Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 129 of 198
Found at i:41083856 original size:29 final size:27
Alignment explanation
Indices: 41083822--41083883 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
41083812 TCATTTTTAA
*
41083822 TAATTTTTATAAATTTCTATATATTTTTT
1 TAATTTTTATAAACTT-TA-ATATTTTTT
* * *
41083851 TTATTTTTTTGAACTTTAATATTTTTT
1 TAATTTTTATAAACTTTAATATTTTTT
41083878 TAATTT
1 TAATTT
41083884 GTATGATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 14 0.50
28 2 0.07
29 12 0.43
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (27 bp):
TAATTTTTATAAACTTTAATATTTTTT
Found at i:41084203 original size:16 final size:16
Alignment explanation
Indices: 41084182--41084212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41084172 CATGTTAGAG
41084182 CATATAAATTTGAAAC
1 CATATAAATTTGAAAC
*
41084198 CATATATATTTGAAA
1 CATATAAATTTGAAA
41084213 AAAATTCAAA
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:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (16 bp):
CATATAAATTTGAAAC
Found at i:41084345 original size:30 final size:28
Alignment explanation
Indices: 41084301--41084367 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 28
41084291 TTTTAGAAAA
41084301 TTTTTAAATTTTTAACT-TTTTAATATATT
1 TTTTTAAATTTTTAA-TATTTT-ATATATT
*
41084330 TTTTTAGACTTTTTAATATTTTATATATT
1 TTTTTA-AATTTTTAATATTTTATATATT
*
41084359 TTTTAAAAT
1 TTTTTAAAT
41084368 ATAAATTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
28 2 0.06
29 19 0.58
30 12 0.36
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.64
Consensus pattern (28 bp):
TTTTTAAATTTTTAATATTTTATATATT
Found at i:41084404 original size:19 final size:20
Alignment explanation
Indices: 41084372--41084424 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
41084362 TAAAATATAA
41084372 ATTTTGATATTTTT-ATAAA-T
1 ATTTTGA-ATTTTTGA-AAATT
41084392 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTGAAAATT
*
41084412 ATTTTGACTTTTT
1 ATTTTGAATTTTT
41084425 TTGTAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (20 bp):
ATTTTGAATTTTTGAAAATT
Found at i:41084854 original size:21 final size:20
Alignment explanation
Indices: 41084828--41084884 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
41084818 CTTTAGCTAA
41084828 TTTTTATGATTTTCTATAATT
1 TTTTTATGATTTT-TATAATT
* *
41084849 TTTTTATTATTTTTATTATT
1 TTTTTATGATTTTTATAATT
*
41084869 TTTTTAATTATTTTTA
1 TTTTT-ATGATTTTTA
41084885 ATATAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.33
21 22 0.67
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.74
Consensus pattern (20 bp):
TTTTTATGATTTTTATAATT
Found at i:41091676 original size:22 final size:21
Alignment explanation
Indices: 41091648--41091700 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 21
41091638 AGCCTGCTAG
*
41091648 GCACAAATCTCGAATATCATC
1 GCACAAAGCTCGAATATCATC
41091669 AGCACAAAGCTCGAATATCATC
1 -GCACAAAGCTCGAATATCATC
41091691 GACACAAAGC
1 G-CACAAAGC
41091701 CCGCTAGGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.42, C:0.28, G:0.13, T:0.17
Consensus pattern (21 bp):
GCACAAAGCTCGAATATCATC
Found at i:41091712 original size:38 final size:38
Alignment explanation
Indices: 41091670--41091911 Score: 283
Period size: 38 Copynumber: 6.4 Consensus size: 38
41091660 AATATCATCA
* * *
41091670 GCACAAAGCTCGAATATCATCGACACAAAGCCCGCTAG
1 GCACAAAGCCCGAATATCACCGACACAAAGCCTGCTAG
*
41091708 GCACAAAGCCCGAATATCACCGACACAAAGCCTACTAG
1 GCACAAAGCCCGAATATCACCGACACAAAGCCTGCTAG
* * * * *
41091746 GCACAAAGCCCAAATACCATCGGCACAAAACCTGCTAG
1 GCACAAAGCCCGAATATCACCGACACAAAGCCTGCTAG
* * *
41091784 GCACAAAGCCCGAATGTCACCGGCACAAAGCTTGCT-G
1 GCACAAAGCCCGAATATCACCGACACAAAGCCTGCTAG
* *
41091821 GTGACAAAGCCCGAA-ACCACC-AGCACAAAGCCTGCTAG
1 G-CACAAAGCCCGAATATCACCGA-CACAAAGCCTGCTAG
* * * *
41091859 GCACAAAGCCTGAATATCACCGGCACAAAGCTTGTTAG
1 GCACAAAGCCCGAATATCACCGACACAAAGCCTGCTAG
41091897 GCACAAAGCCCGAAT
1 GCACAAAGCCCGAAT
41091912 TAACATTACG
Statistics
Matches: 171, Mismatches: 28, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
37 29 0.17
38 142 0.83
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.12
Consensus pattern (38 bp):
GCACAAAGCCCGAATATCACCGACACAAAGCCTGCTAG
Found at i:41091735 original size:60 final size:60
Alignment explanation
Indices: 41091604--41091738 Score: 166
Period size: 60 Copynumber: 2.2 Consensus size: 60
41091594 GATACAATTA
* * * * * *
41091604 CACCAGCATAAAGCCCAAAATATCACTGACACAAAGCCTGCTAGGCACAAATCTCGAATAT
1 CACCAGCACAAAGCTC-GAATATCACTGACACAAAGCCCGCTAGGCACAAAGCCCGAATAT
*
41091665 CATCAGCACAAAGCTCGAATATCA-TCGACACAAAGCCCGCTAGGCACAAAGCCCGAATAT
1 CACCAGCACAAAGCTCGAATATCACT-GACACAAAGCCCGCTAGGCACAAAGCCCGAATAT
41091725 CACC-GACACAAAGC
1 CACCAG-CACAAAGC
41091739 CTACTAGGCA
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
59 2 0.03
60 49 0.77
61 13 0.20
ACGTcount: A:0.40, C:0.32, G:0.15, T:0.13
Consensus pattern (60 bp):
CACCAGCACAAAGCTCGAATATCACTGACACAAAGCCCGCTAGGCACAAAGCCCGAATAT
Found at i:41091767 original size:76 final size:76
Alignment explanation
Indices: 41091670--41091911 Score: 319
Period size: 76 Copynumber: 3.2 Consensus size: 76
41091660 AATATCATCA
* * * *
41091670 GCACAAAGCTCGAATATCATCGACACAAAGCCCGCTAGGCACAAAGCCCGAATATCACCGACACA
1 GCACAAAGCCCGAATACCATCGACACAAAGCCTGCTAGGCACAAAGCCCGAATATCACCGGCACA
* *
41091735 AAGCCTACTAG
66 AAGCTTGCTAG
* * * *
41091746 GCACAAAGCCCAAATACCATCGGCACAAAACCTGCTAGGCACAAAGCCCGAATGTCACCGGCACA
1 GCACAAAGCCCGAATACCATCGACACAAAGCCTGCTAGGCACAAAGCCCGAATATCACCGGCACA
41091811 AAGCTTGCT-G
66 AAGCTTGCTAG
* * *
41091821 GTGACAAAGCCCGAA-ACCA-CCAGCACAAAGCCTGCTAGGCACAAAGCCTGAATATCACCGGCA
1 G-CACAAAGCCCGAATACCATCGA-CACAAAGCCTGCTAGGCACAAAGCCCGAATATCACCGGCA
*
41091884 CAAAGCTTGTTAG
64 CAAAGCTTGCTAG
41091897 GCACAAAGCCCGAAT
1 GCACAAAGCCCGAAT
41091912 TAACATTACG
Statistics
Matches: 143, Mismatches: 19, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
74 1 0.01
75 65 0.45
76 77 0.54
ACGTcount: A:0.36, C:0.32, G:0.19, T:0.12
Consensus pattern (76 bp):
GCACAAAGCCCGAATACCATCGACACAAAGCCTGCTAGGCACAAAGCCCGAATATCACCGGCACA
AAGCTTGCTAG
Found at i:41095304 original size:23 final size:22
Alignment explanation
Indices: 41095273--41095334 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
41095263 ATATTTATTT
41095273 TTTTA-ATATAGTGTAATCATTA
1 TTTTATATATA-TGTAATCATTA
*
41095295 TTTTATATATATATGTAATTATTA
1 -TTT-TATATATATGTAATCATTA
*
41095319 TATATATATATATGTA
1 T-TTTATATATATGTA
41095335 CAGATTTAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 16 0.47
24 13 0.38
25 5 0.15
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (22 bp):
TTTTATATATATGTAATCATTA
Found at i:41095315 original size:21 final size:22
Alignment explanation
Indices: 41095290--41095355 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 22
41095280 ATAGTGTAAT
41095290 CATTATTTTATATATATATGTA
1 CATTATTTTATATATATATGTA
41095312 -ATTATTATATATATATATATGTA
1 CATTATT-T-TATATATATATGTA
* *
41095335 CA-GATTTAATATATATATGTA
1 CATTATTTTATATATATATGTA
41095356 TATGTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 19 0.49
22 2 0.05
23 17 0.44
24 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (22 bp):
CATTATTTTATATATATATGTA
Found at i:41095346 original size:23 final size:23
Alignment explanation
Indices: 41095298--41095366 Score: 77
Period size: 23 Copynumber: 2.8 Consensus size: 23
41095288 ATCATTATTT
*
41095298 TATATATATATGTAATTATTATA
1 TATATATATATGTAAATATTATA
41095321 TATATATATATGTACAGAT-TTAATA
1 TATATATATATGTA-A-ATATT-ATA
41095346 TATATATGTATATGTAAATAT
1 TATATA--TATATGTAAATAT
41095367 ATTGTTATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 14 0.36
24 3 0.08
25 12 0.31
26 2 0.05
27 8 0.21
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (23 bp):
TATATATATATGTAAATATTATA
Found at i:41095347 original size:27 final size:24
Alignment explanation
Indices: 41095298--41095364 Score: 82
Period size: 27 Copynumber: 2.7 Consensus size: 24
41095288 ATCATTATTT
*
41095298 TATATATATATGT-AATTATTATA
1 TATATATATATGTAAATTAATATA
41095321 TATATATATATGTACAGATTTAATATA
1 TATATATATATGTA-A-A-TTAATATA
*
41095348 TATATGTATATGTAAAT
1 TATATATATATGTAAAT
41095365 ATATTGTTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
23 13 0.34
24 1 0.03
25 2 0.05
26 2 0.05
27 20 0.53
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.48
Consensus pattern (24 bp):
TATATATATATGTAAATTAATATA
Found at i:41101836 original size:88 final size:89
Alignment explanation
Indices: 41101667--41101888 Score: 243
Period size: 88 Copynumber: 2.5 Consensus size: 89
41101657 CAATGAAGAC
* * * * *
41101667 AGCAGATTTTGCCTTTCTGTACCGGCAACGAAACAGATC-AAAGACACCAGCCTTGCCTCCCTGG
1 AGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCGAAAGACACCAGCCTTGCCTCCCTGA
*
41101731 GCTGCAGCGGAGCAGGTTAAAAAT
66 GCAGCAGCGGAGCAGGTTAAAAAT
* * * * * *
41101755 AGTAGATCTTGCCTTCCTGTACCGGTAGCGAAGCAGATCGAAA-TCTCCAGCCTTGTCTCCTTGA
1 AGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCGAAAGACACCAGCCTTGCCTCCCTGA
* * *
41101819 GCAGCAGTGGAGTAGGTTGAAAAT
66 GCAGCAGCGGAGCAGGTTAAAAAT
* * * * *
41101843 AGCAGGTCTTGCCTTCCTATACTGGCAGTGAAGTAGATCG-AAGACA
1 AGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCGAAAGACA
41101889 TCAGTTTTAT
Statistics
Matches: 108, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
87 2 0.02
88 103 0.95
89 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.23
Consensus pattern (89 bp):
AGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCGAAAGACACCAGCCTTGCCTCCCTGA
GCAGCAGCGGAGCAGGTTAAAAAT
Found at i:41102474 original size:44 final size:43
Alignment explanation
Indices: 41102405--41103008 Score: 235
Period size: 44 Copynumber: 14.0 Consensus size: 43
41102395 TGCAATGGCG
*
41102405 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * * * **
41102449 AATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAACTTT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * * *** *
41102492 GAATCTTATCTCTCTGATGTTGCAG-AGAGTAGATCGTA-TC-T
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* *
41102533 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG-CA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA--AAGCCAT
* * *
41102577 AGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCA-
1 AATCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAT
*
41102622 AATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC-AT
* * ** * *
41102666 AATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCAC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * ** ** *
41102709 AGATTTTATCTCTCTGAAGTTACA-AAGAGCAGATTGCATCC--
1 A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * **
41102750 AATCTTATCTCCCTGAAGTTACAGT-GAGGCAGACTCAAGAAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGA-GCAGATTAAAGCCAT
* * * * *** *
41102793 CAAGTCTTATCCCCCTAAAATTGCAGTGG-GACAGACTAAATAAACC
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGGAG-CAGATTAAAGCCA-T
* * * **
41102839 AATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTACAATG--AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTA-AA-GCCAT
* * * * ** *
