
* *
389408 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
** * * *
389458 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCA-TGAGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTG-GCACCAAGACG
** * *
389508 AGAACTCCCATGTAAGACCATTTCTGGGATATGGCATTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
389550 GTACAAGAAA
Statistics
Matches: 172, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
49 2 0.01
50 119 0.69
51 5 0.03
52 1 0.01
53 3 0.02
55 5 0.03
56 37 0.22
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
Found at i:398213 original size:56 final size:52
Alignment explanation
Indices: 398141--398386 Score: 270
Period size: 50 Copynumber: 4.8 Consensus size: 52
398131 ACAAATGTAA
*
398141 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-CATG
*
398197 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCATTGGCACCGAGAC--G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
* * * *
398247 AGAGGTCTCATGTAAGACCATGCCTGGGACATGGCGTTGGCAGCGAG--ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
* ** * * *
398297 AAAGGTCCCCCGTAACACCATGTCTGGGACATGGCATGGGCACC--TACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
** * *
398347 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
398387 TGGTACAAGA
Statistics
Matches: 160, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
50 113 0.71
52 1 0.01
53 4 0.03
55 2 0.01
56 40 0.25
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (52 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACATG
Found at i:404535 original size:760 final size:761
Alignment explanation
Indices: 402384--406170 Score: 5428
Period size: 759 Copynumber: 5.0 Consensus size: 761
402374 AAGAAAGTCA
* * *
402384 TATTTTTGTCCCCTAATTTCAACCAGTTCATCCT-AGCCCTTAGCTCCCAATACATTTCATCTTT
1 TATTTTTGTCCCCTAATTTCAACCAGTTTA-CCTGAGCCCTTTGCTCCCAATACATTTCGTCTTT
* *
402448 ATCAATCTCTAAATTAAGATGTACTCCAGTATCAAT-CAAATCAGCCATA-----ATTAGTTCTG
65 ATCAATCTCTAAATTAAGATGTACTCTAGTATCAATCCAAATCAGCCATACTTTCATCAGTTCTG
* * * *
402507 TCATGATTTAAGAGAAATTTTATTTTTTCTATCTGCTTCTTCTTTTGCCCTTCCCTTTTTTGTCT
130 TCTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTGTCT
* * * **
402572 AATTCTAGTAGCCCATCTTACGAGCCCAATTTGTAAAAATTTGAGCTTTTCAAAAATATCACCGT
195 AATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACCGT
*
402637 GATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCATGCCTCA
260 GATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTCA
* * * *
402702 AATTGAAATATCTTACTATACATGTTCTTTGATTCAATATCAAGACCAAGCAGTATGGGATAGTG
325 AATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTG
* * *
402767 ATAGGAAAAA-AATTCGGTAAATGGTGAAAAACTGCTATTGGAAACATATCCCTCCACTCTAAGT
390 ATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCCTCCACTCTAAGT
* *
402831 TCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCCGGCAAATTCCCTCTTTCCCAAGCA
455 TCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTA
* *
402896 AACCAAGTACCTAAGAAGCCAATATCTGTCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCAC
520 AACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGC
* ** * * * * *
402961 CATCCTGCTCTCTTCTCTTGGTTCACCACCCACATTCTCGAAGGAATAAAGTATCACATTAAAAG
585 CATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAAAT
* * * *
403026 CTCCACAAACCATCCAAGGTAGGCCTTGGAATCGATTTAGGTTTTTTAGTATGCCCCAAGTATTT
650 CTTCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATTT
* *
403091 CCTCTATTCTGCGCATAAGGGGAGCCATAAAAACCCT-TAAACCTATG
715 CCTCTATTCTACGCATAAAGGGAGCCATAAAAA-CCTATAAACCTATG
* * * * *
403138 TATTTTTGTCCCCTAATTTCAACCAGTTTACCCT-A-CCCTTTTACACCCAATAAATTTTGCCTT
1 TATTTTTGTCCCCTAATTTCAACCAGTTTA-CCTGAGCCC-TTTGCTCCCAATACATTTCGTCTT
* * *
403201 TATCAATCTCTAAATTAAGATGTACTCTAGTATCAA-CCAACTCAGCTATACTTTCATTAGTTCT
64 TATCAATCTCTAAATTAAGATGTACTCTAGTATCAATCCAAATCAGCCATACTTTCATCAGTTCT
* *
403265 GTCTTGATCTAAGAGAAATTTTATTTTTTCTGTCAGCTTCTTCTTTCGCCCTTCCTTTTTTCTTT
129 GTCTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCC---CTT-TTT
* * *
403330 TGTTTAATTCCAGTAGCCTATCTTACGAGCCGAATCTATAAAAATTTGAATTTTTCAAAAATATC
190 TGTCTAATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATC
* * * * *
403395 ACCGCGATCAACTTGCCATAATCTTCTGATCTCATCCACATAA-ATTCTTCCTTCACCCACCACG
255 ACCGTGATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACG
403459 CCTCAAATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGA
320 CCTCAAATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGA
* * *
403524 TAGTGATCGGAAAAA-AATGCGGTAAATGGTGAAAAACTGCTGTCGGGAACGTATCCCTCCACTC
385 TAGTGATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCCTCCACTC
*
403588 TAAGTTTGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCC
450 TAAGTTCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCC
* *
403653 AAGTAAACCAAGTACTTAAGAAGCTAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAAC
515 AAGTAAACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAAC
403718 TCCGCCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTT
580 TCCGCCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTT
* *
403783 AAAATCTTCACAAACTATCCAAGGTAAGCCTTGGATTTGATTTAGATTTTTTAGTATGCCCCAAG
645 AAAATCTTCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAG
* * * *
403848 TATTTCATCTATTCTACACATAAAAGGGAGACATAAAAACCTGTAAACCTATG
710 TATTTCCTCTATTCTACGCAT-AAAGGGAGCCATAAAAACCTATAAACCTATG
* * * *
403901 TATTTTT-CCCCCTAATTTCAACCAGTTTACTTGAGCCCTTTGCTCCTAATAGATTTCGTCTTTA
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCTGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
*
403965 TCAATCTCTAAATTAAGTTGTACTCTAGTAT-AATCCAAATCAGCCATACTTTCATCAGTTCTGT
66 TCAATCTCTAAATTAAGATGTACTCTAGTATCAATCCAAATCAGCCATACTTTCATCAGTTCTGT
* *
404029 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCACCCTTCCCTTTTTTATCTA
131 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTGTCTA
* * ** *
404094 ATTCCAGTAGCCCATCTTATGAGCCCAATCTGTAAAAAAATGAATTTTTCAAAAATATCACTGTG
196 ATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACCGTG
* *
404159 ATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACACACCACACCTCAA
261 ATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTCAA
* *
404224 ATCGAAATACCTTCCTAGACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTGA
326 ATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTGA
* * * * *
404289 TC-GAAAAAGGAATGCAGTGAATGGTGAAAAACTGCTGTTGGTAACATATCCTTCCACTCTATGT
391 TCGGAAAAA-GAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCCTCCACTCTAAGT
* *
404353 TCGCCACACCCCTATCAAGTCTTTCATGTATATTAGTCTCTAGCAAATTCCCTCTTTCCCAAGTA
455 TCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTA
* * * *
404418 AACCAAGTACCTAAGAAGCCAATATCCATCAATTGACATTCCTCCAAAATTTCCCTAAACTCCGT
520 AACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGC
* * *
404483 AATCCTGCTCTCCTCTCTTAGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAAGT
585 CATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAAAT
* * * *
404548 CTCCATAAACCATCCAAGGTAAGCCTTGGATTCGATTTATATTTTTTAGTATGCCCCAAGTATTG
650 CTTCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATTT
* *
404613 CCTCTATTCTGA-TCATAAAGGGAGCCATAAAAACCCATAAACCTATG
715 CCTCTATTCT-ACGCATAAAGGGAGCCATAAAAACCTATAAACCTATG
* * * *
404660 TACTTTTGTCCCCTAATTTCAACCAGTTTACCCGAGCCCTTTGCTCCCACTTCATTTCGTCTTTA
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCTGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
* * *
404725 TTAATCTCTAAATTAAGATGTACTCTAGTATCAA-CCAAATCAACCATACTTTCATCAGTTCAGT
66 TCAATCTCTAAATTAAGATGTACTCTAGTATCAATCCAAATCAGCCATACTTTCATCAGTTCTGT
* * * *
404789 CTTGATCTAAGAGAAATTTTATTTTTACTGTCAGCTTCTTCTTTCACCCTTCCCTTTTTTCTCTA
131 CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTGTCTA
* * * **
