Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 38 of 50
Found at i:16590988 original size:49 final size:47
Alignment explanation
Indices: 16590911--16591151 Score: 208
Period size: 49 Copynumber: 5.0 Consensus size: 47
16590901 GTTTAAATAT
16590911 TAATGATTAAATTGTAATAAAATATTAATATTTAAAGTATCAATTATTACTA
1 TAATGATTAAA-T-T-ATAAAATATTAATATTTAAA-TATCAATTATTA-TA
* * * * * *
16590963 TAATGACTAAATTATAAATTATTAATATTTAAAAATAAATAATCATAA
1 TAATGATTAAATTATAAAATATTAATATTTAAATATCAATTATTAT-A
* ** *
16591011 TAAT-ATTTAAATTAT-AAATA-AAATA-TT-AATAT-GTTTA-AATA
1 TAATGA-TTAAATTATAAAATATTAATATTTAAATATCAATTATTATA
16591052 TTAATGATTAAATTTGTAATAAAATATTAATATTTAAAGTATCAATTATTAATA
1 -TAATGATTAAA--T-T-ATAAAATATTAATATTTAAA-TATCAATTATT-ATA
16591106 TAATGATTAAATTATAAAATATTAATATTTAAATTATCAATTATTA
1 TAATGATTAAATTATAAAATATTAATATTTAAA-TATCAATTATTA
16591152 ATTTTTTAAA
Statistics
Matches: 154, Mismatches: 19, Indels: 36
0.74 0.09 0.17
Matches are distributed among these distances:
41 1 0.01
42 11 0.07
43 3 0.02
44 5 0.03
45 3 0.02
46 6 0.04
47 11 0.07
48 26 0.17
49 52 0.34
50 4 0.03
51 5 0.03
52 13 0.08
53 11 0.07
54 3 0.02
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (47 bp):
TAATGATTAAATTATAAAATATTAATATTTAAATATCAATTATTATA
Found at i:16591010 original size:142 final size:142
Alignment explanation
Indices: 16590690--16591138 Score: 722
Period size: 142 Copynumber: 3.2 Consensus size: 142
16590680 TAATATTTAG
* * *
16590690 ATTATAAATTATTAATATTTAAAAATTAATAATCATAATAACATTTAACTTATAAATAAAATATT
1 ATTATAAATTATTAATATTTAAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATT
* * * * * * * *
16590755 CATATTTTTAAATATTAATGAATAAAATATAAT-AAATGTTAATATTTTAATTATCAATTATTAA
66 AATATGTTTAAATATTAATGATTAAATTGTAATAAAATATTAATATTTAAAGTATCAATTATTAA
*
16590819 TAT-TTGAACTAA
131 TATAATG-ACTAA
*
16590831 ATTATAAATTATTAATAGTTAAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATT
1 ATTATAAATTATTAATATTTAAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATT
*
16590896 AATATGTTTAAATATTAATGATTAAATTGTAATAAAATATTAATATTTAAAGTATCAATTATTAC
66 AATATGTTTAAATATTAATGATTAAATTGTAATAAAATATTAATATTTAAAGTATCAATTATTAA
16590961 TATAATGACTAA
131 TATAATGACTAA
16590973 ATTATAAATTATTAATATTTAAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATT
1 ATTATAAATTATTAATATTTAAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATT
16591038 AATATGTTTAAATATTAATGATTAAATTTGTAATAAAATATTAATATTTAAAGTATCAATTATTA
66 AATATGTTTAAATATTAATGATTAAA-TTGTAATAAAATATTAATATTTAAAGTATCAATTATTA
*
16591103 ATATAATGATTAA
130 ATATAATGACTAA
*
16591116 ATTATAAAATATTAATATTTAAA
1 ATTATAAATTATTAATATTTAAA
16591139 TTATCAATTA
Statistics
Matches: 287, Mismatches: 18, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
141 89 0.31
142 125 0.44
143 73 0.25
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (142 bp):
ATTATAAATTATTAATATTTAAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATT
AATATGTTTAAATATTAATGATTAAATTGTAATAAAATATTAATATTTAAAGTATCAATTATTAA
TATAATGACTAA
Found at i:16591040 original size:26 final size:25
Alignment explanation
Indices: 16590976--16591042 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 25
16590966 TGACTAAATT
*
16590976 ATAAATTATTAATATTTAAAAATAA
1 ATAAAATATTAATATTTAAAAATAA
* * *
16591001 ATAATCATAATAATATTTAAATTATAA
1 ATAA-AATATTAATATTTAAA-AATAA
16591028 ATAAAATATTAATAT
1 ATAAAATATTAATAT
16591043 GTTTAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
25 4 0.12
26 22 0.65
27 8 0.24
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (25 bp):
ATAAAATATTAATATTTAAAAATAA
Found at i:16591050 original size:48 final size:46
Alignment explanation
Indices: 16590856--16591144 Score: 141
Period size: 49 Copynumber: 6.2 Consensus size: 46
16590846 TAGTTAAAAA
16590856 TAAATAATCATAATAATATTTAAATTATAAATAAAATATTAATATGTT
1 TAAATAATCATAATAATA-TTAAATTATAAATAAAATATTAATAT-TT
* *
16590904 TAAAT-AT--TAAT--GATTAAATTGT-AATAAAATATTAATA-TT
1 TAAATAATCATAATAATATTAAATTATAAATAAAATATTAATATTT
* * * *
16590943 TAAAGT-ATCA-ATTATTACTATAATGACTAAATTATAAATTATTAATATTT
1 TAAA-TAATCATAATAATATTA-AATTA-TAAA-TA-AAA-TATTAATATTT
16590993 AAAAATAAATAATCATAATAATATTTAAATTATAAATAAAATATTAATATGTT
1 -----TAAATAATCATAATAATA-TTAAATTATAAATAAAATATTAATAT-TT
* *
16591046 TAAAT-AT--TAAT--GATTAAATT-TGTAATAAAATATTAATA-TT
1 TAAATAATCATAATAATATTAAATTAT-AAATAAAATATTAATATTT
*
16591086 TAAAGT-ATCAATTATTAATA-TAATGATTA-AATTATAAAATATTAATA-TT
1 TAAA-TAATC-A-TAATAATATTAA--ATTATAA--ATAAAATATTAATATTT
*
16591135 TAAATTATCA
1 TAAATAATCA
16591145 ATTATTAATT
Statistics
Matches: 190, Mismatches: 16, Indels: 70
0.69 0.06 0.25
Matches are distributed among these distances:
39 6 0.03
40 9 0.05
41 21 0.11
42 30 0.16
43 5 0.03
44 3 0.02
45 12 0.06
46 5 0.03
47 8 0.04
48 18 0.09
49 31 0.16
50 2 0.01
52 9 0.05
53 5 0.03
54 3 0.02
55 12 0.06
56 9 0.05
57 2 0.01
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.42
Consensus pattern (46 bp):
TAAATAATCATAATAATATTAAATTATAAATAAAATATTAATATTT
Found at i:16591146 original size:192 final size:193
Alignment explanation
Indices: 16590906--16591328 Score: 543
Period size: 192 Copynumber: 2.2 Consensus size: 193
16590896 AATATGTTTA
* * *
16590906 AATATTAATGATTAAATTGTAATAAAATATTAATATTTAAAGTATCAATTATTACTATAATGACT
1 AATATTAATGATTAAA-T-T-ATAAAATATTAATATTTAAAGTATCAATTATTAATATAATAAAT
* ** *
16590971 AAATTATAAAT-TATTAATATTTAAAA-ATAAATAATCATAATAATATTTAAATTATAAATAAAA
63 AAATTATAAATAT-TTAAAAAATAAAATAAAAATAATCATAATAATATTTAAATTAT-AATAAAA
* *
16591034 TATTAATATGTTTA-AATATTAATGATTAAATT-TGTAATAAAATATTAATATTTAAAGTATCAA
126 TATTAATAT-TTTATAATATTAATGATTAAATTAT-AAATAAAATAATAATATTTAAAGTATCAA
16591097 TTATT
189 TTATT
* * **
16591102 AATA-TAATGATTAAATTATAAAATATTAATATTTAAATTATCAATTATTAATTTTTTAAATAAA
1 AATATTAATGATTAAATTATAAAATATTAATATTTAAAGTATCAATTATTAATATAATAAATAAA
* *
16591166 TTATAAATATTTAAAAAATAAAATAAAAATAATCATAATAGTATTTAAATTATATTAAAATATTA
66 TTATAAATATTTAAAAAATAAAATAAAAATAATCATAATAATATTTAAATTATAATAAAATATTA
* * *
16591231 ATATTTTATAATATTAATTATTAAATTATAAATAAAATAATATTATTTAAATTATCAATTATT
131 ATATTTTATAATATTAATGATTAAATTATAAATAAAATAATAATATTTAAAGTATCAATTATT
* ** *
16591294 TATATTTGTGA-TAAATTATAAATTATTAATATTTA
1 AATATTAATGATTAAATTATAAAATATTAATATTTA
16591329 GAAAATAAAA
Statistics
Matches: 200, Mismatches: 22, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
191 4 0.02
192 146 0.73
193 34 0.17
194 1 0.00
195 11 0.05
196 4 0.02
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (193 bp):
AATATTAATGATTAAATTATAAAATATTAATATTTAAAGTATCAATTATTAATATAATAAATAAA
TTATAAATATTTAAAAAATAAAATAAAAATAATCATAATAATATTTAAATTATAATAAAATATTA
ATATTTTATAATATTAATGATTAAATTATAAATAAAATAATAATATTTAAAGTATCAATTATT
Found at i:16591166 original size:49 final size:49
Alignment explanation
Indices: 16591070--16591176 Score: 153
Period size: 49 Copynumber: 2.2 Consensus size: 49
16591060 TAAATTTGTA
* *
16591070 ATAAAATATTAATATTTAAAGTATCAATTATTAATATAATGATTAAATT
1 ATAAAATATTAATATTTAAAGTATCAATTATTAATATAATAAATAAATT
* * **
16591119 ATAAAATATTAATATTTAAATTATCAATTATTAATTTTTTAAATAAATT
1 ATAAAATATTAATATTTAAAGTATCAATTATTAATATAATAAATAAATT
16591168 AT-AAATATT
1 ATAAAATATT
16591177 TAAAAAATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
48 7 0.13
49 45 0.87
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (49 bp):
ATAAAATATTAATATTTAAAGTATCAATTATTAATATAATAAATAAATT
Found at i:16591278 original size:143 final size:148
Alignment explanation
Indices: 16591119--16591451 Score: 444
Period size: 155 Copynumber: 2.2 Consensus size: 148
16591109 TGATTAAATT
*
16591119 ATAAAATATTAATATTTAAATTATCAATTATTAATTT-T-TTAA-ATAAATTATAAATATTT-AA
1 ATAAAATATTAATATTTAAATTATCAATTATTAATTTGTATAAATATAAATTATAAATATTTAAA
* * * *
16591180 -AAAATAAAATAAAAATAATCATAATAGTATTTAAATTATATTAAAATATTAATATTTTATAATA
66 TAAAATAAAATAAAAACAATCATAATAATATTTAAATTATAATAAAATATTAATATTATATAAT-
*
16591244 T-TAATTATTAAATTATAA
130 TCTAATGATTAAATTATAA
* * *
16591262 ATAAAATAATATTATTTAAATTATCAATTATTTATATTTGTGATAAATTATAAATTATTAATATT
1 ATAAAATATTAATATTTAAATTATCAATTA-TTA-ATTTGT-ATAAA-TATAAATTATAAATATT
*
16591327 TAGAAAATAAAATAAAATAAAAACAATCATAATAATATTTAAATTATAATAAAATTTTAATATTA
62 T---AAATAAAATAAAATAAAAACAATCATAATAATATTTAAATTATAATAAAATATTAATATTA
16591392 TATAATTCTAATGATTAAATTATAA
124 TATAATTCTAATGATTAAATTATAA
* *
16591417 ATAAAATATTAACATTTAAATTATAAATTATTAAT
1 ATAAAATATTAATATTTAAATTATCAATTATTAAT
16591452 ATTTAAAAAA
Statistics
Matches: 163, Mismatches: 14, Indels: 16
0.84 0.07 0.08
Matches are distributed among these distances:
143 28 0.17
144 3 0.02
145 4 0.02
146 1 0.01
148 3 0.02
150 16 0.10
153 2 0.01
154 6 0.04
155 100 0.61
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (148 bp):
ATAAAATATTAATATTTAAATTATCAATTATTAATTTGTATAAATATAAATTATAAATATTTAAA
TAAAATAAAATAAAAACAATCATAATAATATTTAAATTATAATAAAATATTAATATTATATAATT
CTAATGATTAAATTATAA
Found at i:16591291 original size:41 final size:41
Alignment explanation
Indices: 16591210--16591293 Score: 100
Period size: 41 Copynumber: 2.0 Consensus size: 41
16591200 ATAATAGTAT
* * *
16591210 TTAAATTATATTAAAATATTAATATTTTATAATATTAATTA
1 TTAAATTATAATAAAATAATAATATTTTATAATATCAATTA
*
16591251 TTAAATTATAAATAAAATAATATTA-TTTA-AATTATCAATTA
1 TTAAATTAT-AATAAAATAATAATATTTTATAA-TATCAATTA
16591292 TT
1 TT
16591294 TATATTTGTG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.05
41 23 0.62
42 12 0.32
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (41 bp):
TTAAATTATAATAAAATAATAATATTTTATAATATCAATTA
Found at i:16591375 original size:17 final size:19
Alignment explanation
Indices: 16591355--16591397 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
16591345 AAAAACAATC
