Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold158
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: 3161772
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 138004 characters in sequence are not A, C, G, or T
File 2 of 9
Found at i:368049 original size:42 final size:44
Alignment explanation
Indices: 368003--368117 Score: 144
Period size: 44 Copynumber: 2.7 Consensus size: 44
367993 ATCTTCAGTT
*
368003 TGCTCCACTACAACTTCAGGGAGATAAGACT-TT-ACTTCAATC
1 TGCTCCACTACAACTTTAGGGAGATAAGACTATTGACTTCAATC
* * * * *
368045 TGCTCCACTACAACTTTAGGGAGATAGGATTATTGGCTTTAATT
1 TGCTCCACTACAACTTTAGGGAGATAAGACTATTGACTTCAATC
* *
368089 TGCTCCACTGCAACTTTAGAGAGATAAGA
1 TGCTCCACTACAACTTTAGGGAGATAAGA
368118 TTTGCCATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 28 0.45
43 2 0.03
44 32 0.52
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.30
Consensus pattern (44 bp):
TGCTCCACTACAACTTTAGGGAGATAAGACTATTGACTTCAATC
Found at i:368061 original size:225 final size:224
Alignment explanation
Indices: 367773--368257 Score: 573
Period size: 225 Copynumber: 2.2 Consensus size: 224
367763 TCATCATTTT
* * * * *
367773 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTAGTAGTTCAATCTGCTCTACTGCAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTA-TACTTCAATCTGCTCCACTACAACTTT
* * * * **
367837 AGGGAGATAAGATTGGT-ATTTTCAACCTACTCCACTACAACTTTAGGGAGATAAGGTTTGATGT
65 AGGGAGATAAGATTAGTGACTTT-AACCTACTCCACTACAACTTTAGAGAGATAAGATTTGACAT
* *
367901 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTTATGATTTATAGCTTTGATCTATTCCACT
129 GATCTACTCTACTGCAACTTCAGAGAGATAAGAT-TTATGATTTATAGCTTTAATCTATTCCACT
* * *
367966 GCAATCTTCAGGGAAACGAGATTTGCTATCTTC
193 G-AAGCTTCAGGAAAACGAGATTCGCTATCTTC
* * *
367999 AGTTTGCTCCACTACAACTTCAGGGAGATAAGACTT-TACTTCAATCTGCTCCACTACAACTTTA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATACTTCAATCTGCTCCACTACAACTTTA
* * * ** * * *
368063 GGGAGATAGGATTATTGGCTTTAATTTGCTCCACTGCAACTTTAGAGAGATAAGATTTGCCATGA
66 GGGAGATAAGATTAGTGACTTTAACCTACTCCACTACAACTTTAGAGAGATAAGATTTGACATGA
* * * * *
368128 TCTACTCTATTGCAACTTCAGAGAGATAAGATTTGTGATTTATAGCTTTAATCTGTTCCATTGTA
131 TCTACTCTACTGCAACTTCAGAGAGATAAGATTTATGATTTATAGCTTTAATCTATTCCACTGAA
*
368193 GCTTCAGGAAAATGAGATTCGCTATCTTC
196 GCTTCAGGAAAACGAGATTCGCTATCTTC
* * *
368222 AATCTAC-CCTATTGCAACTTCAGGGGGATAAGACTT
1 AATCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTT
368258 GCTTTCTTCA
Statistics
Matches: 217, Mismatches: 39, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
222 2 0.01
223 53 0.24
224 27 0.12
225 102 0.47
226 31 0.14
227 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.33
Consensus pattern (224 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTATACTTCAATCTGCTCCACTACAACTTTA
GGGAGATAAGATTAGTGACTTTAACCTACTCCACTACAACTTTAGAGAGATAAGATTTGACATGA
TCTACTCTACTGCAACTTCAGAGAGATAAGATTTATGATTTATAGCTTTAATCTATTCCACTGAA
GCTTCAGGAAAACGAGATTCGCTATCTTC
Found at i:368103 original size:44 final size:42
Alignment explanation
Indices: 367995--368120 Score: 153
Period size: 42 Copynumber: 3.0 Consensus size: 42
367985 GATTTGCTAT
* * *
367995 CTTCAGTTTGCTCCACTACAACTTCAGGGAGATAAGACTTTA
1 CTTCAATTTGCTCCACTACAACTTTAGGGAGATAAGATTTTA
* * *
368037 CTTCAATCTGCTCCACTACAACTTTAGGGAGATAGGATTATTGG
1 CTTCAATTTGCTCCACTACAACTTTAGGGAGATAAGATT-TT-A
* * *
368081 CTTTAATTTGCTCCACTGCAACTTTAGAGAGATAAGATTT
1 CTTCAATTTGCTCCACTACAACTTTAGGGAGATAAGATTT
368121 GCCATGATCT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
42 34 0.48
43 3 0.04
44 34 0.48
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (42 bp):
CTTCAATTTGCTCCACTACAACTTTAGGGAGATAAGATTTTA
Found at i:368323 original size:44 final size:44
Alignment explanation
Indices: 368268--368721 Score: 296
Period size: 44 Copynumber: 10.2 Consensus size: 44
368258 GCTTTCTTCA
* * *
368268 ATAAGACTTGTAACTTTAATCCGCTCCACTGTAACTTCAAGGAG
1 ATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
** *
368312 ATAAGATTTGTAACTTTAATCTGCTCCACTATAACTTCAGGGAG
1 ATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
** *
368356 ATAAGATTAT-TGGCTTTAATCTGCTCCACTGCAACTAT-AGGGAG
1 ATAAGATT-TGTAACTTTAATCTGCTCCACTGCAACT-TCAAGGAG
* * ** * * * *
368400 ATAAGATTTGCCATCTGCAGTCTGCCCCACTGTAACTTCAAGGGG
1 ATAAGATTTG-TAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
* ** * * * *
368445 ATAAGACTTGTTTTCTTCAGTCTACTCCATTGCAACTTC-AGCGAG
1 ATAAGATTTG-TAACTTTAATCTGCTCCACTGCAACTTCAAG-GAG
* *
368490 ATAAGACTTGTAACTTTAATC-CCTCCACTGCAACTTC-AGTGAG
1 ATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAAG-GAG
* ** * *
368533 ATAGGATTAT-TGGCTTTAATATGCTCCACTGCAACTTCATGGAG
1 ATAAGATT-TGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
* * * * * *
368577 ATAAGATTTGCCATCTTCAGTCTGCCCCACTGCAACTTC-AGGGG
1 ATAAGATTTG-TAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
* ** * * * * * *
368621 AATAAGACTTGCTTTCTTCAGTCTGATCCACTGTAACTTTAGGGAG
1 -ATAAGATTTG-TAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
* * *
368667 ATAAGACTTGTAACTTTAATCCGCTCCATTGCAA-TCTC-AGAGAG
1 ATAAGATTTGTAACTTTAATCTGCTCCACTGCAACT-TCAAG-GAG
368711 ATAAGATTTGT
1 ATAAGATTTGT
368722 GGTTTTACTG
Statistics
Matches: 323, Mismatches: 72, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
43 37 0.11
44 153 0.47
45 130 0.40
46 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (44 bp):
ATAAGATTTGTAACTTTAATCTGCTCCACTGCAACTTCAAGGAG
Found at i:368466 original size:45 final size:44
Alignment explanation
Indices: 368268--368700 Score: 254
Period size: 45 Copynumber: 9.8 Consensus size: 44
368258 GCTTTCTTCA
* * * * *
368268 ATAAGACTTG-TAACTTTAATCCGCTCCACTGTAACTTCAAGGAG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTC-AGGGG
* * * **
368312 ATAAGATTTG-TAACTTTAATCTGCTCCACTATAACTTCAGGGAG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGG-G
* ** *
368356 ATAAGA-TTATTGGCTTTAATCTGCTCCACTGCAACTAT-AGGGAG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACT-TCAGGG-G
* ** * * * *
368400 ATAAGATTTGCCATCTGCAGTCTGCCCCACTGTAACTTCAAGGGG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTC-AGGGG
* * * * *
368445 ATAAGACTTGTTTTCTTCAGTCTACTCCATTGCAACTTCAGCGAG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTCAG-GGG
* * * *
368490 ATAAGACTTG-TAACTTTAATC-CCTCCACTGCAACTTCAGTGAG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTCAG-GGG
* * ** * * *
368533 ATAGGA-TTATTGGCTTTAATATGCTCCACTGCAACTTCATGGAG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTCA-GGGG
* ** * *
368577 ATAAGATTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGG
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGGG
* * * *
368621 AATAAGACTTGCTT-TCTTCAGTCTGATCCACTGTAACTTTAGGGAG
1 -ATAAGACTTG-TTATCTTCAATCTGCTCCACTGCAACTTCAGGG-G
* * * *
368667 ATAAGACTTG-TAACTTTAATCCGCTCCATTGCAA
1 ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAA
368701 TCTCAGAGAG
Statistics
Matches: 307, Mismatches: 67, Indels: 30
0.76 0.17 0.07
Matches are distributed among these distances:
42 2 0.01
43 38 0.12
44 128 0.42
45 134 0.44
46 5 0.02
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (44 bp):
ATAAGACTTGTTATCTTCAATCTGCTCCACTGCAACTTCAGGGG
Found at i:368564 original size:177 final size:177
Alignment explanation
Indices: 368291--368718 Score: 605
Period size: 177 Copynumber: 2.4 Consensus size: 177
368281 CTTTAATCCG
* * ** *
368291 CTCCACTGTAACTTCAAGGAGATAAGATTTGTAACTTTAATCTGCTCCACTATAACTTCAGGGAG
1 CTCCACTGTAACTTC-AGGAGATAAGACTTGTAACTTTAATC-CCTCCACTGCAACTTCAGAGAG
*
368356 ATAAGATTATTGGCTTTAATCTGCTCCACTGCAACTAT-AGGGAGATAAGATTTGCCATCTGCAG
64 ATAAGATTATTGGCTTTAATATGCTCCACTGCAACT-TCAGGGAGATAAGATTTGCCATCTGCAG
* *
368420 TCTGCCCCACTGTAACTTCAAGGGG-ATAAGACTTGTTTTCTTCAGTCT-A
128 TCTGCCCCACTGCAACTTC-AGGGGAATAAGACTTGCTTTCTTCAGTCTGA
* * *
368469 CTCCATTGCAACTTCAGCGAGATAAGACTTGTAACTTTAATCCCTCCACTGCAACTTCAGTGAGA
1 CTCCACTGTAACTTCAG-GAGATAAGACTTGTAACTTTAATCCCTCCACTGCAACTTCAGAGAGA
* * *
368534 TAGGATTATTGGCTTTAATATGCTCCACTGCAACTTCATGGAGATAAGATTTGCCATCTTCAGTC
65 TAAGATTATTGGCTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTGCAGTC
368599 TGCCCCACTGCAACTTCAGGGGAATAAGACTTGCTTTCTTCAGTCTGA
130 TGCCCCACTGCAACTTCAGGGGAATAAGACTTGCTTTCTTCAGTCTGA
* *
368647 -TCCACTGTAACTTTAGGGAGATAAGACTTGTAACTTTAATCCGCTCCATTGCAA-TCTCAGAGA
1 CTCCACTGTAACTTCA-GGAGATAAGACTTGTAACTTTAATCC-CTCCACTGCAACT-TCAGAGA
368710 GATAAGATT
63 GATAAGATT
368719 TGTGGTTTTA
Statistics
Matches: 224, Mismatches: 19, Indels: 14
0.87 0.07 0.05
Matches are distributed among these distances:
176 6 0.03
177 156 0.70
178 62 0.28
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (177 bp):
CTCCACTGTAACTTCAGGAGATAAGACTTGTAACTTTAATCCCTCCACTGCAACTTCAGAGAGAT
AAGATTATTGGCTTTAATATGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCATCTGCAGTCT
GCCCCACTGCAACTTCAGGGGAATAAGACTTGCTTTCTTCAGTCTGA
Found at i:369025 original size:24 final size:24
Alignment explanation
Indices: 368998--369053 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
368988 CAAATTTCCC
368998 CCACTGTAATCTTCAAGGTTCAAA
1 CCACTGTAATCTTCAAGGTTCAAA
* *
369022 CCACTATAATCTTCAAGGTTCAAT
1 CCACTGTAATCTTCAAGGTTCAAA
*
369046 CTACTGTA
1 CCACTGTA
369054 CTTTTGGGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (24 bp):
CCACTGTAATCTTCAAGGTTCAAA
Found at i:375993 original size:22 final size:21
Alignment explanation
Indices: 375958--376015 Score: 53
Period size: 22 Copynumber: 2.7 Consensus size: 21
375948 AAAGGGTATC
* * *
375958 TACAAATTAAATCTCTAAGAT
1 TACAAATCATATCTCTAAAAT
375979 TACAAAATCATATCTTCTAAAAT
1 TAC-AAATCATATC-TCTAAAAT
* *
376002 TGCATATCATATCT
1 TACAAATCATATCT
376016 AAGATTGCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 9 0.30
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (21 bp):
TACAAATCATATCTCTAAAAT
Found at i:379130 original size:25 final size:25
Alignment explanation
Indices: 379102--379170 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
379092 TTTAAATTTA
*
379102 TTATCTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
* *
379127 TTATTTAATATAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAGT
379152 TCTATTTGATGTAATAAAA
1 T-TATTTGATGTAATAAAA
379171 ACCCTAACTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAGT
Found at i:379189 original size:18 final size:18
Alignment explanation
Indices: 379166--379987 Score: 1626
Period size: 18 Copynumber: 45.7 Consensus size: 18
379156 TTTGATGTAA
379166 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
*
379184 TAAAAACCCTAATTTAAT
1 TAAAAACCCTAACTTAAT
*
