Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D12
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: 58873029
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 639818 characters in sequence are not A, C, G, or T
File 145 of 196
Found at i:42912987 original size:16 final size:16
Alignment explanation
Indices: 42912966--42912998 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42912956 TAAGCCATTG
42912966 ATGTGAATAATGTGCC
1 ATGTGAATAATGTGCC
42912982 ATGTGAATAATGTGCC
1 ATGTGAATAATGTGCC
42912998 A
1 A
42912999 AAGTGTGCGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.30
Consensus pattern (16 bp):
ATGTGAATAATGTGCC
Found at i:42914127 original size:14 final size:14
Alignment explanation
Indices: 42914108--42914135 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
42914098 AGTTTCAGTC
42914108 GGCCCAGAATACAA
1 GGCCCAGAATACAA
42914122 GGCCCAGAATACAA
1 GGCCCAGAATACAA
42914136 AATCAGTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.29, G:0.21, T:0.07
Consensus pattern (14 bp):
GGCCCAGAATACAA
Found at i:42914490 original size:14 final size:15
Alignment explanation
Indices: 42914462--42914493 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
42914452 TACAGCAAAA
42914462 AAAGAGCAGAATATC
1 AAAGAGCAGAATATC
42914477 AAAGAGCA-AATATC
1 AAAGAGCAGAATATC
42914491 AAA
1 AAA
42914494 CAAGATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.12
Consensus pattern (15 bp):
AAAGAGCAGAATATC
Found at i:42915448 original size:22 final size:22
Alignment explanation
Indices: 42915422--42915471 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
42915412 CATATTTATA
42915422 TTTTAATGTAATGTAATCATTT
1 TTTTAATGTAATGTAATCATTT
* * *
42915444 TTTT-ATTTTATGTAATTATTT
1 TTTTAATGTAATGTAATCATTT
*
42915465 TTATAAT
1 TTTTAAT
42915472 ATATATATGT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.30, C:0.02, G:0.06, T:0.62
Consensus pattern (22 bp):
TTTTAATGTAATGTAATCATTT
Found at i:42915485 original size:12 final size:12
Alignment explanation
Indices: 42915470--42915520 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
42915460 TATTTTTATA
42915470 ATATATATATGT
1 ATATATATATGT
42915482 ATATATATAT-T
1 ATATATATATGT
*
42915493 -TAT-TCT-TGT
1 ATATATATATGT
42915502 ATATATATATGT
1 ATATATATATGT
*
42915514 ATGTATA
1 ATATATA
42915521 CATATTAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
8 1 0.03
9 3 0.09
10 6 0.19
11 3 0.09
12 19 0.59
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (12 bp):
ATATATATATGT
Found at i:42915491 original size:16 final size:16
Alignment explanation
Indices: 42915466--42915525 Score: 52
Period size: 16 Copynumber: 3.8 Consensus size: 16
42915456 TAATTATTTT
42915466 TATA-ATATATATATG
1 TATATATATATATATG
*
42915481 TATATATATATTTAT-
1 TATATATATATATATG
* *
42915496 TCTTGTATATATATATG
1 T-ATATATATATATATG
* *
42915513 TATGTATACATAT
1 TATATATATATAT
42915526 TAATATTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 5 0.14
16 30 0.83
17 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (16 bp):
TATATATATATATATG
Found at i:42919179 original size:46 final size:46
Alignment explanation
Indices: 42919080--42919369 Score: 390
Period size: 46 Copynumber: 6.6 Consensus size: 46
42919070 TACGTATGAT
*
42919080 CACTTATCAC-TTGTC-CTTAATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
42919123 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* *
42919169 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTGAGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
*
42919215 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
42919261 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T-A----A-
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
42919297 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTGC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
* * *
42919343 CACTTATCACTTTATCTCTTAATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
42919370 AGTACTCAAA
Statistics
Matches: 223, Mismatches: 11, Indels: 23
0.87 0.04 0.09
Matches are distributed among these distances:
36 29 0.13
37 1 0.00
38 3 0.01
40 1 0.00
41 2 0.01
42 1 0.00
43 10 0.04
44 7 0.03
45 20 0.09
46 149 0.67
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAGGCTAC
Found at i:42919309 original size:82 final size:82
Alignment explanation
Indices: 42919215--42919369 Score: 265
Period size: 82 Copynumber: 1.9 Consensus size: 82
42919205 CTGAGGCTAC
*
42919215 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
*
42919280 TGATCAGATAAGTATAA
66 TAATCAGATAAGTATAA
* * *
42919297 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTGCCACTTATCACTTTATCTCT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
42919362 TAATCAGA
66 TAATCAGA
42919370 AGTACTCAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
82 68 1.00
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.35
Consensus pattern (82 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCACT
TAATCAGATAAGTATAA
Found at i:42931222 original size:44 final size:42
Alignment explanation
Indices: 42931159--42931975 Score: 388
Period size: 44 Copynumber: 18.8 Consensus size: 42
42931149 GTTCGCATCT
42931159 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* * *
42931203 AGTCTTATCCTCCTAAAGTTGCAGT-GAGGCAGGCTAAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * *
42931248 AATCTTATATCCCTGAAGTTGCAGTGGAGCAGA-TTAG-AGCCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * * *
42931291 TAATCTTATCCCCCT-AAGGTTGTAGTGGAGCGGATTAA-AACCTT
1 -AGTCTTAT-CTCCTGAA-GTTGCAGTGGAGCAGACTAAGAAGC-A
* * * * *
42931335 AGATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGTATCT
1 AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
42931376 AGTCTTATCTCCCTGAA-TTGCAGTGGAGCAAACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
42931419 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
42931464 AATCTTATCTCTCTGAAATTGCAATGGAGCAGA-TTA-AAGTCGA
1 AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * * * *
42931507 TAATCCTATCTCTCTGAGGTTGCAGTGGAGCGGATTAA-AATCA
1 -AGTCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* * * * * *
42931550 CAGATCTTATCTCTCTGAAGTTACAG-AGAGCAGA-T-CGCATCT
1 -AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
*
42931592 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
* *
42931636 AGTCTTATCCTCCTGACGTTGCAGT-GAGGCAGACTGAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * * *
42931681 AATCTTATCTCCCTAAAGTTACAGTGAAGCAGA-TTA-AAGCCAA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAG-C-A
* * * *
42931724 TAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTAA-AACCA
1 -AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAG-ACTAAGAAGCA
* * * * * * *
42931767 CAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGA-TCA-CATCG
1 -AG-TCTTATCTC-CTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
* *
42931810 GGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTAAGTAAGCA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCA
*
42931854 AGTCTTATCCTCCTGAAGTTGCAGT-GAGGCAGACTAAAGATGGCA
1 AGTCTTAT-CTCCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCA
* * * *
42931899 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAA-AACCGA
1 AGTCTTATCT-CCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-A
* * *
42931942 TAATCTTATCTCCTTGAAGTTACAGTGAAGCAGA
1 -AGTCTTATCTCC-TGAAGTTGCAGTGGAGCAGA
42931976 TTAAAGCCGA
Statistics
Matches: 600, Mismatches: 106, Indels: 134
0.71 0.13 0.16
Matches are distributed among these distances:
39 6 0.01
40 38 0.06
41 43 0.07
42 19 0.03
43 63 0.10
44 285 0.47
45 139 0.23
46 7 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
AGTCTTATCTCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCA
Found at i:42931715 original size:217 final size:217
Alignment explanation
Indices: 42931073--42932007 Score: 1320
Period size: 217 Copynumber: 4.3 Consensus size: 217
42931063 TCGGTGGCCA
* ** * *
42931073 ATAATCCTATCACCCTGAGGTTGCAGTGGAGCGGATTAAAACCTTAAATCTTATCTCTTTGAAGT
1 ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGT
* * *
42931138 TGCAAAGAGTAGTTCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* * * *
42931203 AGTCTTATCCTCCTAAAGTTGCAGTGAGGCAGGCTAAAGATGGCAAATCTTATATCCCTGAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTAAAGTT
* *
42931268 GCAGTGGAGCAGATTAGAGCCG
196 GCAGTGAAGCAGATTAAAGCCG
* * * * **
42931290 ATAATCTTATCCCCCTAAGGTTGTAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGT
* *
42931355 TGCAGAGAGCAGATCGTATCTAGTCTTATCTCCCTGAA-TTGCAGTGGAGCAAACTAAGTAAGCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
*
42931419 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCTCTGAAA-T
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCT-AAAGT
* * *
42931483 TGCAATGGAGCAGATTAAAGTCG
195 TGCAGTGAAGCAGATTAAAGCCG
* *
42931506 ATAATCCTATCTCTCTGAGGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGT
1 ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGT
* *
42931571 TACAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCA
66 TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
* *
42931636 AGTCTTATCCTCCTGACGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTAAAGTT
131 AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTAAAGTT
* *
42931701 ACAGTGAAGCAGATTAAAGCCA
196 GCAGTGAAGCAGATTAAAGCCG
* * *
42931723 ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGAATTAAAACCACAGATCTTATCTCTCTAAAGT
1 ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGT
* * ** *
42931788 TGCAGTAGAGTAGATCACATCGGGTCTTATCTCCCTGAAATTGCAGTGGAGCAGACTAAGTAAGC
66 TGCAG-AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGC
*
42931853 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGT
130 AAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTAAAGT
*
42931918 TGCAGTGGAA-CAGATTAAAACCG
195 TGCAGT-GAAGCAGATTAAAGCCG
* * * * * * * * * *
42931941 ATAATCTTATCTCCTTGAAGTTACAGTGAAGCAGATTAAAGCCGATA-ATCCTATCTCCCTGAAG
1 ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACC-ACAGATCTTATCTCTCTGAAG
42932005 TTG
65 TTG
42932008 TAGTGAAGCG
Statistics
Matches: 644, Mismatches: 68, Indels: 11
0.89 0.09 0.02
Matches are distributed among these distances:
216 197 0.31
217 258 0.40
218 184 0.29
219 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (217 bp):
ATAATCCTATCTCCCTGAGGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGT
TGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCA
AGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTAAAGTT
GCAGTGAAGCAGATTAAAGCCG
Found at i:42931746 original size:89 final size:88
Alignment explanation
Indices: 42931161--42932012 Score: 419
Period size: 89 Copynumber: 9.8 Consensus size: 88
42931151 TCGCATCTAG
* * * *
42931161 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-CA-AGTCTTATC-CTCCTAAAGTT
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGA-TTA--AAGCCATAATCTTATCTC-CCTGAAGTT
* **
42931223 GCAGT-GAGGCAGGC-TAAAGATGGCAAA
62 GCAGTGGA-GCAGACTTAAA-ACCGCAAA
* * * * *
42931250 TCTTATATCCCTGAAGTTGCAGTGGAGCAGATTAGAGCCGATAATCTTATCCCCCT-AAGGTTGT
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCC-ATAATCTTATCTCCCTGAA-GTTGC
* ** *
42931314 AGTGGAGCGGA-TTAAAACCTTAGA
64 AGTGGAGCAGACTTAAAACCGCAAA
* * *** * *
42931338 TCTTATCTCTCTGAAGTTGCAGAG-AGCAGATCGTA-TC-TAGTCTTATCTCCCTGAA-TTGCAG
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCATAATCTTATCTCCCTGAAGTTGCAG
* *
