Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 68 of 144
Found at i:20670217 original size:41 final size:41
Alignment explanation
Indices: 20670156--20670489 Score: 164
Period size: 46 Copynumber: 7.8 Consensus size: 41
20670146 GATTAAAGGA
* *
20670156 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGAGAAGATCACATCAGG
* * *
20670197 TCTTATCTCCCTGAGATTACAGTGGA-ACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGA-AGATC--A-CA--TCAGG
* * * *
20670243 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGAT-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGAAGATC-A-CATCAG--G
* * * ** *
20670287 TCCTATCTCCTTGAGATTACAATGGAGCGGATTA-A--AGG
1 TCTTATCTCCCTGAGATTACAGTGGAGAAGATCACATCAGG
* *
20670325 ATCTTATCTCTCTGA-AGTTACAGTAGAGAAGATCACATCAGG
1 -TCTTATCTCCCTGAGA-TTACAGTGGAGAAGATCACATCAGG
* * *
20670367 TCTTATCTCCCTGAGATTACAGTGGA-ACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGA-AGATC--A-CA--TCAGG
* * * *
20670413 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGA-AGCCAGAG
1 TCTTATCTCCCTGAGATTACAGTGGAGAAGA-TCACA-TCAG-G
* *
20670456 ATCTTATCTCCCTGAGATTACAGCGGAGCAGATC
1 -TCTTATCTCCCTGAGATTACAGTGGAGAAGATC
20670490 GAAGACACTA
Statistics
Matches: 228, Mismatches: 39, Indels: 50
0.72 0.12 0.16
Matches are distributed among these distances:
38 1 0.00
39 24 0.11
40 5 0.02
41 53 0.23
42 10 0.04
43 6 0.03
44 59 0.26
45 5 0.02
46 65 0.29
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (41 bp):
TCTTATCTCCCTGAGATTACAGTGGAGAAGATCACATCAGG
Found at i:20670264 original size:46 final size:45
Alignment explanation
Indices: 20669723--20670668 Score: 373
Period size: 44 Copynumber: 21.8 Consensus size: 45
20669713 ATTATACAGG
*
20669723 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * ** * *
20669769 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA--GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-AATTCAGA
* * * *
20669813 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * **
20669856 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * * *
20669900 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * **
20669943 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * * *
20669987 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * **
20670030 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGAT-TAA-AATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAAT-TCAGA
* * * *
20670074 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * *
20670117 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAG------GA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGAATTCAGA
* * * *
20670156 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATTCAGA
*
20670197 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * * *
20670243 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAGGATAGT-A-A
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * * * *
20670287 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG------GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
* * * *
20670326 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--A-CA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGAATTCAGA
*
20670367 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAA-TTCAGA
* * ** * *
20670413 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCA--GAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-AATTCAGA
* * * *
20670457 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * *
20670500 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAT-AGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGA-ATTCAGA
* * * *
20670544 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCA-GA
* * * * *
20670587 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAT-AGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGA-ATTCAGA
* * *
20670631 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGA
20670669 CACTATCCTA
Statistics
Matches: 696, Mismatches: 127, Indels: 155
0.71 0.13 0.16
Matches are distributed among these distances:
37 2 0.00
38 1 0.00
39 50 0.07
40 2 0.00
41 54 0.08
42 25 0.04
43 178 0.26
44 253 0.36
45 21 0.03
46 107 0.15
47 3 0.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.25
Consensus pattern (45 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGAATTCAGA
Found at i:20670333 original size:170 final size:169
Alignment explanation
Indices: 20669897--20670484 Score: 742
Period size: 170 Copynumber: 3.4 Consensus size: 169
20669887 TTAAAATAAG
20669897 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
* ** * *
20669962 CAGTGGAGCGGATTAAAATAAGAGATCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGA-AGA
66 CAGTGGAGCGGATT---A-AAG-GATCTTATCTCTCTGAAG-TTACAGTAGAGAAGATC-ACA-T
** * * * ** ***
20670025 CACTATCCTATCTCCCTGA-AGTTACAGTGGAGCGGA-TTAA-AATAAG
123 CA-GGTCTTATCTCCCTGAGA-TTACAGTGGAACAGACCAAAGAATTTC
20670071 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
20670136 CAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTT
66 CAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTT
20670201 ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
131 ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
* * *
20670240 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATC-AAGGATAGTAATCCTATCTCCTTG-AGA
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAA-GACACT-ATCCTATCTCCCTGAAG-
*
20670303 TTACAATGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGT
63 TTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGT
20670368 CTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
128 CTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
* * * * ** *
20670410 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGAT
1 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTATCCTATCTCCCTGAAG-T
*
20670474 TACAGCGGAGC
64 TACAGTGGAGC
20670485 AGATCGAAGA
Statistics
Matches: 374, Mismatches: 30, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
167 26 0.07
168 8 0.02
169 74 0.20
170 184 0.49
171 3 0.01
174 79 0.21
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (169 bp):
AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
CAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTT
ATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTC
Found at i:20670507 original size:87 final size:87
Alignment explanation
Indices: 20670367--20670746 Score: 520
Period size: 87 Copynumber: 4.4 Consensus size: 87
20670357 TCACATCAGG
* * * * * * *
20670367 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TATCCTATCTCCCTGAAGTT
* * ***
20670431 ACAGTGGAGCAGATTGAAGCCAGAGA
62 ACAGTGGAGCGGATTAAAATAAGAGA
20670457 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
*
20670522 TGGAGCGGATTAAAATAATAGA
66 TGGAGCGGATTAAAATAAGAGA
20670544 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
*
20670609 TGGAGCGGATTAAAATAATAGA
66 TGGAGCGGATTAAAATAAGAGA
20670631 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
20670696 TGGAGCGGATT---A-AAG-GA
66 TGGAGCGGATTAAAATAAGAGA
* * * *
20670713 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATCG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCG
20670747 CATCAAGTCT
Statistics
Matches: 271, Mismatches: 18, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
82 32 0.12
83 2 0.01
84 1 0.00
87 200 0.74
88 1 0.00
90 34 0.13
91 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.26
Consensus pattern (87 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
TGGAGCGGATTAAAATAAGAGA
Found at i:20670608 original size:174 final size:175
Alignment explanation
Indices: 20670197--20670709 Score: 546
Period size: 174 Copynumber: 3.0 Consensus size: 175
20670187 TCACATCAGG
* *
20670197 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTG-AGATT
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAG-TT
* * * * * * ** * *
20670261 ACAGCGGAGCAGATCAAGGA-TAGTA-ATCCTATCTCCTTGAGATTACAATGGAGCGGAT--TA-
63 ACAGTGGAGCAGATTAA-AACAAG-AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG
** * * * ** * * * *
20670321 A-AGGATCTTATCTCTCTGAAGTTACAGTAGAGAAGA-TCACAT--CAGG
126 ACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAATAGA
* * *
20670367 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAA--TCAGATCCTATCTCCCTGAAGTTA
* * *
20670432 CAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
64 CAGTGGAGCAGATTAAAACAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
20670497 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAATAGA
129 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAATAGA
* * * *
20670544 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A-CACTATCCTATCTCCCTGAAGTTAC
1 TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCA-GATCCTATCTCCCTGAAGTTAC
* * *
20670607 AGTGGAGCGGATTAAAATAATAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAC
65 AGTGGAGCAGATTAAAACAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAC
20670672 TATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
130 TATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAA
20670710 GGATCTTATC
Statistics
Matches: 295, Mismatches: 37, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
169 1 0.00
170 105 0.36
171 1 0.00
172 1 0.00
173 3 0.01
174 144 0.49
175 4 0.01
176 1 0.00
177 35 0.12
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (175 bp):
TCTTATCTCCCTGAGATTACAGCGGAACAGACCAAAGAATCAGATCCTATCTCCCTGAAGTTACA
GTGGAGCAGATTAAAACAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACT
ATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAATAGA
Found at i:20670717 original size:470 final size:461
Alignment explanation
Indices: 20669726--20670745 Score: 1208
Period size: 470 Copynumber: 2.2 Consensus size: 461
20669716 ATACAGGTCT
*
20669726 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTACAG
1 TATCTCCCTGAGATTACAGTGGAACAGACCAAAG------AGATCTTATCTCCCTGAGATTACAG
** * ** * * ** * * *
20669791 TGGAGCAGATTGAA-GCCAG-AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAC
60 CAGAGCAGA-TCAAGGATAGTA-ATCCTATCTCCTTGAGATTACAATGGAGCGGAT--TA-A-AG
* * * * ** * * *
20669854 TATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAGAGATCTTATCTCCCTGAGATTA
119 GATCTTATCTCTCTGAAGTTACAGTAGAGAAGA-TCACATCAG-G-TCTTATCTCCCTGAGATTA
* * * * * *
20669919 CAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAG
181 CAGCGGAACAGACCAAAGACACGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAG
20669984 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
246 AGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTA
20670049 CAGTGGAGCGGATTAAAATAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
311 CAGTGGAGCGGATTAAAATAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA
* * *
20670114 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAGGATCTTATCTCTCTGAAGTTACAGT
376 CTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAGATCTTATCTCCCTGAAGTTACAGC
* * *
20670179 AGAGAAGATCACATCAGGTCT
441 AGAGAAGATCACAACAGATCC
20670200 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGATTACAG
1 TATCTCCCTGAGATTACAGTGGAACAGACCAAAG------AGATCTTATCTCCCTGAGATTACAG
*
20670265 CGGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTT
60 CAGAGCAGATCAAGGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTT
*
20670330 ATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGTGGAAC
125 ATCTCTCTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGCGGAAC
* * * * *
20670395 AGACCAAAGA-ATTTCAGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATC
190 AGACCAAAGACA---C-GATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAGAGATC
20670459 TTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTG
251 TTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTG
*
20670524 GAGCGGATTAAAATAATAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATC
316 GAGCGGATTAAAATAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATC
20670589 CTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAATAGATCTTATCTCCCTG-AGATTACAG
381 CTATCTCCCTGAAGTTACAGTGGAGCGGATT---A-AA-AGATCTTATCTCCCTGAAG-TTACAG
* * *
20670653 CGGAGCAGATCGA-AGACACTATCC
440 CAGAGAAGATC-ACA-ACA-GATCC
* * ** * *
20670677 TATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAG-GATCTTATCTCTCTGAGGTTACAGCAGAG
1 TATCTCCCTGAGA-TTACAGTGGAACAGACCAAAGAGATCTTATCTCCCTGAGATTACAGCAGAG
*
20670740 TAGATC
65 CAGATC
20670746 GCATCAAGTC
Statistics
Matches: 479, Mismatches: 51, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
466 1 0.00
467 34 0.07
468 1 0.00
469 7 0.01
470 259 0.54
471 1 0.00
472 1 0.00
473 4 0.01
474 107 0.22
475 30 0.06
476 4 0.01
477 30 0.06
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (461 bp):
TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAGATCTTATCTCCCTGAGATTACAGCAGAGC
AGATCAAGGATAGTAATCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAGGATCTTATCTCT
CTGAAGTTACAGTAGAGAAGATCACATCAGGTCTTATCTCCCTGAGATTACAGCGGAACAGACCA
AAGACACGATCCTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAACAAGAGATCTTATCTCCCT
GAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTA
AAATAAGAGATCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCT
GAAGTTACAGTGGAGCGGATTAAAAGATCTTATCTCCCTGAAGTTACAGCAGAGAAGATCACAAC
AGATCC
Found at i:20672558 original size:14 final size:12
Alignment explanation
Indices: 20672508--20672553 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
20672498 ATATACATAC
20672508 TTATATATATTT
1 TTATATATATTT
*
20672520 TATATTTTATAATTT
1 T-TA-TATAT-ATTT
20672535 TTATATATATTT
1 TTATATATATTT
20672547 TTATATA
1 TTATATA
20672554 CATATACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 6 0.21
15 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATATATTT
Found at i:20682495 original size:70 final size:70
Alignment explanation
Indices: 20682316--20682559 Score: 255
Period size: 71 Copynumber: 3.5 Consensus size: 70
20682306 CATACAGCTT
* * ** * * **
20682316 ATAAGATGAGATAGAAGTCCTAAGATCGACGTAAATGATCCCGTTTAATTTGTTCTAGACTAGAA
1 ATAAAATGAGATAGAAGTCCTAAAATCGGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAA
20682381 TTCCG
66 TTCCG
* * *
20682386 AAAAAGATGAGACAGAAGTCCTAAAATCAGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGA
1 ATAAA-ATGAGATAGAAGTCCTAAAATCGGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGA
20682451 ATTCCG
65 ATTCCG
* * * *
20682457 ATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTTGTTTGATC---A--AGAA
1 ATAAAATGAGATAGAAGTCCTAAAATCGGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAA
*
20682517 TTCTG
66 TTCCG
* * * * *
20682522 ATAAAATGATATAAAAGTCCTAAGATCAGTGTGAATGA
1 ATAAAATGAGATAGAAGTCCTAAAATCGGTGTAAATGA
20682560 TGAGTCCATC
Statistics
Matches: 147, Mismatches: 26, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
65 39 0.27
67 1 0.01
70 47 0.32
71 60 0.41
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.29
Consensus pattern (70 bp):
ATAAAATGAGATAGAAGTCCTAAAATCGGTGTAAATGACCCCATTTTGTTTGTTCTAGACTAGAA
TTCCG
Found at i:20682559 original size:65 final size:65
Alignment explanation
Indices: 20682377--20682693 Score: 242
Period size: 65 Copynumber: 4.7 Consensus size: 65
20682367 GTTCTAGACT
* * * * * * *
20682377 AGAATTCCGAAAAAGATGAGACAGAAGTCCTAAAATCAGTGTAAATGACCCCATTTTGTTTGTTC
1 AGAATTCTGATAAA-ATGAGATAAAAGTCCTAAGATCAGTGTAAATGACCCCATCTCGTTTGTTC
20682442 TAGA
65 ---A
* * * ** * * *
20682446 CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTTGTTTGAT
1 --AGAATTCTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGACCCCATCTCGTTTGTT
20682511 CA
64 CA
* ** *
20682513 AGAATTCTGATAAAATGATATAAAAGTCCTAAGATCAGTGTGAATGATGAGTCCATCTCCTTTGT
1 AGAATTCTGATAAAATGAGATAAAAGTCCTAAGATCAGTGT-AA--ATGACCCCATCTCGTTTGT
*
20682578 TCT
63 TCA
* * * ** *
20682581 AGAATTCTGATCAAATGAGGA-AGAAAGTCCTAGGCTTGGTGTAAATGACCCCATCTCATTTGTT
1 AGAATTCTGATAAAATGA-GATA-AAAGTCCTAAGATCAGTGTAAATGACCCCATCTCGTTTGTT
20682645 CA
64 CA
* * * *
20682647 AGAATTCCT-ATAAATTGAGATAGATGTTCTAAGATCAGTGTAAATGA
1 AGAATT-CTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGA
20682694 TGATCCCGTC
Statistics
Matches: 200, Mismatches: 39, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
65 54 0.27
66 34 0.17
67 3 0.01
68 36 0.18
69 16 0.08
70 44 0.22
71 13 0.06
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.30
Consensus pattern (65 bp):
AGAATTCTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGACCCCATCTCGTTTGTTCA
Found at i:20682715 original size:134 final size:133
Alignment explanation
Indices: 20682446--20682696 Score: 326
Period size: 134 Copynumber: 1.9 Consensus size: 133
20682436 TTGTTCTAGA
**
20682446 CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTTGTTTGAT
1 CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTCATTTGAT
* *
20682511 CAAGAATTCTGATAAAATGATATAAAAGTCCTAAGATCAGTGTGAATGATGAGTCCATCTCCTTT
66 CAAGAATTCTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGATGAGTCCATCTCCTTT
20682576 GTT
131 GTT
* * *** *
20682579 CTAGAATTCTGATCAAATGAGGA-AGAAAGTCCTAGGCTTGGTGTAAATGACCCCATCTCATTTG
1 CTAGAATTCCGATAAAATGA-GATAG-AAGTCCTAAAATTGGTGCAAATGACCCCATCTCATTTG
* * * * *
20682643 TTCAAGAATTCCT-ATAAATTGAGATAGATGTTCTAAGATCAGTGTAAATGATGA
64 ATCAAGAATT-CTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGATGA
20682697 TCCCGTCTCA
Statistics
Matches: 100, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
133 20 0.20
134 78 0.78
135 2 0.02
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (133 bp):
CTAGAATTCCGATAAAATGAGATAGAAGTCCTAAAATTGGTGCAAATGACCCCATCTCATTTGAT
CAAGAATTCTGATAAAATGAGATAAAAGTCCTAAGATCAGTGTAAATGATGAGTCCATCTCCTTT
GTT
Found at i:20688189 original size:52 final size:52
Alignment explanation
Indices: 20688127--20688277 Score: 230
Period size: 52 Copynumber: 2.9 Consensus size: 52
20688117 AATAATTGTT
* * *
20688127 TTTCACTTTGTGAAAGCAGATTCCCTCTTATTTGCTCGTTTAGCTTTATGTC
1 TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
* *
20688179 TTTCACTTTGTAAAAACAGATTCCCTCTTATCCGCTCGTTTAGCTTTATGAC
1 TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
* * *
20688231 TTACACTTTGTTAAAGCAGATTTCCTCTTATCTGCTCGTTTAGCTTT
1 TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTT
20688278 TATCCCCTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 89 1.00
ACGTcount: A:0.20, C:0.23, G:0.13, T:0.44
Consensus pattern (52 bp):
TTTCACTTTGTAAAAGCAGATTCCCTCTTATCTGCTCGTTTAGCTTTATGAC
Found at i:20689029 original size:3 final size:3
Alignment explanation
Indices: 20689021--20689050 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
20689011 TGATTCTTTA
20689021 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20689051 GGTTAATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20689308 original size:18 final size:19
Alignment explanation
Indices: 20689269--20689310 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
20689259 ATAAATTTTA
*
20689269 AAAAATTAAAAAATTATCT
1 AAAAATTAAAAAATTATAT
20689288 AAAAA-TAAATAAATTA-AT
1 AAAAATTAAA-AAATTATAT
20689306 AAAAA
1 AAAAA
20689311 AGAGTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
AAAAATTAAAAAATTATAT
Found at i:20689310 original size:19 final size:18
Alignment explanation
Indices: 20689261--20689311 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
20689251 TGACGAGCAT
*
20689261 AAATTTTAAAAAATTAAA
1 AAATTATAAAAAATTAAA
*
20689279 AAATTATCTAAAAA-TAAA
1 AAATTAT-AAAAAATTAAA
20689297 TAAATTAATAAAAAA
1 -AAATT-ATAAAAAA
20689312 GAGTATAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 10 0.37
19 15 0.56
20 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATTATAAAAAATTAAA
Found at i:20690780 original size:50 final size:50
Alignment explanation
Indices: 20690721--20690822 Score: 177
Period size: 50 Copynumber: 2.0 Consensus size: 50
20690711 CGAACACGTT
*
20690721 TCCCAACTGGTTTTAATAGTCAAATAGATTAGTTCAAGGTTTTCTTCCGA
1 TCCCAACTGGTTTTAATAGTCAAATAGATAAGTTCAAGGTTTTCTTCCGA
* *
20690771 TCCCAACTGGTTTTAATAGTTAAATAGATAAGTTCAAGGTTTTCTTCTGA
1 TCCCAACTGGTTTTAATAGTCAAATAGATAAGTTCAAGGTTTTCTTCCGA
20690821 TC
1 TC
20690823 TTTTGATTTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (50 bp):
TCCCAACTGGTTTTAATAGTCAAATAGATAAGTTCAAGGTTTTCTTCCGA
Found at i:20696529 original size:25 final size:25
Alignment explanation
Indices: 20696474--20696531 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
20696464 AGTTGTAGTA
*
20696474 AATTTATATTTTAATATTATTATAT
1 AATTTATTTTTTAATATTATTATAT
** *
20696499 TTTTTATTTTTTATTATTATT-TCAT
1 AATTTATTTTTTAATATTATTAT-AT
20696524 AATTTATT
1 AATTTATT
20696532 ATGATTTTTG
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 1 0.04
25 25 0.96
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (25 bp):
AATTTATTTTTTAATATTATTATAT
Found at i:20697441 original size:31 final size:29
Alignment explanation
Indices: 20697406--20697464 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
20697396 ATGTAAACAG
* *
20697406 TGAAATATGAAAAGTAGATGGACTAAATTCC
1 TGAAA-AT-AAAAATAGAGGGACTAAATTCC
*
20697437 TGAAAATAAAAATATAGGGACTAAATTC
1 TGAAAATAAAAATAGAGGGACTAAATTC
20697465 TAAAGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 18 0.72
30 2 0.08
31 5 0.20
ACGTcount: A:0.49, C:0.08, G:0.17, T:0.25
Consensus pattern (29 bp):
TGAAAATAAAAATAGAGGGACTAAATTCC
Found at i:20709426 original size:51 final size:50
Alignment explanation
Indices: 20709403--20709497 Score: 133
Period size: 51 Copynumber: 1.9 Consensus size: 50
20709393 TCATACATAT
* *
20709403 ATATGTATATTTTATATCTTATTTTATATATATATATATATCTTTATATAC
1 ATATATATATTTTATATCTTA-TTTATATACATATATATATCTTTATATAC
*
20709454 ATATATATATTTTATATCTTA-TTATAT--ATATATACATCTTTATA
1 ATATATATATTTTATATCTTATTTATATACATATATATATCTTTATA
20709498 CACGTATTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 16 0.38
49 6 0.14
51 20 0.48
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.56
Consensus pattern (50 bp):
ATATATATATTTTATATCTTATTTATATACATATATATATCTTTATATAC
Found at i:20709427 original size:12 final size:12
Alignment explanation
Indices: 20709400--20709482 Score: 51
Period size: 12 Copynumber: 6.6 Consensus size: 12
20709390 TTTTCATACA
*
20709400 TATATATGTATAT
1 TATATATCT-TAT
*
20709413 TTTATATCTTAT
1 TATATATCTTAT
* *
20709425 TTTATAT-ATAT
1 TATATATCTTAT
20709436 ATATATATCTTTAT
1 -TATATATC-TTAT
* *
20709450 ATACATATATATAT
1 -TATATATCT-TAT
*
20709464 TTTATATCTTAT
1 TATATATCTTAT
20709476 TATATAT
1 TATATAT
20709483 ATATACATCT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
11 3 0.05
12 25 0.45
13 14 0.25
14 13 0.24
ACGTcount: A:0.36, C:0.05, G:0.01, T:0.58
Consensus pattern (12 bp):
TATATATCTTAT
Found at i:20709434 original size:2 final size:2
Alignment explanation
Indices: 20709427--20709487 Score: 56
Period size: 2 Copynumber: 32.0 Consensus size: 2
20709417 TATCTTATTT
* * * *
20709427 TA TA TA TA TA TA TA TA TC TT TA TA TA CA TA TA TA TA T- TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
20709468 TA TC T- TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
20709488 CATCTTTATA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:20709450 original size:18 final size:18
Alignment explanation
Indices: 20709422--20709470 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 18
20709412 TTTTATATCT
20709422 TATTTTATATATATATATA
1 TATTTTATATA-ATATATA
20709441 TATCTTTATATACATATATA
1 TAT-TTTATATA-ATATATA
20709461 TATTTTATAT
1 TATTTTATAT
20709471 CTTATTATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 10 0.36
20 18 0.64
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTATATAATATATA
Found at i:20709496 original size:21 final size:21
Alignment explanation
Indices: 20709455--20709493 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
