Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
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: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 12 of 136
Found at i:3703168 original size:20 final size:19
Alignment explanation
Indices: 3703145--3703191 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
3703135 TAAATTAAAT
*
3703145 ATTAAGATAATAAATTTATG
1 ATTAAGATAATAAA-ATATG
*
3703165 ATTAA-ATTAATAAAATATT
1 ATTAAGA-TAATAAAATATG
3703184 ATTAAGAT
1 ATTAAGAT
3703192 GAGTATAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
ATTAAGATAATAAAATATG
Found at i:3705823 original size:25 final size:25
Alignment explanation
Indices: 3705761--3705823 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
3705751 AACTCTCTTA
* * * *
3705761 AGCTTCTCGATACTTGGCTCTCATG
1 AGCTTCCCGATATTTGGCTCGCAAG
3705786 AGCTTCCCGATATTTGGCTCGCAAG
1 AGCTTCCCGATATTTGGCTCGCAAG
3705811 AGCTTCCCGATAT
1 AGCTTCCCGATAT
3705824 ACAGCTCGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.32
Consensus pattern (25 bp):
AGCTTCCCGATATTTGGCTCGCAAG
Found at i:3705830 original size:25 final size:25
Alignment explanation
Indices: 3705785--3705842 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
3705775 TGGCTCTCAT
***
3705785 GAGCTTCCCGATATTTGGCTCGCAA
1 GAGCTTCCCGATATACAGCTCGCAA
* *
3705810 GAGCTTCCCGATATACAGCTCGTAT
1 GAGCTTCCCGATATACAGCTCGCAA
3705835 GAGCTTCC
1 GAGCTTCC
3705843 TGTTACTCAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (25 bp):
GAGCTTCCCGATATACAGCTCGCAA
Found at i:3709686 original size:26 final size:26
Alignment explanation
Indices: 3709639--3709692 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 26
3709629 TAAATAATTT
3709639 TAAAATTGTAAAAAATAAAAAAGTTCA
1 TAAAATTGTAAAAAATAAAAAAG-TCA
* *
3709666 TAAAATTTTCAAAAA-AAAAAAGTCA
1 TAAAATTGTAAAAAATAAAAAAGTCA
3709691 TA
1 TA
3709693 TGAAGTACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.20
26 7 0.28
27 13 0.52
ACGTcount: A:0.63, C:0.06, G:0.06, T:0.26
Consensus pattern (26 bp):
TAAAATTGTAAAAAATAAAAAAGTCA
Found at i:3713397 original size:18 final size:18
Alignment explanation
Indices: 3713358--3713406 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
3713348 TTATAATTCT
*
3713358 TTTAATAT-TTTTTAAAA
1 TTTAATATATTTATAAAA
*
3713375 TTTAATATATTTATAATA
1 TTTAATATATTTATAAAA
3713393 TTTAA-ATTATTTAT
1 TTTAATA-TATTTAT
3713407 TGATGCGACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAATATATTTATAAAA
Found at i:3717884 original size:20 final size:18
Alignment explanation
Indices: 3717858--3717908 Score: 57
Period size: 20 Copynumber: 2.7 Consensus size: 18
3717848 AAATATAAAA
*
3717858 AAATTATTGAAAATTATAG
1 AAATTATT-AAAAATATAG
*
3717877 AAAGTTATAAAAAAATATAG
1 AAA-TTAT-TAAAAATATAG
3717897 AAATTATTAAAA
1 AAATTATTAAAA
3717909 GAAACAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 4 0.15
19 7 0.26
20 16 0.59
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (18 bp):
AAATTATTAAAAATATAG
Found at i:3717886 original size:31 final size:31
Alignment explanation
Indices: 3717829--3717892 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
3717819 TTTTTATATT
3717829 ATTATTAAAATCTATAAAAAAATATAAAAAA
1 ATTATTAAAATCTATAAAAAAATATAAAAAA
* **
3717860 ATTATTGAAAAT-TATAGAAAGTTATAAAAAA
1 ATTATT-AAAATCTATAAAAAAATATAAAAAA
3717891 AT
1 AT
3717893 ATAGAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.83
32 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (31 bp):
ATTATTAAAATCTATAAAAAAATATAAAAAA
Found at i:3718439 original size:37 final size:37
Alignment explanation
Indices: 3718397--3718468 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
3718387 AGGATATGGT
*
3718397 CCAAAGCGGCGAGCAAAAATCAACAAAAGAATTGAGC
1 CCAAAGCGGCAAGCAAAAATCAACAAAAGAATTGAGC
3718434 CCAAAGCGGCAAGCAAAAATCAACAAAAGAATTGA
1 CCAAAGCGGCAAGCAAAAATCAACAAAAGAATTGA
3718469 ACATTCACCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.08
Consensus pattern (37 bp):
CCAAAGCGGCAAGCAAAAATCAACAAAAGAATTGAGC
Found at i:3719179 original size:2 final size:2
Alignment explanation
Indices: 3719172--3719199 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3719162 ATAAAAATAC
3719172 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3719200 TAAAGAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3725901 original size:41 final size:43
Alignment explanation
Indices: 3725803--3725955 Score: 134
Period size: 41 Copynumber: 3.6 Consensus size: 43
3725793 TTTAATCCGC
* * * * *
3725803 TCCACTGCAACTTCAGGGAGATAGGATTGGTTTCTTATGTGTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTGGATACTGA-GTCTGT
3725847 TCCACTGCAACTTCAGGGAGATAAGATTGGATAC-GA-TCTGT
1 TCCACTGCAACTTCAGGGAGATAAGATTGGATACTGAGTCTGT
* ** * * * * * *
3725888 TCTACTGCAACTTCATAGAGATAAGATCT-AAT-TTTAATCCGC
1 TCCACTGCAACTTCAGGGAGATAAGAT-TGGATACTGAGTCTGT
3725930 TCCACTGCAACTTCAGGGAGATAAGA
1 TCCACTGCAACTTCAGGGAGATAAGA
3725956 CCTGCCCTCT
Statistics
Matches: 90, Mismatches: 16, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 31 0.34
42 27 0.30
43 1 0.01
44 31 0.34
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.30
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGGATACTGAGTCTGT
Found at i:3726377 original size:88 final size:88
Alignment explanation
Indices: 3726264--3726486 Score: 356
Period size: 88 Copynumber: 2.5 Consensus size: 88
3726254 TCAAGGCAAT
* * * * * * * *
3726264 AAGGCTGGTGTCCTCGATCTGCTTCGCTGCCAGTACAAGAAGGCAAGATCTGCTATTTTTAACCT
1 AAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATTTTCAACCT
*
3726329 ACTCCGCTGCTGCTCAGGGAGAC
66 ACTCCACTGCTGCTCAGGGAGAC
3726352 AAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATTTTCAACCT
1 AAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATTTTCAACCT
3726417 ACTCCACTGCTGCTCAGGGAGAC
66 ACTCCACTGCTGCTCAGGGAGAC
*
3726440 AAGGCTAGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAG
1 AAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAG
3726487 TTCTTCATAG
Statistics
Matches: 125, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 125 1.00
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (88 bp):
AAGGCTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATTTTCAACCT
ACTCCACTGCTGCTCAGGGAGAC
Found at i:3726380 original size:43 final size:43
Alignment explanation
Indices: 3726327--3726469 Score: 151
Period size: 43 Copynumber: 3.3 Consensus size: 43
3726317 TATTTTTAAC
*
3726327 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTGGTATCTTCGAT
1 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTAGTATCTTCGAT
* *** * * * * * *
3726370 CTACTTCGCTGCCAATACAGGAAGACAAGATCTACTATTTTCAAC
1 CTACTCCGCTGCTGCT-CAGGGAGACAAG-GCTAGTATCTTCGAT
*
3726415 CTACTCCACTGCTGCTCAGGGAGACAAGGCTAGTATCTTCGAT
1 CTACTCCGCTGCTGCTCAGGGAGACAAGGCTAGTATCTTCGAT
*
3726458 CTACTTCGCTGC
1 CTACTCCGCTGC
3726470 CAATACAGGA
Statistics
Matches: 74, Mismatches: 24, Indels: 4
0.73 0.24 0.04
Matches are distributed among these distances:
43 32 0.43
44 22 0.30
45 20 0.27
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.27
Consensus pattern (43 bp):
CTACTCCGCTGCTGCTCAGGGAGACAAGGCTAGTATCTTCGAT
Found at i:3726440 original size:44 final size:44
Alignment explanation
Indices: 3726307--3726442 Score: 139
Period size: 44 Copynumber: 3.1 Consensus size: 44
3726297 TACAAGAAGG
*
3726307 CAAGATCTGCTATTTTTAACCTACTCCGCTGCTGCTCAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCTCAGGGAGA
* * * * * * *** *
3726351 CAAG-GCTGGTATCTTCGATCTACTTCGCTGCCAATACAGGAAGA
1 CAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCT-CAGGGAGA
* *
3726395 CAAGATCTACTATTTTCAACCTACTCCACTGCTGCTCAGGGAGA
1 CAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCTCAGGGAGA
3726439 CAAG
1 CAAG
3726443 GCTAGTATCT
Statistics
Matches: 67, Mismatches: 23, Indels: 4
0.71 0.24 0.04
Matches are distributed among these distances:
43 21 0.31
44 26 0.39
45 20 0.30
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.26
Consensus pattern (44 bp):
CAAGATCTGCTATTTTCAACCTACTCCGCTGCTGCTCAGGGAGA
Found at i:3726484 original size:44 final size:44
Alignment explanation
Indices: 3726343--3726486 Score: 155
Period size: 44 Copynumber: 3.3 Consensus size: 44
3726333 CGCTGCTGCT
* *
3726343 CAGGGAGACAAGGCTGGTATCTTCGATCTACTTCGCTGCCAATA
1 CAGGAAGACAAGGCTAGTATCTTCGATCTACTTCGCTGCCAATA
* * * * * * * ***
3726387 CAGGAAGACAAGATCTACTATTTTCAACCTACTCCACTGCTGCT-
1 CAGGAAGACAAG-GCTAGTATCTTCGATCTACTTCGCTGCCAATA
*
3726431 CAGGGAGACAAGGCTAGTATCTTCGATCTACTTCGCTGCCAATA
1 CAGGAAGACAAGGCTAGTATCTTCGATCTACTTCGCTGCCAATA
3726475 CAGGAAGACAAG
1 CAGGAAGACAAG
3726487 TTCTTCATAG
Statistics
Matches: 74, Mismatches: 24, Indels: 4
0.73 0.24 0.04
Matches are distributed among these distances:
43 21 0.28
44 33 0.45
45 20 0.27
ACGTcount: A:0.29, C:0.26, G:0.22, T:0.24
Consensus pattern (44 bp):
CAGGAAGACAAGGCTAGTATCTTCGATCTACTTCGCTGCCAATA
Found at i:3728000 original size:25 final size:26
Alignment explanation
Indices: 3727962--3728028 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
3727952 TTAATATGGT
*
3727962 TTAAAATGCATAATATA-TGAAAAAC
1 TTAAAATGAATAATATATTGAAAAAC
**
3727987 TTAAAAT-AATTAAT-TATTGAAAATT
1 TTAAAATGAA-TAATATATTGAAAAAC
3728012 TTAAAATGAATAATATA
1 TTAAAATGAATAATATA
3728029 AAGTTCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
24 3 0.09
25 28 0.80
26 4 0.11
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.36
Consensus pattern (26 bp):
TTAAAATGAATAATATATTGAAAAAC
Found at i:3735817 original size:32 final size:31
Alignment explanation
Indices: 3735756--3735851 Score: 165
Period size: 31 Copynumber: 3.1 Consensus size: 31
3735746 NNNNNNNNNN
*
3735756 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3735787 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
*