404854 ATTCCAATAGCCCATCTTACGAGCCCAATCTATAAAAAATTGAATTTTTCAAAAAT-GCACCACG
196 ATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACCGTG
* * * *
404918 GTCAACTTGCCGCAATCGTCTGATCTCATCCACACAAATTTT-TTCCTTCACCCACCATGCCTCA
261 ATCAACTTGCCACAATCATCTGATCTCATCCACAC-AATTTTCTTCCTTCACCCACCACGCCTCA
* * * * *
404982 AATCGAAATACCTCCCTATACATGTTCTTTGATTCAATATCAATATCAAGTAGTATAGGATAGTA
325 AATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTG
* * * *
405047 ACCGGAAAAAGAATGCGGTAAATGGTGAAAAACTACTATTGGAAACATATCCGTCCACTCTAAGT
390 ATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCCTCCACTCTAAGT
* * * * *
405112 TTGCCACACCCCTATCAAGCCTTTCTTGTACATTAGTCTCTGGAAAATTCCTTCTTTCCCAAGTA
455 TCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTA
*
405177 AACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTTCCTAAACTCCGC
520 AACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGC
* * * *
405242 CATCCTGCTCTGCTCTCTTGGCGCACCACCCACTTTCTCGAAGGGATAAATAATCTCGTTAAAAT
585 CATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAAAT
405307 C-TCTACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATT
650 CTTC-ACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATT
* * * *
405371 TCCTCTATTCTGCGCATAAGGGGAGCTATAAAAA-CTCGTAAACCTATG
714 TCCTCTATTCTACGCATAAAGGGAGCCATAAAAACCT-ATAAACCTATG
*
405419 TATTTTTGTCCCCTAATTTCAACCAGTTTACTTGAGCCCTATT-CTCCCAATACATTTCGTCTTT
1 TATTTTTGTCCCCTAATTTCAACCAGTTTACCTGAGCCCT-TTGCTCCCAATACATTTCGTCTTT
* * * *
405483 ATAAATCTCTAAATTAAAATGTACTCTAGTGTCAAT-CAAATCAGCCATACTTTCATCAGTTTTG
65 ATCAATCTCTAAATTAAGATGTACTCTAGTATCAATCCAAATCAGCCATACTTTCATCAGTTCTG
* *
405547 TCTTTATCTAAGAGAAATTTTATTTTTTCTATTAGC-T-TT-TTTCGCCC-TCCCTTTTTTTGTC
130 TCTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCC-TTTTTTGTC
** * * *
405608 TAATTCCAACAGCCCATCTTATGATCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACTG
194 TAATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACCG
*
405673 TGATCAACTTGCCACAATCGTTCT-ATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCT
259 TGATCAACTTGCCACAATC-ATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCT
* * *
405737 CAAATTGAAATACCTTCCTACACATGTCCTTTGATTCAATATTAATATCAAGCAGTATGGGATAG
323 CAAATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAG
* ** * *
405802 TGATCGGAAAAAGAATGCGGTAAATGGTG-AAAATTATTGTTGGAAACATATCCGTCCACTTTAA
388 TGATCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCCTCCACTCTAA
** * * *
405866 GTTCGCCACACCTTTATCAAGCCTTTCATGTATTTTAGTCTCCGACAAATTCCCTCTTTCCCAAG
453 GTTCGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAG
* * * * * *
405931 TAAACCAAGTACCTAAGAAACAAATTTCCATCACTTGAAATTCCTCCAAAACTTCCCTAAACTCC
518 TAAACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAACTCC
* * ** *
405996 TCCATCCTGCTTTGTTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATATCGTTAAA
583 GCCATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAA
* * *
406061 ATC-TCTACAAACCAT-CAAAGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATTCCCTAAGTA
648 ATCTTC-ACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTA
* * * *
406124 TTTCCTCTATTCTGCGTA-AAAGGGGAGTCATAAAAACCCATAAACCT
712 TTTCCTCTATTCTACGCATAAA-GGGAGCCATAAAAACCTATAAACCT
406171 TAATTCCTTT
Statistics
Matches: 2721, Mismatches: 277, Indels: 69
0.89 0.09 0.02
Matches are distributed among these distances:
753 3 0.00
754 98 0.04
755 85 0.03
756 293 0.11
757 138 0.05
758 110 0.04
759 767 0.28
760 536 0.20
761 7 0.00
762 550 0.20
763 134 0.05
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.33
Consensus pattern (761 bp):
TATTTTTGTCCCCTAATTTCAACCAGTTTACCTGAGCCCTTTGCTCCCAATACATTTCGTCTTTA
TCAATCTCTAAATTAAGATGTACTCTAGTATCAATCCAAATCAGCCATACTTTCATCAGTTCTGT
CTTGATCTAAGAGAAATTTTATTTTTTCTATCAGCTTCTTCTTTCGCCCTTCCCTTTTTTGTCTA
ATTCCAGTAGCCCATCTTACGAGCCCAATCTATAAAAATTTGAATTTTTCAAAAATATCACCGTG
ATCAACTTGCCACAATCATCTGATCTCATCCACACAATTTTCTTCCTTCACCCACCACGCCTCAA
ATTGAAATACCTTCCTATACATGTTCTTTGATTCAATATCAATATCAAGCAGTATGGGATAGTGA
TCGGAAAAAGAATGCGGTAAATGGTGAAAAACTGCTGTTGGAAACATATCCCTCCACTCTAAGTT
CGCCACACCCCTATCAAGCCTTTCATGTATATTAGTCTCTGGCAAATTCCCTCTTTCCCAAGTAA
ACCAAGTACCTAAGAAGCCAATATCCGTCAGTTGACATTCCTCCAAAACTTCCCTAAACTCCGCC
ATCCTGCTCTCCTCTCTTGGCGCACCACCCACCTTCTCGAAGGAATAAAGAATCTCGTTAAAATC
TTCACAAACCATCCAAGGTAAGCCTTGGATTCGATTTAGATTTTTTAGTATGCCCCAAGTATTTC
CTCTATTCTACGCATAAAGGGAGCCATAAAAACCTATAAACCTATG
Found at i:409162 original size:77 final size:76
Alignment explanation
Indices: 409069--409211 Score: 232
Period size: 77 Copynumber: 1.9 Consensus size: 76
409059 TTTTCCTGCA
* *
409069 TTTTCTATAGAGCATTTTTCAAGGTAGGGTGAGAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTTT
1 TTTTCTATAGAGCATTTTTCAAGGTAGAGTGAAAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTTT
409134 TAGCTATGTTC
66 TAGCTATGTTC
* * *
409145 TTTTCTACTAGAGCATTTTTTAAGGTAGAGTGAAAAAGCTTTATTCTAAAGGTTTCTTGTTGTTT
1 TTTTCTA-TAGAGCATTTTTCAAGGTAGAGTGAAAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTT
409210 TT
65 TT
409212 TTGCTAGGTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
76 7 0.11
77 54 0.89
ACGTcount: A:0.24, C:0.10, G:0.20, T:0.45
Consensus pattern (76 bp):
TTTTCTATAGAGCATTTTTCAAGGTAGAGTGAAAAAGCTTTAGTCCAAAGGTTTCTTGTTGTTTT
TAGCTATGTTC
Found at i:411068 original size:41 final size:41
Alignment explanation
Indices: 411011--411232 Score: 444
Period size: 41 Copynumber: 5.4 Consensus size: 41
411001 ATTGAAATTT
411011 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
411052 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
411093 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
411134 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
411175 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
1 GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
411216 GTGATCTGAATCAGGCT
1 GTGATCTGAATCAGGCT
411233 NNNNNNNNNN
Statistics
Matches: 181, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 181 1.00
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.23
Consensus pattern (41 bp):
GTGATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCG
Found at i:426631 original size:262 final size:262
Alignment explanation
Indices: 426166--426683 Score: 1036
Period size: 262 Copynumber: 2.0 Consensus size: 262
426156 TTAAAAAGGT
426166 TTTTGATATGATAATTTATGTTATATGTATAATTAACTAGGTTAAGTGGTATGACCCTAAAGTCA
1 TTTTGATATGATAATTTATGTTATATGTATAATTAACTAGGTTAAGTGGTATGACCCTAAAGTCA
426231 AGTGATTTTAGAAAATGAGGTATTGGGACCTCATTTCTATAAACTGAGCCGTAAATATTTTAATA
66 AGTGATTTTAGAAAATGAGGTATTGGGACCTCATTTCTATAAACTGAGCCGTAAATATTTTAATA
426296 AATATTTATGGAGTGTTATTAAGGTTGTATTAAAGTTTCATTAAAAAATTGTAATGTTTAGATAG
131 AATATTTATGGAGTGTTATTAAGGTTGTATTAAAGTTTCATTAAAAAATTGTAATGTTTAGATAG
426361 TTAATTAATTGAAAAGGACTAAATTGTAAAAGCTATAAAAGTTAAATTTTATTAACTAAATAAAA
196 TTAATTAATTGAAAAGGACTAAATTGTAAAAGCTATAAAAGTTAAATTTTATTAACTAAATAAAA
426426 TG
261 TG
426428 TTTTGATATGATAATTTATGTTATATGTATAATTAACTAGGTTAAGTGGTATGACCCTAAAGTCA
1 TTTTGATATGATAATTTATGTTATATGTATAATTAACTAGGTTAAGTGGTATGACCCTAAAGTCA
426493 AGTGATTTTAGAAAATGAGGTATTGGGACCTCATTTCTATAAACTGAGCCGTAAATATTTTAATA
66 AGTGATTTTAGAAAATGAGGTATTGGGACCTCATTTCTATAAACTGAGCCGTAAATATTTTAATA
426558 AATATTTATGGAGTGTTATTAAGGTTGTATTAAAGTTTCATTAAAAAATTGTAATGTTTAGATAG
131 AATATTTATGGAGTGTTATTAAGGTTGTATTAAAGTTTCATTAAAAAATTGTAATGTTTAGATAG
426623 TTAATTAATTGAAAAGGACTAAATTGTAAAAGCTATAAAAGTTAAATTTTATTAACTAAAT
196 TTAATTAATTGAAAAGGACTAAATTGTAAAAGCTATAAAAGTTAAATTTTATTAACTAAAT
426684 GAGTCAAATA
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
262 256 1.00
ACGTcount: A:0.39, C:0.06, G:0.16, T:0.39
Consensus pattern (262 bp):
TTTTGATATGATAATTTATGTTATATGTATAATTAACTAGGTTAAGTGGTATGACCCTAAAGTCA
AGTGATTTTAGAAAATGAGGTATTGGGACCTCATTTCTATAAACTGAGCCGTAAATATTTTAATA