20709445 TTTATATACA
* *
20709455 TATATATATTTTATATCTTAT
1 TATATATATTATACATCTTAT
20709476 TATATATA-TATACATCTT
1 TATATATATTATACATCTT
20709494 TATACACGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (21 bp):
TATATATATTATACATCTTAT
Found at i:20721450 original size:47 final size:47
Alignment explanation
Indices: 20721318--20721613 Score: 393
Period size: 47 Copynumber: 6.3 Consensus size: 47
20721308 CAACCCTGTT
* * * * *
20721318 TTGGACAGTAATTATTCATCAAATTGGACAGCAAT-AATATGCTTAAAA
1 TTGGACAG-CATTATACATTAAAATGGACAGC-ATCAATATACTTAAAA
* * * * * *
20721366 -TGGACAGCATTATACATCAAATTAGACAGCTTAAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
* *
20721412 TTTGACAGCATTATACATTAAAATGGACAACATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
* *
20721459 TTGGACAGCATTATACATTAAAAT-GAGCAGTATCAATATACTCAAAA
1 TTGGACAGCATTATACATTAAAATGGA-CAGCATCAATATACTTAAAA
*
20721506 TTGGACAGCATTATACATTAAAATGGATAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
20721553 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
1 TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
20721600 -TGGACAGCATTATA
1 TTGGACAGCATTATA
20721614 TATCAAATTT
Statistics
Matches: 222, Mismatches: 22, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
45 1 0.00
46 47 0.21
47 172 0.77
48 2 0.01
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.29
Consensus pattern (47 bp):
TTGGACAGCATTATACATTAAAATGGACAGCATCAATATACTTAAAA
Found at i:20721452 original size:25 final size:24
Alignment explanation
Indices: 20721342--20721609 Score: 210
Period size: 22 Copynumber: 11.4 Consensus size: 24
20721332 TTCATCAAAT
*
20721342 TGGACAGCAAT-AATATGCTTAAAA
1 TGGACAGC-ATCAATATACTTAAAA
* *
20721366 TGGACAGCAT---TATACATCAAAT
1 TGGACAGCATCAATATAC-TTAAAA
* * * *
20721388 TAGACAGCTTAAATATACTCAAAA
1 TGGACAGCATCAATATACTTAAAA
*
20721412 TTTGACAGCAT---TATACATTAAAA
1 -TGGACAGCATCAATATAC-TTAAAA
*
20721435 TGGACAACATCAATATACTTAAAA
1 TGGACAGCATCAATATACTTAAAA
20721459 TTGGACAGCAT---TATACATTAAAA
1 -TGGACAGCATCAATATAC-TTAAAA
* *
20721482 T-GAGCAGTATCAATATACTCAAAA
1 TGGA-CAGCATCAATATACTTAAAA
20721506 TTGGACAGCAT---TATACATTAAAA
1 -TGGACAGCATCAATATAC-TTAAAA
*
20721529 TGGATAGCATCAATATACTTAAAA
1 TGGACAGCATCAATATACTTAAAA
20721553 TTGGACAGCAT---TATACATTAAAA
1 -TGGACAGCATCAATATAC-TTAAAA
20721576 TGGACAGCATCAATATACTTAAAA
1 TGGACAGCATCAATATACTTAAAA
20721600 TGGACAGCAT
1 TGGACAGCAT
20721610 TATATATCAA
Statistics
Matches: 200, Mismatches: 18, Indels: 52
0.74 0.07 0.19
Matches are distributed among these distances:
21 6 0.03
22 65 0.32
23 24 0.12
24 46 0.23
25 57 0.28
26 2 0.01
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.28
Consensus pattern (24 bp):
TGGACAGCATCAATATACTTAAAA
Found at i:20722635 original size:28 final size:27
Alignment explanation
Indices: 20722603--20722701 Score: 103
Period size: 28 Copynumber: 3.6 Consensus size: 27
20722593 TTAATAAGTA
*
20722603 CGCACACTTAGTGCTTAATAATCAAACT
1 CGCACACTTAGTGCTT-ATAATTAAACT
* *
20722631 CGCACACTTAGTGCTT-TACCCTTATACT
1 CGCACACTTAGTGCTTATA--ATTAAACT
20722659 CGCACACTTAGTGCATT-TCAATTAAACT
1 CGCACACTTAGTGC-TTAT-AATTAAACT
*
20722687 CGCACACTTGGTGCT
1 CGCACACTTAGTGCT
20722702 AATCTCATTA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
26 2 0.03
27 1 0.02
28 54 0.89
29 3 0.05
30 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.13, T:0.31
Consensus pattern (27 bp):
CGCACACTTAGTGCTTATAATTAAACT
Found at i:20724824 original size:139 final size:139
Alignment explanation
Indices: 20724528--20724868 Score: 382
Period size: 139 Copynumber: 2.5 Consensus size: 139
20724518 CCCTGAAGTT
* * * * *
20724528 GCAGTGGAACAGACTGAAGCCACTAATCCTATTTCCCTGAAGTTGCAGTGAAGCGGATTAAAACG
1 GCAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACA
* * * * **
20724593 AGAAATCCTATACCTTTGAAGTTGCAGAGGGCCAGATTAAATTTTATTATAGCAATTCTTATCTC
66 AGAAATCATATACCTCTGAAGTTGCAGAGGGCCAGATTAAATCTTATCATAGCAAACCTTATCTC
* *
20724658 CTTGAAGTT
131 CTTGAAATC
* * *
20724667 GCAGTGGGGTAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTCAAACA
1 GCAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACA
* * * *
20724732 ATG-AATCATATACCTCTGAAGTTGCAGTAGGTCGA-ATTAGATCTTATCATATCAAACCTTATC
66 A-GAAATCATATACCTCTGAAGTTGCAG-AGGGCCAGATTAAATCTTATCATAGCAAACCTTATC
20724795 TCCTTGAAATC
129 TCCTTGAAATC
** * * * * * *
20724806 GCAGTGGAGCAGGTTGAAGATAC-AAGTCTTATCCCCCTGAGGTTGCAGTGGAGCAGACTAAAA
1 GCAGTGGAGCAGACTGAAGCTACTAA-TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
20724869 ACCACAAACT
Statistics
Matches: 168, Mismatches: 31, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
138 2 0.01
139 160 0.95
140 6 0.04
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (139 bp):
GCAGTGGAGCAGACTGAAGCTACTAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACA
AGAAATCATATACCTCTGAAGTTGCAGAGGGCCAGATTAAATCTTATCATAGCAAACCTTATCTC
CTTGAAATC
Found at i:20725558 original size:13 final size:13
Alignment explanation
Indices: 20725540--20725564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20725530 GTTCTTGTGT
20725540 TTTTCTTATTTTA
1 TTTTCTTATTTTA
20725553 TTTTCTTATTTT
1 TTTTCTTATTTT
20725565 TTGTATTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTCTTATTTTA
Found at i:20729639 original size:52 final size:51
Alignment explanation
Indices: 20729561--20729661 Score: 121
Period size: 52 Copynumber: 2.0 Consensus size: 51
20729551 GCATAATAAC
* * ***
20729561 AAATTTAGCCCTTAACGTTTATACATTGTGTCAATTTAATCTTAATTTTAAA
1 AAATTTAGCCCTTAACATTTACACATTACCT-AATTTAATCTTAATTTTAAA
* * *
20729613 AAATTTAGCTCTTAATATTTACACATTACCTAATTTTATCTTAATTTTA
1 AAATTTAGCCCTTAACATTTACACATTACCTAATTTAATCTTAATTTTA
20729662 CATGAAAATG
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
51 17 0.41
52 24 0.59
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.47
Consensus pattern (51 bp):
AAATTTAGCCCTTAACATTTACACATTACCTAATTTAATCTTAATTTTAAA
Found at i:20733085 original size:12 final size:12
Alignment explanation
Indices: 20733070--20733094 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20733060 TTATATGTAA
20733070 TTTTAATATTTT
1 TTTTAATATTTT
20733082 TTTTAATATTTT
1 TTTTAATATTTT
20733094 T
1 T
20733095 AAAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTAATATTTT
Found at i:20737187 original size:19 final size:19
Alignment explanation
Indices: 20737163--20737200 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20737153 GAATTGTGTG
*
20737163 ACCCAAATTCTAAGAGATT
1 ACCCAAATTCTAAAAGATT
20737182 ACCCAAATTCTAAAAGATT
1 ACCCAAATTCTAAAAGATT
20737201 GCTTGCAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.08, T:0.26
Consensus pattern (19 bp):
ACCCAAATTCTAAAAGATT
Found at i:20746945 original size:6 final size:6
Alignment explanation
Indices: 20746936--20746961 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
20746926 AAAAATAGAT
20746936 ATTAAA ATTAAA ATTAAA ATTAAA AT
1 ATTAAA ATTAAA ATTAAA ATTAAA AT
20746962 ATGACTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
ATTAAA
Found at i:20749403 original size:18 final size:18
Alignment explanation
Indices: 20749359--20749405 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
20749349 ATTGTAACTT
*
20749359 GAATTCTTAAGAGTAATA
1 GAATTCTTGAGAGTAATA
20749377 GAATTCTTGAGAGTAATA
1 GAATTCTTGAGAGTAATA
20749395 GAATTCTTGAG
1 GAATTCTTGAG
20749406 CATTTACTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.34
Consensus pattern (18 bp):
GAATTCTTGAGAGTAATA
Found at i:20755021 original size:12 final size:14
Alignment explanation
Indices: 20754994--20755027 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
20754984 ATCACTTGTG
20754994 AAGCACTTTTTCAA
1 AAGCACTTTTTCAA
20755008 AA-CACTTTTT-AA
1 AAGCACTTTTTCAA
20755020 AAGCACTT
1 AAGCACTT
20755028 CTCAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.21
13 13 0.68
14 2 0.11
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.35
Consensus pattern (14 bp):
AAGCACTTTTTCAA
Found at i:20767083 original size:29 final size:31
Alignment explanation
Indices: 20767044--20767117 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
20767034 TATATATTCA
20767044 TAAA-TTT-GAAATTTAATCTTTATA-CTTT
1 TAAATTTTAGAAATTTAATCTTTATATCTTT
* * *
20767072 T-ATTTTTAGAAATTTAGTCTTTCTATCTTT
1 TAAATTTTAGAAATTTAATCTTTATATCTTT
20767102 TAAATTTTA-AAATTTA
1 TAAATTTTAGAAATTTA
20767118 GGTTCAATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 15 0.39
30 12 0.32
31 6 0.16
ACGTcount: A:0.34, C:0.07, G:0.04, T:0.55
Consensus pattern (31 bp):
TAAATTTTAGAAATTTAATCTTTATATCTTT
Found at i:20772080 original size:12 final size:11
Alignment explanation
Indices: 20772063--20772106 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
20772053 AAGAGTTTTT
20772063 ATTTTTTTAATA
1 ATTTTTTT-ATA
20772075 A-TTTTTTA-A
1 ATTTTTTTATA
*
20772084 ATTTTTTTGTA
1 ATTTTTTTATA
20772095 ATTTTTTTATA
1 ATTTTTTTATA
20772106 A
1 A
20772107 ATATTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 2 0.07
10 7 0.25
11 18 0.64
12 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (11 bp):
ATTTTTTTATA
Found at i:20773618 original size:15 final size:14
Alignment explanation
Indices: 20773574--20773622 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 14
20773564 TTGTCATTAA
20773574 AATTTAATAAAAAT
1 AATTTAATAAAAAT
* *
20773588 -A-TTATTAAATAT
1 AATTTAATAAAAAT
20773600 AATTTAATAATAAAT
1 AATTTAATAA-AAAT
20773615 AATTTAAT
1 AATTTAAT
20773623 CGTATTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 9 0.32
13 2 0.07
14 6 0.21
15 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AATTTAATAAAAAT
Found at i:20777443 original size:6 final size:6
Alignment explanation
Indices: 20777432--20777460 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
20777422 TATATACATC
20777432 AAAATA AAAATA AAAATA AAAATA AAAAT
1 AAAATA AAAATA AAAATA AAAATA AAAAT
20777461 TTATAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:20779864 original size:20 final size:20
Alignment explanation
Indices: 20779826--20779864 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20779816 CGTGATTCAA
* * *
20779826 TTGAAACATGAGAATTTTTT
1 TTGAAACACGAAAACTTTTT
20779846 TTGAAACACGAAAACTTTT
1 TTGAAACACGAAAACTTTT
20779865 GAAAACATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGAAACACGAAAACTTTTT
Found at i:20779870 original size:18 final size:18
Alignment explanation
Indices: 20779843--20780027 Score: 177
Period size: 18 Copynumber: 10.5 Consensus size: 18
20779833 ATGAGAATTT
20779843 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
20779860 CTTTTGAAAACATGGAAA
1 TTTTTGAAAACACGAAAA
* **
20779878 TTTGTG-AAACACGGGAA
1 TTTTTGAAAACACGAAAA
* *
20779895 TTGTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
20779913 TTTTTG-AAACACGGAAAT
1 TTTTTGAAAACAC-GAAAA
20779931 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
20779949 TTTTT-AAAACACCGGAAA
1 TTTTTGAAAACA-CGAAAA
*
20779967 -TTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
*
20779984 TTTTTG-AAACATCG-GAA
1 TTTTTGAAAACA-CGAAAA
*
20780001 TTTTTGAAAACACGAAGA
1 TTTTTGAAAACACGAAAA
20780019 TTTTTGAAA
1 TTTTTGAAA
20780028 CATGATTTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
17 51 0.38
18 78 0.58
19 6 0.04
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.30
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:20780030 original size:35 final size:34
Alignment explanation
Indices: 20779843--20780029 Score: 221
Period size: 35 Copynumber: 5.3 Consensus size: 34
20779833 ATGAGAATTT
* * * *
20779843 TTTTTGAAACACGAAAACTTTTGAAAACATGGAAA
1 TTTTTGAAACACG-GAATTTTTGAAAACACGAAAA
* * *
20779878 TTTGTGAAACACGGGAATTGTTGAAAACATGAAAA
1 TTTTTGAAACAC-GGAATTTTTGAAAACACGAAAA
20779913 TTTTTGAAACACGGAAATTTTTTGAAAACACGAAAA
1 TTTTTGAAACACGG-AA-TTTTTGAAAACACGAAAA
* * *
20779949 TTTTTAAAACACCGGAAATTTTGAAAACACGAAGA
1 TTTTTGAAACA-CGGAATTTTTGAAAACACGAAAA