16591355 ATAATAATA-TTTAA-ATT
1 ATAATAATATTTTAATATT
*
16591372 ATAATAAAATTTTAATATT
1 ATAATAATATTTTAATATT
16591391 AT-ATAAT
1 ATAATAAT
16591398 TCTAATGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 8 0.36
18 9 0.41
19 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATAATATTTTAATATT
Found at i:16591448 original size:22 final size:22
Alignment explanation
Indices: 16591417--16591468 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
16591407 TAAATTATAA
16591417 ATAAAATATTAACATTTAAATT
1 ATAAAATATTAACATTTAAATT
* * **
16591439 ATAAATTATTAATATTTAAAAA
1 ATAAAATATTAACATTTAAATT
16591461 ATAAAATA
1 ATAAAATA
16591469 AACAATTATA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAATATTAACATTTAAATT
Found at i:16592652 original size:2 final size:2
Alignment explanation
Indices: 16592645--16592679 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
16592635 TAATTAATTA
16592645 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
16592680 AATCCAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16602043 original size:3 final size:3
Alignment explanation
Indices: 16602030--16602062 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
16602020 TCCCTTAGTC
16602030 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TA
16602063 GTAGGAGAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16602534 original size:30 final size:30
Alignment explanation
Indices: 16602488--16602560 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
16602478 AAAAATTTTA
*
16602488 AATAAATTTTTAT-TTTTT-ATTATG-TTT
1 AATAAATTTTTATATTTTTAATTATGATCT
*
16602515 AATCAAATTTTTATATTTTTAATTTTGAATCT
1 AAT-AAATTTTTATATTTTTAATTATG-ATCT
16602547 AATAAATTTTTATA
1 AATAAATTTTTATA
16602561 ACGTTATTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
27 3 0.08
28 10 0.26
29 5 0.13
30 5 0.13
31 11 0.28
32 5 0.13
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (30 bp):
AATAAATTTTTATATTTTTAATTATGATCT
Found at i:16602545 original size:27 final size:25
Alignment explanation
Indices: 16602481--16602545 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 25
16602471 TTATTCCAAA
16602481 AATTTTAAAT-AAATTTTTATTTTTT
1 AATTTT-AATCAAATTTTTATTTTTT
16602506 ATTATGTTTAATCAAATTTTTATATTTTT
1 A--AT-TTTAATCAAATTTTTAT-TTTTT
16602535 AATTTTGAATC
1 AATTTT-AATC
16602546 TAATAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
25 1 0.03
26 3 0.09
27 11 0.32
28 13 0.38
29 6 0.18
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (25 bp):
AATTTTAATCAAATTTTTATTTTTT
Found at i:16603386 original size:30 final size:30
Alignment explanation
Indices: 16603330--16603387 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
16603320 GTTTTTTTAT
*
16603330 TTTTAATTTGAGCTAAATAAATCTTTATAC
1 TTTTAATTTGAGCTAAATAAACCTTTATAC
* *
16603360 TTTTACTTTGAGCTAAATAAGCCTTTAT
1 TTTTAATTTGAGCTAAATAAACCTTTAT
16603388 GGTTAATAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.47
Consensus pattern (30 bp):
TTTTAATTTGAGCTAAATAAACCTTTATAC
Found at i:16606413 original size:61 final size:59
Alignment explanation
Indices: 16606277--16606441 Score: 195
Period size: 61 Copynumber: 2.7 Consensus size: 59
16606267 CATCGTCATT
* * * ** *
16606277 TACTCGTGGGAACTCCCCACGTCACCAAATATAAATCGGGACTTCAAGTCTTTTTTTATC
1 TACTCGTGGG-ACTCCCCACGCCACCAAATATAAGTCGGGGCTTCAAGTCCCTTTTTACC
* *
16606337 TACTCGTGGCACTCCCCATGCCACCAAATATCAAGTCGGGGCTTCAAGTCCCCTTTTTACC
1 TACTCGTGGGACTCCCCACGCCACCAAATAT-AAGTCGGGGCTTCAAGT-CCCTTTTTACC
* * *
16606398 TATTCGTGGGACTCCCCACACCACCAAATATTATGTCGGGGCTT
1 TACTCGTGGGACTCCCCACGCCACCAAATA-TAAGTCGGGGCTT
16606442 TAGGTTCCCT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
59 19 0.21
60 24 0.27
61 45 0.51
62 1 0.01
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (59 bp):
TACTCGTGGGACTCCCCACGCCACCAAATATAAGTCGGGGCTTCAAGTCCCTTTTTACC
Found at i:16615322 original size:8 final size:7
Alignment explanation
Indices: 16615298--16615352 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 7
16615288 ATCAACCAAA
16615298 AATAAAT
1 AATAAAT
16615305 AA-AAAT
1 AATAAAT
16615311 AATAACAT
1 AATAA-AT
16615319 AAT--AT
1 AATAAAT
16615324 AATAAA-
1 AATAAAT
16615330 AATAAA-
1 AATAAAT
16615336 AATAAAT
1 AATAAAT
16615343 AAATAAAT
1 -AATAAAT
16615351 AA
1 AA
16615353 GAAAAAAAAG
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
5 5 0.12
6 18 0.43
7 7 0.17
8 12 0.29
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (7 bp):
AATAAAT
Found at i:16615336 original size:28 final size:27
Alignment explanation
Indices: 16615301--16615358 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 27
16615291 AACCAAAAAT
*
16615301 AAATAAAAAT-AATAACATAATATAATAA
1 AAATAAAAATAAATAA-ATAA-ATAAGAA
16615329 AAATAAAAATAAATAAATAAATAAGAA
1 AAATAAAAATAAATAAATAAATAAGAA
16615356 AAA
1 AAA
16615359 AAAGAAAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 9 0.32
28 14 0.50
29 5 0.18
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.21
Consensus pattern (27 bp):
AAATAAAAATAAATAAATAAATAAGAA
Found at i:16615359 original size:28 final size:28
Alignment explanation
Indices: 16615295--16615359 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
16615285 AAAATCAACC
16615295 AAAAATAAATAAAAATAATAACATAATAT
1 AAAAA-AAATAAAAATAATAACATAATAT
*
16615324 AATAAAAATAAAAATAAATAA-ATAA-AT
1 AAAAAAAATAAAAAT-AATAACATAATAT
16615351 AAGAAAAAA
1 AA-AAAAAA
16615360 AAGAAAACAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 4 0.12
28 19 0.59
29 9 0.28
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.20
Consensus pattern (28 bp):
AAAAAAAATAAAAATAATAACATAATAT
Found at i:16616110 original size:32 final size:32
Alignment explanation
Indices: 16616050--16616110 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
16616040 ATAAGGAAGG
*
16616050 AAAAGAAAAAGAGAGAGAATGAAGGAAAAGAA
1 AAAAGAAAAAGAGAGAGAATGAAAGAAAAGAA
* *
16616082 AAAAGAAAAAGGGGGAGAA-GAAAAGAAAA
1 AAAAGAAAAAGAGAGAGAATG-AAAGAAAA
16616111 AGAGCGACGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 1 0.04
32 24 0.96
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (32 bp):
AAAAGAAAAAGAGAGAGAATGAAAGAAAAGAA
Found at i:16631414 original size:24 final size:24
Alignment explanation
Indices: 16631382--16631484 Score: 68
Period size: 24 Copynumber: 4.4 Consensus size: 24
16631372 CCATGATGTT
16631382 ACAAGCCATGTACAAAAACCTATG
1 ACAAGCCATGTACAAAAACCTATG
** * * *
16631406 ACAAGCCA--TA-ATTAGCGTATT
1 ACAAGCCATGTACAAAAACCTATG
* ** ** *
16631427 ACACGTTATGTACAAAAATATGTG
1 ACAAGCCATGTACAAAAACCTATG
*
16631451 ACACGCCATGTACAAAAACCTATG
1 ACAAGCCATGTACAAAAACCTATG
*
16631475 ACAAGTCATG
1 ACAAGCCATG
16631485 GTTAGCATGT
Statistics
Matches: 54, Mismatches: 22, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
21 11 0.20
22 2 0.04
23 2 0.04
24 39 0.72
ACGTcount: A:0.42, C:0.21, G:0.15, T:0.22
Consensus pattern (24 bp):
ACAAGCCATGTACAAAAACCTATG
Found at i:16631498 original size:69 final size:69
Alignment explanation
Indices: 16631377--16631529 Score: 216
Period size: 69 Copynumber: 2.2 Consensus size: 69
16631367 AATTACCATG
* * * *
16631377 ATGTTACAAGCCATGTACAAAAACCTATGACAAGCCATAATTAGCGTATTACACGTTATGTACAA
1 ATGTGACAAGCCATGTACAAAAACCTATGACAAGCCATAATTAGCATATTACACGCTATATACAA
16631442 AAAT
66 AAAT
* * ** *
16631446 ATGTGACACGCCATGTACAAAAACCTATGACAAGTCATGGTTAGCATGTTACACGCTATATACAA
1 ATGTGACAAGCCATGTACAAAAACCTATGACAAGCCATAATTAGCATATTACACGCTATATACAA
16631511 AAAT
66 AAAT
*
16631515 ATGTGACAAGTCATG
1 ATGTGACAAGCCATG
16631530 ATTAGCTTGT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.25
Consensus pattern (69 bp):
ATGTGACAAGCCATGTACAAAAACCTATGACAAGCCATAATTAGCATATTACACGCTATATACAA
AAAT
Found at i:16631522 original size:45 final size:45
Alignment explanation
Indices: 16631446--16631574 Score: 161
Period size: 45 Copynumber: 2.9 Consensus size: 45
16631436 GTACAAAAAT
* * ** * *
16631446 ATGTGACACGCCATGTACAAAAACCTATGACAAGTCATGGTTAGC
1 ATGTTACACGCTATGTACAAAAATATGTGACAAGTCATGATTAGC
*
16631491 ATGTTACACGCTATATACAAAAATATGTGACAAGTCATGATTAGC
1 ATGTTACACGCTATGTACAAAAATATGTGACAAGTCATGATTAGC
* *
16631536 TTGTTACATG-TCATGTACAAAAATATGTGACAAGTCATG
1 ATGTTACACGCT-ATGTACAAAAATATGTGACAAGTCATG
16631575 TACAAAAACC
Statistics
Matches: 73, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
44 1 0.01
45 72 0.99
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (45 bp):
ATGTTACACGCTATGTACAAAAATATGTGACAAGTCATGATTAGC
Found at i:16631577 original size:24 final size:24
Alignment explanation
Indices: 16631506--16631582 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 24
16631496 ACACGCTATA
16631506 TACAAAAATATGTGACAAGTCATG
1 TACAAAAATATGTGACAAGTCATG
** ** * *
16631530 -A-TTAGCT-TGTTACATGTCATG
1 TACAAAAATATGTGACAAGTCATG
16631551 TACAAAAATATGTGACAAGTCATG
1 TACAAAAATATGTGACAAGTCATG
16631575 TACAAAAA
1 TACAAAAA
16631583 CCTGTAACAA
Statistics
Matches: 38, Mismatches: 12, Indels: 6
0.68 0.21 0.11
Matches are distributed among these distances:
21 12 0.32
22 3 0.08
23 3 0.08
24 20 0.53
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.29
Consensus pattern (24 bp):
TACAAAAATATGTGACAAGTCATG
Found at i:16631577 original size:114 final size:114
Alignment explanation
Indices: 16631377--16631684 Score: 395
Period size: 114 Copynumber: 2.7 Consensus size: 114
16631367 AATTACCATG
* * * * *
16631377 ATGTTACAAGCCATGTACAAAAACCTATGACAAGCCATAATTAGCGTATTACACGTTATGTACAA
1 ATGTTACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAGCGTGTTACACGTCATGTACAA
* *
16631442 AAATATGTGACACGCCATGTACAAAAACCTATGACAAG-TCATGGTTAGC
66 AAATATGTGACAAGCCATGTACAAAAACCTATAACAAGAT-ATGGTTAGC
* * ** * * *
