Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 200 of 202
Found at i:61142448 original size:2 final size:2
Alignment explanation
Indices: 61142441--61142478 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
61142431 CAAACCTAAT
61142441 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61142479 CCCATAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61147058 original size:16 final size:17
Alignment explanation
Indices: 61147032--61147064 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
61147022 GTTCTTTAAA
*
61147032 CATTCCTCTTTTTTTTC
1 CATTCCTCTTTTGTTTC
61147049 CATT-CTCTTTTGTTTC
1 CATTCCTCTTTTGTTTC
61147065 TCCCTCTGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.06, C:0.27, G:0.03, T:0.64
Consensus pattern (17 bp):
CATTCCTCTTTTGTTTC
Found at i:61147196 original size:14 final size:14
Alignment explanation
Indices: 61147160--61147193 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
61147150 TCATCATTTG
61147160 CCTATAACCAAAAC
1 CCTATAACCAAAAC
61147174 CCTATAACCAAAAC
1 CCTATAACCAAAAC
61147188 CC-ATAA
1 CCTATAA
61147194 ACCCATGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:61151488 original size:31 final size:30
Alignment explanation
Indices: 61151426--61151505 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 30
61151416 AATAAATTTT
*
61151426 TTAAATCAATATCAAAGTTTCATGTGAATAA
1 TTAAATCAAAATCAAAGTTTCATGT-AATAA
*
61151457 TTAAATCAAAATTAAAGTTCTACATGT-ATAA
1 TTAAATCAAAATCAAAGTT-T-CATGTAATAA
61151488 TT--ATGC-AAATCAAAGTTT
1 TTAAAT-CAAAATCAAAGTTT
61151506 ATGGATCACA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
28 1 0.02
29 12 0.28
30 1 0.02
31 23 0.53
32 1 0.02
33 5 0.12
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (30 bp):
TTAAATCAAAATCAAAGTTTCATGTAATAA
Found at i:61158383 original size:23 final size:24
Alignment explanation
Indices: 61158332--61158384 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
61158322 GCATAAGTTG
*
61158332 TGAA-TTTAATCTTTGTACTTTGA
1 TGAATTTTAATCTTTATACTTTGA
* *
61158355 TCAATTTTAATCTTTATACTTT-T
1 TGAATTTTAATCTTTATACTTTGA
61158378 TGAATTT
1 TGAATTT
61158385 GTCAATTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.26, C:0.09, G:0.08, T:0.57
Consensus pattern (24 bp):
TGAATTTTAATCTTTATACTTTGA
Found at i:61160425 original size:19 final size:19
Alignment explanation
Indices: 61160388--61160425 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
61160378 TTATTATTCT
*
61160388 TTTTTTTATATTAATCATA
1 TTTTTTTATATTAAACATA
61160407 TTTTTTTAGTA-TAAACATA
1 TTTTTTTA-TATTAAACATA
61160426 AATTTCTATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.58
Consensus pattern (19 bp):
TTTTTTTATATTAAACATA
Found at i:61161127 original size:105 final size:105
Alignment explanation
Indices: 61160969--61161177 Score: 301
Period size: 105 Copynumber: 2.0 Consensus size: 105
61160959 GAGTCCAAAT
* * * * * *
61160969 GATCGTCTAGAGATCAATCTCGAGATTAATGTCAACTAAAAACTCGAATATATATCTTTTGTCAT
1 GATCATCTAGAAATCAATCTCGAGACTAATATCAACTAAAAACTCGAACATATATCTTTTGTCAC
* *
61161034 TTCACTTATGATTCTACCGACTCCTCGTACTTTCATTTAA
66 TTCACTTATGATTCAACCGACTCCTCATACTTTCATTTAA
* *
61161074 GATCATCTAGAAATCGATCTCGAGACTAATATCAATTAAAAACTCGAACATATATCTTTTGTCAC
1 GATCATCTAGAAATCAATCTCGAGACTAATATCAACTAAAAACTCGAACATATATCTTTTGTCAC
* * *
61161139 TTCACTTGTGATTCAACTGACTTCTCATACTTTCATTTA
66 TTCACTTATGATTCAACCGACTCCTCATACTTTCATTTA
61161178 CCGCATGACG
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
105 91 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (105 bp):
GATCATCTAGAAATCAATCTCGAGACTAATATCAACTAAAAACTCGAACATATATCTTTTGTCAC
TTCACTTATGATTCAACCGACTCCTCATACTTTCATTTAA
Found at i:61165989 original size:24 final size:26
Alignment explanation
Indices: 61165961--61166009 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
61165951 TATTAAAATT
*
61165961 TGTTTTTGCC-TT-TTTAAATATTGA
1 TGTTTTTACCATTCTTTAAATATTGA
61165985 TGTTTTTACCATTTCTTTAAATATT
1 TGTTTTTACCA-TTCTTTAAATATT
61166010 AAAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
26 2 0.10
27 10 0.48
ACGTcount: A:0.22, C:0.10, G:0.08, T:0.59
Consensus pattern (26 bp):
TGTTTTTACCATTCTTTAAATATTGA
Found at i:61167650 original size:13 final size:12
Alignment explanation
Indices: 61167632--61167665 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
61167622 TATTTTTCGA
61167632 GTTTAATATTTTT
1 GTTTAAT-TTTTT
61167645 GTTTAATTTTTT
1 GTTTAATTTTTT
61167657 -TTTAATTTT
1 GTTTAATTTT
61167666 CAAAAAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.43
12 5 0.24
13 7 0.33
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
GTTTAATTTTTT
Found at i:61172117 original size:7 final size:7
Alignment explanation
Indices: 61172105--61172139 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
61172095 CAAGAACTTC
61172105 AAATAAA
1 AAATAAA
61172112 AAATAAA
1 AAATAAA
61172119 AAATAAA
1 AAATAAA
61172126 AAATAAA
1 AAATAAA
*
61172133 AACTAAA
1 AAATAAA
61172140 TGCCAAGTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.83, C:0.03, G:0.00, T:0.14
Consensus pattern (7 bp):
AAATAAA
Found at i:61175125 original size:15 final size:15
Alignment explanation
Indices: 61175105--61175142 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
61175095 CAGAATCATA
61175105 TTTTTAACT-ATTTAT
1 TTTTTAA-TGATTTAT
61175120 TTTTTAATGATTTAT
1 TTTTTAATGATTTAT
61175135 TTATTTAA
1 TT-TTTAA
61175143 ATCGGATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 1 0.05
15 15 0.71
16 5 0.24
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTTTAATGATTTAT
Found at i:61182664 original size:29 final size:26
Alignment explanation
Indices: 61182622--61182678 Score: 62
Period size: 30 Copynumber: 2.1 Consensus size: 26
61182612 GAACTATTAT
*
61182622 TTTTTTATATTAATCGAAATAAATAATACA
1 TTTTTTATACTAAT--AAA-AAATAA-ACA
61182652 TTTTTTA-ACTAATAAAAAATAAACA
1 TTTTTTATACTAATAAAAAATAAACA
61182677 TT
1 TT
61182679 AGCAATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 5 0.19
26 6 0.23
27 3 0.12
29 5 0.19
30 7 0.27
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (26 bp):
TTTTTTATACTAATAAAAAATAAACA
Found at i:61205531 original size:18 final size:18
Alignment explanation
Indices: 61205491--61205531 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
61205481 ATTCATATTG
61205491 TTTTTATTTTTATTTTCA
1 TTTTTATTTTTATTTTCA
*
61205509 ATTTTA-TTTTATTTATCA
1 TTTTTATTTTTATTT-TCA
61205527 TTTTT
1 TTTTT
61205532 TAATAAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTATTTTTATTTTCA
Found at i:61207874 original size:31 final size:31
Alignment explanation
Indices: 61207834--61207904 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
61207824 AAATATTTCG
*
61207834 AATAGTTTAATGACCAAAACGTAAACTTGTT
1 AATAGTTTAATGACCAAAACGTAAACTTATT
* * *
61207865 AATAATTTAATGACGAAAACGTAAATTTATT
1 AATAGTTTAATGACCAAAACGTAAACTTATT
61207896 AATAGTTTA
1 AATAGTTTA
61207905 GTAATCTTGG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (31 bp):
AATAGTTTAATGACCAAAACGTAAACTTATT
Found at i:61207945 original size:11 final size:10
Alignment explanation
Indices: 61207920--61207944 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
61207910 CTTGGTGTAG
61207920 TTTTTCTTTT
1 TTTTTCTTTT
61207930 TTTTTCTTTT
1 TTTTTCTTTT
61207940 TTTTT
1 TTTTT
61207945 TTGTTGTTCA
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:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:61211303 original size:22 final size:21
Alignment explanation
Indices: 61211278--61211318 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
61211268 AATATAATTT
61211278 TAAAT-TTAATTATAAGAATATA
1 TAAATATTAA-TATAA-AATATA
61211300 TAAATATTAATATAAAATA
1 TAAATATTAATATAAAATA
61211319 CATTTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.22
22 10 0.56
23 4 0.22
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (21 bp):
TAAATATTAATATAAAATATA
Found at i:61215331 original size:15 final size:15
Alignment explanation
Indices: 61215311--61215360 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
61215301 TTCAGAGTCT
61215311 TCATCTCTTTCAACA
1 TCATCTCTTTCAACA
* *
61215326 TCATCTCTTTCCACC
1 TCATCTCTTTCAACA
*
61215341 TCATCTCTTTCAACT
1 TCATCTCTTTCAACA
61215356 TCATC
1 TCATC
61215361 AGCATCTTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (15 bp):
TCATCTCTTTCAACA
Found at i:61218359 original size:32 final size:32
Alignment explanation
Indices: 61218323--61218398 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 32
61218313 GGTAAACCCC
*
61218323 AAAATTA-TAAGTCATGACTATAAAAGAGAAAG
1 AAAATTATTAA-TCATGACTAGAAAAGAGAAAG
* *
61218355 AAAA-TATTCATCATGACTAGAAAGGAGAAAG
1 AAAATTATTAATCATGACTAGAAAAGAGAAAG
*
61218386 AAAA-TATTCATCA
1 AAAATTATTAATCA
61218399 CTTATGATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
31 34 0.85
32 6 0.15
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.22
Consensus pattern (32 bp):
AAAATTATTAATCATGACTAGAAAAGAGAAAG
Found at i:61218372 original size:31 final size:31
Alignment explanation
Indices: 61218334--61218398 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
61218324 AAATTATAAG
*
61218334 TCATGACTATAAAAGAGAAAGAAAATATTCA
1 TCATGACTAGAAAAGAGAAAGAAAATATTCA
*
61218365 TCATGACTAGAAAGGAGAAAGAAAATATTCA
1 TCATGACTAGAAAAGAGAAAGAAAATATTCA
61218396 TCA
1 TCA
61218399 CTTATGATTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.15, T:0.22
Consensus pattern (31 bp):
TCATGACTAGAAAAGAGAAAGAAAATATTCA
Found at i:61221775 original size:24 final size:24
Alignment explanation
Indices: 61221745--61221798 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
61221735 ACTACTAAGT
*
61221745 TTGAAACTTGAAATTAGAGAAGAG
1 TTGAAACTTGAAATGAGAGAAGAG
61221769 TTGAAACTTGAAATGAGAGAAGAG
1 TTGAAACTTGAAATGAGAGAAGAG
*
61221793 CTGAAA
1 TTGAAA
61221799 AGAAGCAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.26, T:0.22
Consensus pattern (24 bp):
TTGAAACTTGAAATGAGAGAAGAG