42931399 TGGAGCAAAC-TAAGTAA--GCAAG
66 TGGAGCAGACTTAA--AACCGCAAA
* * * * *
42931421 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCA-AATCTTATCTCTCTGAAATT
1 TCTTATCTC-CCTGAAGTTGCAGTGAAGCAGA-TTAA-A-GCCATAATCTTATCTCCCTGAAGTT
* **
42931484 GCAATGGAGCAGA-TTAAAGTCG-ATAA
62 GCAGTGGAGCAGACTTAAAACCGCA-AA
* * * * * ** * * *
42931510 TCCTATCTCTCTGAGGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTACA
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCATA-ATCTTATCTCCCTGAAGTTGCA
* ** ** * *
42931575 G-AGAGCAGA--T--CGCATCTAG
65 GTGGAGCAGACTTAAAACCGCAAA
* * ** *
42931594 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGTAATCAAGTCTTATC-CTCCTGACGTTG
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCAT-AA-TCTTATCTC-CCTGAAGTTG
* * **
42931657 CAGT-GAGGCAGACTGAAGATGGCAAA
63 CAGTGGA-GCAGACTTAAAACCGCAAA
* * *
42931683 TCTTATCTCCCTAAAGTTACAGTGAAGCAGATTAAAGCCAATAATCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCC-ATAATCTTATCTCCCTGAAGTTGCA
* * *
42931748 GTGGAGC-GAATTAAAACCACAGA
65 GTGGAGCAGACTTAAAACCGCAAA
* * * * * * *** *
42931771 TCTTATCTCTCTAAAGTTGCAGT-AGAGTAGATCACA-TC-GGGTCTTATCTCCCTGAAATTGCA
1 TCTTATCTCCCTGAAGTTGCAGTGA-AGCAGATTAAAGCCATAATCTTATCTCCCTGAAGTTGCA
*
42931833 GTGGAGCAGAC-TAAGTAA--GCAAG
65 GTGGAGCAGACTTAA--AACCGCAAA
* * *
42931856 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTAAAGATGGCA-AATCTTATCTCCCTGAAGTT
1 TCTTATCTC-CCTGAAGTTGCAGTGAAGCAGA-TTAA-A-GCCATAATCTTATCTCCCTGAAGTT
*
42931919 GCAGTGGAACAGA-TTAAAACCG-ATAA
62 GCAGTGGAGCAGACTTAAAACCGCA-AA
* * * *
42931945 TCTTATCTCCTTGAAGTTACAGTGAAGCAGATTAAAGCCGATAATCCTATCTCCCTGAAGTTGTA
1 TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCC-ATAATCTTATCTCCCTGAAGTTGCA
42932010 GTG
65 GTG
42932013 AAGCGGGTTA
Statistics
Matches: 577, Mismatches: 128, Indels: 117
0.70 0.16 0.14
Matches are distributed among these distances:
82 1 0.00
83 42 0.07
84 69 0.12
85 64 0.11
86 14 0.02
87 28 0.05
88 135 0.23
89 209 0.36
90 13 0.02
91 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (88 bp):
TCTTATCTCCCTGAAGTTGCAGTGAAGCAGATTAAAGCCATAATCTTATCTCCCTGAAGTTGCAG
TGGAGCAGACTTAAAACCGCAAA
Found at i:42931844 original size:174 final size:174
Alignment explanation
Indices: 42931637--42931953 Score: 382
Period size: 174 Copynumber: 1.8 Consensus size: 174
42931627 AAGTAATCAA
** *
42931637 GTCTTATCCTCCTGACGTTGCAGTGAGGCAGACTGAAG-ATGGCAAATCTTAT-CTCCCTAAAGT
1 GTCTTATCCTCCTGAAATTGCAGTGAGGCAGACT-AAGTA-AGCAAATCTTATCCT-CCTAAAGT
* *
42931700 TACAGTGAAGCAGA-TTAA-A-GCCAATAATCCTATCTCCCTGAAGTTGCAGTGGAGC-GAATTA
63 TACAGTGAAGCAGACTAAAGATGCC-A-AATCCTATCTCCCTGAAGTTGCAGTGGAACAG-ATTA
42931761 AAACC-ACAGATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCACATCGG
125 AAACCGACA-ATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCACATCGG
* *
42931811 GTCTTAT-CTCCCTGAAATTGCAGTG-GAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTT
1 GTCTTATCCT-CCTGAAATTGCAGTGAG-GCAGACTAAGTAAGCAAATCTTATCCTCCTAAAGTT
* * * *
42931874 GCAGTGAGGCAGACTAAAGATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAC
64 ACAGTGAAGCAGACTAAAGATGCCAAATCCTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAAC
*
42931939 CGATAATCTTATCTC
129 CGACAATCTTATCTC
42931954 CTTGAAGTTA
Statistics
Matches: 122, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
173 35 0.29
174 80 0.66
175 5 0.04
176 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (174 bp):
GTCTTATCCTCCTGAAATTGCAGTGAGGCAGACTAAGTAAGCAAATCTTATCCTCCTAAAGTTAC
AGTGAAGCAGACTAAAGATGCCAAATCCTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAACCG
ACAATCTTATCTCTCTAAAGTTGCAGTAGAGTAGATCACATCGG
Found at i:42932077 original size:24 final size:24
Alignment explanation
Indices: 42932050--42932095 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
42932040 TCTCTAGAGT
42932050 TGCAGAGAGCAGATCGCATCTAAA
1 TGCAGAGAGCAGATCGCATCTAAA
*
42932074 TGCAGAGAGCAGATTGCATCTA
1 TGCAGAGAGCAGATCGCATCTA
42932096 GTCTTATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (24 bp):
TGCAGAGAGCAGATCGCATCTAAA
Found at i:42933728 original size:22 final size:21
Alignment explanation
Indices: 42933660--42933732 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 21
42933650 CAAATTAGTC
*
42933660 TTTTATTTATT-TATTTATTTA
1 TTTTATTT-TTATATTTAATTA
* *
42933681 TTTTCATTTTTAT-TTTGTATTT
1 TTTT-ATTTTTATATTT-AATTA
42933703 TTTTATTTTTCATATTTAATTA
1 TTTTATTTTT-ATATTTAATTA
42933725 TTTTATTT
1 TTTTATTT
42933733 AAATTTATGT
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
21 15 0.36
22 24 0.57
23 3 0.07
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTATATTTAATTA
Found at i:42933754 original size:44 final size:44
Alignment explanation
Indices: 42933671--42933756 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 44
42933661 TTTATTTATT
* ** * * *
42933671 TATTTATTTATTTTCATTTTTATTTTGTATTTTTTTATTTTTCA
1 TATTTAATTATTTTCATTTAAATTTTGTATATATGTATTTTTCA
42933715 TATTTAATTATTTT-ATTTAAATTTATGTATATATGTATTTTT
1 TATTTAATTATTTTCATTTAAATTT-TGTATATATGTATTTTT
42933757 TTGTACATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
43 8 0.23
44 27 0.77
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.70
Consensus pattern (44 bp):
TATTTAATTATTTTCATTTAAATTTTGTATATATGTATTTTTCA
Found at i:42933830 original size:25 final size:25
Alignment explanation
Indices: 42933786--42933837 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
42933776 CATACGCATG
42933786 TTTATTTTTTAATGTAATGTAATGTA
1 TTTATTTTTTAATGTAATGTAAT-TA
* *
42933812 TTTATTTTTT-ATTTTATGTAATTA
1 TTTATTTTTTAATGTAATGTAATTA
42933836 TT
1 TT
42933838 ATTATAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 4 0.17
25 10 0.42
26 10 0.42
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (25 bp):
TTTATTTTTTAATGTAATGTAATTA
Found at i:42934907 original size:19 final size:19
Alignment explanation
Indices: 42934883--42934920 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42934873 AATTTCTTGA
42934883 AAATGATTTACTTTTCTGG
1 AAATGATTTACTTTTCTGG
*
42934902 AAATGATTTATTTTTCTGG
1 AAATGATTTACTTTTCTGG
42934921 TGTTTGTATG
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:0.26, C:0.08, G:0.16, T:0.50
Consensus pattern (19 bp):
AAATGATTTACTTTTCTGG
Found at i:42937354 original size:23 final size:22
Alignment explanation
Indices: 42937322--42937383 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
42937312 ACCCGGCCCG
*
42937322 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
42937346 TTTTTATTAAAATTAAAACTAA
1 TTTTTATTAAAATTAAAACTAA
*
42937368 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
42937384 TTGTTATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.44
23 15 0.42
24 5 0.14
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:42937378 original size:16 final size:16
Alignment explanation
Indices: 42937357--42937394 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
42937347 TTTTATTAAA
42937357 ATTAAAACTAATTGTT
1 ATTAAAACTAATTGTT
*
42937373 ATTAAAATTAATTGTT
1 ATTAAAACTAATTGTT
42937389 A-TAAAA
1 ATTAAAA
42937395 ATTGTATCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 5 0.24
16 16 0.76
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (16 bp):
ATTAAAACTAATTGTT
Found at i:42937533 original size:86 final size:86
Alignment explanation
Indices: 42937443--42937614 Score: 326
Period size: 86 Copynumber: 2.0 Consensus size: 86
42937433 TTTGTAAAAT
42937443 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTAATAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTAATAATTGTTACTAAAATTATCAAATT
42937508 ATATCAAATTATTAATTGTTA
66 ATATCAAATTATTAATTGTTA
* *
42937529 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTAATAATTGTTACTAAAATTATCAAATT
42937594 ATATCAAATTATTAATTGTTA
66 ATATCAAATTATTAATTGTTA
42937615 ATTGTATTAA
Statistics
Matches: 84, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
86 84 1.00
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (86 bp):
CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTAATAATTGTTACTAAAATTATCAAATT
ATATCAAATTATTAATTGTTA
Found at i:42938777 original size:22 final size:23
Alignment explanation
Indices: 42938728--42938779 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
42938718 AACAAACACT
42938728 GGAAAAGGCTAAAAAAAATTTCC
1 GGAAAAGGCTAAAAAAAATTTCC
* * *
42938751 GGAAATGGCTGAAAATAATTTCC
1 GGAAAAGGCTAAAAAAAATTTCC
*
42938774 GAAAAA
1 GGAAAA
42938780 TGTTTTCATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (23 bp):
GGAAAAGGCTAAAAAAAATTTCC
Found at i:42944200 original size:18 final size:17
Alignment explanation
Indices: 42944173--42944208 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
42944163 CATTATGTGG
42944173 TCTTCCATTTCCACCGT
1 TCTTCCATTTCCACCGT
42944190 TCTTACCATTTCCACCGT
1 TCTT-CCATTTCCACCGT
42944208 T
1 T
42944209 GCCATCTCCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.14, C:0.39, G:0.06, T:0.42
Consensus pattern (17 bp):
TCTTCCATTTCCACCGT
Found at i:42946773 original size:77 final size:77
Alignment explanation
Indices: 42946613--42946758 Score: 197
Period size: 77 Copynumber: 1.9 Consensus size: 77
42946603 ACACTCGCTA
* ** *
42946613 GATTTAAAATCGCAACTGTCATTTTTACAGTTCAATTGATTTAAGGTCGCGATGTTTGATATTCT
1 GATTTAAAATCGCAACTGTCATTTTTACAGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
42946678 AACAGTTCGATT
66 AACAGTTCGATT
* * *
42946690 GATTTAACATCGCAACTGTCATTTTTTA-GGTT-AACTTGATTTAAGATCGTGACCTTCGATATT
1 GATTTAAAATCGCAACTGTCA-TTTTTACAGTTCAA-TTGATTTAAGATCGCGACCTTCGATATT
42946753 CTAACA
64 CTAACA
42946759 TTTTTCTTGG
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
76 2 0.03
77 52 0.87
78 6 0.10
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.40
Consensus pattern (77 bp):
GATTTAAAATCGCAACTGTCATTTTTACAGTTCAATTGATTTAAGATCGCGACCTTCGATATTCT
AACAGTTCGATT
Found at i:42947518 original size:7 final size:7
Alignment explanation
Indices: 42947506--42947539 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
42947496 TTAAATTTAA
42947506 ATTTCAT
1 ATTTCAT
42947513 ATTTCAT
1 ATTTCAT
42947520 ATTTCAT
1 ATTTCAT
42947527 ATTTCAT
1 ATTTCAT
42947534 ATTTCA
1 ATTTCA
42947540 ACAATAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTCAT
Found at i:42948045 original size:36 final size:38
Alignment explanation
Indices: 42947998--42948092 Score: 104
Period size: 36 Copynumber: 2.5 Consensus size: 38
42947988 GTCTCCAAAT
* *
42947998 TCACATTTCAATTCAATTTCACTTTTTCA-CTTTCAA-
1 TCACAATTCAATTCAATTTCACTTTTCCATCTTTCAAG
* *
42948034 TCACAATTCAATTCAAAATTCACTTTTCCATTTTTCAAG
1 TCACAATTCAATTC-AATTTCACTTTTCCATCTTTCAAG
*
42948073 TCATTATATTCAATTCAATT
1 TCA-CA-ATTCAATTCAATT
42948093 CCAGACATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 13 0.27
37 13 0.27
38 6 0.12
39 3 0.06
40 4 0.08
41 9 0.19
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (38 bp):
TCACAATTCAATTCAATTTCACTTTTCCATCTTTCAAG
Found at i:42950945 original size:42 final size:42
Alignment explanation
Indices: 42950886--42950976 Score: 155
Period size: 42 Copynumber: 2.2 Consensus size: 42
42950876 ATCGCACAAC
*
42950886 TAGTGCCCGTTATTCAACATTGTCATTTTAATTTCACACACT
1 TAGTGCCCGTTATTCAACATCGTCATTTTAATTTCACACACT
* *
42950928 TAGTGCCCGTTATTCAACATCGTCATTTTAGTTTCGCACACT
1 TAGTGCCCGTTATTCAACATCGTCATTTTAATTTCACACACT
42950970 TAGTGCC
1 TAGTGCC
42950977 ATTCGTATAG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (42 bp):
TAGTGCCCGTTATTCAACATCGTCATTTTAATTTCACACACT
Found at i:42956081 original size:20 final size:19
Alignment explanation
