Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 122 of 171
Found at i:38845282 original size:39 final size:42
Alignment explanation
Indices: 38845208--38845300 Score: 111
Period size: 39 Copynumber: 2.3 Consensus size: 42
38845198 AGACATCGCC
* * * *
38845208 AATCTCTTACCCCGATCATGGGGCAGATCGCAA-C-C-ATCT
1 AATCTTTTACCCCGATCATGGGACAGATCGAAACCACAACCT
* *
38845247 AATCTTTTACCCCGATCATGTGACAGATTGAAACCACAACCT
1 AATCTTTTACCCCGATCATGGGACAGATCGAAACCACAACCT
38845289 AATCTTTTACCC
1 AATCTTTTACCC
38845301 TTAAACCAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 28 0.62
40 1 0.02
41 1 0.02
42 15 0.33
ACGTcount: A:0.29, C:0.31, G:0.13, T:0.27
Consensus pattern (42 bp):
AATCTTTTACCCCGATCATGGGACAGATCGAAACCACAACCT
Found at i:38845974 original size:29 final size:29
Alignment explanation
Indices: 38845916--38845975 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
38845906 TTTGCCTCAT
* * **
38845916 CACCGCTGACACCATCACGCCTCTGTCAC
1 CACCACTGACACCACCACGCCTCTACCAC
38845945 CACCACTGACACCACCACGCCTCTACCAC
1 CACCACTGACACCACCACGCCTCTACCAC
38845974 CA
1 CA
38845976 TAGCTACCAC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.25, C:0.52, G:0.10, T:0.13
Consensus pattern (29 bp):
CACCACTGACACCACCACGCCTCTACCAC
Found at i:38847360 original size:17 final size:16
Alignment explanation
Indices: 38847317--38847364 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 16
38847307 AATTTATCCC
38847317 TTTAGTTTCATTTTTTT
1 TTTA-TTTCATTTTTTT
* *
38847334 GTTCTTTCATTTTGTTT
1 TTTATTTCATTTT-TTT
38847351 TTTATTTCATTTTT
1 TTTATTTCATTTTT
38847365 AAAAAAAACC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.10, C:0.08, G:0.06, T:0.75
Consensus pattern (16 bp):
TTTATTTCATTTTTTT
Found at i:38854912 original size:12 final size:12
Alignment explanation
Indices: 38854870--38854913 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
38854860 ACCCAATTCC
*
38854870 ATTTTTCTTATT
1 ATTTTTATTATT
38854882 ATTTTTATTTATT
1 ATTTTTA-TTATT
*
38854895 -TATTTATTATT
1 ATTTTTATTATT
38854906 ATTTTTAT
1 ATTTTTAT
38854914 GAATATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:38854982 original size:63 final size:61
Alignment explanation
Indices: 38854884--38855063 Score: 238
Period size: 63 Copynumber: 2.8 Consensus size: 61
38854874 TTCTTATTAT
38854884 TTTTATTTATTTATTTATTATTATTTTTATGAATATAAATAAATATAAAATAATATTAATTTTA
1 TTTTA-TTATTTATTTATTATTA--TTTATGAATATAAATAAATATAAAATAATATTAATTTTA
38854948 TTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTT
1 TTTTATTATTTATTTA-TTATTATT-TATGAATATAAATAAAT--A--TAAAATAATATTAATTT
*
38855013 TG
60 TA
*
38855015 TTTTATTATTTATTTATTA-T-TTTATGAATATAAATAAATAAATAAATAA
1 TTTTATTATTTATTTATTATTATTTATGAATATAAATAAATATA-AAATAA
38855064 CAAACCAAAA
Statistics
Matches: 107, Mismatches: 2, Indels: 18
0.84 0.02 0.14
Matches are distributed among these distances:
59 1 0.01
60 6 0.06
61 1 0.01
62 2 0.02
63 45 0.42
64 13 0.12
65 2 0.02
66 3 0.03
67 34 0.32
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (61 bp):
TTTTATTATTTATTTATTATTATTTATGAATATAAATAAATATAAAATAATATTAATTTTA
Found at i:38854994 original size:67 final size:65
Alignment explanation
Indices: 38854884--38855058 Score: 245
Period size: 67 Copynumber: 2.7 Consensus size: 65
38854874 TTCTTATTAT
38854884 TTTTATTTATTTATTTATTATTATTT-T---TATGAATATAAATAAATATAAAATAATATTAATT
1 TTTTA-TTATTTATTTATTATTATTTATGAATAT-AA-ATAAATAAATATAAAATAATATTAATT
38854945 TTA
63 TTA
*
38854948 TTTTATTATTTATTTATTTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTT
1 TTTTATTATTTATTTA-TTATTATT-TATGAATATAAATAAATAAATATAAAATAATATTAATTT
*
38855013 TG
64 TA
38855015 TTTTATTATTTATTTATTA-T-TTTATGAATATAAATAAATAAATA
1 TTTTATTATTTATTTATTATTATTTATGAATATAAATAAATAAATA
38855059 AATAACAAAC
Statistics
Matches: 102, Mismatches: 3, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
63 32 0.31
64 15 0.15
65 2 0.02
66 4 0.04
67 44 0.43
68 2 0.02
69 3 0.03
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (65 bp):
TTTTATTATTTATTTATTATTATTTATGAATATAAATAAATAAATATAAAATAATATTAATTTTA
Found at i:38858835 original size:49 final size:49
Alignment explanation
Indices: 38858763--38859523 Score: 481
Period size: 49 Copynumber: 15.6 Consensus size: 49
38858753 CAGGTTTCAT
* * * *
38858763 TACCACGAAGACATGAAGGGAAAGATTTAAGCCGTAACTGTGAATCTAG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * *
38858812 TACCACGAATATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* *
38858861 TACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * * *
38858910 TACCACGAATATATGGAGGCAAA-ATTTAAGTCGCAACGGTGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * *
38858958 TACCTA-AAAAACATGAA-GGAATGATTTAAGCCGCAACGGCGAATCTAG
1 TACC-ACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * * * *
38859006 TACCTCGAAGATATGGAGGGAAAGGTTTAAGTCGCAATGACGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * *
38859055 TACCTCTGAA-ACATGAAGGAAAAGATTTATGCCGTAAAGGCGAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * *** * * * *
38859104 TACCACGAAGATATGGAGGGAAA-AGTTCAAGTCATGACGACAAACCTTG
1 TACCACGAAGATATGAAGGGAAAGA-TTTAAGCCGCAACGGCGAATCTAG
* * * * * * ** *
38859153 TACCTCAAAAACATGAA-GGAAGTGATTTAAGCCGTAACGATGAATCTAA
1 TACCACGAAGATATGAAGGGAA-AGATTTAAGCCGCAACGGCGAATCTAG
* * * * * *
38859202 TACCACGAAGATATGGAGGGAAAGGTTTAA---GTAACGGTGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * **
38859248 TACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCACAACGGTAAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * ** * * * *
38859297 TACCACGAAGATATGGAGGGAAAGGTTTAATTCACAACGGTGAACCTTG
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * *
38859346 TACCTCAGAA-ACATGAAGGGAAAGATTTAAGCCACAATGACGAATCTAG
1 TACCAC-GAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* * * * * *
38859395 TACCATGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGGTGAACCTTA-
1 TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC-TAG
* * * ** * *
38859444 TACCTTAGGAA-CT-TGAAGGGAAAGATTGAAGCCGCAACAACAAATCTGG
1 TACC--ACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
* *
38859493 TACCACGAAGATATGGAGGGAAAGGTTTAAG
1 TACCACGAAGATATGAAGGGAAAGATTTAAG
38859524 TCGTGACGGA
Statistics
Matches: 534, Mismatches: 153, Indels: 50
0.72 0.21 0.07
Matches are distributed among these distances:
46 34 0.06
47 10 0.02
48 83 0.16
49 386 0.72
50 17 0.03
51 4 0.01
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (49 bp):
TACCACGAAGATATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAG
Found at i:38859125 original size:98 final size:98
Alignment explanation
Indices: 38858773--38859602 Score: 1006
Period size: 98 Copynumber: 8.5 Consensus size: 98
38858763 TACCACGAAG
* * * * *
38858773 ACATGAAGGGAAAGATTTAAGCCGTAACTGTGAATCTAGTACCACGAATATATGAAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
*
38858838 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* * *
38858871 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAATATATGGAGGCAAA-AT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* *