AATATTTATGGAGTGTTATTAAGGTTGTATTAAAGTTTCATTAAAAAATTGTAATGTTTAGATAG
TTAATTAATTGAAAAGGACTAAATTGTAAAAGCTATAAAAGTTAAATTTTATTAACTAAATAAAA
TG
Found at i:428803 original size:9 final size:9
Alignment explanation
Indices: 428785--428821 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
428775 TATAGTTTGA
428785 TATTCGAAT
1 TATTCGAAT
*
428794 TATTCAAAT
1 TATTCGAAT
*
428803 TATTCGAGT
1 TATTCGAAT
428812 TATTCGAAT
1 TATTCGAAT
428821 T
1 T
428822 TGAAAACTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:428890 original size:9 final size:9
Alignment explanation
Indices: 428873--428903 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
428863 TCAAGTTGAT
428873 TCGAATAAC
1 TCGAATAAC
*
428882 TCGATTAAC
1 TCGAATAAC
428891 TCGAATAAC
1 TCGAATAAC
428900 TCGA
1 TCGA
428904 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:429678 original size:20 final size:20
Alignment explanation
Indices: 429653--429704 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
429643 AAGTTTATGT
429653 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
* *
429673 TAAGTAAATGGAATGGTAAG
1 TAAGTAAATGAAATGGAAAG
*
429693 AAAGTAAATGAA
1 TAAGTAAATGAA
429705 GTGGTACACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.25, T:0.21
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:429709 original size:20 final size:19
Alignment explanation
Indices: 429654--429710 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
429644 AGTTTATGTT
* *
429654 AAGTAAATGAAATGGAAAGT
1 AAGTAAATG-AATGGTAAGA
429674 AAGTAAATGGAATGGTAAGA
1 AAGTAAAT-GAATGGTAAGA
429694 AAGTAAATGAAGTGGTA
1 AAGTAAATGAA-TGGTA
429711 CACAGTTTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.09
20 29 0.88
21 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.28, T:0.21
Consensus pattern (19 bp):
AAGTAAATGAATGGTAAGA
Found at i:433984 original size:32 final size:31
Alignment explanation
Indices: 433948--434022 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 31
433938 CACACGCTTG
*
433948 TGTGGCCTACACACCCTACCTAGCACATCCCA
1 TGTGGCC-ACACACCCTACCTAGCACAGCCCA
* * * *
433980 TGTGGTCCACACACCTTATCTAGCATAGCCCT
1 TGTGG-CCACACACCCTACCTAGCACAGCCCA
434012 TGTGGCC-CACA
1 TGTGGCCACACA
434023 AAACCTGGCA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
30 4 0.11
31 2 0.05
32 29 0.78
33 2 0.05
ACGTcount: A:0.23, C:0.39, G:0.16, T:0.23
Consensus pattern (31 bp):
TGTGGCCACACACCCTACCTAGCACAGCCCA
Found at i:444193 original size:71 final size:71
Alignment explanation
Indices: 444086--444222 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 71
444076 AATTTGATTA
* * * * * *
444086 TGCTCACTCAAGCTGTCGGGAATTCGCAATACATGTTGGATCACAGTCATCGATAAAGAATAATT
1 TGCTCACTCAAGCTATCGAGAATCCACAACACATGTTGGATCACAGCCATCGATAAAGAATAATT
444151 TAATGT
66 TAATGT
* *
444157 TGCTCACTCAAGCTATCGAGAATCCACAACATATGTTGGATCCCAGCCATCGATAAAGAATAATT
1 TGCTCACTCAAGCTATCGAGAATCCACAACACATGTTGGATCACAGCCATCGATAAAGAATAATT
444222 T
66 T
444223 CTATTCAAAC
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.28
Consensus pattern (71 bp):
TGCTCACTCAAGCTATCGAGAATCCACAACACATGTTGGATCACAGCCATCGATAAAGAATAATT
TAATGT
Found at i:445263 original size:19 final size:19
Alignment explanation
Indices: 445211--445263 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
445201 ATATTTAGTT
* *
445211 TAATAATTAATTAATTAAT
1 TAATAATTAACTAATTAAC
*
445230 TAAT-CTTAACTTAATTAAC
1 TAATAATTAAC-TAATTAAC
*
445249 TAATAGTTAACTAAT
1 TAATAATTAACTAAT
445264 ATTAACCTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.14
19 19 0.68
20 5 0.18
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATAATTAACTAATTAAC
Found at i:450359 original size:15 final size:14
Alignment explanation
Indices: 450330--450364 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
450320 AGGAAAGAAT
*
450330 GATGAGAAGTGAGG
1 GATGATAAGTGAGG
450344 GATGATAAGATGAGG
1 GATGATAAG-TGAGG
450359 GATGAT
1 GATGAT
450365 TGAAGAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.37, C:0.00, G:0.43, T:0.20
Consensus pattern (14 bp):
GATGATAAGTGAGG
Found at i:453221 original size:25 final size:24
Alignment explanation
Indices: 453193--453243 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
453183 ATTAAGCAGG
453193 TCCTTTACAATCATTTTCATAGCTT
1 TCCTTTACAATCATTTTCATAG-TT
*
453218 TCCTTTACAATCCTTTTCATAGTT
1 TCCTTTACAATCATTTTCATAGTT
453242 TC
1 TC
453244 ATAACATAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 4 0.16
25 21 0.84
ACGTcount: A:0.22, C:0.25, G:0.04, T:0.49
Consensus pattern (24 bp):
TCCTTTACAATCATTTTCATAGTT
Found at i:465862 original size:68 final size:68
Alignment explanation
Indices: 465784--465988 Score: 365
Period size: 68 Copynumber: 3.0 Consensus size: 68
465774 GAAGATAATT
* *
465784 TCTCACTTTCTCTATTCTCCTCTCTATGTTACGACATTGGATCCCCCATGTTGCGACATAGCATC
1 TCTCACTTTCTCTATTCTACTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
465849 CAG
66 CAG
*
465852 TCTCACTTTCTCTATTCTGCTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
1 TCTCACTTTCTCTATTCTACTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
465917 CAG
66 CAG
* *
465920 TCTCACTTTCTCTATTCTACTCCCTATGTTGCGACATTGGATCCCCCATGTTGTGACATAGCATC
1 TCTCACTTTCTCTATTCTACTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
465985 CAG
66 CAG
465988 T
1 T
465989 ATTGACCCAA
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 132 1.00
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.36
Consensus pattern (68 bp):
TCTCACTTTCTCTATTCTACTCTCTATGTTGCGACATTGGATCCCCCATGTTGCGACATAGCATC
CAG
Found at i:470111 original size:39 final size:39
Alignment explanation
Indices: 470068--470183 Score: 169
Period size: 39 Copynumber: 2.9 Consensus size: 39
470058 AACATGTTTC
*
470068 TGAGTATTGTGATATATGCTTGAATGTTATGTGATTAAA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTAAA
*
470107 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTAAA
* * * *
470146 TGTGTAATGTGATATATGCTTAAAAGTGAATGTGATTA
1 TGAGTATTGTGATATATGCTTAAATGT-TATGTGATTA
470184 CCATTTAAAT
Statistics
Matches: 70, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 61 0.87
40 9 0.13
ACGTcount: A:0.32, C:0.03, G:0.22, T:0.43
Consensus pattern (39 bp):
TGAGTATTGTGATATATGCTTAAATGTTATGTGATTAAA
Found at i:489112 original size:13 final size:13
Alignment explanation
Indices: 489094--489120 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
489084 GTGATATAGG
489094 TGATATCTAAATA
1 TGATATCTAAATA
489107 TGATATCTAAATA
1 TGATATCTAAATA
489120 T
1 T
489121 TTAAGATATT
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:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (13 bp):
TGATATCTAAATA
Found at i:493782 original size:11 final size:11
Alignment explanation
Indices: 493762--493809 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
493752 TATGAATACA
493762 TTTTTA-AAAT
1 TTTTTATAAAT
493772 TTTTTATAAAT
1 TTTTTATAAAT
*
493783 TTTTT-TAACTT
1 TTTTTATAA-AT
*
493794 TTTTTATTAAT
1 TTTTTATAAAT
493805 TTTTT
1 TTTTT
493810 TGAATTATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
10 9 0.28
11 21 0.66
12 2 0.06
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTATAAAT
Found at i:493789 original size:22 final size:22
Alignment explanation
Indices: 493762--493810 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
493752 TATGAATACA
493762 TTTTTAAAATTTTTTATAAATT
1 TTTTTAAAATTTTTTATAAATT
** *
493784 TTTTTAACTTTTTTTATTAATT
1 TTTTTAAAATTTTTTATAAATT
493806 TTTTT
1 TTTTT
493811 GAATTATGCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTAAAATTTTTTATAAATT
Found at i:493798 original size:10 final size:10
Alignment explanation
Indices: 493762--493815 Score: 54
Period size: 10 Copynumber: 5.1 Consensus size: 10