3735819 AATAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3735850 AA
1 AA
3735852 ATTATCTAAG
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
31 33 0.53
32 29 0.47
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:3738505 original size:11 final size:11
Alignment explanation
Indices: 3738489--3738513 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3738479 TCACAGCTGG
3738489 AACTTGTGCAT
1 AACTTGTGCAT
3738500 AACTTGTGCAT
1 AACTTGTGCAT
3738511 AAC
1 AAC
3738514 ATGCTGCCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (11 bp):
AACTTGTGCAT
Found at i:3743980 original size:12 final size:12
Alignment explanation
Indices: 3743947--3743983 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
3743937 CATTGATAGC
*
3743947 ATAAGTTATCTT
1 ATAAGTTATTTT
3743959 ATAAGTTATTTT
1 ATAAGTTATTTT
3743971 ATAAGTTATTTT
1 ATAAGTTATTTT
3743983 A
1 A
3743984 AATCAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (12 bp):
ATAAGTTATTTT
Found at i:3753454 original size:2 final size:2
Alignment explanation
Indices: 3753447--3753490 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
3753437 AAGCATGTAG
3753447 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3753489 AT
1 AT
3753491 CATGAGTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3756069 original size:49 final size:49
Alignment explanation
Indices: 3756012--3756108 Score: 185
Period size: 49 Copynumber: 2.0 Consensus size: 49
3756002 TCAAGAAACG
3756012 TGGAGTTATTATTTTGAGAAATTGACAAGCTTTTAAAAAACCGGACAAT
1 TGGAGTTATTATTTTGAGAAATTGACAAGCTTTTAAAAAACCGGACAAT
*
3756061 TGGAGTTATTATTTTGAGAAATTGGCAAGCTTTTAAAAAACCGGACAA
1 TGGAGTTATTATTTTGAGAAATTGACAAGCTTTTAAAAAACCGGACAA
3756109 GGCAGAGATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (49 bp):
TGGAGTTATTATTTTGAGAAATTGACAAGCTTTTAAAAAACCGGACAAT
Found at i:3757255 original size:26 final size:27
Alignment explanation
Indices: 3757205--3757257 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3757195 TGCATGTCAA
* *
3757205 ATTTGATTTTAATTAAAAAATTTCAACT
1 ATTTAATTTTAA-TAAAAAAATTCAACT
3757233 ATTTAATTTTAA-AAAAAAATTCAAC
1 ATTTAATTTTAATAAAAAAATTCAAC
3757258 CGTTGAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
28 11 0.48
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.42
Consensus pattern (27 bp):
ATTTAATTTTAATAAAAAAATTCAACT
Found at i:3758857 original size:36 final size:37
Alignment explanation
Indices: 3758795--3758871 Score: 147
Period size: 36 Copynumber: 2.1 Consensus size: 37
3758785 AACACATTTG
3758795 AACAACTTAGTTAGTTAAATAAAACCACATAAATGAC
1 AACAACTTAGTTAGTTAAATAAAACCACATAAATGAC
3758832 AACAACTTAGTTAG-TAAATAAAACCACATAAATGAC
1 AACAACTTAGTTAGTTAAATAAAACCACATAAATGAC
3758868 AACA
1 AACA
3758872 CATTTGGACA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
36 26 0.65
37 14 0.35
ACGTcount: A:0.53, C:0.17, G:0.08, T:0.22
Consensus pattern (37 bp):
AACAACTTAGTTAGTTAAATAAAACCACATAAATGAC
Found at i:3759206 original size:100 final size:99
Alignment explanation
Indices: 3759084--3759269 Score: 293
Period size: 100 Copynumber: 1.9 Consensus size: 99
3759074 TAATTTGTAC
3759084 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGAATTAATATACTCAAAAATGGACAACAATT
1 AAAAATGGACAGCATTTAAGCACCAATTTGGACAGAATTAATATACTCAAAAATGGACAACAATT
3759149 AAGCA-TAAATTTGGACAGCATTAATATGCTAAAA
66 AAGCACT-AATTTGGACAGCATTAATATGCTAAAA
* * * ** *
3759183 AAAAATTGGACAGCATTTAAGCACTAATTTGGACAGCATTAATATGCTCAAAAATGGACAGTATT
1 AAAAA-TGGACAGCATTTAAGCACCAATTTGGACAGAATTAATATACTCAAAAATGGACAACAAT
3759248 TAAGCACTAATTTGGACAGCAT
65 TAAGCACTAATTTGGACAGCAT
3759270 CTTACCATCA
Statistics
Matches: 79, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
99 5 0.06
100 73 0.92
101 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.26
Consensus pattern (99 bp):
AAAAATGGACAGCATTTAAGCACCAATTTGGACAGAATTAATATACTCAAAAATGGACAACAATT
AAGCACTAATTTGGACAGCATTAATATGCTAAAA
Found at i:3759214 original size:52 final size:48
Alignment explanation
Indices: 3759065--3759269 Score: 270
Period size: 48 Copynumber: 4.2 Consensus size: 48
3759055 AACAACAATC
* *
3759065 GGACAGCATTAATTTG-TACAAAAATGGACAGCATTTAAGCACCAATTT
1 GGACAGCATTAATATGCT-CAAAAATGGACAGCATTTAAGCACTAATTT
* * * *
3759113 GGACAGAATTAATATACTCAAAAATGGACAACAATTAAGCA-TAAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCATTTAAGCACT-AATTT
*
3759161 GGACAGCATTAATATGCTAAAAAAAAATTGGACAGCATTTAAGCACTAATTT
1 GGACAGCATTAATATGCT---CAAAAA-TGGACAGCATTTAAGCACTAATTT
*
3759213 GGACAGCATTAATATGCTCAAAAATGGACAGTATTTAAGCACTAATTT
1 GGACAGCATTAATATGCTCAAAAATGGACAGCATTTAAGCACTAATTT
3759261 GGACAGCAT
1 GGACAGCAT
3759270 CTTACCATCA
Statistics
Matches: 137, Mismatches: 13, Indels: 14
0.84 0.08 0.09
Matches are distributed among these distances:
48 87 0.64
49 6 0.04
51 5 0.04
52 38 0.28
53 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.16, T:0.26
Consensus pattern (48 bp):
GGACAGCATTAATATGCTCAAAAATGGACAGCATTTAAGCACTAATTT
Found at i:3759215 original size:23 final size:23
Alignment explanation
Indices: 3759188--3759269 Score: 92
Period size: 23 Copynumber: 3.5 Consensus size: 23
3759178 TAAAAAAAAA
3759188 TTGGACAGCATTTAAGCACTAAT
1 TTGGACAGCATTTAAGCACTAAT
* * * *
3759211 TTGGACAGCATTAATATGCTCAAAA
1 TTGGACAGCATT--TAAGCACTAAT
* *
3759236 ATGGACAGTATTTAAGCACTAAT
1 TTGGACAGCATTTAAGCACTAAT
3759259 TTGGACAGCAT
1 TTGGACAGCAT
3759270 CTTACCATCA
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
23 28 0.62
25 17 0.38
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (23 bp):
TTGGACAGCATTTAAGCACTAAT
Found at i:3760188 original size:60 final size:60
Alignment explanation
Indices: 3760095--3760213 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
3760085 ATGATATGTT
** *
3760095 GAGTTTATGTGAATGATTACATGAAATTGGGTATGGAGGACGGATGAGTTCAGTAGGAGG
1 GAGTTTATGTGAATGATTACATGAAATTGGGTATAAAAGACGGATGAGTTCAGTAGGAGG
*
3760155 GAGTTTATGTGAATGATTACATGAAATTGGGTATAAAAGACGGATGAGTTCCGTAGGAG
1 GAGTTTATGTGAATGATTACATGAAATTGGGTATAAAAGACGGATGAGTTCAGTAGGAG
3760214 AAAGTGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.32, C:0.06, G:0.34, T:0.29
Consensus pattern (60 bp):
GAGTTTATGTGAATGATTACATGAAATTGGGTATAAAAGACGGATGAGTTCAGTAGGAGG
Found at i:3785959 original size:26 final size:25
Alignment explanation
Indices: 3785911--3785961 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3785901 CACTAATTTT
*
3785911 TTTATAATTTTGTATAAATTTTATA
1 TTTATAATTTTGTATAAAATTTATA
* *
3785936 TTTATAATTTTTTTTAAAAATTTATA
1 TTTATAATTTTGTAT-AAAATTTATA
3785962 ATATTTAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTATAATTTTGTATAAAATTTATA
Found at i:3786986 original size:125 final size:125
Alignment explanation
Indices: 3786764--3787052 Score: 497
Period size: 125 Copynumber: 2.3 Consensus size: 125
3786754 TTTTTTTAAG
* *
3786764 GAAATCGCTCCCACATGGACACGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
**
3786829 GTTTCTGAGCAAATAGTGTCAAAAATTCTTTAAGCAGGATGCATTGTCAACAAAAGTACT
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACT
*
3786889 GAAATCGCTCTCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
* * *
3786954 GTTTCTGAGCAAATAGTGTCAAAACCGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTACT
66 GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACT
*
3787014 GAAATCACTCCCACGTGGACGCGCTTTTGCTACAGTAGC
1 GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGC
3787053 GCATGTTTGG
Statistics
Matches: 154, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
125 154 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (125 bp):
GAAATCGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGTAGAC
GTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCATTGTCAACAAAAGTACT
Found at i:3793001 original size:18 final size:18
Alignment explanation
Indices: 3792975--3793017 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3792965 GACTGTAAAA
* * *
3792975 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
3792993 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
3793011 AGGATAC
1 AGGATAC
3793018 GCACTTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:3801308 original size:24 final size:26
Alignment explanation
Indices: 3801263--3801320 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
3801253 AATAAGAATG
*
3801263 ATATTAAATTATATATTTTAAT-ATT
1 ATATTAAATTATATATTGTAATAATT
3801288 -TATTAAATTATAT-TTAGTAATAATT
1 ATATTAAATTATATATT-GTAATAATT
3801313 ATATTAAA
1 ATATTAAA
3801321 ATATGATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 2 0.07
24 17 0.59
25 3 0.10
26 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
ATATTAAATTATATATTGTAATAATT
Found at i:3801341 original size:61 final size:61
Alignment explanation
Indices: 3801265--3801383 Score: 177
Period size: 61 Copynumber: 2.0 Consensus size: 61
3801255 TAAGAATGAT
*
3801265 ATTAAATTATATATTTTAATATTTATTAAATTATATTT-AGTAATAATTATATTAAAATATG
1 ATTAAATTATATATTTTAATATTTATTAAATTATATTTCA-TAATAATCATATTAAAATATG
* * * *
3801326 ATTAAATTATTTATTTTTATTTTTATTAAATTATATTTCATAATAATCCTATTAAAAT
1 ATTAAATTATATATTTTAATATTTATTAAATTATATTTCATAATAATCATATTAAAAT
3801384 TTAATAACAA
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
61 51 0.98
62 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.53
Consensus pattern (61 bp):
ATTAAATTATATATTTTAATATTTATTAAATTATATTTCATAATAATCATATTAAAATATG
Found at i:3807111 original size:15 final size:15
Alignment explanation
Indices: 3807093--3807126 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
3807083 ATAAATGTCG
3807093 CAATAACAAATACAA
1 CAATAACAAATACAA
*
3807108 CAATAATAAATACAA
1 CAATAACAAATACAA
3807123 CAAT
1 CAAT
3807127 GGCATAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.18, G:0.00, T:0.18
Consensus pattern (15 bp):
CAATAACAAATACAA
Found at i:3807931 original size:22 final size:21