38858935 TTAAGTCGCAACGGTGAACCTTGTACCTAAAAA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* *
38858968 ACATGAA-GGAATGATTTAAGCCGCAACGGCGAATCTAGTACCTCGAAGATATGGAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* ** *
38859032 TTAAGTCGCAATGACGAACCTTGTACCTCTGAA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* * * * *
38859065 ACATGAAGGAAAAGATTTATGCCGTAAAGGCGAATCTAGTACCACGAAGATATGGAGGGAAAAGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* *** *** *
38859130 TCAAGTCATGACGACAAACCTTGTACCTCAAAA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* * ** *
38859163 ACATGAA-GGAAGTGATTTAAGCCGTAACGATGAATCTAATACCACGAAGATATGGAGGGAAAGG
1 ACATGAAGGGAA-AGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGG
38859227 TTTAAGT---AACGGTGAACCTTGTACCTCAGAA
65 TTTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* **
38859258 ACATGAAGGGAAAGATTTAAGCCACAACGGTAAATCTAGTACCACGAAGATATGGAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* *
38859323 TTAATTCACAACGGTGAACCTTGTACCTCAGAA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* * * *
38859356 ACATGAAGGGAAAGATTTAAGCCACAATGACGAATCTAGTACCATGAAGATATGGAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* * *
38859421 TTAAGTCGCAACGGTGAACCTTATACCTTAGGA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
* * ** * *
38859454 ACTTGAAGGGAAAGATTGAAGCCGCAACAACAAATCTGGTACCACGAAGATATGGAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
** * *
38859519 TTAAGTCGTGACGGAGAACCTTGTACCTCAAAA
66 TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
** * * * * * * * *
38859552 ACATGCTGGGTAGGATTGAGGCTGCAACGGCGAATCCAATACCATGAAGAT
1 ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGAT
38859603 TCGAAGCGAA
Statistics
Matches: 630, Mismatches: 95, Indels: 14
0.85 0.13 0.02
Matches are distributed among these distances:
95 78 0.12
96 54 0.09
97 76 0.12
98 422 0.67
ACGTcount: A:0.37, C:0.17, G:0.25, T:0.20
Consensus pattern (98 bp):
ACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
TTAAGTCGCAACGGTGAACCTTGTACCTCAGAA
Found at i:38859392 original size:291 final size:289
Alignment explanation
Indices: 38858773--38859556 Score: 1014
Period size: 291 Copynumber: 2.7 Consensus size: 289
38858763 TACCACGAAG
* * *
38858773 ACATGAAGGGAAAGATTTAAGCCGTAACTGTGAATCTAGTACCACGAATATATGAAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGTAA-TGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
*
38858838 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACGGCG
65 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACGACG
* * * *
38858903 AATCTAGTACCACGAATATATGGAGGCAAA-ATTTAAGTCGCAACGGTGAACCTTGTACCTAAAA
130 AATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGT---AACGGTGAACCTTGTACCTCAAA
* * * *
38858967 AACATGAAGGAATGATTTAAGCCGCAACGGCGAATCTAGTACCTCGAAGATATGGAGGGAAAGGT
192 AACATGAAGGAAAGATTTAAGCCACAACGGCAAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* * *
38859032 TTAAGTCGCAATGACGAACCTTGTACCTCTGAA
257 TTAAGTCACAACGACGAACCTTGTACCTCAGAA
* * * *
38859065 ACATGAAGGAAAAGATTTATGCCGTAAAGGCGAATCTAGTACCACGAAGATATGGAGGGAAAAGT
1 ACATGAAGGGAAAGATTTAAGCCGT-AATGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* *** * * * * * *
38859130 TCAAGTCATGACGACAAACCTTGTACCTCAAAAACATGAA-GGAAGTGATTTAAGCCGTAACGAT
65 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAA-AGATTTAAGCCGCAACGAC
* *
38859194 GAATCTAATACCACGAAGATATGGAGGGAAAGGTTTAAGTAACGGTGAACCTTGTACCTCAGAAA
129 GAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTAACGGTGAACCTTGTACCTCAAAAA
*
38859259 CATGAAGGGAAAGATTTAAGCCACAACGGTAAATCTAGTACCACGAAGATATGGAGGGAAAGGTT
194 CATGAA-GGAAAGATTTAAGCCACAACGGCAAATCTAGTACCACGAAGATATGGAGGGAAAGGTT
* **
38859324 TAATTCACAACGGTGAACCTTGTACCTCAGAA
258 TAAGTCACAACGACGAACCTTGTACCTCAGAA
** *
38859356 ACATGAAGGGAAAGATTTAAGCCACAATGACGAATCTAGTACCATGAAGATATGGAGGGAAAGGT
1 ACATGAAGGGAAAGATTTAAGCCGTAATG-CGAATCTAGTACCACGAAGATATGGAGGGAAAGGT
* * * * * * * *
38859421 TTAAGTCGCAACGGTGAACCTTATACCTTAGGAACTTGAAGGGAAAGATTGAAGCCGCAACAACA
65 TTAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACGACG
* * *
38859486 AATCTGGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTGACGGAGAACCTTGTACCTCAAA
130 AATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAA---GTAACGGTGAACCTTGTACCTCAAA
38859551 AACATG
192 AACATG
38859557 CTGGGTAGGA
Statistics
Matches: 418, Mismatches: 65, Indels: 16
0.84 0.13 0.03
Matches are distributed among these distances:
290 32 0.08
291 214 0.51
292 135 0.32
293 9 0.02
294 28 0.07
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.21
Consensus pattern (289 bp):
ACATGAAGGGAAAGATTTAAGCCGTAATGCGAATCTAGTACCACGAAGATATGGAGGGAAAGGTT
TAAGTCGCAACGGCGAACCTTGTACCTCAGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGA
ATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTAACGGTGAACCTTGTACCTCAAAAACA
TGAAGGAAAGATTTAAGCCACAACGGCAAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTAA
GTCACAACGACGAACCTTGTACCTCAGAA
Found at i:38859987 original size:41 final size:38
Alignment explanation
Indices: 38859933--38860051 Score: 114
Period size: 41 Copynumber: 3.0 Consensus size: 38
38859923 GTTACATCAC
*
38859933 CATCCAATTTCTTACCCTGATCATGGGGCAGATTGAAGA
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAA-A
* * *
38859972 CATCGCCAATCTCTTA-CCTCGATCATGGGGAAGATCGCAAC
1 CAT--CCAATCTCTTACCCT-GATCATGGGGCAGATTG-AAA
* * * *
38860013 CATCTAATCTTTTACCCCGATCATGGGACAGATTGAAA
1 CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAA
38860051 C
1 C
38860052 CATAACCCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
38 3 0.05
39 26 0.41
40 5 0.08
41 28 0.44
42 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (38 bp):
CATCCAATCTCTTACCCTGATCATGGGGCAGATTGAAA
Found at i:38860053 original size:39 final size:39
Alignment explanation
Indices: 38859931--38860071 Score: 126
Period size: 39 Copynumber: 3.5 Consensus size: 39
38859921 AAGTTACATC
* *
38859931 ACCATCCAAT-TTCTTACCCTGATCATGGGGCAGATTGAA
1 ACCATCCAATCTT-TTACCCCGATCATGGGACAGATTGAA
* * * *
38859970 GA-CATCGCCAATCTCTTACCTCGATCATGGGGA-AGATCGCA
1 -ACCAT--CCAATCTTTTACCCCGATCAT-GGGACAGATTGAA
*
38860011 ACCATCTAATCTTTTACCCCGATCATGGGACAGATTGAA
1 ACCATCCAATCTTTTACCCCGATCATGGGACAGATTGAA
38860050 ACCATAACCCAATCTTTTACCC
1 ACCAT---CCAATCTTTTACCC
38860072 TTAAACCAAG
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
38 4 0.05
39 32 0.40
40 2 0.03
41 25 0.31
42 17 0.21
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (39 bp):
ACCATCCAATCTTTTACCCCGATCATGGGACAGATTGAA
Found at i:38860443 original size:14 final size:15
Alignment explanation
Indices: 38860424--38860455 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
38860414 AAAAAAATAA
38860424 AAATAAATT-AAATT
1 AAATAAATTAAAATT
38860438 AAATAAATTAAAATT
1 AAATAAATTAAAATT
38860453 AAA
1 AAA
38860456 ATCCATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATAAATTAAAATT
Found at i:38865398 original size:11 final size:12