Found at i:61229345 original size:5 final size:5
Alignment explanation
Indices: 61229335--61229360 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
61229325 TGAGCATTCG
61229335 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
61229361 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:61230397 original size:9 final size:9
Alignment explanation
Indices: 61230383--61230428 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
61230373 TATAGTTTGA
61230383 TATTCGAAT
1 TATTCGAAT
61230392 TATTCGAAT
1 TATTCGAAT
*
61230401 TATTCGAGT
1 TATTCGAAT
*
61230410 TATTCGAGT
1 TATTCGAAT
61230419 TATTCGAAT
1 TATTCGAAT
61230428 T
1 T
61230429 CGAAAACTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 35 1.00
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:61235900 original size:27 final size:27
Alignment explanation
Indices: 61235861--61235923 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
61235851 TCATGCTTTA
* *
61235861 TATTTTTT-TACATACT-TACACATTTT
1 TATTTTTTAAACATA-TATACACAATTT
*
61235887 TATTTTTTAAACATATATACATAATTT
1 TATTTTTTAAACATATATACACAATTT
61235914 TATATTTTTA
1 TAT-TTTTTA
61235924 TTTTATTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
26 9 0.29
27 16 0.52
28 6 0.19
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.57
Consensus pattern (27 bp):
TATTTTTTAAACATATATACACAATTT
Found at i:61237946 original size:19 final size:20
Alignment explanation
Indices: 61237909--61237948 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
61237899 TCTTTTCGCA
* *
61237909 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
61237929 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
61237948 T
1 T
61237949 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:61239904 original size:19 final size:19
Alignment explanation
Indices: 61239880--61239917 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
61239870 AATGTTCTTT
61239880 CATTCTTT-ACGATTTTTTC
1 CATTCTTTCA-GATTTTTTC
61239899 CATTCTTTCAGATTTTTTC
1 CATTCTTTCAGATTTTTTC
61239918 TGCCAAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (19 bp):
CATTCTTTCAGATTTTTTC
Found at i:61241281 original size:13 final size:13
Alignment explanation
Indices: 61241263--61241287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61241253 TAAATCAATT
61241263 TCTTTGTTATCCA
1 TCTTTGTTATCCA
61241276 TCTTTGTTATCC
1 TCTTTGTTATCC
61241288 TCGACAATTT
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:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTGTTATCCA
Found at i:61242273 original size:132 final size:131
Alignment explanation
Indices: 61242036--61243082 Score: 1555
Period size: 132 Copynumber: 8.0 Consensus size: 131
61242026 TTGAAAGCGA
* * *
61242036 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
61242101 TCTACTTTCCTGGGCAACAGTGGAATAGATCGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTA-TTTCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61242166 GG
130 GG
* *
61242168 AGCAGATCGAAGATGGCGGATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * * * *
61242233 TCTACTTTCCTAGACAACAATGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAATAGT
66 TCTA-TTTCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61242298 GG
130 GG
* *
61242300 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCATTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * ** * ** ** *
61242365 TCTACTTCCCTGGACAACAGTGGGATAGATTGAAGATTTGAGGTCTTATCTCCCTCGGTTGCAGT
66 TCTA-TTTCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61242430 GG
130 GG
* **
61242432 ACCAG---GTTGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
61242494 TCTATCTCCATGGGCACCAGTGGAATAGATTGAAGA-TACCAGATCTTATCTCCCTAAGCAGTAG
66 TCTATTTCC-TGGGCAACAGTGGAATAGATTGAAGATTA-CAGATCTTATCTCCCTAAGCAGTAG
61242558 TGG
129 TGG
61242561 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
61242626 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
66 TCTAT-TTCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61242691 GG
130 GG
61242693 AGCAGATC-AATGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCGAA-GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
61242757 TTCTATCTCTCTGGGCAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGTAG
65 TTCTATTTC-CTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
61242822 TGG
129 TGG
* * *
61242825 AGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAC
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
61242890 TCTATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
66 TCTATTTCC-TGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61242955 GG
130 GG
* *
61242957 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * *
61243022 TCTATTTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGTTCTTATCTCCCTAGGCAG
66 TCTATTT-CCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
61243083 CGAAGTAGAT
Statistics
Matches: 836, Mismatches: 67, Indels: 24
0.90 0.07 0.03
Matches are distributed among these distances:
128 4 0.00
129 105 0.13
131 4 0.00
132 715 0.86
133 8 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (131 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATTTCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
G
Found at i:61242560 original size:44 final size:44
Alignment explanation
Indices: 61242512--61242693 Score: 126
Period size: 44 Copynumber: 4.1 Consensus size: 44
61242502 CATGGGCACC
61242512 AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGT
** * ** * * * *
61242556 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAG--GTT
1 AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAG-T
* * ** *
61242599 ACAGTGGAGTACATTGAAG---CCAGTAAT-TCTATCTCCCTGGGCAGC
1 --AGTGGAATAGATTGAAGATACCAG--ATCT-TATCTCCCTAAGCAGT
61242644 AGTGGAATAGATTGAAGATTA-CAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGA-TACCAGATCTTATCTCCCTAAGCAGT
61242688 AGTGGA
1 AGTGGA
61242694 GCAGATCAAT
Statistics
Matches: 103, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
42 3 0.03
43 17 0.17
44 64 0.62
45 15 0.15
46 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGT
Found at i:61242779 original size:393 final size:393
Alignment explanation
Indices: 61242045--61243082 Score: 1600
Period size: 393 Copynumber: 2.6 Consensus size: 393
61242035 AAGCAGATCG
* * * *
61242045 AAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCTAGTAATTCTACTTTC
1 AAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTC
* *
61242110 C-TGGGCAACAGTGGAATAGATCGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
65 CATGGGCAACAGTGGAATAGATTGAAGA-TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
61242174 TCGAAGATGGCGGATTTTACCTTCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-C
129 TCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC
* * * * * * *
61242238 TTTCCTAGACAACAATGGAATAGATTGAAGATTTCAGATATTATCTCCCTAAGCAATAGTGGAGC
194 -TCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
* *
61242303 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCATTAATTCT
258 AGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
* ** ** ** *
61242368 ACTTCCCTGGACAACAGTGGGATAGATTGAAGATTTGAGGTCTTATCTCCCTCGGTTGCAGTGGA
323 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGCAGTGGA
*
61242433 CCAGGT
388 CCAGAT
*
61242439 -TGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCC
1 AAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCC
*
61242503 ATGGGCACCAGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
66 ATGGGCAACAGTGGAATAGATTGAAGATA-CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
61242568 CGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCT
130 CGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCT
*
61242633 CCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
195 CCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
61242698 ATC-AATGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
260 ATCGAA-GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
* * *
61242762 -TCTCTCTGGGCAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGGA
324 CT-TCCCTGGACAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGCAGTGGA
*
61242826 GCAGAT
388 CCAGAT
* *
61242832 CAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTATCT
1 --AAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCT
61242897 CCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
64 CCATGGGCAACAGTGGAATAGATTGAAGA-TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
* *
61242962 ATCGAAGATGGCGGATTTTACCTCCCTGAAGTTATAGTGGAGTACATTGAAGCCAGTAATTCTAT
128 ATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
* * *
61243027 TTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGTTCTTATCTCCCTAGGCAG
193 CTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
61243083 CGAAGTAGAT
Statistics
Matches: 592, Mismatches: 43, Indels: 16
0.91 0.07 0.02
Matches are distributed among these distances:
392 8 0.01
393 346 0.58
394 1 0.00
396 235 0.40
397 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (393 bp):
AAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCC
ATGGGCAACAGTGGAATAGATTGAAGATACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
GAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTC
CCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
TCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACT
TCCCTGGACAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGCAGTGGACCA
GAT
Found at i:61242956 original size:44 final size:44
Alignment explanation
Indices: 61242908--61243082 Score: 124
Period size: 44 Copynumber: 4.0 Consensus size: 44
61242898 CATGGGCAAC
61242908 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
** * ** * * * *
61242952 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTA-T
1 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT-AAG-CAGT
* * * * * * *