Alignment explanation
Indices: 3807906--3808019 Score: 82
Period size: 19 Copynumber: 5.7 Consensus size: 21
3807896 TACAAATTAA
*
3807906 ATCTCTAAGATTTCAAAATCAT
1 ATCTCTAAGATTGC-AAATCAT
* *
3807928 ATCTTCTATGATTGCATATCAT
1 ATC-TCTAAGATTGCAAATCAT
* *
3807950 A--TCTAAGATTACATATCAT
1 ATCTCTAAGATTGCAAATCAT
*
3807969 A--TCTAAGATTGCATATCAT
1 ATCTCTAAGATTGCAAATCAT
* *
3807988 A--TCTAAGATTACATATCAT
1 ATCTCTAAGATTGCAAATCAT
3808007 A--TCTAAGATTGCA
1 ATCTCTAAGATTGCA
3808020 TATCCTTGAA
Statistics
Matches: 83, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
19 64 0.77
22 10 0.12
23 9 0.11
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (21 bp):
ATCTCTAAGATTGCAAATCAT
Found at i:3807959 original size:19 final size:19
Alignment explanation
Indices: 3807932--3808023 Score: 157
Period size: 19 Copynumber: 4.8 Consensus size: 19
3807922 AATCATATCT
*
3807932 TCTATGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
3807951 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
3807970 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
3807989 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
3808008 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
3808024 CTTGAAGATT
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 68 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:3807983 original size:38 final size:38
Alignment explanation
Indices: 3807925--3808023 Score: 175
Period size: 38 Copynumber: 2.7 Consensus size: 38
3807915 ATTTCAAAAT
*
3807925 CATATC-T-TCTATGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTA
3807961 CATATCATATCTAAGATTGCATATCATATCTAAGATTA
1 CATATCATATCTAAGATTGCATATCATATCTAAGATTA
3807999 CATATCATATCTAAGATTGCATATC
1 CATATCATATCTAAGATTGCATATC
3808024 CTTGAAGATT
Statistics
Matches: 60, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
36 6 0.10
37 1 0.02
38 53 0.88
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.38
Consensus pattern (38 bp):
CATATCATATCTAAGATTGCATATCATATCTAAGATTA
Found at i:3810808 original size:42 final size:42
Alignment explanation
Indices: 3810710--3810808 Score: 130
Period size: 43 Copynumber: 2.3 Consensus size: 42
3810700 ATGTAAATGA
*
3810710 CACTAAGTGTGCGGAACTAAAATGATGGAGTTGAATAAAAGGG
1 CACTAAGTGTGCGAAACTAAAATGA-GGAGTTGAATAAAAGGG
* *
3810753 CACTAAGTGTGCGAAATTAAAATG-GAGATGTTGAAT-AACGGG
1 CACTAAGTGTGCGAAACTAAAATGAG-GA-GTTGAATAAAAGGG
3810795 CACTAAGTGTGCGA
1 CACTAAGTGTGCGA
3810809 TACCGGGAGC
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
41 1 0.02
42 21 0.41
43 29 0.57
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.22
Consensus pattern (42 bp):
CACTAAGTGTGCGAAACTAAAATGAGGAGTTGAATAAAAGGG
Found at i:3812900 original size:38 final size:37
Alignment explanation
Indices: 3812857--3812941 Score: 109
Period size: 37 Copynumber: 2.3 Consensus size: 37
3812847 GACCACCATG
* *
3812857 CACACCACATATGAGCTAT-ATCAAGCCCATCCACCCTA
1 CACACCACATAGGA-CCATGAT-AAGCCCATCCACCCTA
* *
3812895 CACACCACATAGGACCATGATAGGTCCATCCACCCTA
1 CACACCACATAGGACCATGATAAGCCCATCCACCCTA
3812932 CACACCACAT
1 CACACCACAT
3812942 TTGTAGAACC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
37 27 0.64
38 15 0.36
ACGTcount: A:0.34, C:0.40, G:0.09, T:0.16
Consensus pattern (37 bp):
CACACCACATAGGACCATGATAAGCCCATCCACCCTA
Found at i:3819742 original size:9 final size:9
Alignment explanation
Indices: 3819728--3819752 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3819718 CCTTACCAAC
3819728 TTCTAACAA
1 TTCTAACAA
3819737 TTCTAACAA
1 TTCTAACAA
3819746 TTCTAAC
1 TTCTAAC
3819753 TTCAAACACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (9 bp):
TTCTAACAA
Found at i:3825792 original size:6 final size:6
Alignment explanation
Indices: 3825781--3825816 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
3825771 CAAGCTCTGA
3825781 GCCTCT GCCTCT GCCTCT GCCTCT GCCTCT GCCTCT
1 GCCTCT GCCTCT GCCTCT GCCTCT GCCTCT GCCTCT
3825817 TGCTACCTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.17, T:0.33
Consensus pattern (6 bp):
GCCTCT
Found at i:3825989 original size:24 final size:23
Alignment explanation
Indices: 3825932--3825984 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
3825922 TTAGCTCTTA
3825932 AAATCTTAATTTTTTAAATTTTAAT
1 AAAT-TTAA-TTTTTAAATTTTAAT
3825957 AAATTTAATTTTT-AATTTTAAT
1 AAATTTAATTTTTAAATTTTAAT
3825979 -AATTTA
1 AAATTTA
3825985 TTAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.21
22 9 0.32
23 5 0.18
24 4 0.14
25 4 0.14
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATTTAATTTTTAAATTTTAAT
Found at i:3850813 original size:2 final size:2
Alignment explanation
Indices: 3850806--3850870 Score: 103
Period size: 2 Copynumber: 32.5 Consensus size: 2
3850796 GCTATACATG
* * *
3850806 AC AC AC AC AC AT AC AC AC GC AC GC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
3850848 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
3850871 TATGAAGAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.48, C:0.48, G:0.03, T:0.02
Consensus pattern (2 bp):
AC
Found at i:3855585 original size:10 final size:10
Alignment explanation
Indices: 3855572--3855596 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3855562 CATTTAATTA
3855572 ATTTTAAAAT
1 ATTTTAAAAT
3855582 ATTTTAAAAT
1 ATTTTAAAAT
3855592 ATTTT
1 ATTTT
3855597 TGTACTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:3855933 original size:27 final size:28
Alignment explanation
Indices: 3855903--3855964 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
3855893 CTCAAATTTG
3855903 GAATTTAGTCCTTACTTTT-AT-TTCCAA
1 GAATTTAGT-CTTACTTTTCATATTCCAA
* *
3855930 GAATTTAGTCTTCCTTTTCATATTTCAA
1 GAATTTAGTCTTACTTTTCATATTCCAA
3855958 -AATTTAG
1 GAATTTAG
3855965 GTCCAATTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
26 8 0.26
27 18 0.58
28 5 0.16
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.48
Consensus pattern (28 bp):
GAATTTAGTCTTACTTTTCATATTCCAA
Found at i:3859794 original size:24 final size:24
Alignment explanation
Indices: 3859736--3859795 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
3859726 CTAAAATTTA
3859736 ATTAAATAAAA-ATTTATATTAAT
1 ATTAAATAAAATATTTATATTAAT
3859759 -TTAAATAAAAATATTTATATTAAT
1 ATTAAAT-AAAATATTTATATTAAT
*
3859783 ATTATATAAAATA
1 ATTAAATAAAATA
3859796 CAAAACATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
22 6 0.18
23 4 0.12
24 18 0.55
25 5 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
ATTAAATAAAATATTTATATTAAT
Found at i:3860604 original size:14 final size:14
Alignment explanation
Indices: 3860585--3860612 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3860575 ATTCTTTCCA
3860585 AAAGAATATAGGAT
1 AAAGAATATAGGAT
3860599 AAAGAATATAGGAT
1 AAAGAATATAGGAT
3860613 TATCCCCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.21, T:0.21
Consensus pattern (14 bp):
AAAGAATATAGGAT
Found at i:3861129 original size:70 final size:70
Alignment explanation
Indices: 3861055--3861272 Score: 181
Period size: 70 Copynumber: 3.2 Consensus size: 70
3861045 TGTATGAGTC
*
3861055 AAATTCATATATTAATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACC
1 AAATTAATATATTAATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACC
3861120 GAAAT
66 GAAAT
** * * * *
3861125 AAATTAATATAACTGTTTATATTA-ATAATTTCGATAA-AATA-T-A--TACA----ATTAATAT
1 AAATTAATAT-A----TTA-ATTATATTCTTTCCA-AAGAATATTAATTTTCATGTCTTTTATAT
* *
3861180 TTTGTA-TG-AGT
59 TTTG-ACCGAAAT
*
3861191 CAAATTCATATATTAATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGAC
1 -AAATTAATATATTAATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGAC
3861256 CGAAAT
65 CGAAAT
3861262 AAATTAATATA
1 AAATTAATATA
3861273 ACTGTTTATA
Statistics
Matches: 108, Mismatches: 19, Indels: 42
0.64 0.11 0.25
Matches are distributed among these distances:
61 6 0.06
62 14 0.13
63 1 0.01
64 1 0.01
66 6 0.06
67 20 0.19
68 1 0.01
69 1 0.01
70 30 0.28
71 6 0.06
73 1 0.01
74 1 0.01
75 14 0.13
76 6 0.06
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (70 bp):
AAATTAATATATTAATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACC
GAAAT
Found at i:3861153 original size:137 final size:137
Alignment explanation
Indices: 3860659--3861349 Score: 1133
Period size: 137 Copynumber: 5.1 Consensus size: 137
3860649 TAGAAAAAAG
* * * * *
3860659 AATTATATTCTTTCTAAAATAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTC-CAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAA
* * * *
3860724 TATAATTGTTTATATTAATAAATTCGATAAAATGTATACAATTATTATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
3860789 CATATATT
130 CATATATT
* * *
3860797 AATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTAATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCC-AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAA
* * *
3860862 TATAA----TTAT-TTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATC
65 TATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
3860922 CATATATT
130 CATATATT
* *
3860930 AGTTATATTCTTTCCAAAAGAATATTAA-TTTCTACGTCTTTTATATTTTGACCGAAATAAATTA
1 AATTATATTCTTTCC-AAAGAATATTAATTTTC-ATGTCTTTTATATTTTGACCGAAATAAATTA
*
3860994 ATATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAGTCAAAT
64 ATATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
3861059 TCATATATT
129 TCATATATT
3861068 AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
1 AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
*
3861133 ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAGTCAAATTC
66 ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
3861198 ATATATT
131 ATATATT
3861205 AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
1 AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
3861270 ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