379202 TAAAACCCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379220 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379238 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379256 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379274 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379292 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379310 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379328 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379346 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379364 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379382 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379400 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379418 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379436 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379454 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379472 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379490 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379508 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379526 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379544 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379562 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379580 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379598 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379616 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379634 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379652 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379670 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379688 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379706 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379724 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379742 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379760 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379778 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379796 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379814 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379832 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379850 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379868 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379886 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379904 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379922 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379940 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379958 TAAAAACCCTAACTTAAT
1 TAAAAACCCTAACTTAAT
379976 TAAAAACCCTAA
1 TAAAAACCCTAA
379988 NNNNNNNNNN
Statistics
Matches: 800, Mismatches: 4, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 800 1.00
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (18 bp):
TAAAAACCCTAACTTAAT
Found at i:384505 original size:111 final size:111
Alignment explanation
Indices: 384282--384489 Score: 321
Period size: 111 Copynumber: 1.9 Consensus size: 111
384272 CCACGAGGGC
* * *
384282 GCGATTTCACAATTTCTTCTCAAATAGCATCCTGGTAGAAGCGATTTTTTACTATTTGACCAGAA
1 GCGATTTCACAATTTCTTCCCAAATAGCATCCTCGTAGAAGCGATTTTATACTATTTGACCAGAA
384347 ACGTCAACTCGAAATAAATTATTCCGGGACCTAAAACCCCTAAAAA
66 ACGTCAACTCGAAATAAATTATTCCGGGACCTAAAACCCCTAAAAA
* * *
384393 GCGATTTCACAATTTCTTCCCAATTAGCATCCTCG-AG-GGCGTGATTTTATACTATTTGTCCAG
1 GCGATTTCACAATTTCTTCCCAAATAGCATCCTCGTAGAAGC--GATTTTATACTATTTGACCAG
*
384456 AAACGTCAACTCGAAATAATTTATTCCGGGACCT
64 AAACGTCAACTCGAAATAAATTATTCCGGGACCT
384490 TTAAACCTTA
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
109 2 0.02
110 2 0.02
111 84 0.95
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (111 bp):
GCGATTTCACAATTTCTTCCCAAATAGCATCCTCGTAGAAGCGATTTTATACTATTTGACCAGAA
ACGTCAACTCGAAATAAATTATTCCGGGACCTAAAACCCCTAAAAA
Found at i:386668 original size:6 final size:6
Alignment explanation
Indices: 386657--386683 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
386647 AATTCAAAAA
386657 AAATTC AAATTC AAATTC AAATTC AAA
1 AAATTC AAATTC AAATTC AAATTC AAA
386684 AATATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTC
Found at i:388649 original size:51 final size:52
Alignment explanation
Indices: 388530--388658 Score: 183
Period size: 51 Copynumber: 2.5 Consensus size: 52
388520 ACTAGTGACT
*
388530 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTATGAAGAAAGATAGCTTTGGTCA
* *
388582 CAAGTGTGGTATTATGTGAAGGCCACTTTATGAAG-AAGGTAGCTTTGG-CTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTATGAAGAAAGATAGCTTTGGTC-A
*
388633 CAAGGGTGGTACTATGT-ACAGGCCAC
1 CAAGTGTGGTACTATGTGA-AGGCCAC
388659 CGGGTATCCG
Statistics
Matches: 70, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
50 2 0.03
51 35 0.50
52 33 0.47
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTATGAAGAAAGATAGCTTTGGTCA
Found at i:396539 original size:43 final size:42
Alignment explanation
Indices: 396468--396631 Score: 190
Period size: 43 Copynumber: 3.8 Consensus size: 42
396458 CAAAAAGCTC
* *
396468 ATACAATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAA
1 ATACGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAA
*
396510 ATAACGATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAATCAT
1 AT-ACGATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAATCAA
* * **
396553 ATACGACGCCAATGTCCCAGATATGGTCTTACACGTAAATGTCAA
1 ATACGATGCCAACGTCCCAGACGTGGTCTTACACGT-AA--TCAA
396598 AT-CGATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATACGATGCCAACGTCCCAGACGTGGTCTTACACG
396632 ATATCACATT
Statistics
Matches: 102, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
42 31 0.30
43 37 0.36
44 29 0.28
45 5 0.05
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (42 bp):
ATACGATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAA
Found at i:400012 original size:29 final size:29
Alignment explanation
Indices: 399970--400027 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
399960 GACTGAAATG
399970 GAGATATAGGAATGGATAATATAAGTACA
1 GAGATATAGGAATGGATAATATAAGTACA
*
399999 GAGATATAGGAATGGATAATATGAGTACA
1 GAGATATAGGAATGGATAATATAAGTACA
400028 CACTTGTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.26, T:0.24
Consensus pattern (29 bp):
GAGATATAGGAATGGATAATATAAGTACA
Found at i:412092 original size:12 final size:12
Alignment explanation
Indices: 412075--412104 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
412065 CCGAACATGC
412075 CCGTGTGCCAGG
1 CCGTGTGCCAGG
*
412087 CCGTGTGCTAGG
1 CCGTGTGCCAGG
412099 CCGTGT
1 CCGTGT
412105 AACAGCCTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.07, C:0.30, G:0.40, T:0.23
Consensus pattern (12 bp):
CCGTGTGCCAGG
Found at i:413276 original size:25 final size:25
Alignment explanation
Indices: 413238--413307 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
413228 CTGTACATGT
413238 ATGCTCACACGAGCTGTGAATCAAA
1 ATGCTCACACGAGCTGTGAATCAAA
* * * *
413263 ATTCTTACATGAGCTGTGAATCAGA
1 ATGCTCACACGAGCTGTGAATCAAA
413288 ATGCTCACACGAGCTGTGAA
1 ATGCTCACACGAGCTGTGAA
413308 AATATGCCTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (25 bp):
ATGCTCACACGAGCTGTGAATCAAA
Found at i:419994 original size:38 final size:38
Alignment explanation
Indices: 419936--420042 Score: 119
Period size: 38 Copynumber: 2.8 Consensus size: 38
419926 AACATTTACT
* *
419936 ACACCGACA-TCAAGCTTGCTACGCACTAAGCCTGAATA
1 ACACCGACACT-AAGCCTGCTAAGCACTAAGCCTGAATA
* *
419974 ACACC-AGCACTAAGCCTGCTAAGCACTAAGCTTGATTA
1 ACACCGA-CACTAAGCCTGCTAAGCACTAAGCCTGAATA
* * *
420012 ACATCGATACTAAGCCTACTAAGCACTAAGC
1 ACACCGACACTAAGCCTGCTAAGCACTAAGC
420043 TTGCTAGACA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
37 1 0.02
38 56 0.95
39 2 0.03
ACGTcount: A:0.36, C:0.30, G:0.15, T:0.20
Consensus pattern (38 bp):
ACACCGACACTAAGCCTGCTAAGCACTAAGCCTGAATA
Found at i:424363 original size:39 final size:39
Alignment explanation
Indices: 424320--424400 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 39
424310 TAACCACACT
* *
424320 AATTAGCTCATGTGTTTTAATTGTCTCCTACACGCCACA
1 AATTAGCTCATATGTTTTAATTGTCTCCTACACACCACA
*
424359 AATTAGCTCATATGTTTTAATTGTCTCCTATACACCACA
1 AATTAGCTCATATGTTTTAATTGTCTCCTACACACCACA
424398 AAT
1 AAT
424401 CTCTCAAGTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (39 bp):
AATTAGCTCATATGTTTTAATTGTCTCCTACACACCACA
Found at i:430928 original size:22 final size:22
Alignment explanation
Indices: 430886--430930 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
430876 ATTAGAAATC
*
430886 CTACCCAACCAGCCTCTACACT
1 CTACCCAACCAGCCTCAACACT
*
430908 CTACTCCATCCAGCC-CAACACT
1 CTAC-CCAACCAGCCTCAACACT
430930 C
1 C
430931 CATGTGGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.27, C:0.51, G:0.04, T:0.18
Consensus pattern (22 bp):
CTACCCAACCAGCCTCAACACT
Found at i:431146 original size:25 final size:27
Alignment explanation
Indices: 431118--431170 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
431108 ATAGTCATAC
*
431118 ATAACATA-GAGCAT-GCAGTTATTTT
1 ATAACATAGGAGCATAACAGTTATTTT
*
431143 ATAACATAGGGGCATAACAGTTATTTT
1 ATAACATAGGAGCATAACAGTTATTTT
431170 A
1 A
431171 CCACGTGGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 5 0.21
27 11 0.46
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (27 bp):
ATAACATAGGAGCATAACAGTTATTTT
Found at i:431168 original size:27 final size:26
Alignment explanation
Indices: 431133--431198 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
431123 ATAGAGCATG
431133 CAGTTATTTTATAACATAGGGGCATAA
1 CAGTTATTTTATAACAT-GGGGCATAA
** * *
431160 CAGTTATTTTACCACGTGGGGGATAA
1 CAGTTATTTTATAACATGGGGCATAA
*
431186 CAGTCATTTTATA
1 CAGTTATTTTATA
431199 TCAGTTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 18 0.56
27 14 0.44
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.35
Consensus pattern (26 bp):
CAGTTATTTTATAACATGGGGCATAA
Found at i:439731 original size:9 final size:9
Alignment explanation
Indices: 439717--439747 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
439707 GTTAAACGAA
439717 TCGAGTTAT
1 TCGAGTTAT
*
439726 TCGAGTTAA
1 TCGAGTTAT
439735 TCGAGTTAT
1 TCGAGTTAT
439744 TCGA
1 TCGA
439748 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:439817 original size:9 final size:9
Alignment explanation
Indices: 439800--439836 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
439790 TGAGTTTTCG
439800 AATTCGAAT
1 AATTCGAAT
439809 -ATCTCGAAT
1 AAT-TCGAAT
439818 AATTCGAAT
1 AATTCGAAT
439827 AATTCGAAT
1 AATTCGAAT
439836 A
1 A
439837 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:440816 original size:5 final size:5
Alignment explanation
Indices: 440806--440832 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
440796 AAATATTTTT
440806 ATTCG ATTCG ATTCG ATTCG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG AT
440833 CAAACGCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.41
Consensus pattern (5 bp):
ATTCG
Found at i:449870 original size:13 final size:13
Alignment explanation
Indices: 449833--449880 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
449823 TTAATTAAAC
449833 TTAATTAAATTAG-
1 TTAATT-AATTAGT
449846 TTAATTACATTAGT
1 TTAATTA-ATTAGT
*
449860 TTACTTAATTAGT
1 TTAATTAATTAGT
449873 CTTAATTA
1 -TTAATTA
449881 TAACAATATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
12 1 0.03
13 17 0.57
14 12 0.40
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (13 bp):
TTAATTAATTAGT
Found at i:459612 original size:5 final size:5
Alignment explanation
Indices: 459595--459627 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
459585 TTCAATTACA
*
459595 TTTAG TTTA- TTTAT TTTAT TTTAT TTTAT TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTA
459628 ACATAATGAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (5 bp):
TTTAT
Found at i:461172 original size:27 final size:27
Alignment explanation
Indices: 461142--461301 Score: 141
Period size: 27 Copynumber: 6.0 Consensus size: 27
461132 CGTAAACAAG
*
461142 TCATGAAAGAAATGCTTTTGTGGCGAA
1 TCATGAAAGAAATGCCTTTGTGGCGAA
* *
461169 TCATGAAAGAAATG-C-ATGTGGTGAA
1 TCATGAAAGAAATGCCTTTGTGGCGAA
* *
461194 TCATGAAAGAAAAGCCTTTGTGGAGAAA
1 TCATGAAAGAAATGCCTTTGTGGCG-AA
**
461222 T-ATGAAAGGAAAT-ATTTTGTGGCGAA
1 TCATGAAA-GAAATGCCTTTGTGGCGAA
** *
461248 TCATGAAAGAAAAACCATTGTGGCGAA
1 TCATGAAAGAAATGCCTTTGTGGCGAA
* * *
461275 TTATGAAAG-GATAGCCTCTGTGGCGAA
1 TCATGAAAGAAAT-GCCTTTGTGGCGAA
461302 CCCTACAAGG
Statistics
Matches: 106, Mismatches: 20, Indels: 14
0.76 0.14 0.10
Matches are distributed among these distances:
25 21 0.20
26 9 0.08
27 69 0.65
28 7 0.07
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (27 bp):
TCATGAAAGAAATGCCTTTGTGGCGAA
Found at i:461257 original size:54 final size:53
Alignment explanation
Indices: 461142--461285 Score: 166
Period size: 54 Copynumber: 2.7 Consensus size: 53
461132 CGTAAACAAG
* * *
461142 TCATGAAAGAAATGCTTTTGTGGCG-AATCATGAAA-GAAATGCATGTGGTGAA
1 TCATGAAAGAAAAGCCTTTGTGGCGAAAT-ATGAAAGGAAATGCATGTGGCGAA
* ***
461194 TCATGAAAGAAAAGCCTTTGTGGAGAAATATGAAAGGAAATATTTTGTGGCGAA
1 TCATGAAAGAAAAGCCTTTGTGGCGAAATATGAAAGGAAAT-GCATGTGGCGAA
* * *
461248 TCATGAAAGAAAAACCATTGTGGCGAATTATGAAAGGA
1 TCATGAAAGAAAAGCCTTTGTGGCGAAATATGAAAGGA
461286 TAGCCTCTGT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
52 28 0.36
53 8 0.10
54 42 0.54
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.25
Consensus pattern (53 bp):
TCATGAAAGAAAAGCCTTTGTGGCGAAATATGAAAGGAAATGCATGTGGCGAA
Found at i:461312 original size:81 final size:79
Alignment explanation
Indices: 461143--461297 Score: 195
Period size: 79 Copynumber: 1.9 Consensus size: 79
461133 GTAAACAAGT
* ** *
461143 CATGAAA-GAAATGCTTTTGTGGCGAATCATGAAAGAAATGCATGTGGTGAATCATGAAAGAAAA
1 CATGAAAGGAAAT-ATTTTGTGGCGAATCATGAAAGAAAACCATGTGGCGAATCATGAAAGAAAA
*
461207 GCCTTTGTGGAGAAA
65 GCCTCTGTGGAGAAA
* * * *
461222 TATGAAAGGAAATATTTTGTGGCGAATCATGAAAGAAAAACCATTGTGGCGAATTATGAAAGGAT
1 CATGAAAGGAAATATTTTGTGGCGAATCATGAAAG-AAAACCA-TGTGGCGAATCATGAAAGAAA
461287 AGCCTCTGTGG
64 AGCCTCTGTGG
461298 CGAACCCTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
79 27 0.42
80 10 0.16
81 27 0.42
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.25
Consensus pattern (79 bp):
CATGAAAGGAAATATTTTGTGGCGAATCATGAAAGAAAACCATGTGGCGAATCATGAAAGAAAAG
CCTCTGTGGAGAAA
Found at i:463041 original size:43 final size:42
Alignment explanation
Indices: 462989--463135 Score: 213
Period size: 42 Copynumber: 3.5 Consensus size: 42
462979 GTGCTAAACA
* **
462989 GAAACCCATAAGGGTTGAACTGAAGCTCGTAAGAGCTGAAGCG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAA-CG
* *
463032 GAAACCCATAAGGGTTAAATTGAAGCTCAAAAGAGTTGAACG
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
* * *
463074 AAAACCCATAAGGGTTAAACTGAAGCTTAAAAGAGCTGAACA
1 GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
463116 GAAACCCATAAGGGTTAAAC
1 GAAACCCATAAGGGTTAAAC
463136 AAAAACTTAT
Statistics
Matches: 93, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
42 58 0.62
43 35 0.38
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (42 bp):
GAAACCCATAAGGGTTAAACTGAAGCTCAAAAGAGCTGAACG
Found at i:471578 original size:5 final size:5
Alignment explanation
Indices: 471568--471607 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
471558 AGTTAAAATA
*
471568 TATAT TATAT TAGAT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
471608 ATGTTGAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:476656 original size:61 final size:61
Alignment explanation
Indices: 476580--476712 Score: 239
Period size: 61 Copynumber: 2.2 Consensus size: 61
476570 TTGGCACAGC
*
476580 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACGGAG
1 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACAGAG
* *
476641 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATGGTGTGTAGGGTTGGACAGAG
1 ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACAGAG
476702 ATGGTGTGTAG
1 ATGGTGTGTAG
476713 AGGTTGGTGA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.20, C:0.11, G:0.39, T:0.30
Consensus pattern (61 bp):
ATGGTGTGTAGGGATGGGTGGCTTGATTTAATCCCCACATAGTATGTAGGGTTGGACAGAG
Found at i:478493 original size:5 final size:5
Alignment explanation
Indices: 478483--478511 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
478473 TAAATGAGGC
478483 TATAT TATAT TATAT TATAT TATAT TATA
1 TATAT TATAT TATAT TATAT TATAT TATA
478512 AGGATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:478564 original size:11 final size:10
Alignment explanation
Indices: 478540--478588 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
478530 AAATAAAAAG
478540 ATAGAAAG--
1 ATAGAAAGAA
478548 ATAGAAACGAA
1 ATAGAAA-GAA
478559 ATAGAAAGAA
1 ATAGAAAGAA
*
478569 AAAGAAAGAA
1 ATAGAAAGAA
*
478579 AGA-AAAGAA
1 ATAGAAAGAA
478588 A
1 A
478589 GAAAAAGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
8 7 0.19
9 8 0.22
10 14 0.39
11 7 0.19
ACGTcount: A:0.71, C:0.02, G:0.20, T:0.06
Consensus pattern (10 bp):
ATAGAAAGAA
Found at i:478576 original size:4 final size:4
Alignment explanation
Indices: 478536--478604 Score: 54
Period size: 4 Copynumber: 17.0 Consensus size: 4
478526 AATAAAATAA
* *
478536 AAAG ATAG AAAG ATAG AAACG AAATAG AAAG -AA- AAAG AAAG AAAG AAAAG
1 AAAG AAAG AAAG AAAG AAA-G -AA-AG AAAG AAAG AAAG AAAG AAAG -AAAG
*
478586 AAAG AAA- AAGG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG
478605 GAAGGAGAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 14
0.72 0.08 0.19
Matches are distributed among these distances:
3 6 0.12
4 35 0.67
5 7 0.13
6 3 0.06
7 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.23, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:478579 original size:33 final size:33
Alignment explanation
Indices: 478517--478603 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 33
478507 TTATAAGGAT
* * *
478517 AAAATAAAG-AATA-AAATAAAAAGATAGAAAG
1 AAAAGAAAGAAATAGAAAGAAAAAGAAAGAAAG
*
478548 -ATAGAAACGAAATAGAAAGAAAAAGAAAGAAAG
1 AAAAGAAA-GAAATAGAAAGAAAAAGAAAGAAAG
*
478581 AAAAGAAAGAAAAAGGAAAGAAA
1 AAAAGAAAGAAATA-GAAAGAAA
478604 GGAAGGAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
30 5 0.11
31 1 0.02
32 4 0.09
33 21 0.47
34 14 0.31
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.07
Consensus pattern (33 bp):
AAAAGAAAGAAATAGAAAGAAAAAGAAAGAAAG
Found at i:478595 original size:29 final size:28
Alignment explanation
Indices: 478534--478604 Score: 72
Period size: 29 Copynumber: 2.5 Consensus size: 28
478524 AGAATAAAAT
* * * *
478534 AAAAAG-ATAGAAAGATAGAAACGAAAT
1 AAAAAGAAAAGAAAGAAAGAAAAGAAAG
*
478561 AGAAAGAAAAAGAAAGAAAGAAAAGAAAG
1 AAAAAG-AAAAGAAAGAAAGAAAAGAAAG
*
478590 AAAAAGGAAAGAAAG
1 AAAAAGAAAAGAAAG
478605 GAAGGAGAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
27 5 0.14
28 8 0.23
29 22 0.63
ACGTcount: A:0.72, C:0.01, G:0.23, T:0.04
Consensus pattern (28 bp):
AAAAAGAAAAGAAAGAAAGAAAAGAAAG
Found at i:478615 original size:20 final size:20
Alignment explanation
Indices: 478563--478615 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
478553 AACGAAATAG
*
478563 AAAGAAAAAGAAA-GAAAGA
1 AAAGAAAGAGAAAGGAAAGA
*
478582 AAAGAAAGAAAAAGGAAAGA
1 AAAGAAAGAGAAAGGAAAGA
* *
478602 AAGGAAGGAGAAAG
1 AAAGAAAGAGAAAG
478616 CTACGGCCAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 11 0.39
20 17 0.61
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAGAAAGGAAAGA
Found at i:479347 original size:21 final size:20
Alignment explanation
Indices: 479296--479358 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
479286 TAGTATATGA
* *
479296 TGAATTTATTGGATTTATAT
1 TGAATATATTGGATATATAT
*
479316 TGATTGA-ATTGGTATATATAT
1 TGAAT-ATATTGG-ATATATAT
479337 TGAATATATT-GAT-TAT-T
1 TGAATATATTGGATATATAT
479354 TGAAT
1 TGAAT
479359 TGAAATGAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 6 0.17
18 3 0.08
19 2 0.06
20 11 0.31
21 14 0.39
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (20 bp):
TGAATATATTGGATATATAT
Found at i:479498 original size:41 final size:41
Alignment explanation
Indices: 479454--479588 Score: 145
Period size: 41 Copynumber: 3.4 Consensus size: 41
479444 GACTTCGAGT
*
479454 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* * * *
479495 CGATGAGGCAGTGGGTGCCAATTTACT--TT-GGTTTAA-C
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* * *
479532 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATT-ATC
1 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
* *
479572 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
479589 CCTAACTGGT
Statistics
Matches: 76, Mismatches: 14, Indels: 9
0.77 0.14 0.09
Matches are distributed among these distances:
37 22 0.29
38 6 0.08
39 5 0.07
40 19 0.25
41 24 0.32
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (41 bp):
CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATC
Found at i:479578 original size:40 final size:40
Alignment explanation
Indices: 479454--479588 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
479444 GACTTCGAGT
* * *
479454 CGATGAGACACTGGGTGTCAATTTACTACTTCGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * * * *
479495 CGATGAGGCAGTGGGTG-CCAA-T-TTACTTTGGTTTAAC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
*
479532 CGATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
* *
479572 CAATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
479589 CCTAACTGGT
Statistics
Matches: 73, Mismatches: 18, Indels: 7
0.74 0.18 0.07
Matches are distributed among these distances:
37 16 0.22
38 12 0.16
39 2 0.03
40 28 0.38
41 15 0.21
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:488669 original size:40 final size:40
Alignment explanation
Indices: 488613--488732 Score: 120
Period size: 40 Copynumber: 3.0 Consensus size: 40
488603 TCAAGATACC
*
488613 ACAATTTTTTTACTATTTTTAAAAATTTTGAATAATTTTTT
1 ACAATTTTTTTACTATTTCTAAAAATTTT-AATAATTTTTT
* *
488654 ACAA-TTTTTTACTATTTCTAATAATTTTTATAATTTTTTT
1 ACAATTTTTTTACTATTTCTAAAAATTTTAATAA-TTTTTT
* *** * *
488694 ATAA-TACCTTACAATTTCTAATAATTTT-ATAATTTTTT
1 ACAATTTTTTTACTATTTCTAAAAATTTTAATAATTTTTT
488732 A
1 A
488733 TAGTTGTTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
38 7 0.10
39 8 0.11
40 51 0.73
41 4 0.06
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (40 bp):
ACAATTTTTTTACTATTTCTAAAAATTTTAATAATTTTTT
Found at i:488841 original size:10 final size:11
Alignment explanation
Indices: 488815--488843 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
488805 TATTATTTAT
488815 ATTTTTTGGTA
1 ATTTTTTGGTA
488826 ATTTTTTGGTA
1 ATTTTTTGGTA
488837 ATTTTTT
1 ATTTTTT
488844 AATATTTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (11 bp):
ATTTTTTGGTA
Found at i:489568 original size:23 final size:23
Alignment explanation
Indices: 489542--489587 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
489532 TGAAATCATC
*
489542 TAATATATAACT-AAGTTAAATAT