61242997 AGTGGAGTACATTGAAGCCAGTA-A-TTC-TATTTCCCTAGGCAGC
1 AGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAGT
* *
61243040 AGTGGAATAGATTGAAGATTACAGTTCTTATCTCCCTAGGCAG
1 AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAG
61243083 CGAAGTAGAT
Statistics
Matches: 96, Mismatches: 27, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
41 3 0.03
42 2 0.02
43 20 0.21
44 50 0.52
45 19 0.20
46 1 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.29
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
Found at i:61243158 original size:44 final size:45
Alignment explanation
Indices: 61243095--61243200 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
61243085 AAGTAGATCA
61243095 AAGTTGCAGTGGGGCAGACT-AAGGA-AGC-AAGTCTTATC-CTCCTG
1 AAGTTGCAGTGGGGCAGACTGAA-GATAGCGAA-TCTTATCTC-CCTG
*
61243139 AAGTTGCAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
* *
61243184 AAGTTGTAGTGGAGCAG
1 AAGTTGCAGTGGGGCAG
61243201 GTTAAAGCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
44 22 0.40
45 30 0.55
46 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (45 bp):
AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
Found at i:61243232 original size:44 final size:44
Alignment explanation
Indices: 61243169--61243299 Score: 176
Period size: 44 Copynumber: 3.0 Consensus size: 44
61243159 GAAGATGGCG
* *
61243169 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGG-TTAAAGCCA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTAAAACCACA
* *
61243212 TAATCCTATCTCCCTGAAGTTGCAGTGGAACGGATTAAAACCACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
* *
61243257 GATCTTATCTCTCTGAAGTTGCAGTGGAGCGGATTAAAACCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCAC
61243300 GGATCGCATC
Statistics
Matches: 77, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
43 2 0.03
44 74 0.96
45 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
Found at i:61243321 original size:3 final size:3
Alignment explanation
Indices: 61243313--61243356 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
61243303 TCGCATCCAG
* *
61243313 TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAC TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
61243357 CTACACATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:61245423 original size:19 final size:20
Alignment explanation
Indices: 61245384--61245423 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
61245374 TCTTTTCGTA
* *
61245384 TTCATTTCATGCATTTGCAT
1 TTCATTACATGCATATGCAT
61245404 TTCATTACAT-CATATGCAT
1 TTCATTACATGCATATGCAT
61245423 T
1 T
61245424 AAACACAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.25, C:0.20, G:0.07, T:0.47
Consensus pattern (20 bp):
TTCATTACATGCATATGCAT
Found at i:61247344 original size:19 final size:19
Alignment explanation
Indices: 61247320--61247357 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
61247310 AATATTCTTT
*
61247320 CATTCTTTAAGATTTTTTC
1 CATTCTTTAAGATGTTTTC
*
61247339 CATTCTTTTAGATGTTTTC
1 CATTCTTTAAGATGTTTTC
61247358 TGCCAAATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.18, C:0.16, G:0.08, T:0.58
Consensus pattern (19 bp):
CATTCTTTAAGATGTTTTC
Found at i:61248334 original size:14 final size:14
Alignment explanation
Indices: 61248302--61248333 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
61248292 AAGTGATGTG
61248302 GAAAATGAAAAGAT
1 GAAAATGAAAAGAT
61248316 GAAAATGAAAA-AT
1 GAAAATGAAAAGAT
61248329 GAAAA
1 GAAAA
61248334 AGTAAAACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (14 bp):
GAAAATGAAAAGAT
Found at i:61248724 original size:13 final size:13
Alignment explanation
Indices: 61248706--61248730 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
61248696 TAAATCAATT
61248706 TCTTTGTTATCCA
1 TCTTTGTTATCCA
61248719 TCTTTGTTATCC
1 TCTTTGTTATCC
61248731 TCGACAATTT
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:0.12, C:0.24, G:0.08, T:0.56
Consensus pattern (13 bp):
TCTTTGTTATCCA
Found at i:61249715 original size:132 final size:131
Alignment explanation
Indices: 61249478--61250525 Score: 1584
Period size: 132 Copynumber: 8.0 Consensus size: 131
61249468 TTGAAAGCGA
* *
61249478 AGCAGATCGAAGATGGCAGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
61249543 TCTACTTCCCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTATT
66 TCTA-TTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61249608 GG
130 GG
* *
61249610 AGCAGATTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * * * *
61249675 TCTACTTTCCTAGACAACAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGT
66 TCTA-TTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61249740 GG
130 GG
*
61249742 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* ** * ** ** *
61249807 TCTACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTGAGGTCTTATCTCCCTCGGTTGCAGT
66 TCTA-TTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61249872 GG
130 GG
* ** * *
61249874 ACCAG---GTTGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAGTACATTGAAGCCAATAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
61249936 TCTATCTCCATGGGCACCAGTGGAATAGATTGAAGA-TACCAGATCTTATCTCCCTAAGCAGTAG
66 TCTAT-TCCCTGGGCAACAGTGGAATAGATTGAAGATTA-CAGATCTTATCTCCCTAAGCAGTAG
61250000 TGG
129 TGG
61250003 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
61250068 TCTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
66 TCTAT-TCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61250133 GG
130 GG
*
61250135 AGCAGATC-AATGATGGCGGATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
1 AGCAGATCGAA-GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
* * *
61250199 TTCTATCTCTCTGGGCAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGTAG
65 TTCTAT-TCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAG
61250264 TGG
129 TGG
* * *
61250267 AGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAC
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* *
61250332 TCTACCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
66 TCTA-TTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGT
61250397 GG
130 GG
* *
61250399 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTATAGTGGAGTACATTGAAGCCAGTAAT
1 AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
* * *
61250464 TCTATCTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGT
66 TCTAT-TCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
61250526 GAGTAGATCA
Statistics
Matches: 841, Mismatches: 65, Indels: 20
0.91 0.07 0.02
Matches are distributed among these distances:
128 2 0.00
129 108 0.13
131 2 0.00
132 725 0.86
133 4 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (131 bp):
AGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TCTATTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTG
G
Found at i:61250002 original size:44 final size:44
Alignment explanation
Indices: 61249954--61250135 Score: 126
Period size: 44 Copynumber: 4.1 Consensus size: 44
61249944 CATGGGCACC
61249954 AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGT
** * ** * * * *
61249998 AGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAG--GTT
1 AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAG-T
* * ** *
61250041 ACAGTGGAGTACATTGAAG---CCAGTAAT-TCTATCTCCCTGGGCAGC
1 --AGTGGAATAGATTGAAGATACCAG--ATCT-TATCTCCCTAAGCAGT
61250086 AGTGGAATAGATTGAAGATTA-CAGATCTTATCTCCCTAAGCAGT
1 AGTGGAATAGATTGAAGA-TACCAGATCTTATCTCCCTAAGCAGT
61250130 AGTGGA
1 AGTGGA
61250136 GCAGATCAAT
Statistics
Matches: 103, Mismatches: 22, Indels: 26
0.68 0.15 0.17
Matches are distributed among these distances:
42 3 0.03
43 17 0.17
44 64 0.62
45 15 0.15
46 4 0.04
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (44 bp):
AGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGT
Found at i:61250091 original size:43 final size:43
Alignment explanation
Indices: 61249910--61250498 Score: 119
Period size: 44 Copynumber: 13.4 Consensus size: 43
61249900 CCTGATGTTA
* * * *
61249910 CAGTGGAGTACATTGAAGCCAATAATTCTATCTCCATGGGCAC
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
* **
61249953 CAGTGGAATAGATTGAAGATACCAG--A-TCTTATCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAG---CCAGTAATTC-TATCTCCCTGGGCAG
* * * *** ** * * *
61249997 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCAG-TAATTCTATCTCCCTG-GG-CAG
*
61250042 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
* * * **
61250085 CAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAG
* * * * * * * * *
61250129 TAGTGGAGCAGATCAATGATGGC-G-GATTTTACCTCTCTGAGGTTA-
1 CAGTGGAGTAGAT---TGAAGCCAGTAATTCTATCTCCCTG-GG-CAG
* * *
61250174 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGGGCAA
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
* * * ** *
61250217 CAGTGGAATAGATTGAAG--ATTACAAATCTTATCTCCCTAAGTAG
1 CAGTGGAGTAGATTGAAGCCAGT--AATTC-TATCTCCCTGGGCAG
* * ** *** * * * *
61250261 TAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCAGT-AATTCTATCTCCCTG-GG-CAG
* * * * *
61250306 CAGTGGAGTACATTGAAGCCAGTAACTCTACCTCCATGGGCAA
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
* * * **
61250349 CAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TATCTCCCTGGGCAG
* * * *** ** * * **
61250393 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAAGTTA-
1 CAGTGGAGTAGATTGAAGCCAG-TAATTCTATCTCCCTG--GGCAG
* * *
61250438 TAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTAGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
*
61250481 CAGTGGAATAGATTGAAG
1 CAGTGGAGTAGATTGAAG
61250499 ATTACAGATC
Statistics
Matches: 370, Mismatches: 135, Indels: 82
0.63 0.23 0.14
Matches are distributed among these distances:
41 9 0.02
42 12 0.03
43 96 0.26
44 174 0.47
45 64 0.17
46 11 0.03
47 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (43 bp):
CAGTGGAGTAGATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
Found at i:61250221 original size:393 final size:392