493752 TATGAATACA
*
493762 TTTTTAAAAT
1 TTTTTTAAAT
493772 TTTTTATAAAT
1 TTTTT-TAAAT
*
493783 TTTTTTAACT
1 TTTTTTAAAT
493793 TTTTTTATTAAT
1 TTTTTTA--AAT
*
493805 TTTTTTGAAT
1 TTTTTTAAAT
493815 T
1 T
493816 ATGCGTGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
10 20 0.54
11 9 0.24
12 8 0.22
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTTTAAAT
Found at i:495043 original size:18 final size:16
Alignment explanation
Indices: 495016--495054 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 16
495006 CTTGAATTTT
495016 TTTTAAATTTCTCTATAA
1 TTTTAAATTT-TCTA-AA
*
495034 TTTTATATTTTCTAAA
1 TTTTAAATTTTCTAAA
495050 TTTTA
1 TTTTA
495055 CATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 4 0.20
18 9 0.45
ACGTcount: A:0.31, C:0.08, G:0.00, T:0.62
Consensus pattern (16 bp):
TTTTAAATTTTCTAAA
Found at i:495569 original size:140 final size:141
Alignment explanation
Indices: 495374--495656 Score: 559
Period size: 140 Copynumber: 2.0 Consensus size: 141
495364 TGAGATAGAA
495374 GTTCTGAAAATTACACATTTAAAAATAATTATAATTTAATTTACAATTATTAGTTAAAATTATTT
1 GTTCTGAAAATTACACATTTAAAAATAATTATAATTTAATTTACAATTATTAGTTAAAATTATTT
495439 TACTAATTTAAAATAAAATTATTACTTAAATAGAACTCTAAGCATGAAATATAGAGAAAAAATTG
66 TACTAATTTAAAATAAAATTATTACTTAAATAGAACTCTAAGCATGAAATATAGAGAAAAAATTG
495504 TCAATTATAAT
131 TCAATTATAAT
495515 GTTCTGAAAA-TACACATTTAAAAATAATTATAATTTAATTTACAATTATTAGTTAAAATTATTT
1 GTTCTGAAAATTACACATTTAAAAATAATTATAATTTAATTTACAATTATTAGTTAAAATTATTT
495579 TACTAATTTAAAATAAAATTATTACTTAAATAGAACTCTAAGCATGAAATATAGAGAAAAAATTG
66 TACTAATTTAAAATAAAATTATTACTTAAATAGAACTCTAAGCATGAAATATAGAGAAAAAATTG
495644 TCAATTATAAT
131 TCAATTATAAT
495655 GT
1 GT
495657 AATTATAATT
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
140 132 0.93
141 10 0.07
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (141 bp):
GTTCTGAAAATTACACATTTAAAAATAATTATAATTTAATTTACAATTATTAGTTAAAATTATTT
TACTAATTTAAAATAAAATTATTACTTAAATAGAACTCTAAGCATGAAATATAGAGAAAAAATTG
TCAATTATAAT
Found at i:496250 original size:31 final size:31
Alignment explanation
Indices: 496212--496311 Score: 141
Period size: 31 Copynumber: 3.3 Consensus size: 31
496202 ACTACCAAAA
*
496212 TAGTCACTTTTGTTTCTCTGGTGTTACATTT
1 TAGTCACTTTTGTTTCTCTGATGTTACATTT
496243 TAGTCACTTTTGTTTCTCTGATGTTACATTT
1 TAGTCACTTTTGTTTCTCTGATGTTACATTT
* ***
496274 TAGTCACTTATG-TT-TGAAATGTTACATTT
1 TAGTCACTTTTGTTTCTCTGATGTTACATTT
496303 TAGTCACTT
1 TAGTCACTT
496312 ACGTTGTCAT
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 21 0.33
30 2 0.03
31 41 0.64
ACGTcount: A:0.19, C:0.15, G:0.14, T:0.52
Consensus pattern (31 bp):
TAGTCACTTTTGTTTCTCTGATGTTACATTT
Found at i:496335 original size:31 final size:29
Alignment explanation
Indices: 496236--496337 Score: 91
Period size: 31 Copynumber: 3.4 Consensus size: 29
496226 TCTCTGGTGT
* *
496236 TACATTTTAGTCACTTTTGTT-TCTCTGATG
1 TACATTTTAGTCACTTATGTTGTC-ATG-TG
**
496266 TTACATTTTAGTCACTTATGTTTGAAATGT-
1 -TACATTTTAGTCACTTATG-TTGTCATGTG
*
496296 TACATTTTAGTCACTTACGTTGTCATGTTG
1 TACATTTTAGTCACTTATGTTGTCATG-TG
496326 TAACATTTTAGT
1 T-ACATTTTAGT
496338 TACTGAATGT
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
28 6 0.10
29 19 0.32
30 1 0.02
31 29 0.49
32 4 0.07
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.50
Consensus pattern (29 bp):
TACATTTTAGTCACTTATGTTGTCATGTG
Found at i:496520 original size:21 final size:20
Alignment explanation
Indices: 496487--496526 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
496477 TTTGACATTA
496487 AAAAGAGAAGGAGAATGAAGG
1 AAAAGAGAAGGAGAA-GAAGG
* *
496508 AAAATAGAGGGAGAAGAAG
1 AAAAGAGAAGGAGAAGAAG
496527 AAGAGAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.05
Consensus pattern (20 bp):
AAAAGAGAAGGAGAAGAAGG
Found at i:498544 original size:13 final size:13
Alignment explanation
Indices: 498526--498550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
498516 TCTCGATTTA
498526 ATCAATCTAATCC
1 ATCAATCTAATCC
498539 ATCAATCTAATC
1 ATCAATCTAATC
498551 AAATTCAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.28, G:0.00, T:0.32
Consensus pattern (13 bp):
ATCAATCTAATCC
Found at i:502527 original size:37 final size:37
Alignment explanation
Indices: 502454--502546 Score: 123
Period size: 37 Copynumber: 2.5 Consensus size: 37
502444 TTAATATAAA
* * *
502454 AATAATTAAATTAAAATTTTTATTAAATTATATTTAAT
1 AATAATTATATTAAAA-TATGATTAAATTATATTTAAT
*
502492 AATAATTATATTAAAATATGATTAAATTATTTTTAAT
1 AATAATTATATTAAAATATGATTAAATTATATTTAAT
**
502529 AATAATCCTATTAAAATA
1 AATAATTATATTAAAATA
502547 ATAATCATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
37 34 0.69
38 15 0.31
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (37 bp):
AATAATTATATTAAAATATGATTAAATTATATTTAAT
Found at i:502670 original size:16 final size:16
Alignment explanation
Indices: 502649--502702 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
502639 TGAATTATTG
502649 ATTACAACTCTATTTC
1 ATTACAACTCTATTTC
**
502665 ATTACAGTTCTATTAT-
1 ATTACAACTCTATT-TC
*
502681 ATTACAACTCTATTCC
1 ATTACAACTCTATTTC
502697 ATTACA
1 ATTACA
502703 TTTCAAAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 30 0.97
17 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.02, T:0.43
Consensus pattern (16 bp):
ATTACAACTCTATTTC
Found at i:504729 original size:18 final size:17
Alignment explanation
Indices: 504708--504750 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
504698 ATTTAAATTT
504708 ATTAAAAATTATAAAAAA
1 ATTAAAAA-TATAAAAAA
*
504726 ATTAAATATATAAAAAA
1 ATTAAAAATATAAAAAA
504743 ATTAAAAA
1 ATTAAAAA
504751 ACACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
ATTAAAAATATAAAAAA
Found at i:504758 original size:19 final size:18
Alignment explanation
Indices: 504708--504768 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 18
504698 ATTTAAATTT
**
504708 ATTAAAAATTATAAAAAA
1 ATTAAAAAACATAAAAAA
* *
504726 ATT-AAATATATAAAAAA
1 ATTAAAAAACATAAAAAA
504743 ATTAAAAAACACTAAAAAA
1 ATTAAAAAACA-TAAAAAA
*
504762 TTTAAAA
1 ATTAAAA
504769 TACTTTTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
17 15 0.42
18 8 0.22
19 13 0.36
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (18 bp):
ATTAAAAAACATAAAAAA
Found at i:505909 original size:432 final size:433
Alignment explanation
Indices: 505095--505962 Score: 1720
Period size: 432 Copynumber: 2.0 Consensus size: 433
505085 TCGAAATTGA
505095 ATCGAATTCTATTTTTATTTAATATATAATTAATTTGAATTTTTATGATATAAAATTAAATATTT
1 ATCGAATTC-ATTTTTATTTAATATATAATTAATTTGAATTTTTATGATATAAAATTAAATATTT
505160 TATATTAAAAATAATTGAAAAATTATTATTTTTACAAACATTTATAAAAAAAAACTTAAAATTTT
65 TATATTAAAAATAATTGAAAAATTATTATTTTTACAAACATTTATAAAAAAAAACTTAAAATTTT
505225 ATCAAATAATATTCAAAATCCTTAAAATAAAATTTATTTCATCAAACTAAATCTAAAAACTTAAG
130 ATCAAATAATATTCAAAATCCTTAAAATAAAATTTATTTCATCAAACTAAATCTAAAAACTTAAG
505290 ATAAAAATACTGATATAAAAACCGAAAAACAAACCGAATCCAATCATAATTAAAGATTAAAAGTT
195 ATAAAAATACTGATATAAAAACCGAAAAACAAACCGAATCCAATCATAATTAAAGATTAAAAGTT
505355 AGAGAAAAAATCCAACTAAACGGATCCGATATCACTTTACTACTTGCAACTAAGAAGATGGTGGT
260 AGAGAAAAAATCCAACTAAACGGATCCGATATCACTTTACTACTTGCAACTAAGAAGATGGTGGT
505420 TGATCGAAAAGCAAATGTTCCGCAAACGATGGAAAAACGCCGCAAAGGACAACGAATGTTGGGTC
325 TGATCGAAAAGCAAATGTTCCGCAAACGATGGAAAAACGCCGCAAAGGACAACGAATGTTGGGTC
505485 GATCCTGATCCTTACCAACAAATGATCTAACAAAAGCACTCATT
390 GATCCTGATCCTTACCAACAAATGATCTAACAAAAGCACTCATT
505529 ATCGAATTC-TTTTTATTTAATATATAATTAATTTGAATTTTTATGATATAAAATTAAATATTTT
1 ATCGAATTCATTTTTATTTAATATATAATTAATTTGAATTTTTATGATATAAAATTAAATATTTT
505593 ATATTAAAAATAATTGAAAAATTATTATTTTTACAAACATTTATAAAAAAAAACTTAAAATTTTA
66 ATATTAAAAATAATTGAAAAATTATTATTTTTACAAACATTTATAAAAAAAAACTTAAAATTTTA