Indices: 42956042--42956080 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42956032 TATTTTAAAA
42956042 TATTTGTACATTTTAATTT
1 TATTTGTACATTTTAATTT
*
42956061 TATTATGTATATTTT-ATTT
1 TATT-TGTACATTTTAATTT
42956080 T
1 T
42956081 TTTCTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (19 bp):
TATTTGTACATTTTAATTT
Found at i:42962774 original size:11 final size:11
Alignment explanation
Indices: 42962760--42962801 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
42962750 TAAATATTAC
42962760 TTTATTAATAT
1 TTTATTAATAT
*
42962771 TTTAATGAGATAT
1 TTT-ATTA-ATAT
42962784 TTTATTAATAT
1 TTTATTAATAT
42962795 TTTATTA
1 TTTATTA
42962802 TAAATAGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 14 0.52
12 6 0.22
13 7 0.26
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.60
Consensus pattern (11 bp):
TTTATTAATAT
Found at i:42977293 original size:17 final size:18
Alignment explanation
Indices: 42977251--42977293 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
42977241 TTAATATGGT
*
42977251 TATATATAAAATTATAAA
1 TATATATTAAATTATAAA
42977269 TA-ATTATTAAA-TATAAA
1 TATA-TATTAAATTATAAA
42977286 TATATATT
1 TATATATT
42977294 TAAAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATATATTAAATTATAAA
Found at i:42979267 original size:18 final size:17
Alignment explanation
Indices: 42979224--42979267 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
42979214 ATGTAGAATT
*
42979224 ATATTTTGAAAAATAAA
1 ATATTTTTAAAAATAAA
* *
42979241 ACATGTTTAAAAATTAAA
1 ATATTTTTAAAAA-TAAA
42979259 ATATTTTTA
1 ATATTTTTA
42979268 TTATACAAAA
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (17 bp):
ATATTTTTAAAAATAAA
Found at i:42984607 original size:261 final size:261
Alignment explanation
Indices: 42984143--42984620 Score: 642
Period size: 261 Copynumber: 1.8 Consensus size: 261
42984133 ACCAACTCAG
* ** *
42984143 TTAAAATGTATAAAAATATAAAATAAAACTTTAATTAAGTGGTAAATTAAATGTTTTACTAATGT
1 TTAAAATATATAAAAATATAAAATAAAACTTTAATTAAGTGGTAAATTAAAAATTTTACTAATGC
* * * * * * * *
42984208 AGTTGACGTGGATTCAAACCCCACTATATGTATATTTTTATTGGATTTGTTTTAAAGTGAAAAGA
66 AATTGACGTGGATTCAAACACCAATATATGCATAGTTTTAATCGATTTGTTTTAAAGTGAAAAAA
** * * * *
42984273 CTAAAATACTCTTGAATAACATTACTTATTTTAATTACGAAAGGGCATTCTCGTAACTTTCTAAC
131 CTAAAATACTCTCAAATAACATTACTTATTTTAATTACAAAAGGACATTCTCATAACTTCCTAAC
*
42984338 TGAGTTGGTGACCCGGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
196 TGAGTTGGTGACCCAGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
42984403 A
261 A
* *
42984404 TTAAAATATATAAAAATATCAAAATAAAACTTTAGTTGAA-TGGTAAATTAAAAATTTTATTAAT
1 TTAAAATATATAAAAATAT-AAAATAAAACTTTAATT-AAGTGGTAAATTAAAAATTTTACTAAT
* * *
42984468 GCAATTGATGTAGG-TTTAAATACCAATATATGCAT-GTTTTAATCGACTTT-TTTTAAAGTGAA
64 GCAATTGACGT-GGATTCAAACACCAATATATGCATAGTTTTAATCGA-TTTGTTTTAAAGTGAA
* *
42984530 AAAACTAAAATA-TCCTCAAATAATATTACTTATTTTAATTACAAAAGGACATTCTCATAAGTTC
127 AAAACTAAAATACT-CTCAAATAACATTACTTATTTTAATTACAAAAGGACATTCTCATAACTTC
42984594 CTAACTGAGTTGGTGACCCAGTTGAGG
191 CTAACTGAGTTGGTGACCCAGTTGAGG
42984621 ATGACACCAA
Statistics
Matches: 186, Mismatches: 26, Indels: 10
0.84 0.12 0.05
Matches are distributed among these distances:
260 1 0.01
261 117 0.63
262 64 0.34
263 4 0.02
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (261 bp):
TTAAAATATATAAAAATATAAAATAAAACTTTAATTAAGTGGTAAATTAAAAATTTTACTAATGC
AATTGACGTGGATTCAAACACCAATATATGCATAGTTTTAATCGATTTGTTTTAAAGTGAAAAAA
CTAAAATACTCTCAAATAACATTACTTATTTTAATTACAAAAGGACATTCTCATAACTTCCTAAC
TGAGTTGGTGACCCAGTTGAGGGTTACATAAACTCGATTAGAGATAATAAGGCGTGCATAATAAA
A
Found at i:42984956 original size:308 final size:310
Alignment explanation
Indices: 42984391--42984963 Score: 794
Period size: 308 Copynumber: 1.9 Consensus size: 310
42984381 ATAATAAGGC
42984391 GTGCATAATAAAATTAAAATATATAAAAATATCAAAATAAAACTTTAGTTGAATGGTAAATTAAA
1 GTGCATAATAAAATTAAAATATATAAAAATATCAAAATAAAACTTTAGTTGAATGGTAAATTAAA
** * * *
42984456 AATTTTATTAATGCAATTGATGTAGGTTTAAATACCAATATATGCATGTTTTAATCGACTTTTTT
66 AATTTTAAAAATGCAATTGATGTAGGTTCAAATACCAATATATGCATATTTTAATCGACATTTTT
* *
42984521 TAAAGTGAAAAAACTAAAATATCCTCAAATAATATTACTTATTTTAATTACAAAAGGACATTCTC
131 TAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCTC
* * *
42984586 ATAAGTTCCTAACTGAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATTAAGAGTTTTATTA
196 ATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATCAAGAGTTTTATTA
42984651 ATAGTGTGTGTATATATATACAAATACACAACCAATAAAGTTCATGGAGT
261 ATAGTGTGTGTATATATATACAAATACACAACCAATAAAGTTCATGGAGT
* * * *
42984701 GTGCATAATAAAATTAAAATGTATAAAAATATTAAAGTAAAACTTTAGATT-AGTGGTAAATTAA
1 GTGCATAATAAAATTAAAATATATAAAAATATCAAAATAAAACTTTAG-TTGAATGGTAAATTAA
** * * * * * * *
42984765 ATGTTTTAAAAATGCAATTGGTGTGGGTTCAAATATC-ATAATGTGTATATTTTTAT-TA-ATTT
65 AAATTTTAAAAATGCAATTGATGTAGGTTCAAATACCAAT-ATATGCATATTTTAATCGACATTT
*** *
42984827 TTTAAAGTGAAAATGTTAAAATACCCTCGAATAATATTACTTATTTCAATTACAAAAGGACATTC
129 TTTAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTC
* * * * * * *
42984892 TCGTAACTTCCTAACTAAGTTGGTGACCCGGTTGAGGGTGACGCCAACTTAGTCAAGGGTTTTAT
194 TCATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATCAAGAGTTTTAT
42984957 TAATAGT
259 TAATAGT
42984964 ATATATATAC
Statistics
Matches: 227, Mismatches: 34, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
308 124 0.55
309 3 0.01
310 98 0.43
311 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (310 bp):
GTGCATAATAAAATTAAAATATATAAAAATATCAAAATAAAACTTTAGTTGAATGGTAAATTAAA
AATTTTAAAAATGCAATTGATGTAGGTTCAAATACCAATATATGCATATTTTAATCGACATTTTT
TAAAGTGAAAAAACTAAAATACCCTCAAATAATATTACTTATTTCAATTACAAAAGGACATTCTC
ATAACTTCCTAACTAAGTTGGTGACCCAGTTGAGGATGACACCAACTCAATCAAGAGTTTTATTA
ATAGTGTGTGTATATATATACAAATACACAACCAATAAAGTTCATGGAGT
Found at i:42985778 original size:16 final size:17
Alignment explanation
Indices: 42985747--42985779 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
42985737 CATTTCATAA
*
42985747 ATTTTTATAATATTAAT
1 ATTTTAATAATATTAAT
42985764 ATTTTAATAAT-TTAAT
1 ATTTTAATAATATTAAT
42985780 TCCCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTTAATAATATTAAT
Found at i:42987132 original size:18 final size:18
Alignment explanation
Indices: 42987105--42987142 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
42987095 ACTCCAAGGC
42987105 GACGACGAAGATGAAGAT
1 GACGACGAAGATGAAGAT
* *
42987123 GACGATGAAGATGGAGAT
1 GACGACGAAGATGAAGAT
42987141 GA
1 GA
42987143 TGAAGATGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.08, G:0.37, T:0.13
Consensus pattern (18 bp):
GACGACGAAGATGAAGAT
Found at i:43007309 original size:2 final size:2
Alignment explanation
Indices: 43007304--43007339 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
43007294 TTAATATATA
*
43007304 TG TG TG TG CG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
43007340 GTACTTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.50, T:0.47
Consensus pattern (2 bp):
TG
Found at i:43010175 original size:16 final size:16
Alignment explanation
Indices: 43010154--43010186 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
43010144 TCATTTAATT
43010154 TCATGTTAAATAAATA
1 TCATGTTAAATAAATA
43010170 TCATGTTAAATAAATA
1 TCATGTTAAATAAATA
43010186 T
1 T
43010187 AAGTGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (16 bp):
TCATGTTAAATAAATA
Found at i:43010514 original size:22 final size:22
Alignment explanation
Indices: 43010489--43010531 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
43010479 TATGTATGTC
* *
43010489 ATATTTAAATTTATTTTGATTT
1 ATATCTAAATATATTTTGATTT
*
43010511 ATATCTAGATATATTTTGATT
1 ATATCTAAATATATTTTGATT
43010532 ACCACTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (22 bp):
ATATCTAAATATATTTTGATTT
Found at i:43012463 original size:15 final size:15
Alignment explanation
Indices: 43012435--43012484 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
43012425 AACCCAACCA
*
43012435 AAACCAAACCAGCCC
1 AAACCAAACAAGCCC
*
43012450 AAACCCAACAAGCCC
1 AAACCAAACAAGCCC
* *
43012465 AAACTAACCCAAGCCC
1 AAACCAA-ACAAGCCC
43012481 AAAC
1 AAAC
43012485 ACTTAAGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.48, C:0.44, G:0.06, T:0.02
Consensus pattern (15 bp):
AAACCAAACAAGCCC
Found at i:43012475 original size:25 final size:26
Alignment explanation
Indices: 43012420--43012482 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
43012410 ACCTAAATCT
43012420 ACCCAAACCCAACCAAAACCAAACCA
1 ACCCAAACCCAACCAAAACCAAACCA
* ** *
43012446 GCCCAAACCCAA-CAAGCCCAAACTA
1 ACCCAAACCCAACCAAAACCAAACCA
*
43012471 ACCCAAGCCCAA
1 ACCCAAACCCAA
43012483 ACACTTAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.48, C:0.46, G:0.05, T:0.02
Consensus pattern (26 bp):
ACCCAAACCCAACCAAAACCAAACCA
Found at i:43013633 original size:3 final size:3
Alignment explanation
Indices: 43013598--43013683 Score: 52
Period size: 3 Copynumber: 29.0 Consensus size: 3
43013588 TTTAGCACTT
* *
43013598 TTA TTA TT- TTA GTTAA TTA TT- TTA ATG TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA -TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*** * * * *
43013643 GCG TTG TCA TTA TTA ATA TTA TTA TTA CTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
43013684 ATATAATTGC
Statistics
Matches: 62, Mismatches: 16, Indels: 10
0.70 0.18 0.11
Matches are distributed among these distances:
2 6 0.10
3 51 0.82
4 4 0.06
5 1 0.02
ACGTcount: A:0.31, C:0.03, G:0.06, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:43015986 original size:19 final size:19
Alignment explanation
Indices: 43015962--43016008 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
43015952 AACGTCTCTT
*
43015962 TTTGCATT-CATTTCATGCA
1 TTTGCATTACATTGCAT-CA
43015981 TTTGCATTACATTGCATCA
1 TTTGCATTACATTGCATCA
*
43016000 TATGCATTA
1 TTTGCATTA
43016009 GATTTTCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCATTACATTGCATCA
Found at i:43017268 original size:17 final size:18
Alignment explanation
Indices: 43017246--43017282 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
43017236 TTATTCTTTT
43017246 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
43017263 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
43017281 AT
1 AT
43017283 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:43018059 original size:16 final size:17
Alignment explanation
Indices: 43018033--43018076 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 17
43018023 AATCAAAGTC
43018033 AAAATAGAAAAAAAG-AG
1 AAAA-AGAAAAAAAGAAG
43018050 AAAAAG-AAAAAAGAAG
1 AAAAAGAAAAAAAGAAG
43018066 AAAAAGAAAAA
1 AAAAAGAAAAA
43018077 GGAGAGGTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.28
16 10 0.40
17 8 0.32
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (17 bp):
AAAAAGAAAAAAAGAAG
Found at i:43018061 original size:15 final size:15
Alignment explanation
Indices: 43018041--43018081 Score: 64
Period size: 16 Copynumber: 2.7 Consensus size: 15
43018031 TCAAAATAGA
43018041 AAAAAAGAGAAAAAG
1 AAAAAAGAGAAAAAG
43018056 AAAAAAGAAGAAAAAG
1 AAAAAAG-AGAAAAAG
*
43018072 AAAAAGGAGA
1 AAAAAAGAGA
43018082 GGTCAAGGCG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAAAAAGAGAAAAAG
Found at i:43021138 original size:29 final size:30
Alignment explanation
Indices: 43021079--43021136 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
43021069 TCCGAGCCTT
*
43021079 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* * *
43021109 GGGGTAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