*
20779984 TTTTTGAAACATCGGAATTTTTGAAAACACGAAGA
1 TTTTTGAAACA-CGGAATTTTTGAAAACACGAAAA
20780019 TTTTTGAAACA
1 TTTTTGAAACA
20780030 TGATTTTTTT
Statistics
Matches: 134, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
34 2 0.01
35 100 0.75
36 29 0.22
37 3 0.02
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.29
Consensus pattern (34 bp):
TTTTTGAAACACGGAATTTTTGAAAACACGAAAA
Found at i:20780046 original size:35 final size:34
Alignment explanation
Indices: 20779892--20780062 Score: 130
Period size: 35 Copynumber: 4.9 Consensus size: 34
20779882 TGAAACACGG
* * * *
20779892 GAATTGTTGAAAACATGAAAATTTTTGAAACA-C
1 GAATTTTTAAAAACACGAAGATTTTTGAAACATC
* * * *
20779925 GGAAATTTTTTGAAAACACGAAAATTTTTAAAACACC
1 -G-AA-TTTTTAAAAACACGAAGATTTTTGAAACATC
* *
20779962 GGAAATTTTGAAAACACGAAGATTTTTGAAACATC
1 -GAATTTTTAAAAACACGAAGATTTTTGAAACATC
*
20779997 GGAATTTTTGAAAACACGAAGATTTTTGAAACAT-
1 -GAATTTTTAAAAACACGAAGATTTTTGAAACATC
* * * *
20780031 GATTTTTTTAAAAAACAAGAAAATTTGTGAAA
1 GA-ATTTTT-AAAAACACGAAGATTTTTGAAA
20780063 ATACGGAAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
33 2 0.02
34 6 0.05
35 80 0.67
36 28 0.24
37 3 0.03
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.31
Consensus pattern (34 bp):
GAATTTTTAAAAACACGAAGATTTTTGAAACATC
Found at i:20780996 original size:20 final size:20
Alignment explanation
Indices: 20780941--20781002 Score: 69
Period size: 20 Copynumber: 3.3 Consensus size: 20
20780931 TTTTTTCTAT
20780941 TTTCTTTTTTTCC--CCTT-
1 TTTCTTTTTTTCCTTCCTTC
* * *
20780958 TTT-TTCTTTCCCTTTCTTC
1 TTTCTTTTTTTCCTTCCTTC
20780977 TTTCTTTTTTTCCTTCCTTC
1 TTTCTTTTTTTCCTTCCTTC
20780997 TTTCTT
1 TTTCTT
20781003 CTCTTCATCT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 7 0.20
17 3 0.09
18 3 0.09
19 3 0.09
20 19 0.54
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTCTTTTTTTCCTTCCTTC
Found at i:20780999 original size:27 final size:25
Alignment explanation
Indices: 20780955--20781004 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 25
20780945 TTTTTTTCCC
*
20780955 CTTTTTTTCTTTCCCTTTCTTCTTT
1 CTTTTTTTCCTTCCCTTTCTTCTTT
20780980 CTTTTTTTCCTTCCTTCTTTCTTCT
1 CTTTTTTTCCTTCC--CTTTCTTCT
20781005 CTTCATCTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 13 0.59
27 9 0.41
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (25 bp):
CTTTTTTTCCTTCCCTTTCTTCTTT
Found at i:20781211 original size:21 final size:20
Alignment explanation
Indices: 20781172--20781213 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20781162 TGTTGACGAC
* *
20781172 GGCGGTGTTGTGGTTACGGT
1 GGCGGTGTTGCGGTGACGGT
20781192 GGCGGTGGTTGCGGTGACGGT
1 GGCGGT-GTTGCGGTGACGGT
20781213 G
1 G
20781214 TTGTTCTTAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.05, C:0.12, G:0.55, T:0.29
Consensus pattern (20 bp):
GGCGGTGTTGCGGTGACGGT
Found at i:20781635 original size:30 final size:30
Alignment explanation
Indices: 20781538--20781637 Score: 96
Period size: 30 Copynumber: 3.4 Consensus size: 30
20781528 TTTAGGGCCC
* ** *
20781538 AAATGTAA-TTTACAAATTATTAGGGTTTA
1 AAATGTAATTTTAGAAAAAATTAGGGGTTA
* * * *
20781567 AGATGTAAATTTAGAAAAAATTAAGGGTCA
1 AAATGTAATTTTAGAAAAAATTAGGGGTTA
*
20781597 AAATGTAATTTTTG-AAAAATTCAGGGGTTA
1 AAATGTAATTTTAGAAAAAATT-AGGGGTTA
20781627 AAATGTAATTT
1 AAATGTAATTT
20781638 GTATTTTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
29 14 0.25
30 43 0.75
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (30 bp):
AAATGTAATTTTAGAAAAAATTAGGGGTTA
Found at i:20782228 original size:75 final size:75
Alignment explanation
Indices: 20781959--20782666 Score: 710
Period size: 75 Copynumber: 9.4 Consensus size: 75
20781949 GATTCGAAGT
* ** * *
20781959 TCAACTCACTTCTCAG-ATTATGAGTTGA--CCTTTGAAAAATAGAATTTGAAAAATACCTCGGC
1 TCAACTCACCTCTC-GCATTATGAGTTGATTTTTTTGAAAAATAGAAATT-AAAAATACCTCAGC
* *
20782021 ATATGACCCTAGGC
64 --GTGACCCGAGGC
* * * * *
20782035 TCAACTCACATCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTAAAAACACCT---CG-
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGT
20782094 G-CCCGAGGC
66 GACCCGAGGC
20782103 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGGAAAACA-AGAAATTAAAAATACCTCAGC
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTT-GAAAA-ATAGAAATTAAAAATACCTCAGC
*
20782167 GTAACCCGAGGC
64 GTGACCCGAGGC
* * * *
20782179 TCAACTCACCTCTCACATTATGAGTTGATTTTTTTGGAAAACAGAAATTAAAAATACCTTAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGT
*
20782244 AACCCGAGGC
66 GACCCGAGGC
* *
20782254 TCAACTCACCTCTTGCATTATGAGTTGA--TTTTTGGAAAATAGAAATTAAAATATACCTCAGCA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAA-ATACCTCAGC-
*
20782317 TGTGACCTGAGGC
64 -GTGACCCGAGGC
* ** * * *
20782330 TTAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGT
20782395 GACCCGAGGC
66 GACCCGAGGC
* * * * * * *
20782405 TCAACTCACCTCTTGCAATATGAGTTGATATTTTTGAAAAGTAGAAATTGAAAATACCTTAGCAT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGT
*
20782470 GGCCCGAGGC
66 GACCCGAGGC
* * * * *
20782480 TTAACTCACTTCTCGCATTATGAGTTGA--TTTTTGAAAAATAGAAATTGAAAAGACCTCAGGAT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAATACCTCA-G-C
*
20782543 GTGACTCGAGGC
64 GTGACCCGAGGC
* * * **
20782555 TCAACCCACCTCTCGCATTATGAGTTAATTTTTTTTTTGAAAAATAGAAATTGAGAAATACCTTG
1 TCAACTCACCTCTCGCATTATGAGTTGA---TTTTTTTGAAAAATAGAAATT-AAAAATACCTCA
*
20782620 GCATGTG-CCCAAGGC
62 GC--GTGACCCGAGGC
* *
20782635 TCAACTCACCTCTTGAATTATGAGTTGATTTT
1 TCAACTCACCTCTCGCATTATGAGTTGATTTT
20782667 AAAAAAAAAC
Statistics
Matches: 536, Mismatches: 70, Indels: 51
0.82 0.11 0.08
Matches are distributed among these distances:
68 33 0.06
69 1 0.00
70 5 0.01
71 20 0.04
72 2 0.00
73 50 0.09
74 13 0.02
75 205 0.38
76 113 0.21
77 14 0.03
78 20 0.04
80 50 0.09
81 10 0.02
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (75 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAATAGAAATTAAAAATACCTCAGCGT
GACCCGAGGC
Found at i:20782276 original size:151 final size:150
Alignment explanation
Indices: 20781959--20782691 Score: 690
Period size: 151 Copynumber: 4.9 Consensus size: 150
20781949 GATTCGAAGT
* ** * *
20781959 TCAACTCACTTCTCAG-ATTATGAGTTGA--CCTTT-GAAAAATAGAATTTGAAAAATACCTCGG
1 TCAACTCACCTCTC-GCATTATGAGTTGATTTTTTTGGAAAAA-AGAAATT-AAAAATACCTCAG
* * * * *
20782020 CATATGACCCTAGGCTCAACTCACATCTCGCAATATGAGTTGA--TTTTTGAAAAACAAAAATTA
63 CGTA--ACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTA
*
20782083 AAAACACCT---CG-G-CCCGAGGC
126 AAAATACCTCAGCGTGACCCGAGGC
20782103 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGGAAAACAAGAAATTAAAAATACCTCAGCG
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGGAAAA-AAGAAATTAAAAATACCTCAGCG
* *
20782168 TAACCCGAGGCTCAACTCACCTCTCACATTATGAGTTGATTTTTTTGGAAAACAGAAATTAAAAA
65 TAACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAA
* *
20782233 TACCTTAGCGTAACCCGAGGC
130 TACCTCAGCGTGACCCGAGGC
* *
20782254 TCAACTCACCTCTTGCATTATGAGTTGA--TTTTTGGAAAATAGAAATTAAAATATACCTCAGCA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGGAAAAAAGAAATTAAAA-ATACCTCAGC-
* * * ** * *
20782317 TGTGACCTGAGGCTTAACTCATTTCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAA
64 -GTAACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAA
20782382 AATACCTCAGCGTGACCCGAGGC
128 AATACCTCAGCGTGACCCGAGGC
* * * * * * *
20782405 TCAACTCACCTCTTGCAATATGAGTTGATATTTTT-GAAAAGTAGAAATTGAAAATACCTTAGCA
1 TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGGAAAA-AAGAAATTAAAAATACCTCAGCG
** * * * *
20782469 TGGCCCGAGGCTTAACTCACTTCTCGCATTATGAGTTGA--TTTTTGAAAAATAGAAATTGAAAA
65 TAACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAA
* * *
20782532 GACCTCAGGATGTGACTCGAGGC
130 TACCTCA-G-CGTGACCCGAGGC
* * * * **
20782555 TCAACCCACCTCTCGCATTATGAGTTAATTTTTTTTTTGAAAAATAGAAATTGAGAAATACCTTG
1 TCAACTCACCTCTCGCATTATGAGTTGA--TTTTTTTGGAAAAA-AGAAATT-AAAAATACCTCA
* * * * ****
20782620 GCATGT-GCCCAAGGCTCAACTCACCTCTTGAATTATGAGTTGATTTTAAAAAAAAACAGAAATT
62 GC--GTAACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATT
20782684 GAAAAATA
125 -AAAAATA
20782692 TTTCTTGAGA
Statistics
Matches: 498, Mismatches: 61, Indels: 46
0.82 0.10 0.08
Matches are distributed among these distances:
143 1 0.00
144 58 0.12
146 44 0.09
147 11 0.02
148 41 0.08
149 24 0.05
150 70 0.14
151 138 0.28
152 20 0.04
153 28 0.06
154 11 0.02
155 32 0.06
156 1 0.00
157 14 0.03
158 5 0.01
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.29
Consensus pattern (150 bp):
TCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGGAAAAAAGAAATTAAAAATACCTCAGCGT
AACCCGAGGCTCAACTCACCTCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTAAAAAT
ACCTCAGCGTGACCCGAGGC
Found at i:20782429 original size:226 final size:225
Alignment explanation
Indices: 20781989--20782666 Score: 784
Period size: 226 Copynumber: 3.0 Consensus size: 225
20781979 TGAGTTGACC
** * ** * *
20781989 TTTGAAAAATAGAATTTGAAAAATACCTCGGCATATGACCCTAGGCTCAACTCACATCTCGCAAT
1 TTTGAAAAGCAGAAATT-AAAAATACCTTAGCATA--ACCCGAGGCTCAACTCACATCTCGCATT
* * *
20782054 ATGAGTTGATTTTTGAAAAACAAAAATTAAAAACACCT---C--G-G-CCCGAGGCTCAACTCAC
63 ATGAGTTGATTTTTGAAAAATAGAAATTAAAAACACCTCAGCATGTGACCTGAGGCTCAACTCAC
* * *
20782112 CTCTCGCATTATGAGTTGATTTTTTTGGAAAACAAGAAATTAAAAATACCTCAGCGTAACCCGAG
128 CTCTCGCATTATGAGTTGATTTTTTTGAAAAAC-AGAAATTGAAAATACCTCAGCGTGACCCGAG
** *
20782177 GCTCAACTCACCTCTCACATTATGAGTTGATTTT
192 GCTCAACTCACCTCTTGCAATATGAGTTGATTTT
* * *
20782211 TTTGGAAAA-CAGAAATTAAAAATACCTTAGCGTAACCCGAGGCTCAACTCACCTCTTGCATTAT
1 TTT-GAAAAGCAGAAATTAAAAATACCTTAGCATAACCCGAGGCTCAACTCACATCTCGCATTAT
* * * **
20782275 GAGTTGATTTTTGGAAAATAGAAATTAAAATATACCTCAGCATGTGACCTGAGGCTTAACTCATT
65 GAGTTGATTTTTGAAAAATAGAAATTAAAA-ACACCTCAGCATGTGACCTGAGGCTCAACTCACC
*
20782340 TCTCGCAATATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGC
129 TCTCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGC
*
20782405 TCAACTCACCTCTTGCAATATGAGTTGATATT
194 TCAACTCACCTCTTGCAATATGAGTTGATTTT
* * ** * *
20782437 TTTGAAAAGTAGAAATTGAAAATACCTTAGCATGGCCCGAGGCTTAACTCACTTCTCGCATTATG
1 TTTGAAAAGCAGAAATTAAAAATACCTTAGCATAACCCGAGGCTCAACTCACATCTCGCATTATG
* * * *
20782502 AGTTGATTTTTGAAAAATAGAAATTGAAAAGACCTCAGGATGTGA-CTCGAGGCTCAACCCACCT
66 AGTTGATTTTTGAAAAATAGAAATTAAAAACACCTCAGCATGTGACCT-GAGGCTCAACTCACCT
* * **
20782566 CTCGCATTATGAGTTAATTTTTTTTTTGAAAAATAGAAATTGAGAAATACCTTGGCATGTG-CCC
130 CTCGCATTATGAGTTGA---TTTTTTTGAAAAACAGAAATTGA-AAATACCTCAGC--GTGACCC
*
20782630 AAGGCTCAACTCACCTCTTG-AATTATGAGTTGATTTT
189 GAGGCTCAACTCACCTCTTGCAA-TATGAGTTGATTTT
20782667 AAAAAAAAAC
Statistics
Matches: 390, Mismatches: 48, Indels: 28
0.84 0.10 0.06
Matches are distributed among these distances:
219 53 0.14
220 5 0.01
221 14 0.04
222 9 0.02
223 6 0.02
224 2 0.01
225 47 0.12
226 138 0.35
227 44 0.11
228 22 0.06
229 12 0.03
230 35 0.09
231 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (225 bp):
TTTGAAAAGCAGAAATTAAAAATACCTTAGCATAACCCGAGGCTCAACTCACATCTCGCATTATG
AGTTGATTTTTGAAAAATAGAAATTAAAAACACCTCAGCATGTGACCTGAGGCTCAACTCACCTC
TCGCATTATGAGTTGATTTTTTTGAAAAACAGAAATTGAAAATACCTCAGCGTGACCCGAGGCTC
AACTCACCTCTTGCAATATGAGTTGATTTT
Found at i:20794530 original size:20 final size:20
Alignment explanation
Indices: 20794492--20794530 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20794482 CGTGATCCAA
* * *
20794492 TTGAAACATGAGAATTTTTT
1 TTGAAACACGAAAACTTTTT
20794512 TTGAAACACGAAAACTTTT
1 TTGAAACACGAAAACTTTT
20794531 GAAATACGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (20 bp):
TTGAAACACGAAAACTTTTT
Found at i:20794596 original size:35 final size:35
Alignment explanation
Indices: 20794509--20794804 Score: 234
Period size: 35 Copynumber: 8.5 Consensus size: 35
20794499 ATGAGAATTT
* * * * *
20794509 TTTTTG-AAACACGAAAACTTTTGAAATACGAGAA
1 TTTTTGAAAACACGGAAATTTTTAAAACACGAAAA
* *
20794543 -TTTT-AAGAACACGAAAATTTTTAAAACACAAAAA
1 TTTTTGAA-AACACGGAAATTTTTAAAACACGAAAA