66 ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
3861335 ATATATT
131 ATATATT
3861342 AATTATAT
1 AATTATAT
3861350 ATATGTTTTC
Statistics
Matches: 524, Mismatches: 21, Indels: 17
0.93 0.04 0.03
Matches are distributed among these distances:
132 4 0.01
133 116 0.22
134 4 0.01
137 264 0.50
138 136 0.26
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (137 bp):
AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATT
Found at i:3861286 original size:274 final size:270
Alignment explanation
Indices: 3860659--3861349 Score: 1125
Period size: 271 Copynumber: 2.5 Consensus size: 270
3860649 TAGAAAAAAG
* * * * *
3860659 AATTATATTCTTTCTAAAATAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTC-CAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAA
* * * *
3860724 TATAATTGTTTATATTAATAAATTCGATAAAATGTATACAATTATTATTTTGTATGAATCAAATT
65 TATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
3860789 CATATATTAATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTAATATTTTGACCGAAA
130 CATATATTAATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTAATATTTTGACCGAAA
* *
3860854 TTAATTAATATAATTATTTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAA
195 TAAATTAATATAATTATTTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAA
3860919 ATCCATATATT
260 ATCCATATATT
* *
3860930 AGTTATATTCTTTCCAAAAGAATATTAA-TTTCTACGTCTTTTATATTTTGACCGAAATAAATTA
1 AATTATATTCTTTCC-AAAGAATATTAATTTTC-ATGTCTTTTATATTTTGACCGAAATAAATTA
*
3860994 ATATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAGTCAAAT
64 ATATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
* *
3861059 TCATATATTAATTATATTCTTTCC-AAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAA
129 TCATATATTAATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTAATATTTTGACCGAA
*
3861123 ATAAATTAATATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATG
194 ATAAATTAATATAA----TTAT-TTAATAAATTCGATAAAATATATACAATTAATATTTTGTATG
* *
3861188 AGTCAAATTCATATATT
254 AATCAAATCCATATATT
3861205 AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
1 AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
3861270 ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
66 ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
3861335 ATATATTAATTATAT
131 ATATATTAATTATAT
3861350 ATATGTTTTC
Statistics
Matches: 390, Mismatches: 22, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
270 54 0.14
271 136 0.35
274 127 0.33
275 73 0.19
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (270 bp):
AATTATATTCTTTCCAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATAAATTAAT
ATAACTGTTTATATTAATAATTTCGATAAAATATATACAATTAATATTTTGTATGAATCAAATTC
ATATATTAATTATATTCTTTCCAAAAGAATATTAACTTTCATGTCTTTAATATTTTGACCGAAAT
AAATTAATATAATTATTTAATAAATTCGATAAAATATATACAATTAATATTTTGTATGAATCAAA
TCCATATATT
Found at i:3870978 original size:2 final size:2
Alignment explanation
Indices: 3870971--3871010 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3870961 AGTATCCTAA
3870971 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3871011 TAAAATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3872401 original size:2 final size:2
Alignment explanation
Indices: 3872394--3872432 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
3872384 GTATCCTAAT
3872394 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3872433 TAAAATTTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3873593 original size:9 final size:9
Alignment explanation
Indices: 3873558--3873603 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
3873548 TACTTCATGC
3873558 TAATTTTTT
1 TAATTTTTT
*
3873567 TGAATTTGTAT
1 T-AATTT-TTT
*
3873578 GAATTTTTT
1 TAATTTTTT
3873587 TAATTTTTT
1 TAATTTTTT
3873596 TAATTTTT
1 TAATTTTT
3873604 AATTTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 19 0.61
10 10 0.32
11 2 0.06
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.70
Consensus pattern (9 bp):
TAATTTTTT
Found at i:3873617 original size:16 final size:16
Alignment explanation
Indices: 3873583--3873622 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3873573 TGTATGAATT
*
3873583 TTTTTAATTTTTTTAA
1 TTTTTAATTTTTATAA
*
3873599 TTTTTAATTTTATATAT
1 TTTTTAATTTT-TATAA
3873616 TTTTTAA
1 TTTTTAA
3873623 ACTATTTGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTAATTTTTATAA
Found at i:3873941 original size:21 final size:20
Alignment explanation
Indices: 3873894--3873945 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
3873884 AGAAATTTAT
* *
3873894 TTATTTTTATAAATAAGTAA
1 TTATTTTTATGAATAAATAA
*
3873914 -CATTTTTATGAATAAATATA
1 TTATTTTTATGAATAAATA-A
3873934 TTATTTTTATGA
1 TTATTTTTATGA
3873946 TATATAAGAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 15 0.58
20 1 0.04
21 10 0.38
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (20 bp):
TTATTTTTATGAATAAATAA
Found at i:3875180 original size:60 final size:60
Alignment explanation
Indices: 3875088--3875237 Score: 164
Period size: 62 Copynumber: 2.5 Consensus size: 60
3875078 AAAATTGTAT
* * *
3875088 GAAATTTTAGTAT-TCTCTTAGATATTTAGATATA-C-CAATAACTAAGGATATGC-TCTTA
1 GAAATTTTAGTATAT-TGTTAGAAATTTAGATATATCAAAATAACTAAGGATATGCAT-TTA
* * **
3875146 GAAATTTTGGTATAATTGTTTAGAAATTTTGATATATCAAAATATTTAAGGATATGCATTTA
1 GAAATTTTAGTAT-ATTG-TTAGAAATTTAGATATATCAAAATAACTAAGGATATGCATTTA
3875208 GAAATTTTAGTATATTGTTAGAAATATTAG
1 GAAATTTTAGTATATTGTTAGAAAT-TTAG
3875238 TATTAACACT
Statistics
Matches: 76, Mismatches: 9, Indels: 11
0.79 0.09 0.11
Matches are distributed among these distances:
58 12 0.16
59 1 0.01
60 24 0.32
61 8 0.11
62 30 0.39
63 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.14, T:0.42
Consensus pattern (60 bp):
GAAATTTTAGTATATTGTTAGAAATTTAGATATATCAAAATAACTAAGGATATGCATTTA
Found at i:3887611 original size:16 final size:16
Alignment explanation
Indices: 3887575--3887613 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3887565 TTGATTCGCT
* *
3887575 GTAATGGAATAGAGGT
1 GTAATAGAATAGAGGC
*
3887591 ATAATAGAATAGAGGC
1 GTAATAGAATAGAGGC
3887607 GTAATAG
1 GTAATAG
3887614 CAATTCAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.31, T:0.23
Consensus pattern (16 bp):
GTAATAGAATAGAGGC
Found at i:3887686 original size:44 final size:45
Alignment explanation
Indices: 3887597--3887687 Score: 132
Period size: 44 Copynumber: 2.0 Consensus size: 45
3887587 AGGTATAATA
*
3887597 GAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGTAATG
1 GAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGGAATG
* *
3887642 GAATAGAGGCGTAATAG-TATTC-TTATGTTTGGTTGAATGGAATG
1 GAATAGAGGCGTAATAGCAATTCAAT-TGTTTGGTTGAATGGAATG
3887686 GA
1 GA
3887688 GGTGTAATAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
43 1 0.02
44 24 0.57
45 17 0.40
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (45 bp):
GAATAGAGGCGTAATAGCAATTCAATTGTTTGGTTGAATGGAATG
Found at i:3891580 original size:14 final size:14
Alignment explanation
Indices: 3891561--3891588 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3891551 AGTAGAAATC
3891561 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
3891575 TGGAGAAAAGAAAA
1 TGGAGAAAAGAAAA
3891589 GAAATGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (14 bp):
TGGAGAAAAGAAAA
Found at i:3891588 original size:19 final size:18
Alignment explanation
Indices: 3891543--3891608 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
3891533 GAAAAAATTT
*
3891543 AGAAGAAAAGTAGAAATCTG
1 AGAAGAAAAG-A-AAATGTG
3891563 -G-AGAAAAGAAAATG-G
1 AGAAGAAAAGAAAATGTG
3891578 AGAAAAGAAAAG-AAATGTG
1 AG--AAGAAAAGAAAATGTG
3891597 AGAAGAAAAGAA
1 AGAAGAAAAGAA
3891609 GCGTACCGTA
Statistics
Matches: 39, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
15 1 0.03
16 5 0.13
17 9 0.23
18 13 0.33
19 11 0.28
ACGTcount: A:0.62, C:0.02, G:0.27, T:0.09
Consensus pattern (18 bp):
AGAAGAAAAGAAAATGTG
Found at i:3893026 original size:15 final size:15
Alignment explanation
Indices: 3893006--3893034 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3892996 GTGGGTCCGT
3893006 TTACTAGGACTTTTG
1 TTACTAGGACTTTTG
3893021 TTACTAGGACTTTT
1 TTACTAGGACTTTT
3893035 TAACAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
TTACTAGGACTTTTG
Found at i:3895695 original size:9 final size:9
Alignment explanation
Indices: 3895666--3895702 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3895656 TCAGTTTTCA
3895666 AATTCGAAT
1 AATTCGAAT
*
3895675 AACTCGAAT
1 AATTCGAAT
3895684 AATTCGAAT
1 AATTCGAAT
*
3895693 AATTTGAAT
1 AATTCGAAT
3895702 A
1 A
3895703 TTAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3906734 original size:13 final size:13
Alignment explanation
Indices: 3906716--3906740 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3906706 ATTTTGCAAA
3906716 ATTGTTGGTTTCC
1 ATTGTTGGTTTCC
3906729 ATTGTTGGTTTC
1 ATTGTTGGTTTC
3906741 TTGACACTTT
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:0.08, C:0.12, G:0.24, T:0.56
Consensus pattern (13 bp):
ATTGTTGGTTTCC
Found at i:3908431 original size:27 final size:27
Alignment explanation
Indices: 3908392--3908455 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
3908382 TCGTAAGTGA
* *
3908392 GGGTTCACTAGTA-TTTCGACGAACTAG
1 GGGTTCACCAGTACTTT-GACAAACTAG
* *
3908419 GGGTTCACCAGTACTTTGGCAAACTGG
1 GGGTTCACCAGTACTTTGACAAACTAG
3908446 GGGTTCACCA
1 GGGTTCACCA
3908456 AAAGGACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 29 0.91
28 3 0.09
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (27 bp):
GGGTTCACCAGTACTTTGACAAACTAG
Found at i:3909301 original size:14 final size:14
Alignment explanation
Indices: 3909279--3909330 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
3909269 TATGCGAGCC
* *
3909279 TATGATTTTAAAGA
1 TATGTTTTTAAAAA