Alignment explanation
Indices: 61249487--61250525 Score: 1620
Period size: 393 Copynumber: 2.6 Consensus size: 392
61249477 AAGCAGATCG
*
61249487 AAGATGGCAGATTTTACCTCCCTG-TGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTC
1 AAGATGGCGGATTTTACCTCCCTGAT-GTTACAGTGGAGTACATTGAAGCCAGTAATTCTAC-TC
* * *
61249551 CCTGGGCAACAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTATTGGAGCAGA
64 CATGGGCAACAGTGGAATAGATTGAAGA-TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGA
* *
61249616 TTGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-C
128 TCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATC
* * * * *
61249680 TTTCCTAGACAACAATGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGC
193 -TCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGC
*
61249745 AGATCGAAGATGGCGGATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
257 AGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCT
** ** ** *
61249810 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTTGAGGTCTTATCTCCCTCGGTTGCAGTGGA
322 ACTTCCCTGGACAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGCAGTGGA
*
61249875 CCAGGT
387 CCAGAT
* *
61249881 -TGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCC
1 AAGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CTCC
*
61249945 ATGGGCACCAGTGGAATAGATTGAAGATACCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
65 ATGGGCAACAGTGGAATAGATTGAAGATA-CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
61250010 CGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCT
129 CGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCT
*
61250075 CCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
194 CCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
*
61250140 ATC-AATGATGGCGGATTTTACCTCTCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
259 ATCGAA-GATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA
* * *
61250204 -TCTCTCTGGGCAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGTAGTGGA
323 CT-TCCCTGGACAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGCAGTGGA
*
61250268 GCAGAT
387 CCAGAT
* * *
61250274 CAAAGATGGTGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAACTCTACCT
1 --AAGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-CT
61250339 CCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
63 CCATGGGCAACAGTGGAATAGATTGAAGA-TACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAG
* *
61250404 ATCGAAGATGGCGGATTTTACCTCCCTGAAGTTATAGTGGAGTACATTGAAGCCAGTAATTCTAT
127 ATCGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
*
61250469 CTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGT
192 CTCCCTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGT
61250526 GAGTAGATCA
Statistics
Matches: 595, Mismatches: 40, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
392 4 0.01
393 351 0.59
394 3 0.01
396 235 0.39
397 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.28
Consensus pattern (392 bp):
AAGATGGCGGATTTTACCTCCCTGATGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTCCA
TGGGCAACAGTGGAATAGATTGAAGATACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
AAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCC
CTAGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGAT
CGAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTT
CCCTGGACAACAGTGGAATAGATTGAAGATTACAAATCTTATCTCCCTAAGTAGCAGTGGACCAG
AT
Found at i:61250599 original size:44 final size:45
Alignment explanation
Indices: 61250536--61250641 Score: 130
Period size: 45 Copynumber: 2.4 Consensus size: 45
61250526 GAGTAGATCA
61250536 AAGTTGCAGTGGGGCAGACT-AAGGA-AGC-AAGTCTTATC-CTCCTG
1 AAGTTGCAGTGGGGCAGACTGAA-GATAGCGAA-TCTTATCTC-CCTG
*
61250580 AAGTTGCAGTGGGGCAGACTGAAGATGGCGAATCTTATCTCCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
* *
61250625 AAGTTGTAGTGGAGCAG
1 AAGTTGCAGTGGGGCAG
61250642 GTTAAAGCCA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
44 22 0.40
45 30 0.55
46 3 0.05
ACGTcount: A:0.26, C:0.18, G:0.32, T:0.24
Consensus pattern (45 bp):
AAGTTGCAGTGGGGCAGACTGAAGATAGCGAATCTTATCTCCCTG
Found at i:61250673 original size:44 final size:44
Alignment explanation
Indices: 61250610--61250835 Score: 153
Period size: 44 Copynumber: 5.2 Consensus size: 44
61250600 GAAGATGGCG
* *
61250610 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGG-TTAAAGCCA-A
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTAAAACCACA
*
61250653 TAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
* * * *** *
61250698 GATCTTATCTCTCTGAAGTTGCAGAGG-GCGGA-TCGCATC-C-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
* * * * * *
61250738 AGTCTTATCTCCCTGAAGTTGCAGTGAAGCAGA-CAGAAGA-AACC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTA-AA-ACCACA
* * * * *
61250782 AATCCTATCTCCTTGAAGTTGCAATGGAGTGGATTAGAACCACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
* *
61250826 GATCTCATCT
1 AATCTTATCT
61250836 ATCGGAGGTT
Statistics
Matches: 137, Mismatches: 36, Indels: 18
0.72 0.19 0.09
Matches are distributed among these distances:
40 22 0.16
41 5 0.04
42 3 0.02
43 10 0.07
44 95 0.69
45 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACA
Found at i:61252207 original size:3 final size:3
Alignment explanation
Indices: 61252199--61252243 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
61252189 CATGTTATAT
61252199 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
61252244 CTACACATAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:61252413 original size:27 final size:27
Alignment explanation
Indices: 61252381--61252443 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
61252371 TCATGCTTTA
*
61252381 TATTTTTTT-ACATACT-TACATATTTT
1 TATTTTTTTAACATA-TATACATAATTT
*
61252407 TATTTTTTAAACATATATACATAATTT
1 TATTTTTTTAACATATATACATAATTT
*
61252434 TATATTTTTA
1 TATTTTTTTA
61252444 TTTTATTGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 9 0.29
27 22 0.71
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (27 bp):
TATTTTTTTAACATATATACATAATTT
Found at i:61256576 original size:13 final size:13
Alignment explanation
Indices: 61256558--61256583 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
61256548 ATAAAATGTT
61256558 AACACATATATAA
1 AACACATATATAA
61256571 AACACATATATAA
1 AACACATATATAA
61256584 GTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.00, T:0.23
Consensus pattern (13 bp):
AACACATATATAA
Found at i:61256722 original size:2 final size:2
Alignment explanation
Indices: 61256715--61256755 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
61256705 ATGAGTGTAC
*
61256715 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61256756 AAAACTATGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 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):
AT
Found at i:61257993 original size:18 final size:19
Alignment explanation
Indices: 61257970--61258006 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
61257960 CGCTGGAGGC
61257970 GAGGGC-TGTTGCGACGCT
1 GAGGGCTTGTTGCGACGCT
*
61257988 GAGGGCTTGTTGCGGCGCT
1 GAGGGCTTGTTGCGACGCT
61258007 CCCTATTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.08, C:0.22, G:0.46, T:0.24
Consensus pattern (19 bp):
GAGGGCTTGTTGCGACGCT
Found at i:61258880 original size:27 final size:26
Alignment explanation
Indices: 61258838--61258900 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
61258828 TAAAAATTAT
61258838 CAAAATAT-TATAATTTTTTTATTTAC
1 CAAAATATATATAA-TTTTTTATTTAC
61258864 CAAAATATATATAATTTTTTATTTAC
1 CAAAATATATATAATTTTTTATTTAC
61258890 CAAAATATATA
1 CAAAATATATA
61258901 AAAAACTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 31 0.86
27 5 0.14
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (26 bp):
CAAAATATATATAATTTTTTATTTAC
Found at i:61262099 original size:3 final size:3
Alignment explanation
Indices: 61262091--61262125 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
61262081 NNNATCTTAT
61262091 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
61262126 CTATAAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:61262489 original size:27 final size:27
Alignment explanation
Indices: 61262439--61262521 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 27
61262429 GGTTGGTAGG
** **
61262439 ACTGGTGCCGCCAACAGGGATCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
**
61262466 ACTGGTGCCGCCAACCTGCTTCCCTTG
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
** *
61262493 TTTGGTGCCACCAACCTGCTTCCCTCC
1 ACTGGTGCCGCCAACCTGCTTCCCTCC
61262520 AC
1 AC
61262522 CCAGGGAGTT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.14, C:0.42, G:0.20, T:0.23
Consensus pattern (27 bp):
ACTGGTGCCGCCAACCTGCTTCCCTCC
Found at i:61262605 original size:26 final size:26
Alignment explanation
Indices: 61262575--61262642 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
61262565 TATTTTTTTG
61262575 ATATATTTTGA-TAAATAAAAAAAATT
1 ATATATTTTGAGTAAAT-AAAAAAATT
*
61262601 ATATATATTTTAGTAAATAAAAAAATT
1 ATATAT-TTTGAGTAAATAAAAAAATT
61262628 ATAATATTTTG-GTAA
1 AT-ATATTTTGAGTAA
61262643 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
26 10 0.27
27 18 0.49
28 9 0.24
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
ATATATTTTGAGTAAATAAAAAAATT
Found at i:61262606 original size:28 final size:28
Alignment explanation
Indices: 61262575--61262642 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
61262565 TATTTTTTTG
61262575 ATATATTTTGA-TAAATAAAAAAAATTAT
1 ATATATTTTGAGTAAAT-AAAAAAATTAT
61262603 ATATATTTT-AGTAAATAAAAAAATTAT
1 ATATATTTTGAGTAAATAAAAAAATTAT
61262630 A-ATATTTTG-GTAA
1 ATATATTTTGAGTAA
61262643 TTTTTTATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
26 11 0.29
27 13 0.34
28 14 0.37
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (28 bp):
ATATATTTTGAGTAAATAAAAAAATTAT
Found at i:61268688 original size:21 final size:21
Alignment explanation