Alignment explanation
Indices: 38865382--38865414 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
38865372 GGGTCACATG
38865382 GCTGACGTGG-C
1 GCTGACGTGGAC
*
38865393 GCTGACGTGGAT
1 GCTGACGTGGAC
38865405 GCTGACGTGG
1 GCTGACGTGG
38865415 TAGGAGGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.21, G:0.45, T:0.21
Consensus pattern (12 bp):
GCTGACGTGGAC
Found at i:38866194 original size:98 final size:98
Alignment explanation
Indices: 38866074--38866574 Score: 705
Period size: 98 Copynumber: 5.1 Consensus size: 98
38866064 CGGTCGTAAC
* * * * *
38866074 CTTTCCTTTCATGTTTCTGAGGTACAAGGTTTGCTGTTACGACTTAAACCTTTCCCTCCATATCT
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* * *
38866139 TCGTGGTACTAGATTCATCATTGTGGCTTAAAT
66 TCGTGGTACTGGATTCACCGTTGTGGCTTAAAT
* * *
38866172 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTTGCCGTTGTGACTTAAACCTTTCTCTCCATATCT
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* *
38866237 TCGTGGTATTGGATTCGCCGTTGTGGCTTAAAT
66 TCGTGGTACTGGATTCACCGTTGTGGCTTAAAT
* * * * *
38866270 CTTTCCCTTCATGCTTTTGAGGTATAAGGTTCACCGTTGGGACTTAAACCTTTCCGTCCATATCT
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* * * *
38866335 TTGTGGTACTGGATTCGCTGTTGCGGCTTAAAT
66 TCGTGGTACTGGATTCACCGTTGTGGCTTAAAT
* * *
38866368 CTTTCCCTTCATGCTTCTAAGATACAAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCT
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* *
38866433 TCGTTGTACTGGATTCACTGTTGTGGCTTAAAT
66 TCGTGGTACTGGATTCACCGTTGTGGCTTAAAT
* *
38866466 CTTTCCCTTCATGCTTCTGAGGTAGAAGGTTCGCCATTGCGACTTAAACCTTTCCCTCCATATCT
1 CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
* * * *
38866531 TCTTGGTACTGGATTCGCCATTGCGGCTTAAAT
66 TCGTGGTACTGGATTCACCGTTGTGGCTTAAAT
38866564 CTTTCCCTTCA
1 CTTTCCCTTCA
38866575 AACTTGTAGA
Statistics
Matches: 360, Mismatches: 43, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
98 360 1.00
ACGTcount: A:0.18, C:0.25, G:0.18, T:0.39
Consensus pattern (98 bp):
CTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCT
TCGTGGTACTGGATTCACCGTTGTGGCTTAAAT
Found at i:38866548 original size:49 final size:49
Alignment explanation
Indices: 38866113--38866571 Score: 294
Period size: 49 Copynumber: 9.4 Consensus size: 49
38866103 TTTGCTGTTA
* * ** *
38866113 CGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCATCATTG
1 CGACTTAAACCTTTCCCTCCATATCTTCTTGGTACTGGATTCGCCGTTG
* * * * * * * *
38866162 TGGCTTAAATCTTTCCCTTCAT-GCTTCTGAGGTACAAGG-TTTGCCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCT-TGGTAC-TGGATTCGCCGTTG
* * * *
38866211 TGACTTAAACCTTTCTCTCCATATCTTCGTGGTATTGGATTCGCCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCTTGGTACTGGATTCGCCGTTG
* * * * * *
38866260 TGGCTTAAATCTTTCCCTTCAT-GCTT-TTGAGGTA-TAAGG-TTCACCGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCTT--GGTACT--GGATTCGCCGTTG
* * *
38866309 GGACTTAAACCTTTCCGTCCATATCTT-TGTGGTACTGGATTCGCTGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTCT-TGGTACTGGATTCGCCGTTG
* * * * * * * *
38866358 CGGCTTAAATCTTTCCCTTCAT-GCTTCTAAGATACAAGG-TTCGCCATTG
1 CGACTTAAACCTTTCCCTCCATATCTTCT-TGGTAC-TGGATTCGCCGTTG
* *
38866407 CGACTTAAACCTTTCCCTCCATATCTTCGTT-GTACTGGATTCACTGTTG
1 CGACTTAAACCTTTCCCTCCATATCTTC-TTGGTACTGGATTCGCCGTTG
* * * * * * ** *
38866456 TGGCTTAAATCTTTCCCTTCAT-GCTTCTGAGGTAGAAGG-TTCGCCATTG
1 CGACTTAAACCTTTCCCTCCATATCTTCT-TGGTA-CTGGATTCGCCGTTG
*
38866505 CGACTTAAACCTTTCCCTCCATATCTTCTTGGTACTGGATTCGCCATTG
1 CGACTTAAACCTTTCCCTCCATATCTTCTTGGTACTGGATTCGCCGTTG
* *
38866554 CGGCTTAAATCTTTCCCT
1 CGACTTAAACCTTTCCCT
38866572 TCAAACTTGT
Statistics
Matches: 307, Mismatches: 81, Indels: 44
0.71 0.19 0.10
Matches are distributed among these distances:
47 2 0.01
48 23 0.07
49 255 0.83
50 25 0.08
51 2 0.01
ACGTcount: A:0.19, C:0.25, G:0.18, T:0.38
Consensus pattern (49 bp):
CGACTTAAACCTTTCCCTCCATATCTTCTTGGTACTGGATTCGCCGTTG
Found at i:38870289 original size:20 final size:21
Alignment explanation
Indices: 38870264--38870302 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
38870254 GTAAGGAATT
38870264 TGAAAC-AACAAAAGTAAAAG
1 TGAAACAAACAAAAGTAAAAG
*
38870284 TGAAACAAATAAAAGTAAA
1 TGAAACAAACAAAAGTAAA
38870303 TAAAAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.67, C:0.08, G:0.13, T:0.13
Consensus pattern (21 bp):
TGAAACAAACAAAAGTAAAAG
Found at i:38876307 original size:13 final size:14
Alignment explanation
Indices: 38876289--38876318 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
38876279 ATCAACGCAA
38876289 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
38876302 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
38876316 TCA
1 TCA
38876319 CTGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:38888833 original size:20 final size:20
Alignment explanation
Indices: 38888810--38888848 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
38888800 TTATTGATGT
* *
38888810 TTGCCATTTTTTACCAATGC
1 TTGCCATTATTGACCAATGC
*
38888830 TTGCTATTATTGACCAATG
1 TTGCCATTATTGACCAATG
38888849 TTTGTAATCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (20 bp):
TTGCCATTATTGACCAATGC
Found at i:38891622 original size:15 final size:15
Alignment explanation
Indices: 38891604--38891635 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
38891594 TTTTATTTAG
38891604 TATTTATTTATTATT
1 TATTTATTTATTATT
*
38891619 TATTTATTTGTTATT
1 TATTTATTTATTATT
38891634 TA
1 TA
38891636 CATTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TATTTATTTATTATT
Found at i:38891626 original size:11 final size:11
Alignment explanation
Indices: 38891564--38891659 Score: 64
Period size: 11 Copynumber: 9.0 Consensus size: 11
38891554 ATATGGTCCC
38891564 ATTTA-TATTT
1 ATTTATTATTT
38891574 -TTTA-TATATT
1 ATTTATTAT-TT
38891584 ATTTTCATTATTTT
1 A-TTT-ATTA-TTT
*
38891598 ATTTAGTATTT
1 ATTTATTATTT
38891609 ATTTATTATTT
1 ATTTATTATTT
38891620 ATTTATT-TGTT
1 ATTTATTAT-TT
*
38891631 ATTTA-CATTT
1 ATTTATTATTT
*
38891641 -TTT-CT-TTT
1 ATTTATTATTT
38891649 ATTTATTATTT
1 ATTTATTATTT
38891660 TTATGCTATT
Statistics
Matches: 69, Mismatches: 5, Indels: 23
0.71 0.05 0.24
Matches are distributed among these distances:
8 3 0.04
9 13 0.19
10 6 0.09
11 31 0.45
12 6 0.09
13 4 0.06
14 5 0.07
15 1 0.01
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (11 bp):
ATTTATTATTT
Found at i:38891670 original size:36 final size:39
Alignment explanation
Indices: 38891606--38891698 Score: 95
Period size: 36 Copynumber: 2.5 Consensus size: 39
38891596 TTATTTAGTA
* * *
38891606 TTTATTTATTATTTATTTATTTGTTATTTACATTTTTTCT
1 TTTATTTATTATTTATTTA-TTGCTATTTACATTTTTGCC
**
38891646 TTTATTTATTA-TT-TTTA-TGCTATTTATGTTTTTGCC
1 TTTATTTATTATTTATTTATTGCTATTTACATTTTTGCC
*
38891682 TTTATTTAAT-TTTATTT
1 TTTATTTATTATTTATTT
38891699 CTTCATGGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
36 25 0.56
37 3 0.07
38 4 0.09
39 2 0.04
40 11 0.24
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.71
Consensus pattern (39 bp):
TTTATTTATTATTTATTTATTGCTATTTACATTTTTGCC