3909293 TATGTTTTTAAAAA
1 TATGTTTTTAAAAA
*
3909307 TATGGTTTTAAAAA
1 TATGTTTTTAAAAA
3909321 T-TGTGTTTTA
1 TATGT-TTTTA
3909331 CAAGATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 2 0.06
14 31 0.94
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TATGTTTTTAAAAA
Found at i:3909710 original size:6 final size:6
Alignment explanation
Indices: 3909698--3909736 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
3909688 TAGTGTGTAT
*
3909698 AAGAAC AAAAAC AAGAAC AAGAAC AAGAAC AAGAAC AAG
1 AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAGAAC AAG
3909737 CATAAGTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.69, C:0.15, G:0.15, T:0.00
Consensus pattern (6 bp):
AAGAAC
Found at i:3912026 original size:11 final size:11
Alignment explanation
Indices: 3912012--3912141 Score: 56
Period size: 11 Copynumber: 11.6 Consensus size: 11
3912002 AGCATTTAAC
*
3912012 CAACATTCGGA
1 CAACATTCAGA
* *
3912023 CAACATTTAAA
1 CAACATTCAGA
3912034 CAACATTCAGA
1 CAACATTCAGA
3912045 CAACATT-AGAA
1 CAACATTCAG-A
**
3912056 TGCTAA-A-AAAGAA
1 --C-AACATTCAG-A
*
3912069 CAACATTTA-A
1 CAACATTCAGA
3912079 CCAACATTC-GAA
1 C-AACATTCAG-A
*
3912091 CAACATTTA-A
1 CAACATTCAGA
*
3912101 CCAACATTCGGA
1 -CAACATTCAGA
* *
3912113 CAACATTTAAA
1 CAACATTCAGA
3912124 CAACATTCAGA
1 CAACATTCAGA
3912135 CAACATT
1 CAACATT
3912142 AGTATGCTAA
Statistics
Matches: 89, Mismatches: 17, Indels: 26
0.67 0.13 0.20
Matches are distributed among these distances:
10 7 0.08
11 70 0.79
12 4 0.04
13 6 0.07
14 2 0.02
ACGTcount: A:0.48, C:0.23, G:0.08, T:0.22
Consensus pattern (11 bp):
CAACATTCAGA
Found at i:3912029 original size:22 final size:22
Alignment explanation
Indices: 3912004--3912227 Score: 182
Period size: 22 Copynumber: 10.0 Consensus size: 22
3911994 AAACGAATAG
3912004 CATTTAACCAACATTCGGACAA
1 CATTTAACCAACATTCGGACAA
* *
3912026 CATTTAAACAACATTCAGACAA
1 CATTTAACCAACATTCGGACAA
* * *** *
3912048 CATTAGAATGCTAA-AAAAGAACAA
1 CATT-TAA--CCAACATTCGGACAA
*
3912072 CATTTAACCAACATTCGAACAA
1 CATTTAACCAACATTCGGACAA
3912094 CATTTAACCAACATTCGGACAA
1 CATTTAACCAACATTCGGACAA
* *
3912116 CATTTAAACAACATTCAGACAA
1 CATTTAACCAACATTCGGACAA
* * * * * *
3912138 CATTAGTATGCTAAAAAAT-GAACAT
1 CATT--TA-AC-CAACATTCGGACAA
* *
3912163 CATTTAACAAACATTCGGACAG
1 CATTTAACCAACATTCGGACAA
*
3912185 CATTTAACCAACATTCGGACAT
1 CATTTAACCAACATTCGGACAA
*
3912207 CATTTAAACAACATTCGGACA
1 CATTTAACCAACATTCGGACA
3912228 GTACCTTGTC
Statistics
Matches: 159, Mismatches: 34, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
21 8 0.05
22 121 0.76
23 6 0.04
24 11 0.07
25 9 0.06
26 4 0.03
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (22 bp):
CATTTAACCAACATTCGGACAA
Found at i:3912083 original size:68 final size:69
Alignment explanation
Indices: 3911978--3912119 Score: 216
Period size: 68 Copynumber: 2.1 Consensus size: 69
3911968 AATTTGGACG
* * *
3911978 ACATTAATATGCTAAAAAACGAATAGCATTTAACCAACATTCGGACAACATTTAAACAACATTCA
1 ACATTAATATGCTAAAAAACGAACAACATTTAACCAACATTCGAACAACATTTAAACAACATTCA
3912043 GACA
66 GACA
*
3912047 ACATTAGA-ATGCTAAAAAA-GAACAACATTTAACCAACATTCGAACAACATTTAACCAACATTC
1 ACATTA-ATATGCTAAAAAACGAACAACATTTAACCAACATTCGAACAACATTTAAACAACATTC
*
3912110 GGACA
65 AGACA
3912115 ACATT
1 ACATT
3912120 TAAACAACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
68 49 0.73
69 17 0.25
70 1 0.01
ACGTcount: A:0.48, C:0.21, G:0.08, T:0.23
Consensus pattern (69 bp):
ACATTAATATGCTAAAAAACGAACAACATTTAACCAACATTCGAACAACATTTAAACAACATTCA
GACA
Found at i:3912215 original size:91 final size:90
Alignment explanation
Indices: 3911997--3912227 Score: 381
Period size: 90 Copynumber: 2.6 Consensus size: 90
3911987 TGCTAAAAAA
*
3911997 CGAATAGCATTTAACCAACATTCGGACAACATTTAAACAACATTCAGACAACATTAGAATGCTAA
1 CGAACAGCATTTAACCAACATTCGGACAACATTTAAACAACATTCAGACAACATTAGAATGCTAA
*
3912062 AAAAGAACAACATTTAACCAACATT
66 AAAAGAACAACATTTAACAAACATT
* *
3912087 CGAACAACATTTAACCAACATTCGGACAACATTTAAACAACATTCAGACAACATTAGTATGCTAA
1 CGAACAGCATTTAACCAACATTCGGACAACATTTAAACAACATTCAGACAACATTAGAATGCTAA
*
3912152 AAAATGAACATCATTTAACAAACATT
66 AAAA-GAACAACATTTAACAAACATT
* * *
3912178 CGGACAGCATTTAACCAACATTCGGACATCATTTAAACAACATTCGGACA
1 CGAACAGCATTTAACCAACATTCGGACAACATTTAAACAACATTCAGACA
3912228 GTACCTTGTC
Statistics
Matches: 131, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
90 66 0.50
91 65 0.50
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (90 bp):
CGAACAGCATTTAACCAACATTCGGACAACATTTAAACAACATTCAGACAACATTAGAATGCTAA
AAAAGAACAACATTTAACAAACATT
Found at i:3912890 original size:43 final size:41
Alignment explanation
Indices: 3912821--3912942 Score: 136
Period size: 42 Copynumber: 2.9 Consensus size: 41
3912811 ATAAAGCTCG
* * * **
3912821 TACAATGCCATATCCCAGATATGGTCTTACATGTTATAATA
1 TACAATGCCATGTCCCAGACATGGTCTTACACGAAATAATA
* *
3912862 TATCAATGCCACTGTCCCAGACAGGGTCTTACACGAAATCATA
1 TA-CAATGCCA-TGTCCCAGACATGGTCTTACACGAAATAATA
* *
3912905 TACGATGCCAATGTCCCAGACATGGTCGTACACGAAAT
1 TACAATGCC-ATGTCCCAGACATGGTCTTACACGAAAT
3912943 CACACCTCGG
Statistics
Matches: 68, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.03
42 39 0.57
43 27 0.40
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (41 bp):
TACAATGCCATGTCCCAGACATGGTCTTACACGAAATAATA
Found at i:3920029 original size:35 final size:36
Alignment explanation
Indices: 3919952--3920045 Score: 113
Period size: 35 Copynumber: 2.7 Consensus size: 36
3919942 GTTTGTGCCT
* *
3919952 AGCGCTAGTCAGATGAACCGA--AAAATGTGTGCCC
1 AGCGCTAGTCAGATAAACCGACGAAAATGTGCGCCC
* * *
3919986 AGCACTAGTCAGATAAACTGACGAAAGT-TGCGCCC
1 AGCGCTAGTCAGATAAACCGACGAAAATGTGCGCCC
*
3920021 AGCGCTAGTCGGATAAACCGACGAA
1 AGCGCTAGTCAGATAAACCGACGAA
3920046 TAATTAGTGA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
34 18 0.36
35 28 0.56
36 4 0.08
ACGTcount: A:0.34, C:0.24, G:0.26, T:0.16
Consensus pattern (36 bp):
AGCGCTAGTCAGATAAACCGACGAAAATGTGCGCCC
Found at i:3920074 original size:39 final size:37
Alignment explanation
Indices: 3919982--3920196 Score: 156
Period size: 35 Copynumber: 5.9 Consensus size: 37
3919972 AAAAATGTGT
* ** * * *
3919982 GCCCAGCACTAGTCAGATAAACTGACG-A-AAGTTGC
1 GCCCAGCGCTAGTTGGATAAACCGACGAATAATTTGA
*
3920017 GCCCAGCGCTAGTCGGATAAACCGACGAATAATTAGTGA
1 GCCCAGCGCTAGTTGGATAAACCGACGAATAATT--TGA
* * * * *
3920056 GCGCAGCTCTAGTTGGATATACCGAAG-GT-ATTT-A
1 GCCCAGCGCTAGTTGGATAAACCGACGAATAATTTGA
* *
3920090 CGCCCAGCGCTAGTTGGATAAACCAACGAATAAATAGTGA
1 -GCCCAGCGCTAGTTGGATAAACCGACGAAT-AAT-TTGA
* ** * *
3920130 GCCCAGCTCTAGTTGGATTTACCAACG-AT-ATTTGC
1 GCCCAGCGCTAGTTGGATAAACCGACGAATAATTTGA
*
3920165 GCCCAGCGGTAGTTGGATAAACCGACGAATAA
1 GCCCAGCGCTAGTTGGATAAACCGACGAATAA
3920197 ACAATTATTT
Statistics
Matches: 140, Mismatches: 28, Indels: 22
0.74 0.15 0.12
Matches are distributed among these distances:
34 1 0.01
35 71 0.51
36 6 0.04
37 7 0.05
38 5 0.04
39 49 0.35
40 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (37 bp):
GCCCAGCGCTAGTTGGATAAACCGACGAATAATTTGA
Found at i:3920111 original size:74 final size:74
Alignment explanation
Indices: 3920016--3920197 Score: 276
Period size: 74 Copynumber: 2.5 Consensus size: 74
3920006 ACGAAAGTTG
* * *
3920016 CGCCCAGCGCTAGTCGGATAAACCGACGAATAATTAGTGAGCGCAGCTCTAGTTGGATATACCGA
1 CGCCCAGCGCTAGTTGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTGGATATACC-A
*
3920081 A-GGTATTTA
65 ACGATATTTA
* *
3920090 CGCCCAGCGCTAGTTGGATAAACCAACGAATAAATAGTGAGCCCAGCTCTAGTTGGATTTACCAA
1 CGCCCAGCGCTAGTTGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTGGATATACCAA
*
3920155 CGATATTTG
66 CGATATTTA
*
3920164 CGCCCAGCGGTAGTTGGATAAACCGACGAATAAA
1 CGCCCAGCGCTAGTTGGATAAACCGACGAATAAA
3920198 CAATTATTTA
Statistics
Matches: 98, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
73 2 0.02
74 96 0.98
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (74 bp):
CGCCCAGCGCTAGTTGGATAAACCGACGAATAAATAGTGAGCCCAGCTCTAGTTGGATATACCAA
CGATATTTA
Found at i:3921220 original size:3 final size:3
Alignment explanation
Indices: 3921212--3921262 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3921202 ATTTCTCATC
3921212 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3921260 TAT
1 TAT
3921263 ATAACCTTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3925109 original size:20 final size:21
Alignment explanation
Indices: 3925071--3925111 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3925061 GAATGGTAAC
*
3925071 TTTTCAAAAGTATTATTTTTA
1 TTTTAAAAAGTATTATTTTTA
*
3925092 TTTTAAAAATTATT-TTTTTA
1 TTTTAAAAAGTATTATTTTTA
3925112 AATATTTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTAAAAAGTATTATTTTTA
Found at i:3926403 original size:156 final size:152
Alignment explanation
Indices: 3926138--3926431 Score: 371
Period size: 156 Copynumber: 1.9 Consensus size: 152
3926128 TAAAGTAATA
* * * * *
3926138 TATATTATAAAAAAATGTATGGAAGTAAAAATGGAAACTTTGAGTTCTAATTTAGTTTTTTGAAT
1 TATATTATAAAAAAATGTATGGAAGAAAAAATGAAAACTTTGAGTTCTAAATTAATTCTTTGAAT
* * * *
3926203 TTCAAAATATTTTTTAATTATATTTAAGGTGTGTCTCATTTTTAAATTAAGTTTTA-AATATAGT
66 TCCAAAATATTTTTTAATTATATTTAAAGTGTATCTCATTTTTAAATTAAGTTTTACAAAATA-T
3926267 -TTTCTTACTGTTAATAGTCATG
130 ATTTCTTACTGTTAATAGTCATG
* * *
3926289 TATATTATAAAAGAATGTA-GGAAAGCAAAAAATGAAAATTTTGAGTTTTAAATTAATTCTTTGA
1 TATATTATAAAAAAATGTATGG-AAG-AAAAAATGAAAACTTTGAGTTCTAAATTAATTCTTTGA
*
3926353 ATTCCAAAATGCTTCATTTTTAATTATATTTAAAGT-TAATCTCATTTTTAAATTAAGTTTTACA
64 ATTCCAAAAT--AT--TTTTTAATTATATTTAAAGTGT-ATCTCATTTTTAAATTAAGTTTTACA
3926417 AAATATATTTCTTAC
124 AAATATATTTCTTAC
3926432 CATTAATCAT
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
150 2 0.02
151 21 0.17
152 40 0.33
154 1 0.01
155 1 0.01
156 43 0.36
157 13 0.11
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (152 bp):