* * *
20794577 TTTTTGAAAACACGGAAATTTGTGAAACACGAGAA
1 TTTTTGAAAACACGGAAATTTTTAAAACACGAAAA
* *
20794612 TTGTTGAAAACACGAAAATTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGGAAATTTTT-AAAACACGAAAA
* * *
20794648 TTTTTGAAAGACA-GGAATTTTTTGAAAATACAAAAA
1 TTTTTGAAA-ACACGGAAATTTTT-AAAACACGAAAA
* * *
20794684 TTTTT-AAAACATCGGAAATTTTGAAAACATGAAGA
1 TTTTTGAAAACA-CGGAAATTTTTAAAACACGAAAA
*
20794719 TTTTTG-AAACACCGG-AATTTTTGAAAACACGAATA
1 TTTTTGAAAACA-CGGAAATTTTT-AAAACACGAAAA
*** *
20794754 TTTTTG-AAACAC-G-AATTAAAAGAAACAAGAAAA
1 TTTTTGAAAACACGGAAATTTTTA-AAACACGAAAA
*
20794787 TTTGTGAAAACACGGAAA
1 TTTTTGAAAACACGGAAA
20794805 AAACACGAAG
Statistics
Matches: 212, Mismatches: 36, Indels: 26
0.77 0.13 0.09
Matches are distributed among these distances:
32 1 0.00
33 24 0.11
34 38 0.18
35 92 0.43
36 54 0.25
37 3 0.01
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (35 bp):
TTTTTGAAAACACGGAAATTTTTAAAACACGAAAA
Found at i:20794769 original size:17 final size:17
Alignment explanation
Indices: 20794509--20794768 Score: 220
Period size: 18 Copynumber: 14.9 Consensus size: 17
20794499 ATGAGAATTT
20794509 TTTTTGAAACACGAAAA
1 TTTTTGAAACACGAAAA
* * *
20794526 CTTTTGAAATACGAGAA
1 TTTTTGAAACACGAAAA
*
20794543 -TTTTAAGAACACGAAAA
1 TTTTTGA-AACACGAAAA
* *
20794560 TTTTTAAAACACAAAAA
1 TTTTTGAAACACGAAAA
*
20794577 TTTTTGAAAACACGGAAA
1 TTTTTG-AAACACGAAAA
* *
20794595 TTTGTGAAACACGAGAA
1 TTTTTGAAACACGAAAA
*
20794612 TTGTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
20794630 TTTTTGAAAACACGAAAA
1 TTTTTG-AAACACGAAAA
* * *
20794648 TTTTTGAAAGACAGGAAT
1 TTTTTGAAACAC-GAAAA
* *
20794666 TTTTTGAAAATACAAAAA
1 TTTTTG-AAACACGAAAA
* *
20794684 TTTTTAAAACATCGGAAA
1 TTTTTGAAACA-CGAAAA
* *
20794702 -TTTTGAAAACATGAAGA
1 TTTTTG-AAACACGAAAA
*
20794719 TTTTTGAAACACCG-GAA
1 TTTTTGAAACA-CGAAAA
*
20794736 TTTTTGAAAACACGAATA
1 TTTTTG-AAACACGAAAA
20794754 TTTTTGAAACACGAA
1 TTTTTGAAACACGAA
20794769 TTAAAAGAAA
Statistics
Matches: 194, Mismatches: 37, Indels: 24
0.76 0.15 0.09
Matches are distributed among these distances:
16 5 0.03
17 88 0.45
18 96 0.49
19 5 0.03
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (17 bp):
TTTTTGAAACACGAAAA
Found at i:20795386 original size:15 final size:15
Alignment explanation
Indices: 20795366--20795409 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
20795356 CTTTTTTGGC
20795366 TGGGCTGCTGGCTGT
1 TGGGCTGCTGGCTGT
20795381 TGGGCTGCT-GCTGT
1 TGGGCTGCTGGCTGT
* *
20795395 TAGGTTGCCTGGCTG
1 TGGGCTG-CTGGCTG
20795410 CTAGGCCTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.40
15 11 0.44
16 4 0.16
ACGTcount: A:0.02, C:0.20, G:0.43, T:0.34
Consensus pattern (15 bp):
TGGGCTGCTGGCTGT
Found at i:20795686 original size:13 final size:14
Alignment explanation
Indices: 20795670--20795707 Score: 62
Period size: 13 Copynumber: 2.9 Consensus size: 14
20795660 TTTCTTTTTT
20795670 CTTTTTT-TTTCCC
1 CTTTTTTCTTTCCC
20795683 CTTTTTTCTTT-CC
1 CTTTTTTCTTTCCC
20795696 CTTTTTTCTTTC
1 CTTTTTTCTTTC
20795708 TTTTTTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 20 0.87
14 3 0.13
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (14 bp):
CTTTTTTCTTTCCC
Found at i:20795713 original size:13 final size:13
Alignment explanation
Indices: 20795651--20795719 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 13
20795641 GACCCGACTA
20795651 TTCTATTTTTTTCT
1 TTCT-TTTTTTTCT
*
20795665 TT-TTTCTTTTTTT
1 TTCTTT-TTTTTCT
**
20795678 TTCCCCTTTTTTCT
1 TT-CTTTTTTTTCT
**
20795692 TTCCCTTTTTTCT
1 TTCTTTTTTTTCT
20795705 TTCTTTTTTTTCT
1 TTCTTTTTTTTCT
20795718 TT
1 TT
20795720 TTCTTCCTTC
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
12 2 0.04
13 33 0.72
14 10 0.22
15 1 0.02
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTTTTTTTTCT
Found at i:20795730 original size:22 final size:22
Alignment explanation
Indices: 20795698--20795751 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
20795688 TTCTTTCCCT
*
20795698 TTTTTCTTTCTT-TTT-TT-TC
1 TTTTTCTTCCTTCTTTCTTCTC
20795717 TTTTTCTTCCTTCTTTCTTCTC
1 TTTTTCTTCCTTCTTTCTTCTC
*
20795739 TTCTTCTTCCTTC
1 TTTTTCTTCCTTC
20795752 CCTTCGACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 11 0.37
20 3 0.10
21 2 0.07
22 14 0.47
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (22 bp):
TTTTTCTTCCTTCTTTCTTCTC
Found at i:20795746 original size:15 final size:14
Alignment explanation
Indices: 20795661--20795751 Score: 55
Period size: 13 Copynumber: 6.7 Consensus size: 14
20795651 TTCTATTTTT
*
20795661 TTCTTTTTTCTTT-
1 TTCTTTCTTCTTTC
* ** *
20795674 TTTTTTCCCCTTTT
1 TTCTTTCTTCTTTC
* *
20795688 TTCTTTC-CCTTTT
1 TTCTTTCTTCTTTC
*
20795701 TTCTTTCTT-TTTT
1 TTCTTTCTTCTTTC
*
20795714 TTCTTT-TTCTTCC
1 TTCTTTCTTCTTTC
20795727 TTCTTTCTTCTCTTC
1 TTCTTTCTTCT-TTC
*
20795742 TTCTTCCTTC
1 TTCTTTCTTC
20795752 CCTTCGACCT
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
12 2 0.03
13 40 0.63
14 10 0.16
15 11 0.17
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTTCTTCTTTC
Found at i:20795855 original size:18 final size:19
Alignment explanation
Indices: 20795814--20795855 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
20795804 GTCTCTGGCA
*
20795814 TCTCCTCTTCTCTTCTTCT
1 TCTCTTCTTCTCTTCTTCT
*
20795833 T-TCTTCTTCTTTTCTT-T
1 TCTCTTCTTCTCTTCTTCT
20795850 TCTCTT
1 TCTCTT
20795856 TTTTTTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 17 0.85
19 1 0.05
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (19 bp):
TCTCTTCTTCTCTTCTTCT
Found at i:20796290 original size:29 final size:30
Alignment explanation
Indices: 20796257--20796320 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
20796247 GTAAAAGTGA
*
20796257 AATTT-TAGAAA-TATATGGGGCCAAAATGT
1 AATTTCTAGAAAGTATA-GGGACCAAAATGT
* *
20796286 AATTTCTAGAAAGTTTAGGGACCCAAATGT
1 AATTTCTAGAAAGTATAGGGACCAAAATGT
20796316 AATTT
1 AATTT
20796321 ACAAATTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.17
30 22 0.73
31 3 0.10
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.33
Consensus pattern (30 bp):
AATTTCTAGAAAGTATAGGGACCAAAATGT
Found at i:20796379 original size:33 final size:32
Alignment explanation
Indices: 20796328--20796389 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 32
20796318 TTTACAAATT
* *
20796328 ATTAGGGGTTAAGATGTAAATTTAGAAAAAAA
1 ATTAGGGGTCAAAATGTAAATTTAGAAAAAAA
* *
20796360 ATTAGAGGGTCAAAATGTAATTTTTGAAAA
1 ATTAG-GGGTCAAAATGTAAATTTAGAAAA
20796390 GTTCAGGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 5 0.20
33 20 0.80
ACGTcount: A:0.47, C:0.02, G:0.21, T:0.31
Consensus pattern (32 bp):
ATTAGGGGTCAAAATGTAAATTTAGAAAAAAA
Found at i:20809703 original size:7 final size:7
Alignment explanation
Indices: 20809691--20809718 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
20809681 TTTATTCTTA
20809691 TTTGTTC
1 TTTGTTC
20809698 TTTGTTC
1 TTTGTTC
20809705 TTTGTTC
1 TTTGTTC
20809712 TTTGTTC
1 TTTGTTC
20809719 CAAAATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.71
Consensus pattern (7 bp):
TTTGTTC
Found at i:20810399 original size:20 final size:20
Alignment explanation
Indices: 20810374--20810414 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20810364 TTTTTAGCAG
*
20810374 ACTTAGTTGACCCAATGTTA
1 ACTTAGTTGACCCAAAGTTA
20810394 ACTTAGTTGACCCAAAGTTA
1 ACTTAGTTGACCCAAAGTTA
20810414 A
1 A
20810415 TTCGGTCTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.32
Consensus pattern (20 bp):
ACTTAGTTGACCCAAAGTTA
Found at i:20812978 original size:18 final size:18
Alignment explanation
Indices: 20812941--20812984 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20812931 TTTAATAATT
20812941 AATTAAGATAAAAAATTAA
1 AATTAA-ATAAAAAATTAA
* *
20812960 AATTAAATTAAACATTAA
1 AATTAAATAAAAAATTAA
*
20812978 AGTTAAA
1 AATTAAA
20812985 ATCAACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (18 bp):
AATTAAATAAAAAATTAA
Found at i:20815061 original size:22 final size:23
Alignment explanation
Indices: 20815036--20815085 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
20815026 AAAAAAATGG
*
20815036 GTATTCATTTATT-TATAATTT-T
1 GTATTCATTT-TTATAAAATTTAT
*
20815058 GTATTTATTTTTATAAAATTTAT
1 GTATTCATTTTTATAAAATTTAT
20815081 GTATT
1 GTATT
20815086 TTTTTAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (23 bp):
GTATTCATTTTTATAAAATTTAT
Found at i:20822256 original size:15 final size:15
Alignment explanation
Indices: 20822236--20822267 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
20822226 CATTTCACTA
*
20822236 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
20822251 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
20822266 TT
1 TT
20822268 TGCATGCATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:20823849 original size:56 final size:56
Alignment explanation
Indices: 20823783--20823951 Score: 338
Period size: 56 Copynumber: 3.0 Consensus size: 56
20823773 TTTATCAAGA
20823783 TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
1 TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
20823839 TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
1 TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
20823895 TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
1 TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
20823951 T
1 T
20823952 CTTTATATAA
Statistics
Matches: 113, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 113 1.00
ACGTcount: A:0.44, C:0.09, G:0.05, T:0.41
Consensus pattern (56 bp):
TAAATATTAGATTAAATTTAATATTAAAGTTAATTATAATTGAACTCTCTAAACTC
Found at i:20836293 original size:50 final size:50
Alignment explanation
Indices: 20836233--20836334 Score: 204
Period size: 50 Copynumber: 2.0 Consensus size: 50
20836223 TATAAAAATT
20836233 AAATAATAATAAAAATTTGGTAATTACAAATTTTTAACTTTTGAGCTAAA
1 AAATAATAATAAAAATTTGGTAATTACAAATTTTTAACTTTTGAGCTAAA
20836283 AAATAATAATAAAAATTTGGTAATTACAAATTTTTAACTTTTGAGCTAAA
1 AAATAATAATAAAAATTTGGTAATTACAAATTTTTAACTTTTGAGCTAAA
20836333 AA
1 AA
20836335 TTAAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (50 bp):
AAATAATAATAAAAATTTGGTAATTACAAATTTTTAACTTTTGAGCTAAA
Found at i:20838056 original size:16 final size:17
Alignment explanation
Indices: 20838035--20838074 Score: 64
Period size: 16 Copynumber: 2.4 Consensus size: 17
20838025 GAATAGATTT
20838035 TTAATTAAAATTTT-AA
1 TTAATTAAAATTTTAAA
*
20838051 TTAATTAGAATTTTAAA
1 TTAATTAAAATTTTAAA
20838068 TTAATTA
1 TTAATTA
20838075 CACATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTAATTAAAATTTTAAA
Found at i:20841055 original size:42 final size:42
Alignment explanation
Indices: 20841000--20841157 Score: 217
Period size: 42 Copynumber: 3.8 Consensus size: 42
20840990 TTCTGCTGTG
* * * * *
20841000 TCCGTCGACGGTTTCGTCGCTGATTGTTTAGATTCCGAGGTT
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
** *
20841042 TCTTTCGAAGGTTTCGTCGCCGGTGGTTTGGATTCCGGGGTT
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
*
20841084 TCCGTCGAAGGTTTCGTCGCCGGTTTTTTGGATTCCGGGGTT
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
* *
20841126 TCCGACGAAGGTTTCGTCGCCGGTTGCTTGGA
1 TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGA
20841158 GTCAGCGGTT
Statistics
Matches: 101, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 101 1.00
ACGTcount: A:0.09, C:0.22, G:0.33, T:0.36
Consensus pattern (42 bp):
TCCGTCGAAGGTTTCGTCGCCGGTTGTTTGGATTCCGGGGTT
Found at i:20841190 original size:33 final size:33
Alignment explanation
Indices: 20841160--20841269 Score: 193
Period size: 33 Copynumber: 3.3 Consensus size: 33
20841150 TGCTTGGAGT
*
20841160 CAGCGGTTTCTGTCGTCTCCGGCGGTTTGGAAC
1 CAGCGGTTTCCGTCGTCTCCGGCGGTTTGGAAC
20841193 CAGCGGTTTCCGTCGTCTCCGGCGGTTTGGAAC
1 CAGCGGTTTCCGTCGTCTCCGGCGGTTTGGAAC
* *
20841226 CAGCGGTTTCCGTCGTCTCCGGTGGTTTGGAAT
1 CAGCGGTTTCCGTCGTCTCCGGCGGTTTGGAAC
20841259 CAGCGGTTTCC