16631491 ATGTTACACGCTATATACAAAAATATGTGACAAGTCATGATTAGCTTGTTACATGTCATGTACAA
1 ATGTTACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAGCGTGTTACACGTCATGTACAA
* *
16631556 AAATATGTGACAAGTCATGTACAAAAACCTGTAACAAGATATGGTTAGC
66 AAATATGTGACAAGCCATGTACAAAAACCTATAACAAGATATGGTTAGC
* * * * *
16631605 TTGTTACACGCCATGTACAAAAACCTGTAACAAACCATGGTTAGCGTGTTACACG-CTATATACA
1 ATGTTACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAGCGTGTTACACGTC-ATGTACA
16631669 AAAATATGTGACAAGC
65 AAAATATGTGACAAGC
16631685 TATGGTTAGC
Statistics
Matches: 163, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
113 1 0.01
114 161 0.99
115 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (114 bp):
ATGTTACACGCCATGTACAAAAACCTGTGACAAGCCATGATTAGCGTGTTACACGTCATGTACAA
AAATATGTGACAAGCCATGTACAAAAACCTATAACAAGATATGGTTAGC
Found at i:16631592 original size:24 final size:24
Alignment explanation
Indices: 16631545--16631593 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
16631535 CTTGTTACAT
* *
16631545 GTCATGTACAAAAATATGTGACAA
1 GTCATGTACAAAAACATGTAACAA
*
16631569 GTCATGTACAAAAACCTGTAACAA
1 GTCATGTACAAAAACATGTAACAA
16631593 G
1 G
16631594 ATATGGTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.22
Consensus pattern (24 bp):
GTCATGTACAAAAACATGTAACAA
Found at i:16631733 original size:90 final size:90
Alignment explanation
Indices: 16631575--16631738 Score: 247
Period size: 90 Copynumber: 1.8 Consensus size: 90
16631565 ACAAGTCATG
* *
16631575 TACAAAAACCTGTAACAAGATATGGTTAGCTTGTTACACGCCATGTACAAAAACCTGTAACAAAC
1 TACAAAAACATGTAACAAGATATGGTTAGCTTGTTACACGCCATATACAAAAACCTGTAACAAAC
*
16631640 CATGGTTAGCGTGTTACACGCTATA
66 CATGATTAGCGTGTTACACGCTATA
* * * * * *
16631665 TACAAAAATATGTGACAAGCTATGGTTAGCTTGTTACACGTCATATACAAAAACCTGTGACAAGC
1 TACAAAAACATGTAACAAGATATGGTTAGCTTGTTACACGCCATATACAAAAACCTGTAACAAAC
16631730 CATGATTAG
66 CATGATTAG
16631739 ATTGTTACGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
90 65 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (90 bp):
TACAAAAACATGTAACAAGATATGGTTAGCTTGTTACACGCCATATACAAAAACCTGTAACAAAC
CATGATTAGCGTGTTACACGCTATA
Found at i:16631762 original size:45 final size:45
Alignment explanation
Indices: 16631575--16631753 Score: 223
Period size: 45 Copynumber: 4.0 Consensus size: 45
16631565 ACAAGTCATG
** *
16631575 TACAAAAACCTGTAACAAGATATGGTTAGCTTGTTACACGCCATG
1 TACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATA
* * *
16631620 TACAAAAACCTGTAACAAACCATGGTTAGCGTGTTACACGCTATA
1 TACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATA
** * * *
16631665 TACAAAAATATGTGACAAGCTATGGTTAGCTTGTTACACGTCATA
1 TACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATA
* * * *
16631710 TACAAAAACCTGTGACAAGCCATGATTAGATTGTTACGCGCCAT
1 TACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCAT
16631754 GTTGAAAAAA
Statistics
Matches: 113, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 113 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (45 bp):
TACAAAAACCTGTAACAAGCCATGGTTAGCTTGTTACACGCCATA
Found at i:16631807 original size:26 final size:26
Alignment explanation
Indices: 16631772--16631822 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
16631762 AAAAATATTA
* *
16631772 TTGTTGCACGTCATGGTT-AAAAAAAG
1 TTGTTACACGCCAT-GTTGAAAAAAAG
16631798 TTGTTACACGCCATGTTGAAAAAAA
1 TTGTTACACGCCATGTTGAAAAAAA
16631823 AAATTATTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.29
Consensus pattern (26 bp):
TTGTTACACGCCATGTTGAAAAAAAG
Found at i:16631861 original size:29 final size:29
Alignment explanation
Indices: 16631761--16631868 Score: 107
Period size: 29 Copynumber: 3.7 Consensus size: 29
16631751 CATGTTGAAA
* *
16631761 AAAAAATATTATTGTTGCACGTCATGGTT-
1 AAAAAATATTGTTGTTACACGTCAT-GTTG
*
16631790 AAAAAA-A--GTTGTTACACGCCATGTTG
1 AAAAAATATTGTTGTTACACGTCATGTTG
16631816 AAAAAAAAAATTATTGTTGTTACACGTCATGTTG
1 ----AAAAAA-TATTGTTGTTACACGTCATGTTG
16631850 AAAAAATATTGTTGTTACA
1 AAAAAATATTGTTGTTACA
16631869 TGACATATTC
Statistics
Matches: 66, Mismatches: 4, Indels: 18
0.75 0.05 0.20
Matches are distributed among these distances:
25 3 0.05
26 12 0.18
28 1 0.02
29 19 0.29
30 12 0.18
32 1 0.02
34 18 0.27
ACGTcount: A:0.40, C:0.10, G:0.16, T:0.34
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACACGTCATGTTG
Found at i:16631862 original size:60 final size:57
Alignment explanation
Indices: 16631739--16631862 Score: 171
Period size: 58 Copynumber: 2.1 Consensus size: 57
16631729 CCATGATTAG
*
16631739 ATTGTTACGCGCCATGTTGAAAAAAAAATATTATTGTTGCACGTCATGGTTAAAAAA
1 ATTGTTACACGCCATGTTGAAAAAAAAATATTATTGTTGCACGTCATGGTTAAAAAA
16631796 AGTTGTTACACGCCATGTTGAAAAAAAAA-ATTATTGTTGTTACACGTCAT-GTTGAAAAAA
1 A-TTGTTACACGCCATGTTGAAAAAAAAATATTATTGTTG---CACGTCATGGTT-AAAAAA
16631856 TATTGTT
1 -ATTGTT
16631863 GTTACATGAC
Statistics
Matches: 60, Mismatches: 1, Indels: 9
0.86 0.01 0.13
Matches are distributed among these distances:
57 11 0.18
58 26 0.43
59 3 0.05
60 19 0.32
61 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (57 bp):
ATTGTTACACGCCATGTTGAAAAAAAAATATTATTGTTGCACGTCATGGTTAAAAAA
Found at i:16631882 original size:29 final size:29
Alignment explanation
Indices: 16631820--16631896 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 29
16631810 ATGTTGAAAA
* * *
16631820 AAAAAATTATTGTTGTTACACGTCATGTTG
1 AAAAAA-TATTGTTGTTACACGACATATTC
*
16631850 AAAAAATATTGTTGTTACATGACATATTC
1 AAAAAATATTGTTGTTACACGACATATTC
*
16631879 -AAAAACATT-TTGTTACAC
1 AAAAAATATTGTTGTTACAC
16631897 TTTAATGCCT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
27 8 0.20
28 8 0.20
29 19 0.46
30 6 0.15
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (29 bp):
AAAAAATATTGTTGTTACACGACATATTC
Found at i:16632641 original size:42 final size:42
Alignment explanation
Indices: 16632594--16632677 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
16632584 AAAACCATAC
16632594 CTCCTACCTTTGAATCATCGTGGTTGTTTAATGCAAAGTTAT
1 CTCCTACCTTTGAATCATCGTGGTTGTTTAATGCAAAGTTAT
*
16632636 CTCCTACCTTTGAATTATCGTGGTTGTTTAATGCAAAGTTAT
1 CTCCTACCTTTGAATCATCGTGGTTGTTTAATGCAAAGTTAT
16632678 GTACCACATA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.17, T:0.42
Consensus pattern (42 bp):
CTCCTACCTTTGAATCATCGTGGTTGTTTAATGCAAAGTTAT
Found at i:16651952 original size:33 final size:33
Alignment explanation
Indices: 16651868--16651958 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 33
16651858 TCATTTAATT
* * **
16651868 ATATT-ATCATGTTATATTATTATCAATTATGGT
1 ATATTAAT-ATGTTATATTATCATCAAATATGAC
* *
16651901 ATGTTAATATGTCATATTATCATCAAATATGAC
1 ATATTAATATGTTATATTATCATCAAATATGAC
* *
16651934 ATATTAATATGTTTTATTAACATCA
1 ATATTAATATGTTATATTATCATCA
16651959 CATAATATAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
33 45 0.96
34 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (33 bp):
ATATTAATATGTTATATTATCATCAAATATGAC
Found at i:16652941 original size:18 final size:18
Alignment explanation
Indices: 16652918--16652954 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
16652908 TTTGAAAAAC
16652918 TTTTAAAAAATAATATTT
1 TTTTAAAAAATAATATTT
16652936 TTTTAAAAAATAATATTT
1 TTTTAAAAAATAATATTT
16652954 T
1 T
16652955 CTAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTTAAAAAATAATATTT
Found at i:16652947 original size:15 final size:16
Alignment explanation
Indices: 16652924--16652970 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
16652914 AAACTTTTAA
*
16652924 AAAATAATATTTTTTT
1 AAAATAATATTTTTCT
16652940 AAAA-AATAATATTTTCT
1 AAAATAAT-AT-TTTTCT
*
16652957 AAAATAAAATTTTT
1 AAAATAATATTTTT
16652971 AAAAAAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 11 0.42
18 2 0.08
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATAATATTTTTCT
Found at i:16655814 original size:22 final size:21
Alignment explanation
Indices: 16655776--16655832 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 21
16655766 AAATAATTGA
*
16655776 TTAAAATATTTTTTTATTAGTT
1 TTAAAATATTTTATTA-TAGTT
*
16655798 TTAAAA-ATTATTATTATATTT
1 TTAAAATATT-TTATTATAGTT
*
16655819 TTAAATAAATTTTA
1 TTAAA-ATATTTTA
16655833 AAGATGTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
21 12 0.40
22 15 0.50
23 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTAAAATATTTTATTATAGTT
Found at i:16660438 original size:18 final size:18
Alignment explanation
Indices: 16660383--16660438 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
16660373 ACAAGTATAC
* *
16660383 ATCCACTTTTGGTGGGTG
1 ATCCACTTATGGTGGGTT
* *
16660401 ATCCACATATGATGGGTT
1 ATCCACTTATGGTGGGTT
* *
16660419 ATCCACTTCTGGTGGATT
1 ATCCACTTATGGTGGGTT
16660437 AT
1 AT
16660439 ACATTTTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (18 bp):
ATCCACTTATGGTGGGTT
Found at i:16661167 original size:22 final size:23
Alignment explanation
Indices: 16661124--16661169 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
16661114 TGTTATGAAA
*
16661124 ATAACTTAAAAGAACAAATAAAG
1 ATAACTGAAAAGAACAAATAAAG
*
16661147 ATAACTGAAAA-AACAATTAAAG
1 ATAACTGAAAAGAACAAATAAAG
16661169 A
1 A
16661170 GAAGAAAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.65, C:0.09, G:0.09, T:0.17
Consensus pattern (23 bp):
ATAACTGAAAAGAACAAATAAAG
Found at i:16665366 original size:15 final size:15
Alignment explanation
Indices: 16665325--16665367 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
16665315 GAAAGAGGAA
*
16665325 AAAGAAGAAAATAAAG
1 AAAGTAGAAAA-AAAG
* *
16665341 AAAATAAAAAAAAAG
1 AAAGTAGAAAAAAAG
16665356 AAAGTAGAAAAA
1 AAAGTAGAAAAA
16665368 CAAAACAAAG
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.07
Consensus pattern (15 bp):
AAAGTAGAAAAAAAG