41102882 GAATCTTATCTCTCTGAAATTACAGTAGAGCAGATTGCA-TCA-
1 -AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
* * * * * * *
41102924 AAT-TCATCT---TTAAGTTGTAGCGGATCA-AGTTCAAGCTAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGCCAT
* *
41102963 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCTAT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
41103007 AA
1 AA
41103009 AATTTTGTTC
Statistics
Matches: 413, Mismatches: 106, Indels: 82
0.69 0.18 0.14
Matches are distributed among these distances:
36 1 0.00
37 14 0.03
38 1 0.00
39 2 0.00
40 49 0.12
41 23 0.06
42 4 0.01
43 28 0.07
44 223 0.54
45 64 0.15
46 4 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAT
Found at i:41102670 original size:217 final size:218
Alignment explanation
Indices: 41102399--41102829 Score: 582
Period size: 217 Copynumber: 2.0 Consensus size: 218
41102389 CAACATTGCA
* * * *
41102399 ATGGCGAATCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCCTG
1 ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAATAATCCTATCTCCCTA
*** * * * *
41102464 AAGTTACAGTGGAGCGGATTAAAA-CTTTGAATCTTATCTCTCTGATGTTGCAGAGAGTAGATCG
66 AAGTTACAGTGGAGCGGATTAAAACCACAG-ATCTTATCTCTCTGAAGTTACAAAGAGCAGATCG
* * * * * *
41102528 TATCTAGTCTTATCTCCCTGAAGTTGCAGTG-GAGCAGACT-AAGTAAGCAAGTCTTATCCTCCT
130 CATCCAATCTTATCTCCCTGAAGTTACAGTGAG-GCAGACTCAAGAAAGCAAGTCTTATCCCCCT
* *
41102591 GAAGTTGCAGTGAGG-CAGACTGAAG
194 AAAATTGCAGTG-GGACAGACTGAAG
*
41102616 ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCGATAATCCTATCTCCCTA
1 ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAATAATCCTATCTCCCTA
* * * *
41102681 AAGTTGCAGTGGAGTGGATTAAAACCACAGATTTTATCTCTCTGAAGTTACAAAGAGCAGATTGC
66 AAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAAAGAGCAGATCGC
*
41102746 ATCCAATCTTATCTCCCTGAAGTTACAGTGAGGCAGACTCAAGAAATCAAGTCTTATCCCCCTAA
131 ATCCAATCTTATCTCCCTGAAGTTACAGTGAGGCAGACTCAAGAAAGCAAGTCTTATCCCCCTAA
41102811 AATTGCAGTGGGACAGACT
196 AATTGCAGTGGGACAGACT
41102830 AAATAAACCA
Statistics
Matches: 185, Mismatches: 25, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
217 146 0.79
218 39 0.21
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (218 bp):
ATGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGATTAAAGCCAATAATCCTATCTCCCTA
AAGTTACAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTACAAAGAGCAGATCGC
ATCCAATCTTATCTCCCTGAAGTTACAGTGAGGCAGACTCAAGAAAGCAAGTCTTATCCCCCTAA
AATTGCAGTGGGACAGACTGAAG
Found at i:41102758 original size:173 final size:174
Alignment explanation
Indices: 41102579--41102922 Score: 426
Period size: 173 Copynumber: 2.0 Consensus size: 174
41102569 AGTAAGCAAG
* * ** * * *
41102579 TCTTATC-CTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTG
1 TCTTATCTC-CCTGAAGTTACAGTGAGGCAGACTCAAGAAAGCAAATCTTATCCCCCTAAAATTG
* ** *
41102643 CAGTGGAACAGATTAAAGCCGA-TAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACC
65 CAGTGGAACAGACTAAA-CAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACC
* *
41102707 ACAG-ATTTTATCTCTCTGAAGTTACA-AAGAGCAGATTGCATCCAA
129 A-AGAATCTTATCTCTCTGAAATTACAGAAGAGCAGATTGCATCCAA
* *
41102752 TCTTATCTCCCTGAAGTTACAGTGAGGCAGACTCAAGAAATCAAGTCTTATCCCCCTAAAATTGC
1 TCTTATCTCCCTGAAGTTACAGTGAGGCAGACTCAAGAAAGCAAATCTTATCCCCCTAAAATTGC
* * * * ** *
41102817 AGTGGGACAGACTAAATAAACCAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGATTACAATGAT
66 AGTGGAACAGACTAAACAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCAA
*
41102882 GAATCTTATCTCTCTGAAATTACAGTAGAGCAGATTGCATC
131 GAATCTTATCTCTCTGAAATTACAGAAGAGCAGATTGCATC
41102923 AAATTCATCT
Statistics
Matches: 144, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
172 2 0.01
173 126 0.88
174 16 0.11
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (174 bp):
TCTTATCTCCCTGAAGTTACAGTGAGGCAGACTCAAGAAAGCAAATCTTATCCCCCTAAAATTGC
AGTGGAACAGACTAAACAAACCAATCCTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAACCAA
GAATCTTATCTCTCTGAAATTACAGAAGAGCAGATTGCATCCAA
Found at i:41104429 original size:29 final size:28
Alignment explanation
Indices: 41104390--41104448 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
41104380 TATTTTTTTA
*
41104390 ATATAGTGTAATCATTATTATTATTTATAT
1 ATATAGTGTAATCATT-TT-TTATATATAT
*
41104420 ATATA-TGTAATTATTTTTTATATATAT
1 ATATAGTGTAATCATTTTTTATATATAT
41104447 AT
1 AT
41104449 GTACAGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 11 0.41
28 2 0.07
29 9 0.33
30 5 0.19
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.56
Consensus pattern (28 bp):
ATATAGTGTAATCATTTTTTATATATAT
Found at i:41104460 original size:27 final size:24
Alignment explanation
Indices: 41104406--41104486 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 24
41104396 TGTAATCATT
41104406 ATTATTATTTATATATATATGT-A
1 ATTATTATTTATATATATATGTAA
*
41104429 ATTATTTTTTATATATATATGTACA
1 ATTATTATTTATATATATATGTA-A
* *
41104454 GATTTATTATATATATGTATATGTAA
1 -A-TTATTATTTATATATATATGTAA
41104480 ATATATT
1 AT-TATT
41104487 GTTATATTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
23 21 0.43
24 1 0.02
25 6 0.12
26 2 0.04
27 19 0.39
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (24 bp):
ATTATTATTTATATATATATGTAA
Found at i:41125250 original size:24 final size:25
Alignment explanation
Indices: 41125214--41125264 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
41125204 AAATAAAGGG
41125214 GAAATGAAGGGTTTA-TGAATGA-GA
1 GAAATGAAGGG-TTAGTGAATGATGA
41125238 GAAATG-AGAGGTTAGTGAATGATGA
1 GAAATGAAG-GGTTAGTGAATGATGA
41125263 GA
1 GA
41125265 GGAAATAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.21
24 15 0.62
25 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.24
Consensus pattern (25 bp):
GAAATGAAGGGTTAGTGAATGATGA
Found at i:41128362 original size:17 final size:17
Alignment explanation
Indices: 41128336--41128369 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41128326 GATTATTCTA
41128336 CAATTATTGAGAAAGTT
1 CAATTATTGAGAAAGTT
*
41128353 CAATTGTTGAGAAAGTT
1 CAATTATTGAGAAAGTT
41128370 GTAGAAATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (17 bp):
CAATTATTGAGAAAGTT
Found at i:41131895 original size:20 final size:20
Alignment explanation
Indices: 41131855--41131913 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
41131845 AATTTAATAC
* *
41131855 TTATCTTAATAGT-ATTTTA
1 TTATCTTAATATTAAATTTA
41131874 TTAAT-TTAATATTAAATTTA
1 TT-ATCTTAATATTAAATTTA
41131894 TTATCTTAATATTAAATTTA
1 TTATCTTAATATTAAATTTA
41131914 ATTTAATGTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 11 0.31
20 24 0.69
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (20 bp):
TTATCTTAATATTAAATTTA
Found at i:41131895 original size:25 final size:25
Alignment explanation
Indices: 41131867--41131918 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
41131857 ATCTTAATAG
*
41131867 TATTTTATTAAT-TTAATATTAAATT
1 TATTATATTAATATTAA-ATTAAATT
* *
41131892 TATTATCTTAATATTAAATTTAATT
1 TATTATATTAATATTAAATTAAATT
41131917 TA
1 TA
41131919 ATGTTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATATTAATATTAAATTAAATT
Found at i:41132713 original size:25 final size:25
Alignment explanation
Indices: 41132673--41132841 Score: 133
Period size: 25 Copynumber: 6.8 Consensus size: 25
41132663 CGGCTAATTC
*
41132673 TTTGGAAAGCCCTTGTGGTGAATCC
1 TTTGGAAAGCCCTTGTGGTGAATCA
* * **
41132698 TTTGGAAAACCTTTGTGGAAAATTC-
1 TTTGGAAAGCCCTTGTGGTGAA-TCA
* * *
41132723 TTTGGAAAGCCCTTCTGGCGTATCA
1 TTTGGAAAGCCCTTGTGGTGAATCA
* * *
41132748 TTTGGAAAGCCTTTATGGTGAATTA
1 TTTGGAAAGCCCTTGTGGTGAATCA
* *
41132773 TTTGGAAAGCCCTTGTGGCGTATCA
1 TTTGGAAAGCCCTTGTGGTGAATCA
* * * * * *
41132798 TTTGAAAAACCTTTATGGTAAATTA
1 TTTGGAAAGCCCTTGTGGTGAATCA
* *
41132823 TTTGGAATGCCATTGTGGT
1 TTTGGAAAGCCCTTGTGGT
41132842 AAGTTGTTAT
Statistics
Matches: 109, Mismatches: 33, Indels: 4
0.75 0.23 0.03
Matches are distributed among these distances:
24 2 0.02
25 105 0.96
26 2 0.02
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (25 bp):
TTTGGAAAGCCCTTGTGGTGAATCA
Found at i:41132752 original size:50 final size:50
Alignment explanation
Indices: 41132668--41132840 Score: 229
Period size: 50 Copynumber: 3.5 Consensus size: 50
41132658 AGTATCGGCT
* * * * * *
41132668 AATTCTTTGGAAAGCCCTTGTGGTGAATCCTTTGGAAAACCTTTGTGGAA
1 AATTATTTGGAAAGCCCTTGTGGCGTATCATTTGGAAAACCTTTATGGTA
* * * *
41132718 AATTCTTTGGAAAGCCCTTCTGGCGTATCATTTGGAAAGCCTTTATGGTG
1 AATTATTTGGAAAGCCCTTGTGGCGTATCATTTGGAAAACCTTTATGGTA
*
41132768 AATTATTTGGAAAGCCCTTGTGGCGTATCATTTGAAAAACCTTTATGGTA
1 AATTATTTGGAAAGCCCTTGTGGCGTATCATTTGGAAAACCTTTATGGTA
* *
41132818 AATTATTTGGAATGCCATTGTGG
1 AATTATTTGGAAAGCCCTTGTGG
41132841 TAAGTTGTTA
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 108 1.00
ACGTcount: A:0.26, C:0.15, G:0.23, T:0.36
Consensus pattern (50 bp):
AATTATTTGGAAAGCCCTTGTGGCGTATCATTTGGAAAACCTTTATGGTA
Found at i:41134583 original size:3 final size:3
Alignment explanation
Indices: 41134575--41134606 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
41134565 CAATCTTAAC
41134575 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
41134607 GAATGTTGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41136389 original size:21 final size:21
Alignment explanation
Indices: 41136363--41136408 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
41136353 TTAGTTCGAA
* *
41136363 GTTCCATTTCGCTACTCCAGG
1 GTTCCATTTCGCGACACCAGG
41136384 GTTCCATTTCGCGACACCAGG
1 GTTCCATTTCGCGACACCAGG
41136405 GTTC
1 GTTC
41136409 AATCTCGTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.15, C:0.33, G:0.22, T:0.30
Consensus pattern (21 bp):
GTTCCATTTCGCGACACCAGG
Found at i:41136420 original size:21 final size:21
Alignment explanation
Indices: 41136379--41136420 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41136369 TTTCGCTACT
* *
41136379 CCAGGGTTCCATTTCGCGACA
1 CCAGGGTTCAATCTCGCGACA
*
41136400 CCAGGGTTCAATCTCGTGACA
1 CCAGGGTTCAATCTCGCGACA
41136421 TTGCCCCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.24, T:0.24
Consensus pattern (21 bp):
CCAGGGTTCAATCTCGCGACA
Found at i:41142537 original size:17 final size:16
Alignment explanation
Indices: 41142511--41142542 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41142501 TGATAGATAT
41142511 CTGACGAGCTTCCAAA
1 CTGACGAGCTTCCAAA
41142527 CTGATCGAGCTTCCAA
1 CTGA-CGAGCTTCCAA
41142543 TAATCTATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (16 bp):
CTGACGAGCTTCCAAA
Found at i:41161687 original size:2 final size:2
Alignment explanation
Indices: 41161676--41161732 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
41161666 CCCATAAAGT
41161676 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41161717 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
41161733 AAACACTTTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:41163778 original size:22 final size:22
Alignment explanation
Indices: 41163750--41163792 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41163740 TTTATTGTTC
41163750 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
41163772 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
41163793 TAGCCAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:41164964 original size:42 final size:43