Indices: 61268636--61268688 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
61268626 TCAAAATCAA
*
61268636 TTTAAATGTTATTCTTTTATC
1 TTTAAATATTATTCTTTTATC
* *
61268657 GTTATATTATTATTCTTTATAT-
1 TTTA-AATATTATTCTTT-TATC
61268679 TTTAAATATT
1 TTTAAATATT
61268689 TCACGAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
21 8 0.32
22 14 0.56
23 3 0.12
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (21 bp):
TTTAAATATTATTCTTTTATC
Found at i:61268745 original size:14 final size:14
Alignment explanation
Indices: 61268726--61268755 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61268716 TGTCAAAATG
61268726 TTATAATAATCATT
1 TTATAATAATCATT
*
61268740 TTATAATAATTATT
1 TTATAATAATCATT
61268754 TT
1 TT
61268756 GATTCAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (14 bp):
TTATAATAATCATT
Found at i:61272039 original size:17 final size:17
Alignment explanation
Indices: 61272017--61272075 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
61272007 ATGATTGATT
61272017 TAATGTTGATTTTTTTA
1 TAATGTTGATTTTTTTA
61272034 TAATG-T-ATTTTGAATGATT-
1 TAATGTTGATTTT---T--TTA
61272053 TAATGTTGATTTTTTTA
1 TAATGTTGATTTTTTTA
61272070 TAATGT
1 TAATGT
61272076 ATTTTGAATG
Statistics
Matches: 34, Mismatches: 0, Indels: 16
0.68 0.00 0.32
Matches are distributed among these distances:
15 5 0.15
16 3 0.09
17 11 0.32
18 2 0.06
19 5 0.15
20 3 0.09
21 5 0.15
ACGTcount: A:0.27, C:0.00, G:0.14, T:0.59
Consensus pattern (17 bp):
TAATGTTGATTTTTTTA
Found at i:61272046 original size:21 final size:21
Alignment explanation
Indices: 61272022--61272082 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
61272012 TGATTTAATG
61272022 TTGATTTTTTTATAATGTATT
1 TTGATTTTTTTATAATGTATT
* **
61272043 TTGA-ATGATT-TAATG----
1 TTGATTTTTTTATAATGTATT
61272058 TTGATTTTTTTATAATGTATT
1 TTGATTTTTTTATAATGTATT
61272079 TTGA
1 TTGA
61272083 ATGTTAATAT
Statistics
Matches: 28, Mismatches: 6, Indels: 12
0.61 0.13 0.26
Matches are distributed among these distances:
15 4 0.14
16 3 0.11
17 5 0.18
19 5 0.18
20 3 0.11
21 8 0.29
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (21 bp):
TTGATTTTTTTATAATGTATT
Found at i:61272052 original size:36 final size:36
Alignment explanation
Indices: 61272012--61272085 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
61272002 TTTGAATGAT
61272012 TGATTTAATGTTGATTTTTTTATAATGTATTTTGAA
1 TGATTTAATGTTGATTTTTTTATAATGTATTTTGAA
61272048 TGATTTAATGTTGATTTTTTTATAATGTATTTTGAA
1 TGATTTAATGTTGATTTTTTTATAATGTATTTTGAA
61272084 TG
1 TG
61272086 TTAATATATG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (36 bp):
TGATTTAATGTTGATTTTTTTATAATGTATTTTGAA
Found at i:61272315 original size:42 final size:42
Alignment explanation
Indices: 61272242--61272470 Score: 259
Period size: 42 Copynumber: 5.4 Consensus size: 42
61272232 ACGTCGCTAA
* *
61272242 CTTTTGCGGCGCTTACAGAAAAGAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTA-TGAAAA-AACGCCGCTAAAGATCATGTT
* *
61272286 CTTTAGCGGCACTTATGAAAAAACACCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
* *
61272328 CTTTAGCGACGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
*
61272370 CTTTAGCGGCGCTT-TGGAAGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAT-GAA-AAAACGCCGCTAAAGA-TCATGTT
* * **
61272413 CTATAGCGGCGCTTGTTCAAAAACGCCGCTAACAG-T-AGTGTT
1 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAA-AGATCA-TGTT
*
61272455 CTTTAGCAGCGCTTAT
1 CTTTAGCGGCGCTTAT
61272471 TTCACAAACA
Statistics
Matches: 161, Mismatches: 17, Indels: 16
0.83 0.09 0.08
Matches are distributed among these distances:
41 1 0.01
42 106 0.66
43 40 0.25
44 14 0.09
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
Found at i:61272426 original size:85 final size:84
Alignment explanation
Indices: 61272247--61272470 Score: 260
Period size: 85 Copynumber: 2.6 Consensus size: 84
61272237 GCTAACTTTT
* *
61272247 GCGGCGCTTACAGAAAAGAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTATGAAAAAACAC
1 GCGGCGCTTA-GGAAAA-AACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAAAAACAC
* *
61272312 CGCTAAAGATCATGTTCTTTA
64 CGCTAAAGATAATGTTCTATA
* *
61272333 GCGACGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTT-TGGAAGAAAACGC
1 GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAT-GAA-AAAACAC
61272397 CGCTAAA-AGTAATGTTCTATA
64 CGCTAAAGA-TAATGTTCTATA
** *
61272418 GCGGCGCTT-GTTCAAAAACGCCGCTAACAG-T-AGTGTTCTTTAGCAGCGCTTAT
1 GCGGCGCTTAG-GAAAAAACGCCGCTAA-AGATCA-TGTTCTTTAGCGGCGCTTAT
61272471 TTCACAAACA
Statistics
Matches: 121, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
83 1 0.01
84 40 0.33
85 68 0.56
86 12 0.10
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (84 bp):
GCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTATGAAAAAACACCG
CTAAAGATAATGTTCTATA
Found at i:61272942 original size:21 final size:21
Alignment explanation
Indices: 61272918--61272986 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
61272908 GCTTCTATCG
*
61272918 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
*
61272939 CTGCTTCTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* * *
61272960 CTGCTTCCCTCACTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
61272981 CTGCTT
1 CTGCTT
61272987 TAAGTTGTTG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.03, C:0.43, G:0.19, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:61275258 original size:9 final size:9
Alignment explanation
Indices: 61275244--61275327 Score: 123
Period size: 9 Copynumber: 9.3 Consensus size: 9
61275234 GAACGCACTA
61275244 TATGTAAGT
1 TATGTAAGT
61275253 TATGTAAGT
1 TATGTAAGT
* *
61275262 TATTTAATT
1 TATGTAAGT
61275271 TATGTAAGT
1 TATGTAAGT
61275280 TATGTAAGT
1 TATGTAAGT
* *
61275289 TATTTAATT
1 TATGTAAGT
*
61275298 TATGTAATT
1 TATGTAAGT
61275307 TATGTAAGT
1 TATGTAAGT
61275316 TATGTAAGT
1 TATGTAAGT
61275325 TAT
1 TAT
61275328 ATACTAAATT
Statistics
Matches: 67, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (9 bp):
TATGTAAGT
Found at i:61275282 original size:27 final size:27
Alignment explanation
Indices: 61275244--61275327 Score: 141
Period size: 27 Copynumber: 3.1 Consensus size: 27
61275234 GAACGCACTA
61275244 TATGTAAGTTATGTAAGTTATTTAATT
1 TATGTAAGTTATGTAAGTTATTTAATT
61275271 TATGTAAGTTATGTAAGTTATTTAATT
1 TATGTAAGTTATGTAAGTTATTTAATT
* * *
61275298 TATGTAATTTATGTAAGTTATGTAAGT
1 TATGTAAGTTATGTAAGTTATTTAATT
61275325 TAT
1 TAT
61275328 ATACTAAATT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (27 bp):
TATGTAAGTTATGTAAGTTATTTAATT
Found at i:61276345 original size:36 final size:36
Alignment explanation
Indices: 61276305--61276380 Score: 152
Period size: 36 Copynumber: 2.1 Consensus size: 36
61276295 TTTATACCAA
61276305 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
1 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
61276341 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
1 AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
61276377 AAAT
1 AAAT
61276381 TTTGAACAGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (36 bp):
AAATATTACTTTGCTCAGAATGTAATTTGAACTTAC
Found at i:61276721 original size:52 final size:52
Alignment explanation
Indices: 61276654--61276752 Score: 189
Period size: 52 Copynumber: 1.9 Consensus size: 52
61276644 GTTATGCAAA
*
61276654 ATTATTACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
61276706 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTT
1 ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTT
61276753 TCTTATTTCA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.44
Consensus pattern (52 bp):
ATTAATACCTAAAAATGTTCTTACTTTCTTAACCCTAATTTGAATTTACCGT
Found at i:61276742 original size:26 final size:26
Alignment explanation
Indices: 61276661--61276743 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 26
61276651 AAAATTATTA
61276661 CCTAAAAATGTTCTTACTTTCTTAAC
1 CCTAAAAATGTTCTTACTTTCTTAAC
** * ** * *
61276687 CCT-AATTTGAAT-TTACCGTATTAATA
1 CCTAAAAATG-TTCTTACTTTCTTAA-C
61276713 CCTAAAAATGTTCTTACTTTCTTAAC
1 CCTAAAAATGTTCTTACTTTCTTAAC
61276739 CCTAA
1 CCTAA
61276744 TTTGAATTTT
Statistics
Matches: 39, Mismatches: 14, Indels: 8
0.64 0.23 0.13
Matches are distributed among these distances:
25 13 0.33
26 13 0.33
27 13 0.33
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.41
Consensus pattern (26 bp):
CCTAAAAATGTTCTTACTTTCTTAAC
Found at i:61278667 original size:14 final size:14
Alignment explanation
Indices: 61278650--61278696 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
61278640 TTGTAACTCT
*
61278650 TAAATCTTAAACCA
1 TAAACCTTAAACCA
*
61278664 TAAACCTTAAAGCA
1 TAAACCTTAAACCA
* *
61278678 TAACCCTTAAACCC
1 TAAACCTTAAACCA
61278692 TAAAC
1 TAAAC
61278697 TGCAAAAACC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.47, C:0.28, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACCTTAAACCA
Found at i:61278696 original size:35 final size:35
Alignment explanation
Indices: 61278614--61278696 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
61278604 ACATAATCAC
* *** *
61278614 TAAACCCATAATCCATAAACCTTAAATTGTAACTCT
1 TAAACCC-TAAACCATAAACCTTAAAGCATAACCCT
* *
61278650 TAAATCTTAAACCATAAACCTTAAAGCATAACCCT
1 TAAACCCTAAACCATAAACCTTAAAGCATAACCCT
61278685 TAAACCCTAAAC
1 TAAACCCTAAAC
61278697 TGCAAAAACC
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
35 33 0.87
36 5 0.13
ACGTcount: A:0.45, C:0.27, G:0.02, T:0.27
Consensus pattern (35 bp):
TAAACCCTAAACCATAAACCTTAAAGCATAACCCT
Found at i:61279119 original size:99 final size:96
Alignment explanation
Indices: 61279009--61279195 Score: 259
Period size: 99 Copynumber: 1.9 Consensus size: 96
61278999 TAAATCCCTG
* * * * *
61279009 AGCATTAGCGGCGCTTTATTAAAAACGCCGCTAAACCCCCTAAAAGCT-AAGAAAACGGTGTCGT
1 AGCATTAGCGGCACATTATTAAAAACGCCACTAAACCCCCCAAAAGCTCAA-AAAACGGCGTCGT
*
61279073 TGGGTTTAATTTTATTTGCGGCGCTTTTATGCCTT
65 TGGGCTT-A-TTT-TTTGCGGCGCTTTTATGCCTT
* *