Found at i:16667498 original size:108 final size:108
Alignment explanation
Indices: 16667384--16667589 Score: 310
Period size: 108 Copynumber: 1.9 Consensus size: 108
16667374 AGAAATTCTG
** * * *
16667384 AGTAAATTTAAATAAAA-AGTAAATTGGGTAAGAGTTGAATAATTTTA-AAAGAATGTTTATTTG
1 AGTAAATTTAAATAAAAGA-TAAATTAAGTAAAAGTTGAATAATTTCATAAA-AATGTGTATTTG
*
16667447 TAAATTGTGAAAGTTGTAACTAAA-CTAACATATTTTACTAATTTT
64 TAAATTGTGAAAATTGTAACTAAATCT-ACATATTTTACTAATTTT
16667492 AGTAAATTTAAATAAAAGATAAATTAAGTAAAAGTTGAATAATTTCATAAAAATGTGTATTTGTA
1 AGTAAATTTAAATAAAAGATAAATTAAGTAAAAGTTGAATAATTTCATAAAAATGTGTATTTGTA
16667557 AATTGTGAAAATTGTAACTAAATCTACATATTT
66 AATTGTGAAAATTGTAACTAAATCTACATATTT
16667590 AGTTATTTTA
Statistics
Matches: 89, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
108 83 0.93
109 6 0.07
ACGTcount: A:0.46, C:0.04, G:0.13, T:0.38
Consensus pattern (108 bp):
AGTAAATTTAAATAAAAGATAAATTAAGTAAAAGTTGAATAATTTCATAAAAATGTGTATTTGTA
AATTGTGAAAATTGTAACTAAATCTACATATTTTACTAATTTT
Found at i:16668528 original size:3 final size:3
Alignment explanation
Indices: 16668522--16668555 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
16668512 TATTATCAGC
* *
16668522 ATA ATA ATA ATA ATA ATA ATA ATA CTA ATC ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16668556 AACTTTCGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:16675409 original size:2 final size:2
Alignment explanation
Indices: 16675402--16675426 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16675392 TGTATGTACA
16675402 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
16675427 AATTTATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:16676566 original size:33 final size:31
Alignment explanation
Indices: 16676492--16676573 Score: 101
Period size: 33 Copynumber: 2.6 Consensus size: 31
16676482 CCTACTAATG
**
16676492 CTAAAATGTTCCAACAAACATGGTTAACACA
1 CTAAAATGTTCCAACAAACATGGAAAACACA
* * *
16676523 TTAAAATGTTCCAACAAACATAATGAAAATACA
1 CTAAAATGTTCCAACAAACAT--GGAAAACACA
16676556 CTAAAATGTTCCAACAAA
1 CTAAAATGTTCCAACAAA
16676574 GTTATGCAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 20 0.47
33 23 0.53
ACGTcount: A:0.50, C:0.20, G:0.07, T:0.23
Consensus pattern (31 bp):
CTAAAATGTTCCAACAAACATGGAAAACACA
Found at i:16678825 original size:11 final size:12
Alignment explanation
Indices: 16678800--16678832 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
16678790 AGTCAAACAC
16678800 AAAAAAGAAAGT
1 AAAAAAGAAAGT
*
16678812 AAAAAATAAA-T
1 AAAAAAGAAAGT
16678823 AAAAAAGAAA
1 AAAAAAGAAA
16678833 AAGACGAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.82, C:0.00, G:0.09, T:0.09
Consensus pattern (12 bp):
AAAAAAGAAAGT
Found at i:16681845 original size:21 final size:21
Alignment explanation
Indices: 16681808--16681855 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
16681798 AATGGAGAAT
** *
16681808 TTTATTTATTCTTTCTTTTTA
1 TTTATTTATTCAATCTTATTA
16681829 TTTATTTATTCAATCTTATTA
1 TTTATTTATTCAATCTTATTA
16681850 -TTATTT
1 TTTATTT
16681856 TTATTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (21 bp):
TTTATTTATTCAATCTTATTA
Found at i:16683671 original size:74 final size:74
Alignment explanation
Indices: 16683585--16683724 Score: 237
Period size: 74 Copynumber: 1.9 Consensus size: 74
16683575 ACCTATACTT
* *
16683585 ATAAATATGTATTCA-CTAAATGATGATCGTTGAAATATTTTTTATTATAATTATTACTAAGATT
1 ATAAATATGTATTCATC-AAATGATGATCATTGAAATATTTTTTATTATAATTATTACAAAGATT
16683649 TAAACCTATC
65 TAAACCTATC
*
16683659 ATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTAGAAAGATTT
1 ATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTACAAAGATTT
16683724 A
66 A
16683725 TTCCATTTAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 61 0.98
75 1 0.02
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.44
Consensus pattern (74 bp):
ATAAATATGTATTCATCAAATGATGATCATTGAAATATTTTTTATTATAATTATTACAAAGATTT
AAACCTATC
Found at i:16684216 original size:20 final size:19
Alignment explanation
Indices: 16684191--16684231 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
16684181 TTATTTTTCT
16684191 TTTTTTAATTTTTATTATTA
1 TTTTTTAATTTTTATT-TTA
*
16684211 TTTTTTAGTTTTTATTTTA
1 TTTTTTAATTTTTATTTTA
16684230 TT
1 TT
16684232 GATTTGTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTAATTTTTATTTTA
Found at i:16684222 original size:27 final size:28
Alignment explanation
Indices: 16684168--16684228 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
16684158 TTTATTTCAA
*
16684168 AATTTATTATTTATTATTTTTCTTTTTTT
1 AATTT-TTATTTATTATTTTTCTGTTTTT
16684197 AATTTTTA-TTATTATTTTT-TAGTTTTT
1 AATTTTTATTTATTATTTTTCT-GTTTTT
16684224 -ATTTT
1 AATTTT
16684229 ATTGATTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.20
27 16 0.53
28 3 0.10
29 5 0.17
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (28 bp):
AATTTTTATTTATTATTTTTCTGTTTTT
Found at i:16684223 original size:35 final size:34
Alignment explanation
Indices: 16684171--16684244 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 34
16684161 ATTTCAAAAT
* * *
16684171 TTATTATTTATTATTTTTCTTTTTTTAATTTTTA
1 TTATTATTTATTATTTTTATTTTATTAATTTGTA
* *
16684205 TTATTATTTTTTAGTTTTTATTTTATTGATTTGTA
1 TTATTATTTATTA-TTTTTATTTTATTAATTTGTA
16684240 TTATT
1 TTATT
16684245 GAGACAACCC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 12 0.35
35 22 0.65
ACGTcount: A:0.20, C:0.01, G:0.04, T:0.74
Consensus pattern (34 bp):
TTATTATTTATTATTTTTATTTTATTAATTTGTA
Found at i:16685591 original size:18 final size:17
Alignment explanation
Indices: 16685568--16685612 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
16685558 ACTGCATTCA
*
16685568 TTTTTATTTCTTTTTTTC
1 TTTTTATTT-TATTTTTC
16685586 TTTTTATTTTATTTTTC
1 TTTTTATTTTATTTTTC
*
16685603 ATTTTATTTT
1 TTTTTATTTT
16685613 CTATCGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTATTTTATTTTTC
Found at i:16690647 original size:31 final size:31
Alignment explanation
Indices: 16690612--16690948 Score: 451
Period size: 31 Copynumber: 10.8 Consensus size: 31
16690602 CACGACATTA
*
16690612 GTTATATGCATGGCGTGTTACAACAATTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
** *
16690643 GTTATATGCATGATGTGTTACAACATTGTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
*
16690674 GTTATATGCATGGCGTGTTACAAGATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
* * *
16690705 GTTATATGCATGACATGTTACAACATTTTAA
1 GTTATATGCATGGCGTGTTACAACATTTTAC
*
16690736 GCTATATGCATGGCGTGTTACAACATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
* * * *
16690767 GCTATATGCATGACGAGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
* *
16690798 GCTATATGCATGGCGTGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
** * *
16690829 ACTATATGCATGCCGTGTTACAACATTTTTAT
1 GTTATATGCATGGCGTGTTACAACA-TTTTAC
*
16690861 GTTATATGCATGGCGTGTTATC-ATATTTTAC
1 GTTATATGCATGGCGTGTTA-CAACATTTTAC
*
16690892 GTTATATGCATGGCGTGTTACCACATTTTAC
1 GTTATATGCATGGCGTGTTACAACATTTTAC
*
16690923 GTTATATGCATGGCGTGTAACAACAT
1 GTTATATGCATGGCGTGTTACAACAT
16690949 GATTGACAAA
Statistics
Matches: 270, Mismatches: 33, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
30 1 0.00
31 244 0.90
32 24 0.09
33 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.18, T:0.37
Consensus pattern (31 bp):
GTTATATGCATGGCGTGTTACAACATTTTAC
Found at i:16694686 original size:15 final size:14
Alignment explanation
Indices: 16694666--16694713 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
16694656 AAGCACTTTT
16694666 ATTTATATTTATATA
1 ATTTATATTTAT-TA
* *
16694681 ATTTATATGTCATGA
1 ATTTATAT-TTATTA
16694696 ATTTATATTT-TTA
1 ATTTATATTTATTA
16694709 ATTTA
1 ATTTA
16694714 AAAAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 7 0.25
14 1 0.04
15 17 0.61
16 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (14 bp):
ATTTATATTTATTA
Found at i:16699260 original size:86 final size:85
Alignment explanation
Indices: 16699103--16699605 Score: 532
Period size: 86 Copynumber: 5.9 Consensus size: 85
16699093 AAGCAGATGC
* * * * *
16699103 TTGTGGTGGCACGTTGACTGCAA-GCAGACTTATGGCGTGACACGCTGACTTGTTGCAATCTTAT
1 TTGTGGTGACACGCTGAGTG-AATGCAGACTT-TGGCGTGACACGCTGACTTGTTGCAGTCTTGT
* * * **
16699167 GGAGTGACACGGTACGACCCAA
64 GGGGTGACACGGCAAGGGCCAA
*
16699189 TTGTGGTGACACGCTGAGTGAATGCAGACTTCTGGCGTGACACGTTGACTTGTTGCAGTCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTT-TGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
*
16699254 GGGTGACACAGC-AGGAGCCAA
65 GGGTGACACGGCAAGG-GCCAA
* *
16699275 TTGTGGTGACACGCTGAGTAAATGCA-AGCTTATGGCATGACACGCTGACTTGTTGCAGTCTTGT
1 TTGTGGTGACACGCTGAGTGAATGCAGA-CTT-TGGCGTGACACGCTGACTTGTTGCAGTCTTGT
* * *
16699339 GGGGTGACACGGTATGGCCCAA
64 GGGGTGACACGGCAAGGGCCAA
** * * * * * *
16699361 TTGTGGTGACACTATGAGTGCATGCACACTTCTGACGTCACACGTTGACTTGTTACAGTCTTGTG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTT-TGGCGTGACACGCTGACTTGTTGCAGTCTTGTG
*
16699426 GGGTGACACGACAAGGGCCAA
65 GGGTGACACGGCAAGGGCCAA
* * * ** * *
16699447 TTGTGGTGACACGCTGAGTGCATTCAGAC-TTGGAGTGACACGCCAAATTGTTGCAGTCTTAT-G
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTTGGCGTGACACGCTGACTTGTTGCAGTCTTGTGG
16699510 GGTGACACGGCAAGGGCCAA
66 GGTGACACGGCAAGGGCCAA
* * * ** * *
16699530 TTGTGGTGACACGTTGAGTGCATACAGAC-TTGGCGTGACACGCCAAATTGTTGCAGTCTTGTCG
1 TTGTGGTGACACGCTGAGTGAATGCAGACTTTGGCGTGACACGCTGACTTGTTGCAGTCTTGTGG
*
16699594 GGTGACATGGCA
66 GGTGACACGGCA
16699606 CAAAATTAAT
Statistics
Matches: 357, Mismatches: 54, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
83 78 0.22
84 35 0.10
85 5 0.01
86 236 0.66
87 3 0.01
ACGTcount: A:0.22, C:0.21, G:0.31, T:0.26
Consensus pattern (85 bp):