Alignment explanation
Indices: 41164884--41164969 Score: 156
Period size: 42 Copynumber: 2.0 Consensus size: 43
41164874 GAGAGATGTG
*
41164884 TCCAACGACACAACCACAAAAAAAATTAAAATCGGTGGTTGCA
1 TCCAACGACACAACCACAAAAAAAATTAAAATCAGTGGTTGCA
41164927 TCCAACGACACAACCAC-AAAAAAATTAAAATCAGTGGTTGCA
1 TCCAACGACACAACCACAAAAAAAATTAAAATCAGTGGTTGCA
41164969 T
1 T
41164970 ACTCCTACAA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
42 25 0.60
43 17 0.40
ACGTcount: A:0.47, C:0.23, G:0.13, T:0.17
Consensus pattern (43 bp):
TCCAACGACACAACCACAAAAAAAATTAAAATCAGTGGTTGCA
Found at i:41168651 original size:18 final size:18
Alignment explanation
Indices: 41168625--41168664 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41168615 ATTGTCGAAT
* *
41168625 TCAGATCCCTTTTCATTC
1 TCAGATCCCTCTTCATCC
*
41168643 TCAGCTCCCTCTTCATCC
1 TCAGATCCCTCTTCATCC
41168661 TCAG
1 TCAG
41168665 TTGCCTTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.15, C:0.40, G:0.07, T:0.38
Consensus pattern (18 bp):
TCAGATCCCTCTTCATCC
Found at i:41180763 original size:13 final size:13
Alignment explanation
Indices: 41180745--41180769 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41180735 CAATAATAAA
41180745 AAGTTTAAAAATT
1 AAGTTTAAAAATT
41180758 AAGTTTAAAAAT
1 AAGTTTAAAAAT
41180770 ACTTATTAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAGTTTAAAAATT
Found at i:41184417 original size:15 final size:15
Alignment explanation
Indices: 41184399--41184429 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41184389 AAAGGCTCGT
41184399 GAAAAAAAAAGAAAA
1 GAAAAAAAAAGAAAA
*
41184414 GAAAAAAAGAGAAAA
1 GAAAAAAAAAGAAAA
41184429 G
1 G
41184430 CGTACATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAGAAAA
Found at i:41186585 original size:26 final size:26
Alignment explanation
Indices: 41186549--41186601 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
41186539 TAAGTATGTT
41186549 CATAAGTTAGCAAATTACCGAGTTGC
1 CATAAGTTAGCAAATTACCGAGTTGC
41186575 CATAAGTTAGCAAATTACCGAGTTGC
1 CATAAGTTAGCAAATTACCGAGTTGC
41186601 C
1 C
41186602 GTGAATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (26 bp):
CATAAGTTAGCAAATTACCGAGTTGC
Found at i:41198493 original size:12 final size:13
Alignment explanation
Indices: 41198462--41198486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41198452 AAATAACAAA
41198462 AAGTTTAAAAATC
1 AAGTTTAAAAATC
41198475 AAGTTTAAAAAT
1 AAGTTTAAAAAT
41198487 ATGTTTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (13 bp):
AAGTTTAAAAATC
Found at i:41208168 original size:89 final size:89
Alignment explanation
Indices: 41208017--41208181 Score: 269
Period size: 89 Copynumber: 1.9 Consensus size: 89
41208007 TAAGTAGAAG
*
41208017 AAATCAATGAGAGAATTAAAGAAAAGCAAGCTAAATCCAAGGAAAATCAAAGAACAAGTCAAATC
1 AAATCAATGAGAGAATTAAAGAAAAGCAAGATAAATCCAAGGAAAATCAAAGAACAAGTCAAATC
*
41208082 TTATTTTTCATTTGAAAATTTCAA
66 TAATTTTTCATTTGAAAATTTCAA
* * *
41208106 AAATCAATGAGAGAATTAAAGGAAATCAAGATAAATCCAAGGGAAATCCAAA-AACAAGTCAAAT
1 AAATCAATGAGAGAATTAAAGAAAAGCAAGATAAATCCAAGGAAAAT-CAAAGAACAAGTCAAAT
41208170 CTAATTTTTCAT
65 CTAATTTTTCAT
41208182 AGTAAAGTAC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
89 66 0.94
90 4 0.06
ACGTcount: A:0.51, C:0.13, G:0.13, T:0.24
Consensus pattern (89 bp):
AAATCAATGAGAGAATTAAAGAAAAGCAAGATAAATCCAAGGAAAATCAAAGAACAAGTCAAATC
TAATTTTTCATTTGAAAATTTCAA
Found at i:41232908 original size:25 final size:24
Alignment explanation
Indices: 41232867--41232920 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
41232857 CCCAATTAAT
* *
41232867 TGGCTCTCTGAAGCTTCCTGATAC
1 TGGCTCGCTGAACCTTCCTGATAC
*
41232891 TGGCTCGCTTGAACCTTCCTGATAT
1 TGGCTCGC-TGAACCTTCCTGATAC
41232916 TGGCT
1 TGGCT
41232921 TGTATAAGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.15, C:0.28, G:0.22, T:0.35
Consensus pattern (24 bp):
TGGCTCGCTGAACCTTCCTGATAC
Found at i:41233969 original size:404 final size:405
Alignment explanation
Indices: 41233214--41234027 Score: 1477
Period size: 404 Copynumber: 2.0 Consensus size: 405
41233204 ATATATATGT
41233214 ATATGCAAAATTTGATTGATATTGAGCTCAAACATGTTTCTTGATATTCAAGTGAATTACATGAC
1 ATATGCAAAATTTGATTGATATTGAGCTCAAACATGTTTCTTGATATTCAAGTGAATTACATGAC
**
41233279 TAACATGCTTGATGAGGATATGTGTTTAGGCATGTGGTCAAATTGGTTTGAGCATGTTTATTTGC
66 TAACATGCTTGATGAGGATATGTGTTTAGGCATGTGACCAAATTGGTTTGAGCATGTTTATTTGC
41233344 TTACCTTAAATGTGAATTAATTGGTAAGTTAAATTCAATGTTATACGAACTTACTAAGCTTTAAA
131 TTACCTTAAATGTGAATTAATTGGTAAGTTAAATTCAATGTTATACGAACTTACTAAGCTTTAAA
* * * *
41233409 GCTTACTTTGTTTTATTTTCCTTTGTTCTATAGTAATTCGGAGGCTCGTTGGGTTGGAAGCTTGG
196 GCTTACTTTGGTTTATTTTCCTCTGTTCTACAGTAATTCGGAGGCTCGTTAGGTTGGAAGCTTGG
* *
41233474 CGGAGATATCATCACACTATCCATCGGCCCATTTCGGTACAAATATAAAATTAATTTTGGTTATA
261 AGGAGATATCATCACACTATCCATCGGCCCATTTCGGTACAAATATAAAACTAATTTTGGTTATA
* *
41233539 ATGACATGTATAGGTTAATTGGCCAGTGTTGGCATATAAATGTTTTGGTTGTAAATGGCCATTGG
326 ATGACATGTATAGGATAATTGGCCAGTGTTGGCATATAAATGTTTTGGTTGTAAATAGCCATTGG
41233604 AATGGCTTATGATTA
391 AATGGCTTATGATTA
*
41233619 ATATG-AAAATTTGATTGATATTGAGCTCAAACATGTTTCTTGATATTCATGTGAATTACATGAC
1 ATATGCAAAATTTGATTGATATTGAGCTCAAACATGTTTCTTGATATTCAAGTGAATTACATGAC
41233683 TAACATGCTTGATGAGGATATGTGTTTAGGCATGTGACCAAATTGGTTTGAGCATGTTTATTTGC
66 TAACATGCTTGATGAGGATATGTGTTTAGGCATGTGACCAAATTGGTTTGAGCATGTTTATTTGC
*
41233748 TTACCTTAAATGTGAATTAATTGGTAAGTTAAATTCAATGTTATATGAACTTACTAAGCTTTAAA
131 TTACCTTAAATGTGAATTAATTGGTAAGTTAAATTCAATGTTATACGAACTTACTAAGCTTTAAA
41233813 GCTTACTTTGGTTTATTTTCCTCTGTTCTACAGTAATTCGGAGGCTCGTTAGGTTGGAAGCTTGG
196 GCTTACTTTGGTTTATTTTCCTCTGTTCTACAGTAATTCGGAGGCTCGTTAGGTTGGAAGCTTGG
** * *
41233878 AGGAGATATCATCACGTTATCCATCTGCCCATTTTGGTACAAATATAAAACTAATTTTGGTTATA
261 AGGAGATATCATCACACTATCCATCGGCCCATTTCGGTACAAATATAAAACTAATTTTGGTTATA
41233943 ATGACATGTATAGGATAATTGGCCAGTGTTGGCATATAAATGTTTTGGTTGTAAATAGCCATTGG
326 ATGACATGTATAGGATAATTGGCCAGTGTTGGCATATAAATGTTTTGGTTGTAAATAGCCATTGG
41234008 AATGGCTTATGATTA
391 AATGGCTTATGATTA
41234023 ATATG
1 ATATG
41234028 TTTTGATGTA
Statistics
Matches: 393, Mismatches: 16, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
404 388 0.99
405 5 0.01
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.38
Consensus pattern (405 bp):
ATATGCAAAATTTGATTGATATTGAGCTCAAACATGTTTCTTGATATTCAAGTGAATTACATGAC
TAACATGCTTGATGAGGATATGTGTTTAGGCATGTGACCAAATTGGTTTGAGCATGTTTATTTGC
TTACCTTAAATGTGAATTAATTGGTAAGTTAAATTCAATGTTATACGAACTTACTAAGCTTTAAA
GCTTACTTTGGTTTATTTTCCTCTGTTCTACAGTAATTCGGAGGCTCGTTAGGTTGGAAGCTTGG
AGGAGATATCATCACACTATCCATCGGCCCATTTCGGTACAAATATAAAACTAATTTTGGTTATA
ATGACATGTATAGGATAATTGGCCAGTGTTGGCATATAAATGTTTTGGTTGTAAATAGCCATTGG
AATGGCTTATGATTA
Found at i:41240987 original size:24 final size:24
Alignment explanation
Indices: 41240960--41241024 Score: 67
Period size: 25 Copynumber: 2.7 Consensus size: 24
41240950 CGAAAGAGTG
* *
41240960 TCCCGTTATTAGCTCTCATGATCT
1 TCCCGTTATTAGCTCTCACGAACT
* * *
41240984 TCCCGTTATATGGTTCTTACGAACT
1 TCCCGTTAT-TAGCTCTCACGAACT
*
41241009 TCCCGTTAATAGCTCT
1 TCCCGTTATTAGCTCT
41241025 TCGGAGCATC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
24 14 0.44
25 18 0.56
ACGTcount: A:0.18, C:0.28, G:0.14, T:0.40
Consensus pattern (24 bp):
TCCCGTTATTAGCTCTCACGAACT
Found at i:41241788 original size:33 final size:33
Alignment explanation
Indices: 41241742--41241807 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
41241732 TGGAGGCTCG
41241742 TTGGGTTGGAAGCTTGGCAGAGATATCATCACA
1 TTGGGTTGGAAGCTTGGCAGAGATATCATCACA
*
41241775 TTGGGTTGTAAGCTTGGCAGAGATATCATCACA
1 TTGGGTTGGAAGCTTGGCAGAGATATCATCACA
41241808 CTATCCATCG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.29
Consensus pattern (33 bp):
TTGGGTTGGAAGCTTGGCAGAGATATCATCACA
Found at i:41244762 original size:18 final size:18
Alignment explanation
Indices: 41244735--41244774 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
41244725 CAGGTGCGTA
*
41244735 TCCTAGCCCTTATATGTG
1 TCCTAACCCTTATATGTG
*
41244753 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTG
41244771 TCCT
1 TCCT
41244775 TTTCTCAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTG
Found at i:41245262 original size:62 final size:60
Alignment explanation
Indices: 41245147--41245263 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 60
41245137 TTGTATAAAC
* ***
41245147 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAGCCAAT
1 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGTAATAGCCAAT
* *
41245207 TATTTTTATATTTTTTCGTATTTAATAAAATAGAAGTTCTTTTGAATAAGGTAATAG
1 TATTTTTATATTGTTTC--ATTTAATAAAATAAAAGTTCTTTTGAATAAGGTAATAG
41245264 AAATAATGCA
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
60 16 0.33
62 33 0.67
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (60 bp):
TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGTAATAGCCAAT
Found at i:41246803 original size:16 final size:16
Alignment explanation
Indices: 41246782--41246822 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
41246772 CCTCGCGTGT
41246782 TGCGCCTCCGCGCGCG
1 TGCGCCTCCGCGCGCG
*
41246798 TGCGCCTCCGCGTGCG
1 TGCGCCTCCGCGCGCG
41246814 TGCGCCTCC
1 TGCGCCTCC
41246823 AGCTGGATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.00, C:0.49, G:0.34, T:0.17
Consensus pattern (16 bp):
TGCGCCTCCGCGCGCG
Found at i:41247910 original size:26 final size:27
Alignment explanation
Indices: 41247881--41247942 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
41247871 TTTTATATGA
41247881 TTATTTTAACTTGCTT-TGTAAATTA-T
1 TTATTTTAACTTG-TTCTGTAAATTATT
* *
41247907 TTATGTTT-ATTTGTTCTGTATATTATT
1 TTAT-TTTAACTTGTTCTGTAAATTATT
41247934 TTATTTTAA
1 TTATTTTAA
41247943 ATTATTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
25 2 0.07
26 19 0.63
27 9 0.30
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (27 bp):
TTATTTTAACTTGTTCTGTAAATTATT
Found at i:41247982 original size:34 final size:35
Alignment explanation
Indices: 41247939--41248008 Score: 133
Period size: 34 Copynumber: 2.0 Consensus size: 35
41247929 TTATTTTATT
41247939 TTAAATTATTTTATATATTAATTA-TTTAAAATTA
1 TTAAATTATTTTATATATTAATTATTTTAAAATTA
41247973 TTAAATTATTTTATATATTAATTATTTTAAAATTA
1 TTAAATTATTTTATATATTAATTATTTTAAAATTA
41248008 T
1 T
41248009 CCTATACTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 24 0.69
35 11 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
TTAAATTATTTTATATATTAATTATTTTAAAATTA
Found at i:41248608 original size:17 final size:18
Alignment explanation
Indices: 41248570--41248613 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
41248560 ATTATTGCTC
* *
41248570 TTATGTGTATTGTATTGC
1 TTATTTGTATTGTATTGA
41248588 TTATTTGTATT-TATTGA
1 TTATTTGTATTGTATTGA
41248605 TTATTTGTA
1 TTATTTGTA
41248614 GTTCATTAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.20, C:0.02, G:0.16, T:0.61
Consensus pattern (18 bp):
TTATTTGTATTGTATTGA
Found at i:41251878 original size:97 final size:98
Alignment explanation
Indices: 41251700--41251897 Score: 281
Period size: 97 Copynumber: 2.0 Consensus size: 98
41251690 TAAGGCAAAG
* * * * *
41251700 CAAGAACTATTTTAGAAAAAGAGCGTCCTCGTGGGATTTTTTTTCAATAATTTTGCTGACAGTAC