1 TAATAT-TAACTGAAATTAAATAT
*
489565 TAATATTAATTGAAATTAAATAT
1 TAATATTAACTGAAATTAAATAT
489588 ATATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.41
Consensus pattern (23 bp):
TAATATTAACTGAAATTAAATAT
Found at i:490412 original size:72 final size:72
Alignment explanation
Indices: 490295--490436 Score: 257
Period size: 72 Copynumber: 2.0 Consensus size: 72
490285 TCTCGGATTT
* *
490295 AAAAAAGGGATCATACCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATACCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
490360 CTTGATA
66 CTTGATA
*
490367 AAAAAAGGGATCATGCCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGATCATACCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
490432 CTTGA
66 CTTGA
490437 GTTTGAAAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (72 bp):
AAAAAAGGGATCATACCCAATAAGTTAGGACACGATCTCTTCTTAATTCCCGAGATCGTTTAAAA
CTTGATA
Found at i:492773 original size:44 final size:45
Alignment explanation
Indices: 492720--492931 Score: 153
Period size: 44 Copynumber: 4.6 Consensus size: 45
492710 CAGCTTCATT
* *
492720 CTGCTCCACTGCAACTTCAGGGAGATAATACTTGTATA-TTCAAC
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTATACTTCAAC
* * **
492764 TTGCCCCACTACAACTTCAAGGG-GATAAGGTTTGT-TACTTCAAC
1 CTGCCCCACTGCAACTTC-AGGGAGATAAGACTTGTATACTTCAAC
* * * * *
492808 CTGCTCTACTGCAACTTCAGAGAGATAAGACTTGTAGCCTGTCTTCAAT
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTA---T-ACTTCAAC
* * * * * *
492857 CTGCTCTACAGCAACTTCAGGGAGATAAGA-TTGGTTTATTTTTAAC
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTT-GTATA-CTTCAAC
* * *
492903 CTACTCCACTGCAATTTCAGGGAGATAAG
1 CTGCCCCACTGCAACTTCAGGGAGATAAG
492932 GTTTGATATG
Statistics
Matches: 132, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
43 5 0.04
44 54 0.41
45 4 0.03
46 30 0.23
48 3 0.02
49 36 0.27
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.30
Consensus pattern (45 bp):
CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGTATACTTCAAC
Found at i:493292 original size:50 final size:50
Alignment explanation
Indices: 493238--493922 Score: 574
Period size: 50 Copynumber: 13.7 Consensus size: 50
493228 TCAAAGAAAT
* * *
493238 AAGATTCGCTGTTATAGCTTCAATCTATTTAACTGCAATGTCGGGGAAAC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * ** * * *
493288 AAGATTCACTGTTGTAGCTTCAATATGTTCCACTACACTG-CTAGGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
* * *
493338 AAGATTCACTGTTGCAGCTTCAACCTATTTAACTGCAATGTC-GGGAAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGG-AAGC
* * * * ** *
493388 AAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCG-CTAGGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
* *
493438 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATATCAGGGAGGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* ** * * * **
493488 AAGATTCGCTGTTGTAGCTTCAATCTGTTCCACTAC-ATCGCCAAGGAAAT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAAT-GTCAGGGAAGC
* **
493538 AAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * * ** ** *
493588 AAGATTCACTATTGTAGCTTCAATATGTTCCACTGCACCG-CTAGGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTC-AGGGAAGC
* *
493638 AAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * * * *** * * **
493688 AAGACTCGCTACCTT-TAGCTTTAATTTGTTCCGCTGCAACGTTAGGGAAAT
1 AAGATTCGCT--GTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * *
493739 AAGATTCGCTGTTATAGCTTCAATCTATTTAACTGTAATGTCGGGGAAAC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * * **
493789 AAGATTCACTGTTGCAGCTTCAATCTATTTAACCGTAATGTTGGGGAAGC
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
* * * ** * * *
493839 AAGATTCGCTGTTGTAGCTTCAACCTGTTCT-ACTGTACCGCCAAGGAAGT
1 AAGATTCGCTGTTGTAGCTTCAATCTATT-TAACTGCAATGTCAGGGAAGC
493889 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACT
1 AAGATTCGCTGTTGTAGCTTCAATCTATTTAACT
493923 TTAGTCTTAA
Statistics
Matches: 493, Mismatches: 127, Indels: 30
0.76 0.20 0.05
Matches are distributed among these distances:
49 10 0.02
50 438 0.89
51 43 0.09
52 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (50 bp):
AAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGC
Found at i:493360 original size:100 final size:100
Alignment explanation
Indices: 493237--493812 Score: 787
Period size: 100 Copynumber: 5.8 Consensus size: 100
493227 GTCAAAGAAA
*
493237 TAAGATTCGCTGTTATAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
* *
493302 TAGCTTCAATATGTTCCACTACACTGCTAGGGAAG
66 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * *
493337 TAAGATTCACTGTTGCAGCTTCAACCTATTTAACTGCAATGTC-GGGAAAGCAAGATTCACTGTT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAA-CAAGATTCACTGTT
*
493401 GTAGCTTCAATATGTTTCACTGCACCGCTAGGGAAG
65 GTAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * ** *
493437 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATATCAGGGAGGCAAGATTCGCTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
* * * * * *
493502 TAGCTTCAATCTGTTCCACTACATCGCCAAGGAAA
66 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * * *
493537 TAAGATTCGTTGTTGTAGCTTCAATCTATTTAACTGCAATGTTGGGGAAGCAAGATTCACTATTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
493602 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
66 TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* * * * *
493637 TAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGCTACCT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACT--GT
* * * * * *
493702 T-TAGCTTTAATTTGTTCCGCTGCAACGTTAGGGAAA
64 TGTAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
* *
493738 TAAGATTCGCTGTTATAGCTTCAATCTATTTAACTGTAATGTCGGGGAAACAAGATTCACTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
*
493803 CAGCTTCAAT
66 TAGCTTCAAT
493813 CTATTTAACC
Statistics
Matches: 417, Mismatches: 54, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
99 8 0.02
100 318 0.76
101 89 0.21
102 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.32
Consensus pattern (100 bp):
TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
TAGCTTCAATATGTTCCACTGCACCGCTAGGGAAG
Found at i:493590 original size:200 final size:199
Alignment explanation
Indices: 493237--493914 Score: 847
Period size: 200 Copynumber: 3.4 Consensus size: 199
493227 GTCAAAGAAA
* * * *
493237 TAAGATTCGCTGTTATAGCTTCAATCTATTTAACTGCAATGTCGGGGAAACAAGATTCACTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
* * * * *
493302 TAGCTTCAATATGTTCCACTACACTGCTAGGGAAGTAAGATTCACTGTTGCAGCTTCAACCTATT
66 TAGCTTCAATCTGTTCCACTACAC-GCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTATT
*
493367 TAACTGCAATGTCGGGAAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAG
130 TAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAG
493432 GGAAG
195 GGAAG
* *
493437 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATATCAGGGAGGCAAGATTCGCTGTTG
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
* * *
493502 TAGCTTCAATCTGTTCCACTACATCGCCAAGGAAATAAGATTCGTTGTTGTAGCTTCAATCTATT
66 TAGCTTCAATCTGTTCCACTACA-CGCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTATT
* * *
493567 TAACTGCAATGTTGGGGAAGCAAGATTCACTATTGTAGCTTCAATATGTTCCACTGCACCGCTAG
130 TAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAG
493632 GGAAG
195 GGAAG
* * * *
493637 TAAGATTCGCTGTTTTAGCTTCAATCTATTTAACTGCAATGTCGGGGAAGCAAGACTCGCTACCT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCT--GT
* * * * * *
493702 T-TAGCTTTAATTTGTTCCGCTGCAACGTTAGGGAAATAAGATTCGCTGTTATAGCTTCAATCTA
64 TGTAGCTTCAATCTGTTCCACTAC-ACGCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTA
* * * * * * * * ** *
493766 TTTAACTGTAATGTCGGGGAAACAAGATTCACTGTTGCAGCTTCAATCTATTTAACCGTAATGTT
128 TTTAACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCT
*
493831 GGGGAAG
193 AGGGAAG
* * * * ** * * *
493838 CAAGATTCGCTGTTGTAGCTTCAACCTGTTCT-ACTGTACCGCCAAGGAAGTAAGATTCGCTGTT
1 TAAGATTCGCTGTTGTAGCTTCAATCTATT-TAACTGCAATGTCAGGGAAGCAAGATTCGCTGTT
493902 GTAGCTTCAATCT
65 GTAGCTTCAATCT
493915 ATTTAACTTT
Statistics
Matches: 409, Mismatches: 63, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
199 2 0.00
200 246 0.60
201 157 0.38
202 4 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (199 bp):
TAAGATTCGCTGTTGTAGCTTCAATCTATTTAACTGCAATGTCAGGGAAGCAAGATTCGCTGTTG
TAGCTTCAATCTGTTCCACTACACGCTAGGGAAATAAGATTCGCTGTTGTAGCTTCAATCTATTT
AACTGCAATGTCGGGGAAGCAAGATTCACTGTTGTAGCTTCAATATGTTTCACTGCACCGCTAGG
GAAG
Found at i:494800 original size:48 final size:48
Alignment explanation
Indices: 494729--494823 Score: 190
Period size: 48 Copynumber: 2.0 Consensus size: 48
494719 ACTTGGTGTG
494729 TTCTAAACAACAGTCCTGTTTCAGGTTCCTATATTATTTAGAAGCTTC
1 TTCTAAACAACAGTCCTGTTTCAGGTTCCTATATTATTTAGAAGCTTC
494777 TTCTAAACAACAGTCCTGTTTCAGGTTCCTATATTATTTAGAAGCTT
1 TTCTAAACAACAGTCCTGTTTCAGGTTCCTATATTATTTAGAAGCTT
494824 TCTAGAGTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.20, G:0.13, T:0.40
Consensus pattern (48 bp):
TTCTAAACAACAGTCCTGTTTCAGGTTCCTATATTATTTAGAAGCTTC
Found at i:495390 original size:15 final size:15
Alignment explanation
Indices: 495370--495419 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
495360 TGGCCTCTCT
495370 TTTTTCTTTTTCTTC
1 TTTTTCTTTTTCTTC
495385 TTTTTCTTTTTCTT-
1 TTTTTCTTTTTCTTC
* *
495399 TTCTTTCTTCTTCTCC
1 TT-TTTCTTTTTCTTC
495415 TTTTT
1 TTTTT
495420 TTAAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTTCTTTTTCTTC
Found at i:495402 original size:11 final size:12
Alignment explanation
Indices: 495378--495410 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
495368 CTTTTTTCTT
495378 TTTCTTCTTTTTC
1 TTTCTTC-TTTTC
495391 TTT-TTCTTTTC
1 TTTCTTCTTTTC
495402 TTTCTTCTT
1 TTTCTTCTT
495411 CTCCTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 8 0.42
13 3 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTCTTCTTTTC
Found at i:495406 original size:21 final size:21
Alignment explanation
Indices: 495370--495412 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
495360 TGGCCTCTCT
*
495370 TTTTTCTTTTTCTTCTTTTTC
1 TTTTTCTTTTTCTTCTTCTTC
495391 TTTTTC-TTTTCTTTCTTCTTC
1 TTTTTCTTTTTC-TTCTTCTTC
495412 T
1 T
495413 CCTTTTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (21 bp):
TTTTTCTTTTTCTTCTTCTTC
Found at i:498744 original size:106 final size:107
Alignment explanation
Indices: 498610--498823 Score: 421
Period size: 106 Copynumber: 2.0 Consensus size: 107
498600 GAAAAAAAAA
498610 ACAATGGACACCCTTTCTTTTTATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTG
1 ACAATGGACACCCTTTCTTTTTATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTG
498675 CATATAATGAGAAGTTAAATTCTACTTCTAA-AATATAACTT
66 CATATAATGAGAAGTTAAATTCTACTTCTAATAATATAACTT
498716 ACAATGGACACCCTTTCTTTTTATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTG
1 ACAATGGACACCCTTTCTTTTTATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTG
498781 CATATAATGAGAAGTTAAATTCTACTTCTAATAATATAACTT
66 CATATAATGAGAAGTTAAATTCTACTTCTAATAATATAACTT
498823 A
1 A
498824 AATTATTATA
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
106 96 0.90
107 11 0.10
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (107 bp):
ACAATGGACACCCTTTCTTTTTATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTG
CATATAATGAGAAGTTAAATTCTACTTCTAATAATATAACTT
Found at i:498841 original size:3 final size:3
Alignment explanation
Indices: 498831--498874 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
498821 TTAAATTATT
498831 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
498875 TAAAGAATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:498856 original size:106 final size:106
Alignment explanation
Indices: 498632--498856 Score: 285
Period size: 106 Copynumber: 2.1 Consensus size: 106
498622 CTTTCTTTTT
*
498632 ATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTGCATATAATGAGAAGTTAAATTC
1 ATATATAATAATATAGATGTTAATTATAAATTAACAAAAGTTGCATATAATGAGAAGTTAAATTC
**** ** ** *
498697 TACTTCTAAAATATAACTTACAATGGACACCCTTTCTTTTT
66 TACTTCTAAAATATAACTTACAATGGACAAAAATAATAATA
*
498738 ATATATAGTAATATAGATGTTAATTATAAATTAACAAAAGTTGCATATAATGAGAAGTTAAATTC
1 ATATATAATAATATAGATGTTAATTATAAATTAACAAAAGTTGCATATAATGAGAAGTTAAATTC
* *
498803 TACTTCTAATAATATAACTTA-AAT-TATTATAAAATAATAATA
66 TACTTCTAA-AATATAACTTACAATGGA-CA-AAAATAATAATA
498845 ATA-ATAATAATA
1 ATATATAATAATA
498857 ATAATAATAA
Statistics
Matches: 104, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
105 1 0.01
106 86 0.83
107 17 0.16
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (106 bp):
ATATATAATAATATAGATGTTAATTATAAATTAACAAAAGTTGCATATAATGAGAAGTTAAATTC
TACTTCTAAAATATAACTTACAATGGACAAAAATAATAATA
Found at i:499075 original size:17 final size:17
Alignment explanation
Indices: 499055--499087 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
499045 GTGAAGAGTC
499055 AAGGAAAATGAAAGGTT
1 AAGGAAAATGAAAGGTT
*
499072 AAGGAAGATGAAAGGT
1 AAGGAAAATGAAAGGT
499088 GAAAAGTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.33, T:0.15
Consensus pattern (17 bp):
AAGGAAAATGAAAGGTT
Found at i:506105 original size:22 final size:21
Alignment explanation
Indices: 506080--506159 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 21
506070 TACAAATTAA
* *
506080 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTGC-ATATCAT
506102 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTGCATATCAT
506124 ATC-C-AAGATTGCATATCAT
1 ATCTCTAAGATTGCATATCAT
506143 A--TCTAAGATTGCATATC
1 ATCTCTAAGATTGCATATC
506160 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.02
19 29 0.55
20 1 0.02
22 12 0.23
23 10 0.19
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCTAAGATTGCATATCAT
Found at i:506758 original size:44 final size:45
Alignment explanation
Indices: 506684--506845 Score: 112
Period size: 45 Copynumber: 3.6 Consensus size: 45
506674 ATTCTAATCC
* * * * *
506684 ACCCCACTACAACTTT-AGGGAGACAGGATTT-GTTTATTTAGTCT
1 ACCCCACTGCAA-TTTCAGGGAGATAAGATTTACTTTATTGAGTCT
* *
506728 ACCCCACTGCAATTTCAGGGGGATAAGATTTACTTTCTTGAGTCT
1 ACCCCACTGCAATTTCAGGGAGATAAGATTTACTTTATTGAGTCT
*** * * ** * *
506773 GTTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCT
1 ACCCCACTGCAATTTCAGGGAGATAAGATTTACTTTATTGAGTCT
* * * * *
506818 GCTCCTCCGCAACTTCAGGGAGATAAGA
1 ACCCCACTGCAATTTCAGGGAGATAAGA
506846 CCTGATATCT
Statistics
Matches: 97, Mismatches: 19, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
43 3 0.03
44 23 0.24
45 71 0.73
ACGTcount: A:0.25, C:0.23, G:0.22, T:0.30
Consensus pattern (45 bp):
ACCCCACTGCAATTTCAGGGAGATAAGATTTACTTTATTGAGTCT
Found at i:506780 original size:45 final size:45
Alignment explanation
Indices: 506731--506846 Score: 151
Period size: 45 Copynumber: 2.6 Consensus size: 45
506721 TTAGTCTACC
* * * * *
506731 CCACTGCAATTTCAGGGGGATAAGATTTACTTTCTTGAGTCTGTT
1 CCACTGCAACTTCAGGGAGATAAGACTCACTTTCTTGAGTCTGCT
* *
506776 CCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTCACTTTCTTGAGTCTGCT
* *
506821 CCTCCGCAACTTCAGGGAGATAAGAC
1 CCACTGCAACTTCAGGGAGATAAGAC
506847 CTGATATCTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 62 1.00
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.29
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTCACTTTCTTGAGTCTGCT
Found at i:507093 original size:44 final size:45
Alignment explanation
Indices: 506969--507184 Score: 116
Period size: 44 Copynumber: 4.9 Consensus size: 45
506959 ATAAGACTGG
* * * * *
506969 TGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTAC
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* * * * * ** *
507014 TATCTTCAGTCTGCTCCGCT-ACAACCCAGGGAGGCAAG-GCTAA
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* * *
507057 TGTCTTTGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTAC
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* **** * * * ** * **
507102 TATCTTTAACCTGCTCCACT-ACGACCCAGGGAGGCAAG-GCTGG
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
* * *
507145 TATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGA
1 TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGA
507185 TCTGCTGTCT
Statistics
Matches: 120, Mismatches: 47, Indels: 8
0.69 0.27 0.05
Matches are distributed among these distances:
43 36 0.30
44 51 0.43
45 33 0.28
ACGTcount: A:0.22, C:0.26, G:0.26, T:0.26
Consensus pattern (45 bp):
TGTCTTCGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGAGCTAA
Found at i:507118 original size:88 final size:88
Alignment explanation
Indices: 506965--507406 Score: 643
Period size: 88 Copynumber: 5.0 Consensus size: 88
506955 TTCGATAAGA
* * * * **
506965 CTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAAGAAGGCAAGATCTACTATCTTCAGTCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
*
507030 CGCTACAACCCAGGGAGGCAAGG
66 CACTACAACCCAGGGAGGCAAGG
** * * * * *
507053 CTAATGTCTTTGGTCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTACTATCTTTAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
*
507118 CACTACGACCCAGGGAGGCAAGG
66 CACTACAACCCAGGGAGGCAAGG
* *
507141 CTGGTATCTTCGATCTGCTTCGCTGTCAATGCAGGAAGGCAAGATCTGCTGTCTTCAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
*
507206 TACTACAACCCAGGGAGGCAAGG
66 CACTACAACCCAGGGAGGCAAGG
* *
507229 CTGGTATCTTCGATCTACTTCGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
* *
507294 CACTACGACCCAGGGAGGCAAGA
66 CACTACAACCCAGGGAGGCAAGG
*
507317 CTGGTATCTTCGATCTGCTTCGCTATCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
1 CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
* *
507382 CACAACGAA-CCAGGGAGACAAGG
66 CACTAC-AACCCAGGGAGGCAAGG
507405 CT
1 CT
507407 TTGTGATTTC
Statistics
Matches: 317, Mismatches: 36, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
88 316 1.00
89 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (88 bp):
CTGGTATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTC
CACTACAACCCAGGGAGGCAAGG
Found at i:507225 original size:44 final size:44
Alignment explanation
Indices: 507084--507395 Score: 195
Period size: 44 Copynumber: 7.1 Consensus size: 44
507074 GCTGTCGATG
* * *
507084 CAGGAAGGCAAGATCTACTATCTTTAACCTGCTCCACTACGACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
* * * * * * * * **
507128 CAGGGAGGCAAG-GCTGGTATCTTCGATCTGCT-TCGCTGTCAATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCT-ACT-ACGACC
* *
507172 CAGGAAGGCAAGATCTGCTGTCTTCAACCTGCTCTACTACAACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
* * * * * * * * **
507216 CAGGGAGGCAAG-GCTGGTATCTTCGATCTACT-TCGCTGTCGATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCT-ACT-ACGACC
* *
507260 TAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACTACGACC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
* * * * * **
507304 CAGGGAGGCAAGA-CTGGTATCTTCGATCTGCT-TCGCTATCGATG
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCT-ACTA-CGACC
* * *
507348 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACAACGAAC
1 CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
507392 CAGG
1 CAGG
507396 GAGACAAGGC
Statistics
Matches: 191, Mismatches: 65, Indels: 24
0.68 0.23 0.09
Matches are distributed among these distances:
42 1 0.01
43 51 0.27
44 86 0.45
45 52 0.27
46 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.24
Consensus pattern (44 bp):
CAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCTACTACGACC
Found at i:511753 original size:41 final size:41
Alignment explanation
Indices: 511696--511922 Score: 357
Period size: 41 Copynumber: 5.5 Consensus size: 41
511686 TTTAACAATT
* *
511696 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
511737 TCACCAGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
511778 TCA-CGGCACTTCGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
*
511818 TCACCGGCACTTAGCTTGGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCT-GCTAGGTTTATAACCTGATTCAGA
* ** *
511860 TTACTAGAACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
511901 TCACCGGCACTTAGCCTGCTAG
1 TCACCGGCACTTAGCCTGCTAG
511923 ACGTATAGTC
Statistics
Matches: 168, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
40 38 0.23
41 94 0.56
42 36 0.21
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAGA
Found at i:511897 original size:83 final size:81
Alignment explanation
Indices: 511704--511922 Score: 348
Period size: 83 Copynumber: 2.7 Consensus size: 81
511694 TTTCACCGGC
* * *
511704 ACTTAGCCTGCTAGGCTTATAGCCTGATTCAGATCACCAGCACTTAGCCTGCTAGGTTTATAACC
1 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACC
* *
511769 TGATTCAGATCACGGC
66 TGATTCAGATCACAGA
* *
511785 ACTTCGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCTTGGCTAGGTTTATAAC
1 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCT-GCTAGGTTTATAAC
*
511850 CTGATTCAGATTACTAGA
65 CTGATTCAGATCAC-AGA
511868 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAG
1 ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAG
511923 ACGTATAGTC
Statistics
Matches: 126, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
81 45 0.36
82 32 0.25
83 49 0.39
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (81 bp):
ACTTAGCCTGCTAGGTTTATAACCTGATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACC
TGATTCAGATCACAGA
Found at i:516158 original size:22 final size:21
Alignment explanation
Indices: 516133--516212 Score: 96
Period size: 19 Copynumber: 3.9 Consensus size: 21
516123 TACAAATTAA
* *
516133 ATCTCTAAGATTACAAAATCAT
1 ATCTCTAAGATTGC-ATATCAT
516155 ATCTTCTAAGATTGCATATCAT
1 ATC-TCTAAGATTGCATATCAT
516177 ATC-C-AAGATTGCATATCAT
1 ATCTCTAAGATTGCATATCAT
516196 A--TCTAAGATTGCATATC
1 ATCTCTAAGATTGCATATC
516213 CTTGAAGATT
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
18 1 0.02
19 29 0.55
20 1 0.02
22 12 0.23
23 10 0.19
ACGTcount: A:0.38, C:0.19, G:0.09, T:0.35
Consensus pattern (21 bp):
ATCTCTAAGATTGCATATCAT
Found at i:517711 original size:105 final size:106
Alignment explanation
Indices: 517566--517777 Score: 297
Period size: 105 Copynumber: 2.0 Consensus size: 106
517556 ATGGATTGAG
* * *
517566 ATTTAAGAGGATATTAGGCTATTTGGTTCAACAAGAAATCGAAACCCAGCACGTTAGGGCACGTT
1 ATTTAAAAGGATATTAGGCTATTTGGTTCAACAAGAAATCGAAACCCAGCACATTAGGGCACGAT
* *
517631 TTCTCGAATTTCCAAATGCAAAATATTG-CCTATTTTGAAA
66 TTCTCGAATTTCCAAACGCAAAATATTGTCCTATTTAGAAA
*
517671 ATTTAAAAGGATATTTTA-GCTATTTGG-TCGAACGA-AAATCGAAACCCAGCACATTAGGGCAC