TTGTGGTGACACGCTGAGTGAATGCAGACTTTGGCGTGACACGCTGACTTGTTGCAGTCTTGTGG
GGTGACACGGCAAGGGCCAA
Found at i:16701219 original size:81 final size:81
Alignment explanation
Indices: 16701052--16701202 Score: 221
Period size: 81 Copynumber: 1.9 Consensus size: 81
16701042 CACGAGTGAC
** *
16701052 TGAAGGTCCCCCTCCTTTCCCTCAGATACATCGATAACCAAATCAGCCTCAGGAACATGGACTCC
1 TGAAGGTCCCCCTCCCCTCCCGCAGATACATCGATAACCAAATCAGCCTCAGGAACATGGACTCC
*
16701117 TTTAGCCATGAGCTAA
66 TTCAGCCATGAGCTAA
* * * * *
16701133 TGAAGGTCCCCCTCCCCTCCCGCATATGCATCGATAATCGAATCAGCCTGAGGAACATGGACTCC
1 TGAAGGTCCCCCTCCCCTCCCGCAGATACATCGATAACCAAATCAGCCTCAGGAACATGGACTCC
16701198 TTCAG
66 TTCAG
16701203 TAGCATCTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 61 1.00
ACGTcount: A:0.26, C:0.33, G:0.18, T:0.23
Consensus pattern (81 bp):
TGAAGGTCCCCCTCCCCTCCCGCAGATACATCGATAACCAAATCAGCCTCAGGAACATGGACTCC
TTCAGCCATGAGCTAA
Found at i:16703422 original size:55 final size:55
Alignment explanation
Indices: 16703352--16703466 Score: 160
Period size: 55 Copynumber: 2.1 Consensus size: 55
16703342 CAAGAAGCAA
* *
16703352 AACACTCCAAAAACAGCCGTGACATGCTGAAAATCC-AAAAACTCAATTAACCCAC
1 AACACTCCAAAAACAGCCGTGACAAGCTAAAAATCCAAAAAAC-CAATTAACCCAC
* * * *
16703407 AACACTCTAAGAACAGCTGTGACAAGCTAAAAATCCAAAAAACCAGTTAACCCAC
1 AACACTCCAAAAACAGCCGTGACAAGCTAAAAATCCAAAAAACCAATTAACCCAC
16703462 AACAC
1 AACAC
16703467 GCCATATGTA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 47 0.89
56 6 0.11
ACGTcount: A:0.47, C:0.30, G:0.10, T:0.14
Consensus pattern (55 bp):
AACACTCCAAAAACAGCCGTGACAAGCTAAAAATCCAAAAAACCAATTAACCCAC
Found at i:16703941 original size:23 final size:23
Alignment explanation
Indices: 16703914--16703966 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
16703904 ATACCATGGC
16703914 TGTCACATATTAAACCCATGACG
1 TGTCACATATTAAACCCATGACG
* * *
16703937 TGTCACATGTTTAACCCATGCCG
1 TGTCACATATTAAACCCATGACG
16703960 TGTCACA
1 TGTCACA
16703967 CGTCTGACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (23 bp):
TGTCACATATTAAACCCATGACG
Found at i:16703983 original size:22 final size:23
Alignment explanation
Indices: 16703926--16704012 Score: 72
Period size: 23 Copynumber: 3.8 Consensus size: 23
16703916 TCACATATTA
* *
16703926 AACCCATGACGTGTCACATGTTT
1 AACCCATGACGTGTCACACGTCT
*
16703949 AACCCATGCCGTGTCACACGTCT
1 AACCCATGACGTGTCACACGTCT
* *
16703972 GA-CCATGGCGTGTCCCACAC-TCT
1 AACCCATGACGTGT--CACACGTCT
* *
16703995 AACGC-TGTCGTGTCACAC
1 AACCCATGACGTGTCACAC
16704013 CCGTCCCACA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
21 5 0.09
22 10 0.19
23 32 0.60
24 6 0.11
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (23 bp):
AACCCATGACGTGTCACACGTCT
Found at i:16704126 original size:81 final size:80
Alignment explanation
Indices: 16703980--16704130 Score: 194
Period size: 81 Copynumber: 1.9 Consensus size: 80
16703970 CTGACCATGG
* * * * **
16703980 CGTGTCCCACACTCTAACGCTGTCGTGTCACACCCGTCCCACATATTCTCACTGTGCTGTCTCAC
1 CGTGTCACACACTCTAACCCTGTCGTGTCACACCCGTCCCACACATTATCACTGTGCCATCTCAC
16704045 ACATTTTCACCCTGA
66 ACATTTTCACCCTGA
** ** *
16704060 CGTGTCACACACTCTAAACCCTGTCGTGTCACACTGGTGTCACACATTATCACTGTGCCATTTCA
1 CGTGTCACACACTCT-AACCCTGTCGTGTCACACCCGTCCCACACATTATCACTGTGCCATCTCA
16704125 CACATT
65 CACATT
16704131 ATGACCCTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
80 14 0.24
81 45 0.76
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (80 bp):
CGTGTCACACACTCTAACCCTGTCGTGTCACACCCGTCCCACACATTATCACTGTGCCATCTCAC
ACATTTTCACCCTGA
Found at i:16704138 original size:81 final size:80
Alignment explanation
Indices: 16703971--16704138 Score: 192
Period size: 81 Copynumber: 2.1 Consensus size: 80
16703961 GTCACACGTC
* * * * * *
16703971 TGACCATGGCGTGTCCCACACTCTAACGCTGTCGTGTCACACCCGTCCCACATATTCTCACTGTG
1 TGACCCTGACGTGTCACACACTCTAACCCTGTCGTGTCACACCCGTCCCACACATTATCACTGTG
** *
16704036 CTGTCTCACACATTT
66 CCATCTCACACATTA
* ** **
16704051 TCACCCTGACGTGTCACACACTCTAAACCCTGTCGTGTCACACTGGTGTCACACATTATCACTGT
1 TGACCCTGACGTGTCACACACTCT-AACCCTGTCGTGTCACACCCGTCCCACACATTATCACTGT
*
16704116 GCCATTTCACACATTA
65 GCCATCTCACACATTA
16704132 TGACCCT
1 TGACCCT
16704139 ATTATAACCC
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
80 20 0.28
81 51 0.72
ACGTcount: A:0.21, C:0.35, G:0.15, T:0.29
Consensus pattern (80 bp):
TGACCCTGACGTGTCACACACTCTAACCCTGTCGTGTCACACCCGTCCCACACATTATCACTGTG
CCATCTCACACATTA
Found at i:16704183 original size:115 final size:113
Alignment explanation
Indices: 16704044--16704253 Score: 285
Period size: 115 Copynumber: 1.8 Consensus size: 113
16704034 TGCTGTCTCA
* * ** *
16704044 CACATTTTCACCCTGACGTGTCACACACTCTAAACCCTGTCGTGTCACACTGGTGTCACACATTA
1 CACATTTTCACCATGACGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTA
* * *
16704109 TCACTGTGCCATTTCACACATTATGACCCTATTATAACCCTGTCGTGT
66 TCACCGTGCCATCTCACACATTATCACCCTATTATAACCCTGTCGTGT
* * *
16704157 CACATTTTCTGACCATGGCGTGTCACACACTCTAAACGCTGTCATGTCACACCCGTCTCACATAT
1 CACATTTTC--ACCATGACGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACAT
* *
16704222 TCTCACCGTGCCGTCTCACACATTATCACCCT
64 TATCACCGTGCCATCTCACACATTATCACCCT
16704254 GCCGTGTCAC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
113 9 0.11
115 73 0.89
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (113 bp):
CACATTTTCACCATGACGTGTCACACACTCTAAACCCTGTCATGTCACACCCGTCTCACACATTA
TCACCGTGCCATCTCACACATTATCACCCTATTATAACCCTGTCGTGT
Found at i:16704235 original size:23 final size:23
Alignment explanation
Indices: 16704209--16704269 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
16704199 CATGTCACAC
* *
16704209 CCGTCTCACATATTCTCACCGTG
1 CCGTCTCACACATTCTCACCCTG
*
16704232 CCGTCTCACACATTATCACCCTG
1 CCGTCTCACACATTCTCACCCTG
* *
16704255 CCGTGTCACAGATTC
1 CCGTCTCACACATTC
16704270 CCTTCATGGC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.39, G:0.13, T:0.28
Consensus pattern (23 bp):
CCGTCTCACACATTCTCACCCTG
Found at i:16704335 original size:162 final size:163
Alignment explanation
Indices: 16704164--16704484 Score: 477
Period size: 162 Copynumber: 2.0 Consensus size: 163
16704154 TGTCACATTT
* * *
16704164 TCTGACCATGGCGTGTCACACACTCTAAACGCTGTCATGTCACACCCGTCTCACATATTCTCACC
1 TCTGACCATGGCGTGTCACACACTCTAAACACTGCCATGTCACACCCATCTCACATATTCTCACC
* * *
16704229 GTGCCGTCTCACACATTATCACCCTGCCGTGTCACAGATTCCCTTC-ATGGC-ATGTCACACACT
66 ATGCCGTCTCACACATTATCACCCTGCCATGTCACAAATTCCC-TCAATGGCGATGTCACACACT
16704292 CTAAACCCTG-CAGCGTCACACCCGTGTCATACGC
130 CTAAACCCTGTC-GCGTCACACCCGTGTCATACGC
* * * *
16704326 TCTGACCATGGCGTGTCACACACTCTAAACACTGCCATGTTACACCCATGTCACATGTTTTCACC
1 TCTGACCATGGCGTGTCACACACTCTAAACACTGCCATGTCACACCCATCTCACATATTCTCACC
*
16704391 ATGCCGTCTCACACATTATCACCCTGCCATGTCACAAATTCCCTCAATGGCGTGTGTCACACACT
66 ATGCCGTCTCACACATTATCACCCTGCCATGTCACAAATTCCCTCAATGGCG-ATGTCACACACT
* *
16704456 CTAAACCTTGTCGCGTCACACTCGTGTCA
130 CTAAACCCTGTCGCGTCACACCCGTGTCA
16704485 CACATTATCA
Statistics
Matches: 142, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
161 2 0.01
162 103 0.73
164 36 0.25
165 1 0.01
ACGTcount: A:0.23, C:0.36, G:0.15, T:0.26
Consensus pattern (163 bp):
TCTGACCATGGCGTGTCACACACTCTAAACACTGCCATGTCACACCCATCTCACATATTCTCACC
ATGCCGTCTCACACATTATCACCCTGCCATGTCACAAATTCCCTCAATGGCGATGTCACACACTC
TAAACCCTGTCGCGTCACACCCGTGTCATACGC
Found at i:16704392 original size:58 final size:58
Alignment explanation
Indices: 16704274--16704405 Score: 140
Period size: 58 Copynumber: 2.3 Consensus size: 58
16704264 AGATTCCCTT
* * * * *
16704274 CATGGCATGTCACACACTCTAAACCCTGCAGCGTCACACCCGTGTCATACGCTCTGAC
1 CATGGCGTGTCACACACTCTAAACACTGCAGCGTCACACCCATGTCACACGCTCTCAC
* * * * *
16704332 CATGGCGTGTCACACACTCTAAACACTGCCA-TGTTACACCCATGTCACATGTTTTCAC
1 CATGGCGTGTCACACACTCTAAACACTG-CAGCGTCACACCCATGTCACACGCTCTCAC
* *
16704390 CATGCCGTCTCACACA
1 CATGGCGTGTCACACA
16704406 TTATCACCCT
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 59 0.97
59 2 0.03
ACGTcount: A:0.25, C:0.36, G:0.15, T:0.23
Consensus pattern (58 bp):
CATGGCGTGTCACACACTCTAAACACTGCAGCGTCACACCCATGTCACACGCTCTCAC
Found at i:16704425 original size:23 final size:23
Alignment explanation
Indices: 16704371--16704426 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
16704361 CATGTTACAC
** *
16704371 CCATGTCACATGTTTTCACCATG
1 CCATGTCACACATTATCACCATG
* * *
16704394 CCGTCTCACACATTATCACCCTG
1 CCATGTCACACATTATCACCATG
16704417 CCATGTCACA
1 CCATGTCACA
16704427 AATTCCCTCA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.23, C:0.38, G:0.11, T:0.29
Consensus pattern (23 bp):
CCATGTCACACATTATCACCATG
Found at i:16704531 original size:23 final size:23
Alignment explanation
Indices: 16704477--16704533 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
16704467 CGCGTCACAC
** *
16704477 TCGTGTCACACATTATCACTGTG
1 TCGTGTCACACATTATCACCCTA
* * *
16704500 CCGTTTCACACATTATGACCCTA
1 TCGTGTCACACATTATCACCCTA
16704523 TCGTGTCACAC
1 TCGTGTCACAC
16704534 GTTCTAACCA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.32
Consensus pattern (23 bp):
TCGTGTCACACATTATCACCCTA
Found at i:16704576 original size:24 final size:23
Alignment explanation
Indices: 16704517--16704580 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
16704507 ACACATTATG
*
16704517 ACCCTATCGTGTCACACGTTCTA
1 ACCCTGTCGTGTCACACGTTCTA
* * *
16704540 ACCATGGCATGTCACACGCTT-TAA
1 ACCCTGTCGTGTCACACG-TTCT-A
16704564 ACCCTGTCGTGTCACAC
1 ACCCTGTCGTGTCACAC
16704581 CTATCTCACA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (23 bp):
ACCCTGTCGTGTCACACGTTCTA
Found at i:16704635 original size:81 final size:81
Alignment explanation
Indices: 16704540--16704719 Score: 198