1 CAAGAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGTTTTTTTCAATAATTTTGCTGACAGTAC
*
41251765 ATCTTGCTTAAAGCATTTTTGACACTATTTTTT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTTTT
* * * * *
41251798 CAAGAACTACTGTAAAAAAAGAGTGTCCACGTGGGAGTTTTTTT-AGTAATTTTGTTGATAGTGC
1 CAAGAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGTTTTTTTCAATAATTTTGCTGACAGTAC
*
41251862 ATCCTGCTTGAAGCATTTTTGACACTATTTTTT
66 ATCCTGCTTAAAGCATTTTTGACACTATTTTTT
41251895 CAA
1 CAA
41251898 AACCGTCTTC
Statistics
Matches: 88, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 50 0.57
98 38 0.43
ACGTcount: A:0.29, C:0.15, G:0.17, T:0.39
Consensus pattern (98 bp):
CAAGAACTACTGTAAAAAAAGAGCGTCCACGTGGGAGTTTTTTTCAATAATTTTGCTGACAGTAC
ATCCTGCTTAAAGCATTTTTGACACTATTTTTT
Found at i:41252047 original size:125 final size:126
Alignment explanation
Indices: 41251790--41252319 Score: 726
Period size: 126 Copynumber: 4.2 Consensus size: 126
41251780 TTTTTGACAC
* * * * * *
41251790 TATTTTTTCAAGAACTACTGTAAAAAAAGAGTGTCCACGTGGGAG-TTTTTTTAGTAATTTTGTT
1 TATTTTTTCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCCTTTTTCAGTAATTTTGCT
*
41251854 GATAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
66 GACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
*
41251915 TATTTTTTCAGGAACTA-TAGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGC
1 TATTTTTTCAGGAACTACT-GTAGAAAAAGAGCGTCCACGTGGGAGCCTTTTTCAGTAATTTTGC
* * * *
41251979 TGATAGTGCATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAAT
65 TGACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
* * * *
41252041 TATTTTTTCAGGAACTACTGTATAAAAAGAGAGTCCACGTGGTAGCCTTTTTCAAG-ACTTTTGC
1 TATTTTTTCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCCTTTTTC-AGTAATTTTGC
* * * * * * *
41252105 TGACATTGCATACTGCTTGAAGTATTTTTGACATTA-TTTTTCAGAACTGCCTTCTCAAAAT
65 TGACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
* * * * *
41252166 TATTTTTTCAGAAACTACTGTAGAAAAAGAGCATCCATGTGGGAGCCCTTTTCAGTACTTTTGCT
1 TATTTTTTCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCCTTTTTCAGTAATTTTGCT
* *
41252231 GACAGTGCATCCTGCTTGAAGCATTTTTGTCACTATTTTTTCAGAACCGTCTTCTCAAAAT
66 GACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
* *
41252292 TAATTTTTCAGAAACTACTGTAGAAAAA
1 TATTTTTTCAGGAACTACTGTAGAAAAA
41252320 AGATCAAAAT
Statistics
Matches: 362, Mismatches: 37, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
124 3 0.01
125 148 0.41
126 208 0.57
127 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (126 bp):
TATTTTTTCAGGAACTACTGTAGAAAAAGAGCGTCCACGTGGGAGCCTTTTTCAGTAATTTTGCT
GACAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
Found at i:41252240 original size:251 final size:251
Alignment explanation
Indices: 41251790--41252322 Score: 739
Period size: 251 Copynumber: 2.1 Consensus size: 251
41251780 TTTTTGACAC
* * ** *
41251790 TATTTTTTCAAGAACTACTGTAAAAAAAGAGTGTCCACGTGGGAGTTTTTTTAGTAATTTTGTTG
1 TATTTTTTCAGGAACTACTGTAAAAAAAGAGAGTCCACGTGGGAGTTTTTCAAGTAATTTTGCTG
* * *
41251855 ATAGTGCATCCTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAATTATTT
66 ACAGTGCATACTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGCCTTCTCAAAATTATTT
* * ** *
41251920 TTTCAGGAACTATAGTAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTCAGTAATTTTGCTGATAG
131 TTTCAGAAACTATAGTAGAAAAAGAGCATCCACGTGGGAGCCCTTTTCAGTAATTTTGCTGACAG
* *
41251985 TGCATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAAT
196 TGCATCCTACTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
* * *
41252041 TATTTTTTCAGGAACTACTGTATAAAAAGAGAGTCCACGTGGTAGCCTTTTTCAAG-ACTTTTGC
1 TATTTTTTCAGGAACTACTGTAAAAAAAGAGAGTCCACGTGGGAG--TTTTTCAAGTAATTTTGC
* * * * *
41252105 TGACATTGCATACTGCTTGAAGTATTTTTGACATTA-TTTTTCAGAACTGCCTTCTCAAAATTAT
64 TGACAGTGCATACTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGCCTTCTCAAAATTAT
* *
41252169 TTTTTCAGAAACTACT-GTAGAAAAAGAGCATCCATGTGGGAGCCCTTTTCAGTACTTTTGCTGA
129 TTTTTCAGAAACTA-TAGTAGAAAAAGAGCATCCACGTGGGAGCCCTTTTCAGTAATTTTGCTGA
* * *
41252233 CAGTGCATCCTGCTTGAAGCATTTTTGTCACTATTTTTTCAGAACCGTCTTCTCAAAAT
193 CAGTGCATCCTACTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
* *
41252292 TAATTTTTCAGAAACTACTGTAGAAAAAAGA
1 TATTTTTTCAGGAACTACTGTA-AAAAAAGA
41252323 TCAAAATCCT
Statistics
Matches: 247, Mismatches: 31, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
251 195 0.79
252 45 0.18
253 7 0.03
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (251 bp):
TATTTTTTCAGGAACTACTGTAAAAAAAGAGAGTCCACGTGGGAGTTTTTCAAGTAATTTTGCTG
ACAGTGCATACTGCTTGAAGCATTTTTGACACTATTTTTTCAAAACCGCCTTCTCAAAATTATTT
TTTCAGAAACTATAGTAGAAAAAGAGCATCCACGTGGGAGCCCTTTTCAGTAATTTTGCTGACAG
TGCATCCTACTTGAAGCATTTTTGACACTATTTTTTCAAAACCGTCTTCTCAAAAT
Found at i:41252976 original size:23 final size:23
Alignment explanation
Indices: 41252946--41252992 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
41252936 TCACTTAACT
41252946 TCAAAAAGTTACAAAACT-GTCAC
1 TCAAAAAGTTACAAAA-TAGTCAC
41252969 TCAAAAAGTTACAAAATAGTCAC
1 TCAAAAAGTTACAAAATAGTCAC
41252992 T
1 T
41252993 GAATTATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 1 0.04
23 22 0.96
ACGTcount: A:0.49, C:0.19, G:0.09, T:0.23
Consensus pattern (23 bp):
TCAAAAAGTTACAAAATAGTCAC
Found at i:41254126 original size:10 final size:10
Alignment explanation
Indices: 41254111--41254138 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
41254101 CTTATTTTCT
41254111 AATTTTCACA
1 AATTTTCACA
41254121 AATTTTCACA
1 AATTTTCACA
41254131 AATTTTCA
1 AATTTTCA
41254139 TTTTCATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.39, C:0.18, G:0.00, T:0.43
Consensus pattern (10 bp):
AATTTTCACA
Found at i:41254672 original size:27 final size:27
Alignment explanation
Indices: 41254623--41254674 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
41254613 AAATCTTTGA
* *
41254623 AATTTTAAAAAATAAAATTAAAAATAT
1 AATTATAAAAAATAAAATCAAAAATAT
41254650 AATTATAAAAAATATAAA-CAAAAAT
1 AATTATAAAAAATA-AAATCAAAAAT
41254675 TCCAAAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 19 0.86
28 3 0.14
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (27 bp):
AATTATAAAAAATAAAATCAAAAATAT
Found at i:41256778 original size:53 final size:53
Alignment explanation
Indices: 41256673--41256779 Score: 169
Period size: 53 Copynumber: 2.0 Consensus size: 53
41256663 TAAGGAGACC
* *
41256673 TTTTTAATGTTGTGGATTATTGTTGGATCATTAGTTGACTGATGAACGGTCTA
1 TTTTTAATGTTGTGGATTATTGTTGGATCATTAGTTGACTAATGAACAGTCTA
* * *
41256726 TTTTTAATGTTGTGGATTATTGTTGGATTATTAGTTGTCTAATGAATAGTCTA
1 TTTTTAATGTTGTGGATTATTGTTGGATCATTAGTTGACTAATGAACAGTCTA
41256779 T
1 T
41256780 CCATAACATG
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.23, C:0.06, G:0.22, T:0.49
Consensus pattern (53 bp):
TTTTTAATGTTGTGGATTATTGTTGGATCATTAGTTGACTAATGAACAGTCTA
Found at i:41256901 original size:14 final size:14
Alignment explanation
Indices: 41256882--41256908 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41256872 TTTTATTTTT
41256882 ATTAGATTAAAATC
1 ATTAGATTAAAATC
41256896 ATTAGATTAAAAT
1 ATTAGATTAAAAT
41256909 TGTTTTCTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.07, T:0.37
Consensus pattern (14 bp):
ATTAGATTAAAATC
Found at i:41257637 original size:159 final size:156
Alignment explanation
Indices: 41257348--41257806 Score: 510
Period size: 159 Copynumber: 2.9 Consensus size: 156
41257338 TATGCCATCC
* * * * * * * *
41257348 TTTTTTGGCTTCTAGTTCTCATACTTGTACCAAACTGAGAACAAAAATCATAACCCTAAATTAAA
1 TTTTTTGGCTTCTAGTTCTCGTACTAGTACCAGACTAAGAAAAAAAATCAGAACCCCAAATTAGA
* *
41257413 TTTAAATAATTTGGAATTGACATTAAAAAAGTGTTTACGATATAAATGTGATCCAGTTGTGTTAG
66 TTTAAATATTTTGGAATTGACATT-AAAAAGTGTTTACGATATACATGTGATCCAGTTGTGTTAG
* *
41257478 GTTGAATGCATGG-AGTTATGTTATTCT
130 GTTGAATACATGGTA-TTATGTTATTAT
*
41257505 TTTTTTGGCTTCTAGTTCAT-GTACTCGTACCAGACTAAGACCAAAAAAATCAGAACCCCAAATT
1 TTTTTTGGCTTCTAGTTC-TCGTACTAGTACCAGACTAAGA--AAAAAAATCAGAACCCCAAATT
* * * * * * *
41257569 AGATTAAAATATTTTTGAGTTGACATTAAAATAGTGTATACGATATACCTATGATCCAGTTGTAT
63 AGATTTAAATATTTTGGAATTGACATTAAAA-AGTGTTTACGATATACATGTGATCCAGTTGTGT
* *
41257634 TAGGCTGAATACATGGTATTATGTTGTTAT
127 TAGGTTGAATACATGGTATTATGTTATTAT
** * * * *
41257664 TTTTGGGGCTTTTAGTTCTCGCACTAGTACCAGACTAAGATAAAAAAAGTTAGAA-CCCAAATGA
1 TTTTTTGGCTTCTAGTTCTCGTACTAGTACCAGACTAAGA-AAAAAAA-TCAGAACCCCAAATTA
* * * * * *
41257728 GATTTTAATATTTTGGAATTGACAATGAAAAAGTGTTTATGATATACTTGTGTTCCCGTTGTGTT
64 GATTTAAATATTTTGGAATTGAC-ATTAAAAAGTGTTTACGATATACATGTGATCCAGTTGTGTT
41257793 AGGTTGAATACATG
128 AGGTTGAATACATG
41257807 ATCTTTTGTT
Statistics
Matches: 252, Mismatches: 42, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
157 34 0.13
158 80 0.32
159 137 0.54
160 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (156 bp):
TTTTTTGGCTTCTAGTTCTCGTACTAGTACCAGACTAAGAAAAAAAATCAGAACCCCAAATTAGA
TTTAAATATTTTGGAATTGACATTAAAAAGTGTTTACGATATACATGTGATCCAGTTGTGTTAGG
TTGAATACATGGTATTATGTTATTAT
Found at i:41261541 original size:40 final size:39
Alignment explanation
Indices: 41261476--41261636 Score: 135
Period size: 41 Copynumber: 3.9 Consensus size: 39
41261466 ACTATGTTTA
*
41261476 GCACTTAGTGTGTGATTCGAGATAGCTTCGGCTATTTATG
1 GCACTTAGTGTGTGATTAGA-ATAGCTTCGGCTATTTATG
* *
41261516 GCAGTTAGTGTGTGATTTAGAATAGCTTTGGCTATATATATATG
1 GCACTTAGTGTGTGA-TTAGAATAGCTTCGGC--TAT-T-TATG
* * * * *
41261560 GCACTTAGTGTGCAAGACT-GAGATAGCTTCAGCTATGTAAG
1 GCACTTAGTGTG--TGATTAGA-ATAGCTTCGGCTATTTATG
*
41261601 GCACTTAGTGTGTGGGATTATAATAGCTTCGGCTAT
1 GCACTTAGTGTGT--GATTAGAATAGCTTCGGCTAT
41261637 GCGATGGCAT
Statistics
Matches: 96, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
40 24 0.25
41 35 0.36
42 4 0.04
43 4 0.04
44 17 0.18
45 10 0.10
46 2 0.02
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (39 bp):
GCACTTAGTGTGTGATTAGAATAGCTTCGGCTATTTATG
Found at i:41266927 original size:17 final size:17
Alignment explanation
Indices: 41266905--41266938 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41266895 CACCCACAAA
41266905 CGAATGGTTAATCTGAG
1 CGAATGGTTAATCTGAG
41266922 CGAATGGTTAATCTGAG
1 CGAATGGTTAATCTGAG
41266939 TGATTCGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.29
Consensus pattern (17 bp):
CGAATGGTTAATCTGAG
Found at i:41267056 original size:34 final size:34
Alignment explanation
Indices: 41267013--41267080 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
41267003 AGATATTGAG
41267013 TTTCAGATTAGGGATCGAATGTTTTTGAAAGTAT
1 TTTCAGATTAGGGATCGAATGTTTTTGAAAGTAT
41267047 TTTCAGATTAGGGATCGAATGTTTTTGAAAGTAT
1 TTTCAGATTAGGGATCGAATGTTTTTGAAAGTAT
41267081 CTCCGTGGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (34 bp):
TTTCAGATTAGGGATCGAATGTTTTTGAAAGTAT
Found at i:41268697 original size:40 final size:39
Alignment explanation
Indices: 41268642--41268780 Score: 143
Period size: 40 Copynumber: 3.4 Consensus size: 39
41268632 ACTATGTTTA
* *
41268642 GCACTTAGTGTGCGATTCGAGATAGCTTCGGCTATTTATG
1 GCACTTAGTATGCGATT-GAGATAGCTTTGGCTATTTATG
*
41268682 GCACTTAGTATGCGATTGATAATAGCTTTGGCTATATATATATG
1 GCACTTAGTATGCGATTGA-GATAGCTTTGGC--TAT-T-TATG
* * *
41268726 ACACTTAGTATGCAAGACTGAGATAGCTTTGGCTATGTATG
1 GCACTTAGTATGC--GATTGAGATAGCTTTGGCTATTTATG