61279108 AGCATTAGCGGCACATTATTGAAAACGCCACTAAACCCCCCGAAAGCTCAAAAAACGGCGTCGTT
1 AGCATTAGCGGCACATTATTAAAAACGCCACTAAACCCCCCAAAAGCTCAAAAAACGGCGTCGTT
61279173 GGGCTTATTTTTTGCGGCGCTTT
66 GGGCTTATTTTTTGCGGCGCTTT
61279196 GTCAAAACCG
Statistics
Matches: 79, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
96 13 0.16
97 3 0.04
98 1 0.01
99 60 0.76
100 2 0.03
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (96 bp):
AGCATTAGCGGCACATTATTAAAAACGCCACTAAACCCCCCAAAAGCTCAAAAAACGGCGTCGTT
GGGCTTATTTTTTGCGGCGCTTTTATGCCTT
Found at i:61290509 original size:21 final size:20
Alignment explanation
Indices: 61290485--61290525 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
61290475 AAATTGTACG
*
61290485 GATTGATTGAACCAAATAAAA
1 GATTAATTGAACCAAA-AAAA
61290506 GATTAATTGAACCAAAAAAA
1 GATTAATTGAACCAAAAAAA
61290526 TTGAATTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (20 bp):
GATTAATTGAACCAAAAAAA
Found at i:61294159 original size:11 final size:11
Alignment explanation
Indices: 61294143--61294167 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
61294133 TTCAGTTCGG
61294143 TTTTTATATTT
1 TTTTTATATTT
61294154 TTTTTATATTT
1 TTTTTATATTT
61294165 TTT
1 TTT
61294168 AAGCTTATTT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:61295969 original size:344 final size:344
Alignment explanation
Indices: 61295342--61296034 Score: 1368
Period size: 344 Copynumber: 2.0 Consensus size: 344
61295332 ACCTAGAGTT
61295342 AATTGCTTTTATGCTTGAAAGAGATATTAGTATAAGTTAGGGATTTCTACGGATTAAGGAAACTA
1 AATTGCTTTTATGCTTGAAAGAGATATTAGTATAAGTTAGGGATTTCTACGGATTAAGGAAACTA
61295407 AGGAAATGAATTGCATAAAGTAGATTGAGAATTTTAGATGAATTCTAGGTGGATTCTTACCTAGG
66 AGGAAATGAATTGCATAAAGTAGATTGAGAATTTTAGATGAATTCTAGGTGGATTCTTACCTAGG
*
61295472 TATTGTTTGGTCAATCTGTAACAACCCAAAAGTCAGTAGAGTCGAAAATGGTGGTTTCGAGATGA
131 TATTGTTTGGTCAATCTGTAACAACCCAAAAGTCAGTAGAGTCGAAAATGGTGGTTTCGAAATGA
61295537 TGTTTTCCAATTATAGAATTTGTGAATATTATTTATTAATATATACGAGGGTATTACAATATTAT
196 TGTTTTCCAATTATAGAATTTGTGAATATTATTTATTAATATATACGAGGGTATTACAATATTAT
*
61295602 ACTGAGGTTTGGTCTAATAATTTTAATTATCTGAAAAGTTTAACAAGGTACAGGTGTATCGGTTC
261 ACTGAGGTTTGGTCTAATAATTTTAATTATCTAAAAAGTTTAACAAGGTACAGGTGTATCGGTTC
61295667 TAAAGTTGGTGGTTTTGGA
326 TAAAGTTGGTGGTTTTGGA
61295686 AATTGCTTTTATGCTTGAAAGAGATATTAGTATAAGTTAGGGATTTCTACGGATTAAGGAAACTA
1 AATTGCTTTTATGCTTGAAAGAGATATTAGTATAAGTTAGGGATTTCTACGGATTAAGGAAACTA
61295751 AGGAAATGAATTGCATAAAGTAGATTGAGAATTTTAGATGAATTCTAGGTGGATTCTTACCTAGG
66 AGGAAATGAATTGCATAAAGTAGATTGAGAATTTTAGATGAATTCTAGGTGGATTCTTACCTAGG
61295816 TATTGTTTGGTCAATCTGTAACAACCCAAAAGTCAGTAGAGTCGAAAATGGTGGTTTCGAAATGA
131 TATTGTTTGGTCAATCTGTAACAACCCAAAAGTCAGTAGAGTCGAAAATGGTGGTTTCGAAATGA
61295881 TGTTTTCCAATTATAGAATTTGTGAATATTATTTATTAATATATACGAGGGTATTACAATATTAT
196 TGTTTTCCAATTATAGAATTTGTGAATATTATTTATTAATATATACGAGGGTATTACAATATTAT
61295946 ACTGAGGTTTGGTCTAATAATTTTAATTATCTAAAAAGTTTAACAAGGTACAGGTGTATCGGTTC
261 ACTGAGGTTTGGTCTAATAATTTTAATTATCTAAAAAGTTTAACAAGGTACAGGTGTATCGGTTC
61296011 TAAAGTTGGTGGTTTTGGA
326 TAAAGTTGGTGGTTTTGGA
61296030 AATTG
1 AATTG
61296035 AGGTATCAGG
Statistics
Matches: 347, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
344 347 1.00
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (344 bp):
AATTGCTTTTATGCTTGAAAGAGATATTAGTATAAGTTAGGGATTTCTACGGATTAAGGAAACTA
AGGAAATGAATTGCATAAAGTAGATTGAGAATTTTAGATGAATTCTAGGTGGATTCTTACCTAGG
TATTGTTTGGTCAATCTGTAACAACCCAAAAGTCAGTAGAGTCGAAAATGGTGGTTTCGAAATGA
TGTTTTCCAATTATAGAATTTGTGAATATTATTTATTAATATATACGAGGGTATTACAATATTAT
ACTGAGGTTTGGTCTAATAATTTTAATTATCTAAAAAGTTTAACAAGGTACAGGTGTATCGGTTC
TAAAGTTGGTGGTTTTGGA
Found at i:61307062 original size:16 final size:17
Alignment explanation
Indices: 61307033--61307065 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
61307023 TGTGTTTGGA
61307033 TATTCTTATATTTGTAT
1 TATTCTTATATTTGTAT
*
61307050 TATTTTTAT-TTTGTAT
1 TATTCTTATATTTGTAT
61307066 CAAAATGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.21, C:0.03, G:0.06, T:0.70
Consensus pattern (17 bp):
TATTCTTATATTTGTAT
Found at i:61312808 original size:31 final size:31
Alignment explanation
Indices: 61312770--61312831 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
61312760 TTACACCACA
* * *
61312770 AGTCACCCAACTATTGTCTCCTTTCTTTTTT
1 AGTCACCCAACCATTGACTCCTTTATTTTTT
*
61312801 AGTCACCCAACCATTGACTCTTTTATTTTTT
1 AGTCACCCAACCATTGACTCCTTTATTTTTT
61312832 GATCGCGCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.19, C:0.27, G:0.06, T:0.47
Consensus pattern (31 bp):
AGTCACCCAACCATTGACTCCTTTATTTTTT
Found at i:61317030 original size:8 final size:7
Alignment explanation
Indices: 61317002--61317027 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
61316992 GAAGCCAAAA
61317002 TTTTTAT
1 TTTTTAT
61317009 TTTTTAT
1 TTTTTAT
61317016 TTTTTAT
1 TTTTTAT
61317023 TTTTT
1 TTTTT
61317028 TATGGATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:61344056 original size:20 final size:20
Alignment explanation
Indices: 61344022--61344063 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
61344012 AACTATTGAA
** *
61344022 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
61344042 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
61344062 AT
1 AT
61344064 GTCTCTATGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:61350326 original size:19 final size:20
Alignment explanation
Indices: 61350302--61350342 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
61350292 TTTAACAATG
*
61350302 TTTTTGTCTCAAAAGTA-TT
1 TTTTTGTCCCAAAAGTACTT
61350321 TTTTTGTCCCAAAAGTACTT
1 TTTTTGTCCCAAAAGTACTT
61350341 TT
1 TT
61350343 GAGAAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.24, C:0.15, G:0.10, T:0.51
Consensus pattern (20 bp):
TTTTTGTCCCAAAAGTACTT
Found at i:61359121 original size:14 final size:14
Alignment explanation
Indices: 61359087--61359131 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
61359077 TTTTTAATAT
61359087 AAATTTAGTACTTATA
1 AAATTTAGTA-TTA-A
*
61359103 AAATTTAATATTAA
1 AAATTTAGTATTAA
*
61359117 AAATTCAGTATTAA
1 AAATTTAGTATTAA
61359131 A
1 A
61359132 TTTTTTAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 14 0.54
15 3 0.12
16 9 0.35
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (14 bp):
AAATTTAGTATTAA
Found at i:61359359 original size:16 final size:16
Alignment explanation
Indices: 61359336--61359374 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
61359326 ATTAAAATTT
61359336 AAAT-TTTTAAAA-AA
1 AAATATTTTAAAATAA
61359350 AAAGTATTTTAAAATAA
1 AAA-TATTTTAAAATAA
61359367 AAATATTT
1 AAATATTT
61359375 ATTATATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 1 0.05
16 13 0.59
17 5 0.23
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAATATTTTAAAATAA
Found at i:61359789 original size:13 final size:14
Alignment explanation
Indices: 61359771--61359799 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
61359761 AATAAAAAAA
61359771 TTAAAATAAT-ATT
1 TTAAAATAATGATT
61359784 TTAAAATAATGATT
1 TTAAAATAATGATT
61359798 TT
1 TT
61359800 TTTAAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
TTAAAATAATGATT
Found at i:61369253 original size:30 final size:29
Alignment explanation
Indices: 61369188--61369253 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
61369178 GTTTAATGTT
* * *
61369188 CAATTGTATACATGAAATTTGATTTTATG
1 CAATTTTATACATGAAATTTGATTTGATC
* *
61369217 CAATTTTATATATGAAATTTTTATTTGATC
1 CAATTTTATACATGAAA-TTTGATTTGATC
61369247 CAATTTT
1 CAATTTT
61369254 TGAAAATTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
29 15 0.48
30 16 0.52
ACGTcount: A:0.33, C:0.08, G:0.09, T:0.50
Consensus pattern (29 bp):
CAATTTTATACATGAAATTTGATTTGATC
Found at i:61369466 original size:29 final size:29
Alignment explanation
Indices: 61369383--61369474 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
61369373 ATAATTAAAT
*
61369383 CAAAATTAAAGTTTCAAGTATA-AATTTGAA
1 CAAAATTAAAGTTT-AAGTATATAA-TTGCA
* * *
61369413 CTACAATTAGAATTTTAAGTGTATAATTGCA
1 C-AAAATTA-AAGTTTAAGTATATAATTGCA
*
61369444 CAAAATTAAAGTTTATGTATATAATTGCA
1 CAAAATTAAAGTTTAAGTATATAATTGCA
61369473 CA
1 CA
61369475 TTAAATCAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
29 20 0.39
30 7 0.14
31 17 0.33
32 7 0.14
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.36
Consensus pattern (29 bp):
CAAAATTAAAGTTTAAGTATATAATTGCA
Found at i:61369493 original size:29 final size:28
Alignment explanation
Indices: 61369434--61369498 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
61369424 ATTTTAAGTG
* *
61369434 TATAATTGCACAAAATTAAAGTTTATGTA
1 TATAATTGCACAAAATCAAAGTTCA-GTA
61369463 TATAATTGCACATTAAATCAAAGTTCA-TA
1 TATAATTGCACA--AAATCAAAGTTCAGTA
61369492 TATAATT
1 TATAATT
61369499 TTGAAATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 21 0.66
31 11 0.34
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.38
Consensus pattern (28 bp):
TATAATTGCACAAAATCAAAGTTCAGTA
Found at i:61370355 original size:18 final size:18
Alignment explanation
Indices: 61370308--61370357 Score: 50
Period size: 18 Copynumber: 2.8 Consensus size: 18
61370298 TGTGACGAGC
*
61370308 ATAAATTAA-AAAATTAA
1 ATAAATTAATAAAAATAA
* *
61370325 ACAAATCT-TTAAAAATAA
1 ATAAAT-TAATAAAAATAA
61370343 ATAAATTAATAAAAA
1 ATAAATTAATAAAAA
61370358 AGTATAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 5
0.71 0.14 0.14
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAATTAATAAAAATAA
Found at i:61370425 original size:20 final size:20
Alignment explanation
Indices: 61370400--61370437 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
61370390 GCGAACATAA
61370400 TTATAT-TTTTTATAATTAAT
1 TTATATATTTTTA-AATTAAT
61370420 TTATATATTTTTAAATTA
1 TTATATATTTTTAAATTA
61370438 TTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATATATTTTTAAATTAAT
Found at i:61372527 original size:16 final size:16
Alignment explanation
Indices: 61372503--61372541 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