Period size: 81 Copynumber: 2.2 Consensus size: 81
16704530 ACACGTTCTA
* * * ** * * *
16704540 ACCATGGCATGTCACACGCTTTAAACCCTGTCGTGTCACACCTATCTCACATAGTCTCACCATGA
1 ACCATGCCATGTCACACACTCTAAACCCTACCATGTCACACCCATCTCACAAAGTCTCACCATGA
*
16704605 CGTATCACACATTGCC
66 CGTATCACACATTCCC
* * * * * * *
16704621 ACTATGCCGTGTCACAAACTCTATACCCTACCATGTCACACCCGTTTCACAAATTCTCACCATGA
1 ACCATGCCATGTCACACACTCTAAACCCTACCATGTCACACCCATCTCACAAAGTCTCACCATGA
* *
16704686 TGTGTCACACATTCCC
66 CGTATCACACATTCCC
16704702 ACCATGCCATGTCACACA
1 ACCATGCCATGTCACACA
16704720 TTCCCACCAT
Statistics
Matches: 78, Mismatches: 21, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.27, C:0.36, G:0.12, T:0.26
Consensus pattern (81 bp):
ACCATGCCATGTCACACACTCTAAACCCTACCATGTCACACCCATCTCACAAAGTCTCACCATGA
CGTATCACACATTCCC
Found at i:16704713 original size:25 final size:21
Alignment explanation
Indices: 16704667--16704729 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
16704657 CACACCCGTT
* *
16704667 TCACAAATTCTCACCATGATGTG
1 TCACACATTCCCACCATGA--TG
16704690 TCACACATTCCCACCATGCCATG
1 TCACACATTCCCACCATG--ATG
16704713 TCACACATTCCCACCAT
1 TCACACATTCCCACCAT
16704730 TCCGTTTCAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
23 35 0.97
25 1 0.03
ACGTcount: A:0.29, C:0.38, G:0.08, T:0.25
Consensus pattern (21 bp):
TCACACATTCCCACCATGATG
Found at i:16705291 original size:40 final size:40
Alignment explanation
Indices: 16705245--16705327 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
16705235 TTAGGCCAAA
16705245 TGGGGCAAGGCTCAAGTCTAGAATTCTATGCCCAAAGATC
1 TGGGGCAAGGCTCAAGTCTAGAATTCTATGCCCAAAGATC
*
16705285 TGGGGCAAGGTTCAAGTCTAGAATTCTATGCCCAAAGATC
1 TGGGGCAAGGCTCAAGTCTAGAATTCTATGCCCAAAGATC
16705325 TGG
1 TGG
16705328 CCTGTGGAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (40 bp):
TGGGGCAAGGCTCAAGTCTAGAATTCTATGCCCAAAGATC
Found at i:16722386 original size:19 final size:20
Alignment explanation
Indices: 16722362--16722400 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16722352 CTGTAAGATA
*
16722362 GAGAGAGA-GAGAGAGAAAG
1 GAGAGAGATGAGAGAAAAAG
16722381 GAGAGAGATGAGAGAAAAAG
1 GAGAGAGATGAGAGAAAAAG
16722401 ATTTTGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.03
Consensus pattern (20 bp):
GAGAGAGATGAGAGAAAAAG
Found at i:16725424 original size:19 final size:19
Alignment explanation
Indices: 16725400--16725437 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
16725390 ACTTCTTAAC
16725400 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
*
16725419 CTCAAATCATACTCTAATA
1 CTCAAATCATACTCCAATA
16725438 AGTCAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.29, G:0.00, T:0.29
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:16726920 original size:2 final size:2
Alignment explanation
Indices: 16726913--16726957 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
16726903 TGTTTAGAAT
16726913 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
16726955 AG A
1 AG A
16726958 TGCATANGTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16727111 original size:203 final size:202
Alignment explanation
Indices: 16726762--16727168 Score: 789
Period size: 203 Copynumber: 2.0 Consensus size: 202
16726752 CTAACGGTAC
16726762 GTAAGCTCTATTGTTGTTGTTTGTGGTTGTTGCTACTTTCTTTTCTTGAGTCAGCTAAGTTAACT
1 GTAAGCTCTATTGTTGTTGTTTGTGGTTGTTGCTACTTTCTTTTCTTGAGTCAGCTAAGTTAACT
16726827 CGAATGAATGGTTAGGTTCTCTGTTTTTTCCATTTTCCTTTTTGGATGTCGTTTCGAAGACATTT
66 CGAATGAATGGTTAGGTTCTCTGTTTTTTCCATTTTCCTTTTTGGATGTCGTTTCGAAGACATTT
16726892 TCTAATAGTACTGTTTAGAATAGAGAGAGAGAGAGAGAGA-GAGAGAGAGAGAGAGAGAGAGAGA
131 TCTAATAGTACTGTTTAGAATAGAGAGAGAGAGAGAGAGACGAGAGAGAGAGAGAGAGAGAGAGA
16726956 GATGCATA
196 GAT-CATA
16726964 NGTAAGCTCTATTGTTGTTGTTTGTGGTTGTTGCTACTTTCTTTTCTTGAGTCAGCTAAGTTAAC
1 -GTAAGCTCTATTGTTGTTGTTTGTGGTTGTTGCTACTTTCTTTTCTTGAGTCAGCTAAGTTAAC
16727029 TCGAATGAATGGTTAGGTTCTCTGTTTTTTCCATTTTCCTTTTTGGATGTCGTTTCGAAGACATT
65 TCGAATGAATGGTTAGGTTCTCTGTTTTTTCCATTTTCCTTTTTGGATGTCGTTTCGAAGACATT
16727094 TTCTAATAGTACTGTTTAGAATAGAGAGAGAGAGAGAGAGACGAGAGAGAGAGAGAGAGAGAGAG
130 TTCTAATAGTACTGTTTAGAATAGAGAGAGAGAGAGAGAGACGAGAGAGAGAGAGAGAGAGAGAG
16727159 AGATCATA
195 AGATCATA
16727167 GT
1 GT
16727169 CCTTTCTTCA
Statistics
Matches: 203, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
202 2 0.01
203 174 0.86
204 27 0.13
ACGTcount: A:0.26, C:0.11, G:0.26, T:0.37
Consensus pattern (202 bp):
GTAAGCTCTATTGTTGTTGTTTGTGGTTGTTGCTACTTTCTTTTCTTGAGTCAGCTAAGTTAACT
CGAATGAATGGTTAGGTTCTCTGTTTTTTCCATTTTCCTTTTTGGATGTCGTTTCGAAGACATTT
TCTAATAGTACTGTTTAGAATAGAGAGAGAGAGAGAGAGACGAGAGAGAGAGAGAGAGAGAGAGA
GATCATA
Found at i:16727123 original size:2 final size:2
Alignment explanation
Indices: 16727116--16727161 Score: 83
Period size: 2 Copynumber: 22.5 Consensus size: 2
16727106 TGTTTAGAAT
16727116 AG AG AG AG AG AG AG AG AG ACG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG
16727159 AG A
1 AG A
16727162 TCATAGTCCT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16738563 original size:45 final size:45
Alignment explanation
Indices: 16738512--16738605 Score: 179
Period size: 45 Copynumber: 2.1 Consensus size: 45
16738502 TATATTTCAC
*
16738512 CTTTTTGTGTTGTTTTTGATAAATTCATGGCTTATGTATAAATCT
1 CTTTTTGTGTTGTTTTTGATAAATTCATGGCTTATATATAAATCT
16738557 CTTTTTGTGTTGTTTTTGATAAATTCATGGCTTATATATAAATCT
1 CTTTTTGTGTTGTTTTTGATAAATTCATGGCTTATATATAAATCT
16738602 CTTT
1 CTTT
16738606 CATTAATCAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.22, C:0.10, G:0.14, T:0.54
Consensus pattern (45 bp):
CTTTTTGTGTTGTTTTTGATAAATTCATGGCTTATATATAAATCT
Found at i:16740324 original size:2 final size:2
Alignment explanation
Indices: 16740317--16740353 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
16740307 NNNNNNNNNN
16740317 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 T
16740354 GTAAATATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:16743415 original size:16 final size:18
Alignment explanation
Indices: 16743394--16743427 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
16743384 AACTTTTTTC
16743394 AAATATT-ATACA-AAAA
1 AAATATTAATACATAAAA
16743410 AAATATTAATACATAAAA
1 AAATATTAATACATAAAA
16743428 CTCAATCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATATTAATACATAAAA
Found at i:16756160 original size:20 final size:20
Alignment explanation
Indices: 16756135--16756173 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
16756125 CTCGATTGAG
* *
16756135 GCTCCCTAAGGGAGCATCGA
1 GCTCCCCAAGGAAGCATCGA
16756155 GCTCCCCAAGGAAGCATCG
1 GCTCCCCAAGGAAGCATCG
16756174 GTGCTCCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.33, G:0.28, T:0.13
Consensus pattern (20 bp):
GCTCCCCAAGGAAGCATCGA
Found at i:16759550 original size:31 final size:30
Alignment explanation
Indices: 16759518--16759623 Score: 121
Period size: 30 Copynumber: 3.5 Consensus size: 30
16759508 AATCATTAAT
*
16759518 TATAAAGATTTATTTACATTTCAAAA-AAAAT
1 TATAAAGATTTATTTACA--TCAAAATAAAAA
16759549 TATAAAGATTTATTTGAC-TCAAAATAAAAA
1 TATAAAGATTTATTT-ACATCAAAATAAAAA
16759579 TAT-AAGAGTTTATTTA-ACTCAAAATAAAAA
1 TATAAAGA-TTTATTTACA-TCAAAATAAAAA
*
16759609 TATAAAAATTTATTT
1 TATAAAGATTTATTT
16759624 TAATTTTTTT
Statistics
Matches: 67, Mismatches: 2, Indels: 13
0.82 0.02 0.16
Matches are distributed among these distances:
29 11 0.16
30 36 0.54
31 18 0.27
32 2 0.03
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.38
Consensus pattern (30 bp):
TATAAAGATTTATTTACATCAAAATAAAAA
Found at i:16772874 original size:16 final size:16
Alignment explanation
Indices: 16772836--16772884 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
16772826 TTTGAGCTTG
*
16772836 AATTAATTTGAATTCGA
1 AATTAATTTGAATT-AA
16772853 AA-TAATTTGAATTAA
1 AATTAATTTGAATTAA
*
16772868 AATTAATTTCAATTAA
1 AATTAATTTGAATTAA
16772884 A
1 A
16772885 TATTTTATCG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 3 0.10
16 24 0.83
17 2 0.07
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.41
Consensus pattern (16 bp):
AATTAATTTGAATTAA
Found at i:16773563 original size:6 final size:7
Alignment explanation
Indices: 16773536--16773561 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
16773526 TTTCTAGCTT
16773536 TTTTTTC
1 TTTTTTC
16773543 TTTTTTC
1 TTTTTTC
16773550 TTTTTTC
1 TTTTTTC
16773557 TTTTT
1 TTTTT
16773562 CTGTATGTTG
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:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:16785202 original size:21 final size:21
Alignment explanation
Indices: 16785170--16785224 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
16785160 ATACTGTCAC
16785170 AGAAAA-CATTTTCCCAGCAA
1 AGAAAATCATTTTCCCAGCAA
16785190 AGAAAATCATTTTCCCAGCAA
1 AGAAAATCATTTTCCCAGCAA
16785211 AGAAAATCATTTTC
1 AGAAAATCATTTTC
16785225 TGTTGTTTGC
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.44, C:0.22, G:0.09, T:0.25
Consensus pattern (21 bp):
AGAAAATCATTTTCCCAGCAA
Found at i:16795340 original size:90 final size:90
Alignment explanation
Indices: 16795185--16795348 Score: 240
Period size: 90 Copynumber: 1.8 Consensus size: 90
16795175 GTTAATTTTT
* * *
16795185 GTGTTTTTGTCTCACAAATGGTACTTGGCGGATTTAAATAGGAGTGGGTGGGAGTTTAAAGAGCA
1 GTGTTTCTGTCTCACAAATGGTACTTAGCGGATTTAAATAGGAATGGGTGGGAGTTTAAAGAGCA
*
16795250 GTCAGAGAAGGAAGAGCCGTCACTG
66 GTAAGAGAAGGAAGAGCCGTCACTG
* * * *
16795275 GTGTTTCTGTCTTACGAATGGTACTTAGCGGATTTAGATGGGAATGGGTGGGAGTTTAGAA-AGC
1 GTGTTTCTGTCTCACAAATGGTACTTAGCGGATTTAAATAGGAATGGGTGGGAGTTTA-AAGAGC
16795339 AGTAAGAGAA
65 AGTAAGAGAA
16795349 AAGGAGAGCC
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