*
41268767 GCACTTAGTGTGCG
1 GCACTTAGTATGCG
41268781 GGATTATAAT
Statistics
Matches: 83, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
39 3 0.04
40 26 0.31
41 15 0.18
42 3 0.04
43 4 0.05
44 16 0.19
45 11 0.13
46 5 0.06
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (39 bp):
GCACTTAGTATGCGATTGAGATAGCTTTGGCTATTTATG
Found at i:41268793 original size:41 final size:39
Alignment explanation
Indices: 41268633--41268823 Score: 123
Period size: 40 Copynumber: 4.6 Consensus size: 39
41268623 GATAAATCAA
* * **
41268633 CTATGTTTAGCACTTAGTGTGCGATTCGAGATAGCTTCGG
1 CTATGTATGGCACTTAGTGTGCGATTATA-ATAGCTTCGG
* * *
41268673 CTATTTATGGCACTTAGTATGCGATTGATAATAGCTTTGG
1 CTATGTATGGCACTTAGTGTGCGATT-ATAATAGCTTCGG
* * * * * *
41268713 CTATATATATATGACACTTAGTATGCAAGACTGA-GATAGCTTTGG
1 C----TATGTATGGCACTTAGTGTGC--GA-TTATAATAGCTTCGG
*
41268758 CTATGTATGGCACTTAGTGTGCGGGATTATAATAGCTTCAG
1 CTATGTATGGCACTTAGTGTGC--GATTATAATAGCTTCGG
* *
41268799 CTATGCGATGGCATTTAGTGTGCGA
1 CTATG-TATGGCACTTAGTGTGCGA
41268824 AACATTGAGT
Statistics
Matches: 119, Mismatches: 22, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
40 36 0.30
41 34 0.29
42 15 0.13
44 19 0.16
45 11 0.09
46 3 0.03
47 1 0.01
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (39 bp):
CTATGTATGGCACTTAGTGTGCGATTATAATAGCTTCGG
Found at i:41278190 original size:19 final size:19
Alignment explanation
Indices: 41278153--41278190 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
41278143 CTAATTAAGT
*
41278153 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
41278172 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
41278191 GAAAATGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:41283015 original size:42 final size:40
Alignment explanation
Indices: 41282959--41283069 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 40
41282949 GATTTATGTA
* * *
41282959 TAAGACCATGTCTGGGACATCGGCATTATATTTGATTTCGTG
1 TAAGACCCTGTCTGGGACAT-GGCATTATA-TTGATTACATG
*
41283001 TAAGACCCTGTCTGGGACAGTGGCATCGATATTGATTACATG
1 TAAGACCCTGTCTGGGACA-TGGCAT-TATATTGATTACATG
*
41283043 TAAGACCAC-GTCTGGGACGTTGGCATT
1 TAAGACC-CTGTCTGGGAC-ATGGCATT
41283070 GTACGAGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
42 54 0.92
43 5 0.08
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (40 bp):
TAAGACCCTGTCTGGGACATGGCATTATATTGATTACATG
Found at i:41283410 original size:17 final size:18
Alignment explanation
Indices: 41283366--41283410 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
41283356 TATGAAATTT
41283366 TGATATGAAATGTGAGTA
1 TGATATGAAATGTGAGTA
*
41283384 TGAT-TAAAATGATGA-TA
1 TGATATGAAATG-TGAGTA
41283401 T-ATATGAAAT
1 TGATATGAAAT
41283411 ATATGATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
16 2 0.09
17 14 0.61
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.20, T:0.36
Consensus pattern (18 bp):
TGATATGAAATGTGAGTA
Found at i:41285707 original size:20 final size:20
Alignment explanation
Indices: 41285682--41285720 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
41285672 CATTCATTTA
41285682 TTTATAAATATTTTTATAAT
1 TTTATAAATATTTTTATAAT
**
41285702 TTTATATGTATTTTTATAA
1 TTTATAAATATTTTTATAA
41285721 AATCTTATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTATAAATATTTTTATAAT
Found at i:41287307 original size:14 final size:14
Alignment explanation
Indices: 41287288--41287319 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
41287278 AATACGAGCT
41287288 GAGAGAGACAGAGA
1 GAGAGAGACAGAGA
41287302 GAGAGAGACAGAGA
1 GAGAGAGACAGAGA
41287316 GAGA
1 GAGA
41287320 CAAAGAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (14 bp):
GAGAGAGACAGAGA
Found at i:41287664 original size:17 final size:17
Alignment explanation
Indices: 41287626--41287668 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
41287616 GTTTAAAACG
*
41287626 ATTTTTATTTTTAATAA
1 ATTTTTAATTTTAATAA
*
41287643 TTTTTTAATTTT-ATGAA
1 ATTTTTAATTTTAAT-AA
41287660 ATTTTTAAT
1 ATTTTTAAT
41287669 GATTTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 20 0.91
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
ATTTTTAATTTTAATAA
Found at i:41292684 original size:31 final size:30
Alignment explanation
Indices: 41292649--41292708 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
41292639 AGAGGTGGGA
*
41292649 TGGGAAAGGAATAAAAGTTTTAGGGGAAAAG
1 TGGGAAA-GAATAAAAATTTTAGGGGAAAAG
* * *
41292680 TGGGAGAGAGTAAAAATTTTGGGGGAAAA
1 TGGGAAAGAATAAAAATTTTAGGGGAAAA
41292709 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 19 0.76
31 6 0.24
ACGTcount: A:0.43, C:0.00, G:0.37, T:0.20
Consensus pattern (30 bp):
TGGGAAAGAATAAAAATTTTAGGGGAAAAG
Found at i:41292936 original size:9 final size:9
Alignment explanation
Indices: 41292922--41292958 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
41292912 TATAGTTTGA
41292922 TATTCGAAT
1 TATTCGAAT
41292931 TATTCGAAT
1 TATTCGAAT
*
41292940 TATTCGAGT
1 TATTCGAAT
*
41292949 TATTCAAAT
1 TATTCGAAT
41292958 T
1 T
41292959 CGAAAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:41294674 original size:5 final size:5
Alignment explanation
Indices: 41294664--41294700 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
41294654 CTAGGAGATC
*
41294664 TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCACA TC
1 TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TCTCA TC
41294701 CTCAAGAGCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.22, C:0.41, G:0.00, T:0.38
Consensus pattern (5 bp):
TCTCA
Found at i:41298462 original size:22 final size:22
Alignment explanation
Indices: 41298408--41298450 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41298398 TTTATTGTTC
41298408 AAACATGAGAGCTTAGTACGTG
1 AAACATGAGAGCTTAGTACGTG
41298430 AAACATGAGAGCTTAGTACGT
1 AAACATGAGAGCTTAGTACGT
41298451 TAGCCATGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.23
Consensus pattern (22 bp):
AAACATGAGAGCTTAGTACGTG
Found at i:41302192 original size:7 final size:7
Alignment explanation
Indices: 41302157--41302221 Score: 53
Period size: 7 Copynumber: 9.0 Consensus size: 7
41302147 GTTCAGATTC
*
41302157 AAAAAAC
1 AAAAAAG
41302164 AAAAAAG
1 AAAAAAG
41302171 AAAAAAAG
1 -AAAAAAG
41302179 AGGAAAAAG
1 A--AAAAAG
41302188 AAAAAA-
1 AAAAAAG
*
41302194 ATAAGAAG
1 A-AAAAAG
41302202 AAAAAAG
1 AAAAAAG
*
41302209 AAAAGA-
1 AAAAAAG
41302215 AAAAAAG
1 AAAAAAG
41302222 GAAGGAGAGG
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
6 6 0.13
7 26 0.55
8 8 0.17
9 7 0.15
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:41302199 original size:20 final size:20
Alignment explanation
Indices: 41302171--41302218 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
41302161 AACAAAAAAG
*
41302171 AAAAAAAG-AGGAAAAAGAA
1 AAAAAAAGAAGAAAAAAGAA
41302190 AAAAATAAGAAGAAAAAAGAA
1 AAAAA-AAGAAGAAAAAAGAA
41302211 AAGAAAAA
1 AA-AAAAA
41302219 AAGGAAGGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 5 0.20
20 3 0.12
21 14 0.56
22 3 0.12
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (20 bp):
AAAAAAAGAAGAAAAAAGAA
Found at i:41302207 original size:13 final size:12
Alignment explanation
Indices: 41302159--41302219 Score: 52
Period size: 12 Copynumber: 4.9 Consensus size: 12
41302149 TCAGATTCAA
*
41302159 AAAACAAAAAAG
1 AAAAGAAAAAAG
* *
41302171 AAAA-AAAGAGG
1 AAAAGAAAAAAG
*
41302182 AAAAAGAAAAAAAT
1 -AAAAG-AAAAAAG
41302196 AAGAAGAAAAAAG
1 AA-AAGAAAAAAG
41302209 AAAAGAAAAAA
1 AAAAGAAAAAA
41302220 AGGAAGGAGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
11 5 0.13
12 17 0.44
13 10 0.26
14 7 0.18
ACGTcount: A:0.82, C:0.02, G:0.15, T:0.02
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:41303531 original size:44 final size:44
Alignment explanation
Indices: 41303459--41303662 Score: 230
Period size: 44 Copynumber: 4.6 Consensus size: 44
41303449 GGGGAATTGT
* **
41303459 AAGTCCTAGCTCCCTGACCAGTATTGGAATAGGTGGAAGACTGC
1 AAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGC
** * * *
41303503 AAGTCCTAGCTCCCTGAATAGTAGTGGAATAGACAGAAGATTGT
1 AAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGC
* *
41303547 AAGTCCTAGCTCCCTGACCAGCAGTGGAATAGGCAGAAGATTGTC
1 AAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTG-C
** ** **
41303592 AA-TCCTAGCTCCCTGACCAGCGGTGGAATAGGTGGAAGACTTT
1 AAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGC
* *
41303635 AAGTCTTAGCTCCCTGAACAGTAGTGGA
1 AAGTCCTAGCTCCCTGACCAGTAGTGGA
41303663 GCAGATCGAA
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
43 2 0.01
44 131 0.97
45 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (44 bp):
AAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGC
Found at i:41303564 original size:88 final size:88
Alignment explanation
Indices: 41303454--41303662 Score: 260
Period size: 88 Copynumber: 2.4 Consensus size: 88
41303444 AAACCGGGGA
* **
41303454 ATTGTAAGTCCTAGCTCCCTGACCAGTATTGGAATAGGTGGAAGACTG-CAAGTCCTAGCTCCCT
1 ATTGTAAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGTCAA-TCCTAGCTCCCT
* *
41303518 GAATAGTAGTGGAATAGACAGAAG
65 GAACAGCAGTGGAATAGACAGAAG
* *
41303542 ATTGTAAGTCCTAGCTCCCTGACCAGCAGTGGAATAGGCAGAAGATTGTCAATCCTAGCTCCCTG
1 ATTGTAAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGTCAATCCTAGCTCCCTG
* * ***
41303607 ACCAGCGGTGGAATAGGTGGAAG
66 AACAGCAGTGGAATAGACAGAAG
* *
41303630 ACTT-TAAGTCTTAGCTCCCTGAACAGTAGTGGA
1 A-TTGTAAGTCCTAGCTCCCTGACCAGTAGTGGA
41303663 GCAGATCGAA
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
88 99 0.95
89 5 0.05
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (88 bp):
ATTGTAAGTCCTAGCTCCCTGACCAGTAGTGGAATAGGCAGAAGACTGTCAATCCTAGCTCCCTG
AACAGCAGTGGAATAGACAGAAG
Found at i:41303762 original size:132 final size:132
Alignment explanation
Indices: 41303614--41304782 Score: 1616
Period size: 132 Copynumber: 8.9 Consensus size: 132
41303604 CTGACCAGCG
* * *
41303614 GTGGAATAGGTGGAAGACTTTAAG-TCTTAGCTCCCTGAA-CAGTAGTGGAGCAGATCGAAGATG
1 GTGGAATAGATTGAAGA-TTTAAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATG
* *
41303677 ACAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCTTGGTT
64 GCAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTT
41303742 GGCA
129 GGCA
* * * *
41303746 GTAGAAAAGATTGAAGATTTCAGACCTTATCTCCCT----A--AGTGGAGCAGATCGAAGATGGC
1 GTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* * * *
41303805 GGATTTTACCTCCCTGTGATTACAGT--AG-AGATTGAAGCTAGTAATTCTATCTCCCTAGTTGG
66 AGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGG
*
41303867 AA
131 CA
41303869 GTGGAATAGATTGAAGATTTCAA-ATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 GTGGAATAGATTGAAGATTT-AAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* * *
41303933 CAGATTTTACCTCCCTATGACTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTGGTTG
65 CAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTG
41303998 GCA
130 GCA
* * *
41304001 GTGGAATAGATTGAAGATTTCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAGATGGT
1 GTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* * * *
41304066 AGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTAGTTGG
66 AGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGG
41304131 CA