1 ATTTAAAAGGATA--TTAGGCTATTTGGTTC-AACAAGAAATCGAAACCCAGCACATTAGGGCAC
* *
517733 GATTTCTCGGATTTCCAAACGCAAAATATTGTCTTATTTAGAAA
63 GATTTCTCGAATTTCCAAACGCAAAATATTGTCCTATTTAGAAA
517777 A
1 A
517778 ATTTTCCTTT
Statistics
Matches: 95, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
105 68 0.72
106 24 0.25
107 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (106 bp):
ATTTAAAAGGATATTAGGCTATTTGGTTCAACAAGAAATCGAAACCCAGCACATTAGGGCACGAT
TTCTCGAATTTCCAAACGCAAAATATTGTCCTATTTAGAAA
Found at i:518170 original size:12 final size:12
Alignment explanation
Indices: 518155--518185 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
518145 ATATAATAAG
518155 ATATAAAGATAT
1 ATATAAAGATAT
*
518167 ATATAAAGATGT
1 ATATAAAGATAT
518179 ATATAAA
1 ATATAAA
518186 TAGTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.10, T:0.32
Consensus pattern (12 bp):
ATATAAAGATAT
Found at i:518333 original size:3 final size:3
Alignment explanation
Indices: 518325--518391 Score: 50
Period size: 3 Copynumber: 23.3 Consensus size: 3
518315 ATATATAAAT
** * * *
518325 ATA ATA ATA ATA ACG ATA ATA ATA ATA ATA ATA CT- ATA TTA ATG AT-
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* *
518371 ATA AT- ATA ATA GTA GTA ATA A
1 ATA ATA ATA ATA ATA ATA ATA A
518392 GACTTAAAAT
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
2 5 0.10
3 45 0.90
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:520570 original size:25 final size:25
Alignment explanation
Indices: 520546--520593 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
520536 AAAATGGTTA
*
520546 TAAGA-AAATGAAAGGTGAAGAG-T
1 TAAGAGAAATGAAAGGTGAAAAGTT
*
520569 TAAGAGAGATGAAAGGTGAAAAGTT
1 TAAGAGAAATGAAAGGTGAAAAGTT
520594 GAACATTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 15 0.71
25 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.31, T:0.19
Consensus pattern (25 bp):
TAAGAGAAATGAAAGGTGAAAAGTT
Found at i:523476 original size:18 final size:19
Alignment explanation
Indices: 523450--523485 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
523440 ATAAGTGTGT
*
523450 GATTCAACA-ATATTTAAA
1 GATTAAACAGATATTTAAA
523468 GATTAAACAGATATTTAA
1 GATTAAACAGATATTTAA
523486 TAAAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (19 bp):
GATTAAACAGATATTTAAA
Found at i:528974 original size:21 final size:21
Alignment explanation
Indices: 528932--528974 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
528922 GTCGAAAAAT
*
528932 ATATAAAATTTTATATTATCC
1 ATATAAAAATTTATATTATCC
*
528953 ATATAATAAATTTA-ATTCTCC
1 ATATAA-AAATTTATATTATCC
528974 A
1 A
528975 ATATTTACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (21 bp):
ATATAAAAATTTATATTATCC
Found at i:533018 original size:16 final size:16
Alignment explanation
Indices: 532997--533036 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
532987 CGTTTGGTTC
*
532997 ACTGTAATGGAATAGA
1 ACTGTAATGAAATAGA
533013 ACTGTAATGAAATAGA
1 ACTGTAATGAAATAGA
*
533029 GCTGTAAT
1 ACTGTAAT
533037 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.42, C:0.07, G:0.23, T:0.28
Consensus pattern (16 bp):
ACTGTAATGAAATAGA
Found at i:536507 original size:30 final size:30
Alignment explanation
Indices: 536471--536546 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
536461 TGGTTGACAC
* *
536471 ATCCCTTTTCATAATTCGATAACCGAAGTT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
* **
536501 ATCCCTTTTCATAGTTCGACAGTCGAAGCT
1 ATCCCTTTTCATAATTCGACAACCGAAGCT
536531 ATCCCTTTTCATAATT
1 ATCCCTTTTCATAATT
536547 TGATGGTCGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.26, C:0.25, G:0.11, T:0.38
Consensus pattern (30 bp):
ATCCCTTTTCATAATTCGACAACCGAAGCT
Found at i:536631 original size:30 final size:31
Alignment explanation
Indices: 536590--536663 Score: 91
Period size: 30 Copynumber: 2.5 Consensus size: 31
536580 CGGTCGTCAC
* **
536590 CATCCATTTTCATAAT-TTGATAGCCGAAGAT
1 CATCCCTTTTCATAATATCAATAGCCGAAG-T
536621 -ATCCCTTTTCAT-ATATCAATAGCCGAAGT
1 CATCCCTTTTCATAATATCAATAGCCGAAGT
536650 CATCCCTTTTCATA
1 CATCCCTTTTCATA
536664 GTTGGATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 3 0.08
30 34 0.92
ACGTcount: A:0.30, C:0.24, G:0.09, T:0.36
Consensus pattern (31 bp):
CATCCCTTTTCATAATATCAATAGCCGAAGT
Found at i:536683 original size:120 final size:119
Alignment explanation
Indices: 536470--536777 Score: 361
Period size: 120 Copynumber: 2.6 Consensus size: 119
536460 ATGGTTGACA
* * * *
536470 CATCCCTTTTCATAATTCGATAACCGAAGTTATCCCTTTTCATAGT-TCGACAGTCGAAG-CTAT
1 CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATA-TATCAATAGTCGAAGTC-AT
* ** *
536533 CCCTTTTCATAATTTGATGGTCGTCACCATCCATTTTAATTTTTCGACGGTCGTCAC
64 CCCTTTTCATAATTGGATAATCGTCACCATCCATTTTAATTGTTC-ACGGTCGTCAC
* * *
536590 CATCCATTTTCATAATTTGATAGCCGAAGATATCCCTTTTCATATATCAATAGCCGAAGTCATCC
1 CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATATATCAATAGTCGAAGTCATCC
* * * * * * *
536655 CTTTTCATAGTTGGATAATCGTCCCCATCCCTTTTCATTGTTCATGGTTGTCTC
66 CTTTTCATAATTGGATAATCGTCACCATCCATTTTAATTGTTCACGGTCGTCAC
* * * * *
536709 CTTCCCTTTTCATAA-TCGATAGCTGAAGCTATCCCTTTTCATAGATCAATAGTCGAAGTTATCC
1 CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATATATCAATAGTCGAAGTCATCC
536773 CTTTT
66 CTTTT
536778 TATTCATCGA
Statistics
Matches: 160, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
118 48 0.30
119 22 0.14
120 89 0.56
121 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (119 bp):
CATCCCTTTTCATAATTCGATAGCCGAAGATATCCCTTTTCATATATCAATAGTCGAAGTCATCC
CTTTTCATAATTGGATAATCGTCACCATCCATTTTAATTGTTCACGGTCGTCAC
Found at i:536743 original size:29 final size:30
Alignment explanation
Indices: 536711--536777 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
536701 GTTGTCTCCT
*
536711 TCCCTTTTCATA-ATCGATAG-CTGAAGCTA
1 TCCCTTTTCATAGATCAATAGTC-GAAGCTA
*
536740 TCCCTTTTCATAGATCAATAGTCGAAGTTA
1 TCCCTTTTCATAGATCAATAGTCGAAGCTA
536770 TCCCTTTT
1 TCCCTTTT
536778 TATTCATCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 12 0.35
30 21 0.62
31 1 0.03
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (30 bp):
TCCCTTTTCATAGATCAATAGTCGAAGCTA
Found at i:543739 original size:25 final size:25
Alignment explanation
Indices: 543707--543762 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
543697 ATCATCATCA
*
543707 AAAT-GCTAAACCACAAGCCAAAAC
1 AAATGGCTAAACCAAAAGCCAAAAC
** *
543731 AAATGGCTATTCCAAAATCCAAAAC
1 AAATGGCTAAACCAAAAGCCAAAAC
*
543756 ACATGGC
1 AAATGGC
543763 CAACATTAGC
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 4 0.15
25 22 0.85
ACGTcount: A:0.48, C:0.27, G:0.11, T:0.14
Consensus pattern (25 bp):
AAATGGCTAAACCAAAAGCCAAAAC
Found at i:544222 original size:30 final size:30
Alignment explanation
Indices: 544188--544251 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
544178 AGCCGAAGCT
*
544188 ATCCCTGTTCATTATTTGATGGTCATCACC
1 ATCCCTGTTCATTATTCGATGGTCATCACC
* * **
544218 ATCCCTTTTCATTGTTCGATGGTTTTCACC
1 ATCCCTGTTCATTATTCGATGGTCATCACC
544248 ATCC
1 ATCC
544252 TTTTTAATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.17, C:0.28, G:0.12, T:0.42
Consensus pattern (30 bp):
ATCCCTGTTCATTATTCGATGGTCATCACC
Found at i:546122 original size:16 final size:14
Alignment explanation
Indices: 546104--546149 Score: 62
Period size: 13 Copynumber: 3.5 Consensus size: 14
546094 GGTCTAGTTT
546104 AGTA-TTGCTTTTG
1 AGTAGTTGCTTTTG
546117 AGTAG-TGCTTTTG
1 AGTAGTTGCTTTTG
546130 AGTAG-TGCTTTTG
1 AGTAGTTGCTTTTG
*
546143 AGAAGTT
1 AGTAGTT
546150 TTGTTTAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 29 0.97
14 1 0.03
ACGTcount: A:0.20, C:0.07, G:0.28, T:0.46
Consensus pattern (14 bp):
AGTAGTTGCTTTTG
Found at i:546125 original size:13 final size:13
Alignment explanation
Indices: 546104--546144 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
546094 GGTCTAGTTT
*
546104 AGTATTGCTTTTG
1 AGTAGTGCTTTTG
546117 AGTAGTGCTTTTG
1 AGTAGTGCTTTTG
546130 AGTAGTGCTTTTG
1 AGTAGTGCTTTTG
546143 AG
1 AG
546145 AAGTTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.17, C:0.07, G:0.29, T:0.46
Consensus pattern (13 bp):
AGTAGTGCTTTTG
Found at i:550928 original size:72 final size:72
Alignment explanation
Indices: 550715--550974 Score: 285
Period size: 72 Copynumber: 3.6 Consensus size: 72
550705 AATAAACTTT
* * * * *
550715 ATATCCAAAATC-AAATATAAACAACTATTGATAAAACTA-ATTTAGTATAACTAAGTAGAACAT
1 ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAGACTTAATATAAATAAGTAGAACAT
550778 AAATTCA
66 AAATTCA
* * * * * *
550785 ATATCCAAAAAAAAAAAAAACATAAACAATTATTAATAAAAAT-GACCCTAAGCATAAATAAGTA
1 ATATCC----AAAAACAAAACATAAACAACTATTGATAAAACTAGA-CTTAA-TATAAATAAGTA
*
550849 GACCATAAATTCA
60 GAACATAAATTCA
* *
550862 ATATCCAAAAACCAAACATAAACAACCATTGATAAAACTAGA-TTACATATAAATAAGTAGAACA
1 ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAGACTTA-ATATAAATAAGTAGAACA
550926 TAAATTCA
65 TAAATTCA
**
550934 ATATTAAAAAACAAAACATAAACAACTATTGATAAAACTAG
1 ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAG
550975 TTTAGCATTG
Statistics
Matches: 155, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
70 6 0.04
72 62 0.40
73 28 0.18
74 6 0.04
75 23 0.15
76 2 0.01
77 28 0.18
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.23
Consensus pattern (72 bp):
ATATCCAAAAACAAAACATAAACAACTATTGATAAAACTAGACTTAATATAAATAAGTAGAACAT
AAATTCA
Found at i:564075 original size:9 final size:9
Alignment explanation
Indices: 564061--564121 Score: 50
Period size: 9 Copynumber: 6.6 Consensus size: 9
564051 ATAATTTTAT
564061 TTTTTAAAA
1 TTTTTAAAA
564070 TTTTTAATAA
1 TTTTTAA-AA
*
564080 TTTTAAAAA
1 TTTTTAAAA
* *
564089 TTTTCATAA
1 TTTTTAAAA
**
564098 TTGTTTGCAA
1 TT-TTTAAAA
*
564108 TTTTTATAA
1 TTTTTAAAA
564117 TTTTT
1 TTTTT
564122 TATTATTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
9 28 0.67
10 14 0.33
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:564083 original size:18 final size:18
Alignment explanation
Indices: 564032--564099 Score: 59
Period size: 18 Copynumber: 3.7 Consensus size: 18
564022 CATTTTTAAT
564032 ATTTCTAATAATTTCTTAAATA
1 ATTT-TAATAA-TT-TTAAA-A
*
564054 ATTTT-AT-TTTTTAAAA
1 ATTTTAATAATTTTAAAA
*
564070 TTTTTAATAATTTTAAAA
1 ATTTTAATAATTTTAAAA
*
564088 ATTTTCATAATT
1 ATTTTAATAATT
564100 GTTTGCAATT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
16 5 0.13
17 7 0.18
18 20 0.51
20 2 0.05
21 1 0.03
22 4 0.10
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTAATAATTTTAAAA
Found at i:568839 original size:30 final size:30
Alignment explanation
Indices: 568774--568841 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
568764 ATAGTTGGAT
* * * *
568774 ACCAGATTATTCTAGATTATCATCTTACTTT
1 ACCA-ATTATTCCAGATTATCACCTCACTTC
*
568805 ACCAATTATTCCAGATTATCGCCTCACTTC
1 ACCAATTATTCCAGATTATCACCTCACTTC
568835 ACCAATT
1 ACCAATT
568842 TTTATGAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.29, C:0.26, G:0.06, T:0.38
Consensus pattern (30 bp):
ACCAATTATTCCAGATTATCACCTCACTTC
Found at i:570466 original size:19 final size:20
Alignment explanation
Indices: 570424--570472 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
570414 TTAGTATTTG
*
570424 TAAAATATAATTTGAATATA