505658 TCAAATAATATTCAAAATCCTTAAAATAAAATTTATTTCATCAAACTAAATCTAAAAACTTAAGA
131 TCAAATAATATTCAAAATCCTTAAAATAAAATTTATTTCATCAAACTAAATCTAAAAACTTAAGA
505723 TAAAAATACTGATATAAAAACCGAAAAACAAACCGAATCCAATCATAATTAAAGATTAAAAGTTA
196 TAAAAATACTGATATAAAAACCGAAAAACAAACCGAATCCAATCATAATTAAAGATTAAAAGTTA
505788 GAGAAAAAATCCAACTAAACGGATCCGATATCACTTTACTACTTGCAACTAAGAAGATGGTGGTT
261 GAGAAAAAATCCAACTAAACGGATCCGATATCACTTTACTACTTGCAACTAAGAAGATGGTGGTT
505853 GATCGAAAAGCAAATGTTCCGCAAACGATGGAAAAACGCCGCAAAGGACAACGAATGTTGGGTCG
326 GATCGAAAAGCAAATGTTCCGCAAACGATGGAAAAACGCCGCAAAGGACAACGAATGTTGGGTCG
505918 ATCCTGATCCTTACCAACAAATGATCTAACAAAAGCACTCATT
391 ATCCTGATCCTTACCAACAAATGATCTAACAAAAGCACTCATT
505961 AT
1 AT
505963 TTTTATTCAT
Statistics
Matches: 434, Mismatches: 0, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
432 425 0.98
434 9 0.02
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.30
Consensus pattern (433 bp):
ATCGAATTCATTTTTATTTAATATATAATTAATTTGAATTTTTATGATATAAAATTAAATATTTT
ATATTAAAAATAATTGAAAAATTATTATTTTTACAAACATTTATAAAAAAAAACTTAAAATTTTA
TCAAATAATATTCAAAATCCTTAAAATAAAATTTATTTCATCAAACTAAATCTAAAAACTTAAGA
TAAAAATACTGATATAAAAACCGAAAAACAAACCGAATCCAATCATAATTAAAGATTAAAAGTTA
GAGAAAAAATCCAACTAAACGGATCCGATATCACTTTACTACTTGCAACTAAGAAGATGGTGGTT
GATCGAAAAGCAAATGTTCCGCAAACGATGGAAAAACGCCGCAAAGGACAACGAATGTTGGGTCG
ATCCTGATCCTTACCAACAAATGATCTAACAAAAGCACTCATT
Found at i:506115 original size:40 final size:41
Alignment explanation
Indices: 506071--506161 Score: 148
Period size: 41 Copynumber: 2.2 Consensus size: 41
506061 AAAAATTTGC
* *
506071 CACAAGTTTTGTAC-TTTTTGAAAATTTAACCCTTCATATT
1 CACAAATTCTGTACTTTTTTGAAAATTTAACCCTTCATATT
506111 CACAAATTCTGTACTTTTTTGAAAATTTAACCCTTCATATT
1 CACAAATTCTGTACTTTTTTGAAAATTTAACCCTTCATATT
*
506152 TACAAATTCT
1 CACAAATTCT
506162 ATCAATTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 12 0.26
41 35 0.74
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (41 bp):
CACAAATTCTGTACTTTTTTGAAAATTTAACCCTTCATATT
Found at i:517172 original size:132 final size:132
Alignment explanation
Indices: 516929--517175 Score: 332
Period size: 132 Copynumber: 1.9 Consensus size: 132
516919 CAGCTCGCAT
* ** * * *
516929 ACCTACGTTCCCAACTGATGTTTAAAGGTTAGAGGAGTTATACTTACAACCTTCATTTATTTGAG
1 ACCTACGTTACCAACTGATGTTTAAAGGCCAGAGGAGTTATACTCACAACCTTCACTTATTTAAG
* * *
516994 TAACCTGAGTTAAGCTCACTACTCCAGAACAGCTTGCGGACCTACGCTCCCAGTTGATAGCTCAC
66 TAACCTGAGTTAAGCTCACTACTCCAGAACAGCTCGCGAACATACGCTCCCAGTTGATAGCTCAC
517059 TG
131 TG
* * * *
517061 ACCTATGTTACCAGCTGATGTTTAAAGGCCAGATGAGTTATACTCATAACCTTCACTTATTTAAG
1 ACCTACGTTACCAACTGATGTTTAAAGGCCAGAGGAGTTATACTCACAACCTTCACTTATTTAAG
** * * *
517126 TAAGTTGAGTTAAGCTCACTATTCTAGAATAGCTCGCGAACATACGCTCC
66 TAACCTGAGTTAAGCTCACTACTCCAGAACAGCTCGCGAACATACGCTCC
517176 AACTGATAAA
Statistics
Matches: 97, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
132 97 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (132 bp):
ACCTACGTTACCAACTGATGTTTAAAGGCCAGAGGAGTTATACTCACAACCTTCACTTATTTAAG
TAACCTGAGTTAAGCTCACTACTCCAGAACAGCTCGCGAACATACGCTCCCAGTTGATAGCTCAC
TG
Found at i:524483 original size:21 final size:21
Alignment explanation
Indices: 524427--524498 Score: 99
Period size: 21 Copynumber: 3.4 Consensus size: 21
524417 GGTAGTTATA
*
524427 AAATGTTCGGTGATTTGAAAC
1 AAATGTACGGTGATTTGAAAC
* *
524448 ATATGTATTGGTGATTTGAAAC
1 AAATGTA-CGGTGATTTGAAAC
*
524470 AGATGTACGGTGATTTGAAAC
1 AAATGTACGGTGATTTGAAAC
524491 AAATGTAC
1 AAATGTAC
524499 TGGTAGTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
21 25 0.57
22 19 0.43
ACGTcount: A:0.35, C:0.08, G:0.24, T:0.33
Consensus pattern (21 bp):
AAATGTACGGTGATTTGAAAC
Found at i:527076 original size:16 final size:16
Alignment explanation
Indices: 527051--527097 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
527041 GGCCCATATC
*
527051 AAATAAATAAACAAAA
1 AAATATATAAACAAAA
527067 AAATATATAAA-AAATA
1 AAATATATAAACAAA-A
*
527083 AAA-ATAAAAACAAAA
1 AAATATATAAACAAAA
527098 TTATTAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATATATAAACAAAA
Found at i:527081 original size:23 final size:25
Alignment explanation
Indices: 527046--527092 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
527036 TGCCTGGCCC
527046 ATATCAAATAAATAAACAA-AAAAAT
1 ATATCAAATAAATAAA-AATAAAAAT
527071 ATAT-AAA-AAATAAAAATAAAAA
1 ATATCAAATAAATAAAAATAAAAA
527093 CAAAATTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 2 0.10
23 12 0.57
24 3 0.14
25 4 0.19
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (25 bp):
ATATCAAATAAATAAAAATAAAAAT
Found at i:527219 original size:26 final size:27
Alignment explanation
Indices: 527178--527228 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
527168 CAAACAGATC
*
527178 CCAAATACCCACTTAACCTAGCCCAAA
1 CCAAATACCCAATTAACCTAGCCCAAA
527205 CCAAA-ACCCAATTAACCTAGCCCA
1 CCAAATACCCAATTAACCTAGCCCA
527229 GCTAATGTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.41, C:0.41, G:0.04, T:0.14
Consensus pattern (27 bp):
CCAAATACCCAATTAACCTAGCCCAAA
Found at i:527645 original size:20 final size:19
Alignment explanation
Indices: 527608--527675 Score: 68
Period size: 20 Copynumber: 3.6 Consensus size: 19
527598 TTTAAGGTGG
*
527608 TTCTCTTTTCT--TTTTCT
1 TTCTCTTTTCTGCGTTTCT
527625 TTCTCTTTCTCTGCGTTTCT
1 TTCTCTTT-TCTGCGTTTCT
* **
527645 TTACTGTTTTCTTTGTTTCT
1 TT-CTCTTTTCTGCGTTTCT
527665 TTCTCTTTTCT
1 TTCTCTTTTCT
527676 ATACGAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
17 8 0.19
18 3 0.07
19 8 0.19
20 18 0.43
21 5 0.12
ACGTcount: A:0.01, C:0.24, G:0.06, T:0.69
Consensus pattern (19 bp):
TTCTCTTTTCTGCGTTTCT
Found at i:528395 original size:24 final size:24
Alignment explanation
Indices: 528359--528404 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
528349 AATATTATAT
* *
528359 AAATTTACCATGTTTTATTATTCA
1 AAATTTACCATGTATCATTATTCA
**
528383 AAATTTATTATGTATCATTATT
1 AAATTTACCATGTATCATTATT
528405 TAAATTTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATTTACCATGTATCATTATTCA
Found at i:528689 original size:28 final size:28
Alignment explanation
Indices: 528657--528738 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
528647 ATTTTATCCC
528657 TTTCAAATATTTTCACATTTTTAATTTA
1 TTTCAAATATTTTCACATTTTTAATTTA
* *
528685 TTTCAACT-TATTTCA-ATATTGTTACTTTA
1 TTTCAAATAT-TTTCACAT-TT-TTAATTTA
*
528714 TTT-AAATTATTTTAACA-TTTTAATT
1 TTTCAAA-TATTTTCACATTTTTAATT
528739 CATATATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 13
0.70 0.08 0.21
Matches are distributed among these distances:
27 8 0.19
28 18 0.42
29 15 0.35
30 2 0.05
ACGTcount: A:0.32, C:0.10, G:0.01, T:0.57
Consensus pattern (28 bp):
TTTCAAATATTTTCACATTTTTAATTTA
Found at i:540931 original size:44 final size:44
Alignment explanation
Indices: 540874--541283 Score: 125
Period size: 44 Copynumber: 9.4 Consensus size: 44
540864 TAATCCTATT
*
540874 TCCCTG-AGATTACAGTGGAACGGATTAAAATAAAGGATCTTATC
1 TCCCTGAAG-TTACAGTGGAACAGATTAAAATAAAGGATCTTATC
* * ** *** *
540918 TCTCTGAAGTTACAGTAGAGTAGA-TCGCAT-CAGG-TCTTATC
1 TCCCTGAAGTTACAGTGGAACAGATTAAAATAAAGGATCTTATC
* ** *
540959 TCCCTG-AGATTACAGTGGAATAGACCGAAGAATTACA-GATCTTATC
1 TCCCTGAAG-TTACAGTGGAACAGA-TTAA-AA-TAAAGGATCTTATC
* * * * * *** * * *
541005 TCCCTAAAATTACAGCGGAGCAGATTGAAGCCAATGATCCTATT
1 TCCCTGAAGTTACAGTGGAACAGATTAAAATAAAGGATCTTATC
* *
541049 TCCCTG-AGATTACAGTGGAACGGATTAAAATAAATGATCTTATC
1 TCCCTGAAG-TTACAGTGGAACAGATTAAAATAAAGGATCTTATC
* * ** * * *
541093 TCTCTGAAGTTACAGTAGAGTAGA-TCACAT-CAGG-TCTTATC
1 TCCCTGAAGTTACAGTGGAACAGATTAAAATAAAGGATCTTATC
* ** * *
541134 TCCCTG-AGATTACAGTGGAATAGACCGAAGAATTACA-GATCTTTTC
1 TCCCTGAAG-TTACAGTGGAACAGA-TTAA-AA-TAAAGGATCTTATC
* ** * ** * *
541180 TCACTG-AGATTACAGCT-GAGGAGATT--GATGCCAGTAATCTTATT