131 CA
41304133 GTGGAATAGATTGAAGA-TTAGAGATCTTATCTCCCTAAGCAGTA-TGGAGCAGATCGAAGATGG
1 GTGGAATAGATTGAAGATTTA-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
*
41304196 CAGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTG
65 CAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTG
41304261 GCA
130 GCA
* * * *
41304264 GTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGCAGTAGTGGAGCAAATCGAAGATGAC
1 GTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* * * * * * ***
41304329 AGATTTTACTTCCCTGTGGTTACAGTGGAGTACATTGAAGCAACTAATTCTATCTTCCAGGGCAG
66 AGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGG
41304394 CA
131 CA
*
41304396 GTGGAATAGATTGAAGA-TTACAGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
1 GTGGAATAGATTGAAGATTTA-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* * * * * ***
41304460 CAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCTAATAATTCTATCTCCTTGGGCA
65 CAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTG
41304525 GCA
130 GCA
* * **
41304528 GTGGAATAGATTGAAGA-TTACAGATCTTATCTCCTTAAGTAGTAGTGGAATAGATCGAAGATGG
1 GTGGAATAGATTGAAGATTTA-AGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGG
* * * *
41304592 CGGATTTTACGTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTG
65 CAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTG
41304657 GCA
130 GCA
* * *
41304660 GTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATTGAAGATGGC
1 GTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
* *
41304725 -GAATTTTACCTCTCTGTGACTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
66 AG-ATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
41304783 CGACGTTGCG
Statistics
Matches: 930, Mismatches: 89, Indels: 36
0.88 0.08 0.03
Matches are distributed among these distances:
123 61 0.07
124 3 0.00
126 46 0.05
127 1 0.00
128 1 0.00
129 45 0.05
131 135 0.15
132 636 0.68
133 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (132 bp):
GTGGAATAGATTGAAGATTTAAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATGGC
AGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGTTGG
CA
Found at i:41303916 original size:44 final size:45
Alignment explanation
Indices: 41303868--41304049 Score: 99
Period size: 44 Copynumber: 4.1 Consensus size: 45
41303858 CCTAGTTGGA
*
41303868 AGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAG-CAGT
1 AGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGACAGC
** * ** * * * *
41303912 AGTGGAGCAGATCGAAGATGGCAGATTTTACCTCCCTATGACTA-C
1 AGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGAC-AGC
* * * * * ***
41303957 AGTGGAGTACATTGAAGCCA-AT-AATTC-TATCTCCCT-GGTTGGC
1 AGTGGAATAGATTGAAG--ATTTCAAATCTTATCTCCCTAAGACAGC
* * *
41304000 AGTGGAATAGATTGAAGATTTCAGATCTTATCTCTCTAAG-CAGT
1 AGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGACAGC
41304044 AGTGGA
1 AGTGGA
41304050 GCAGATCGAA
Statistics
Matches: 96, Mismatches: 33, Indels: 18
0.65 0.22 0.12
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 20 0.21
44 54 0.56
45 18 0.19
46 1 0.01
47 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (45 bp):
AGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGACAGC
Found at i:41304380 original size:395 final size:393
Alignment explanation
Indices: 41303609--41304782 Score: 1729
Period size: 395 Copynumber: 3.0 Consensus size: 393
41303599 GCTCCCTGAC
* * * * *
41303609 CAGCGGTGGAATAGGTGGAAGACTTTAAG-TCTTAGCTCCCTGAA-CAGTAGTGGAGCAGATCGA
1 CAGCAGTGGAATAGATTGAAGA-TTTCAGATCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGA
* * * *
41303672 AGATGACAGATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCT
64 AGATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCT
* * * *
41303737 TGGTTGGCAGTAGAAAAGATTGAAGATTTCAGACCTTATCTCCCT-A-AG--TGGAGCAGATCGA
129 TGGTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGAGTATGGAGCAGATCGA
*
41303798 AGATGGCGGATTTTACCTCCCTGTGATTACAGTAGAG---ATTGAAGCTAGTAATTCTATCTCCC
194 AGATGGCGGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCC
* * *
41303860 TAGTTGGAAGTGGAATAGATTGAAGATTTCAAATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
259 TGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
*
41303925 GAAGATGGCAGATTTTACCTCCCTATGACTACAGTGGAGTACATTGAAGCCAATAATTCTATCTC
324 GAAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAG-CAATAATTCTATCTC
* *
41303990 CCTGGT
388 CCAGGG
** *
41303996 TGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGAAG
1 CAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
* * *
41304061 ATGGTAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCCTA
66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCTTG
*
41304126 GTTGGCAGTGGAATAGATTGAAGATTAGAGATCTTATCTCCCTAAGCAGTATGGAGCAGATCGAA
131 GTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAG-AGTATGGAGCAGATCGAA
*
41304191 GATGGCAGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCT
195 GATGGCGGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCT
* *
41304256 GGTTGGCAGTGGAATAGATTGAAGATTTCAGATTTTATCTCCCTAAGCAGTAGTGGAGCAAATCG
260 GGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG
* * ** *
41304321 AAGATGACAGATTTTACTTCCCTGTGGTTACAGTGGAGTACATTGAAGCAACTAATTCTATCTTC
325 AAGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCAA-TAATTCTATCTCC
41304386 CAGGG
389 CAGGG
* *
41304391 CAGCAGTGGAATAGATTGAAGATTACAGATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
1 CAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
*
41304456 ATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCTAATAATTCTATCTCCTTG
66 ATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCTTG
*** * **
41304521 GGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCTTAAGTAGTAGTGGAATAGATCGA
131 GTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAG-AGTA-TGGAGCAGATCGA
* * * *
41304586 AGATGGCGGATTTTACGTCCCTGTGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCC
194 AGATGGCGGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCC
* *
41304651 TGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGTAGATT
259 TGGTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATC
* *
41304716 GAAGATGGC-GAATTTTACCTCTCTGTGACTACAGTGGAGTACATTGAAGCCAGTAATTCTATCT
324 GAAGATGGCAG-ATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAG-CAATAATTCTATCT
41304780 CCC
387 CCC
41304783 CGACGTTGCG
Statistics
Matches: 705, Mismatches: 68, Indels: 19
0.89 0.09 0.02
Matches are distributed among these distances:
386 7 0.01
387 144 0.20
388 1 0.00
390 2 0.00
392 49 0.07
394 3 0.00
395 310 0.44
396 187 0.27
397 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.30
Consensus pattern (393 bp):
CAGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAG
ATGGCAGATTTTACCTCCCTGTGGTTACAGTAGAGTACATTGAAGCCAATAATTCTATCTCCTTG
GTTGGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGAGTATGGAGCAGATCGAAG
ATGGCGGATTTTACCTCCCTGTGATTACAGTAGAGTACATTGAAGCCAGTAATTCTATCTCCCTG
GTTGGCAGTGGAATAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
AGATGGCAGATTTTACCTCCCTGTGACTACAGTGGAGTACATTGAAGCAATAATTCTATCTCCCA
GGG
Found at i:41305904 original size:3 final size:3
Alignment explanation
Indices: 41305896--41306013 Score: 150
Period size: 3 Copynumber: 40.0 Consensus size: 3
41305886 ATTAAGTTAG
* *
41305896 TAT TAT TAT TAT TAT TAT TAT TAT TAT TTT TAT TAT TAT TTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
41305944 TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT T-T T-T TAT TTT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
41305990 TAT TTT TAA TAT TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
41306014 CATCATATCT
Statistics
Matches: 98, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
2 4 0.04
3 94 0.96
ACGTcount: A:0.27, C:0.00, G:0.01, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:41306410 original size:2 final size:2
Alignment explanation
Indices: 41306403--41306428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41306393 ATGCTTACTC
41306403 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
41306429 TATTTAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41306456 original size:35 final size:35
Alignment explanation
Indices: 41306406--41306482 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
41306396 CTTACTCATA
* * *
41306406 TATATATATATATATATATATATTATTTAATAATTT
1 TATAAATACATATATACATATATT-TTTAATAATTT
* *
41306442 TA-AAATACATATATACATATATTTTTCATATTTT
1 TATAAATACATATATACATATATTTTTAATAATTT
41306476 TATAAAT
1 TATAAAT
41306483 TTATGTACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
34 11 0.31
35 22 0.63
36 2 0.06
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (35 bp):
TATAAATACATATATACATATATTTTTAATAATTT
Found at i:41306773 original size:15 final size:15
Alignment explanation
Indices: 41306755--41306785 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41306745 TTATTATTTG
*
41306755 TTTTTGTTCATATTA
1 TTTTTGTTCACATTA
41306770 TTTTTGTTCACATTA
1 TTTTTGTTCACATTA
41306785 T
1 T
41306786 CATATTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.06, T:0.65
Consensus pattern (15 bp):
TTTTTGTTCACATTA
Found at i:41307036 original size:108 final size:109
Alignment explanation
Indices: 41306846--41307268 Score: 658
Period size: 108 Copynumber: 3.9 Consensus size: 109
41306836 AAAGAAAAGT
* * *
41306846 TTTCAAAGTAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCGTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
41306911 CGATTTTTCTTGTTCAACCAAATAGCTAAATATCTTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
*
41306955 TTTCAAAATAAGGCAATGTTTT-CGTTTAGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
41307019 CGATTTTTCTTGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * *
41307063 TTT-TAAATAAGGCAATGTTTTGCGTCTGGAAATTCGAGGAAACGTGCCCTAATGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
41307127 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCGTTTTAAAAA
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
* * * *
41307171 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTTGAG-GAACGTGCCCTATTGTGCTGGGTTT
1 TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* *
41307235 CGA--TTTCTCGTTTAACCAAATAGCCAAATATCCT
66 CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCT
41307269 CTTGAATTTT
Statistics
Matches: 292, Mismatches: 20, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
106 28 0.10
107 17 0.06
108 196 0.67
109 51 0.17
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.36
Consensus pattern (109 bp):
TTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCTCGTTCAACCAAATAGCTAAATATCCTTTTAAAAA
Found at i:41307864 original size:28 final size:28
Alignment explanation
Indices: 41307825--41307909 Score: 127
Period size: 28 Copynumber: 3.1 Consensus size: 28
41307815 CTATACAGAT
*
41307825 CAGT-ACAGTGTGGGTCTTAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
*
41307852 CAGTAACAGTGTGTGCCTTAGCCCATTA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
* *
41307880 CAGTAATAGTGTGGGCCTTAGCCCAATA
1 CAGTAACAGTGTGGGCCTTAGCCCATTA
41307908 CA
1 CA
41307910 ATAATCAATA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