43021137 AGAGTCGAGG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:43021366 original size:13 final size:13
Alignment explanation
Indices: 43021348--43021379 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
43021338 TTTCCAGCAA
43021348 TTATGAATTTATT
1 TTATGAATTTATT
43021361 TTATGAATTTATT
1 TTATGAATTTATT
*
43021374 TGATGA
1 TTATGA
43021380 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:43021587 original size:50 final size:50
Alignment explanation
Indices: 43021474--43021715 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
43021464 ATTTGGGTAA
* * *
43021474 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
43021530 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
43021580 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
43021630 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
43021680 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
43021716 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:43021663 original size:100 final size:103
Alignment explanation
Indices: 43021474--43021723 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
43021464 ATTTGGGTAA
43021474 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
43021539 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
43021580 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
43021642 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
43021680 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
43021724 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:43023451 original size:50 final size:49
Alignment explanation
Indices: 43023327--43024106 Score: 782
Period size: 50 Copynumber: 15.9 Consensus size: 49
43023317 GCAGCAGAAC
* * *
43023327 AGATTGAAGCTACAACGGCGGATCTCACTTCCCTGACATTGCAATCAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAAA
* * * * * * * ** *
43023376 AGATTGAGGCCATAACGGTGAATCTTACTTTCCT-AGCATTGCGGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAAT-GAAA
*
43023426 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAA-A
* * * **
43023476 AGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCGTTGCAGTGGAGC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAAT-GAAA
* ** *
43023526 AGATTGAAGCTATAACAGCAAATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAA-A
* * * *
43023576 AGATTGAAGCTACAACAGCGGATCTTACTTTCCT-AGCGTTGCAGTGGAAT
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAAT-GAAA
* *
43023626 AGATTGAAGCTACAATAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAA-TGAAA
* * * * * *
43023676 AGATTGATGCTACAACAGCAGATCTTACTTTCCCAG-CGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTAC-TTCCCTGACATTGCAAT-GAAA
* *
43023726 AGATTGAAGCTGCAACAGCGGATCTTACTTCCCTGACATTGCAATTAAGA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAA-A
* * * * *
43023776 AGATTGAAGCTACAACAACGGATCTTACTTTCCT-AGCGTTGCAGTGGAAC
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGA-CATTGCAAT-GAAA
*
43023826 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAAA
* ** * *
43023875 AGATTGAAGCTACAACAGCGAATCTTGTTTCCCCGGCAGTT---A--AAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA-TTGCAATGAAA
*
43023920 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAA-TGAAA
** * *
43023970 AGATTGAAGCTACAACAGCGGATCTTGTTTCCCCGGCAGTT---A--AAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA-TTGCAATGAAA
*
43024015 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATTAAAA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAA-TGAAA
* *
43024065 AGATTGAAGCTACAACAGCAGATCTTAC-CCCCTGACATTGCA
1 AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCA
43024107 GTGGAACAAA
Statistics
Matches: 598, Mismatches: 100, Indels: 66
0.78 0.13 0.09
Matches are distributed among these distances:
44 4 0.01
45 73 0.12
47 3 0.01
48 2 0.00
49 97 0.16
50 401 0.67
51 18 0.03
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (49 bp):
AGATTGAAGCTACAACAGCGGATCTTACTTCCCTGACATTGCAATGAAA
Found at i:43023543 original size:100 final size:100
Alignment explanation
Indices: 43023264--43024092 Score: 1135
Period size: 100 Copynumber: 8.4 Consensus size: 100
43023254 TAACCATAGT
* * ** * * * **
43023264 TTGCAATTTAAAAGATTG-AGGTCACAATGGCGAATCTTACTTTCTCAAGCGGTGCAGCAGAACA
1 TTGCAATTAAAAAGATTGAAGCT-ACAACAGCGGATCTTACTTTC-CTAGCGTTGCAGTGGAACA
* *
43023328 GATTGAAGCTACAACGGCGGATCTCACTTCCCTGACA
64 GATTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * * * * * * *
43023365 TTGCAA-TCAAAAGATTGAGGCCATAACGGTGAATCTTACTTTCCTAGCATTGCGGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
43023429 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
43023464 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAGCAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
* **
43023529 TTGAAGCTATAACAGCAAATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
43023564 TTGCAATTAAGAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAATAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
43023629 TTGAAGCTACAATAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * *
43023664 TTGCAATTAAAAAGATTGATGCTACAACAGCAGATCTTACTTTCCCAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
*
43023729 TTGAAGCTGCAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* *
43023764 TTGCAATTAAGAAGATTGAAGCTACAACAACGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
43023829 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * * ** *
43023864 TTGCAATT-AAAAGATTGAAGCTACAACAGCGAATCTT-GTTTCC--CCG--GCAGTTAAAAAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
43023923 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
* * ** *
43023958 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTT-GTTTCC--CCG--GCAGTTAAAAAGA
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
43024018 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
66 TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
*
43024053 TTGCAATTAAAAAGATTGAAGCTACAACAGCAGATCTTAC
1 TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTAC
43024093 CCCCTGACAT
Statistics
Matches: 665, Mismatches: 59, Indels: 13
0.90 0.08 0.02
Matches are distributed among these distances:
94 53 0.08
95 122 0.18
96 2 0.00
98 5 0.01
99 80 0.12
100 396 0.60
101 7 0.01
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (100 bp):
TTGCAATTAAAAAGATTGAAGCTACAACAGCGGATCTTACTTTCCTAGCGTTGCAGTGGAACAGA
TTGAAGCTACAACAGCGGATCTTACTTCCCTGACA
Found at i:43024455 original size:15 final size:15
Alignment explanation
Indices: 43024427--43024476 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
43024417 AACCCAACCA
*
43024427 AAACCAAACCAGCCC
1 AAACCAAACAAGCCC
*
43024442 AAACCCAACAAGCCC
1 AAACCAAACAAGCCC
* *
43024457 AAACTAACCCAAGCCC
1 AAACCAA-ACAAGCCC
43024473 AAAC
1 AAAC
43024477 ACTTAAGATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.48, C:0.44, G:0.06, T:0.02
Consensus pattern (15 bp):
AAACCAAACAAGCCC
Found at i:43024467 original size:25 final size:26
Alignment explanation
Indices: 43024412--43024474 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 26
43024402 ACCTAAATCT
43024412 ACCCAAACCCAACCAAAACCAAACCA
1 ACCCAAACCCAACCAAAACCAAACCA
* ** *
43024438 GCCCAAACCCAA-CAAGCCCAAACTA
1 ACCCAAACCCAACCAAAACCAAACCA
*
43024463 ACCCAAGCCCAA
1 ACCCAAACCCAA
43024475 ACACTTAAGA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.48, C:0.46, G:0.05, T:0.02
Consensus pattern (26 bp):
ACCCAAACCCAACCAAAACCAAACCA
Found at i:43027561 original size:20 final size:20
Alignment explanation
Indices: 43027538--43027605 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
43027528 CCTTGATCCT
43027538 TGTCTCAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
* *** *
43027558 TGTCTCAAGACCTTG-ATCCT
1 TGTCTCAATACAACGAAT-CG
43027578 TGTCTCAATACAACGAATCG
1 TGTCTCAATACAACGAATCG
43027598 TGTCTCAA
1 TGTCTCAA
43027606 GACCTTGGAT
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 2 0.06
20 32 0.89
21 2 0.06
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.29
Consensus pattern (20 bp):
TGTCTCAATACAACGAATCG
Found at i:43027562 original size:40 final size:40
Alignment explanation
Indices: 43027525--43027612 Score: 176
Period size: 40 Copynumber: 2.2 Consensus size: 40
43027515 CTATGTCTAG
43027525 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
43027565 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
1 AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
43027605 AGACCTTG
1 AGACCTTG
43027613 GATCGAATTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (40 bp):
AGACCTTGATCCTTGTCTCAATACAACGAATCGTGTCTCA
Found at i:43027617 original size:20 final size:20
Alignment explanation
Indices: 43027554--43027617 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
43027544 AATACAACGA
43027554 ATCGTGTCTCAAGACCTT-G
1 ATCGTGTCTCAAGACCTTGG
* * *** *
43027573 ATCCTTGTCTCAATACAACGA
1 AT-CGTGTCTCAAGACCTTGG
43027594 ATCGTGTCTCAAGACCTTGG
1 ATCGTGTCTCAAGACCTTGG
43027614 ATCG
1 ATCG
43027618 AATTTGATTG
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (20 bp):
ATCGTGTCTCAAGACCTTGG
Found at i:43031054 original size:181 final size:174
Alignment explanation
Indices: 43030747--43031097 Score: 470
Period size: 181 Copynumber: 2.0 Consensus size: 174
43030737 TATATATATA
* *
43030747 TTTATCTATTTAACCAGCTTTCTGCGACTAATATTTTTTTCAGCTTGCACATGTGTCTTGTGAGC
1 TTTATCTATTTAACCAGCTTTCTGCAACTAATATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
** * * *
43030812 AGTTGAATTCATCAAAAGACATTACAGAAGAAATTCTTTTATCATATTCTTGGTTGCATCACCTA
66 ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATATTCTCGGTAGCATCACCTA
* * * *
43030877 TTAAGGAAACATATATTTCCTTAGTATGTCTCTCAATAAGGCATTTCT
131 TTAA-G-AA-A-ACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
* *
43030925 TTTATCTATTTAACCAGCTTTCTGCAAGTAA-ATTTTTCCTTCATCTTGCAGGCACGTGTCTTGT
1 TTTATCTATTTAACCAGCTTTCTGCAACTAATATTTTT--TTCAGCTTGCA--CACGTGTCTTGT
* * * *
43030989 GAGTACATGAATTCATCTAAAGACATTACAAAAGAAATTCTTTTGTCATGTTCTCGGTAGCATCA
62 GAGCACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATATTCTCGGTAGCATCA
43031054 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
127 CCTATTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCAT
43031098 CTTTTTTTGG
Statistics
Matches: 152, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
177 34 0.22
178 30 0.20
179 12 0.08
180 1 0.01
181 75 0.49
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (174 bp):
TTTATCTATTTAACCAGCTTTCTGCAACTAATATTTTTTTCAGCTTGCACACGTGTCTTGTGAGC
ACATGAATTCATCAAAAGACATTACAAAAGAAATTCTTTTATCATATTCTCGGTAGCATCACCTA
TTAAGAAAACATTTCATTAGCATGTCTCTCAATAAAGCATTTCT
Found at i:43033157 original size:21 final size:20
Alignment explanation
Indices: 43033128--43033166 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
43033118 GTCAAATATA
43033128 AATGCCACAAGCGCCAATAG
1 AATGCCACAAGCGCCAATAG
*
43033148 AATGCACACAAGTGCCAAT
1 AATGC-CACAAGCGCCAAT
43033167 CTTCCTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.28, G:0.18, T:0.13
Consensus pattern (20 bp):
AATGCCACAAGCGCCAATAG
Found at i:43049848 original size:932 final size:931
Alignment explanation
Indices: 43048037--43050442 Score: 4319
Period size: 931 Copynumber: 2.6 Consensus size: 931
43048027 AACATAAACT
* * * * *
43048037 ATTTGTTGGGGATGAGGAGGAGCAAAGAAAGGAAATAAAGAGCACAGAACAATGAAACAAGATGC
1 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
* *
43048102 AAGAAATATTTTTACTTGCTCACAAATGTGCAGCAAGGGAGCTTATGGCTAATAGCTCATTTTGC
66 AAGAAATATTTTTACTTGCTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
* * *
43048167 TCATTCATTCAAGTAG-AAAAAATAATACATTTATAGCCAAATACATCACCAAATACTACTTACT
131 TCATTCATTCAACTAGAAAAAAATAATACATTTATAGGCAAATACATCACCAAATACTACCTACT
*
43048231 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAGC
196 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
** *
43048296 ACAAAAAAAATATCAAAACAATACCAACCTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAAC
261 AC-CTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAAC
43048361 TAAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAA
325 TAAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAA
* *
43048426 CCAAAAATATAACAGTAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGTAA
390 CCAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAA
43048491 ATACCAATCATTCATCAAGTTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACT
455 ATACCAATCATTCATCAAG-TTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACT
* * *
43048556 CTGCTCAAGTAATTCATTTTCAACCTTGGCTTTATTCTCAACCAAATCTGACTTGCACGCTTGAC
519 CTGCTCAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGACTTACACGCTTGAC
* *
43048621 TATCCCAGTCTTTTGATCCAAAGATTTGTTCATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTG
584 TATCCCAATCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTG
* *
43048686 GTTGACAACTTGCCTTCAAAAACATCTTGCCTTGTTTCTTTGTTCATTACAGTCCTGTTTCTTCT
649 GTTGACAACTTGCCTTCAAAAACATATTGCCTTGTTTCTTTGTTCATTACAGTCCTGTTTCTTAT
* * * *
43048751 TGCACATACTCCCTCCTGCTGTAGAGTGTCTTCATGCATACACTCCATCAACTCCTCCTTTAGCT
714 TGCACATACTCCCTCCTGCTGTAGAGTGACTTCATGCACACAATCCATCAACTCCTCCTTCAGCT
*
43048816 TATCCCAAGCTTGTTTAGGAGTCTCACATGGGTGAGCTGTTGCTATCTTTTTTACAAGCAGTCCT
779 TATCCCAAGCTTGTTTAGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGCAGTCCT
43048881 CAAAGATGACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAAACAAGCCC
844 CAAAGATGACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGC-AAAACAAGCCC
*
43048946 TCAAAGAGTTGGGCTCATGATACC
908 TCAAAGACTTGGGCTCATGATACC
*
43048970 ATTTGTTGGGGATGAGGAGGAGTAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
1 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
*
43049035 AAGAAATATTTTTACTTACTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
66 AAGAAATATTTTTACTTGCTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
43049100 TCATTCATTCAACTAGAAAAAAATAATACATTTATAGGCAAATACATCACCAAATACTACCTACT
131 TCATTCATTCAACTAGAAAAAAATAATACATTTATAGGCAAATACATCACCAAATACTACCTACT
43049165 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
196 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
*
43049230 ACCTAAAAATATTAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
261 ACCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
43049295 AAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
326 AAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
43049360 CAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
391 CAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
43049425 TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
456 TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
* *
43049490 GCTTAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATTTGACTTACACGCTTGACTA
521 GCTCAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGACTTACACGCTTGACTA
*
43049555 TCCCAATCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTTCTTCACAGCCTTGGT
586 TCCCAATCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTGGT
*
43049620 TGACAACTTGCCTTCAAACACATATTGCCTTGTTTCTTTGTTCATTACAGTCCTGTTTCTTATTG
651 TGACAACTTGCCTTCAAAAACATATTGCCTTGTTTCTTTGTTCATTACAGTCCTGTTTCTTATTG
43049685 CACATACTCCCTCCTGCTGTAGAGTGACTTCATGCACACAATCCATCAACTCCTCCTTCAGCTTA
716 CACATACTCCCTCCTGCTGTAGAGTGACTTCATGCACACAATCCATCAACTCCTCCTTCAGCTTA
* *
43049750 TCCCAAGCTTGTTTGGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGTAGTCCTCA
781 TCCCAAGCTTGTTTAGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGCAGTCCTCA
* * *
43049815 AAGATGACAGGCTTTAATAGCTTCTTGTCTTTCTTAACAAGCAGCAGAAGCAAAACAAGCCTTCA
846 AAGATGACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAACAAGCCCTCA
43049880 AAGACTTGGGCTCATGATACC
911 AAGACTTGGGCTCATGATACC
*
43049901 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAAAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
1 ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
43049966 AAGAAATATTTTTACTTGCTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
66 AAGAAATATTTTTACTTGCTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
*
43050031 TCATTCATTCAACTAGAAAAAAATAATACATTTATAGGCAAATACATCACCAAATACTATCTACT
131 TCATTCATTCAACTAGAAAAAAATAATACATTTATAGGCAAATACATCACCAAATACTACCTACT
*
43050096 ACCACTAGTCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
196 ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
*
43050161 ACCTAAAAATGTCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
261 ACCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
* * *
43050226 AAACAACCTTGCTATTACAACAAACATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
326 AAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
**
43050291 CAAAAATATAACAGCAATATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
391 CAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
*
43050356 TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCA
456 TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
43050421 GCTCAAGCAATTCATTTTCAAC
521 GCTCAAGCAATTCATTTTCAAC
43050443 ACTATTATCA
Statistics
Matches: 1417, Mismatches: 55, Indels: 4
0.96 0.04 0.00
Matches are distributed among these distances:
931 561 0.40
932 403 0.28
933 341 0.24
934 112 0.08
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (931 bp):
ATTTGTTGGGGATGAGGAGGAGCAAAGGAAGAAAACAGAGAGCACAGAACAATGAAGCAAGATGC
AAGAAATATTTTTACTTGCTCACAAATATGCAGCAAGGGAGCTTATGGCTGATAGCTCATTTTGC
TCATTCATTCAACTAGAAAAAAATAATACATTTATAGGCAAATACATCACCAAATACTACCTACT
ACCACTAATCATACTTTGAAACAAGTAAAACTTAACTTGCACACAAGCTGATTATGTCAATCAAC
ACCTAAAAATATCAAAACAATACCAACTTAGTTCATTTTCAACTAAGTAGCTTAACAAAGTAACT
AAACAACCTTGCTGTTACAGCAAGCATACGTGCTGCAGCATGTTTACAAGCTGCATGCACTTAAC
CAAAAATATAACAGCAGCATGGTTGGCCAATTTTCAACACTCCTCCTTGGACTCCATGCCGCAAA
TACCAATCATTCATCAAGTTTTTTGAACTTGGCAGTCCTTAGATGCTTTGTTTCAAGCTGACTCT
GCTCAAGCAATTCATTTTCAACCTTGGCTTCATTCTCAACCAAATCTGACTTACACGCTTGACTA
TCCCAATCTTTTGATCCAAAGATTTGTCCATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTGGT
TGACAACTTGCCTTCAAAAACATATTGCCTTGTTTCTTTGTTCATTACAGTCCTGTTTCTTATTG
CACATACTCCCTCCTGCTGTAGAGTGACTTCATGCACACAATCCATCAACTCCTCCTTCAGCTTA
TCCCAAGCTTGTTTAGGAGTCTCACAAGGGTGAGCTGTTGCTATCTTTTTTACAAGCAGTCCTCA
AAGATGACAGGCTTTAACAGCTTCTTATCTTTCTTAACAAGCAGCAGAAGCAAAACAAGCCCTCA
AAGACTTGGGCTCATGATACC
Found at i:43059064 original size:19 final size:19
Alignment explanation
Indices: 43059040--43059077 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
43059030 TTTTCTCTAT
43059040 TTTGTTTGCTTGTGATTTG
1 TTTGTTTGCTTGTGATTTG
43059059 TTTGTTTGCTTGTGATTTG
1 TTTGTTTGCTTGTGATTTG
43059078 CTTTTGCAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.05, C:0.05, G:0.26, T:0.63
Consensus pattern (19 bp):
TTTGTTTGCTTGTGATTTG
Found at i:43059077 original size:11 final size:11
Alignment explanation
Indices: 43059044--43059080 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
43059034 CTCTATTTTG
43059044 TTTGCTTGTGA
1 TTTGCTTGTGA
43059055 TTTG-TT-TG-
1 TTTGCTTGTGA
43059063 TTTGCTTGTGA
1 TTTGCTTGTGA
43059074 TTTGCTT
1 TTTGCTT
43059081 TTGCAGGTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
8 4 0.17
9 4 0.17
10 4 0.17
11 11 0.48
ACGTcount: A:0.05, C:0.08, G:0.24, T:0.62
Consensus pattern (11 bp):
TTTGCTTGTGA
Found at i:43060392 original size:144 final size:143
Alignment explanation
Indices: 43060128--43060418 Score: 510
Period size: 144 Copynumber: 2.0 Consensus size: 143
43060118 TTATTTAGAC
* *
43060128 CTTTAGTCCATTTCTTTGCTTGTAATGACTTTTCAACCTTTTAATTTAATGTATTTTAGTTTCTT
1 CTTTAGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAATTTAATGTATTTTAATTTCTT
* * *
43060193 TTAATTTAATCTGTTAAAGGCTTCAACTTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATACC
66 TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATACC
43060258 TCTCATTACTTTT
131 TCTCATTACTTTT
* *
43060271 CTTTGAGTCCATTTCTTTGTTTGTAATGAATTTTCAACCTTTTAGTTTAATGTATTTTAATTTCT
1 CTTT-AGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAATTTAATGTATTTTAATTTCT
43060336 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATAC
65 TTTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATAC
43060401 CTCTCATTACTTTT
130 CTCTCATTACTTTT
43060415 CTTT
1 CTTT
43060419 TATGTTTTCT
Statistics
Matches: 140, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
143 4 0.03
144 136 0.97
ACGTcount: A:0.20, C:0.14, G:0.10, T:0.55
Consensus pattern (143 bp):
CTTTAGTCCATTTCTTTGCTTGTAATGAATTTTCAACCTTTTAATTTAATGTATTTTAATTTCTT
TTAACTTAATCTGTTAAAGACTTCAAATTTTATGTTTCTTGTTCTTTATTTTGTTGTTGGATACC
TCTCATTACTTTT
Found at i:43060450 original size:144 final size:142
Alignment explanation
Indices: 43060158--43060450 Score: 401
Period size: 144 Copynumber: 2.0 Consensus size: 142
43060148 TGTAATGACT
* * * *
43060158 TTTCAACCTTTTAATTTAATGTATTTTAGTTTCTTTTAATTTAATCTGTTAAAGGCTTCAACTTT
1 TTTCAACCTTTTAATTTAATGTATTTTAATTTCTTTTAACTTAATCTGTTAAAGACTTCAAATTT
43060223 TATGTTTCTTGTTCTTTATTTTGTTGTTGGATACCTCTCATTACTTTTCTTTGAGTCCATTTCTT
66 TATGTTTCTTGTTCTTTATTTTGTTGTTGGATACCTCTCATTACTTTTCTTTGAGT-C-TTTCTT
* * *** * *
43060288 TGTTTGTAATGAAT
129 AGGTAAAAATCAAC
*
43060302 TTTCAACCTTTTAGTTTAATGTATTTTAATTTCTTTTAACTTAATCTGTTAAAGACTTCAAATTT
1 TTTCAACCTTTTAATTTAATGTATTTTAATTTCTTTTAACTTAATCTGTTAAAGACTTCAAATTT
*
43060367 TATGTTTCTTGTTCTTTATTTTGTTGTTGGATACCTCTCATTACTTTTCTTTTATGT-TTTC-TA
66 TATGTTTCTTGTTCTTTATTTTGTTGTTGGATACCTCTCATTACTTTTCTTTGA-GTCTTTCTTA
43060430 GAGTAAAAATCCAAGC
130 G-GTAAAAAT-CAA-C
43060446 TTTCA
1 TTTCA
43060451 TCTTTTTTCT
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
141 2 0.02
142 8 0.06
143 2 0.02
144 118 0.89
145 2 0.02
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (142 bp):
TTTCAACCTTTTAATTTAATGTATTTTAATTTCTTTTAACTTAATCTGTTAAAGACTTCAAATTT
TATGTTTCTTGTTCTTTATTTTGTTGTTGGATACCTCTCATTACTTTTCTTTGAGTCTTTCTTAG
GTAAAAATCAAC
Found at i:43062623 original size:187 final size:188
Alignment explanation
Indices: 43062304--43062676 Score: 694
Period size: 187 Copynumber: 2.0 Consensus size: 188
43062294 TGGAAGAAAA
43062304 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
1 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
*
43062369 TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGTATTGTTTACAGTTCTTGTTAACAATT
66 TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
43062434 GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATCT
131 GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATCT
*
43062492 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATATGAATTGCTTGTGAATTTATTGAA
1 TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
*
43062557 -TATCCTTAGCATGTAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
66 TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
* *
43062621 GGTATCTTAGTTTAAGTATCAATTAGTATCTTCATTAGTCATGAATTTGGTTGAAT
131 GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAAT
43062677 TTTTATGCAA
Statistics
Matches: 180, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