1 TAAAATATAATTTAAATATA
* *
570444 TAAATTATATTTTAAATAT-
1 TAAAATATAATTTAAATATA
570463 TAAAATATAA
1 TAAAATATAA
570473 CATTATAAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TAAAATATAATTTAAATATA
Found at i:589217 original size:19 final size:18
Alignment explanation
Indices: 589195--589239 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
589185 TCTATTTTAG
589195 TTATTTTT-TTAGTTGTGAT
1 TTATTTTTGTTAGTTGT--T
589214 TTATTTATTGTTAGTTGTT
1 TTATTT-TTGTTAGTTGTT
589233 TTATTTT
1 TTATTTT
589240 ATTTTTGAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 13 0.54
20 2 0.08
21 8 0.33
ACGTcount: A:0.16, C:0.00, G:0.13, T:0.71
Consensus pattern (18 bp):
TTATTTTTGTTAGTTGTT
Found at i:589221 original size:23 final size:21
Alignment explanation
Indices: 589189--589245 Score: 55
Period size: 21 Copynumber: 2.7 Consensus size: 21
589179 TAGTTTTCTA
*
589189 TTTTAGTTATTTTTTTAGTTG
1 TTTTATTTATTTTTTTAGTTG
*
589210 TGATTTATTTA--TTGTTAGTTG
1 T--TTTATTTATTTTTTTAGTTG
589231 TTTTATTTTATTTTT
1 TTTTA-TTTATTTTT
589246 GAGACTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 9
0.70 0.08 0.22
Matches are distributed among these distances:
19 4 0.14
20 4 0.14
21 11 0.39
22 2 0.07
23 7 0.25
ACGTcount: A:0.16, C:0.00, G:0.12, T:0.72
Consensus pattern (21 bp):
TTTTATTTATTTTTTTAGTTG
Found at i:592295 original size:30 final size:30
Alignment explanation
Indices: 592261--592321 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
592251 TCCGGTGATA
* *
592261 GAAAAATGCAACGCTTGTTCGTTGATCGTT
1 GAAAAATGCAACGCTTATTCATTGATCGTT
*
592291 GAAAAATGCAACGTTTATTCATTGATCGTT
1 GAAAAATGCAACGCTTATTCATTGATCGTT
592321 G
1 G
592322 TAGAGGTGCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (30 bp):
GAAAAATGCAACGCTTATTCATTGATCGTT
Found at i:593083 original size:88 final size:86
Alignment explanation
Indices: 592786--593195 Score: 328
Period size: 88 Copynumber: 4.7 Consensus size: 86
592776 TTGTTTCCAA
* ** ** * *
592786 ATTAAAAGTAAATAAAATCCGTTTCATGATTTATTCCCGCCATTCAACGGATTTTATTCTATTAT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAAC-GATTTTA-T-TA-CA-
* * ***
592851 TTTTAATTTTATTTCCAAACGGGA-T
61 TTTTGATTTTTTTTCCAAAAATGAGT
* * ** * * *
592876 ATTAAAGTTAAATAAAACCCGTTTCGGGATTTATTCCCGTCGTTCAATGGATTTTATTCCAATTT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAA-CGATTTTATTAC-ATTT
* *
592941 TGATTTTATTACCAAAAATGAGT
64 TGATTTTTTTTCCAAAAATGAGT
* * * *
592964 ATTAAAATTAAAATAAAATCTGTTTCAGGATTTATTCCCACCGTTCAACGAATTTATTACATTTT
1 ATTAAAATT-AAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAACGATTTTATTACATTTT
*
593029 GATTTTTTTTGCCAAAAATGAGAA
65 GATTTTTTTT-CCAAAAATGAG-T
* *
593053 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCTGCCGTTTAACAAGATTTTATTTA-ATT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAAC--GATTTTA-TTACATT
* * *
593117 TT-ATGTTGTTTCC--AAATTAGT
63 TTGATTTTTTTTCCAAAAATGAGT
* * * *
593138 ATT-AAATTAAATAAAATCTATTTTGAGATTTATTCCCGCTGTTTAACAAGATTTTATT
1 ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAAC--GATTTTATT
593196 TTATTTTATT
Statistics
Matches: 270, Mismatches: 41, Indels: 25
0.80 0.12 0.07
Matches are distributed among these distances:
83 2 0.01
84 49 0.18
85 3 0.01
86 6 0.02
87 32 0.12
88 67 0.25
89 50 0.19
90 58 0.21
91 3 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (86 bp):
ATTAAAATTAAATAAAATCTATTTCGGGATTTATTCCCGCCGTTCAACGATTTTATTACATTTTG
ATTTTTTTTCCAAAAATGAGT
Found at i:597471 original size:389 final size:389
Alignment explanation
Indices: 596754--597532 Score: 1531
Period size: 389 Copynumber: 2.0 Consensus size: 389
596744 TATATTAATT
596754 TTTTTAAAATAATACATATGGAGTGGAAACTTAATATTTATAAAAGTTAAAATTAGCAAAATATA
1 TTTTTAAAATAATACATATGGAGTGGAAACTTAATATTTATAAAAGTTAAAATTAGCAAAATATA
* *
596819 TAAAAGAAATAAATTAGGTATTTATAAAGATAGATTTAAACCAATATATATACAAATATGCTAAA
66 TAAAAGAAATAAATTAGATACTTATAAAGATAGATTTAAACCAATATATATACAAATATGCTAAA
596884 GAAAGAACTTAAAATTAATGGCTTTAATAATATGAAATCCATAACATACAAAAGGAAAATAATTT
131 GAAAGAACTTAAAATTAATGGCTTTAATAATATGAAATCCATAACATACAAAAGGAAAATAATTT
596949 GATATAAAGTATGTTTTATAAAATAAAACCAGTAAAAAAAATCTATTGGATTAACATAAAAAAAA
196 GATATAAAGTATGTTTTATAAAATAAAACCAGTAAAAAAAATCTATTGGATTAACATAAAAAAAA
597014 TGAAATAATGATAATAATATAAAACCCTTAAAATAAAAGTACATAATACAAAAAAATTTAGGTAA
261 TGAAATAATGATAATAATATAAAACCCTTAAAATAAAAGTACATAATACAAAAAAATTTAGGTAA
597079 ATAAATATAAACAAAAATAAAATAATAAAACCAATAATAATAGTAATAATAGTAATAACAATAA
326 ATAAATATAAACAAAAATAAAATAATAAAACCAATAATAATAGTAATAATAGTAATAACAATAA
597143 TTTTTAAAATAATACATATGGAGTGGAAACTTAATATTTATAAAAGTTAAAATTAGCAAAATATA
1 TTTTTAAAATAATACATATGGAGTGGAAACTTAATATTTATAAAAGTTAAAATTAGCAAAATATA
597208 TAAAAGAAATAAATTAGATACTTATAAAGATAGATTTAAACCAATATATATACAAATATGCTAAA
66 TAAAAGAAATAAATTAGATACTTATAAAGATAGATTTAAACCAATATATATACAAATATGCTAAA
597273 GAAAGAACTTAAAATTAATGGCTTTAATAATATGAAATCCATAACATACAAAAGGAAAATAATTT
131 GAAAGAACTTAAAATTAATGGCTTTAATAATATGAAATCCATAACATACAAAAGGAAAATAATTT
*
597338 GATATAAAGTATGTTTTATAAAATAAAACCAGTAAAAAAAATCTATTGGATTAACATTAAAAAAA
196 GATATAAAGTATGTTTTATAAAATAAAACCAGTAAAAAAAATCTATTGGATTAACATAAAAAAAA
597403 TGAAATAATGATAATAATATAAAACCCTTAAAATAAAAGTACATAATACAAAAAAATTTAGGTAA
261 TGAAATAATGATAATAATATAAAACCCTTAAAATAAAAGTACATAATACAAAAAAATTTAGGTAA
597468 ATAAATATAAACAAAAATAAAATAATAAAACCAATAATAATAGTAATAATAGTAATAACAATAA
326 ATAAATATAAACAAAAATAAAATAATAAAACCAATAATAATAGTAATAATAGTAATAACAATAA
597532 T
1 T
597533 AATACTAATA
Statistics
Matches: 387, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
389 387 1.00
ACGTcount: A:0.56, C:0.07, G:0.08, T:0.29
Consensus pattern (389 bp):
TTTTTAAAATAATACATATGGAGTGGAAACTTAATATTTATAAAAGTTAAAATTAGCAAAATATA
TAAAAGAAATAAATTAGATACTTATAAAGATAGATTTAAACCAATATATATACAAATATGCTAAA
GAAAGAACTTAAAATTAATGGCTTTAATAATATGAAATCCATAACATACAAAAGGAAAATAATTT
GATATAAAGTATGTTTTATAAAATAAAACCAGTAAAAAAAATCTATTGGATTAACATAAAAAAAA
TGAAATAATGATAATAATATAAAACCCTTAAAATAAAAGTACATAATACAAAAAAATTTAGGTAA
ATAAATATAAACAAAAATAAAATAATAAAACCAATAATAATAGTAATAATAGTAATAACAATAA
Found at i:597506 original size:3 final size:3
Alignment explanation
Indices: 597483--597554 Score: 60
Period size: 3 Copynumber: 24.3 Consensus size: 3
597473 TATAAACAAA
* * * *
597483 AAT AA- AAT AAT AA- AACC AAT AAT AAT AGT AAT AAT AGT AAT AAC
1 AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
597527 AAT AAT AAT ACT AAT AAAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT A
597555 TTAAACTAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
2 6 0.11
3 44 0.80
4 5 0.09
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (3 bp):
AAT
Found at i:597554 original size:24 final size:24
Alignment explanation
Indices: 597491--597573 Score: 78
Period size: 27 Copynumber: 3.3 Consensus size: 24
597481 AAAATAAAAT
*
597491 AATAAAACCAATAATAATAGTAATA
1 AATAAAA-CAATAATAATACTAATA
597516 ATAGTAATAACAATAATAATACTAATA
1 A-A-TAA-AACAATAATAATACTAATA
* * *
597543 AATAAAATAATATTAA-ACTAAAAA
1 AATAAAACAATAATAATACT-AATA
597567 AATAAAA
1 AATAAAA
597574 TAGCACAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
23 3 0.06
24 19 0.38
25 4 0.08
26 2 0.04
27 20 0.40
28 2 0.04
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.25
Consensus pattern (24 bp):
AATAAAACAATAATAATACTAATA
Found at i:604230 original size:13 final size:14
Alignment explanation
Indices: 604214--604251 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
604204 TGTCCATTCA
604214 ACATTTCATAT-TT
1 ACATTTCATATGTT
*
604227 ACATTTCATGTGTT
1 ACATTTCATATGTT
*
604241 CCATTTCATAT
1 ACATTTCATAT
604252 ATTTGTTTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.26, C:0.18, G:0.05, T:0.50
Consensus pattern (14 bp):
ACATTTCATATGTT
Found at i:615572 original size:24 final size:24
Alignment explanation
Indices: 615545--615601 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
615535 AAGATTTAGT
*
615545 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGCATAATATATTTAAC
*
615569 ATTTATTAGCATAATATATTTGAC
1 ATTTATTAGCATAATATATTTAAC
*
615593 ATTGATTAG
1 ATTTATTAG
615602 AATTAGTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTATTAGCATAATATATTTAAC
Found at i:616962 original size:30 final size:30
Alignment explanation
Indices: 616926--616994 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
616916 TGAAGCAAGT
616926 AGAGCTACAGATTGATCCAGAATATACAAC
1 AGAGCTACAGATTGATCCAGAATATACAAC
*
616956 AGAGCTATAGATTGATCCAGAATATACAAC
1 AGAGCTACAGATTGATCCAGAATATACAAC
616986 AGAGTCTAC
1 AGAG-CTAC
616995 TCCTCATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 33 0.92
31 3 0.08
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (30 bp):
AGAGCTACAGATTGATCCAGAATATACAAC
Found at i:618954 original size:24 final size:24
Alignment explanation
Indices: 618898--618955 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
618888 GAAGAATTAG
* *
618898 TATTTATTAGTATGATATATTTAA
1 TATTTATTAGCATAATATATTTAA
* *
618922 CATTTATTAGCATAATATATTTCA
1 TATTTATTAGCATAATATATTTAA
*
618946 TATTGATTAG
1 TATTTATTAG
618956 AATTAGGTTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (24 bp):
TATTTATTAGCATAATATATTTAA
Found at i:621994 original size:54 final size:54
Alignment explanation
Indices: 621903--622026 Score: 142
Period size: 54 Copynumber: 2.3 Consensus size: 54
621893 TCTTAAATCC
* * * * *
621903 TGTAACTCACTGAGTT-AGATCACACGGCCGTGTCGCAGGCCATGTGCCAGATCG
1 TGTAACTCACTGACTTGTGA-CACACGGCCATGTCGCAGGCCATGTGCCAGACCA
* * * *
621957 TGTAACTCTCTGACTTGTGACACATGGCCATGTCGCAGGCCGTGTGCTAGACCA
1 TGTAACTCACTGACTTGTGACACACGGCCATGTCGCAGGCCATGTGCCAGACCA
*
622011 TGTTACTCACTGACTT
1 TGTAACTCACTGACTT
622027 CAAATAACAA
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 56 0.97
55 2 0.03
ACGTcount: A:0.21, C:0.27, G:0.25, T:0.27
Consensus pattern (54 bp):
TGTAACTCACTGACTTGTGACACACGGCCATGTCGCAGGCCATGTGCCAGACCA
Found at i:626012 original size:17 final size:17
Alignment explanation
Indices: 625990--626050 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
625980 GACTTGATTT
*
625990 TTATTTTTGTTTTTTTA
1 TTATTTGTGTTTTTTTA
626007 TTATTTGTGTTTTTTT-
1 TTATTTGTGTTTTTTTA
* *
626023 TTGTGTGTGTGTTTGTTTA
1 TTAT-T-TGTGTTTTTTTA
626042 TT-TTTGTGT
1 TTATTTGTGT
626051 ATAGCATTCC
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.21
17 17 0.45
18 11 0.29
19 2 0.05
ACGTcount: A:0.07, C:0.00, G:0.18, T:0.75
Consensus pattern (17 bp):
TTATTTGTGTTTTTTTA
Found at i:626021 original size:16 final size:15
Alignment explanation
Indices: 625987--626050 Score: 67
Period size: 16 Copynumber: 4.0 Consensus size: 15
625977 TTGGACTTGA
625987 TTTTTATTTTTGT-T
1 TTTTTATTTTTGTGT
626001 TTTTTATTATTTGTGT
1 TTTTTATT-TTTGTGT
*
626017 TTTTTTTTGTGTGTGTGT
1 TTTTTATT-T-T-TGTGT
626035 TTGTTTATTTTTGTGT
1 TT-TTTATTTTTGTGT
626051 ATAGCATTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 8 0.19
15 5 0.12
16 14 0.33
17 2 0.05
18 8 0.19
19 5 0.12
ACGTcount: A:0.06, C:0.00, G:0.17, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTTGTGT
Found at i:628688 original size:19 final size:20
Alignment explanation
Indices: 628651--628689 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
628641 TTTTGGATGA
*
628651 TGAACTAAGTTGTAATAAAC
1 TGAACTAAATTGTAATAAAC