1 CAGCGGTTTCC
20841270 ATGGAAGGTT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 74 1.00
ACGTcount: A:0.09, C:0.28, G:0.33, T:0.30
Consensus pattern (33 bp):
CAGCGGTTTCCGTCGTCTCCGGCGGTTTGGAAC
Found at i:20845447 original size:23 final size:23
Alignment explanation
Indices: 20845420--20845475 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
20845410 AATGATGAAA
* *
20845420 TTATAAATTCATACATAATAAAT
1 TTATAAATTAATACATAAAAAAT
** *
20845443 TTATATTTTAATATATAAAAAAT
1 TTATAAATTAATACATAAAAAAT
20845466 TTAT-AATTAA
1 TTATAAATTAA
20845476 ATTCCGATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATAAATTAATACATAAAAAAT
Found at i:20846463 original size:18 final size:18
Alignment explanation
Indices: 20846440--20846481 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
20846430 GTTATTACCT
*
20846440 TGAAGGAGCAGGTGAAAG
1 TGAAGGAGAAGGTGAAAG
* *
20846458 TGAAGGTGAAGGTGAAGG
1 TGAAGGAGAAGGTGAAAG
20846476 TGAAGG
1 TGAAGG
20846482 TTCGGTTGAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.48, T:0.14
Consensus pattern (18 bp):
TGAAGGAGAAGGTGAAAG
Found at i:20846466 original size:6 final size:6
Alignment explanation
Indices: 20846449--20846482 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
20846439 TTGAAGGAGC
*
20846449 AGGTGA AAGTGA AGGTGA AGGTGA AGGTGA AGGT
1 AGGTGA AGGTGA AGGTGA AGGTGA AGGTGA AGGT
20846483 TCGGTTGAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.47, T:0.18
Consensus pattern (6 bp):
AGGTGA
Found at i:20848032 original size:15 final size:15
Alignment explanation
Indices: 20848014--20848044 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20848004 GTGTTACTAA
20848014 GAAATGTGACATGAC
1 GAAATGTGACATGAC
20848029 GAAATGTGACATGAC
1 GAAATGTGACATGAC
20848044 G
1 G
20848045 GAAGTACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.19
Consensus pattern (15 bp):
GAAATGTGACATGAC
Found at i:20850694 original size:20 final size:20
Alignment explanation
Indices: 20850645--20850695 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 20
20850635 TCTAAATTTT
* *
20850645 AAAATTTTAAAATAATATAT
1 AAAATTTGAAAATAATATAA
**
20850665 AAAA-TTGAAAATTTTATAA
1 AAAATTTGAAAATAATATAA
20850684 AAAATTTGAAAA
1 AAAATTTGAAAA
20850696 AAAAGTAGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAATTTGAAAATAATATAA
Found at i:20852459 original size:15 final size:15
Alignment explanation
Indices: 20852435--20852477 Score: 61
Period size: 14 Copynumber: 2.9 Consensus size: 15
20852425 ATTTAATAAA
*
20852435 TAAAAATAAAAATCC
1 TAAAACTAAAAATCC
20852450 TAAAACTAAAAAT-C
1 TAAAACTAAAAATCC
*
20852464 TAAACCTAAAAATC
1 TAAAACTAAAAATC
20852478 GCGACAGGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.63, C:0.16, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAACTAAAAATCC
Found at i:20853776 original size:14 final size:14
Alignment explanation
Indices: 20853735--20853777 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
20853725 AAAACTTATC
*
20853735 AAAGAAAAGAAAGAA
1 AAAG-AAAGAGAGAA
20853750 AAAGAAAGAGAGAA
1 AAAGAAAGAGAGAA
20853764 AAAGCAAAG-GAGAA
1 AAAG-AAAGAGAGAA
20853778 CGCACGGCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 18 0.69
15 8 0.31
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAGAGAA
Found at i:20856510 original size:22 final size:23
Alignment explanation
Indices: 20856482--20856531 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
20856472 TGTTATTGAT
20856482 CAGTGGT-GCTTCGGCTACATAA
1 CAGTGGTAGCTTCGGCTACATAA
*
20856504 CAGTGGTAGCTTCGGCTACATAT
1 CAGTGGTAGCTTCGGCTACATAA
20856527 CAGTG
1 CAGTG
20856532 TTGCACTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (23 bp):
CAGTGGTAGCTTCGGCTACATAA
Found at i:20860685 original size:24 final size:25
Alignment explanation
Indices: 20860658--20860738 Score: 74
Period size: 25 Copynumber: 3.3 Consensus size: 25
20860648 TTCCCCATAT
*
20860658 TGGCTCGTATGAGCTTCTTGTTA-A
1 TGGCTCGTATGAGCTTCCTGTTACA
** ** * *
20860682 TGGCTTTTCGGAGCTTCCCGCTACA
1 TGGCTCGTATGAGCTTCCTGTTACA
* *
20860707 TGGCTCATATGAGCTTCCTGTTATA
1 TGGCTCGTATGAGCTTCCTGTTACA
20860732 TGGCTCG
1 TGGCTCG
20860739 AAAGAGATTC
Statistics
Matches: 41, Mismatches: 15, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
24 16 0.39
25 25 0.61
ACGTcount: A:0.15, C:0.23, G:0.25, T:0.37
Consensus pattern (25 bp):
TGGCTCGTATGAGCTTCCTGTTACA
Found at i:20860734 original size:25 final size:25
Alignment explanation
Indices: 20860692--20860770 Score: 81
Period size: 25 Copynumber: 3.2 Consensus size: 25
20860682 TGGCTTTTCG
* *
20860692 GAGCTTCCCGCTACATGGCTCATAT
1 GAGCTTCCCGTTATATGGCTCATAT
* *
20860717 GAGCTTCCTGTTATATGGCTCGA-AA
1 GAGCTTCCCGTTATATGGCTC-ATAT
*
20860742 GAGATTCCCGTT-TATGTGCTCATAT
1 GAGCTTCCCGTTATATG-GCTCATAT
20860767 GAGC
1 GAGC
20860771 ATTCTCGAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 5 0.12
25 37 0.86
26 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.32
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCATAT
Found at i:20864991 original size:107 final size:106
Alignment explanation
Indices: 20864797--20865010 Score: 331
Period size: 107 Copynumber: 2.0 Consensus size: 106
20864787 CCAAAACTCA
* *
20864797 TACTTTGAAACTTTAAAAGGGTATTTGGCTATTTGGCTAAACGAGAAATCGAAACCCATCACATT
1 TACTTTGAAACTTTAAAAGGATATTTGGCTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
* * *
20864862 AGGGCATGTTTTCTCGACTTTCCAAACGCAGAATATTACCT
66 AGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTACCT
* * *
20864903 TACTTTGAAATTTTAAAAGGATATTTGGCTATTTGG-TCGAACGAAGAAATCGAAACTCAGCACA
1 TACTTTGAAACTTTAAAAGGATATTTGGCTATTTGGCT-AAACG-AGAAATCGAAACCCAGCACA
20864967 TTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTACCT
64 TTAGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTACCT
20865010 T
1 T
20865011 TATTATTTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
105 1 0.01
106 38 0.39
107 59 0.60
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (106 bp):
TACTTTGAAACTTTAAAAGGATATTTGGCTATTTGGCTAAACGAGAAATCGAAACCCAGCACATT
AGGGCACGTTTTCTCGAATTTCCAAACGCAAAATATTACCT
Found at i:20865772 original size:3 final size:3
Alignment explanation
Indices: 20865757--20865835 Score: 65
Period size: 3 Copynumber: 26.7 Consensus size: 3
20865747 TGAATGGGTA
*
20865757 AAT AAT TAT AAT AAT AAT AA- AAT AAGT AAT AAT AAT AAAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT -AAT AAT AAT
* * * * *
20865802 ACT AAT AAT AGT AAT AGT AGT AAA AAT -AT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20865836 ATAAAAGGGG
Statistics
Matches: 61, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 6 0.10
3 49 0.80
4 6 0.10
ACGTcount: A:0.63, C:0.01, G:0.05, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20866836 original size:9 final size:9
Alignment explanation
Indices: 20866824--20866848 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
20866814 TTCTATCTTT
20866824 GCAGGTGGA
1 GCAGGTGGA
20866833 GCAGGTGGA
1 GCAGGTGGA
20866842 GCAGGTG
1 GCAGGTG
20866849 AGGCCGTGCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.56, T:0.12
Consensus pattern (9 bp):
GCAGGTGGA
Found at i:20875255 original size:24 final size:24
Alignment explanation
Indices: 20875228--20875274 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
20875218 CAAAAAGTAA
20875228 ACTAATATTTT-TATTAAAAATTTC
1 ACTAAT-TTTTATATTAAAAATTTC
20875252 ACTAATTTTTACTATTAAAAATT
1 ACTAATTTTTA-TATTAAAAATT
20875275 GATTCATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 11 0.52
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (24 bp):
ACTAATTTTTATATTAAAAATTTC
Found at i:20893704 original size:46 final size:45
Alignment explanation
Indices: 20893638--20893753 Score: 180
Period size: 46 Copynumber: 2.6 Consensus size: 45
20893628 TTTGAGTACT
* * *
20893638 TCTGATCAGTGGCAAAGTGATAAGTGTTAGCTTTAGCTACACTTA
1 TCTGATCAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
20893683 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATC-AGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
20893729 TCTGATCAGGGAC-AAGTGATAAGTG
1 TCTGATCAGTGACAAAGTGATAAGTG
20893754 ATCATACGTA
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
44 12 0.18
45 12 0.18
46 42 0.64
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (45 bp):
TCTGATCAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:20898955 original size:31 final size:32
Alignment explanation
Indices: 20898919--20898987 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
20898909 TTAACAACCT
* ** *
20898919 AGTGACTCAAAT-AGAAACTTTTGAATAGTTC
1 AGTGACTCAAATGAAAAACTTTCAAATAGCTC
*
20898950 AGTGACTTAAATGAAAAACTTTCAAATAGCTC
1 AGTGACTCAAATGAAAAACTTTCAAATAGCTC
20898982 AGTGAC
1 AGTGAC
20898988 AATTTTATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (32 bp):
AGTGACTCAAATGAAAAACTTTCAAATAGCTC
Found at i:20899175 original size:20 final size:21
Alignment explanation
Indices: 20899131--20899175 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
20899121 TAATTTATTA
*
20899131 ATTATCAACATATTAAAGTAT
1 ATTATAAACATATTAAAGTAT
20899152 -TTATAAACAT-TTAAA-TAT
1 ATTATAAACATATTAAAGTAT
20899170 GATTAT
1 -ATTAT
20899176 GACATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 3 0.14
19 5 0.24
20 13 0.62
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (21 bp):
ATTATAAACATATTAAAGTAT
Found at i:20899437 original size:58 final size:58
Alignment explanation
Indices: 20899371--20899486 Score: 223
Period size: 58 Copynumber: 2.0 Consensus size: 58
20899361 TTTATAGGTT
20899371 GGTATTTTTTATTATTAACTTTTATTCAAAATAAAATAATTGGTGAAATTTGCATTCA
1 GGTATTTTTTATTATTAACTTTTATTCAAAATAAAATAATTGGTGAAATTTGCATTCA
*
20899429 GGTATTTTTTATTCTTAACTTTTATTCAAAATAAAATAATTGGTGAAATTTGCATTCA
1 GGTATTTTTTATTATTAACTTTTATTCAAAATAAAATAATTGGTGAAATTTGCATTCA
20899487 CAAAATTCCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (58 bp):
GGTATTTTTTATTATTAACTTTTATTCAAAATAAAATAATTGGTGAAATTTGCATTCA
Found at i:20901487 original size:41 final size:39
Alignment explanation
Indices: 20901401--20901480 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 39
20901391 ATGGTACTTG
* * *
20901401 ATATACATATATACAAGCATACAGACACAGACATACATA
1 ATATACATACATACAAGCATACAGACACACACATACAGA
* *
20901440 ATATACATACATACACAGACATACATATACACACATACAGA
1 ATATACATACATACA-AG-CATACAGACACACACATACAGA
20901481 CAATACACTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
39 14 0.41
40 2 0.06
41 18 0.53
ACGTcount: A:0.51, C:0.23, G:0.06, T:0.20
Consensus pattern (39 bp):
ATATACATACATACAAGCATACAGACACACACATACAGA
Found at i:20902325 original size:16 final size:17
Alignment explanation
Indices: 20902298--20902339 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
20902288 AATACTTACT
20902298 ATATACATACATATATAC
1 ATATA-ATACATATATAC
*
20902316 ATA-AATACATATATGC
1 ATATAATACATATATAC
20902332 ATATAATA
1 ATATAATA
20902340 TATACAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 14 0.64
17 5 0.23
18 3 0.14
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (17 bp):
ATATAATACATATATAC
Found at i:20904904 original size:322 final size:322
Alignment explanation
Indices: 20904319--20905289 Score: 1816
Period size: 322 Copynumber: 3.0 Consensus size: 322
20904309 GTAGATAGGC
* * * *
20904319 ACTAATCTTAGCTGTTGATATAATTCAATATGTACCGTTGGATCCGGGGGAGATCAATTATAAAT
1 ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
20904384 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
66 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
20904449 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
131 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
20904514 TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
196 TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
20904579 AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
261 AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