90 63 0.97
91 2 0.03
ACGTcount: A:0.28, C:0.10, G:0.34, T:0.28
Consensus pattern (90 bp):
GTGTTTCTGTCTCACAAATGGTACTTAGCGGATTTAAATAGGAATGGGTGGGAGTTTAAAGAGCA
GTAAGAGAAGGAAGAGCCGTCACTG
Found at i:16795402 original size:58 final size:58
Alignment explanation
Indices: 16795303--16795417 Score: 167
Period size: 58 Copynumber: 2.0 Consensus size: 58
16795293 TGGTACTTAG
* *
16795303 CGGATTTAGATGGGAATGGGTGGGAGTTTAGAAAGCAGTAAGAGAAAAGGAGAGCCTA
1 CGGATTTAGATGGGAATGGGTGGGAGTTCAGAAAGCAGTAAGAGAAAAGGAAAGCCTA
* * ** *
16795361 CGGATTTAGATGGGAGTGGGTGGGAGTTCAGAGAGTGGTAAGAGAAAATGAAAGCCT
1 CGGATTTAGATGGGAATGGGTGGGAGTTCAGAAAGCAGTAAGAGAAAAGGAAAGCCT
16795418 TCACTAGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 50 1.00
ACGTcount: A:0.34, C:0.07, G:0.39, T:0.20
Consensus pattern (58 bp):
CGGATTTAGATGGGAATGGGTGGGAGTTCAGAAAGCAGTAAGAGAAAAGGAAAGCCTA
Found at i:16795482 original size:149 final size:148
Alignment explanation
Indices: 16795213--16795502 Score: 386
Period size: 149 Copynumber: 2.0 Consensus size: 148
16795203 TGGTACTTGG
* * *
16795213 CGGATTTAAATAGGAGTGGGTGGGAGTTTAAAGAGCAGTCAGAGAAGGAAGAGCCGTCACTGGTG
1 CGGATTTAAATAGGAGTGGGTGGGAGTTCAAAGAGCAGTAAGAGAAGGAAGAGCCGTCACTAGTG
16795278 TTTCTGTCTTACGAATGGTACTTAGCGGATTTAGATGGGAATGGGTGGGAGTTTAGAAAGCAGTA
66 TTTCTGTCTTACGAATGGTACTTAGCGGATTTAGATGGGAATGGGTGGGAGTTTAGAAAGCAGTA
*
16795343 AGAGAAAAGGAGAGCCTA
131 AAAGAAAAGGAGAGCCTA
* * * ** * *
16795361 CGGATTTAGATGGGAGTGGGTGGGAGTTCAGAGAGTGGTAAGAGAAAATGAA-AGCCTTCACTAG
1 CGGATTTAAATAGGAGTGGGTGGGAGTTCAAAGAGCAGTAAGAG--AAGGAAGAGCCGTCACTAG
* * * * * *
16795425 TGTTTCTGT-TTCGCGAATGGTACTTGGCGGATTTCGATGGGAGTGGGTGGGAGTTTAGAGAGCG
64 TGTTTCTGTCTT-ACGAATGGTACTTAGCGGATTTAGATGGGAATGGGTGGGAGTTTAGAAAGCA
16795489 GTAAAAGAAAAGGA
128 GTAAAAGAAAAGGA
16795503 AAACCTTCAC
Statistics
Matches: 122, Mismatches: 17, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
148 39 0.32
149 78 0.64
150 5 0.04
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (148 bp):
CGGATTTAAATAGGAGTGGGTGGGAGTTCAAAGAGCAGTAAGAGAAGGAAGAGCCGTCACTAGTG
TTTCTGTCTTACGAATGGTACTTAGCGGATTTAGATGGGAATGGGTGGGAGTTTAGAAAGCAGTA
AAAGAAAAGGAGAGCCTA
Found at i:16809290 original size:24 final size:24
Alignment explanation
Indices: 16809258--16809307 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
16809248 TAAAAAAGGG
*
16809258 CAAACTATTCAATATCTTCCTATC
1 CAAACTATTCAATATATTCCTATC
16809282 CAAACTATTCAATATATTCCTATC
1 CAAACTATTCAATATATTCCTATC
16809306 CA
1 CA
16809308 CTAAGTCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.28, G:0.00, T:0.36
Consensus pattern (24 bp):
CAAACTATTCAATATATTCCTATC
Found at i:16818199 original size:22 final size:22
Alignment explanation
Indices: 16818167--16818209 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
16818157 AGTCATTACA
*
16818167 CAAAATACCACTTGTCGTTTTT
1 CAAAATACCACTTGTCATTTTT
*
16818189 CAAAATGCCACTTGTCATTTT
1 CAAAATACCACTTGTCATTTT
16818210 ATACTTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (22 bp):
CAAAATACCACTTGTCATTTTT
Found at i:16818465 original size:29 final size:30
Alignment explanation
Indices: 16818385--16818465 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
16818375 TTATTTGACT
* * **
16818385 CAAAATAAAAATATAAAAGCTTGTTTAGCT
1 CAAAATAAAAATATAAGAGCTTGCTTAGAA
* *
16818415 CAAAATAAAAGTAT-AGTTGCTTGCTTA-AA
1 CAAAATAAAAATATAAG-AGCTTGCTTAGAA
*
16818444 CATAATAAAAATATAAGAGCTT
1 CAAAATAAAAATATAAGAGCTT
16818466 ATTTGAATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.49, C:0.10, G:0.11, T:0.30
Consensus pattern (30 bp):
CAAAATAAAAATATAAGAGCTTGCTTAGAA
Found at i:16818676 original size:2 final size:2
Alignment explanation
Indices: 16818669--16818719 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
16818659 GAACTCGCAA
16818669 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
16818711 AT AT AT AT A
1 AT AT AT AT A
16818720 AACAAAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:16824296 original size:21 final size:21
Alignment explanation
Indices: 16824272--16824320 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
16824262 ATATTATATG
* **
16824272 ATTATATCACTATACTATGTC
1 ATTATATCACTATAATACCTC
*
16824293 ATTATATCATTATAATACCTC
1 ATTATATCACTATAATACCTC
16824314 ATTATAT
1 ATTATAT
16824321 TACATCAGAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.37, C:0.16, G:0.02, T:0.45
Consensus pattern (21 bp):
ATTATATCACTATAATACCTC
Found at i:16827086 original size:2 final size:2
Alignment explanation
Indices: 16827079--16827107 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
16827069 TCTTTTGTAG
16827079 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
16827108 TTTGCGCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:16843565 original size:71 final size:71
Alignment explanation
Indices: 16843485--16843628 Score: 213
Period size: 71 Copynumber: 2.0 Consensus size: 71
16843475 TAATCATGTG
* *
16843485 AATCTATTTGATTTAAAATAAAAGTATAATAACTTT-ATTAAACATAAT-AAAAAAATTATTT-A
1 AATCTATTTGATTCAAAATAAAAATATAAT-ACTTTGATTAAACATAATAAAAAAAATTATTTAA
16843547 ATTATTT
65 ATTATTT
*
16843554 ANNATCTATTTGATTCAAAATAAAAATATAATATTTTGATTAAACATAATAAAAAAAATTATTTA
1 A--ATCTATTTGATTCAAAATAAAAATATAATACTTTGATTAAACATAATAAAAAAAATTATTTA
16843619 AATTATTT
64 AATTATTT
16843627 AA
1 AA
16843629 AATAATTCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
69 1 0.01
70 4 0.06
71 40 0.60
72 13 0.19
73 9 0.13
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.40
Consensus pattern (71 bp):
AATCTATTTGATTCAAAATAAAAATATAATACTTTGATTAAACATAATAAAAAAAATTATTTAAA
TTATTT
Found at i:16849923 original size:2 final size:2
Alignment explanation
Indices: 16849916--16849959 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
16849906 ACATAACCCT
16849916 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16849957 TA T
1 TA T
16849960 GGAGAAAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16853098 original size:25 final size:25
Alignment explanation
Indices: 16853064--16853138 Score: 150
Period size: 25 Copynumber: 3.0 Consensus size: 25
16853054 CAGCAGCCTT
16853064 TTCTTCTTCTCCATCTTCATTTTTG
1 TTCTTCTTCTCCATCTTCATTTTTG
16853089 TTCTTCTTCTCCATCTTCATTTTTG
1 TTCTTCTTCTCCATCTTCATTTTTG
16853114 TTCTTCTTCTCCATCTTCATTTTTG
1 TTCTTCTTCTCCATCTTCATTTTTG
16853139 CCAGCTAGCG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 50 1.00
ACGTcount: A:0.08, C:0.28, G:0.04, T:0.60
Consensus pattern (25 bp):
TTCTTCTTCTCCATCTTCATTTTTG
Found at i:16854464 original size:2 final size:2
Alignment explanation
Indices: 16854459--16854483 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16854449 AAAACTTAAT
16854459 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 T
16854484 TTTAAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16856183 original size:2 final size:2
Alignment explanation
Indices: 16856172--16856205 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
16856162 AAGTTACTTT
16856172 TA TA TA -A 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 T
16856206 TTCTGATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16856973 original size:2 final size:2
Alignment explanation
Indices: 16856966--16856990 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16856956 AAAATAACAA
16856966 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
16856991 ACTAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16861077 original size:22 final size:22
Alignment explanation
Indices: 16861052--16861093 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
16861042 GTATTGCAAG
16861052 ATTGATATT-TAGGCATTGCGTC
1 ATTGAT-TTATAGGCATTGCGTC
*
16861074 ATTGGTTTATAGGCATTGCG
1 ATTGATTTATAGGCATTGCG
16861094 AGACAAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.21, C:0.12, G:0.26, T:0.40
Consensus pattern (22 bp):
ATTGATTTATAGGCATTGCGTC
Found at i:16864510 original size:23 final size:23
Alignment explanation
Indices: 16864477--16864539 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 23
16864467 ACTTGCTAGT
*
16864477 GCAATACCATATCAACTAATCAC
1 GCAATATCATATCAACTAATCAC
* *
16864500 GCAATGTCATATCATTAACTAGTCAC
1 GCAATATCATATC---AACTAATCAC
16864526 GCAATATCATATCA
1 GCAATATCATATCA
16864540 TTAACTAGTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 12 0.36
26 21 0.64
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.27
Consensus pattern (23 bp):
GCAATATCATATCAACTAATCAC
Found at i:16864526 original size:26 final size:26
Alignment explanation
Indices: 16864490--16864557 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
16864480 ATACCATATC
*
16864490 AACTAATCACGCAATGTCATATCATT
1 AACTAGTCACGCAATGTCATATCATT
*
16864516 AACTAGTCACGCAATATCATATCATT
1 AACTAGTCACGCAATGTCATATCATT
*
16864542 AACTAGTCATGCAATG
1 AACTAGTCACGCAATG
16864558 ACTACAAACC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (26 bp):
AACTAGTCACGCAATGTCATATCATT
Found at i:16866818 original size:25 final size:25
Alignment explanation
Indices: 16866790--16866852 Score: 65
Period size: 25 Copynumber: 2.6 Consensus size: 25
16866780 TTTTCTTATA
* **
16866790 AAATAATATTTATAGAGTTACTGAT
1 AAATAATATTTATAGAGTAAAAGAT
* * *
16866815 AAATAATTTTTAAAGCGTAAAAGAT
1 AAATAATATTTATAGAGTAAAAGAT
16866840 AAATAA-ATTTATA
1 AAATAATATTTATA
16866853 CACACTGTAA
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
24 5 0.17
25 25 0.83
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.37
Consensus pattern (25 bp):
AAATAATATTTATAGAGTAAAAGAT
Found at i:16871388 original size:25 final size:26
Alignment explanation
Indices: 16871360--16871429 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 26