628671 TGAACTAAATTG-AATAAAC
1 TGAACTAAATTGTAATAAAC
628690 CTAAAAACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.49, C:0.10, G:0.13, T:0.28
Consensus pattern (20 bp):
TGAACTAAATTGTAATAAAC
Found at i:644251 original size:24 final size:24
Alignment explanation
Indices: 644224--644274 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
644214 TGGTTTGTAT
644224 TTGTAATATGATTAATAACGCTCG
1 TTGTAATATGATTAATAACGCTCG
644248 TTGTAATATGATTAATAACGCTCG
1 TTGTAATATGATTAATAACGCTCG
644272 TTG
1 TTG
644275 AGTTAATTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.39
Consensus pattern (24 bp):
TTGTAATATGATTAATAACGCTCG
Found at i:646881 original size:13 final size:13
Alignment explanation
Indices: 646863--646887 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
646853 AGAAGAATGG
646863 AAAAAAGGAAATA
1 AAAAAAGGAAATA
646876 AAAAAAGGAAAT
1 AAAAAAGGAAAT
646888 GAAGTAAAAA
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:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (13 bp):
AAAAAAGGAAATA
Found at i:648028 original size:21 final size:21
Alignment explanation
Indices: 648004--648053 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
647994 CTTTTTTCTG
*
648004 TTTT-TTAATTGTTTTTCCTTT
1 TTTTATTAATTGGTTTT-CTTT
*
648025 TTTTATTATTTGGTTTTCTTT
1 TTTTATTAATTGGTTTTCTTT
648046 TTTTATTA
1 TTTTATTA
648054 TTTATTATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 16 0.62
22 10 0.38
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.76
Consensus pattern (21 bp):
TTTTATTAATTGGTTTTCTTT
Found at i:648054 original size:21 final size:22
Alignment explanation
Indices: 648016--648056 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
648006 TTTTAATTGT
648016 TTTTCCTTTTTTTATTATTTGG
1 TTTTCCTTTTTTTATTATTTGG
648038 TTTT-CTTTTTTTATTATTT
1 TTTTCCTTTTTTTATTATTT
648057 ATTATTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (22 bp):
TTTTCCTTTTTTTATTATTTGG
Found at i:652183 original size:25 final size:25
Alignment explanation
Indices: 652155--652210 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
652145 GCTCACATGT
*
652155 GCTTACCATTATTTAG-CTCGGAGGA
1 GCTTACCATTATTCAGCCT-GGAGGA
* *
652180 GCTTATCGTTATTCAGCCTGGAGGA
1 GCTTACCATTATTCAGCCTGGAGGA
652205 GCTTAC
1 GCTTAC
652211 TGTTTATAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 24 0.92
26 2 0.08
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.32
Consensus pattern (25 bp):
GCTTACCATTATTCAGCCTGGAGGA
Found at i:659102 original size:12 final size:12
Alignment explanation
Indices: 659085--659205 Score: 72
Period size: 12 Copynumber: 10.0 Consensus size: 12
659075 TTATAATAAT
* *
659085 AATAAACAAATA
1 AATAAAAAAACA
659097 AATAAAAAAACA
1 AATAAAAAAACA
659109 AATAAAAAAGA-A
1 AATAAAAAA-ACA
* *
659121 AA-AGGACAAACA
1 AATA-AAAAAACA
659133 AAT-AAAAAACA
1 AATAAAAAAACA
* *
659144 GA-AAAAAGACA
1 AATAAAAAAACA
*
659155 AACAAATAAAA-A
1 AATAAA-AAAACA
**
659167 AATAGAAAAAGGA
1 AATA-AAAAAACA
659180 AATAAAGAAAAACA
1 AAT-AA-AAAAACA
659194 AATAAAAAAACA
1 AATAAAAAAACA
659206 TAAAAAGGAC
Statistics
Matches: 84, Mismatches: 14, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
11 17 0.20
12 45 0.54
13 13 0.15
14 9 0.11
ACGTcount: A:0.78, C:0.07, G:0.07, T:0.07
Consensus pattern (12 bp):
AATAAAAAAACA
Found at i:659148 original size:26 final size:25
Alignment explanation
Indices: 659104--659179 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 25
659094 ATAAATAAAA
659104 AAACAAAT-AAAAAAGAAAAAGGAC
1 AAACAAATAAAAAAAGAAAAAGGAC
*
659128 AAACAAATAAAAAACAGAAAAAAGAC
1 AAACAAATAAAAAA-AGAAAAAGGAC
659154 AAACAAATAAAAAAATAGAAAAAGGA
1 AAACAAAT-AAAAAA-AGAAAAAGGA
659180 AATAAAGAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 8 0.17
25 5 0.11
26 18 0.39
27 15 0.33
ACGTcount: A:0.76, C:0.08, G:0.11, T:0.05
Consensus pattern (25 bp):
AAACAAATAAAAAAAGAAAAAGGAC
Found at i:659156 original size:62 final size:62
Alignment explanation
Indices: 659090--659217 Score: 152
Period size: 62 Copynumber: 2.1 Consensus size: 62
659080 ATAATAATAA
* * * *
659090 ACAAATAAATAAAAAAACAAATAAAAAAGAAA-AAGGACAAACAAAT-AAAAAACAGAAAAAAG
1 ACAAACAAAT-AAAAAA-AAAGAAAAAAGAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAG
* * * *
659152 ACAAACAAATAAAAAAATAGAAAAAGGAAATAAAGAAAAACAAATAAAAAAACATAAAAAGG
1 ACAAACAAATAAAAAAAAAGAAAAAAGAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAG
659214 ACAA
1 ACAA
659218 TAGGCAGCAG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 11 0.20
61 18 0.32
62 27 0.48
ACGTcount: A:0.77, C:0.08, G:0.09, T:0.07
Consensus pattern (62 bp):
ACAAACAAATAAAAAAAAAGAAAAAAGAAATAAAGAAAAACAAATAAAAAAACAGAAAAAAG
Found at i:659176 original size:35 final size:34
Alignment explanation
Indices: 659088--659212 Score: 105
Period size: 35 Copynumber: 3.7 Consensus size: 34
659078 TAATAATAAT
* *
659088 AAACAAATAAATAAAA-AAACAAATAAA-AAAGAA
1 AAACAAATAAA-AAAATAAAAAAAGAAATAAAGAA
** * * *
659121 AAA-GGACAAACAAATAAAAAACAGAAA-AAAGAC
1 AAACAAATAAAAAAATAAAAAA-AGAAATAAAGAA
*
659154 AAACAAATAAAAAAATAGAAAAAGGAAATAAAGAA
1 AAACAAATAAAAAAATA-AAAAAAGAAATAAAGAA
* *
659189 AAACAAATAAAAAAACATAAAAAG
1 AAACAAATAAAAAAATAAAAAAAG
659213 GACAATAGGC
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
31 3 0.04
32 9 0.13
33 15 0.21
34 18 0.25
35 26 0.37
ACGTcount: A:0.78, C:0.07, G:0.08, T:0.07
Consensus pattern (34 bp):
AAACAAATAAAAAAATAAAAAAAGAAATAAAGAA
Found at i:659198 original size:61 final size:60
Alignment explanation
Indices: 659103--659217 Score: 153
Period size: 62 Copynumber: 1.9 Consensus size: 60
659093 AATAAATAAA
* *
659103 AAAACAAATAAAAAAGAAAAAGGACAAACAAAT-AAAAAACAGAAAAAAGACAAACAAAT
1 AAAACAAATAAAAAAGAAAAAAGAAAAACAAATAAAAAAACAGAAAAAAGACAAACAAAT
* *
659162 AAAA-AAATAGAAAAAGGAAATAAAGAAAAACAAATAAAAAAACATAAAAAGGACAA
1 AAAACAAATA-AAAAA-GAAA-AAAGAAAAACAAATAAAAAAACAGAAAAAAGACAA
659218 TAGGCAGCAG
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
58 5 0.10
59 9 0.19
60 4 0.08
61 12 0.25
62 18 0.38
ACGTcount: A:0.77, C:0.08, G:0.10, T:0.06
Consensus pattern (60 bp):
AAAACAAATAAAAAAGAAAAAAGAAAAACAAATAAAAAAACAGAAAAAAGACAAACAAAT
Found at i:659213 original size:35 final size:35
Alignment explanation
Indices: 659144--659219 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
659134 ATAAAAAACA
* *
659144 GAAA-AAAGACAAACAAATAAAAAAATAGAAAAAG
1 GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
*
659178 GAAATAAAGAAAAACAAATAAAAAAACATAAAAAG
1 GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
659213 GACAATA
1 GA-AATA
659220 GGCAGCAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 4 0.11
35 29 0.78
36 4 0.11
ACGTcount: A:0.75, C:0.07, G:0.11, T:0.08
Consensus pattern (35 bp):
GAAATAAAGAAAAACAAATAAAAAAACAGAAAAAG
Found at i:661241 original size:26 final size:23
Alignment explanation
Indices: 661160--661241 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
661150 CAGCTTGTAT
* * * **
661160 GAGCTTATCGTTTCAGCTCTACG
1 GAGCTTACCGTTTTAGCTCGATA
661183 GAGCTTACCGTTTTAGCTCGATA
1 GAGCTTACCGTTTTAGCTCGATA
*
661206 CAGCTTACCGTTTATCAGCTCGGA-A
1 GAGCTTACCGTTT-T-AGCTC-GATA
661231 TGAGCTTACCG
1 -GAGCTTACCG
661242 ATCATGGCTC
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
23 30 0.62
24 1 0.02
25 6 0.12
26 11 0.23
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGTTTTAGCTCGATA
Found at i:666712 original size:151 final size:152
Alignment explanation
Indices: 666539--666843 Score: 603
Period size: 151 Copynumber: 2.0 Consensus size: 152
666529 TATGTGAATT
666539 ATGCTTTTATTTCATTAAGGTTAATTTGGTAAAATGGTTATTATTTCTAAATATTATATTTAAAT
1 ATGCTTTTATTTCATTAAGGTTAATTTGGTAAAATGGTTATTATTTCTAAATATTATATTTAAAT
666604 ATGAAACGTTGCTTAAAAAACGAAATGTCTTATTATTTTTATTTGTTTCTATTTAGGTTTTTTTT
66 ATGAAACGTTGCTTAAAAAACGAAATGTCTTATTATTTTTATTTGTTTCTATTTAGGTTTTTTTT
666669 TTTAAAAAGTG-AGAATTACAA
131 TTTAAAAAGTGTAGAATTACAA
666690 ATGCTTTTATTTCATTAAGGTTAATTTGGTAAAATGGTTATTATTTCTAAATATTATATTTAAAT
1 ATGCTTTTATTTCATTAAGGTTAATTTGGTAAAATGGTTATTATTTCTAAATATTATATTTAAAT
666755 ATGAAACGTTGCTTAAAAAACGAAATGTCTTATTATTTTTATTTGTTTCTATTTAGGTTTTTTTT
66 ATGAAACGTTGCTTAAAAAACGAAATGTCTTATTATTTTTATTTGTTTCTATTTAGGTTTTTTTT
666820 TTTAAAAAGTGTAGAATTACAA
131 TTTAAAAAGTGTAGAATTACAA
666842 AT
1 AT
666844 ATATATATAT
Statistics
Matches: 153, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
151 141 0.92
152 12 0.08
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.49
Consensus pattern (152 bp):
ATGCTTTTATTTCATTAAGGTTAATTTGGTAAAATGGTTATTATTTCTAAATATTATATTTAAAT
ATGAAACGTTGCTTAAAAAACGAAATGTCTTATTATTTTTATTTGTTTCTATTTAGGTTTTTTTT
TTTAAAAAGTGTAGAATTACAA
Found at i:670085 original size:71 final size:72
Alignment explanation
Indices: 669969--670112 Score: 272
Period size: 71 Copynumber: 2.0 Consensus size: 72
669959 AATCTAATCG
669969 TCAACCTGTCCACATTAATTTCATAGATTGGTTCTTTAGTGTTTTTTTTTTTTTTTTTTTTTT-C
1 TCAACCTGTCCACATTAATTTCATAGATTGGTTCTTTAGTGTTTTTTTTTTTTTTTTTTTTTTGC
*
670033 GGTAAAA
66 AGTAAAA
670040 TCAACCTGTCCACATTAATTTCATAGATTGGTTCTTTAGTGTTTTTTTTTTTTTTTTTTTTTTGC
1 TCAACCTGTCCACATTAATTTCATAGATTGGTTCTTTAGTGTTTTTTTTTTTTTTTTTTTTTTGC
670105 AGTAAAA
66 AGTAAAA
670112 T
1 T
670113 TTGGAAAACT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
71 63 0.89
72 8 0.11
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.56
Consensus pattern (72 bp):
TCAACCTGTCCACATTAATTTCATAGATTGGTTCTTTAGTGTTTTTTTTTTTTTTTTTTTTTTGC
AGTAAAA
Found at i:693160 original size:15 final size:15
Alignment explanation
Indices: 693136--693169 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
693126 TTAACCCGAA
*
693136 AACCCTAAAAAAAAG
1 AACCCGAAAAAAAAG
*
693151 AACCCGAAAACAAAG
1 AACCCGAAAAAAAAG
693166 AACC
1 AACC
693170 TTTAAAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.26, G:0.09, T:0.03
Consensus pattern (15 bp):
AACCCGAAAAAAAAG
Found at i:701394 original size:12 final size:14
Alignment explanation
Indices: 701365--701400 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
701355 CTCAAATTTT
701365 AATTTATCATATTC
1 AATTTATCATATTC
701379 AATTTATCA-A-TC
1 AATTTATCATATTC
701391 AATTTATCAT
1 AATTTATCAT
701401 CTCTTTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.52
13 1 0.05
14 9 0.43
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (14 bp):
AATTTATCATATTC
Found at i:702891 original size:13 final size:13
Alignment explanation
Indices: 702873--702898 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
702863 TACAACAAAT
702873 TTAAGTAGAATCA
1 TTAAGTAGAATCA
702886 TTAAGTAGAATCA
1 TTAAGTAGAATCA
702899 ACTTTTGCAC
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:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (13 bp):
TTAAGTAGAATCA
Found at i:703826 original size:19 final size:20
Alignment explanation
Indices: 703788--703827 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
703778 AACATTCCTT
*
703788 AACTTAAGATAACATAAAAA
1 AACTTAAGATAAAATAAAAA
*
703808 AACTT-AGATAAAATCAAAA
1 AACTTAAGATAAAATAAAAA
703827 A
1 A
703828 TCATACTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.65, C:0.10, G:0.05, T:0.20
Consensus pattern (20 bp):
AACTTAAGATAAAATAAAAA
Done.