61372493 TGAATTACTG
*
61372503 ATTATAGCTATATTCC
1 ATTACAGCTATATTCC
*
61372519 ATTACAGCTCTATTCC
1 ATTACAGCTATATTCC
*
61372535 GTTACAG
1 ATTACAG
61372542 TAAACTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.38
Consensus pattern (16 bp):
ATTACAGCTATATTCC
Found at i:61390399 original size:15 final size:16
Alignment explanation
Indices: 61390376--61390412 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
61390366 CCCAAATTTC
61390376 AACAAATAAAT-TATA
1 AACAAATAAATATATA
*
61390391 AACATATAAATATAT-
1 AACAAATAAATATATA
61390406 AACAAAT
1 AACAAAT
61390413 CCTAAATCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 16 0.84
16 3 0.16
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (16 bp):
AACAAATAAATATATA
Found at i:61395358 original size:60 final size:58
Alignment explanation
Indices: 61395293--61395445 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 58
61395283 CAAGTTCAGC
* * *
61395293 TACCAATTTGAACTAAGAAGCCAAATTTAGGTACCTAATTGGA-CAAAACTAAACTTTAGG
1 TACCAATTTGAACTTAGAAGCCAAGTTTAGGTACCTAATTGGACCAAAA--AAACCTTA-G
* * * *
61395353 TACCAAATTGAACCTTA-AAGCCAAGTTCAAGTACTTAATTGGACCAAAAAAACCTTAG
1 TACCAATTTGAA-CTTAGAAGCCAAGTTTAGGTACCTAATTGGACCAAAAAAACCTTAG
*
61395411 TACCAATTTGAACTTTGAAGCCAAGTTTAGGTACC
1 TACCAATTTGAACTTAGAAGCCAAGTTTAGGTACC
61395446 AAAATGTATA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
57 3 0.04
58 27 0.35
59 7 0.09
60 33 0.42
61 8 0.10
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (58 bp):
TACCAATTTGAACTTAGAAGCCAAGTTTAGGTACCTAATTGGACCAAAAAAACCTTAG
Found at i:61397852 original size:266 final size:266
Alignment explanation
Indices: 61397369--61397907 Score: 807
Period size: 266 Copynumber: 2.0 Consensus size: 266
61397359 AACAACTAAG
* * * *
61397369 TTAATCCCACTTGAAAAAAATCATTTAGGGTAAACTATAAAAATAGTTATTTTTGTTTCCTCAGT
1 TTAATCCCACGTGAAAAAAATCATTTAGGGTAAACTATAAAAATAGTCACTTTTGTTCCCTCAGT
* * *
61397434 TTATATTTTAGTCACTTATGTTTAAAATATTATGTTTTATCCACATGCGTTAACGTGTTGTAACA
66 TTACATTTTAATCACTTATGTTTAAAATATTATGTTTTATCCACATACGTTAACGTGTTGTAACA
*
61397499 TTTTAGTCACCGAGCCATTAACGGTGTAATAGTAAGCTGACGTGGCATGTTAAACCATCATTTCA
131 TTTTAGT-------CCATTAACGGTGTAATAATAAGCTGACGTGGCATGTTAAACCATCATTTCA
61397564 AACAAAAATTTTAGGTTAAATTATACAATTGATACCAATTTTTTTTCGTTTTGAGCAATTTAATT
189 AACAAAAATTTTAGGTTAAATTATACAATTGATACCAA-TTTTTTTCGTTTTGAGCAATTTAA-T
61397629 TTTTTCTTTTATGTT
252 TTTTTCTTTTATGTT
* * *
61397644 TTAATCCCACGTGAAAAAAATTATTTAGGGTCAACTATGAAAATAGTCACTTTTGCTTCCCTCAG
1 TTAATCCCACGTGAAAAAAATCATTTAGGGTAAACTATAAAAATAGTCACTTTTG-TTCCCTCAG
* * * *
61397709 TTTACATTTTAATCACTTATGTTTGAAATGTTATGTTTTAGT-TACTTACGTTAACGTGTTGTAA
65 TTTACATTTTAATCACTTATGTTTAAAATATTATGTTTTA-TCCACATACGTTAACGTGTTGTAA
*
61397773 CATTTTAGT-CA-T-ACGGTGTAATAATAAGCTGACGTGGCATGTTAAACTATCATTTCAAACAA
129 CATTTTAGTCCATTAACGGTGTAATAATAAGCTGACGTGGCATGTTAAACCATCATTTCAAACAA
61397835 AAATTTTAGGTTAAATTATACAATTGATACCAATTTTTTTCGTTTTGAGCAATTTAATTTTTTCT
194 AAATTTTAGGTTAAATTATACAATTGATACCAATTTTTTTCGTTTTGAGCAATTTAATTTTTTCT
61397900 TTTATGTT
259 TTTATGTT
61397908 CTTTTAACTT
Statistics
Matches: 246, Mismatches: 16, Indels: 15
0.89 0.06 0.05
Matches are distributed among these distances:
264 16 0.07
265 24 0.10
266 81 0.33
267 1 0.00
268 2 0.01
275 49 0.20
276 72 0.29
277 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.42
Consensus pattern (266 bp):
TTAATCCCACGTGAAAAAAATCATTTAGGGTAAACTATAAAAATAGTCACTTTTGTTCCCTCAGT
TTACATTTTAATCACTTATGTTTAAAATATTATGTTTTATCCACATACGTTAACGTGTTGTAACA
TTTTAGTCCATTAACGGTGTAATAATAAGCTGACGTGGCATGTTAAACCATCATTTCAAACAAAA
ATTTTAGGTTAAATTATACAATTGATACCAATTTTTTTCGTTTTGAGCAATTTAATTTTTTCTTT
TATGTT
Found at i:61397925 original size:29 final size:28
Alignment explanation
Indices: 61397893--61397949 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
61397883 GCAATTTAAT
61397893 TTTTTCTTTTATGT-TCTTTTAACTTTTCC
1 TTTTTCTTTTAT-TATCTTTT-ACTTTTCC
* *
61397922 TTTTTTTTTTATTATCTTTTGCTTTTCC
1 TTTTTCTTTTATTATCTTTTACTTTTCC
61397950 CTCTATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.09, C:0.16, G:0.04, T:0.72
Consensus pattern (28 bp):
TTTTTCTTTTATTATCTTTTACTTTTCC
Found at i:61399327 original size:16 final size:16
Alignment explanation
Indices: 61399286--61399331 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
61399276 AAAATTGAAA
*
61399286 ATAA-ATATATAT-AT
1 ATAATATATAAATGAT
*
61399300 ATAATATGTAAATGAT
1 ATAATATATAAATGAT
*
61399316 ATATTATATAAATGAT
1 ATAATATATAAATGAT
61399332 TAAATATGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 4 0.15
15 6 0.23
16 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (16 bp):
ATAATATATAAATGAT
Found at i:61400116 original size:22 final size:23
Alignment explanation
Indices: 61400083--61400141 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
61400073 TGCCACTATT
61400083 TTGCTA-TAATTTTATTATT-ATG
1 TTGCTACT-ATTTTATTATTAATG
* *
61400105 TTGTTACTATTTTATTATTAATT
1 TTGCTACTATTTTATTATTAATG
61400128 TTGCTACTATTTTA
1 TTGCTACTATTTTA
61400142 GAGGCATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 16 0.50
23 16 0.50
ACGTcount: A:0.25, C:0.07, G:0.07, T:0.61
Consensus pattern (23 bp):
TTGCTACTATTTTATTATTAATG
Found at i:61402525 original size:2 final size:2
Alignment explanation
Indices: 61402518--61402550 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
61402508 GACCACAGAA
*
61402518 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
61402551 ACATTTTTGC
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:61414775 original size:11 final size:11
Alignment explanation
Indices: 61414761--61414797 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
61414751 AAAAACAAAA
*
61414761 AAAATTATTTT
1 AAAAGTATTTT
61414772 AAAAGTATTTT
1 AAAAGTATTTT
61414783 AAAAGTATTTT
1 AAAAGTATTTT
61414794 AAAA
1 AAAA
61414798 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.43
Consensus pattern (11 bp):
AAAAGTATTTT
Found at i:61415883 original size:2 final size:2
Alignment explanation
Indices: 61415876--61415918 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
61415866 TATTAATTGT
*
61415876 TA TA TA TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61415918 T
1 T
61415919 TTCGAGTGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:61416840 original size:27 final size:28
Alignment explanation
Indices: 61416791--61416859 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
61416781 AATAAAAAAA
*
61416791 TACCTAAATAT-TATAACTTTTTTTTATT
1 TACCAAAATATATATAAC-TTTTTTTATT
61416819 TACCAAAATATATATAA-TTTTTTTATT
1 TACCAAAATATATATAACTTTTTTTATT
61416846 TACCAAAATATATA
1 TACCAAAATATATA
61416860 AAAAAACAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 24 0.62
28 10 0.26
29 5 0.13
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (28 bp):
TACCAAAATATATATAACTTTTTTTATT
Found at i:61416872 original size:10 final size:10
Alignment explanation
Indices: 61416859--61416894 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
61416849 CAAAATATAT
*
61416859 AAAAAAACAA
1 AAAAAAAGAA
*
61416869 AAAAATAGAA
1 AAAAAAAGAA
61416879 AAAAAAAGAA
1 AAAAAAAGAA
61416889 AAAAAA
1 AAAAAA
61416895 CCTGAACTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.89, C:0.03, G:0.06, T:0.03
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:61416965 original size:27 final size:27
Alignment explanation
Indices: 61416935--61417001 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 27
61416925 AGGGAAGCAG
*
61416935 GTTGGCGGCACCAAACAAGGGATCCCT
1 GTTGGCGGCACCAAACAAGGAATCCCT
****
61416962 GTTGGCGGCACCAGTGGAGGAATCCCT
1 GTTGGCGGCACCAAACAAGGAATCCCT
61416989 GTTGGCGGCACCA
1 GTTGGCGGCACCA
61417002 GTCCTGCCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.21, C:0.28, G:0.34, T:0.16
Consensus pattern (27 bp):
GTTGGCGGCACCAAACAAGGAATCCCT
Found at i:61417805 original size:18 final size:17
Alignment explanation
Indices: 61417778--61417817 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 17
61417768 ATATATTTAC
61417778 AAAAATAAAGTATATAT
1 AAAAATAAAGTATATAT
61417795 AAAATATAAAGTATATAT
1 AAAA-ATAAAGTATATAT
61417813 AAAAA
1 AAAAA
61417818 AGTAAAAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.28
Consensus pattern (17 bp):
AAAAATAAAGTATATAT
Found at i:61417836 original size:13 final size:15
Alignment explanation
Indices: 61417814--61417845 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
61417804 AGTATATATA
61417814 AAAAAGT-AAAAAAC
1 AAAAAGTAAAAAAAC
61417828 AAAAA-TAAAAAAAC
1 AAAAAGTAAAAAAAC
61417842 AAAA
1 AAAA
61417846 CATACGTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 1 0.06
14 16 0.94
ACGTcount: A:0.84, C:0.06, G:0.03, T:0.06
Consensus pattern (15 bp):
AAAAAGTAAAAAAAC
Found at i:61417992 original size:3 final size:3
Alignment explanation
Indices: 61417978--61418043 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
61417968 AGAAAATATG
* * *
61417978 ATA ATA ATTA ATA ATA ATAA ATA AT- ATA ATA AAA ATA ATTA ATT TTA
1 ATA ATA A-TA ATA ATA AT-A ATA ATA ATA ATA ATA ATA A-TA ATA ATA
61418025 ATA ATA A-A ATA ATTA ATA A
1 ATA ATA ATA ATA A-TA ATA A
61418044 CAAGGAACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 4 0.08
3 35 0.69
4 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:61418018 original size:31 final size:32
Alignment explanation
Indices: 61417980--61418043 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 32
61417970 AAAATATGAT
61417980 AATAATTAA-TAATAAT-AAATAATATAATAAA
1 AATAATTAATTAATAATAAAATAAT-TAATAAA
61418011 AATAATTAATTTTAATAATAAAATAATTAATAA
1 AATAATTAA--TTAATAATAAAATAATTAATAA
61418044 CAAGGAACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 9 0.31
34 13 0.45
35 7 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (32 bp):
AATAATTAATTAATAATAAAATAATTAATAAA
Found at i:61418880 original size:22 final size:23
Alignment explanation
Indices: 61418849--61418893 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