187 116 0.64
188 64 0.36
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (188 bp):
TCATCAAGATATGCATCTAGTAAAGGGGAGTACTAGAAATAGGAATTGCTTGTGAATTTATTGAA
TTATCCTTAGCATGCAATTCTTTAAATATTAATCCATGCATTGTTTACAGTTCTTGTTAACAATT
GGTATCTTAGTTAAAGTATCAATTAGTATCTTAATTAGTCATGAATTTGGTTGAATCT
Found at i:43063610 original size:22 final size:22
Alignment explanation
Indices: 43063583--43063638 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
43063573 TGGTAGTTAA
43063583 GTCTCAAGACATAAGACCATAT
1 GTCTCAAGACATAAGACCATAT
*
43063605 GTCTCAAGACATAGGACCATAT
1 GTCTCAAGACATAAGACCATAT
43063627 GTCTCAAGACAT
1 GTCTCAAGACAT
43063639 GAAAGTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (22 bp):
GTCTCAAGACATAAGACCATAT
Found at i:43064042 original size:14 final size:15
Alignment explanation
Indices: 43064023--43064051 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
43064013 TGAGTCCAAA
43064023 AATAACCC-AATTAC
1 AATAACCCAAATTAC
43064037 AATAACCCAAATTAC
1 AATAACCCAAATTAC
43064052 TAGCCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
AATAACCCAAATTAC
Found at i:43064258 original size:23 final size:22
Alignment explanation
Indices: 43064208--43064259 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
43064198 CGCACACCTC
*
43064208 CGTACGTGCCACGTCCGCGCCT
1 CGTACGTGCCACGTCCCCGCCT
*
43064230 CTGTACGTGCCACGTCCCCGATCT
1 C-GTACGTGCCACGTCCCCG-CCT
43064254 CGTACG
1 CGTACG
43064260 CCGTACCTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.04
23 22 0.85
24 3 0.12
ACGTcount: A:0.12, C:0.42, G:0.25, T:0.21
Consensus pattern (22 bp):
CGTACGTGCCACGTCCCCGCCT
Found at i:43067569 original size:19 final size:20
Alignment explanation
Indices: 43067545--43067598 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
43067535 GCAATTAAGC
*
43067545 CTAGAAATTTTGGTAT-AGG
1 CTAGAAATTTTGGTATCAGA
*
43067564 CTAGAAATTTTAGTATCAGA
1 CTAGAAATTTTGGTATCAGA
*
43067584 TTA-AAATTTTGGTAT
1 CTAGAAATTTTGGTAT
43067599 TGCTTAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 26 0.87
20 4 0.13
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.41
Consensus pattern (20 bp):
CTAGAAATTTTGGTATCAGA
Found at i:43073504 original size:21 final size:21
Alignment explanation
Indices: 43073461--43073574 Score: 95
Period size: 21 Copynumber: 5.5 Consensus size: 21
43073451 TCGAAAACTG
* * *
43073461 AACAGAAGCTCATGATAGCTA
1 AACAGAAGCTCATAAGAGTTA
43073482 AACAGAAGCTCATAAGAGTTA
1 AACAGAAGCTCATAAGAGTTA
* * * * * *
43073503 AATAAAAACACATAAGGGTTG
1 AACAGAAGCTCATAAGAGTTA
* *
43073524 AACAGAAGCTCGTAAGAGCTA
1 AACAGAAGCTCATAAGAGTTA
* * *
43073545 AACAAAAACTCATAA-AGTTG
1 AACAGAAGCTCATAAGAGTTA
43073565 AACAGAAGCT
1 AACAGAAGCT
43073575 TGTGAGAGCT
Statistics
Matches: 69, Mismatches: 24, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
20 11 0.16
21 58 0.84
ACGTcount: A:0.48, C:0.16, G:0.18, T:0.18
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGTTA
Found at i:43073594 original size:42 final size:42
Alignment explanation
Indices: 43073482--43073631 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 42
43073472 ATGATAGCTA
* * * *
43073482 AACAGAAGCTCATAAGAGTTAAATAAAAACACATAAGGGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAAAAACACATAAGAGTTG
*
43073524 AACAGAAGCTCGTAAGAGCTAAACAAAAACTCATAA-AGTTG
1 AACAGAAGCTCGTAAGAGCTAAACAAAAACACATAAGAGTTG
* * * ** * *
43073565 AACAGAAGCTTGTGAGAGCTGAACAAAAA-ATTGTATGAGTTA
1 AACAGAAGCTCGTAAGAGCTAAACAAAAACA-CATAAGAGTTG
* *
43073607 AACGGAAGCTCGTAAGAGCTTAACA
1 AACAGAAGCTCGTAAGAGCTAAACA
43073632 GAAAGTAAAA
Statistics
Matches: 89, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
41 32 0.36
42 57 0.64
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (42 bp):
AACAGAAGCTCGTAAGAGCTAAACAAAAACACATAAGAGTTG
Found at i:43076804 original size:18 final size:18
Alignment explanation
Indices: 43076781--43076828 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
43076771 AAAAAGCCTA
*
43076781 ACACAATATTTTTTTTTG
1 ACACAATATTTTTTTCTG
*
43076799 ACACAAT-TTTTTATCTG
1 ACACAATATTTTTTTCTG
43076816 ACA-AATATTTTTT
1 ACACAATATTTTTT
43076829 AAAATTTCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 3 0.12
17 16 0.62
18 7 0.27
ACGTcount: A:0.31, C:0.12, G:0.04, T:0.52
Consensus pattern (18 bp):
ACACAATATTTTTTTCTG
Found at i:43086538 original size:27 final size:28
Alignment explanation
Indices: 43086486--43086540 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
43086476 TAAATATTGA
43086486 AATTTATGATTTAAAATAAATTAATAATAT
1 AATTTAT-ATTTAAAATAAA-TAATAATAT
43086516 AATTTAT-TTTAAATATAAA-AATAAT
1 AATTTATATTTAAA-ATAAATAATAAT
43086541 TTTTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 6 0.25
28 6 0.25
29 5 0.21
30 7 0.29
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (28 bp):
AATTTATATTTAAAATAAATAATAATAT
Found at i:43087852 original size:14 final size:15
Alignment explanation
Indices: 43087833--43087871 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
43087823 TTTTATTTTT
43087833 TATTAATTATAAAAA
1 TATTAATTATAAAAA
* *
43087848 T-TTAATTTTAAAAT
1 TATTAATTATAAAAA
43087862 TATTAATTAT
1 TATTAATTAT
43087872 TATCATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTAATTATAAAAA
Found at i:43087856 original size:30 final size:35
Alignment explanation
Indices: 43087790--43087857 Score: 83
Period size: 32 Copynumber: 2.1 Consensus size: 35
43087780 TATGTTTATA
*
43087790 TTATCTTTTTATATATATAATATAAATTTCACATT
1 TTATCTTTTTATATATATAATAAAAATTTCACATT
*
43087825 TTAT-TTTTTAT-TA-ATTATAAAAATTT-A-ATT
1 TTATCTTTTTATATATATAATAAAAATTTCACATT
43087855 TTA
1 TTA
43087858 AAATTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 6 0.19
31 1 0.03
32 11 0.35
33 2 0.06
34 7 0.23
35 4 0.13
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATCTTTTTATATATATAATAAAAATTTCACATT
Found at i:43097414 original size:3 final size:3
Alignment explanation
Indices: 43097406--43097430 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43097396 CAAAAAGGAA
43097406 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
43097431 TTAAACATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:43107730 original size:20 final size:21
Alignment explanation
Indices: 43107684--43107762 Score: 67
Period size: 21 Copynumber: 3.8 Consensus size: 21
43107674 TACTAATTAC
43107684 AAATATTTAATAATTATATTT
1 AAATATTTAATAATTATATTT
43107705 AAATATTTAA-AA-TATAGTTT
1 AAATATTTAATAATTATA-TTT
* *
43107725 ATATATTCTAATTAATT-T-TAT
1 AAATATT-TAA-TAATTATATTT
* *
43107746 AAATAATTAATATTTAT
1 AAATATTTAATAATTAT
43107763 TGCTTAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
19 8 0.17
20 15 0.32
21 20 0.43
23 3 0.06
24 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (21 bp):
AAATATTTAATAATTATATTT
Found at i:43107978 original size:28 final size:26
Alignment explanation
Indices: 43107932--43108003 Score: 72
Period size: 26 Copynumber: 2.7 Consensus size: 26
43107922 ATTTTATTTC
43107932 TCAAAAACACTGCTAAACACCAAACTTT
1 TCAAAAACACTGCTAAACA--AAACTTT
* * *
43107960 TCAAAAACACTTCTCAACAATACTTT
1 TCAAAAACACTGCTAAACAAAACTTT
* * *
43107986 TCAAGAACATTGTTAAAC
1 TCAAAAACACTGCTAAAC
43108004 GTCAGCGGCT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
26 19 0.53
28 17 0.47
ACGTcount: A:0.44, C:0.25, G:0.04, T:0.26
Consensus pattern (26 bp):
TCAAAAACACTGCTAAACAAAACTTT
Found at i:43110084 original size:7 final size:7
Alignment explanation
Indices: 43110068--43110100 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
43110058 ACTCTCTTAT
*
43110068 AATTAAG
1 AATTAGG
43110075 AATTAGG
1 AATTAGG
43110082 AATTAGG
1 AATTAGG
43110089 AATTAGG
1 AATTAGG
43110096 AATTA
1 AATTA
43110101 AATCTCATAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (7 bp):
AATTAGG
Found at i:43117854 original size:19 final size:19
Alignment explanation
Indices: 43117830--43117873 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
43117820 TAGCAAAAAC
*
43117830 ATAAAATGTTAAAATATAA
1 ATAAAATATTAAAATATAA
*
43117849 ATAAAATATTATAATATAA
1 ATAAAATATTAAAATATAA
*
43117868 TTAAAA
1 ATAAAA
43117874 GTTGTCCAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (19 bp):
ATAAAATATTAAAATATAA
Found at i:43135947 original size:22 final size:22
Alignment explanation
Indices: 43135915--43135962 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
43135905 AATTATGATC
*
43135915 ATTACTTTAATTGCACT-ATTTA
1 ATTACTATAATT-CACTGATTTA
*
43135937 ATTACTATAATTCATTGATTTA
1 ATTACTATAATTCACTGATTTA
43135959 ATTA
1 ATTA
43135963 TTAATTTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTACTATAATTCACTGATTTA
Found at i:43138058 original size:20 final size:21
Alignment explanation
Indices: 43138019--43138059 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
43138009 GTAATTATAT
*
43138019 TAATTAAATGAAATAAAAATA
1 TAATTAAATGAAACAAAAATA
*
43138040 TAATTAACT-AAACAAAAATA
1 TAATTAAATGAAACAAAAATA
43138060 ATTACACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (21 bp):
TAATTAAATGAAACAAAAATA
Found at i:43139809 original size:66 final size:66
Alignment explanation
Indices: 43139686--43139818 Score: 162
Period size: 66 Copynumber: 2.0 Consensus size: 66
43139676 GCTTAGGTAC
* * *
43139686 AAACTTGGCTCTAAAAACATGTTCCTCTCGATGAACAAAATAAGTGCTTTCTCTAATTTGTACAC
1 AAACTTGGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTTCCTCTAATTTGTACAC
43139751 A
66 A
* * * * *
43139752 AAACTTTGG-TCTAAATACATATTTCTTTCGATAAACAAAATAAGTGC-TCCATTTAATTTTTAC
1 AAAC-TTGGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTTCC-TCTAATTTGTAC
43139815 ACA
64 ACA
43139818 A
1 A
43139819 TTAAATAAAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
65 2 0.04
66 51 0.89
67 4 0.07
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (66 bp):
AAACTTGGCTCTAAAAACATATTCCTCTCGATAAACAAAATAAGTGCTTCCTCTAATTTGTACAC
A
Found at i:43142440 original size:20 final size:20
Alignment explanation
Indices: 43142415--43142454 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
43142405 TTACAGCAAC
43142415 ATGCTGATGTTTGCAAGACT
1 ATGCTGATGTTTGCAAGACT
43142435 ATGCTGATGTTTGCAAGACT
1 ATGCTGATGTTTGCAAGACT
43142455 TGCGAGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (20 bp):
ATGCTGATGTTTGCAAGACT
Found at i:43150867 original size:30 final size:31
Alignment explanation
Indices: 43150813--43150876 Score: 121
Period size: 31 Copynumber: 2.1 Consensus size: 31
43150803 TTTCAAAACT
43150813 AAATGATTAACACATAGTTTTTTTTACTTAA
1 AAATGATTAACACATAGTTTTTTTTACTTAA
43150844 AAATGATTAACACATAG-TTTTTTTACTTAA
1 AAATGATTAACACATAGTTTTTTTTACTTAA
43150874 AAA
1 AAA
43150877 CCCATACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.42
Consensus pattern (31 bp):
AAATGATTAACACATAGTTTTTTTTACTTAA
Found at i:43154330 original size:34 final size:33
Alignment explanation
Indices: 43154230--43154327 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 33
43154220 TAATTTTTTT
* *
43154230 TAAATTAATTAAATTAGGTTTTAAGGGTTTTAAA
1 TAAATTAATTAAATTAGGGTTTAA-GTTTTTAAA
* **
43154264 TAAATAAATTAAATTAAAGTTTAGAGTTTTTAAGA
1 TAAATTAATTAAATTAGGGTTTA-AGTTTTTAA-A
*
43154299 -AAATTAATTAAATTAGGGTTTAATTTTTT
1 TAAATTAATTAAATTAGGGTTTAAGTTTTT
43154328 TAAAAATAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
33 6 0.11
34 45 0.85
35 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (33 bp):
TAAATTAATTAAATTAGGGTTTAAGTTTTTAAA
Found at i:43154579 original size:126 final size:126
Alignment explanation
Indices: 43154423--43155071 Score: 854
Period size: 126 Copynumber: 5.2 Consensus size: 126