Found at i:38895974 original size:30 final size:30
Alignment explanation
Indices: 38895940--38896025 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
38895930 AAAAAGTTGC
38895940 TTTAATGACTAAATTGGAAATTTTA-TGAAA
1 TTTAATGACTAAATTGG-AATTTTAGTGAAA
38895970 TTTAATGACTAAATTGTG-ATTTTAGTGAAA
1 TTTAATGACTAAATTG-GAATTTTAGTGAAA
* ** *
38896000 CTTAGGGACTAAATTGTAATTTTAGT
1 TTTAATGACTAAATTGGAATTTTAGT
38896026 AGAATTAAGG
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.12
30 42 0.86
31 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (30 bp):
TTTAATGACTAAATTGGAATTTTAGTGAAA
Found at i:38896037 original size:30 final size:30
Alignment explanation
Indices: 38895946--38896041 Score: 99
Period size: 30 Copynumber: 3.2 Consensus size: 30
38895936 TTGCTTTAAT
* * **
38895946 GACTAAATTGGAAATTTTA-TGAAATTTAAT
1 GACTAAATT-GTAATTTTAGTGAAACTTAGG
*
38895976 GACTAAATTGTGATTTTAGTGAAACTTAGG
1 GACTAAATTGTAATTTTAGTGAAACTTAGG
38896006 GACTAAATTGTAATTTTAGT-AGAA-TTAAGG
1 GACTAAATTGTAATTTTAGTGA-AACTT-AGG
38896036 GACTAA
1 GACTAA
38896042 TTTAAACTTT
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.18
30 47 0.82
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (30 bp):
GACTAAATTGTAATTTTAGTGAAACTTAGG
Found at i:38897292 original size:30 final size:30
Alignment explanation
Indices: 38897257--38897322 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
38897247 GCCGCTAGAG
*
38897257 GTGTGTCTCTG-TCCGTGCTACATATTTGTT
1 GTGTGTCTCTGCTCCGTGCTACATA-CTGTT
* *
38897287 GTGTGTCTTTGCTCTGTGCTACATACTGTT
1 GTGTGTCTCTGCTCCGTGCTACATACTGTT
38897317 GTGTGT
1 GTGTGT
38897323 TTCTTTTTGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
30 20 0.62
31 12 0.38
ACGTcount: A:0.09, C:0.18, G:0.26, T:0.47
Consensus pattern (30 bp):
GTGTGTCTCTGCTCCGTGCTACATACTGTT
Found at i:38898745 original size:30 final size:31
Alignment explanation
Indices: 38898705--38898791 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 31
38898695 CCAAAAATTG
* *
38898705 ATTTAAGGACTAAATTAGAAATTTTA-TGAA
1 ATTTAAGGACTAAATTAGTAATTTTAGTAAA
* *
38898735 ATTTAGGGACTAAATT-GTGATTTTAGTAAA
1 ATTTAAGGACTAAATTAGTAATTTTAGTAAA
* *
38898765 ACTTATGGACTAAATTA-TAATTTTAGT
1 ATTTAAGGACTAAATTAGTAATTTTAGT
38898792 GGAACTAGGG
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
29 7 0.15
30 41 0.85
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (31 bp):
ATTTAAGGACTAAATTAGTAATTTTAGTAAA
Found at i:38902906 original size:18 final size:18
Alignment explanation
Indices: 38902879--38902920 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
38902869 CAAATTCTTC
* * *
38902879 TTCTTTTTCTTTCTTTCT
1 TTCTTCTTCTTGCTTCCT
38902897 TTCTTCTTCTTGCTTCCT
1 TTCTTCTTCTTGCTTCCT
38902915 TTCTTC
1 TTCTTC
38902921 CTCCTCTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.00, C:0.29, G:0.02, T:0.69
Consensus pattern (18 bp):
TTCTTCTTCTTGCTTCCT
Found at i:38926963 original size:43 final size:43
Alignment explanation
Indices: 38926905--38927101 Score: 245
Period size: 43 Copynumber: 4.6 Consensus size: 43
38926895 TTATACTCTA
* *
38926905 CCGAGACATAAGTCTTCCTTTTA-ATCATAATCTCATGCTCACC
1 CCGAGACATGAGTCTTCCTTTTATA-CATAATCTCATGCTCATC
* * *
38926948 CCGAGACATGAGTCTTTCTCTTATACATAATCTCATGCTTATC
1 CCGAGACATGAGTCTTCCTTTTATACATAATCTCATGCTCATC
* * *
38926991 CCGAGACATGAGTCATCCCTTTATACGTAATCTCATGCTCATC
1 CCGAGACATGAGTCTTCCTTTTATACATAATCTCATGCTCATC
** *
38927034 CCGAGTTACGAGTCTT-CTATTTATACATAATCTCATGCTCATC
1 CCGAGACATGAGTCTTCCT-TTTATACATAATCTCATGCTCATC
* *
38927077 CTGAGACATGAGTCTTCCATTTATA
1 CCGAGACATGAGTCTTCCTTTTATA
38927102 TATTAAGTGT
Statistics
Matches: 129, Mismatches: 22, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.01
43 126 0.98
44 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.35
Consensus pattern (43 bp):
CCGAGACATGAGTCTTCCTTTTATACATAATCTCATGCTCATC
Found at i:38929008 original size:18 final size:18
Alignment explanation
Indices: 38928982--38929037 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
38928972 GCATGAACAT
*
38928982 CATGATCAAATGCAGTCA
1 CATGCTCAAATGCAGTCA
38929000 CATGCTCAAATGCAGTCA
1 CATGCTCAAATGCAGTCA
* *
38929018 CATGCTCGAATGCAGCCA
1 CATGCTCAAATGCAGTCA
38929036 CA
1 CA
38929038 GCAGACTGCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.20
Consensus pattern (18 bp):
CATGCTCAAATGCAGTCA
Found at i:38935118 original size:12 final size:12
Alignment explanation
Indices: 38935097--38935148 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
38935087 GGGTATCGAG
*
38935097 GAGAAGGAAGAA
1 GAGAAAGAAGAA
38935109 GAGAAAGAAGAA
1 GAGAAAGAAGAA
*
38935121 GAAAAGAAAGAAGGA
1 G---AGAAAGAAGAA
*
38935136 GAGAAAGAGGAA
1 GAGAAAGAAGAA
38935148 G
1 G
38935149 TTTTTGTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 22 0.67
15 11 0.33
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GAGAAAGAAGAA
Found at i:38935123 original size:15 final size:15
Alignment explanation
Indices: 38935098--38935143 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
38935088 GGTATCGAGG
*
38935098 AGAAGGAAGAAGAGAA
1 AGAA-GAAGAAAAGAA
38935114 AGAAGAAGAAAAGAA
1 AGAAGAAGAAAAGAA
*
38935129 AGAAGGAGAGAAAGA
1 AGAAGAAGA-AAAGA
38935144 GGAAGTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 18 0.67
16 9 0.33
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAAGAA
Found at i:38935608 original size:17 final size:17
Alignment explanation
Indices: 38935573--38935611 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
38935563 ATTTTCATCA
**
38935573 CATTTTAATTGTCCCTG
1 CATTTTAATTGTCAATG
*
38935590 CATTTTATTTGTCAATG
1 CATTTTAATTGTCAATG
38935607 CATTT
1 CATTT
38935612 GCATTGTAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.51
Consensus pattern (17 bp):
CATTTTAATTGTCAATG
Found at i:38936076 original size:38 final size:38
Alignment explanation
Indices: 38936025--38936100 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
38936015 GGGAATACTC
38936025 CAATGCAAGTGTTAGAAAAAAAATCTAGCCAAAGGCTA
1 CAATGCAAGTGTTAGAAAAAAAATCTAGCCAAAGGCTA
*
38936063 CAATGCAAGTGTTAGAAAAAATATCTAGCCAAAGGCTA
1 CAATGCAAGTGTTAGAAAAAAAATCTAGCCAAAGGCTA
38936101 TCACTGTAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.46, C:0.16, G:0.18, T:0.20
Consensus pattern (38 bp):
CAATGCAAGTGTTAGAAAAAAAATCTAGCCAAAGGCTA
Found at i:38938972 original size:41 final size:41
Alignment explanation
Indices: 38938922--38939057 Score: 104
Period size: 41 Copynumber: 3.4 Consensus size: 41
38938912 TCGTTAATTC
*
38938922 ATCCAACTAGAGCTGGGCTCACATTTGATATTCGTCGGTTT
1 ATCCAACTAGAGCTGGGCTCACATTTAATATTCGTCGGTTT
* * * * *
38938963 ATCCGACTAGCGCTAGG-TGCA-A---AACA-TCGTTGGTTT
1 ATCCAACTAGAGCTGGGCT-CACATTTAATATTCGTCGGTTT
* * * *
38938999 ATCCAACTAGAGTTGGGCTCACATTTTATATTCATCAGTTT
1 ATCCAACTAGAGCTGGGCTCACATTTAATATTCGTCGGTTT
* * *
38939040 ATTCGACTAGCGCTGGGC
1 ATCCAACTAGAGCTGGGC
38939058 ACAAAACATC
Statistics
Matches: 69, Mismatches: 19, Indels: 14
0.68 0.19 0.14
Matches are distributed among these distances:
36 24 0.35
37 4 0.06