TATATTATAAAAAAATGTATGGAAGAAAAAATGAAAACTTTGAGTTCTAAATTAATTCTTTGAAT
TCCAAAATATTTTTTAATTATATTTAAAGTGTATCTCATTTTTAAATTAAGTTTTACAAAATATA
TTTCTTACTGTTAATAGTCATG
Found at i:3929686 original size:42 final size:42
Alignment explanation
Indices: 3929631--3929727 Score: 158
Period size: 42 Copynumber: 2.3 Consensus size: 42
3929621 GCTCTCGGTA
* *
3929631 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
* *
3929673 TCGCACACGTAGTGCCCATTATCCAACATCATTATTTTAATT
1 TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
3929715 TCGCACACTTAGT
1 TCGCACACTTAGT
3929728 TCCGTTCATA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATCCAACATCATCATTTTAATT
Found at i:3930631 original size:16 final size:17
Alignment explanation
Indices: 3930598--3930631 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
3930588 CATAAAGTTA
*
3930598 ATATTTACCTTATTACT
1 ATATTAACCTTATTACT
3930615 ATATTAACCTT-TTACT
1 ATATTAACCTTATTACT
3930631 A
1 A
3930632 ATAATTATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTAACCTTATTACT
Found at i:3932064 original size:49 final size:49
Alignment explanation
Indices: 3931963--3932075 Score: 131
Period size: 49 Copynumber: 2.3 Consensus size: 49
3931953 TGGTAGAAAA
* * *
3931963 CCATCGTTGTCGAGCTATTCTGGATGATAGAATGTATATATAGTGAGAG
1 CCATCGTTGTCGAGCTATTCAGGATGATAGAATATATAGATAGTGAGAG
* * * *
3932012 CCATTGTTGTTGAGCTATTCAGGATGGTAGAATA-ATTAGATATTGA-ATG
1 CCATCGTTGTCGAGCTATTCAGGATGATAGAATATA-TAGATAGTGAGA-G
3932061 CCATCGTTGTCGAGC
1 CCATCGTTGTCGAGC
3932076 CATCCGGGAC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
48 2 0.04
49 51 0.96
ACGTcount: A:0.27, C:0.13, G:0.26, T:0.34
Consensus pattern (49 bp):
CCATCGTTGTCGAGCTATTCAGGATGATAGAATATATAGATAGTGAGAG
Found at i:3932133 original size:49 final size:49
Alignment explanation
Indices: 3932060--3932168 Score: 114
Period size: 49 Copynumber: 2.2 Consensus size: 49
3932050 GATATTGAAT
*
3932060 GCCATCGTTGTCGAGCCATCCGGGACGATAAAATGTAAGAATAGT-TAAA
1 GCCATCATTGTCGAGCCATCCGGGACGATAAAATGT-AGAATAGTGTAAA
* * * * * ** *
3932109 GCCATCATTGTTGGGCCATTCGGGATGGTAATTTGTTGAATAGTGTAAA
1 GCCATCATTGTCGAGCCATCCGGGACGATAAAATGTAGAATAGTGTAAA
3932158 -CCATCATTGTC
1 GCCATCATTGTC
3932169 AGGTCACTCG
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
48 17 0.35
49 32 0.65
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.29
Consensus pattern (49 bp):
GCCATCATTGTCGAGCCATCCGGGACGATAAAATGTAGAATAGTGTAAA
Found at i:3937234 original size:37 final size:37
Alignment explanation
Indices: 3937193--3937287 Score: 102
Period size: 37 Copynumber: 2.6 Consensus size: 37
3937183 TAAATATTAG
* *
3937193 TCAGTATAACAGTAAGATTTGCTTAGTTAAG-CTCTAT
1 TCAGTATAACAGTAAGATTTGCTCAATTAAGTCTC-AT
* * * *
3937230 TCAGTATAACGGTATGATTTGCTCAATTGAGTTTCAT
1 TCAGTATAACAGTAAGATTTGCTCAATTAAGTCTCAT
* *
3937267 TTAGTATAACAATAAGATTTG
1 TCAGTATAACAGTAAGATTTG
3937288 GCTCGATAGC
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
37 45 0.96
38 2 0.04
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (37 bp):
TCAGTATAACAGTAAGATTTGCTCAATTAAGTCTCAT
Found at i:3939497 original size:20 final size:20
Alignment explanation
Indices: 3939472--3939514 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
3939462 TACTCTCAGT
3939472 GAAAGACTCAATACATAAAA
1 GAAAGACTCAATACATAAAA
*
3939492 GAAAGATTCAATACATAAAA
1 GAAAGACTCAATACATAAAA
3939512 GAA
1 GAA
3939515 TATGTTCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (20 bp):
GAAAGACTCAATACATAAAA
Found at i:3941615 original size:50 final size:50
Alignment explanation
Indices: 3941551--3941717 Score: 182
Period size: 50 Copynumber: 3.3 Consensus size: 50
3941541 TTTATATATA
3941551 AAAAATTATAATTTTTAGTTACATATAAGATATTTCATTTATAAGACCAT
1 AAAAATTATAATTTTTAGTTACATATAAGATATTTCATTTATAAGACCAT
* * ** * *
3941601 AAAAA-TATATATTTTTATGGT-CTTATAA-ATGAAAT-ATCTTATATGTAAC-T
1 AAAAATTATA-ATTTTTA-GTTACATATAAGAT-ATTTCAT-TTATAAG-ACCAT
3941651 AAAAATTATAATTTTTAGTTACATATAAGATATTTCATTTATAAGACCAT
1 AAAAATTATAATTTTTAGTTACATATAAGATATTTCATTTATAAGACCAT
*
3941701 AAAAATATATATTTTTT
1 AAAAAT-TATAATTTTT
3941718 CACCTAGGAA
Statistics
Matches: 93, Mismatches: 13, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
49 12 0.13
50 60 0.65
51 21 0.23
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (50 bp):
AAAAATTATAATTTTTAGTTACATATAAGATATTTCATTTATAAGACCAT
Found at i:3948136 original size:6 final size:7
Alignment explanation
Indices: 3948111--3948135 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3948101 ATAATAAATA
3948111 TTTTTAT
1 TTTTTAT
3948118 TTTTTAT
1 TTTTTAT
3948125 TTTTTAT
1 TTTTTAT
3948132 TTTT
1 TTTT
3948136 AACTTTAAAA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:3948204 original size:12 final size:11
Alignment explanation
Indices: 3948168--3948218 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
3948158 ATTTTTTTAA
3948168 TTTTAAAATTT
1 TTTTAAAATTT
*
3948179 TTTTGAAATTT
1 TTTTAAAATTT
3948190 TTTTAAAATACTT
1 TTTTAAAAT--TT
*
3948203 TTTT-TAATTT
1 TTTTAAAATTT
3948213 TTTTAA
1 TTTTAA
3948219 TTTTAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 6 0.18
11 18 0.55
12 3 0.09
13 6 0.18
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTTAAAATTT
Found at i:3948205 original size:40 final size:38
Alignment explanation
Indices: 3948179--3948260 Score: 114
Period size: 40 Copynumber: 2.2 Consensus size: 38
3948169 TTTAAAATTT
* *
3948179 TTTTGAAATTTTTTTAAAATACTTTTTTTAATTTTTTTAA
1 TTTTAAAATATTTTTAAAATAC-TTTTTTAATTTTTTT-A
3948219 TTTTAAAATATTTTTAAAATACTTTTTTAA--TTTTTA
1 TTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTA
3948255 TTTTAA
1 TTTTAA
3948261 TTTTTAAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 7 0.17
37 5 0.12
39 8 0.20
40 20 0.50
ACGTcount: A:0.33, C:0.02, G:0.01, T:0.63
Consensus pattern (38 bp):
TTTTAAAATATTTTTAAAATACTTTTTTAATTTTTTTA
Found at i:3948205 original size:51 final size:53
Alignment explanation
Indices: 3948139--3948248 Score: 179
Period size: 51 Copynumber: 2.1 Consensus size: 53
3948129 TATTTTTAAC
* *
3948139 TTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATTTTTTTGAAAT-TTT
1 TTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATATTT
3948191 TTTAAAATAC-TTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTT
1 TTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATA-TTT
3948244 TTTAA
1 TTTAA
3948249 TTTTTATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
51 36 0.67
52 10 0.19
53 8 0.15
ACGTcount: A:0.34, C:0.03, G:0.01, T:0.63
Consensus pattern (53 bp):
TTTAAAATACTTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATATTT
Found at i:3948215 original size:8 final size:9
Alignment explanation
Indices: 3948150--3948222 Score: 58
Period size: 9 Copynumber: 7.4 Consensus size: 9
3948140 TTAAAATACT
3948150 TTTTTTTAA
1 TTTTTTTAA
3948159 TTTTTTTAA
1 TTTTTTTAA
**
3948168 -TTTTAAAA
1 TTTTTTTAA
3948176 TTTTTTTGAAA
1 TTTTTTT--AA
3948187 TTTTTTTAAAATA
1 TTTTTTT---A-A
3948200 CTTTTTTTAA
1 -TTTTTTTAA
3948210 TTTTTTTAA
1 TTTTTTTAA
3948219 TTTT
1 TTTT
3948223 AAAATATTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
8 6 0.11
9 26 0.49
10 1 0.02
11 10 0.19
12 2 0.04
13 1 0.02
14 7 0.13
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:3948217 original size:23 final size:22
Alignment explanation
Indices: 3948168--3948218 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
3948158 ATTTTTTTAA
3948168 TTTTAAAATTTTTTTGAAATTT
1 TTTTAAAATTTTTTTGAAATTT
*
3948190 TTTTAAAATACTTTTTT-TAATTT
1 TTTTAAAAT--TTTTTTGAAATTT
3948213 TTTTAA
1 TTTTAA
3948219 TTTTAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 9 0.35
23 11 0.42
24 6 0.23
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTAAAATTTTTTTGAAATTT
Found at i:3948259 original size:51 final size:50
Alignment explanation
Indices: 3948143--3948265 Score: 160
Period size: 51 Copynumber: 2.4 Consensus size: 50
3948133 TTTAACTTTA
* *
3948143 AAATACTTTTTTTTAATTTTTTTAATTTTAAAATTTTTTTGAAATTTTTTT
1 AAATA-TTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATTTTTTT
*
3948194 AAAATACTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT
1 -AAATATTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAAT--TTTTTT
3948247 -AAT-TTTTATTTTAATTTTT
1 AAATATTTT-TTTTAATTTTT
3948266 AAAACTCTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
50 3 0.05
51 50 0.78
52 5 0.08
53 6 0.09
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (50 bp):
AAATATTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATTTTTTT
Found at i:3951155 original size:28 final size:28
Alignment explanation
Indices: 3951112--3951178 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
3951102 TAAAGTAATG
*
3951112 AGCTCACCACTTACTACTCATTTGAGGT
1 AGCTCACCACTCACTACTCATTTGAGGT
*
3951140 AGCTCACCACTCACTATTCATTTGAGGT
1 AGCTCACCACTCACTACTCATTTGAGGT
*
3951168 TGCTCACCACT
1 AGCTCACCACT
3951179 TACTGTGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.24, C:0.31, G:0.13, T:0.31
Consensus pattern (28 bp):
AGCTCACCACTCACTACTCATTTGAGGT
Found at i:3951210 original size:18 final size:18
Alignment explanation
Indices: 3951187--3951231 Score: 74
Period size: 18 Copynumber: 2.5 Consensus size: 18
3951177 CTTACTGTGA
3951187 GTTCGCCAATCTTAGG-GG
1 GTTCGCCAATCTT-GGAGG
3951205 GTTCGCCAATCTTGGAGG
1 GTTCGCCAATCTTGGAGG
3951223 GTTCGCCAA
1 GTTCGCCAA
3951232 ATGTTGCATG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (18 bp):
GTTCGCCAATCTTGGAGG
Found at i:3953709 original size:66 final size:66
Alignment explanation
Indices: 3953572--3953718 Score: 206
Period size: 66 Copynumber: 2.2 Consensus size: 66
3953562 CGAGACATGT
* * *
3953572 TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTTTGGGATATGTTCGACTTTATGACTCA
1 TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTATGGGACATGTTCGACTCTATGACTCA