20904641 ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
1 ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
*
20904706 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAAGTAAGAGAATACTTTTGAGAGCATTTA
66 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
20904771 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
131 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
20904836 TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
196 TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
20904901 AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
261 AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
20904963 ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
1 ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
20905028 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
66 AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
20905093 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
131 CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
* *
20905158 TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTATCACTTTTGAA
196 TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
* * * * * * *
20905223 AGGTAGGATGACTTAGGCAGATTTAAAGTAAAGGAATGACCTAAGGCCGCACGGTTTGCCTA
261 AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
20905285 ACTAA
1 ACTAA
20905290 AGTTCTAGCC
Statistics
Matches: 634, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
322 634 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (322 bp):
ACTAATCTTAGCTGTTGATGTAATTCAATATGTACCATTGGATCTGGGGGAGATCAACTATAAAT
AGAGTTCTCCCTCTTCATTTGTAAGCATTCCATTCAAATTAAGAGAATACTTTTGAGAGCATTTA
CTCAAACATTTGGTGTGCTATTGTTTTCTTGTGGCTTTGTTGTTCAATTCAAGTCCATTTGTCTT
TTCGAGTATCTTCCGCTTTACTTCGATGCATTGGAGAATCTCTCTTGAGAATTCTCACTTTCGAA
AGATAGGATAACTTAGGCGGATTTAAAGCAAAGGAATGGCCTAAGGCCACACGGTTTGCCAA
Found at i:20908749 original size:17 final size:16
Alignment explanation
Indices: 20908722--20908811 Score: 69
Period size: 17 Copynumber: 5.6 Consensus size: 16
20908712 ATCTATAAGA
*
20908722 TAAACATTAAATTAAAT
1 TAAATATTAAATT-AAT
*
20908739 TTAATATTAAATTAAT
1 TAAATATTAAATTAAT
* *
20908755 AAAATACT--ATTAAT
1 TAAATATTAAATTAAT
20908769 ATAAATATTAAATTTAAT
1 -TAAATATTAAA-TTAAT
* *
20908787 TTAATATTACATT-AT
1 TAAATATTAAATTAAT
20908802 TAAAATATTA
1 T-AAATATTA
20908812 TTATTTTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
14 6 0.10
15 9 0.16
16 17 0.29
17 21 0.36
18 5 0.09
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATATTAAATTAAT
Found at i:20908779 original size:48 final size:48
Alignment explanation
Indices: 20908721--20908814 Score: 143
Period size: 48 Copynumber: 2.0 Consensus size: 48
20908711 TATCTATAAG
20908721 ATAAACATTAAATTAAATTTAATATTAAATTAATAAAATACTATTAAT
1 ATAAACATTAAATTAAATTTAATATTAAATTAATAAAATACTATTAAT
* * * * *
20908769 ATAAATATTAAATTTAATTTAATATTACATTATTAAAATATTATTA
1 ATAAACATTAAATTAAATTTAATATTAAATTAATAAAATACTATTA
20908815 TTTTTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (48 bp):
ATAAACATTAAATTAAATTTAATATTAAATTAATAAAATACTATTAAT
Found at i:20912732 original size:27 final size:27
Alignment explanation
Indices: 20912702--20912761 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
20912692 CGACTAACAT
*
20912702 TGAAGGGATAGTATGTATGGCAAACTC
1 TGAAGGGATAGTATGTACGGCAAACTC
20912729 TGAAGGGATAGTATGTACGGCAAACTC
1 TGAAGGGATAGTATGTACGGCAAACTC
*
20912756 TAAAGG
1 TGAAGG
20912762 AACGGTAGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.23
Consensus pattern (27 bp):
TGAAGGGATAGTATGTACGGCAAACTC
Found at i:20926667 original size:22 final size:24
Alignment explanation
Indices: 20926642--20926685 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20926632 AATTCGAGAC
20926642 ATTATATA-TTT-ATATAAATTTT
1 ATTATATATTTTAATATAAATTTT
*
20926664 ATTATTTATTTTAATATAAATT
1 ATTATATATTTTAATATAAATT
20926686 GTGATAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATATATTTTAATATAAATTTT
Found at i:20929132 original size:25 final size:26
Alignment explanation
Indices: 20929095--20929165 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
20929085 GATTAAATAA
* *
20929095 AATTATTAGTATTTATTTATAAG-TCAT
1 AATT-TTATTATTTATTAATAAGAT-AT
* *
20929122 -ATTTTTTTATTTAATAATAAGATAT
1 AATTTTATTATTTATTAATAAGATAT
20929147 AATTTTATTATTTATTAAT
1 AATTTTATTATTTATTAAT
20929166 GATGTATAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
25 16 0.44
26 20 0.56
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.56
Consensus pattern (26 bp):
AATTTTATTATTTATTAATAAGATAT
Found at i:20929339 original size:10 final size:10
Alignment explanation
Indices: 20929308--20929369 Score: 53
Period size: 9 Copynumber: 6.7 Consensus size: 10
20929298 TGTAAAATAT
20929308 ATTTATTATA
1 ATTTATTATA
*
20929318 ATTAATTA-A
1 ATTTATTATA
*
20929327 ATTTTTTATA
1 ATTTATTATA
20929337 ATTTA-TAT-
1 ATTTATTATA
*
20929345 -TTTATTAGA
1 ATTTATTATA
*
20929354 TTTTA-TATA
1 ATTTATTATA
20929363 ATTTATT
1 ATTTATT
20929370 TTTTAAAAGT
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
7 4 0.10
8 2 0.05
9 17 0.43
10 17 0.43
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (10 bp):
ATTTATTATA
Found at i:20929351 original size:26 final size:26
Alignment explanation
Indices: 20929313--20929374 Score: 79
Period size: 26 Copynumber: 2.4 Consensus size: 26
20929303 AATATATTTA
* * *
20929313 TTATAATTAATTAAATTTTTTATAAT
1 TTATATTTTATTAAATTTTATATAAT
*
20929339 TTATATTTTATTAGATTTTATATAAT
1 TTATATTTTATTAAATTTTATATAAT
*
20929365 TTATTTTTTA
1 TTATATTTTA
20929375 AAAGTTAGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (26 bp):
TTATATTTTATTAAATTTTATATAAT
Found at i:20939877 original size:48 final size:48
Alignment explanation
Indices: 20939806--20939905 Score: 191
Period size: 48 Copynumber: 2.1 Consensus size: 48
20939796 ACTTAAAGAA
*
20939806 AAATGATGAGTTAGAGTAACATAGGTTAAAATTGAACTAGTGTTTGAT
1 AAATGATGAGTTAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
20939854 AAATGATGAGTTAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
1 AAATGATGAGTTAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
20939902 AAAT
1 AAAT
20939906 TAAAAATTTA
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.41, C:0.05, G:0.22, T:0.32
Consensus pattern (48 bp):
AAATGATGAGTTAGAGTAACATAGGTTAAAACTGAACTAGTGTTTGAT
Found at i:20942146 original size:29 final size:31
Alignment explanation
Indices: 20942100--20942158 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
20942090 AAACATTTTA
*
20942100 TTTTCCCCCAAAATTTTTA-CTCCTTCCCAC
1 TTTTCCCCCAAAACTTTTATCTCCTTCCCAC
* *
20942130 TTTT-CCCTAAAACTTTTATTTCCTTCCCA
1 TTTTCCCCCAAAACTTTTATCTCCTTCCCA
20942159 TCTCACCTCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
30 13 0.52
ACGTcount: A:0.20, C:0.36, G:0.00, T:0.44
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTATCTCCTTCCCAC
Found at i:20946483 original size:50 final size:50
Alignment explanation
Indices: 20946408--20946506 Score: 189
Period size: 50 Copynumber: 2.0 Consensus size: 50
20946398 ATTTAAAATT
*
20946408 CAGCAGGATTAAAGCGCATAAAGAAAGAATCAAACTTGAACAAAAAAAAA
1 CAGCAGGATTAAAGCGCATAAAGAAAGAATCAAAATTGAACAAAAAAAAA
20946458 CAGCAGGATTAAAGCGCATAAAGAAAGAATCAAAATTGAACAAAAAAAA
1 CAGCAGGATTAAAGCGCATAAAGAAAGAATCAAAATTGAACAAAAAAAA
20946507 CTTAGAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.59, C:0.13, G:0.16, T:0.12
Consensus pattern (50 bp):
CAGCAGGATTAAAGCGCATAAAGAAAGAATCAAAATTGAACAAAAAAAAA
Found at i:20950356 original size:93 final size:93
Alignment explanation
Indices: 20950135--20950639 Score: 368
Period size: 93 Copynumber: 5.4 Consensus size: 93
20950125 CAAAAGGAAG
* * * * *
20950135 AAACCCAAAGAAGAGCTTGAAAAAGGTGGCAACAAA-CTATAAACTTAAACAAAAGCGACTATCG
1 AAACCCGAAGAAGAGCTTG-AAAAGGTGACAA-AAAGGTATAAACTTAAACAAAAGAGACCATCG
* * * *
20950199 T-TGTTATCGAAA-CC-AAGAAGAAGATCAAT
64 TCT-TCATTGAAACCCGAA-AAGGAGATCGAT
*
20950228 AAACTCGAAGAAGAAGAGCTTGAAAAGGT-AGCAAAAAGGTATAAACTTAAACAAAAGAGACCAT
1 AAAC-C--CGAAGAAGAGCTTGAAAAGGTGA-CAAAAAGGTATAAACTTAAACAAAAGAGACCAT
* ** *
20950292 TGTCTTCATT-AGAACTTGAAAAGGAGATCGGT
62 CGTCTTCATTGA-AACCCGAAAAGGAGATCGAT
* * * *
20950324 AAACCCGAAGAAGAGCTTGAAAAGGTGACAAAAAGGTACATTA-TTAAACAAAA-ATGGCTATCG
1 AAACCCGAAGAAGAGCTTGAAAAGGTGACAAAAAGGTATA-AACTTAAACAAAAGA-GACCATCG
* *
20950387 TCTTCA-TCAGAACCCGAAAAGGAGATCGGT
64 TCTTCATTGA-AACCCGAAAAGGAGATCGAT
* * * ** * * *
20950417 AAACCTGAAGAAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAATTTAAATGAAGGCGACTATC
1 AAACC---CGAAGAAGAGCTTGAAAAGGTGACAAAAAGGTATAAACTTAAACAAAAGAGACCATC
* *
20950482 GTCTTTATTGAAACCCGAAAAGAAGA-CTGAT
63 GTCTTCATTGAAACCCGAAAAGGAGATC-GAT
* * * * * * * *
20950513 AAATCC-AAGAAGAACTTTAAAAGGTGACAGAAAGCTATAAACTTAAACGGAAATA-ACCATCAT
1 AAACCCGAAGAAGAGCTTGAAAAGGTGACAAAAAGGTATAAACTTAAAC-AAAAGAGACCATCGT
* *
20950576 CTTCATTGAAACCCGAAAAGGACATTGAT
65 CTTCATTGAAACCCGAAAAGGAGATCGAT
* * ** *
20950605 AAACTCGAAGAATAGCTCAAAAATGTGACAAAAAG
1 AAACCCGAAGAAGAGCTTGAAAAGGTGACAAAAAG
20950640 CTATCATCTT
Statistics
Matches: 328, Mismatches: 61, Indels: 46
0.75 0.14 0.11
Matches are distributed among these distances:
92 71 0.22
93 106 0.32
94 7 0.02
95 43 0.13
96 97 0.30
97 4 0.01
ACGTcount: A:0.47, C:0.15, G:0.19, T:0.19
Consensus pattern (93 bp):
AAACCCGAAGAAGAGCTTGAAAAGGTGACAAAAAGGTATAAACTTAAACAAAAGAGACCATCGTC
TTCATTGAAACCCGAAAAGGAGATCGAT
Found at i:20950481 original size:96 final size:93
Alignment explanation
Indices: 20950142--20950503 Score: 297
Period size: 96 Copynumber: 3.8 Consensus size: 93
20950132 AAGAAACCCA
** * * * *
20950142 AAGAAGAGCTTGAAAAAGGTGGCAACAAA-CTATAAACTTAAACAAAAGCGACTATCGT-TGTTA
1 AAGAAGAGCTTG-AAAAGGTAACAA-AAAGGTATAAATTTAAAAAAAAG-GACTATCGTCT-TCA
* * * **
20950205 TCGAAACC-AAGAAGAAGATCAATAAACTCGAAG
62 TAGAACCCGAA-AAGGAGATCGGTAAAC-CGAAG
* * * * *
20950238 AAGAAGAGCTTGAAAAGGTAGCAAAAAGGTATAAACTTAAACAAAAGAGACCATTGTCTTCATTA
1 AAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAATTTAAAAAAAAG-GACTATCGTCTTCA-TA
** *
20950303 GAACTTGAAAAGGAGATCGGTAAACC--CG
64 GAACCCGAAAAGGAGATCGGTAAACCGAAG
* * *
20950331 AAGAAGAGCTTGAAAAGGTGACAAAAAGGTA-CATTATTAAACAAAAATGG-CTATCGTCTTCAT
1 AAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAAT-TTAAA-AAAAA-GGACTATCGTCTTCAT
20950394 CAGAACCCGAAAAGGAGATCGGTAAACCTGAAG
63 -AGAACCCGAAAAGGAGATCGGTAAACC-GAAG
** * * *
20950427 AAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAATTTAAATGAAGGCGACTATCGTCTTTATTG
1 AAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAATTTAAAAAAAAG-GACTATCGTCTTCATAG
20950492 AAACCCGAAAAG
65 -AACCCGAAAAG
20950504 AAGACTGATA
Statistics
Matches: 218, Mismatches: 33, Indels: 30
0.78 0.12 0.11
Matches are distributed among these distances:
92 2 0.01
93 70 0.32
94 9 0.04
95 44 0.20
96 89 0.41
97 4 0.02
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (93 bp):
AAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAATTTAAAAAAAAGGACTATCGTCTTCATAGA
ACCCGAAAAGGAGATCGGTAAACCGAAG
Found at i:20950597 original size:188 final size:189
Alignment explanation
Indices: 20950234--20950597 Score: 414
Period size: 189 Copynumber: 1.9 Consensus size: 189
20950224 CAATAAACTC
* *
20950234 GAAGAAGAAGAGCTTGAAAAGGTAGCAAAAAGGTATAAACTTAAACAAAAGAGACCATTGTCTTC
1 GAAGAAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAACTTAAACAAAAGAGACCATCGTCTTC
** * * * *
20950299 ATTAGAACTTGAAAAGGAGATCGGTAAACCCGAAGAAGAGCTTGAAAAGGTGACAAAAAGGTACA
66 ATTAGAACCCGAAAAGAAGATCGATAAACCCGAAGAAGAACTTGAAAAGGTGACAAAAAGCTACA
* ** * *
20950364 TTATTAAACAAAAATGGCTATCGTCTTCATCAGAACCCGAAAAGGAGATCGGTAAACCT
131 TAATTAAACAAAAATAACCATCATCTTCATCAGAACCCGAAAAGGAGATCGGTAAACCT
* ** * * * *
20950423 GAAGAAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAATTTAAATGAAGGCGACTATCGTCTTT
1 GAAGAAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAACTTAAACAAAAGAGACCATCGTCTTC
* * *