1 TCCCTGAAG-TTACAG-TGGAACAGATTAAAAT-AAAG-GATCTTATC
*
541224 TCCCTG-AGATTACAGTGGAACGGATTAAAATAAAGGATCTTATC
1 TCCCTGAAG-TTACAGTGGAACAGATTAAAATAAAGGATCTTATC
* *
541268 TCTCTAAAGTTACAGT
1 TCCCTGAAGTTACAGT
541284 AGAGTAGATC
Statistics
Matches: 261, Mismatches: 78, Indels: 54
0.66 0.20 0.14
Matches are distributed among these distances:
40 4 0.02
41 51 0.20
42 8 0.03
43 11 0.04
44 117 0.45
45 13 0.05
46 55 0.21
47 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
TCCCTGAAGTTACAGTGGAACAGATTAAAATAAAGGATCTTATC
Found at i:541118 original size:175 final size:175
Alignment explanation
Indices: 540822--541520 Score: 1077
Period size: 175 Copynumber: 4.1 Consensus size: 175
540812 AAAATGGTGA
*
540822 ATCTGATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
540887 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
540952 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* * * *
540997 ATCTTATCTCCCTAAAATTACAGCGGAGCAGATTGAAGCCAATGATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* *
541062 AGTGGAACGGATTAAAATAAATGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCACATCAGG
66 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
541127 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* * * * * *
541172 ATCTTTTCTCACTGAGATTACAGCTGAGGAGATTGATGCCAGTAATCTTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
*
541237 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTAAAGTTACAGTAGAGTAGATCGCATCAGG
66 AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
* *
541302 TCTTATCTTCTTGAGATTACAGTGGAATAGACCGAAGAATTACAG
131 TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
* *
541347 ATCTTA-----C--AG--T---GC--AGCAGATCGAAGCCAGTTATCCTATTTCCCTGAGATTAC
1 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
* * *
541398 AGT-GAAGCGGATCAAAATAAAGGATCTTATCTCTCTGAATTTACAATAGAGTAGATCGCATCAG
66 AGTGGAA-CGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
541462 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAAATTACAG
130 GTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG-AATTACAG
*
541509 AACTTATCTCCC
1 ATCTTATCTCCC
541521 AAGCGGTGTA
Statistics
Matches: 482, Mismatches: 35, Indels: 22
0.89 0.06 0.04
Matches are distributed among these distances:
160 3 0.01
161 126 0.26
162 13 0.03
163 2 0.00
166 1 0.00
167 1 0.00
168 2 0.00
170 1 0.00
175 333 0.69
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (175 bp):
ATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAGTAATCCTATTTCCCTGAGATTAC
AGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGG
TCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAGAATTACAG
Found at i:541421 original size:161 final size:162
Alignment explanation
Indices: 541209--541514 Score: 508
Period size: 161 Copynumber: 1.9 Consensus size: 162
541199 GGAGATTGAT
* *
541209 GCCAGTAATCTTATTTCCCTGAGATTACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTA
1 GCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACGGATCAAAATAAAGGATCTTATCTCTCTA
* * *
541274 AAGTTACAGTAGAGTAGATCGCATCAGGTCTTATCTTCTTGAGATTACAGTGGAATAGACCGAAG
66 AAGTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
*
541339 -AATTACAGATCTTACAGTGCAGCAGATCGAA
131 AAATTACAGAACTTACAGTGCAGCAGATCGAA
*
541370 GCCAGTTATCCTATTTCCCTGAGATTACAGT-GAAGCGGATCAAAATAAAGGATCTTATCTCTCT
1 GCCAGTAATCCTATTTCCCTGAGATTACAGTGGAA-CGGATCAAAATAAAGGATCTTATCTCTCT
* *
541434 GAATTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAA
65 AAAGTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAA
541499 GAAATTACAGAACTTA
130 GAAATTACAGAACTTA
541515 TCTCCCAAGC
Statistics
Matches: 134, Mismatches: 9, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
160 3 0.02
161 118 0.88
162 13 0.10
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (162 bp):
GCCAGTAATCCTATTTCCCTGAGATTACAGTGGAACGGATCAAAATAAAGGATCTTATCTCTCTA
AAGTTACAATAGAGTAGATCGCATCAGGTCTTATCTCCCTGAGATTACAGTGGAATAGACCGAAG
AAATTACAGAACTTACAGTGCAGCAGATCGAA
Found at i:541613 original size:50 final size:51
Alignment explanation
Indices: 541559--541689 Score: 119
Period size: 50 Copynumber: 2.6 Consensus size: 51
541549 ACAAGGGCGG
* * *
541559 ATCTTGCTTCCCCAACATTGCAGTTAGAA-AGATTGAAGCTGCAATAATGA
1 ATCTTGCTTCCCCAACATTGCAGTTAGAACAGATTGAAGCTACAACAACGA
* * ** * *
541609 ATCTTAC-T-GCCAAGTCGGTGCAG-TGGAACATATTGAAGCTACAACAACGA
1 ATCTTGCTTCCCCAA--CATTGCAGTTAGAACAGATTGAAGCTACAACAACGA
*
541659 ATCTTGCTTCCCCGACATTGCAGTTA-AACAG
1 ATCTTGCTTCCCCAACATTGCAGTTAGAACAG
541690 TTTAAAGTTC
Statistics
Matches: 59, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
48 4 0.07
49 5 0.08
50 45 0.76
51 2 0.03
52 3 0.05
ACGTcount: A:0.32, C:0.23, G:0.19, T:0.26
Consensus pattern (51 bp):
ATCTTGCTTCCCCAACATTGCAGTTAGAACAGATTGAAGCTACAACAACGA
Found at i:541954 original size:28 final size:27
Alignment explanation
Indices: 541911--541963 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 27
541901 GCCCAAATCA
541911 AAAAATAAACAAAAAATATATAAAAAAT
1 AAAAATAAACAAAAAAT-TATAAAAAAT
*
541939 AAAAATAAA-AACAAAATTATTAAAA
1 AAAAATAAACAA-AAAATTATAAAAA
541964 GTCCATCAGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (27 bp):
AAAAATAAACAAAAAATTATAAAAAAT
Found at i:543257 original size:24 final size:24
Alignment explanation
Indices: 543221--543266 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
543211 AATATTATAT
* *
543221 AAATTTACCATGTTTTATTATTCA
1 AAATTTACCATGTATCATTATTCA
**
543245 AAATTTATTATGTATCATTATT
1 AAATTTACCATGTATCATTATT
543267 TAAATTTCCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.04, T:0.52
Consensus pattern (24 bp):
AAATTTACCATGTATCATTATTCA
Found at i:543587 original size:29 final size:28
Alignment explanation
Indices: 543528--543605 Score: 104
Period size: 28 Copynumber: 2.8 Consensus size: 28
543518 CTCTTTCCAA
543528 TATTTTAACATTTTAATTTATCTCAACT
1 TATTTTAACATTTTAATTTATCTCAACT
* *
543556 TATTTCAACATTGTTAATTTAT-TCAAATT
1 TATTTTAACATT-TTAATTTATCTC-AACT
*
543585 TATTTTAACCTTTTAATTTAT
1 TATTTTAACATTTTAATTTAT
543606 ACATATTATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
28 22 0.50
29 22 0.50
ACGTcount: A:0.32, C:0.12, G:0.01, T:0.55
Consensus pattern (28 bp):
TATTTTAACATTTTAATTTATCTCAACT
Found at i:546317 original size:8 final size:8
Alignment explanation
Indices: 546304--546330 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
546294 TCCATACTAC
546304 GACTTGGA
1 GACTTGGA
546312 GACTTGGA
1 GACTTGGA
546320 GACTTGGA
1 GACTTGGA
546328 GAC
1 GAC
546331 GTACAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (8 bp):
GACTTGGA
Found at i:547945 original size:12 final size:12
Alignment explanation
Indices: 547924--547973 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
547914 AAAAACGAAA
*
547924 TGATTAAAAACT
1 TGATGAAAAACT
* *
547936 TGATGGAAAATT
1 TGATGAAAAACT
*
547948 TTATGAAAAGACT
1 TGATGAAAA-ACT
547961 TGATGAAAAACT
1 TGATGAAAAACT
547973 T
1 T
547974 AAAAAGTACT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
12 20 0.67
13 10 0.33
ACGTcount: A:0.46, C:0.06, G:0.16, T:0.32
Consensus pattern (12 bp):
TGATGAAAAACT
Found at i:548063 original size:18 final size:18
Alignment explanation
Indices: 548040--548077 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
548030 AGAACTAAAT
*
548040 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
548058 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
548076 GA
1 GA
548078 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:549459 original size:22 final size:20
Alignment explanation
Indices: 549406--549466 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 20
549396 GTTTTCCTGC
*
549406 AAAAATAAAA-ATG-AAAAT
1 AAAAATAAAATAGGAAAAAT
549424 -AAAATAAAATAGGAAAAAT
1 AAAAATAAAATAGGAAAAAT
549443 AAATAATAATAATAGGAAAAAT