40 4 0.06
41 37 0.54
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (41 bp):
ATCCAACTAGAGCTGGGCTCACATTTAATATTCGTCGGTTT
Found at i:38939005 original size:77 final size:77
Alignment explanation
Indices: 38938922--38939084 Score: 245
Period size: 77 Copynumber: 2.1 Consensus size: 77
38938912 TCGTTAATTC
* * **
38938922 ATCCAACTAGAGCTGGGCTCACATTTGATATTCGTCGGTTTATCCGACTAGCGCTAGGTGCAAAA
1 ATCCAACTAGAGCTGGGCTCACATTTGATATTCATCAGTTTATCCGACTAGCGCTAGGCACAAAA
*
38938987 CATCGTTGGTTT
66 CATCATTGGTTT
* * * *
38938999 ATCCAACTAGAGTTGGGCTCACATTTTATATTCATCAGTTTATTCGACTAGCGCTGGGCACAAAA
1 ATCCAACTAGAGCTGGGCTCACATTTGATATTCATCAGTTTATCCGACTAGCGCTAGGCACAAAA
38939064 CATCATTGGTTT
66 CATCATTGGTTT
38939076 ATCCAACTA
1 ATCCAACTA
38939085 ACGTTAGGCA
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (77 bp):
ATCCAACTAGAGCTGGGCTCACATTTGATATTCATCAGTTTATCCGACTAGCGCTAGGCACAAAA
CATCATTGGTTT
Found at i:38939076 original size:36 final size:36
Alignment explanation
Indices: 38939036--38939120 Score: 107
Period size: 36 Copynumber: 2.4 Consensus size: 36
38939026 ATATTCATCA
* * * *
38939036 GTTTATTCGACTAGCGCTGGGCACAAAACATCATTG
1 GTTTATCCAACTAACGCTAGGCACAAAACATCATTG
* *
38939072 GTTTATCCAACTAACGTTAGGCAGAAAACATCATTG
1 GTTTATCCAACTAACGCTAGGCACAAAACATCATTG
*
38939108 GTATATCCAACTA
1 GTTTATCCAACTA
38939121 GAGTTGGGCT
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (36 bp):
GTTTATCCAACTAACGCTAGGCACAAAACATCATTG
Found at i:38939154 original size:77 final size:77
Alignment explanation
Indices: 38939073--38939219 Score: 215
Period size: 77 Copynumber: 1.9 Consensus size: 77
38939063 ACATCATTGG
*
38939073 TTTATCCAACTAACGTTAGGCAG-AAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACATT
1 TTTATCCAACTAACGTTAGGC-GCAAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACAAT
38939137 TGATATTCGTCGA
65 TGATATTCGTCGA
** * ** *
38939150 TTTATCCAACTAGTGTTAGGCGCAAAATATTGTTGGTATATCTAACTAGAGTTGGGCTCACAATT
1 TTTATCCAACTAACGTTAGGCGCAAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACAATT
38939215 GATAT
66 GATAT
38939220 CATCAGTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 1 0.02
77 61 0.98
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (77 bp):
TTTATCCAACTAACGTTAGGCGCAAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACAATT
GATATTCGTCGA
Found at i:38939186 original size:113 final size:113
Alignment explanation
Indices: 38938983--38939197 Score: 279
Period size: 113 Copynumber: 1.9 Consensus size: 113
38938973 CGCTAGGTGC
* * * * *
38938983 AAAACATCGTTGGTTTATCCAACTAGAGTTGGGCTCACATTTTATATTCATCAGTTTATTCGACT
1 AAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACATTTGATATTCATCAGTTTATCCAACT
* *
38939048 AGCGCTGGGCACAAAACATCATTGGTTTATCCAACTAACGTTAGGCAG
66 AGCGCTAGGCACAAAACATCATTGGTATATCCAACTAACGTTAGGCAG
*
38939096 AAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACATTTGATATTCGTC-GATTTATCCAAC
1 AAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACATTTGATATTCATCAG-TTTATCCAAC
* * * * ** *
38939160 TAGTGTTAGGCGCAAAATATTGTTGGTATATCTAACTA
65 TAGCGCTAGGCACAAAACATCATTGGTATATCCAACTA
38939198 GAGTTGGGCT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
112 1 0.01
113 85 0.99
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (113 bp):
AAAACATCATTGGTATATCCAACTAGAGTTGGGCTCACATTTGATATTCATCAGTTTATCCAACT
AGCGCTAGGCACAAAACATCATTGGTATATCCAACTAACGTTAGGCAG
Found at i:38941633 original size:55 final size:55
Alignment explanation
Indices: 38941567--38941703 Score: 159
Period size: 55 Copynumber: 2.5 Consensus size: 55
38941557 AGCAATACGG
* * * * * * *
38941567 CTAGGCCTTACACTATATAGA-CTTCACATACTCGATTTGATGTCATAATCCCAAA
1 CTAGGTCTTACACGATAT-GATCTTCACAAACCCCATATGATGCCATAATCCCAAA
* *
38941622 CTAGGTCTTACACGATATGATCTTCACAAACCCCATATGATGCCATAGTCCCAGA
1 CTAGGTCTTACACGATATGATCTTCACAAACCCCATATGATGCCATAATCCCAAA
* *
38941677 CTAGGTCTTACATGATATGGTCTTCAC
1 CTAGGTCTTACACGATATGATCTTCAC
38941704 TTGTCATGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
54 2 0.03
55 68 0.97
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (55 bp):
CTAGGTCTTACACGATATGATCTTCACAAACCCCATATGATGCCATAATCCCAAA
Found at i:38946672 original size:15 final size:14
Alignment explanation
Indices: 38946650--38946683 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
38946640 AAAATTTAAT
*
38946650 TATTTTTTAAAAAA
1 TATTTTTTTAAAAA
38946664 TATTTTTTTAAAAA
1 TATTTTTTTAAAAA
38946678 TATTTT
1 TATTTT
38946684 AAAATTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATTTTTTTAAAAA
Found at i:38946991 original size:22 final size:22
Alignment explanation
Indices: 38946963--38947004 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
38946953 ATCATCATCA
38946963 TCATCATCATCCATGGGTTGAT
1 TCATCATCATCCATGGGTTGAT
38946985 TCATCATCATCCATGGGTTG
1 TCATCATCATCCATGGGTTG
38947005 TTCTACTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (22 bp):
TCATCATCATCCATGGGTTGAT
Found at i:38947838 original size:11 final size:11
Alignment explanation
Indices: 38947820--38947855 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
38947810 GTATGATTTT
38947820 AATAATTTTAA
1 AATAATTTTAA
*
38947831 ATTAATTTTAA
1 AATAATTTTAA
38947842 AAT-ATTTTAA
1 AATAATTTTAA
38947852 AATA
1 AATA
38947856 TATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AATAATTTTAA
Found at i:38947850 original size:10 final size:10
Alignment explanation
Indices: 38947815--38947856 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
38947805 AATGAGTATG
*
38947815 ATTTTAATA-
1 ATTTTAAAAT
*
38947824 ATTTTAAATT
1 ATTTTAAAAT
38947834 AATTTTAAAAT
1 -ATTTTAAAAT
38947845 ATTTTAAAAT
1 ATTTTAAAAT
38947855 AT
1 AT
38947857 ATATATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 7 0.25
10 12 0.43
11 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTTAAAAT
Found at i:38952921 original size:24 final size:24
Alignment explanation
Indices: 38952893--38952938 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
38952883 TCTTCACCCT
*
38952893 CTTCATCATCACCATCATCCTCTG
1 CTTCATCATCACCATCACCCTCTG
* *
38952917 CTTCATCTTCACCCTCACCCTC
1 CTTCATCATCACCATCACCCTC
38952939 AGCCTCTCCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.48, G:0.02, T:0.33
Consensus pattern (24 bp):
CTTCATCATCACCATCACCCTCTG
Found at i:38957241 original size:17 final size:18
Alignment explanation
Indices: 38957219--38957252 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
38957209 GCATTATTTC
38957219 TCAAAAA-TACTTTTGAA
1 TCAAAAAGTACTTTTGAA
38957236 TCAAAAAGTACTTTTGA
1 TCAAAAAGTACTTTTGA
38957253 GCAAAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (18 bp):
TCAAAAAGTACTTTTGAA
Found at i:38957257 original size:17 final size:17
Alignment explanation
Indices: 38957220--38957258 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
38957210 CATTATTTCT
*
38957220 CAAAAATACTTTTGAAT
1 CAAAAATACTTTTGAAG
38957237 CAAAAAGTACTTTTG-AG
1 CAAAAA-TACTTTTGAAG
38957254 CAAAA
1 CAAAA
38957259 GATAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.49, C:0.13, G:0.10, T:0.28