27 4 0.08
28 48 0.92
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.27
Consensus pattern (28 bp):
CAGTAACAGTGTGGGCCTTAGCCCATTA
Found at i:41308084 original size:26 final size:27
Alignment explanation
Indices: 41308055--41308128 Score: 89
Period size: 26 Copynumber: 2.8 Consensus size: 27
41308045 AATGACGCAA
41308055 CAAAGCTGCCAGTAACAGTA-ATGCAG
1 CAAAGCTGCCAGTAACAGTATATGCAG
* **
41308081 CAAAGCTGCCAATAACAGTATATGTGG
1 CAAAGCTGCCAGTAACAGTATATGCAG
**
41308108 CAAAGCCACCAGT-ACAGTATA
1 CAAAGCTGCCAGTAACAGTATA
41308129 CTTCTCCTAT
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 27 0.66
27 14 0.34
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (27 bp):
CAAAGCTGCCAGTAACAGTATATGCAG
Found at i:41308307 original size:27 final size:27
Alignment explanation
Indices: 41308277--41308498 Score: 209
Period size: 27 Copynumber: 8.3 Consensus size: 27
41308267 GGGTATAACA
* *
41308277 GTCATTTTATCCTATAG-GGGTATTTTG
1 GTCATTTTA-CCCATAGAGGGTATTTCG
* * *
41308304 GTCATTTTA-TCTTATGAAGGTATTTCG
1 GTCATTTTACCCATA-GAGGGTATTTCG
* *
41308331 GTTATTTTACCCATAGGGGGTATTTCG
1 GTCATTTTACCCATAGAGGGTATTTCG
* *
41308358 ATCATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCATAGAGGGTATTTCG
* * ** *
41308385 ATAATTTTACCCATCTAGGGTATTTTG
1 GTCATTTTACCCATAGAGGGTATTTCG
* *
41308412 GTCA-TTTACCCATCGAGGCTATTTCG
1 GTCATTTTACCCATAGAGGGTATTTCG
* * *
41308438 ATCATTTTACCCATTGAGGGTATTTTG
1 GTCATTTTACCCATAGAGGGTATTTCG
*
41308465 GTCATTTTACCCATCA-AGGGTATTTCA
1 GTCATTTTACCCAT-AGAGGGTATTTCG
41308492 GTCATTT
1 GTCATTT
41308499 GCCCACGAAT
Statistics
Matches: 160, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
25 2 0.01
26 23 0.14
27 132 0.82
28 3 0.02
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCATAGAGGGTATTTCG
Found at i:41308447 original size:80 final size:80
Alignment explanation
Indices: 41308322--41308503 Score: 247
Period size: 80 Copynumber: 2.3 Consensus size: 80
41308312 ATCTTATGAA
* * *
41308322 GGTATTTCGGTTATTTTACCCATAGGGGGTATTTCGATCATTTTACCCATCGAGGGTATTTCGAT
1 GGTATTTCGGTCA-TTTACCCATAGAGGCTATTTCGATCATTTTACCCATCGAGGGTATTTCGAT
*
41308387 AATTTTACCCATCTAG
65 AATTTTACCCATCAAG
* * * * * *
41308403 GGTATTTTGGTCATTTACCCATCGAGGCTATTTCGATCATTTTACCCATTGAGGGTATTTTGGTC
1 GGTATTTCGGTCATTTACCCATAGAGGCTATTTCGATCATTTTACCCATCGAGGGTATTTCGATA
41308468 ATTTTACCCATCAAG
66 ATTTTACCCATCAAG
* *
41308483 GGTATTTCAGTCATTTGCCCA
1 GGTATTTCGGTCATTTACCCA
41308504 CGAATCGTAA
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 77 0.88
81 11 0.12
ACGTcount: A:0.21, C:0.20, G:0.19, T:0.40
Consensus pattern (80 bp):
GGTATTTCGGTCATTTACCCATAGAGGCTATTTCGATCATTTTACCCATCGAGGGTATTTCGATA
ATTTTACCCATCAAG
Found at i:41308498 original size:54 final size:53
Alignment explanation
Indices: 41308277--41308498 Score: 234
Period size: 54 Copynumber: 4.1 Consensus size: 53
41308267 GGGTATAACA
* ** *
41308277 GTCATTTTATCCTATAG-GGGTATTTTGGTCATTTTATCTTATGAA-GGTATTTC
1 GTCATTTTA-CCCATAGAGGGTATTTTGGTCATTTTA-CCCATCAAGGGTATTTC
* * * * *
41308330 GGTTATTTTACCCATAGGGGGTATTTCGATCATTTTACCCATCGAGGGTATTTC
1 -GTCATTTTACCCATAGAGGGTATTTTGGTCATTTTACCCATCAAGGGTATTTC
* ** * *
41308384 GATAATTTTACCCATCTAGGGTATTTTGGTCA-TTTACCCATCGAGGCTATTTC
1 G-TCATTTTACCCATAGAGGGTATTTTGGTCATTTTACCCATCAAGGGTATTTC
*
41308437 GATCATTTTACCCATTGAGGGTATTTTGGTCATTTTACCCATCAAGGGTATTTC
1 G-TCATTTTACCCATAGAGGGTATTTTGGTCATTTTACCCATCAAGGGTATTTC
41308491 AGTCATTT
1 -GTCATTT
41308499 GCCCACGAAT
Statistics
Matches: 143, Mismatches: 20, Indels: 10
0.83 0.12 0.06
Matches are distributed among these distances:
53 60 0.42
54 82 0.57
55 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (53 bp):
GTCATTTTACCCATAGAGGGTATTTTGGTCATTTTACCCATCAAGGGTATTTC
Found at i:41316820 original size:27 final size:28
Alignment explanation
Indices: 41316758--41316820 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 28
41316748 TTTAACCATT
* * * *
41316758 TTTTATTTTATTATATTTTTATTTTTAG
1 TTTTATTTTATTACATTCTAATTTTTAC
* *
41316786 TTTAATTTT-TTACATTCTAATTTTTTC
1 TTTTATTTTATTACATTCTAATTTTTAC
41316813 TTTTATTT
1 TTTTATTT
41316821 GCTTCTAGCA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 20 0.71
28 8 0.29
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTTATTTTATTACATTCTAATTTTTAC
Found at i:41323151 original size:29 final size:29
Alignment explanation
Indices: 41323114--41323180 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
41323104 CACGGTCATG
* * *
41323114 TGGCCCACACAAGAGTGTTCTAGGTCGTT
1 TGGCACACACAAGAGTGTCCTAAGTCGTT
* * *
41323143 TGGCACACAGAGGCGTGTCCTAAGTCGTT
1 TGGCACACACAAGAGTGTCCTAAGTCGTT
41323172 TGGCACACA
1 TGGCACACA
41323181 GGGGCGTGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.22, C:0.25, G:0.28, T:0.24
Consensus pattern (29 bp):
TGGCACACACAAGAGTGTCCTAAGTCGTT
Found at i:41323181 original size:29 final size:29
Alignment explanation
Indices: 41323128--41323199 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
41323118 CCACACAAGA
*
41323128 GTGTTCTAGGTCGTTTGGCACACAGAGGC
1 GTGTCCTAGGTCGTTTGGCACACAGAGGC
* *
41323157 GTGTCCTAAGTCGTTTGGCACACAGGGGC
1 GTGTCCTAGGTCGTTTGGCACACAGAGGC
41323186 GTGTCCTAGGTCGT
1 GTGTCCTAGGTCGT
41323200 ATGTGTACTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.15, C:0.22, G:0.35, T:0.28
Consensus pattern (29 bp):
GTGTCCTAGGTCGTTTGGCACACAGAGGC
Found at i:41326094 original size:16 final size:16
Alignment explanation
Indices: 41326073--41326103 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41326063 TATATATGTT
41326073 TGTACATTGAGGATAA
1 TGTACATTGAGGATAA
41326089 TGTACATTGAGGATA
1 TGTACATTGAGGATA
41326104 TTTTGTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (16 bp):
TGTACATTGAGGATAA
Found at i:41326133 original size:59 final size:59
Alignment explanation
Indices: 41326041--41326154 Score: 210
Period size: 59 Copynumber: 1.9 Consensus size: 59
41326031 CCTCTCTTAT
41326041 GATATTTTATTTATTTTATGTTTATATATGTTTGTACATTGAGGATAATGTACATTGAG
1 GATATTTTATTTATTTTATGTTTATATATGTTTGTACATTGAGGATAATGTACATTGAG
* *
41326100 GATATTTTGTTTATTTTATGTTTATATCTGTTTGTACATTGAGGATAATGTACAT
1 GATATTTTATTTATTTTATGTTTATATATGTTTGTACATTGAGGATAATGTACAT
41326155 CTTAAGTGTG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.27, C:0.04, G:0.17, T:0.52
Consensus pattern (59 bp):
GATATTTTATTTATTTTATGTTTATATATGTTTGTACATTGAGGATAATGTACATTGAG
Found at i:41331709 original size:16 final size:17
Alignment explanation
Indices: 41331690--41331722 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
41331680 TATATAATGT
41331690 ACTACTATTAT-ATATA
1 ACTACTATTATAATATA
*
41331706 ACTATTATTATAATATA
1 ACTACTATTATAATATA
41331723 GATTATAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (17 bp):
ACTACTATTATAATATA
Found at i:41332011 original size:19 final size:19
Alignment explanation
Indices: 41331968--41332026 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
41331958 ATAGTATGTG
* *
41331968 ATATAGTTTTATAATGAAATA
1 ATATA-TTTTATAA-GTATTA
41331989 ATATATTTTATAAGTATTA
1 ATATATTTTATAAGTATTA
*
41332008 ATATATATTT-TAACTATTA
1 ATATAT-TTTATAAGTATTA
41332027 TCATATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.53
20 11 0.32
21 5 0.15
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (19 bp):
ATATATTTTATAAGTATTA
Found at i:41337888 original size:13 final size:11
Alignment explanation
Indices: 41337848--41337883 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
41337838 CCAGCCCGCC
41337848 TTTAT-TAATT
1 TTTATATAATT
*
41337858 TTTATATTATT
1 TTTATATAATT
41337869 TTTATATAATT
1 TTTATATAATT
41337880 TTTA
1 TTTA
41337884 AATATTTCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATAATT
Found at i:41337998 original size:30 final size:30
Alignment explanation
Indices: 41337964--41338023 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
41337954 ACTTAACAAG
41337964 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
*
41337994 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAATTAA
41338024 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.57, C:0.15, G:0.03, T:0.25
Consensus pattern (30 bp):
CAAATGCCTCTAAAATAATAACAAAATTAA
Found at i:41338656 original size:21 final size:21
Alignment explanation
Indices: 41338631--41338697 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
41338621 ATTTTATTTA
41338631 ATTATATTATTATCATACATT
1 ATTATATTATTATCATACATT
* *
41338652 TTTATATTATT-TCAT-TATT
1 ATTATATTATTATCATACATT
* *
41338671 ATTATCATTATTATCATATAGT
1 ATTAT-ATTATTATCATACATT
41338693 ATTAT
1 ATTAT
41338698 TAATTGAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
19 7 0.18
20 10 0.26
21 14 0.36
22 8 0.21
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (21 bp):
ATTATATTATTATCATACATT
Found at i:41339046 original size:50 final size:51
Alignment explanation
Indices: 41338987--41339089 Score: 199
Period size: 50 Copynumber: 2.0 Consensus size: 51
41338977 CTAAAATTCA
41338987 AGACACATAGGACTTAGGTAATAATCAAATGATGAGTA-TTTTTGTTTTTG
1 AGACACATAGGACTTAGGTAATAATCAAATGATGAGTATTTTTTGTTTTTG
41339037 AGACACATAGGACTTAGGTAATAATCAAATGATGAGTATTTTTTGTTTTTG
1 AGACACATAGGACTTAGGTAATAATCAAATGATGAGTATTTTTTGTTTTTG
41339088 AG
1 AG
41339090 GATTCGAGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 38 0.73
51 14 0.27
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (51 bp):
AGACACATAGGACTTAGGTAATAATCAAATGATGAGTATTTTTTGTTTTTG
Found at i:41346870 original size:94 final size:94
Alignment explanation
Indices: 41346740--41347341 Score: 661
Period size: 94 Copynumber: 6.4 Consensus size: 94
41346730 TACAATGGTG
* *
41346740 AATCTTATCTCCCTGAAGTTGCAATAGAGTAAGATGAAGCTACAAATCCTATACCCTTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
* ** *
41346805 CAGTGGGTT-GAAAGGAATTTACAATAACA
66 CAGTGGGTTAG-AATGAAGCTACAATAGCA
* * *
41346834 AATCTTATCTCCCTGAAATTGCAATTGAGAAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
* * ** * *
41346899 CAGTAGGTCAGCTTGAAGCTATAATAGCG
66 CAGTGGGTTAGAATGAAGCTACAATAGCA
* * *
41346928 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCTTATACCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
* * ***
41346993 CAATGGGTTGGAATGAAGCTACAATAATG
66 CAGTGGGTTAGAATGAAGCTACAATAGCA
* * * ** * * *
41347022 AATCTTGTCCCCCTAAAGTTATAGTGGAGCAAGATTAAGCTACAAATCCTATACCCCTGAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
*
41347087 CAGTGGGTTAGAATGAAGCTACCATAGCA
66 CAGTGGGTTAGAATGAAGCTACAATAGCA
* * *
41347116 AATCTTATCTCCCTGAAGTTG-AAGTAGAGCAAGATAAAGATATAAATCCTATACCCCTGAAGTT
1 AATCTTATCTCCCTGAAGTTGCAA-TAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTT
* * ** *
41347180 GCAATAGGTTAGAATGAAATTACAATGGCA
65 GCAGTGGGTTAGAATGAAGCTACAATAGCA
* * * * *
41347210 AACCTTATCTCCCTGAAGTTACATTAGAGCAAGATGAAGCTACAAATCCTATATCCCTAAAGTTG
1 AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
** * * * *
41347275 CAGTGGAAT-GAATTAAAACTACAACAACA
66 CAGTGGGTTAGAA-TGAAGCTACAATAGCA
* ** *
41347304 AATATTATCTCTTTGAAGTTGCAATGGAGCAAGATGAA
1 AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAA
41347342 ACTATAACAC
Statistics
Matches: 424, Mismatches: 80, Indels: 8
0.83 0.16 0.02
Matches are distributed among these distances:
93 4 0.01
94 418 0.99
95 2 0.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (94 bp):
AATCTTATCTCCCTGAAGTTGCAATAGAGCAAGATGAAGCTACAAATCCTATACCCCTGAAGTTG
CAGTGGGTTAGAATGAAGCTACAATAGCA
Found at i:41346966 original size:50 final size:47
Alignment explanation
Indices: 41346740--41347182 Score: 157
Period size: 44 Copynumber: 9.5 Consensus size: 47
41346730 TACAATGGTG
* * *
41346740 AATCTTATCTCCCTGAAGTTGCAATAGAGTAAGATGAAGC----TACA
1 AATCTTATC-CCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAAATACA
* * * * **
41346784 AATCCTATACCCTTGAAGTTGCAGTGG-GTTGAA-AGGAATTTACAATAACA
1 AATCTTAT-CCCCTGAAGTTGCAGTGGAG--CAAGATGAAGCTA-AAT-ACA
* * * *
41346834 AATCTTATCTCCCTGAAATTGCAATTGAGAAAGATGAAGC----TACA
1 AATCTTATC-CCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAAATACA
* * * *
41346878 AATCCTATACCCCTGAAGTTGCAGTAGG-TC-AGCTTGAAGCTATAATAGCG
1 AATCTTAT-CCCCTGAAGTTGCAGT-GGAGCAAG-ATGAAGCTA-AATA-CA
41346928 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGC----TACA
1 AATCTTATC-CCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAAATACA
* ***
41346972 AATCTTATACCCCTGAAGTTGCAATGG-GTTGGAATGAAGCTACAATA-A
1 AATCTTAT-CCCCTGAAGTTGCAGTGGAGCAAG-ATGAAGCTA-AATACA
* * ** *
41347020 TGAATCTTGTCCCCCTAAAGTTATAGTGGAGCAAGATTAAGC----TACA
1 --AATCTTAT-CCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAAATACA
* ** *
41347066 AATCCTATACCCCTGAAGTTGCAGTGG-GTTAGAATGAAGCTACCATAGCA
1 AATCTTAT-CCCCTGAAGTTGCAGTGGAGCAAG-ATGAAGCTA-AATA-CA
* * * *
41347116 AATCTTATCTCCCTGAAGTTGAAGTAGAGCAAGAT-AA---AGATATA
1 AATCTTATC-CCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAAATACA
*
41347160 AATCCTATACCCCTGAAGTTGCA
1 AATCTTAT-CCCCTGAAGTTGCA
41347183 ATAGGTTAGA
Statistics
Matches: 293, Mismatches: 61, Indels: 90
0.66 0.14 0.20
Matches are distributed among these distances:
43 8 0.03
44 133 0.45
45 15 0.05
46 2 0.01
48 1 0.00
49 16 0.05
50 110 0.38
51 8 0.03
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (47 bp):
AATCTTATCCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTAAATACA
Found at i:41354514 original size:43 final size:43
Alignment explanation
Indices: 41354466--41354552 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
41354456 TTCAAAAGCA
41354466 GACACAGTTAACTGACGCCTATAATGCTAATTTAGAAAGTAAT
1 GACACAGTTAACTGACGCCTATAATGCTAATTTAGAAAGTAAT
41354509 GACACAGTTAACTGACGCCTATAATGCTAATTTAGAAAGTAAT
1 GACACAGTTAACTGACGCCTATAATGCTAATTTAGAAAGTAAT
41354552 G
1 G
41354553 TCCTGCAACT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.39, C:0.16, G:0.17, T:0.28
Consensus pattern (43 bp):
GACACAGTTAACTGACGCCTATAATGCTAATTTAGAAAGTAAT
Found at i:41357956 original size:20 final size:20
Alignment explanation
Indices: 41357933--41357975 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
41357923 CACAACATTA
41357933 CATTATTCATGAAGTAACAC
1 CATTATTCATGAAGTAACAC
41357953 CATTATTCATGAAGTAACAC
1 CATTATTCATGAAGTAACAC
41357973 CAT
1 CAT
41357976 CATACTCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.30
Consensus pattern (20 bp):
CATTATTCATGAAGTAACAC
Found at i:41359948 original size:22 final size:23
Alignment explanation
Indices: 41359902--41359950 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
41359892 AATATAAATG
*
41359902 TTTGTTTATATTAATTTGTTTTA
1 TTTGTTTATATTAATTTGTTATA
41359925 TTTGTTTATA-TAATTAT-TTATA
1 TTTGTTTATATTAATT-TGTTATA
41359947 TTTG
1 TTTG
41359951 ACTTGGATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 13 0.54
23 11 0.46
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.67
Consensus pattern (23 bp):
TTTGTTTATATTAATTTGTTATA
Found at i:41361741 original size:20 final size:19
Alignment explanation
Indices: 41361718--41361761 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
41361708 CTAAATAATG
* *
41361718 TTTTTATCATTTATATAAAA
1 TTTTAATCATTTAAAT-AAA
*
41361738 TTTTAATTATTTAAATAAA
1 TTTTAATCATTTAAATAAA
41361757 TTTTA
1 TTTTA
41361762 TTATATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTAATCATTTAAATAAA
Found at i:41361770 original size:18 final size:19
Alignment explanation
Indices: 41361735--41361770 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
41361725 CATTTATATA
*
41361735 AAATTTTAATTATTTAAAT
1 AAATTTTAATTATATAAAT
41361754 AAATTTT-ATTATATAAA
1 AAATTTTAATTATATAAA
41361771 ATATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATTTTAATTATATAAAT
Found at i:41361772 original size:19 final size:19
Alignment explanation
Indices: 41361735--41361773 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41361725 CATTTATATA
*
41361735 AAATTTTAATTATTTAAAT
1 AAATTTTAATTATTAAAAT
41361754 AAATTTT-ATTATATAAAAT
1 AAATTTTAATTAT-TAAAAT
41361773 A
1 A
41361774 TTTTTTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTTAATTATTAAAAT
Found at i:41361778 original size:18 final size:17
Alignment explanation
Indices: 41361728--41361778 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
41361718 TTTTTATCAT
*
41361728 TTATATAAA-ATTTTAA
1 TTATATAAATATTTTTA
* *
41361744 TTATTTAAATAAATTTTA
1 TTATATAAAT-ATTTTTA
41361762 TTATATAAAATATTTTT
1 TTATAT-AAATATTTTT
41361779 TAACTTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
16 8 0.30
18 15 0.56
19 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATAAATATTTTTA
Found at i:41363940 original size:32 final size:32
Alignment explanation
Indices: 41363863--41363943 Score: 119
Period size: 32 Copynumber: 2.5 Consensus size: 32
41363853 AGACAAGGCT
* *
41363863 GTGTGGGCCACACAGGCTAGGCCAAGTTGGGC
1 GTGTGGGCCACACGGGCAAGGCCAAGTTGGGC
*
41363895 ATGTGGGCCACACGGGCAAGGCCAA-TCTGGGC
1 GTGTGGGCCACACGGGCAAGGCCAAGT-TGGGC
41363927 GTGTGGGCCACACGGGC
1 GTGTGGGCCACACGGGC
41363944 GTGTGGGCCC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 1 0.02
32 43 0.98
ACGTcount: A:0.19, C:0.27, G:0.41, T:0.14
Consensus pattern (32 bp):
GTGTGGGCCACACGGGCAAGGCCAAGTTGGGC
Found at i:41363945 original size:17 final size:18
Alignment explanation
Indices: 41363923--41363966 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
41363913 AGGCCAATCT
41363923 GGGCGTGTGGG-CCACAC
1 GGGCGTGTGGGCCCACAC
*
41363940 GGGCGTGTGGGCCCACAT
1 GGGCGTGTGGGCCCACAC
*
41363958 GGGCATGTG
1 GGGCGTGTG
41363967 AGCCTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.11, C:0.25, G:0.48, T:0.16
Consensus pattern (18 bp):
GGGCGTGTGGGCCCACAC
Found at i:41364124 original size:2 final size:2
Alignment explanation
Indices: 41364117--41364147 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
41364107 GACTATTCTG
41364117 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
41364148 TGTACACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41366368 original size:18 final size:20
Alignment explanation
Indices: 41366327--41366370 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
41366317 ATTTTTCCAT
41366327 AAAAAATATTAACAAATTAGA
1 AAAAAATATTAACAAATTA-A
*
41366348 AAAAAATATTAA-ATATTAA
1 AAAAAATATTAACAAATTAA
41366367 AAAA
1 AAAA
41366371 TGAAAATTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.23
20 5 0.23
21 12 0.55
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (20 bp):
AAAAAATATTAACAAATTAA
Found at i:41366411 original size:17 final size:16
Alignment explanation
Indices: 41366389--41366442 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 16
41366379 GATATAAGCT
41366389 TATAAAAATTATCAAAA
1 TATAAAAATTAT-AAAA
*
41366406 TATAAAAATTCTAATAAAT
1 TATAAAAA-T-T-ATAAAA
41366425 TATAAAAAATTATAAAA
1 TAT-AAAAATTATAAAA
41366442 T
1 T
41366443 TAATAAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
17 14 0.45
18 2 0.06
19 8 0.26
20 7 0.23
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
TATAAAAATTATAAAA
Found at i:41366424 original size:10 final size:10
Alignment explanation
Indices: 41366388--41366502 Score: 59
Period size: 10 Copynumber: 11.9 Consensus size: 10
41366378 TGATATAAGC
41366388 TTAT-AAAAA
1 TTATAAAAAA
*
41366397 TTAT-CAAAA
1 TTATAAAAAA
41366406 -TAT-AAAAA
1 TTATAAAAAA
* *
41366414 TTCTAATAAA
1 TTATAAAAAA
41366424 TTATAAAAAA
1 TTATAAAAAA
41366434 TTAT--AAAA
1 TTATAAAAAA
41366442 TTAATAAAATATA
1 TT-ATAAAA-A-A
**
41366455 TT-TAAAATT
1 TTATAAAAAA
41366464 TTAT-AAAAA
1 TTATAAAAAA
*
41366473 TGTAT-TAAAA
1 T-TATAAAAAA
41366483 TTATATAAAAA
1 TTATA-AAAAA
*
41366494 TCATAAAAA
1 TTATAAAAA
41366503 CTTTAATTGG
Statistics
Matches: 82, Mismatches: 13, Indels: 21
0.71 0.11 0.18
Matches are distributed among these distances:
8 13 0.16
9 21 0.26
10 29 0.35
11 15 0.18
12 1 0.01
13 3 0.04
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:41366430 original size:19 final size:18
Alignment explanation
Indices: 41366388--41366502 Score: 81
Period size: 21 Copynumber: 6.0 Consensus size: 18
41366378 TGATATAAGC
*
41366388 TTATAAAAATTATCAAAA
1 TTATAAAAATTATAAAAA
*
41366406 -TATAAAAATTCTAATAAA
1 TTATAAAAATTATAA-AAA
41366424 TTATAAAAAATTAT-AAAA
1 TTAT-AAAAATTATAAAAA
* *
41366442 TTAATAAAATATATTTAAAATT
1 TT-ATAAAA-AT-TATAAAA-A
*
41366464 TTATAAAAATGTATTAAAAT
1 TTATAAAAAT-TA-TAAAAA
*
41366484 TATATAAAAATCATAAAAA
1 T-TATAAAAATTATAAAAA
41366503 CTTTAATTGG
Statistics
Matches: 78, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
17 12 0.15
18 12 0.15
19 13 0.17
20 16 0.21
21 23 0.29
22 2 0.03
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (18 bp):
TTATAAAAATTATAAAAA
Found at i:41367020 original size:8 final size:8
Alignment explanation
Indices: 41367007--41367062 Score: 58
Period size: 8 Copynumber: 6.4 Consensus size: 8
41366997 AATACTTTAA
41367007 ATAATTTT
1 ATAATTTT
41367015 ATAATTTATT
1 ATAA-TT-TT
*
41367025 ATATTTTT
1 ATAATTTT
41367033 ATAATATTT
1 ATAAT-TTT
41367042 ATAAGTTTTT
1 ATAA--TTTT
41367052 ATAATTTT
1 ATAATTTT
41367060 ATA
1 ATA
41367063 TCAATTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
8 17 0.41
9 11 0.27
10 12 0.29
11 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (8 bp):
ATAATTTT
Found at i:41367026 original size:10 final size:9
Alignment explanation
Indices: 41367007--41367079 Score: 71
Period size: 9 Copynumber: 8.0 Consensus size: 9
41366997 AATACTTTAA
41367007 ATAA-TTTT
1 ATAATTTTT
41367015 ATAATTTATT
1 ATAATTT-TT
41367025 AT-ATTTTT
1 ATAATTTTT
*
41367033 ATAATATTT
1 ATAATTTTT
41367042 ATAAGTTTTT
1 ATAA-TTTTT
41367052 ATAATTTTAT
1 ATAATTTT-T
41367062 ATCAA-TTTT
1 AT-AATTTTT
*
41367071 ATTATTTTT
1 ATAATTTTT
41367080 TAAATATTGG
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
8 9 0.16
9 26 0.47
10 18 0.33
11 2 0.04
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
ATAATTTTT
Found at i:41367070 original size:19 final size:18
Alignment explanation
Indices: 41367002--41367078 Score: 68
Period size: 19 Copynumber: 4.2 Consensus size: 18
41366992 TTTTAAATAC
*
41367002 TTTAAATAATTTTATAA-
1 TTTATATAATTTTATAAT
*
41367019 TTTATTATATTTTTATAAT
1 TTTA-TATAATTTTATAAT
*
41367038 ATTTATA-AGTTTTTATAAT
1 -TTTATATA-ATTTTATAAT
*
41367057 TTTATATCAATTTTATTAT
1 TTTATAT-AATTTTATAAT
41367076 TTT
1 TTT
41367079 TTAAATATTG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 4 0.08
18 18 0.36
19 23 0.46
20 5 0.10
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (18 bp):
TTTATATAATTTTATAAT
Done.