3953637 A
66 A
* * * *
3953638 TTGGTGTGTTGGAGAGTGTTAGTTTTATGCTTCAC-TTATGGGACATGTTTGACTCTATGAGTCT
1 TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTATGGGACATGTTCGACTCTATGACTCA
3953702 A
66 A
*
3953703 TCTGGTGTGATGGAGA
1 T-TGGTGTGTTGGAGA
3953719 TCCGTGTATC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
65 25 0.35
66 47 0.65
ACGTcount: A:0.18, C:0.11, G:0.29, T:0.42
Consensus pattern (66 bp):
TTGGTGTGTTGGAGAGTGTTAGCTTTATGCTTCACTTTATGGGACATGTTCGACTCTATGACTCA
A
Found at i:3966004 original size:48 final size:48
Alignment explanation
Indices: 3965928--3966124 Score: 207
Period size: 48 Copynumber: 4.1 Consensus size: 48
3965918 AATAGATTTC
* * * *
3965928 TCGGTGACCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTC
1 TCGGTGACCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
* * * * * ** *
3965976 TTGGTGGCCTACACATAGTTCGTGCCACCCTTGTACCTTAACA-AGTTA
1 TCGGTGACCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGA-TTA
* * * * * *
3966024 TTGGTGACCTGCACACTGGCTGTGCCACCCTTGTGTCACAACAGAATA
1 TCGGTGACCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
*
3966072 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
1 TCGGTGACCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
3966120 TCGGT
1 TCGGT
3966125 ACGCATAGTA
Statistics
Matches: 116, Mismatches: 31, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
47 1 0.01
48 114 0.98
49 1 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
TCGGTGACCTGCACACAGTCCGTGCCACCCTTGTGTCATAACAGATTA
Found at i:3966096 original size:96 final size:96
Alignment explanation
Indices: 3965930--3966105 Score: 235
Period size: 96 Copynumber: 1.8 Consensus size: 96
3965920 TAGATTTCTC
* * * * * * *
3965930 GGTGACCTGCACACAGTCCGTACCACCTTTGTGTAATAACAGATTCTTGGTGGCCTACACATAGT
1 GGTGACCTGCACACAGGCCGTACCACCCTTGTGTAACAACAGAATATCGGTGGCCTACACACAGT
*
3965995 TCGTGCCACCCTTGTACCTTAACAAGTTATT
66 CCGTGCCACCCTTGTACCTTAACAAGTTATT
* * * * *
3966026 GGTGACCTGCACACTGGCTGTGCCACCCTTGTGTCACAACAGAATATCGGTGGCCTGCACACAGT
1 GGTGACCTGCACACAGGCCGTACCACCCTTGTGTAACAACAGAATATCGGTGGCCTACACACAGT
3966091 CCGTGCCACCCTTGT
66 CCGTGCCACCCTTGT
3966106 GTCATAACAG
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 67 1.00
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (96 bp):
GGTGACCTGCACACAGGCCGTACCACCCTTGTGTAACAACAGAATATCGGTGGCCTACACACAGT
CCGTGCCACCCTTGTACCTTAACAAGTTATT
Found at i:3967984 original size:48 final size:48
Alignment explanation
Indices: 3967795--3967995 Score: 215
Period size: 48 Copynumber: 4.2 Consensus size: 48
3967785 GCGTACTGAT
* *
3967795 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTACAGGCCACCAAT
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCAAG
* * * * * *
3967843 ATTCTGTTTTGACACAAGGGTGGCACGGATTGTGTGCAAGTCACCAAT
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCAAG
* * * * *
3967891 AA-CTTGTTAAGATACAAGGGTGGCACGGACTATGCGCAGGCCACCGAG
1 AATC-TGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCAAG
* * * * *
3967939 AATCTGTTATTACACAAAGGTGGTACAGACTGTGTGCAGGCCACCGAG
1 AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCAAG
3967987 AAATCTGTT
1 -AATCTGTT
3967996 TTTATTCCGA
Statistics
Matches: 125, Mismatches: 25, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 115 0.92
49 9 0.07
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.23
Consensus pattern (48 bp):
AATCTGTTATGACACAAGGGTGGCACGGACTGTGTGCAGGCCACCAAG
Found at i:3969595 original size:13 final size:13
Alignment explanation
Indices: 3969577--3969603 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3969567 GAATTTGTAG
3969577 ACCATAAACATAT
1 ACCATAAACATAT
3969590 ACCATAAACATAT
1 ACCATAAACATAT
3969603 A
1 A
3969604 ACGATAATAA
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:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (13 bp):
ACCATAAACATAT
Found at i:3978466 original size:91 final size:91
Alignment explanation
Indices: 3978281--3978469 Score: 231
Period size: 91 Copynumber: 2.1 Consensus size: 91
3978271 AGCAAAAAAA
* *
3978281 TATGTTATTTTAAGGGCTATTGTTTAGTGTATTAATGCAGCAGAAAAATTCTTGTTTAGTCGTCA
1 TATGTTATTTTAAGGGCTATTGTTTAGTGTATTAAAGCAACAGAAAAATTCTTGTTTAGTCGTCA
* * * *
3978346 ATTAATGTTGTTTAAGTGACTGTATT
66 ATAAATGTGGTTGAAGTGACTGTAAT
* * * *
3978372 TATGTTGTTTTAAGGGCTATTGTTTGGTGTATTAAAGCAACAG-TAAATTGTTGTTTAGAT-GTC
1 TATGTTATTTTAAGGGCTATTGTTTAGTGTATTAAAGCAACAGAAAAATTCTTGTTTAG-TCGTC
*
3978435 AATAAATGTGGTCTGAA-TGACTTTAAAT
65 AATAAATGTGGT-TGAAGTGACTGT-AAT
3978463 TATGTTA
1 TATGTTA
3978470 ATAATGGTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
90 32 0.39
91 51 0.61
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.44
Consensus pattern (91 bp):
TATGTTATTTTAAGGGCTATTGTTTAGTGTATTAAAGCAACAGAAAAATTCTTGTTTAGTCGTCA
ATAAATGTGGTTGAAGTGACTGTAAT
Found at i:3979588 original size:43 final size:42
Alignment explanation
Indices: 3979489--3979602 Score: 112
Period size: 43 Copynumber: 2.7 Consensus size: 42
3979479 TGTGTTTAAG
* * * *
3979489 TGTAAGACCATGTCTGGGACA-TCGACA-TCATATTCGATTCG
1 TGTAAGACCACGTCTGGGACAGT-GGCATTGATATTCGATTCA
3979530 TGTAAGACC-CTGTCTGGGACAGTGGCATTGATATAT-GATTACA
1 TGTAAGACCAC-GTCTGGGACAGTGGCATTGATAT-TCGATT-CA
3979573 TGTAAGACCACGTCTGGGAC-GTTGGCATTG
1 TGTAAGACCACGTCTGGGACAG-TGGCATTG
3979603 TACGAGCTTT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
41 22 0.35
42 11 0.18
43 28 0.45
44 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACAGTGGCATTGATATTCGATTCA
Found at i:3979791 original size:36 final size:36
Alignment explanation
Indices: 3979751--3979846 Score: 140
Period size: 36 Copynumber: 2.7 Consensus size: 36
3979741 GTATATTTGA
*
3979751 ATTGATGTACTTGTGATATTATAAGTAATTCGGCCT
1 ATTGATATACTTGTGATATTATAAGTAATTCGGCCT
* *
3979787 ATTGATATACTTGTGATATTATAAGTGATTTGGCCT
1 ATTGATATACTTGTGATATTATAAGTAATTCGGCCT
* *
3979823 AATGATATAGTTGTGATATT-TAAG
1 ATTGATATACTTGTGATATTATAAG
3979847 AGTGATAATT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 4 0.07
36 51 0.93
ACGTcount: A:0.30, C:0.07, G:0.20, T:0.43
Consensus pattern (36 bp):
ATTGATATACTTGTGATATTATAAGTAATTCGGCCT
Found at i:3985794 original size:23 final size:26
Alignment explanation
Indices: 3985765--3985824 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 26
3985755 GTATGTTCTT
* *
3985765 ATATTATAAAAT-ATAA-GTAATTAA
1 ATATTATAAAATGAAAATGTAATAAA
3985789 A-ATTATAAAATGAAAATGTAATAAA
1 ATATTATAAAATGAAAATGTAATAAA
3985814 ATATTATAAAA
1 ATATTATAAAA
3985825 CTTAACGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 10 0.32
24 4 0.13
25 8 0.26
26 9 0.29
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (26 bp):
ATATTATAAAATGAAAATGTAATAAA
Found at i:3986583 original size:16 final size:16
Alignment explanation
Indices: 3986562--3986610 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
3986552 TTCGCTGTAT
*
3986562 TGGAATAGAGCCGTAA
1 TGGAATAGAGGCGTAA
*
3986578 TGGAATAAAGGCGTAA
1 TGGAATAGAGGCGTAA
3986594 TGGAATAGAGGCGTAA
1 TGGAATAGAGGCGTAA
3986610 T
1 T
3986611 AGCAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.39, C:0.08, G:0.33, T:0.20
Consensus pattern (16 bp):
TGGAATAGAGGCGTAA
Found at i:3986641 original size:45 final size:44
Alignment explanation
Indices: 3986590--3986678 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 44
3986580 GAATAAAGGC
3986590 GTAATGGAATAGAGGCGTAATAGCAAATCAAT-TGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAG-AAATC-ATGTGTTTGGTTGAAT
* *
3986635 GTAATGGAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAAT
1 GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
3986679 AGAATAGAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
43 1 0.02
44 17 0.41
45 23 0.56
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.34
Consensus pattern (44 bp):
GTAATGGAATAGAGGCGTAATAGAAATCATGTGTTTGGTTGAAT
Found at i:3986861 original size:16 final size:16
Alignment explanation
Indices: 3986824--3986865 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3986814 TTAATCATAT
*
3986824 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3986840 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3986855 TTAAAATATAT
1 TTAAAATATAT
3986866 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3986872 original size:14 final size:15
Alignment explanation
Indices: 3986833--3986874 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3986823 TTTAAACATA
*
3986833 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3986848 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3986862 A-TATAATTTAATA
1 ATTATAATTAAATA
3986875 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3992760 original size:5 final size:5
Alignment explanation
Indices: 3992743--3992799 Score: 69
Period size: 5 Copynumber: 11.4 Consensus size: 5
3992733 TTATGTTTTA
* * * * *
3992743 TATAT TATTT TATAT TATAT TATTT TATAT CATAT TATAT TATAT TAAAA
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
3992793 TATAT TA
1 TATAT TA
3992800 AAAAACTAAA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
5 42 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:3992763 original size:15 final size:15
Alignment explanation
Indices: 3992743--3992789 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
3992733 TTATGTTTTA
3992743 TATATTATTTTATAT
1 TATATTATTTTATAT
3992758 TATATTATTTTATAT
1 TATATTATTTTATAT
* *
3992773 CATATTATATTATAT
1 TATATTATTTTATAT
3992788 TA
1 TA
3992790 AAATATATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATTTTATAT
Found at i:3993917 original size:23 final size:23
Alignment explanation
Indices: 3993890--3993943 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
3993880 CGGCTTTGAT
*
3993890 CATCAGGCACTTTATGTGTCGTA
1 CATCAGACACTTTATGTGTCGTA
3993913 CATCAGACACTTTATGTGTCGT-