Consensus pattern (17 bp):
CAAAAATACTTTTGAAG
Found at i:38957387 original size:18 final size:18
Alignment explanation
Indices: 38957364--38957398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
38957354 TTTAACACTA
*
38957364 TTTTTATCTCAAAAGTAT
1 TTTTTATATCAAAAGTAT
*
38957382 TTTTTATATTAAAAGTA
1 TTTTTATATCAAAAGTA
38957399 ATGTCAACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (18 bp):
TTTTTATATCAAAAGTAT
Found at i:38959010 original size:31 final size:31
Alignment explanation
Indices: 38958961--38959033 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
38958951 TTTATTCTAT
* *
38958961 TTTTTAAATTAAATCCTTTTATTTTTATTT-
1 TTTTAAAATTAAACCCTTTTATTTTTATTTC
* *
38958991 TTGTTAAAATTTAACCCTTTTATTTTTGTTTC
1 TT-TTAAAATTAAACCCTTTTATTTTTATTTC
38959023 TTTTAAAATTA
1 TTTTAAAATTA
38959034 CCTTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 2 0.06
31 32 0.89
32 2 0.06
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (31 bp):
TTTTAAAATTAAACCCTTTTATTTTTATTTC
Found at i:38959501 original size:106 final size:107
Alignment explanation
Indices: 38959379--38959585 Score: 301
Period size: 106 Copynumber: 1.9 Consensus size: 107
38959369 AAAATAGAGG
* * * * *
38959379 CAATGTTCTTTTATTTTAGGGAACTCGAGAAATTGTGTCCTAATGTACTT-GGTATGGTTTTTCT
1 CAATGCTCTTTTATTTTAGGGAACTCAAGAAATTGTGCCCTAAAGTA-TTGGGTATGATTTTTCT
*
38959443 TTGAACCT-TAATTGAATATACTATTTAAAATCGACAAATGTT
65 TTGAACCTATAACTGAATATACTATTTAAAATCGACAAATGTT
*
38959485 CAATGCTCTTTTATTTTAGGGGACTCAAGAAATTGTGCCCTAAAGTATTGGGTATGATTTTTCTT
1 CAATGCTCTTTTATTTTAGGGAACTCAAGAAATTGTGCCCTAAAGTATTGGGTATGATTTTTCTT
*
38959550 TGAACCTAAGTAACTGAATATCCTATTTAAAATCGA
66 TGAACCT-A-TAACTGAATATACTATTTAAAATCGA
38959586 TAAGTGTTTT
Statistics
Matches: 89, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
105 2 0.02
106 63 0.71
109 24 0.27
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (107 bp):
CAATGCTCTTTTATTTTAGGGAACTCAAGAAATTGTGCCCTAAAGTATTGGGTATGATTTTTCTT
TGAACCTATAACTGAATATACTATTTAAAATCGACAAATGTT
Found at i:38972745 original size:21 final size:22
Alignment explanation
Indices: 38972719--38972760 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
38972709 AATCAAAAAG
38972719 AAAAGAAAAATGAGT-AGAAAC
1 AAAAGAAAAATGAGTAAGAAAC
**
38972740 AAAAGAATCATGAGTAAGAAA
1 AAAAGAAAAATGAGTAAGAAA
38972761 ACATGTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.64, C:0.05, G:0.19, T:0.12
Consensus pattern (22 bp):
AAAAGAAAAATGAGTAAGAAAC
Found at i:38976394 original size:17 final size:16
Alignment explanation
Indices: 38976365--38976397 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38976355 ACAGCATAAT
*
38976365 TTTTTTTTCTTTTCTC
1 TTTTCTTTCTTTTCTC
38976381 TTTTCTTTCTTTT-TC
1 TTTTCTTTCTTTTCTC
38976396 TT
1 TT
38976398 ATTTTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTCTTTCTTTTCTC
Found at i:38990967 original size:16 final size:17
Alignment explanation
Indices: 38990946--38990982 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
38990936 GCAATGAGAA
38990946 ATTTTGCTAAAACC-AT
1 ATTTTGCTAAAACCAAT
*
38990962 ATTTTGTTAAAACCAAT
1 ATTTTGCTAAAACCAAT
38990979 ATTT
1 ATTT
38990983 CATGTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (17 bp):
ATTTTGCTAAAACCAAT
Found at i:38992915 original size:19 final size:18
Alignment explanation
Indices: 38992870--38992916 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
38992860 TCCGAACTTA
*
38992870 ACCCATTGACTTTGATCG
1 ACCCATTGACTTTGACCG
*
38992888 ACCCGTTGACTTTGACCCG
1 ACCCATTGACTTTGA-CCG
*
38992907 ACTCATTGAC
1 ACCCATTGAC
38992917 CGTTGATCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.21, C:0.32, G:0.17, T:0.30
Consensus pattern (18 bp):
ACCCATTGACTTTGACCG
Found at i:38998180 original size:22 final size:22
Alignment explanation
Indices: 38998155--38998219 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
38998145 GCTTTCCATT
*
38998155 TAGCACGATTGTGCTCTTCGTC
1 TAGCACGATTGTGCTCTCCGTC
38998177 TAGCACGATTGTGCTCTCCGTC
1 TAGCACGATTGTGCTCTCCGTC
*
38998199 TAGCAC-CTTGGTGCTCTCCGT
1 TAGCACGATT-GTGCTCTCCGT
38998220 TCTTTAGGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
21 2 0.05
22 38 0.95
ACGTcount: A:0.12, C:0.31, G:0.23, T:0.34
Consensus pattern (22 bp):
TAGCACGATTGTGCTCTCCGTC
Found at i:39001545 original size:16 final size:18
Alignment explanation
Indices: 39001514--39001548 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
39001504 TGTTGCTCTA
39001514 ACAACTTAACTTGCATTG
1 ACAACTTAACTTGCATTG
39001532 ACAACTT-A-TTGCATTG
1 ACAACTTAACTTGCATTG
39001548 A
1 A
39001549 TAGTACTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 1 0.06
18 7 0.41
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (18 bp):
ACAACTTAACTTGCATTG
Found at i:39016976 original size:18 final size:17
Alignment explanation
Indices: 39016953--39017000 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
39016943 CTCTTTTTCC
*
39016953 TCTTTTTCAATTTCTTTT
1 TCTTTTTCAATTT-TATT
39016971 TCTTTTTC-ATCCTTTATT
1 TCTTTTTCAAT--TTTATT
39016989 TCTTTTTCAATT
1 TCTTTTTCAATT
39017001 CCTTCTCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
17 3 0.12
18 19 0.73
19 4 0.15
ACGTcount: A:0.12, C:0.19, G:0.00, T:0.69
Consensus pattern (17 bp):
TCTTTTTCAATTTTATT
Found at i:39017056 original size:27 final size:28
Alignment explanation
Indices: 39017003--39017062 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 28
39016993 TTTCAATTCC
* *
39017003 TTCTCTCACACTTTCTTTTTCTTTCTCTT
1 TTCTCTCACACTCTCTTTTTC-TTCTCAT
39017032 TTCTCTCA-AGCTCTCTTTTTC-TCTCAT
1 TTCTCTCACA-CTCTCTTTTTCTTCTCAT
39017059 TTCT
1 TTCT
39017063 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 9 0.32
28 1 0.04
29 18 0.64
ACGTcount: A:0.08, C:0.32, G:0.02, T:0.58
Consensus pattern (28 bp):
TTCTCTCACACTCTCTTTTTCTTCTCAT
Found at i:39018053 original size:21 final size:22
Alignment explanation
Indices: 39018028--39018081 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
39018018 AATTTTTTTT
39018028 GAATATTTTTATTTTCAC-TTC
1 GAATATTTTTATTTTCACTTTC
* * *
39018049 GAATATATATATTTTCTCTTTTC
1 GAATATTTTTATTTTCAC-TTTC
39018072 GAATATTTTT
1 GAATATTTTT
39018082 TTCAACTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 15 0.58
23 11 0.42
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (22 bp):
GAATATTTTTATTTTCACTTTC
Found at i:39021579 original size:24 final size:24
Alignment explanation
Indices: 39021552--39021615 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
39021542 ACTCTGTTTG
*
39021552 GGCTCGAATGAGCTAACTTATCTA
1 GGCTCGAATGAGCTAACCTATCTA
*
39021576 GGCTCGTAA-GAGCTAACCTATCTG
1 GGCTCG-AATGAGCTAACCTATCTA
*
39021600 GGCTCGTATGAGCTAA
1 GGCTCGAATGAGCTAA
39021616 TTTTGTTTGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 1 0.03
24 32 0.91
25 2 0.06
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (24 bp):
GGCTCGAATGAGCTAACCTATCTA
Found at i:39022972 original size:65 final size:65
Alignment explanation