16871350 ACAGTCATGT
* *
16871360 AATGCCATACAGATAATAG-TCACAC
1 AATGCCATATAGATAATAGACCACAC
* * *
16871385 AATGCCATATAAATAA-CGACCACAT
1 AATGCCATATAGATAATAGACCACAC
16871410 AATGCCATATAGATAATAGA
1 AATGCCATATAGATAATAGA
16871430 ATGCAAGCAA
Statistics
Matches: 36, Mismatches: 7, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 1 0.03
25 33 0.92
26 2 0.06
ACGTcount: A:0.47, C:0.20, G:0.11, T:0.21
Consensus pattern (26 bp):
AATGCCATATAGATAATAGACCACAC
Found at i:16871503 original size:25 final size:26
Alignment explanation
Indices: 16871435--16871503 Score: 79
Period size: 25 Copynumber: 2.7 Consensus size: 26
16871425 ATAGAATGCA
* *
16871435 AGCAATGTCATACAGATAACAATCAT
1 AGCAATGACCTACAGATAACAATCAT
* *
16871461 AG-AATGCCCGACAGATAACAATCAT
1 AGCAATGACCTACAGATAACAATCAT
*
16871486 -GCAATGACCTACAAATAA
1 AGCAATGACCTACAGATAA
16871504 TAGTCACGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
24 1 0.03
25 33 0.92
26 2 0.06
ACGTcount: A:0.46, C:0.22, G:0.13, T:0.19
Consensus pattern (26 bp):
AGCAATGACCTACAGATAACAATCAT
Found at i:16894461 original size:6 final size:6
Alignment explanation
Indices: 16894437--16894476 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
16894427 TTGGTGGCAG
16894437 GAAAGGA GAAAG- G-AAGA GAAAGA GAAAGA GAAAGA -AAAGA
1 GAAA-GA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA
16894477 AAGAGAGGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
4 3 0.10
5 7 0.23
6 17 0.55
7 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:16894463 original size:16 final size:16
Alignment explanation
Indices: 16894437--16894482 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
16894427 TTGGTGGCAG
16894437 GAAAGGAGAAAG-GAAGA
1 GAAA-GAGAAAGAGAA-A
16894454 GAAAGAGAAAGAGAAA
1 GAAAGAGAAAGAGAAA
16894470 GAAA-AGAAAGAGA
1 GAAAGAGAAAGAGA
16894483 GGGTTTAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.32
16 12 0.43
17 7 0.25
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GAAAGAGAAAGAGAAA
Found at i:16894479 original size:21 final size:23
Alignment explanation
Indices: 16894437--16894482 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
16894427 TTGGTGGCAG
*
16894437 GAAAGGAGAAAGGAAGAGAAAGA
1 GAAAGGAGAAAGGAAAAGAAAGA
16894460 GAAA-GAGAAA-GAAAAGAAAGA
1 GAAAGGAGAAAGGAAAAGAAAGA
16894481 GA
1 GA
16894483 GGGTTTAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 12 0.55
22 6 0.27
23 4 0.18
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (23 bp):
GAAAGGAGAAAGGAAAAGAAAGA
Found at i:16894732 original size:7 final size:7
Alignment explanation
Indices: 16894720--16894752 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
16894710 TTAGGGGGGC
16894720 TTTTTTA
1 TTTTTTA
16894727 TTTTTTA
1 TTTTTTA
16894734 TTTTTTA
1 TTTTTTA
*
16894741 TGTTTTA
1 TTTTTTA
16894748 TTTTT
1 TTTTT
16894753 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.85
Consensus pattern (7 bp):
TTTTTTA
Found at i:16896428 original size:44 final size:44
Alignment explanation
Indices: 16896380--16896463 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
16896370 CTTTTTTATT
* *
16896380 TTTTTTTCTTTCTGCACTGGACGCAAGCTATC-GATCGTCGATTA
1 TTTTTTTCTTTATGCACTAGACGCAAGCTATCAG-TCGTCGATTA
*
16896424 TTTTTTTCTTTATTCACTAGACGCAAGCTATCAGTCGTCG
1 TTTTTTTCTTTATGCACTAGACGCAAGCTATCAGTCGTCG
16896464 GTCCTTAAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.42
Consensus pattern (44 bp):
TTTTTTTCTTTATGCACTAGACGCAAGCTATCAGTCGTCGATTA
Found at i:16896667 original size:16 final size:16
Alignment explanation
Indices: 16896646--16896684 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16896636 GAGAAGAAAG
16896646 AGAAAAAAACA-AAAAA
1 AGAAAAAAA-ATAAAAA
*
16896662 AGAAAAAAAATAAGAA
1 AGAAAAAAAATAAAAA
16896678 AGAAAAA
1 AGAAAAA
16896685 GAGGAAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 20 0.95
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (16 bp):
AGAAAAAAAATAAAAA
Found at i:16896676 original size:12 final size:12
Alignment explanation
Indices: 16896646--16896704 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
16896636 GAGAAGAAAG
*
16896646 AGAAAAAAACAAA
1 AGAAGAAAA-AAA
*
16896659 AAAAGAAAAAAA
1 AGAAGAAAAAAA
*
16896671 ATAAGAAAGAAAA
1 AGAAGAAA-AAAA
* *
16896684 AGAGGAAAGAAA
1 AGAAGAAAAAAA
16896696 AGAAGAAAA
1 AGAAGAAAA
16896705 GAAACAAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
12 20 0.54
13 17 0.46
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.02
Consensus pattern (12 bp):
AGAAGAAAAAAA
Found at i:16896683 original size:13 final size:12
Alignment explanation
Indices: 16896639--16896714 Score: 59
Period size: 13 Copynumber: 6.2 Consensus size: 12
16896629 AAAAGGTGAG
*
16896639 AAGAAAG-AGAA
1 AAGAAAGAAAAA
*
16896650 AA-AAACAAAAA
1 AAGAAAGAAAAA
16896661 AAGAAA-AAAAA
1 AAGAAAGAAAAA
16896672 TAAGAAAGAAAAA
1 -AAGAAAGAAAAA
* *
16896685 GAGGAAAGAAAAG
1 -AAGAAAGAAAAA
16896698 AAGAAAAGAAACAA
1 AAG-AAAGAAA-AA
16896712 AAG
1 AAG
16896715 TAATATATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
10 3 0.06
11 12 0.23
12 11 0.21
13 22 0.42
14 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.18, T:0.01
Consensus pattern (12 bp):
AAGAAAGAAAAA
Found at i:16896796 original size:94 final size:95
Alignment explanation
Indices: 16896633--16896818 Score: 295
Period size: 94 Copynumber: 2.0 Consensus size: 95
16896623 TAAGGGAAAA
*
16896633 GGTGAGAAGAAAGAGAAAAAAACAAAAAAAGAAAAAAAATAAGAAAGAAAAAGAGGAAAGAAAAG
1 GGTGAGAAGAAAGAGAAAAAAACAAAAAAAG-AAAAAAATAAAAAAGAAAAAGAGGAAAGAAAAG
16896698 AAGAAAAGAAACAAAAGTAATATATAATTAT
65 AAGAAAAGAAACAAAAGTAATATATAATTAT
* * * *
16896729 GGTGAGAGGAGAGAGAGAAAGAA-AAAAAAAG-AAAAAATAAAAAAGAATAAGAGGAAAGAAAAG
1 GGTGAGAAGAAAGAGA-AAAAAACAAAAAAAGAAAAAAATAAAAAAGAAAAAGAGGAAAGAAAAG
16896792 AAGAAAAGAAACAAAAGTAATATATAA
65 AAGAAAAGAAACAAAAGTAATATATAA
16896819 CTAAATATAA
Statistics
Matches: 84, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
94 57 0.68
96 22 0.26
97 5 0.06
ACGTcount: A:0.69, C:0.02, G:0.21, T:0.09
Consensus pattern (95 bp):
GGTGAGAAGAAAGAGAAAAAAACAAAAAAAGAAAAAAATAAAAAAGAAAAAGAGGAAAGAAAAGA
AGAAAAGAAACAAAAGTAATATATAATTAT
Found at i:16897081 original size:16 final size:16
Alignment explanation
Indices: 16897060--16897098 Score: 71
Period size: 15 Copynumber: 2.5 Consensus size: 16
16897050 TATTGCTTTG
16897060 TTTCTTTTCTTATTTT
1 TTTCTTTTCTTATTTT
16897076 TTTC-TTTCTTATTTT
1 TTTCTTTTCTTATTTT
16897091 TTTCTTTT
1 TTTCTTTT
16897099 TTCATCTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTCTTATTTT
Found at i:16897182 original size:15 final size:15
Alignment explanation
Indices: 16897162--16897199 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
16897152 TCTTTTCTTC
16897162 TTTTCTTTCCTT-TTT
1 TTTTCTTT-CTTATTT
16897177 TTTTCTTTCTTATTT
1 TTTTCTTTCTTATTT
16897192 TTTTCTTT
1 TTTTCTTT
16897200 TTTCATCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 3 0.14
15 19 0.86
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTTCTTATTT
Found at i:16897185 original size:27 final size:26
Alignment explanation
Indices: 16897145--16897202 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
16897135 TATATATTGC
* *
16897145 TTTTGTTTCTTTTCTTCTTTTCTTTCCT
1 TTTTTTTTCTTTTCTTATTTT-TTT-CT
16897173 TTTTTTTTC-TTTCTTATTTTTTTCT
1 TTTTTTTTCTTTTCTTATTTTTTTCT
16897198 TTTTT
1 TTTTT
16897203 CATCTGTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 7 0.25
26 3 0.11
27 10 0.36
28 8 0.29
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (26 bp):
TTTTTTTTCTTTTCTTATTTTTTTCT
Found at i:16897196 original size:11 final size:11
Alignment explanation
Indices: 16897145--16897203 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 11
16897135 TATATATTGC
*
16897145 TTTTGTTTCTT
1 TTTTCTTTCTT
*
16897156 TTCTTCTTT-TC
1 TT-TTCTTTCTT
*
16897167 TTTCCTTT-TT
1 TTTTCTTTCTT
16897177 TTTTCTTTCTT
1 TTTTCTTTCTT
16897188 ATTTT-TTTCTT
1 -TTTTCTTTCTT
16897199 TTTTC
1 TTTTC
16897204 ATCTGTCATG
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 17 0.44
11 13 0.33
12 9 0.23
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:16897438 original size:14 final size:14
Alignment explanation
Indices: 16897412--16897467 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
16897402 TATATATTGC
*
16897412 TTTTGTTTC-TTTCG
1 TTTT-TTTCTTTTCA
*
16897426 TTTTTTTCTTTTCTT
1 TTTTTTTCTTTTC-A
*
16897441 TTTTTTTCTTTTTTA
1 TTTTTTTC-TTTTCA
16897456 TTTTTTTCTTTT
1 TTTTTTTCTTTT
16897468 ATCATTGGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
13 4 0.11
14 12 0.33
15 16 0.44
16 4 0.11
ACGTcount: A:0.02, C:0.11, G:0.04, T:0.84
Consensus pattern (14 bp):
TTTTTTTCTTTTCA
Found at i:16897444 original size:15 final size:15
Alignment explanation
Indices: 16897426--16897467 Score: 68
Period size: 15 Copynumber: 2.8 Consensus size: 15
16897416 GTTTCTTTCG
16897426 TTTTTTTCTTTTCTT-
1 TTTTTTTCTTTT-TTA
16897441 TTTTTTTCTTTTTTA
1 TTTTTTTCTTTTTTA
16897456 TTTTTTTCTTTT
1 TTTTTTTCTTTT
16897468 ATCATTGGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 2 0.08
15 24 0.92
ACGTcount: A:0.02, C:0.10, G:0.00, T:0.88
Consensus pattern (15 bp):
TTTTTTTCTTTTTTA
Found at i:16904827 original size:19 final size:22
Alignment explanation
Indices: 16904786--16904827 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
16904776 AATAGTTAAA
*
16904786 TAGTATTTATATACAATATTTT
1 TAGTATTTATATAAAATATTTT
16904808 TAGTA-TTATA-AAAATATTTT
1 TAGTATTTATATAAAATATTTT
16904828 GGATGTAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 5 0.26
22 5 0.26
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TAGTATTTATATAAAATATTTT
Done.