1 AAA-AATAA-AATAGGAAAAAT
549465 AA
1 AA
549467 TTTTTTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
17 9 0.24
18 2 0.05
19 5 0.14
20 2 0.05
21 5 0.14
22 14 0.38
ACGTcount: A:0.74, C:0.00, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAATAAAATAGGAAAAAT
Found at i:554130 original size:18 final size:18
Alignment explanation
Indices: 554107--554144 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
554097 TGAACTAAAT
*
554107 GAAAAATACTTGAA-GAAA
1 GAAAAACACTT-AATGAAA
554125 GAAAAACACTTAATGAAA
1 GAAAAACACTTAATGAAA
554143 GA
1 GA
554145 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 2 0.11
18 16 0.89
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (18 bp):
GAAAAACACTTAATGAAA
Found at i:556766 original size:30 final size:30
Alignment explanation
Indices: 556713--556840 Score: 143
Period size: 30 Copynumber: 4.3 Consensus size: 30
556703 TGCAAATTCA
* * *
556713 ACCCTATAATCATTCAT-AGTTACACATCAT
1 ACCCTGTAATCATTC-TCAATTACATATCAT
*
556743 ACCTTGTAATCATTCTCAATTACATATCAT
1 ACCCTGTAATCATTCTCAATTACATATCAT
* * *
556773 GCCCTATAATCATTTTCAATTACATATCAT
1 ACCCTGTAATCATTCTCAATTACATATCAT
* *
556803 ACCCTGTAACCATT-TGAAATTACATATCAT
1 ACCCTGTAATCATTCT-CAATTACATATCAT
556833 ACCCTGTA
1 ACCCTGTA
556841 CAATGTGTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
29 2 0.02
30 82 0.98
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.36
Consensus pattern (30 bp):
ACCCTGTAATCATTCTCAATTACATATCAT
Found at i:561678 original size:4 final size:4
Alignment explanation
Indices: 561669--562411 Score: 1486
Period size: 4 Copynumber: 185.8 Consensus size: 4
561659 TATTAAATAA
561669 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
561717 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
561765 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
561813 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
561861 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
561909 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
561957 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562005 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562053 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562101 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562149 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562197 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562245 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562293 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562341 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
562389 GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTA
562412 GATTGAACAT
Statistics
Matches: 739, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 739 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
GTAT
Found at i:562595 original size:41 final size:42
Alignment explanation
Indices: 562507--562599 Score: 125
Period size: 42 Copynumber: 2.2 Consensus size: 42
562497 GGCTTAGCGC
* *
562507 CTAGCAGGCTTATTGCCAGTGAAACAATATCAGACTTTACGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTATACGT
* * * *
562549 CTAGCAGGCTTAATGCCGGTGAAAC-ATTTTAGACTATATGT
1 CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTATACGT
562590 CTAGCAGGCT
1 CTAGCAGGCT
562600 AAGTACCAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
41 22 0.49
42 23 0.51
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
CTAGCAGGCTTAATGCCAGTGAAACAATATCAGACTATACGT
Found at i:569170 original size:76 final size:75
Alignment explanation
Indices: 568995--569362 Score: 220
Period size: 76 Copynumber: 5.0 Consensus size: 75
568985 ACCGTAGCAA
* * * * *
568995 TGTTTTGCTCCCAGCGCTAGTCGGATAAATTGAC-A-A-T--AGGTGTGCCCAGCACTGGTCGGG
1 TGTTTTGCACCCAGCGCTAGTCGGATAAACTGACGATATTAAATGTGTGCCCAGCACTAGT-GGA
* * *
569055 TAAACCGACAA
65 TAAACCAATAT
**** * ** *
569066 TGTTTTATGGCCAGTGCTAGTCAAATAAACTGACGATATTAAATCTGTGCCCAGCACTAGTAGGA
1 TGTTTTGCACCCAGCGCTAGTCGGATAAACTGACGATATTAAATGTGTGCCCAGCACTAGT-GGA
569131 TAAACCAATAT
65 TAAACCAATAT
*** * * * *
569142 TGTTTTGCGTTCAGCGCTAGTTGGATAAA-TCGAC-A-A-TAGA--TGTGCCCAGCACTGGTCGA
1 TGTTTTGCACCCAGCGCTAGTCGGATAAACT-GACGATATTAAATGTGTGCCCAGCACTAGTGGA
* * * *
569201 GTAAATCGACAA
65 -TAAACCAATAT
* * * ** *
569213 TGTTTTGCACCCAACGCAAGTCGGAT-AATTGATTATATTAAATGTGTGCCCAACACTAGTCGGA
1 TGTTTTGCACCCAGCGCTAGTCGGATAAACTGACGATATTAAATGTGTGCCCAGCACTAGT-GGA
***
569277 TAAATTGATAT
65 TAAACCAATAT
* * * * *
569288 TGCTTTGCACCCAGTGCTAGTCGGATAAACTGATGATATTAAATGTGTGCCCAGCACAAGTTGGT
1 TGTTTTGCACCCAGCGCTAGTCGGATAAACTGACGATATTAAATGTGTGCCCAGCACTAG-TGGA
*
569353 TAGACCAATA
65 TAAACCAATA
569363 ATTATCTGTA
Statistics
Matches: 223, Mismatches: 58, Indels: 27
0.72 0.19 0.09
Matches are distributed among these distances:
70 6 0.03
71 70 0.31
72 2 0.01
73 7 0.03
74 2 0.01
75 46 0.21
76 89 0.40
77 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (75 bp):
TGTTTTGCACCCAGCGCTAGTCGGATAAACTGACGATATTAAATGTGTGCCCAGCACTAGTGGAT
AAACCAATAT
Found at i:569217 original size:71 final size:70
Alignment explanation
Indices: 568982--569240 Score: 207
Period size: 71 Copynumber: 3.6 Consensus size: 70
568972 GCCTAACGAA
* *
568982 TAAACCGTAGCAATGTTTTGC-TCCCAGCGCTAGTCGGATAAATTGACAATAGGTGTGCCCAGCA
1 TAAACCG-A-CAATGTTTTGCGT-CCAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCA
569046 CTGGTCGGG
63 CTGGTC-GG
** * * ** *
569055 TAAACCGACAATGTTTTATGGCCAGTGCTAGTCAAATAAA-CTGACGATATTAAATCTGTGCCCA
1 TAAACCGACAATGTTTTGCGTCCAGCGCTAGTCGGATAAATC-GAC-A-A-TAGA--TGTGCCCA
* *
569119 GCACTAGTAGG
60 GCACTGGTCGG
* * * * *
569130 ATAAACCAATATTGTTTTGCGTTCAGCGCTAGTTGGATAAATCGACAATAGATGTGCCCAGCACT
1 -TAAACCGACAATGTTTTGCGTCCAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACT
569195 GGTCGAG
65 GGTCG-G
* ** * *
569202 TAAATCGACAATGTTTTGCACCCAACGCAAGTCGGATAA
1 TAAACCGACAATGTTTTGCGTCCAGCGCTAGTCGGATAA
569241 TTGATTATAT
Statistics
Matches: 141, Mismatches: 35, Indels: 22
0.71 0.18 0.11
Matches are distributed among these distances:
71 73 0.52
72 3 0.02
73 11 0.08
74 3 0.02
75 3 0.02
76 47 0.33
77 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (70 bp):
TAAACCGACAATGTTTTGCGTCCAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTG
GTCGG
Found at i:569314 original size:146 final size:147
Alignment explanation
Indices: 568998--569316 Score: 370
Period size: 147 Copynumber: 2.2 Consensus size: 147
568988 GTAGCAATGT
* * * *
568998 TTTGCTCCCAGCGCTAGTCGGATAAATTGACAATAGGTGTGCCCAGCACTGGTCGGGTAAACCGA
1 TTTGCACCCAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTGGTCGAGTAAACCGA
*** ** * *
569063 CAATGTTTTATGGCCAGTGCTAGTCAAATAAACTGACGATATTAAATCTGTGCCCAGCACTAGTA
66 CAATGTTTTACACCCAACGCAAGTCAAATAAACTGACGATATTAAATCTGTGCCCAACACTAGTA
*
569128 GGATAAACCAATATTGT
131 GGATAAACCAATATTGC
*** * *
569145 TTTGCGTTCAGCGCTAGTTGGATAAATCGACAATAGATGTGCCCAGCACTGGTCGAGTAAATCGA
1 TTTGCACCCAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTGGTCGAGTAAACCGA
* ** * ** * *
569210 CAATGTTTTGCACCCAACGCAAGTCGGAT-AATTGATTATATTAAATGTGTGCCCAACACTAGTC
66 CAATGTTTTACACCCAACGCAAGTCAAATAAACTGACGATATTAAATCTGTGCCCAACACTAGTA
***
569274 GGATAAATTGATATTGC
131 GGATAAACCAATATTGC
*
569291 TTTGCACCCAGTGCTAGTCGGATAAA
1 TTTGCACCCAGCGCTAGTCGGATAAA
569317 CTGATGATAT
Statistics
Matches: 140, Mismatches: 32, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
146 63 0.45
147 77 0.55
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (147 bp):
TTTGCACCCAGCGCTAGTCGGATAAATCGACAATAGATGTGCCCAGCACTGGTCGAGTAAACCGA
CAATGTTTTACACCCAACGCAAGTCAAATAAACTGACGATATTAAATCTGTGCCCAACACTAGTA
GGATAAACCAATATTGC
Found at i:571334 original size:3 final size:3
Alignment explanation
Indices: 571326--572005 Score: 1351