Indices: 39022868--39022997 Score: 206
Period size: 65 Copynumber: 2.0 Consensus size: 65
39022858 TGCCAAATAT
* **
39022868 TATTCCTGGCATGGTATATTCTTTTGATATTATTCATTGGGTATGCACTAATTAAGATTGAGTTA
1 TATTCCTGACATGGTATATTCTTTCAATATTATTCATTGGGTATGCACTAATTAAGATTGAGTTA
* * *
39022933 TATTCCTGATATGGTATATTCTTTCAATATTATTTATTGGGTATGCACTGATTAAGATTGAGTTA
1 TATTCCTGACATGGTATATTCTTTCAATATTATTCATTGGGTATGCACTAATTAAGATTGAGTTA
39022998 ATATATATAT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (65 bp):
TATTCCTGACATGGTATATTCTTTCAATATTATTCATTGGGTATGCACTAATTAAGATTGAGTTA
Found at i:39025648 original size:24 final size:24
Alignment explanation
Indices: 39025615--39025722 Score: 85
Period size: 24 Copynumber: 4.5 Consensus size: 24
39025605 ATACTGGTTA
39025615 AACTCTATCTGGGCTCGAATGAGCT
1 AACT-TATCTGGGCTCGAATGAGCT
*
39025640 AACTTATCTGGGCTCGTAA-AAGCT
1 AACTTATCTGGGCTCG-AATGAGCT
* * **
39025664 ACCCTATCTGGGCTCCTATGAGCT
1 AACTTATCTGGGCTCGAATGAGCT
* * * *
39025688 AATTTTGTTTGGGCTCGTATGAGCT
1 AA-CTTATCTGGGCTCGAATGAGCT
*
39025713 AAATT-TCTGG
1 AACTTATCTGG
39025723 AAGACTCAGT
Statistics
Matches: 66, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
23 5 0.08
24 36 0.55
25 25 0.38
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.33
Consensus pattern (24 bp):
AACTTATCTGGGCTCGAATGAGCT
Found at i:39026916 original size:51 final size:49
Alignment explanation
Indices: 39026809--39026923 Score: 167
Period size: 51 Copynumber: 2.3 Consensus size: 49
39026799 ACAGAAATTT
* * *
39026809 CAGTGGGCATGCTTAACATGAGTATCAAATTTTATTAATATAAGCGTTA
1 CAGTGGGCATGCTTAACATGAGAATCAAATTTTATTAATAGAAGCGATA
* *
39026858 CAATGGGCATGCTTAACATGCGAATCAAAATCTTTATTAATAGAAGCGATA
1 CAGTGGGCATGCTTAACATGAGAATC-AAAT-TTTATTAATAGAAGCGATA
39026909 CAGTGGGCATGCTTA
1 CAGTGGGCATGCTTA
39026924 TCAAAACAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
49 23 0.40
50 4 0.07
51 31 0.53
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (49 bp):
CAGTGGGCATGCTTAACATGAGAATCAAATTTTATTAATAGAAGCGATA
Found at i:39027941 original size:20 final size:21
Alignment explanation
Indices: 39027903--39027941 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39027893 AAATTAGAGT
*
39027903 GAAATTGTTTGAGTTTTGATA
1 GAAATTGTTAGAGTTTTGATA
39027924 GAAATTGTTAGA-TTTTGA
1 GAAATTGTTAGAGTTTTGA
39027942 AGCTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.31, C:0.00, G:0.23, T:0.46
Consensus pattern (21 bp):
GAAATTGTTAGAGTTTTGATA
Found at i:39028978 original size:24 final size:24
Alignment explanation
Indices: 39028951--39029067 Score: 171
Period size: 24 Copynumber: 4.9 Consensus size: 24
39028941 AATGTTTCTT
39028951 ATATTAGCTGGCGAGCGTAAACGC
1 ATATTAGCTGGCGAGCGTAAACGC
* *
39028975 ATATTAGCTGACGAGCGTAAACGT
1 ATATTAGCTGGCGAGCGTAAACGC
*
39028999 ATATTAGCTGGCTAGCGTAAACGC
1 ATATTAGCTGGCGAGCGTAAACGC
* *
39029023 ATATTAGCTGGTGAGCGTAAACGT
1 ATATTAGCTGGCGAGCGTAAACGC
* *
39029047 ATCTTAGCTGACGAGCGTAAA
1 ATATTAGCTGGCGAGCGTAAA
39029068 TGTACTGAAC
Statistics
Matches: 82, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 82 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (24 bp):
ATATTAGCTGGCGAGCGTAAACGC
Found at i:39029006 original size:48 final size:48
Alignment explanation
Indices: 39028950--39029067 Score: 191
Period size: 48 Copynumber: 2.5 Consensus size: 48
39028940 CAATGTTTCT
39028950 TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGACGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGACGAGCGTAAACG
* **
39028998 TATATTAGCTGGCTAGCGTAAACGCATATTAGCTGGTGAGCGTAAACG
1 TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGACGAGCGTAAACG
* *
39029046 TATCTTAGCTGACGAGCGTAAA
1 TATATTAGCTGGCGAGCGTAAA
39029068 TGTACTGAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 64 1.00
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (48 bp):
TATATTAGCTGGCGAGCGTAAACGCATATTAGCTGACGAGCGTAAACG
Found at i:39033169 original size:57 final size:56
Alignment explanation
Indices: 39033116--39033226 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 56
39033106 GGTGAAATGG
* * * *
39033116 AGAAATGGGAAACATTTGGAAATGATTATGGTTTTCTCCAAAATGAAAATGAAAATAA
1 AGAAAT-GCAAACATTTGAAAATGAATATGGCTTTCTCCAAAATGAAAATG-AAATAA
* * *
39033174 AGAAATGCAATCGTTTGAAAATGAATGTGGCTTTCTCCAAAATGAAAATGAAA
1 AGAAATGCAAACATTTGAAAATGAATATGGCTTTCTCCAAAATGAAAATGAAA
39033227 ACAAAAATGA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
56 3 0.07
57 37 0.80
58 6 0.13
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (56 bp):
AGAAATGCAAACATTTGAAAATGAATATGGCTTTCTCCAAAATGAAAATGAAATAA
Found at i:39037580 original size:33 final size:33
Alignment explanation
Indices: 39037538--39037603 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
39037528 GAACCAAATC
*
39037538 CAAATTTTAACATTTTTATGTGGATCGAGATTA
1 CAAATTTTAACATTTTTATGTGGATCAAGATTA
*
39037571 CAAATTTTAACATTTTTATGTGGGTCAAGATTA
1 CAAATTTTAACATTTTTATGTGGATCAAGATTA
39037604 AACAAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (33 bp):
CAAATTTTAACATTTTTATGTGGATCAAGATTA
Found at i:39042229 original size:15 final size:15
Alignment explanation
Indices: 39042211--39042241 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
39042201 TAGAAAATTC
39042211 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
39042226 AAAAAAAGAAGAAAG
1 AAAAAAAGAAAAAAG
39042241 A
1 A
39042242 CTAGGCAAAG
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:39045960 original size:2 final size:2
Alignment explanation
Indices: 39045953--39045980 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39045943 TTGGAAACTA
39045953 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
39045981 TTTAGCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39047980 original size:37 final size:37
Alignment explanation
Indices: 39047939--39048011 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
39047929 TAATAACATC
39047939 AATTGTATCTAAAAATACCAATAAAAC-ATCTAAGTTG
1 AATTGTATCTAAAAATACCAATAAAACAATC-AAGTTG
39047976 AATTGTATCTAAAAATACCAATAAAACAATCAAGTT
1 AATTGTATCTAAAAATACCAATAAAACAATCAAGTT
39048012 CAATCAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
37 32 0.91
38 3 0.09
ACGTcount: A:0.51, C:0.14, G:0.07, T:0.29
Consensus pattern (37 bp):
AATTGTATCTAAAAATACCAATAAAACAATCAAGTTG
Found at i:39050608 original size:20 final size:20
Alignment explanation
Indices: 39050583--39050632 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
39050573 ATCAATTACG
**
39050583 AGTATCAATATTTTTAAAAA
1 AGTATCAATAAGTTTAAAAA
* **
39050603 AGTATCGATAAGTTTAAATC
1 AGTATCAATAAGTTTAAAAA
39050623 AGTATCAATA
1 AGTATCAATA
39050633 CTAAATTGCA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
AGTATCAATAAGTTTAAAAA
Found at i:39053114 original size:23 final size:26
Alignment explanation
Indices: 39053088--39053141 Score: 78
Period size: 23 Copynumber: 2.2 Consensus size: 26
39053078 GGGGAATAAT
*
39053088 ATTCAGAG-ATTTTTTT-ATACA-AC
1 ATTCAGAGAATTTTTTTGAGACATAC
39053111 ATTCAGAGAATTTTTTTGAGACATAC
1 ATTCAGAGAATTTTTTTGAGACATAC