1 CATCAGACACTTTATGTGTCGTA
3993935 -ATCAGACAC
1 CATCAGACAC
3993944 CTCGTGTGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 9 0.30
23 21 0.70
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (23 bp):
CATCAGACACTTTATGTGTCGTA
Found at i:3993940 original size:21 final size:21
Alignment explanation
Indices: 3993891--3993977 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
3993881 GGCTTTGATC
*
3993891 ATCAGGCACTTTATGTGTCGT
1 ATCAGACACTTTATGTGTCGT
3993912 ACATCAGACACTTTATGTGTCGT
1 --ATCAGACACTTTATGTGTCGT
* ** *
3993935 ATCAGACACCTCGTGTGTCAT
1 ATCAGACACTTTATGTGTCGT
* *
3993956 TTCAGGCAC-TTATGTGTCGT
1 ATCAGACACTTTATGTGTCGT
3993976 AT
1 AT
3993978 ATAGATCAGG
Statistics
Matches: 53, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
20 9 0.17
21 24 0.45
23 20 0.38
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (21 bp):
ATCAGACACTTTATGTGTCGT
Found at i:3997721 original size:56 final size:56
Alignment explanation
Indices: 3997659--3997854 Score: 202
Period size: 56 Copynumber: 3.5 Consensus size: 56
3997649 ATTCTGATAA
*
3997659 GCAAACTGGTCTTACGACCTAAGGCAAACCTTGTTCATGTTTTCTAACAAGTATGT
1 GCAAACTGGTCTTACGACCTAAGGCAAACCTTGTTCATGTTTTCTAAAAAGTATGT
* * *
3997715 GCAAACTGGTCTCT-CGACCTAAGGCAAACCCTGTTCATGTTTTCTGATAAGTATGT
1 GCAAACTGGTCT-TACGACCTAAGGCAAACCTTGTTCATGTTTTCTAAAAAGTATGT
** ** *** * *
3997771 GCAAACCAGTCTTGTGACCTAAGGTGGACCTTTTTGA-GTTTTCTAAAAAGTATGT
1 GCAAACTGGTCTTACGACCTAAGGCAAACCTTGTTCATGTTTTCTAAAAAGTATGT
* *
3997826 GCGAGA-T-GACTTCACGACCTAAGGCAAAC
1 GC-AAACTGGTCTT-ACGACCTAAGGCAAAC
3997855 TTAGACTCGA
Statistics
Matches: 114, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
54 4 0.04
55 30 0.26
56 79 0.69
57 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.30
Consensus pattern (56 bp):
GCAAACTGGTCTTACGACCTAAGGCAAACCTTGTTCATGTTTTCTAAAAAGTATGT
Found at i:4002264 original size:51 final size:50
Alignment explanation
Indices: 4002188--4002323 Score: 193
Period size: 50 Copynumber: 2.7 Consensus size: 50
4002178 TCAGTTCACA
* *
4002188 TAGTAGCCTGCATATAGTACTACACATGTGACCATTCCTATCTGATACACG
1 TAGTAGCCTGCATATAGTACTACACATGTGACCATTCAT-TCCGATACACG
* *
4002239 TAGTAGCCTGCATATAGTACTACACATGCGACCCA-TCATTCCGGTACACG
1 TAGTAGCCTGCATATAGTACTACACATGTGA-CCATTCATTCCGATACACG
* *
4002289 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCATATAGTACTACACATGTGACCAT
4002324 CACTTTCACT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
49 3 0.04
50 37 0.49
51 33 0.43
52 3 0.04
ACGTcount: A:0.29, C:0.28, G:0.17, T:0.26
Consensus pattern (50 bp):
TAGTAGCCTGCATATAGTACTACACATGTGACCATTCATTCCGATACACG
Found at i:4012266 original size:11 final size:11
Alignment explanation
Indices: 4012250--4012276 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4012240 TAATTTATTC
4012250 TTTATGATTTA
1 TTTATGATTTA
4012261 TTTATGATTTA
1 TTTATGATTTA
4012272 TTTAT
1 TTTAT
4012277 CAAGTGTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.07, T:0.67
Consensus pattern (11 bp):
TTTATGATTTA
Found at i:4013631 original size:25 final size:24
Alignment explanation
Indices: 4013603--4013685 Score: 96
Period size: 25 Copynumber: 3.4 Consensus size: 24
4013593 GATTACGGAT
* *
4013603 TTCAGCTCGTACGAGCTTACCGCTA
1 TTCAGCTCGAAGGAGCTTACCG-TA
*
4013628 TTCAGCTCAAAGGAGCTTACCGTTA
1 TTCAGCTCGAAGGAGCTTACCG-TA
*
4013653 TTCAGCTGGAAGGAGCTTACCGT-
1 TTCAGCTCGAAGGAGCTTACCGTA
4013676 TTACAGCTCG
1 TT-CAGCTCG
4013686 TATGAGCATA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
23 2 0.04
24 7 0.14
25 41 0.82
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.28
Consensus pattern (24 bp):
TTCAGCTCGAAGGAGCTTACCGTA
Found at i:4014378 original size:24 final size:25
Alignment explanation
Indices: 4014341--4014387 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
4014331 CTTATCATGT
*
4014341 TTGATGTGCATTTT-TGTGAGAAGG
1 TTGATGTGCATTTTGGGTGAGAAGG
4014365 TTGATGT-CATTTTTGGGTGAGAA
1 TTGATGTGCA-TTTTGGGTGAGAA
4014388 ATGTGGCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 2 0.10
24 11 0.55
25 7 0.35
ACGTcount: A:0.21, C:0.04, G:0.32, T:0.43
Consensus pattern (25 bp):
TTGATGTGCATTTTGGGTGAGAAGG
Found at i:4030723 original size:72 final size:71
Alignment explanation
Indices: 4030647--4030796 Score: 282
Period size: 72 Copynumber: 2.1 Consensus size: 71
4030637 AAAATTACTA
4030647 TAAAATCTATAAAACTAATTAAAATCATAACTTTTATAAATATTTAAATATGTATAAATTTAAAA
1 TAAAATCTATAAAA-TAATTAAAATCATAACTTTTATAAATATTTAAATATGTATAAATTTAAAA
4030712 ATAGTTT
65 ATAGTTT
4030719 TAAAAATCTATAAAATAATTAAAATCATAACTTTTATAAATATTTAAATATGTATAAATTTAAAA
1 T-AAAATCTATAAAATAATTAAAATCATAACTTTTATAAATATTTAAATATGTATAAATTTAAAA
4030784 ATAGTTT
65 ATAGTTT
4030791 TAAAAT
1 TAAAAT
4030797 TAAGCTAAAA
Statistics
Matches: 77, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
71 5 0.06
72 59 0.77
73 13 0.17
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.40
Consensus pattern (71 bp):
TAAAATCTATAAAATAATTAAAATCATAACTTTTATAAATATTTAAATATGTATAAATTTAAAAA
TAGTTT
Found at i:4043031 original size:20 final size:20
Alignment explanation
Indices: 4043008--4043054 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4042998 AGATATATAT
**
4043008 ATATATAATAAGACATATGG
1 ATATATAATAAGACATAAAG
*
4043028 ATATATAATAAGATATAAAG
1 ATATATAATAAGACATAAAG
4043048 ATATATA
1 ATATATA
4043055 GATATAAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (20 bp):
ATATATAATAAGACATAAAG
Found at i:4043059 original size:16 final size:17
Alignment explanation
Indices: 4043038--4043071 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
4043028 ATATATAATA
4043038 AGATATAAAG-ATATAT
1 AGATATAAAGTATATAT
*
4043054 AGATATAAGGTATATAT
1 AGATATAAAGTATATAT
4043071 A
1 A
4043072 TACGTATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.32
Consensus pattern (17 bp):
AGATATAAAGTATATAT
Found at i:4044974 original size:6 final size:6
Alignment explanation
Indices: 4044963--4044988 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4044953 AATAAATATA
4044963 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
4044989 AAANNNNNNN
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:4057037 original size:43 final size:42
Alignment explanation
Indices: 4056990--4057090 Score: 132
Period size: 43 Copynumber: 2.4 Consensus size: 42
4056980 TTATATAAAC
4056990 GGCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAAG
1 GGCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTG-ATAAAAG
* * * * *
4057033 GGCACTGAGTGTGCGAAATTAAAATGGAGATGTTGATTAATG
1 GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGATAAAAG
4057075 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
4057091 TATAGAGAGC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
42 20 0.39
43 29 0.57
44 2 0.04
ACGTcount: A:0.36, C:0.11, G:0.31, T:0.23
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGATAAAAG
Found at i:4058027 original size:2 final size:2
Alignment explanation
Indices: 4058020--4058052 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
4058010 AATAATACTA
*
4058020 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4058053 GGATTTGGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4058621 original size:373 final size:370
Alignment explanation
Indices: 4058133--4058876 Score: 1235
Period size: 373 Copynumber: 2.0 Consensus size: 370
4058123 AAAATAAAAT
*
4058133 TATATTCGGCTAAAGTTGAAAAAAAAATTGCCCATATGAATAGTAACTTTATTTGTTTGATGAAC
1 TATATTCGGCTAAAGTTGAAAAAAAAATTGACCATATGAATAGTAACTTTATTTGTTTGATGAAC
* * *
4058198 AAGAAGTTATATACAGCTTGATTAACAGTTTTGTGTAATTGAATATTAATATGCGGATATACTAT
66 AAAAAGTTATATACAACTTGATTAACAGTTTTGTGTAATTGAATATTAATATGCGAATATACTAT
*
4058263 GAAATCATATAAATGCT-TATGGAATGTTCGGCCCAATGATTATAAATGTTGGTAATTATAAGGT
131 GAAATCATATAAAT-ATATATGGAATGTTCGGCCCAATGATTATAAATGTTGGTAATTATAAGGT
*
4058327 TGGTATAGGTACATATATTAAAACATAATGATTAC-ATGTAAAATGAGTAAATTTTAAATGGGAA
195 TGGTATAGGTACATATATTAAAACATAATGACTACGA-GTAAAATGAGTAAATTTTAAATGGGAA
* *
4058391 TTTTATATACATAATTGGTCTTTGTTGTTTA-TAATAGATTTATTAGTCGAGTAGGGGAAATGTG
259 TTTTATATACATAATTGGTCTTTGTTG-TTACTAATAGATTTATTAGTCGAATAGGCGAAATGTG
*
4058455 ATATGACCGATAGTGGTGTTTGAAATATTCTGGATAAACTTTTAATTA
323 ATATGACCGATAGCGGTGTTTGAAATATTCTGGATAAACTTTTAATTA
** *
4058503 TATATTCGGCTAAAGTT-TTAAAAAAATTGACTATATGAATAGTAACTTTATTTGTTTGATGAAC
1 TATATTCGGCTAAAGTTGAAAAAAAAATTGACCATATGAATAGTAACTTTATTTGTTTGATGAAC
*
4058567 AAAAAAATTTTTATATACAACTTGATTAACAGTTTTGTGTAATTGAATATTAATATGCGAATATA
66 --AAAAA--GTTATATACAACTTGATTAACAGTTTTGTGTAATTGAATATTAATATGCGAATATA
* *
4058632 CTATGAAATCATATATATATATATGGAATGTTCGGCCCAATGGTTATAAATGTTGGTAATTATAA
127 CTATGAAATCATATAAATATATATGGAATGTTCGGCCCAATGATTATAAATGTTGGTAATTATAA
* *
4058697 GGTTGGTATAGGTACATATATTAAAATATAATGACTACGAGTAAAATGAGTAAATTTTAAATGTG
192 GGTTGGTATAGGTACATATATTAAAACATAATGACTACGAGTAAAATGAGTAAATTTTAAATGGG
*
4058762 AGTTTTATATACATAATTGGTCTTTGTTGTTACTAATAGATTTATTAGTCGAATAGGCGAAATGT
257 AATTTTATATACATAATTGGTCTTTGTTGTTACTAATAGATTTATTAGTCGAATAGGCGAAATGT
4058827 GATATGACCGATAGCGGTGTTTGAAATATTCTGGATAAACTTTTAATTA
322 GATATGACCGATAGCGGTGTTTGAAATATTCTGGATAAACTTTTAATTA
4058876 T
1 T
4058877 TAATTATATG
Statistics
Matches: 349, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
369 43 0.12
370 17 0.05
371 4 0.01
372 4 0.01
373 280 0.80
374 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.17, T:0.38
Consensus pattern (370 bp):
TATATTCGGCTAAAGTTGAAAAAAAAATTGACCATATGAATAGTAACTTTATTTGTTTGATGAAC
AAAAAGTTATATACAACTTGATTAACAGTTTTGTGTAATTGAATATTAATATGCGAATATACTAT
GAAATCATATAAATATATATGGAATGTTCGGCCCAATGATTATAAATGTTGGTAATTATAAGGTT
GGTATAGGTACATATATTAAAACATAATGACTACGAGTAAAATGAGTAAATTTTAAATGGGAATT
TTATATACATAATTGGTCTTTGTTGTTACTAATAGATTTATTAGTCGAATAGGCGAAATGTGATA
TGACCGATAGCGGTGTTTGAAATATTCTGGATAAACTTTTAATTA
Done.