61418839 GGAGGCGAAC
61418849 GTGCGCGGAG-GATCAGGCGCGAT
1 GTGCGCGGAGCGA-CAGGCGCGAT
*
61418872 GTGCG-GGAGCGACGGGCGCGAT
1 GTGCGCGGAGCGACAGGCGCGAT
61418894 ATTCGGGGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.16, C:0.22, G:0.51, T:0.11
Consensus pattern (23 bp):
GTGCGCGGAGCGACAGGCGCGAT
Found at i:61421951 original size:15 final size:15
Alignment explanation
Indices: 61421927--61421965 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
61421917 CAATAACCAC
*
61421927 AATAACTAAAACTAG
1 AATAATTAAAACTAG
*
61421942 AATAATT-AAATTAG
1 AATAATTAAAACTAG
61421956 AATAATTAAA
1 AATAATTAAA
61421966 TTGATACAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 13 0.62
15 8 0.38
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (15 bp):
AATAATTAAAACTAG
Found at i:61421958 original size:14 final size:14
Alignment explanation
Indices: 61421939--61421967 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
61421929 TAACTAAAAC
61421939 TAGAATAATTAAAT
1 TAGAATAATTAAAT
61421953 TAGAATAATTAAAT
1 TAGAATAATTAAAT
61421967 T
1 T
61421968 GATACAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (14 bp):
TAGAATAATTAAAT
Found at i:61424992 original size:27 final size:28
Alignment explanation
Indices: 61424956--61425013 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
61424946 TTGTTTTTTT
*
61424956 TTATATAT-TTTTG-TAAATATAAAAA-
1 TTATATATATTTTGATAAATAAAAAAAG
61424981 TTATATATATTTTGATAAATAAAAAAAG
1 TTATATATATTTTGATAAATAAAAAAAG
61425009 TTATA
1 TTATA
61425014 ACATTTTAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.28
26 5 0.17
27 11 0.38
28 5 0.17
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (28 bp):
TTATATATATTTTGATAAATAAAAAAAG
Found at i:61425019 original size:27 final size:27
Alignment explanation
Indices: 61424956--61425025 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
61424946 TTGTTTTTTT
* *
61424956 TTATATA-TTTTTG-TAAATATAAAAA
1 TTATATACATTTTGATAAATAAAAAAA
*
61424981 TTATATATATTTTGATAAATAAAAAAA
1 TTATATACATTTTGATAAATAAAAAAA
*
61425008 GTTATA-ACATTTTAATAA
1 -TTATATACATTTTGATAA
61425026 TTTTTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
25 7 0.18
26 5 0.13
27 21 0.55
28 5 0.13
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (27 bp):
TTATATACATTTTGATAAATAAAAAAA
Found at i:61428365 original size:32 final size:31
Alignment explanation
Indices: 61428301--61428367 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
61428291 TTTAAACTAT
*
61428301 AAAGTCAAGTTCAAGTACTAATTTGAACAAA
1 AAAGTCAAGTTCAAGTACTAATTGGAACAAA
** *
61428332 AAAGTCATTTTCAAGTAGCTAATTGGATAAAAA
1 AAAGTCAAGTTCAAGTA-CTAATTGGA-ACAAA
61428365 AAA
1 AAA
61428368 TTAGGTACCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 15 0.50
32 8 0.27
33 7 0.23
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.27
Consensus pattern (31 bp):
AAAGTCAAGTTCAAGTACTAATTGGAACAAA
Found at i:61453628 original size:27 final size:28
Alignment explanation
Indices: 61453598--61453651 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
61453588 AAATAAATAT
61453598 TTTTA-TTTTTATTTTAAAATACTTTTA
1 TTTTATTTTTTATTTTAAAATACTTTTA
*
61453625 TTTTATTTTTTATTTTAAAATATTTTT
1 TTTTATTTTTTATTTTAAAATACTTTT
61453652 TTGGTGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTATTTTTTATTTTAAAATACTTTTA
Found at i:61453634 original size:22 final size:22
Alignment explanation
Indices: 61453592--61453633 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
61453582 TTTAATAAAT
*
61453592 AAATATTTTTATTTTTATTTTA
1 AAATACTTTTATTTTTATTTTA
61453614 AAATACTTTTA-TTTTATTTT
1 AAATACTTTTATTTTTATTTT
61453634 TTATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
AAATACTTTTATTTTTATTTTA
Found at i:61454066 original size:14 final size:14
Alignment explanation
Indices: 61454047--61454077 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
61454037 AATAATACAA
61454047 TAAAAACATTAAAT
1 TAAAAACATTAAAT
*
61454061 TAAAAACATTACAT
1 TAAAAACATTAAAT
61454075 TAA
1 TAA
61454078 TATTACTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAAACATTAAAT
Found at i:61454893 original size:29 final size:30
Alignment explanation
Indices: 61454850--61454927 Score: 88
Period size: 31 Copynumber: 2.6 Consensus size: 30
61454840 TTTTAATCAC
* *
61454850 AATCAAAGTTTCATATGT-ATAATTGCAC-TA
1 AATCAAAG-TTCATATATGA-AACTGCACATA
*
61454880 AATTAAAGTTCATATATGAAACTGCACATTA
1 AATCAAAGTTCATATATGAAACTGCACA-TA
61454911 AATCAAAGTTCATATAT
1 AATCAAAGTTCATATAT
61454928 AATTTTGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 15 0.37
30 8 0.20
31 18 0.44
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.35
Consensus pattern (30 bp):
AATCAAAGTTCATATATGAAACTGCACATA
Found at i:61466310 original size:7 final size:7
Alignment explanation
Indices: 61466300--61466326 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
61466290 NAACCCCAAA
61466300 CCCTAAG
1 CCCTAAG
61466307 CCCTAAG
1 CCCTAAG
61466314 CCCTAAG
1 CCCTAAG
61466321 CCCTAA
1 CCCTAA
61466327 AACCCCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.44, G:0.11, T:0.15
Consensus pattern (7 bp):
CCCTAAG
Found at i:61466403 original size:7 final size:7
Alignment explanation
Indices: 61466386--61466456 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
61466376 AACACCAAAC
*
61466386 CCCTAAG
1 CCCTAAA
61466393 CCCTAAA
1 CCCTAAA
61466400 CCCTAAAAA
1 CCCT--AAA
*
61466409 CCCTACA
1 CCCTAAA
61466416 CCCTAAAAA
1 CCCT--AAA
61466425 CCCTAAA
1 CCCTAAA
*
61466432 CCCCAAA
1 CCCTAAA
61466439 CCCCTAAA
1 -CCCTAAA
**
61466447 TACTAAA
1 CCCTAAA
61466454 CCC
1 CCC
61466457 AAGCCAGGAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
7 31 0.62
8 6 0.12
9 13 0.26
ACGTcount: A:0.42, C:0.44, G:0.01, T:0.13
Consensus pattern (7 bp):
CCCTAAA
Found at i:61466418 original size:16 final size:16
Alignment explanation
Indices: 61466393--61466434 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
61466383 AACCCCTAAG
61466393 CCCTAAACCCTAAAAA
1 CCCTAAACCCTAAAAA
*
61466409 CCCTACACCCTAAAAA
1 CCCTAAACCCTAAAAA
61466425 CCCTAAACCC
1 CCCTAAACCC
61466435 CAAACCCCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.12
Consensus pattern (16 bp):
CCCTAAACCCTAAAAA
Found at i:61466441 original size:14 final size:14
Alignment explanation
Indices: 61466291--61466446 Score: 64
Period size: 14 Copynumber: 10.6 Consensus size: 14
61466281 NNNNNNNNNN
* *
61466291 AACCCCAAACCCTA
1 AACCCTAAACCCCA
* * *
61466305 AGCCCTAAGCCCTA
1 AACCCTAAACCCCA
*
61466319 AGCCCTAAAACCCCA
1 AACCCT-AAACCCCA
*
61466334 AACCCTAGACCCCA
1 AACCCTAAACCCCA
* * ***
61466348 GACCCCAGGTCCCA
1 AACCCTAAACCCCA
*
61466362 AACACC-AAACACCA
1 AAC-CCTAAACCCCA
61466376 AACACC-AAACCCCTA
1 AAC-CCTAAACCCC-A
* *
61466391 AGCCCTAAACCCTAAA
1 AACCCTAAACCC--CA
* *
61466407 AACCCTACACCCTAAA
1 AACCCTAAACCC--CA
61466423 AACCCTAAACCCCA
1 AACCCTAAACCCCA
61466437 AACCCCTAAA
1 AA-CCCTAAA
61466447 TACTAAACCC
Statistics
Matches: 112, Mismatches: 23, Indels: 13
0.76 0.16 0.09
Matches are distributed among these distances:
14 57 0.51
15 29 0.26
16 26 0.23
ACGTcount: A:0.41, C:0.46, G:0.05, T:0.08
Consensus pattern (14 bp):
AACCCTAAACCCCA
Found at i:61466515 original size:32 final size:32
Alignment explanation
Indices: 61466474--61466543 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
61466464 GATATGCAAA
* *
61466474 GAATAGAATAAATCC-AAACCGGGATATGCTTG
1 GAATAGAATAAA-CCTAAACCGGGATATCCGTG
* *
61466506 GAATGGAATAAACCTAAGCCGGGATATCCGTG
1 GAATAGAATAAACCTAAACCGGGATATCCGTG
61466538 GAATAG
1 GAATAG
61466544 GATATCCCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 2 0.06
32 30 0.94
ACGTcount: A:0.39, C:0.16, G:0.26, T:0.20
Consensus pattern (32 bp):
GAATAGAATAAACCTAAACCGGGATATCCGTG
Found at i:61476402 original size:31 final size:31
Alignment explanation
Indices: 61476367--61476500 Score: 216
Period size: 31 Copynumber: 4.3 Consensus size: 31
61476357 ACCCCTAATG
61476367 TGGGATATCCCAAACCGGGATAAGCGCAGAA
1 TGGGATATCCCAAACCGGGATAAGCGCAGAA
*
61476398 TGGGATATCCCAGACCGGGATAAGCGCAGAA
1 TGGGATATCCCAAACCGGGATAAGCGCAGAA
*
61476429 TGGGATATCCCAGACCGGGATAAGCGCAGAA
1 TGGGATATCCCAAACCGGGATAAGCGCAGAA
* *
61476460 TGGGATATCCTC-ATCAGGGATAAGCGCAGAA
1 TGGGATATCC-CAAACCGGGATAAGCGCAGAA
61476491 TGGGATATCC
1 TGGGATATCC
61476501 GGCCCGGGCT
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
31 97 0.99
32 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.31, T:0.16
Consensus pattern (31 bp):
TGGGATATCCCAAACCGGGATAAGCGCAGAA
Found at i:61476404 original size:16 final size:16
Alignment explanation
Indices: 61476383--61476497 Score: 92
Period size: 16 Copynumber: 7.4 Consensus size: 16
61476373 ATCCCAAACC
61476383 GGGATAAGCGCAGAAT
1 GGGATAAGCGCAGAAT
* * **
61476399 GGGAT-ATCCCAGACC
1 GGGATAAGCGCAGAAT
61476414 GGGATAAGCGCAGAAT
1 GGGATAAGCGCAGAAT
* * **
61476430 GGGAT-ATCCCAGACC
1 GGGATAAGCGCAGAAT
61476445 GGGATAAGCGCAGAAT
1 GGGATAAGCGCAGAAT
** * **
61476461 GGGATATCCTCATCA-
1 GGGATAAGCGCAGAAT
61476476 GGGATAAGCGCAGAAT
1 GGGATAAGCGCAGAAT
61476492 GGGATA
1 GGGATA
61476498 TCCGGCCCGG
Statistics
Matches: 70, Mismatches: 26, Indels: 6
0.69 0.25 0.06
Matches are distributed among these distances:
15 32 0.46
16 38 0.54
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.15
Consensus pattern (16 bp):
GGGATAAGCGCAGAAT
Found at i:61476538 original size:21 final size:21
Alignment explanation
Indices: 61476514--61476581 Score: 109
Period size: 21 Copynumber: 3.2 Consensus size: 21
61476504 CCGGGCTCAT
* *
61476514 AAAACAACAGAACCGGTCACC
1 AAAACAGCCGAACCGGTCACC
61476535 AAAACAGCCGAACCGGTCACC
1 AAAACAGCCGAACCGGTCACC
61476556 AAAACAGCCGAACCGGTCACC
1 AAAACAGCCGAACCGGTCACC
61476577 TAAAA
1 -AAAA
61476582 TTCTGAACCG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 40 0.91
22 4 0.09
ACGTcount: A:0.44, C:0.34, G:0.16, T:0.06
Consensus pattern (21 bp):
AAAACAGCCGAACCGGTCACC
Done.