43154413 ATTTTGTTTT
** * * * * **
43154423 TTTTTCTTTAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTTGAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* *
43154488 ACGCTTCAAGTAAGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
*
43154549 TTTTTCTACAGTTGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * *
43154614 AAGCTTCAAGCAAGATGCATTGTCAGCAAAATTACTGAAAAATGCTCCCACGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* * * * * *
43154675 TTTTTCTATAGTAGTTCTTGAAAAAATGATTTTGAAAAGACAATTCTGAAAAAATAGTATCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * * * *
43154740 ACGCTTCAAGCAAGATGCACTGTTAGCAAAGTTACTGAAAAATGCTCCCACGTGGACGCTT
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* *
43154801 TTTTTCTACAGTAGTTCTTGAAAAAATTATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
* * * * * *
43154866 ACGCTTCAAACAGGATGCATTGTTAGCAAAATTATTG-AAAAAGCTCCTACGTAGACGCTC
66 ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
* * * *
43154926 TTTTTGTACAATAGTTCCTGAAAAAATAATACTT-AGAAGACGGTTCTGAAAAAATAGTGT-AAG
1 TTTTTCTACAGTAGTTCCTGAAAAAATAAT-TTTGAGAAGACAGTTCTGAAAAAATAGTGTCAA-
** * * * * * *
43154989 AAATACTTCAAGTAGGATGCACTATCAGCAAAATTACTGAAAAAAGCTCCCACATGGACACTC
64 AAACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
43155052 TTTTTCTACAGTAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
43155072 TTTGGCCTTA
Statistics
Matches: 459, Mismatches: 61, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
124 2 0.00
125 101 0.22
126 356 0.78
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACAGTTCTGAAAAAATAGTGTCAAAA
ACGCTTCAAGCAAGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTAGACGCTC
Found at i:43160872 original size:16 final size:16
Alignment explanation
Indices: 43160847--43160877 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43160837 ATTTGATGTG
*
43160847 TATCTCTTTTTTTAAA
1 TATCTATTTTTTTAAA
43160863 TATCTATTTTTTTAA
1 TATCTATTTTTTTAA
43160878 TATTTTAGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.65
Consensus pattern (16 bp):
TATCTATTTTTTTAAA
Found at i:43162920 original size:25 final size:24
Alignment explanation
Indices: 43162892--43162938 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
43162882 CAAATATTTA
43162892 ATAGTTATAT-TTAAATATTTAAAAT
1 ATAGTTATATATT--ATATTTAAAAT
*
43162917 ATAGTTTTATATTATATTTAAA
1 ATAGTTATATATTATATTTAAA
43162939 TTTTATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 9 0.45
26 2 0.10
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (24 bp):
ATAGTTATATATTATATTTAAAAT
Found at i:43163244 original size:50 final size:50
Alignment explanation
Indices: 43163187--43163283 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
43163177 AAACCAAATA
* * * *
43163187 TTTCAAAAGTACTTATCAAAATTAATTTTCCAAAGCACTTTTTAAAAGCT
1 TTTCAAAAATACTTATAAAAATCAATTTTCCAAAGCACTTCTTAAAAGCT
* *
43163237 TTTCAAAAATACTTCTAAAAATCACTTTTCCAAAGCACTTCTTAAAA
1 TTTCAAAAATACTTATAAAAATCAATTTTCCAAAGCACTTCTTAAAA
43163284 ACAATGCTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (50 bp):
TTTCAAAAATACTTATAAAAATCAATTTTCCAAAGCACTTCTTAAAAGCT
Found at i:43169839 original size:23 final size:23
Alignment explanation
Indices: 43169811--43169857 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
43169801 CCATTTTTAA
43169811 ATAAATGAAACAAAATGTAATCT
1 ATAAATGAAACAAAATGTAATCT
43169834 ATAAATGAAACAAAATGTAATCT
1 ATAAATGAAACAAAATGTAATCT
43169857 A
1 A
43169858 ACTCTTAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.26
Consensus pattern (23 bp):
ATAAATGAAACAAAATGTAATCT
Found at i:43172013 original size:46 final size:46
Alignment explanation
Indices: 43171906--43172111 Score: 319
Period size: 46 Copynumber: 4.5 Consensus size: 46
43171896 CATACGATCT
* *
43171906 CTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
*
43171949 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
* * *
43171995 CTTATCACTTTATCACTTGATGAGATAAGTGTAGTTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
* *
43172041 CTTATCAGTTTGTCACTTGATCAGATAAGTGTAGTTAAAGCTACCA
1 CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
43172087 CTTATCACTTTGTCACTTGATCAGA
1 CTTATCACTTTGTCACTTGATCAGA
43172112 AGTACTCAAA
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
43 8 0.05
44 5 0.03
45 20 0.13
46 116 0.78
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (46 bp):
CTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCA
Found at i:43174264 original size:13 final size:13
Alignment explanation
Indices: 43174246--43174275 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43174236 AAAAAATTCT
43174246 AAAATTATGATAA
1 AAAATTATGATAA
*
43174259 AAAATTATTATAA
1 AAAATTATGATAA
43174272 AAAA
1 AAAA
43174276 CTAATTTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (13 bp):
AAAATTATGATAA
Found at i:43174455 original size:15 final size:16
Alignment explanation
Indices: 43174431--43174462 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
43174421 TTTAGATTAT
43174431 TTTTTATTTAAAAATA
1 TTTTTATTTAAAAATA
43174447 TTTTT-TTTAAAAATA
1 TTTTTATTTAAAAATA
43174462 T
1 T
43174463 AATACACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTTTATTTAAAAATA
Found at i:43180133 original size:5 final size:5
Alignment explanation
Indices: 43180123--43180149 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
43180113 TTAATTGATG
43180123 ATAAT ATAAT ATAAT ATAAT ATAAT AT
1 ATAAT ATAAT ATAAT ATAAT ATAAT AT
43180150 TATGATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATAAT
Found at i:43187350 original size:2 final size:2
Alignment explanation
Indices: 43187343--43187388 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
43187333 CTAAGAATTT
*
43187343 GA GA GA GA GA GA GA GA GC GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
43187385 GA GA
1 GA GA
43187389 ATGAGTAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.02, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:43193172 original size:45 final size:45
Alignment explanation
Indices: 43193121--43193224 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
43193111 TCTAATTTAT
* *
43193121 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACGTGCCAATTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTACCAATTAAA
* * *
43193166 ATTACAAAGTTTGTTCCAAGTTTGTTTCAACACCTATCATTTAAA
1 ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTACCAATTAAA
43193211 ATTACAAAGTTTGT
1 ATTACAAAGTTTGT
43193225 ATTTTTGCAT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.38
Consensus pattern (45 bp):
ATTACAAAGTTTGTTCCAAGTTTGTTCCAACACCTACCAATTAAA
Found at i:43200464 original size:3 final size:3
Alignment explanation
Indices: 43200456--43200480 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
43200446 TAAATACAAA
43200456 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
43200481 GAACAATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:43207683 original size:152 final size:152
Alignment explanation
Indices: 43207402--43207683 Score: 555
Period size: 152 Copynumber: 1.9 Consensus size: 152
43207392 TGAGAAGTAC
*
43207402 AATGGAACTAGTAGCCTCGAAGCCCATATTACCACGTTTTGTAGGCGGATGACTGGGTATGTTAA
1 AATGAAACTAGTAGCCTCGAAGCCCATATTACCACGTTTTGTAGGCGGATGACTGGGTATGTTAA
43207467 TAACGACCAGCTGTTGATACATTGTTTTCAGGATAGCCTCACAGGGGCAGCATCCAAGTGGTACA
66 TAACGACCAGCTGTTGATACATTGTTTTCAGGATAGCCTCACAGGGGCAGCATCCAAGTGGTACA
43207532 TTGTTTTCAGGATAGCCTCACA
131 TTGTTTTCAGGATAGCCTCACA
43207554 AATGAAACTAGTAGCCTCGAAGCCCATATTACCACGTTTTGTAGGCGGATGACTGGGTATGTTAA
1 AATGAAACTAGTAGCCTCGAAGCCCATATTACCACGTTTTGTAGGCGGATGACTGGGTATGTTAA
43207619 TAACGACCAGCTGTTGATACATTGTTTTCAGGATAGCCTCACAGGGGCAGCATCCAAGTGGTACA
66 TAACGACCAGCTGTTGATACATTGTTTTCAGGATAGCCTCACAGGGGCAGCATCCAAGTGGTACA
43207684 ATCAACTGAG
Statistics
Matches: 129, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 129 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (152 bp):
AATGAAACTAGTAGCCTCGAAGCCCATATTACCACGTTTTGTAGGCGGATGACTGGGTATGTTAA
TAACGACCAGCTGTTGATACATTGTTTTCAGGATAGCCTCACAGGGGCAGCATCCAAGTGGTACA
TTGTTTTCAGGATAGCCTCACA
Found at i:43214482 original size:24 final size:26
Alignment explanation
Indices: 43214433--43214482 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
43214423 TGAATTTGTT
*
43214433 TGTTCTTGCGATACTTCATTCTTTTC
1 TGTTCTTGCAATACTTCATTCTTTTC
*
43214459 TGTTCTTG-AATACTT-TTTCTTTTC
1 TGTTCTTGCAATACTTCATTCTTTTC
43214483 AAGACATTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 6 0.27
26 8 0.36
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.58
Consensus pattern (26 bp):
TGTTCTTGCAATACTTCATTCTTTTC
Found at i:43215777 original size:44 final size:43
Alignment explanation
Indices: 43215697--43215946 Score: 143
Period size: 44 Copynumber: 5.8 Consensus size: 43
43215687 GAAGATGGCG
* * * *
43215697 AATCTTATCTCCTTGAAGTTGCAGTGGAGCATATTAAAGCTAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA-ATAAC
* * *
43215741 AATCTTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAATCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAC
* * ***
43215784 AATTCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT--C
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAC
* * * * * * *
43215824 TAGTCTTATCTCCTTGAAGTTGCAGAGGAGTAGACT-GAGTAAGC
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAA-C
* * * ** *
43215868 AGGTCTGATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAA-AGC
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAA-AATAAC
* *
43215913 GAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGA
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA
43215947 CTCAAGAAAG
Statistics
Matches: 163, Mismatches: 31, Indels: 23
0.75 0.14 0.11
Matches are distributed among these distances:
40 21 0.13
41 9 0.06
42 4 0.02
43 11 0.07
44 84 0.52
45 31 0.19
46 2 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAATAAC
Found at i:43215936 original size:45 final size:44
Alignment explanation
Indices: 43215825--43215967 Score: 164
Period size: 45 Copynumber: 3.2 Consensus size: 44
43215815 GATCGCATCT
* ** *
43215825 AGTCTTATC-TCCTTGAAGTTGCAGAGGAGTAGA-CTGAGTAAGC
1 AGTCTTATCTTCC-TGAAGTTGCAGTGGAGTAGACCCAAGAAAGC
* *
43215868 AGGTCTGATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGC
1 A-GTCTTATCTTCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGC
* *
43215913 GAGTCTTATCTTCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGC
1 -AGTCTTATCTTCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGC
43215958 AAGTCTTATC
1 -AGTCTTATC
43215968 CCCCAGAAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
43 1 0.01
44 26 0.31
45 57 0.67
46 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.25
Consensus pattern (44 bp):
AGTCTTATCTTCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGC
Found at i:43215984 original size:45 final size:45
Alignment explanation
Indices: 43215890--43215985 Score: 120
Period size: 45 Copynumber: 2.1 Consensus size: 45
43215880 CCTGAAGTTG
* * ** * * *
43215890 CAGTGGAGTAGACCCAAGAAAGCGAGTCTTATCTTCCTGAAGTTG
1 CAGTGGAGCAGACCCAAGAAAGCAAGTCTTATCCCCCAGAAATTA
*
43215935 CAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCCCCCAGAAATTA
1 CAGTGGAGCAGACCCAAGAAAGCAAGTCTTATCCCCCAGAAATTA
43215980 CAGTGG
1 CAGTGG
43215986 GGCAAACTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.21
Consensus pattern (45 bp):
CAGTGGAGCAGACCCAAGAAAGCAAGTCTTATCCCCCAGAAATTA
Found at i:43219351 original size:58 final size:57