Period size: 3 Copynumber: 226.7 Consensus size: 3
571316 GATCTTAACA
*
571326 AAG AAG AAG AAG AAG AAG AAG GAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571374 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571422 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571470 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571518 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571566 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571614 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571662 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571710 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571758 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571806 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571854 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571902 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571950 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
571998 AAG AAG AA
1 AAG AAG AA
572006 TAGAATGTTC
Statistics
Matches: 675, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 675 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:587148 original size:26 final size:26
Alignment explanation
Indices: 587113--587174 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
587103 CTTACAAGCC
587113 ATAC-TAATCATGCCAAAATAGTTTA
1 ATACATAATCATGCCAAAATAGTTTA
*
587138 ATACATAATCATGCCAAAATATTTTA
1 ATACATAATCATGCCAAAATAGTTTA
587164 ATACATAATCA
1 ATACATAATCA
587175 CACTTACAAG
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 4 0.11
26 31 0.89
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.32
Consensus pattern (26 bp):
ATACATAATCATGCCAAAATAGTTTA
Found at i:590944 original size:17 final size:17
Alignment explanation
Indices: 590893--590944 Score: 50
Period size: 21 Copynumber: 2.8 Consensus size: 17
590883 ATCTTTTCCA
*
590893 TCTATCTTATTTATTAT
1 TCTATTTTATTTATTAT
*
590910 TCTAACTCTTTGATTTATTGT
1 TCT-A-T-TTT-ATTTATTAT
590931 TCTATTTTATTTAT
1 TCTATTTTATTTAT
590945 CTTAGTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
17 9 0.31
18 4 0.14
19 2 0.07
20 3 0.10
21 11 0.38
ACGTcount: A:0.21, C:0.12, G:0.04, T:0.63
Consensus pattern (17 bp):
TCTATTTTATTTATTAT
Found at i:590981 original size:12 final size:13
Alignment explanation
Indices: 590958--590982 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
590948 AGTTATTTAA
590958 TTTAATTTTTTTC
1 TTTAATTTTTTTC
590971 TTTAATTTTTTT
1 TTTAATTTTTTT
590983 ATTTGACTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTAATTTTTTTC
Found at i:593135 original size:90 final size:89
Alignment explanation
Indices: 593041--593273 Score: 278
Period size: 90 Copynumber: 2.6 Consensus size: 89
593031 TAATTTTTTT
* * *
593041 TAAAAAAA-AATAGAAACTTCAAAAAATACTAGTT-AGAATTATAGAAA-AT-TATAAAAAGTAT
1 TAAAAAAAGAATACAAAATTCAAAAAATA-TA-TTAAAAATTATA-AAATATATATAAAAAGTAT
593102 AATCTTTTTTTAAAAAAATGTTATAAAAA
63 --TCTTTTTTTAAAAAAATGTTATAAAAA
* ** *
593131 TAAAAAAAGCATACAAAATTTTAAAATTATATTAAAAATTATAAAATTATATATAAAAAGTATTC
1 TAAAAAAAGAATACAAAATTCAAAAAATATATTAAAAATTATAAAA-TATATATAAAAAGTATTC
593196 TTTTTTTAAAAAAATGTTATAAAAA
65 TTTTTTTAAAAAAATGTTATAAAAA
* ** *
593221 TAAAAAAAGCATACAAAATTTTAAAATTATATTAAAAATTATAAAAT-TATATA
1 TAAAAAAAGAATACAAAATTCAAAAAATATATTAAAAATTATAAAATATATATA
593274 GAATTACAAA
Statistics
Matches: 131, Mismatches: 7, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
88 6 0.05
89 6 0.05
90 91 0.69
91 16 0.12
92 12 0.09
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (89 bp):
TAAAAAAAGAATACAAAATTCAAAAAATATATTAAAAATTATAAAATATATATAAAAAGTATTCT
TTTTTTAAAAAAATGTTATAAAAA
Found at i:593168 original size:20 final size:21
Alignment explanation
Indices: 593145--593189 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
593135 AAAAGCATAC
*
593145 AAAATTTTAAAATTATAT-TA
1 AAAATTATAAAATTATATATA
593165 AAAATTATAAAATTATATATA
1 AAAATTATAAAATTATATATA
593186 AAAA
1 AAAA
593190 GTATTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAATTATAAAATTATATATA
Found at i:593258 original size:20 final size:20
Alignment explanation
Indices: 593235--593272 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
593225 AAAAGCATAC
*
593235 AAAATTTTAAAATTATATTA
1 AAAATTATAAAATTATATTA
593255 AAAATTATAAAATTATAT
1 AAAATTATAAAATTATAT
593273 AGAATTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAAATTATAAAATTATATTA
Found at i:593284 original size:18 final size:20
Alignment explanation
Indices: 593243--593284 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
593233 ACAAAATTTT
*
593243 AAAATTATATTAAAAATTAT
1 AAAATTATATTAAAAATTAC
*
593263 AAAATTATA-T-AGAATTAC
1 AAAATTATATTAAAAATTAC
593281 AAAA
1 AAAA
593285 ATCTAGAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 1 0.05
20 9 0.45
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (20 bp):
AAAATTATATTAAAAATTAC
Found at i:593776 original size:16 final size:17
Alignment explanation
Indices: 593749--593792 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
593739 AACCATTTCC
*
593749 AATATTTCTATATTTTT
1 AATATTTTTATATTTTT
*
593766 TA-ATTTTTATATTTTT
1 AATATTTTTATATTTTT
593782 AATATTTTTAT
1 AATATTTTTAT
593793 TGATTAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
AATATTTTTATATTTTT
Found at i:595043 original size:19 final size:19
Alignment explanation
Indices: 595002--595067 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
594992 AAAAATATAA
*
595002 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAA-TTTTAGAAATT
*
595022 ATTTTGAGTTTTAGAAATT
1 ATTTTGAATTTTAGAAATT
*
595041 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTAG-AAATT
595061 ATTTTGA
1 ATTTTGA
595068 TTCTTTTTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
18 8 0.20
19 15 0.38
20 17 0.43
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (19 bp):
ATTTTGAATTTTAGAAATT
Found at i:595059 original size:20 final size:20
Alignment explanation
Indices: 595002--595067 Score: 75
Period size: 19 Copynumber: 3.4 Consensus size: 20
594992 AAAAATATAA
595002 ATTTTAGAATTTTT-ATAAA-T
1 ATTTT-GAATTTTTGA-AAATT
* *
595022 ATTTTGAGTTTTAG-AAATT
1 ATTTTGAATTTTTGAAAATT
595041 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
595061 ATTTTGA
1 ATTTTGA
595068 TTCTTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 3 0.08
19 19 0.49
20 17 0.44
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.55
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:596204 original size:11 final size:11
Alignment explanation
Indices: 596182--596232 Score: 68
Period size: 11 Copynumber: 4.6 Consensus size: 11
596172 AACTAATCCT
596182 CTCTCAAATTTC
1 CTCTC-AATTTC
596194 CTCTCAATTTC
1 CTCTCAATTTC
*
596205 CTCTTAATTTC
1 CTCTCAATTTC
*
596216 CTCTCAAGTTC
1 CTCTCAATTTC
596227 CT-TCAA
1 CTCTCAA
596233 AAATTCTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
10 4 0.11
11 27 0.75
12 5 0.14
ACGTcount: A:0.22, C:0.33, G:0.02, T:0.43
Consensus pattern (11 bp):
CTCTCAATTTC
Found at i:596255 original size:11 final size:11
Alignment explanation
Indices: 596236--596277 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
596226 CCTTCAAAAA
596236 TTCTCTTAAGT
1 TTCTCTTAAGT
*
596247 TTTTCTTAAGT
1 TTCTCTTAAGT
*
596258 TCCTCTTAAGT
1 TTCTCTTAAGT
596269 TTCTCTTAA
1 TTCTCTTAA
596278 CTCTATTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.07, T:0.55
Consensus pattern (11 bp):
TTCTCTTAAGT
Found at i:597441 original size:7 final size:7
Alignment explanation
Indices: 597429--597453 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
597419 AGTCGATTGA
597429 TATTTAG
1 TATTTAG
597436 TATTTAG
1 TATTTAG
597443 TATTTAG
1 TATTTAG
597450 TATT
1 TATT
597454 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Done.