20950488 ATT-GAAACCCGAAAAGAAGA-CTGATAAATCC-AAGAAGAACTTTAAAAGGTGACAGAAAGCTA
66 ATTAG-AACCCGAAAAGAAGATC-GATAAACCCGAAGAAGAACTTGAAAAGGTGACAAAAAGCTA
* ** *
20950550 TA-AACTTAAACGGAAATAACCATCATCTTCAT-TGAAACCCGAAAAGGA
129 CATAA-TTAAACAAAAATAACCATCATCTTCATCAG-AACCCGAAAAGGA
20950598 CATTGATAAA
Statistics
Matches: 144, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
187 2 0.01
188 64 0.44
189 78 0.54
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (189 bp):
GAAGAAGAAGAGCTTGAAAAGGTAACAAAAAGGTATAAACTTAAACAAAAGAGACCATCGTCTTC
ATTAGAACCCGAAAAGAAGATCGATAAACCCGAAGAAGAACTTGAAAAGGTGACAAAAAGCTACA
TAATTAAACAAAAATAACCATCATCTTCATCAGAACCCGAAAAGGAGATCGGTAAACCT
Found at i:20950949 original size:26 final size:27
Alignment explanation
Indices: 20950920--20950970 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
20950910 TAATTATCTT
* *
20950920 AATTAGACTGATTAAATT-GAAAAAAA
1 AATTAGAATGACTAAATTAGAAAAAAA
20950946 AATTAGAATGACTAAATTAGAAAAA
1 AATTAGAATGACTAAATTAGAAAAA
20950971 CGTTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (27 bp):
AATTAGAATGACTAAATTAGAAAAAAA
Found at i:20952407 original size:25 final size:25
Alignment explanation
Indices: 20952379--20952426 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
20952369 TATCTTGTTG
20952379 AATTTCCATATCTGAGGAATCAAGA
1 AATTTCCATATCTGAGGAATCAAGA
20952404 AATTTCCATATCTGAGGAATCAA
1 AATTTCCATATCTGAGGAATCAA
20952427 ATTCATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (25 bp):
AATTTCCATATCTGAGGAATCAAGA
Found at i:20953220 original size:23 final size:22
Alignment explanation
Indices: 20953175--20953216 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
20953165 TAGTGGAGAA
*
20953175 AAAAATTAGTCACTAAAATTAT
1 AAAAACTAGTCACTAAAATTAT
*
20953197 AAAAACTAGTCACTATAATT
1 AAAAACTAGTCACTAAAATT
20953217 TATAGTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAAACTAGTCACTAAAATTAT
Found at i:20954545 original size:23 final size:24
Alignment explanation
Indices: 20954519--20954572 Score: 67
Period size: 22 Copynumber: 2.3 Consensus size: 24
20954509 GGAACAAAAG
*
20954519 AATAAAAATAAAATAATAATG-AC-
1 AATAAAAAT-AAATAAAAATGCACA
*
20954542 AATAATAATAAATAAAAATGCACA
1 AATAAAAATAAATAAAAATGCACA
20954566 AATAAAA
1 AATAAAA
20954573 GAATGTATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 10 0.38
23 10 0.38
24 6 0.23
ACGTcount: A:0.70, C:0.06, G:0.04, T:0.20
Consensus pattern (24 bp):
AATAAAAATAAATAAAAATGCACA
Found at i:20956283 original size:44 final size:44
Alignment explanation
Indices: 20956199--20956763 Score: 429
Period size: 44 Copynumber: 12.6 Consensus size: 44
20956189 TTATTCTAAC
* * * ** *
20956199 CCACTGTAACTTTAGGGGGTATAAGAAGTGTAGTTTCAATCTACT
1 CCACTGCAACTTCAGGGAG-ATAAGACTTGTAGCTTCAATCTACT
* * *
20956244 CCGCTGCAACTTCAGGGAGATGAGACTCGTAGCTTCAATCTACT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
* * * * * *
20956288 CCACTGCCACCTCAAGGAGATAAGATTCACTATGGTAGATTTAATCCGAC-
1 CCACTGCAACTTCAGGGAGATAAG----ACT-T-GTAGCTTCAAT-CTACT
* * * *
20956338 CTACTGCAACTTCAGAGG-TATAGGA-TT-TAGTTTCAATCTACT
1 CCACTGCAACTTCAG-GGAGATAAGACTTGTAGCTTCAATCTACT
* * * *
20956380 CTACTGCAACTTCGGGGAGATAAGACTTGTAACTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
* * * **
20956424 CCACTGCAACTTTAGGGAGATAAGATTTGTAACTTGTATCTACT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
* * * **
20956468 CCACTGCAACTTCAGGGAGATAATATTTGTAACTTGTATCTACT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
* * *
20956512 CCACTACAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTATT
1 CCACTGCAACTTCAGGGAGAT-A-A---G--ACTTGTAGCTTCAATCTACT
* * * * * * **
20956563 CTACTACAACTTCAAGGAAACAAGATTTGTAGCTTCAATCTGTT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
* * *
20956607 CCACTGCAACTTTAGGGAAATAAGACTTGTGACCTT-AATCTACT
1 CCACTGCAACTTCAGGGAGATAAGACTTGT-AGCTTCAATCTACT
* * *
20956651 CCACTGCAACTTCAGAGAGATAAGACTTGTGGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
* ** * * *
20956695 CCACTGCAACTTCAGGGAGATTAGGTTTATAGCTTTAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
*
20956739 CCAATGCAACTTCAGGGAGATAAGA
1 CCACTGCAACTTCAGGGAGATAAGA
20956764 TTCACTATGG
Statistics
Matches: 418, Mismatches: 81, Indels: 43
0.77 0.15 0.08
Matches are distributed among these distances:
41 5 0.01
42 27 0.06
43 5 0.01
44 291 0.70
45 21 0.05
46 3 0.01
48 3 0.01
49 1 0.00
50 25 0.06
51 37 0.09
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (44 bp):
CCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATCTACT
Found at i:20956618 original size:183 final size:183
Alignment explanation
Indices: 20956372--20956715 Score: 474
Period size: 183 Copynumber: 1.9 Consensus size: 183
20956362 ATTTAGTTTC
* ** * *
20956372 AATCTACTCTACTGCAACTTCGGGGAGATAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTT
1 AATCTACTCTACTACAACTTCAAGGAAACAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTT
* * * * * *
20956437 AGGGAGATAAGATTTGT-AACTTGTATCTACTCCACTGCAACTTCAGGGAGATAATATTTGTAAC
66 AGGGAAATAAGACTTGTGAACTT-AATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAAC
**
20956501 TTGTATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTT
130 TTCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTT
* * * *
20956555 AATCTATTCTACTACAACTTCAAGGAAACAAGATTTGTAGCTTCAATCTGTTCCACTGCAACTTT
1 AATCTACTCTACTACAACTTCAAGGAAACAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTT
* **
20956620 AGGGAAATAAGACTTGTGACCTTAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTGGCT
66 AGGGAAATAAGACTTGTGAACTTAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAACT
* *
20956685 TCAATCTGCTCCACTGCAACTTCAGGGAGAT
131 TCAATCTACTCCACTACAACTTCAGGGAGAT
20956716 TAGGTTTATA
Statistics
Matches: 138, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
183 134 0.97
184 4 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (183 bp):
AATCTACTCTACTACAACTTCAAGGAAACAAGACTTGTAACTTCAATCTGCTCCACTGCAACTTT
AGGGAAATAAGACTTGTGAACTTAATCTACTCCACTGCAACTTCAGAGAGATAAGACTTGTAACT
TCAATCTACTCCACTACAACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTT
Found at i:20958526 original size:35 final size:35
Alignment explanation
Indices: 20958487--20958557 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
20958477 CCACATAGAG
*
20958487 AAAGACCATGGAGAAGTCATAACATGAAGATGTGA
1 AAAGACCATGGAGAAGTCATAACATGAAGAGGTGA
*
20958522 AAAGACCATGGAGAATTCATAACATGAAGAGGTGA
1 AAAGACCATGGAGAAGTCATAACATGAAGAGGTGA
20958557 A
1 A
20958558 TGAGGTACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.46, C:0.11, G:0.25, T:0.17
Consensus pattern (35 bp):
AAAGACCATGGAGAAGTCATAACATGAAGAGGTGA
Found at i:20968740 original size:14 final size:14
Alignment explanation
Indices: 20968684--20968742 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
20968674 TGAAAGTACC
*
20968684 AAAAATAATAA-AAG
1 AAAAATAA-AATAAT
*
20968698 AAATAATAAAATAAC
1 AAA-AATAAAATAAT
* *
20968713 AAGAACAAAATAAT
1 AAAAATAAAATAAT
20968727 AAAAATAAAATAAT
1 AAAAATAAAATAAT
20968741 AA
1 AA
20968743 TGACAATAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
14 28 0.76
15 9 0.24
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.17
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:20968763 original size:26 final size:27
Alignment explanation
Indices: 20968721--20968775 Score: 78
Period size: 26 Copynumber: 2.1 Consensus size: 27
20968711 ACAAGAACAA
*
20968721 AATAATAAAAATAAAATAATAATG-AC
1 AATAATAAAAATAAAATAAAAATGCAC
20968747 AATAATAATAAAT-AAATAAAAATGCAC
1 AATAATAA-AAATAAAATAAAAATGCAC
20968774 AA
1 AA
20968776 ATAAAACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 18 0.69
27 8 0.31
ACGTcount: A:0.69, C:0.05, G:0.04, T:0.22
Consensus pattern (27 bp):
AATAATAAAAATAAAATAAAAATGCAC
Found at i:20968764 original size:31 final size:31
Alignment explanation
Indices: 20968690--20968767 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 31
20968680 TACCAAAAAT
*
20968690 AATAA-AAGAAAT-AATAAAATAACAAGAAC
1 AATAATAATAAATAAATAAAATAACAAGAAC
*
20968719 AA-AATAAT-AA-AAATAAAATAATAATG-AC
1 AATAATAATAAATAAATAAAATAACAA-GAAC
20968747 AATAATAATAAATAAATAAAA
1 AATAATAATAAATAAATAAAA
20968768 ATGCACAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
28 20 0.49
29 11 0.27
30 2 0.05
31 8 0.20
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (31 bp):
AATAATAATAAATAAATAAAATAACAAGAAC
Found at i:20972110 original size:30 final size:30
Alignment explanation
Indices: 20972026--20972110 Score: 116
Period size: 30 Copynumber: 2.8 Consensus size: 30
20972016 ATCACCATCT
* *
20972026 CCATCACCGGCACCATCACCTGTACAAGTG
1 CCATCACCGGCACCGTCACCTGTAGAAGTG
* *
20972056 TCATCACCAGCACCGTCACCTGTAGAAGTG
1 CCATCACCGGCACCGTCACCTGTAGAAGTG
* *
20972086 CCCTCACCGGCACCGTCGCCTGTAG
1 CCATCACCGGCACCGTCACCTGTAG
20972111 GAGCTCCACA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.22, C:0.40, G:0.20, T:0.18
Consensus pattern (30 bp):
CCATCACCGGCACCGTCACCTGTAGAAGTG
Found at i:20972958 original size:9 final size:9
Alignment explanation
Indices: 20972941--20972983 Score: 61
Period size: 9 Copynumber: 4.8 Consensus size: 9
20972931 TAATTTATAA
*
20972941 TTTATAATT
1 TTTAAAATT
20972950 TTTAAAATT
1 TTTAAAATT
20972959 ATTT-AAATT
1 -TTTAAAATT
20972968 TTTAAAATT
1 TTTAAAATT
20972977 TTTAAAA
1 TTTAAAA
20972984 ATAACTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
8 3 0.10
9 25 0.81
10 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTTAAAATT
Found at i:20972969 original size:18 final size:18
Alignment explanation
Indices: 20972940--20972982 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
20972930 ATAATTTATA
20972940 ATTTATAATTTTTAAAATT
1 ATTTA-AATTTTTAAAATT
20972959 ATTTAAATTTTTAAAATT
1 ATTTAAATTTTTAAAATT
20972977 -TTTAAA
1 ATTTAAA
20972983 AATAACTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 6 0.25
18 13 0.54
19 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTAAATTTTTAAAATT
Found at i:20972992 original size:27 final size:27
Alignment explanation
Indices: 20972941--20972993 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
20972931 TAATTTATAA
* * **
20972941 TTTATAATTTTTAAAATTATTTAAATT
1 TTTAAAATTTTTAAAAATAACTAAATT
20972968 TTTAAAATTTTTAAAAATAACTAAAT
1 TTTAAAATTTTTAAAAATAACTAAAT
20972994 ACTGACGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (27 bp):
TTTAAAATTTTTAAAAATAACTAAATT
Found at i:20974608 original size:30 final size:30
Alignment explanation
Indices: 20974574--20974635 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 30
20974564 ACCATCTCCA
* *
20974574 TCACCACTACAAGTGTCGTCACCAGCACCG
1 TCACCACTACAAGTGCCATCACCAGCACCG
** * *
20974604 TCACCTGTAGAAGTGCCATCACCTGCACCG
1 TCACCACTACAAGTGCCATCACCAGCACCG
20974634 TC
1 TC
20974636 GCCTATAGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.19
Consensus pattern (30 bp):
TCACCACTACAAGTGCCATCACCAGCACCG
Found at i:20976711 original size:13 final size:13
Alignment explanation
Indices: 20976693--20976747 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
20976683 AGATTTTTCT
20976693 TAAATATTATCAC
1 TAAATATTATCAC
*
20976706 TAAATA--ATC-T
1 TAAATATTATCAC
* *
20976716 TAAATGTTATTAC
1 TAAATATTATCAC
*
20976729 TAAATATTATTAC
1 TAAATATTATCAC
20976742 TAAATA
1 TAAATA
20976748 ATTCAAAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 5 0.15
11 3 0.09
12 2 0.06
13 24 0.71
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (13 bp):
TAAATATTATCAC
Found at i:20976716 original size:23 final size:23
Alignment explanation
Indices: 20976690--20976734 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
20976680 GCTAGATTTT
20976690 TCTTAAATATTATCACTAAATAA
1 TCTTAAATATTATCACTAAATAA
* *
20976713 TCTTAAATGTTATTACTAAATA
1 TCTTAAATATTATCACTAAATA
20976735 TTATTACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.44, C:0.11, G:0.02, T:0.42
Consensus pattern (23 bp):
TCTTAAATATTATCACTAAATAA
Done.