Alignment explanation
Indices: 43219280--43219414 Score: 153
Period size: 58 Copynumber: 2.3 Consensus size: 57
43219270 ATGTTATTTT
* * *
43219280 GATTTTGGCTTAGGGTTTTGAAGGTTGGGAATTTTGCTTTAGGATTTTTTACTTTTGA
1 GATTTTGGTTTAGGGTTTTGAAGGTTGAGAATTTTG-TTTAGGATTTTTGACTTTTGA
*** * * * *
43219338 GATTTTGGTTTAGGGTTTTTGATTTTTGATATTTTTGTTTAGGGTTTTTGATTTTTGA
1 GATTTTGGTTTAGGG-TTTTGAAGGTTGAGAATTTTGTTTAGGATTTTTGACTTTTGA
*
43219396 GATATTGGTTTAGGGTTTT
1 GATTTTGGTTTAGGGTTTT
43219415 CTATTTGACT
Statistics
Matches: 65, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
57 4 0.06
58 46 0.71
59 15 0.23
ACGTcount: A:0.16, C:0.02, G:0.27, T:0.56
Consensus pattern (57 bp):
GATTTTGGTTTAGGGTTTTGAAGGTTGAGAATTTTGTTTAGGATTTTTGACTTTTGA
Found at i:43219420 original size:29 final size:29
Alignment explanation
Indices: 43219310--43219414 Score: 147
Period size: 29 Copynumber: 3.6 Consensus size: 29
43219300 AAGGTTGGGA
* * * *
43219310 ATTTTGCTTTAGGATTTTTTACTTTTGAG
1 ATTTTGGTTTAGGGTTTTTGATTTTTGAG
*
43219339 ATTTTGGTTTAGGGTTTTTGATTTTTGAT
1 ATTTTGGTTTAGGGTTTTTGATTTTTGAG
*
43219368 ATTTTTGTTTAGGGTTTTTGATTTTTGAG
1 ATTTTGGTTTAGGGTTTTTGATTTTTGAG
*
43219397 ATATTGGTTTAGGGTTTT
1 ATTTTGGTTTAGGGTTTT
43219415 CTATTTGACT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 67 1.00
ACGTcount: A:0.15, C:0.02, G:0.23, T:0.60
Consensus pattern (29 bp):
ATTTTGGTTTAGGGTTTTTGATTTTTGAG
Found at i:43221660 original size:10 final size:9
Alignment explanation
Indices: 43221633--43221857 Score: 99
Period size: 10 Copynumber: 24.0 Consensus size: 9
43221623 TTAAATGACT
43221633 TTTTTAT-A
1 TTTTTATAA
*
43221641 GTTTTA-AA
1 TTTTTATAA
43221649 TTTTTAATAA
1 TTTTT-ATAA
43221659 TTTTTATAA
1 TTTTTATAA
**
43221668 TTTATTGGAA
1 TTT-TTATAA
43221678 TTTTTA-ATA
1 TTTTTATA-A
43221687 TTATTTATAA
1 TT-TTTATAA
*
43221697 GTTTTTATGAT
1 -TTTTTAT-AA
*
43221708 TTTTTATATG
1 TTTTTATA-A
43221718 TTTTTATAAA
1 TTTTTAT-AA
* *
43221728 CTTTTAAACA
1 TTTTTATA-A
43221738 TATTTTATTAA
1 T-TTTTA-TAA
43221749 --TTTATAA
1 TTTTTATAA
43221756 TTTTT-TAA
1 TTTTTATAA
*
43221764 TATTTATAA
1 TTTTTATAA
*
43221773 GTTTATATAA
1 -TTTTTATAA
*
43221783 TTTTAAT-A
1 TTTTTATAA
43221791 TATTTTA-AA
1 T-TTTTATAA
* *
43221800 TACTTAATAA
1 T-TTTTATAA
43221810 TTTTTATAA
1 TTTTTATAA
* *
43221819 TTTTTTTTTA
1 -TTTTTATAA
43221829 TTTTTA-ACGA
1 TTTTTATA--A
43221839 TTTTTATAA
1 TTTTTATAA
43221848 CTTTTTATAA
1 -TTTTTATAA
43221858 CCATAAGCTA
Statistics
Matches: 165, Mismatches: 26, Indels: 50
0.68 0.11 0.21
Matches are distributed among these distances:
7 3 0.02
8 24 0.15
9 48 0.29
10 77 0.47
11 12 0.07
12 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (9 bp):
TTTTTATAA
Found at i:43230704 original size:20 final size:21
Alignment explanation
Indices: 43230679--43230723 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
43230669 AAAAATGAAA
43230679 TTTGAAATTTTT-ATAAA-TAT
1 TTTGAAATTTTTGA-AAATTAT
43230699 TTTG-AATTTTTGAAAATTAT
1 TTTGAAATTTTTGAAAATTAT
43230719 TTTGA
1 TTTGA
43230724 TTTTTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTGAAATTTTTGAAAATTAT
Found at i:43230706 original size:19 final size:20
Alignment explanation
Indices: 43230679--43230728 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
43230669 AAAAATGAAA
43230679 TTTGAAATTTTT-ATAAA-TAT
1 TTTG-AATTTTTGA-AAATTAT
43230699 TTTGAATTTTTGAAAATTAT
1 TTTGAATTTTTGAAAATTAT
43230719 TTTG-ATTTTT
1 TTTGAATTTTT
43230729 TTTGTAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTGAATTTTTGAAAATTAT
Found at i:43232432 original size:23 final size:23
Alignment explanation
Indices: 43232401--43232454 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
43232391 TCGTACTCAA
*
43232401 AACTCGAATTACTT-ATTCGAGTT
1 AACTCGAATAACTTAATTCGA-TT
* *
43232424 GACTCGAATAATTTAATTCGATT
1 AACTCGAATAACTTAATTCGATT
43232447 AACTCGAA
1 AACTCGAA
43232455 ATTCTATTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (23 bp):
AACTCGAATAACTTAATTCGATT
Found at i:43235949 original size:17 final size:17
Alignment explanation
Indices: 43235906--43235950 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
43235896 CTACAGTTTA
* * *
43235906 TTGGAAGCTCGATTGGG
1 TTGGAAACTTGATTAGG
43235923 TTGGAAACTTGATTAGG
1 TTGGAAACTTGATTAGG
43235940 TTGGAAACTTG
1 TTGGAAACTTG
43235951 TCGGAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.24, C:0.09, G:0.33, T:0.33
Consensus pattern (17 bp):
TTGGAAACTTGATTAGG
Found at i:43244457 original size:3 final size:3
Alignment explanation
Indices: 43244449--43244474 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
43244439 AGTTATGGAG
43244449 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
43244475 ATCCAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:43251106 original size:73 final size:73
Alignment explanation
Indices: 43250986--43251132 Score: 186
Period size: 73 Copynumber: 2.0 Consensus size: 73
43250976 TTTTATCATC
* * * * *
43250986 TTAATTCGATTTAAAATTTTTTTGAGTTGAGTTAAACGAGATAAAATTCAAATTGAAGTGAATTG
1 TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
43251051 AATATATT
66 AATATATT
** * ** * *
43251059 TTAATTCGATTTAATTTTTTTTTGAATTCAGTCGAGTGAGATCAAATTTAAATCGAAGCGAATTG
1 TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
43251124 AATATATT
66 AATATATT
43251132 T
1 T
43251133 GTTTGAACTA
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
73 62 1.00
ACGTcount: A:0.37, C:0.06, G:0.15, T:0.42
Consensus pattern (73 bp):
TTAATTCGATTTAAAATTTTTTTGAATTCAGTCAAACGAGATAAAATTCAAATCGAAGCGAATTG
AATATATT
Found at i:43254122 original size:25 final size:25
Alignment explanation
Indices: 43254045--43254122 Score: 61
Period size: 25 Copynumber: 3.1 Consensus size: 25
43254035 TACACCACAA
* * *
43254045 CTCTCTTGAGCTTTCCAATACTTGG
1 CTCTCTTGAGCTTCCCGATATTTGG
* ***
43254070 CTCT-TATGAGCTTCTCGAT-TAACAG
1 CTCTCT-TGAGCTTCCCGATAT-TTGG
43254095 CTCTCTTGAGCTTCCCGATATTTGG
1 CTCTCTTGAGCTTCCCGATATTTGG
43254120 CTC
1 CTC
43254123 GCAAGAGCTT
Statistics
Matches: 38, Mismatches: 11, Indels: 8
0.67 0.19 0.14
Matches are distributed among these distances:
24 1 0.03
25 35 0.92
26 2 0.05
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.38
Consensus pattern (25 bp):
CTCTCTTGAGCTTCCCGATATTTGG
Found at i:43254162 original size:25 final size:25
Alignment explanation
Indices: 43254102--43254163 Score: 88
Period size: 25 Copynumber: 2.5 Consensus size: 25
43254092 CAGCTCTCTT
* *
43254102 GAGCTTCCCGATATTTGGCTCGCAA
1 GAGCTTCCCGTTATATGGCTCGCAA
* *
43254127 GAGCTTTCCGTTATATGGCTCGGAA
1 GAGCTTCCCGTTATATGGCTCGCAA
43254152 GAGCTTCCCGTT
1 GAGCTTCCCGTT
43254164 TACATGCTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (25 bp):
GAGCTTCCCGTTATATGGCTCGCAA
Found at i:43256337 original size:42 final size:42
Alignment explanation
Indices: 43256281--43256425 Score: 184
Period size: 42 Copynumber: 3.4 Consensus size: 42
43256271 TTACTAAGAT
43256281 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
1 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
*
43256323 GACCATATTTGGGATATGACATCGATATGAGAATTCGTGTAA
1 GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
*** * * * *
43256365 GACCATGGATGGGTTATTGGCATCAATACGAG-ATTACATGTAA
1 GACCATATTTGGGATA-TGGCATCGATATGAGAATT-CGTGTAA
*
43256408 GACCATATCTGGGATATG
1 GACCATATTTGGGATATG
43256426 AAATTGTTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
42 58 0.66
43 30 0.34
ACGTcount: A:0.32, C:0.13, G:0.26, T:0.30
Consensus pattern (42 bp):
GACCATATTTGGGATATGGCATCGATATGAGAATTCGTGTAA
Found at i:43267673 original size:21 final size:21
Alignment explanation
Indices: 43267647--43267686 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43267637 CTATTTAGTT
*
43267647 ACTATCTCTGACAGCATGGTA
1 ACTATCTCTAACAGCATGGTA
43267668 ACTATCTCTAACAGCATGG
1 ACTATCTCTAACAGCATGG
43267687 GCGGCGCAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.25, G:0.17, T:0.28
Consensus pattern (21 bp):
ACTATCTCTAACAGCATGGTA
Found at i:43268217 original size:37 final size:37
Alignment explanation
Indices: 43268162--43268235 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
43268152 TAAAAGTTTT
43268162 GGGGAAAGCAAAAGG-AAAAA-GTTTTGAGAGGGTTTGG
1 GGGGAAAGCAAAAGGAAAAAAGGTTTTG-G-GGGTTTGG
*
43268199 GGGGAAAAGTAAAA-GAAAAAAGGTTTTGGGGGTTTGG
1 GGGG-AAAGCAAAAGGAAAAAAGGTTTTGGGGGTTTGG
43268236 AGGAAGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
37 13 0.39
38 14 0.42
39 6 0.18
ACGTcount: A:0.38, C:0.01, G:0.41, T:0.20
Consensus pattern (37 bp):
GGGGAAAGCAAAAGGAAAAAAGGTTTTGGGGGTTTGG
Found at i:43268277 original size:19 final size:19
Alignment explanation
Indices: 43268237--43268278 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
43268227 GGGGTTTGGA
* *
43268237 GGAAGTAAAAATTTTGAGG
1 GGAAGTAAAAATTTTAAAG
*
43268256 GGAAGTAAAAGTTTTAAAG
1 GGAAGTAAAAATTTTAAAG
43268275 GGAA
1 GGAA
43268279 AATAAAAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (19 bp):
GGAAGTAAAAATTTTAAAG
Found at i:43268338 original size:73 final size:74
Alignment explanation
Indices: 43268200--43268338 Score: 160
Period size: 73 Copynumber: 1.9 Consensus size: 74
43268190 AGGGTTTGGG
* * * * *
43268200 GGGAAAAGTAAAAGAAAAAAGGTTTTGGGGGTTTGGAGGAAGTAAAAATTTTGAGGGGAAGTAAA
1 GGGAAAAGTAAAAGAAAAAAGGTTTTCGAGGTTTGGAGGAAATAAAAATTTTGAGGGAAAATAAA
43268265 AGTTTTAAA
66 AGTTTTAAA
* *
43268274 GGGAAAA-TAAAAAGAAAAAA-G-TTTCGAGGTTTGGGGGGAAATAAAATTTTTG-GGAGAAAAT
1 GGGAAAAGT-AAAAGAAAAAAGGTTTTCGAGGTTT-GGAGGAAATAAAAATTTTGAGG-GAAAAT
43268335 AAAA
63 AAAA
43268339 AGGTTTGAGG
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
72 11 0.20
73 26 0.47
74 18 0.33
ACGTcount: A:0.46, C:0.01, G:0.30, T:0.23
Consensus pattern (74 bp):
GGGAAAAGTAAAAGAAAAAAGGTTTTCGAGGTTTGGAGGAAATAAAAATTTTGAGGGAAAATAAA
AGTTTTAAA
Found at i:43276541 original size:40 final size:40
Alignment explanation
Indices: 43276497--43276588 Score: 121
Period size: 40 Copynumber: 2.3 Consensus size: 40
43276487 ATCTAATGTT
* *
43276497 CCATTTCATATATCTATTTCCATATAACTGATTCATATCA
1 CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
* * * *
43276537 CCATTTCGTACATTTATTTCTATATAACCGATTCATATAA
1 CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
*
43276577 CTATTTCATATA
1 CCATTTCATATA
43276589 AACACTTCAT
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.03, T:0.43
Consensus pattern (40 bp):
CCATTTCATATATCTATTTCCATATAACCGATTCATATAA
Found at i:43276574 original size:13 final size:13
Alignment explanation
Indices: 43276558--43276605 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
43276548 ATTTATTTCT
43276558 ATATAACCGA-TTC
1 ATATAACC-ACTTC
* *
43276571 ATATAACTATTTC
1 ATATAACCACTTC
*
43276584 ATATAAACACTTC
1 ATATAACCACTTC
43276597 ATATAACCA
1 ATATAACCA
43276606 TTTCTATTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
12 1 0.03
13 28 0.97
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (13 bp):
ATATAACCACTTC
Found at i:43276589 original size:26 final size:27
Alignment explanation
Indices: 43276551--43276612 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 27
43276541 TTCGTACATT
*
43276551 TATTTCTATATAACCGA-TTCATATAAC
1 TATTTCTATATAAAC-ACTTCATATAAC
43276578 TATTTC-ATATAAACACTTCATATAAC
1 TATTTCTATATAAACACTTCATATAAC
*
43276604 CATTTCTAT
1 TATTTCTAT
43276613 TTACTCATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 1 0.03
26 22 0.71
27 8 0.26
ACGTcount: A:0.37, C:0.19, G:0.02, T:0.42
Consensus pattern (27 bp):
TATTTCTATATAAACACTTCATATAAC
Done.