39053137 ATTCA
1 ATTCA
39053142 AAAAAATTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 8 0.30
25 4 0.15
26 7 0.26
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (26 bp):
ATTCAGAGAATTTTTTTGAGACATAC
Found at i:39060476 original size:25 final size:26
Alignment explanation
Indices: 39060448--39060503 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
39060438 GAATAAGATT
*
39060448 GAGAGATTTTTTT-ATACA-ACATTCA
1 GAGA-ATTTTTTTGAGACATACATTCA
39060473 GAGAATTTTTTTGAGACATACATTCA
1 GAGAATTTTTTTGAGACATACATTCA
*
39060499 AAGAA
1 GAGAA
39060504 AATTCAAAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 8 0.30
25 8 0.30
26 11 0.41
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (26 bp):
GAGAATTTTTTTGAGACATACATTCA
Found at i:39060747 original size:24 final size:25
Alignment explanation
Indices: 39060708--39060754 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
39060698 TTTTATTATT
39060708 ATTTATATTTAGTTGTTTATTTTGAC
1 ATTTATATTTAGTTGTTT-TTTTGAC
39060734 ATTTA-ATTTA-TTGTTTTTTTG
1 ATTTATATTTAGTTGTTTTTTTG
39060755 TTTATTTATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 6 0.29
25 5 0.24
26 5 0.24
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (25 bp):
ATTTATATTTAGTTGTTTTTTTGAC
Found at i:39060846 original size:11 final size:12
Alignment explanation
Indices: 39060830--39060872 Score: 58
Period size: 11 Copynumber: 3.9 Consensus size: 12
39060820 TTATTTCAAC
39060830 ATTTAATTT-TT
1 ATTTAATTTATT
39060841 ATTTAATTTATT
1 ATTTAATTTATT
39060853 A-TT-ATTTATT
1 ATTTAATTTATT
39060863 ATTT-ATTTAT
1 ATTTAATTTAT
39060873 GTGTTGTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.27
11 19 0.63
12 3 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTAATTTATT
Found at i:39063423 original size:57 final size:57
Alignment explanation
Indices: 39063335--39063449 Score: 230
Period size: 57 Copynumber: 2.0 Consensus size: 57
39063325 TTGAGATAAT
39063335 TTGTGACTACCAGAGGCAAGAGAACATCCCCGAGGAGAAGTGGATGGCGATACTCTA
1 TTGTGACTACCAGAGGCAAGAGAACATCCCCGAGGAGAAGTGGATGGCGATACTCTA
39063392 TTGTGACTACCAGAGGCAAGAGAACATCCCCGAGGAGAAGTGGATGGCGATACTCTA
1 TTGTGACTACCAGAGGCAAGAGAACATCCCCGAGGAGAAGTGGATGGCGATACTCTA
39063449 T
1 T
39063450 AGTCTTTGAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.31, C:0.21, G:0.30, T:0.18
Consensus pattern (57 bp):
TTGTGACTACCAGAGGCAAGAGAACATCCCCGAGGAGAAGTGGATGGCGATACTCTA
Found at i:39065900 original size:17 final size:18
Alignment explanation
Indices: 39065863--39065902 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
39065853 TAACAAAATG
39065863 ATGCAGTGACAAAATAAA
1 ATGCAGTGACAAAATAAA
* *
39065881 ATGCAGTGATAATA-AAA
1 ATGCAGTGACAAAATAAA
39065898 ATGCA
1 ATGCA
39065903 TTAAAACTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.53, C:0.10, G:0.17, T:0.20
Consensus pattern (18 bp):
ATGCAGTGACAAAATAAA
Found at i:39081831 original size:95 final size:96
Alignment explanation
Indices: 39081641--39081861 Score: 236
Period size: 95 Copynumber: 2.3 Consensus size: 96
39081631 TGCAATGAAG
* * * ** *
39081641 TGAAGCTAACACATCCAATCTTATACCTCTAAATCTAAAGGGTCGGATTGAAACTACCATATCCA
1 TGAAGCTAACACATCCAATCTTATACCCCTAAATCCAAAGAGTAAGATTGAAACTACCACATCCA
* *
39081706 ATCTTATACCCCAAAATTCAAAGGGTCAGAT
66 ATCTTATACCCCAAAATCCAAAAGGTCAGAT
* * * * *
39081737 TGAAGCTACCACATCTAATCTTATACCCCTAAATCCAGATAG-AAGATTGAAGCTACCACATCCA
1 TGAAGCTAACACATCCAATCTTATACCCCTAAATCCAAAGAGTAAGATTGAAACTACCACATCCA
**
39081801 ATCTTATACCCTTAAATCCAGAAAGG-CAGAT
66 ATCTTATACCCCAAAATCCA-AAAGGTCAGAT
* *
39081832 TGAAG---ACACCATCCAATATTTTACCCCTAA
1 TGAAGCTAACA-CATCCAATCTTATACCCCTAA
39081862 TTGTGAGGGG
Statistics
Matches: 104, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
92 2 0.02
93 18 0.17
95 45 0.43
96 39 0.38
ACGTcount: A:0.38, C:0.26, G:0.11, T:0.25
Consensus pattern (96 bp):
TGAAGCTAACACATCCAATCTTATACCCCTAAATCCAAAGAGTAAGATTGAAACTACCACATCCA
ATCTTATACCCCAAAATCCAAAAGGTCAGAT
Found at i:39081887 original size:45 final size:45
Alignment explanation
Indices: 39081701--39082360 Score: 601
Period size: 45 Copynumber: 14.4 Consensus size: 45
39081691 AAACTACCAT
* * * * *
39081701 ATCCAATCTTATACCCCAAAATTCAAAGGGTCAGATTGAAGCTACCAC
1 ATCCAATCTTTTACCCC-TAATTCAGAGGGGCAGATTGAAGCCA-C-C
* * * ** * *
39081749 ATCTAATCTTATACCCCTAAATCCAGA-TAGAAGATTGAAGCTACCAC
1 ATCCAATCTTTTACCCCT-AATTCAGAGGGGCAGATTGAAGCCA-C-C
* * * ** *
39081796 ATCCAATCTTATACCCTTAAATCCAGAAAGGCAGATTGAAGACACC
1 ATCCAATCTTTTACCCCT-AATTCAGAGGGGCAGATTGAAGCCACC
* **
39081842 ATCCAATATTTTACCCCTAATTGTGAGGGGCAGATTGAAGCCACC
1 ATCCAATCTTTTACCCCTAATTCAGAGGGGCAGATTGAAGCCACC
* * * *
39081887 ATCTAATCTTTTACCCCTAAATCTAGAGGGGCAAATTGAAGCCACA
1 ATCCAATCTTTTACCCCTAATTC-AGAGGGGCAGATTGAAGCCACC
* * * *
39081933 ATCCAATGTTTTACCCCTAATCCAGAGGGACAGATTGAAGCCACT
1 ATCCAATCTTTTACCCCTAATTCAGAGGGGCAGATTGAAGCCACC
* * * * **
39081978 ATCTAATGTTTTACCCCTAATCCAGAGGGACAGATTGAAGTTACC
1 ATCCAATCTTTTACCCCTAATTCAGAGGGGCAGATTGAAGCCACC
* * *
39082023 ATCCAATCTTTCACACCTAAATCTAGAGGGGCAGATTGAAGCCACC
1 ATCCAATCTTTTACCCCTAATTC-AGAGGGGCAGATTGAAGCCACC
* *
39082069 ATCCAATCTTTTACCCCTAATCCAGAGGGGCAGATTGAAGCCATC
1 ATCCAATCTTTTACCCCTAATTCAGAGGGGCAGATTGAAGCCACC
* * * * * *
39082114 ATCCAATCTTTTACCCCGAAATTCAAATGGGTAAATTGAGGCCACC
1 ATCCAATCTTTTACCCC-TAATTCAGAGGGGCAGATTGAAGCCACC
*
39082160 ATCCAATCTTTTACCCCT-ATATCTAGAGGGGCAGATTAAAGCCACC
1 ATCCAATCTTTTACCCCTAAT-TC-AGAGGGGCAGATTGAAGCCACC
* * * *
39082206 ATCTAATCTTTTACCCCTAA-TCTAAAGGGGCATATTGAAGTCA-C
1 ATCCAATCTTTTACCCCTAATTC-AGAGGGGCAGATTGAAGCCACC
* * * * *
39082250 ATCTAATCTTTTACCCTTAAATCTAGAGGGACATATTGAAGCCACC
1 ATCCAATCTTTTACCCCTAATTC-AGAGGGGCAGATTGAAGCCACC
* * **
39082296 ATCCAATCTTTTACCCCTAAATCCAAAAAGGCAGATTGAAGCCA-C
1 ATCCAATCTTTTACCCCT-AATTCAGAGGGGCAGATTGAAGCCACC
*
39082341 ATCCAATCTTTTACGCCTAA
1 ATCCAATCTTTTACCCCTAA
39082361 ACCCAAAGGG
Statistics
Matches: 511, Mismatches: 90, Indels: 26
0.81 0.14 0.04
Matches are distributed among these distances:
44 24 0.05
45 214 0.42
46 194 0.38
47 46 0.09
48 33 0.06
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (45 bp):
ATCCAATCTTTTACCCCTAATTCAGAGGGGCAGATTGAAGCCACC
Found at i:39081925 original size:91 final size:91
Alignment explanation
Indices: 39081652--39082381 Score: 662
Period size: 91 Copynumber: 8.0 Consensus size: 91
39081642 GAAGCTAACA
* * * * * * * *
39081652 CATCCAATCTTATACCTCTAAATCTAAAGGGTCGGATTGAAACTACCATATCCAATCTTATACCC
1 CATCCAATCTTTTACCCCTAATTC-AAAGGGGCAGATTGAAGCCACC--ATCCAATCTTTTACCC
* * * * *
39081717 CAAAATTCAAAGGGTCAGATTGAAGCTACC
63 CTAAATCCAGAGGGGCAGATTGAAGCCA-C
* * * * ** * * *
39081747 ACATCTAATCTTATACCCCTAAATC-CAGATAGAAGATTGAAGCTACCACATCCAATCTTATACC
1 -CATCCAATCTTTTACCCCTAATTCAAAG-GGGCAGATTGAAGCCA-C-CATCCAATCTTTTACC
* ** *
39081811 CTTAAATCCAGAAAGGCAGATTGAAGACAC
62 CCTAAATCCAGAGGGGCAGATTGAAGCCAC
* *** *
39081841 CATCCAATATTTTACCCCTAATTGTGAGGGGCAGATTGAAGCCACCATCTAATCTTTTACCCCTA
1 CATCCAATCTTTTACCCCTAATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTA
* *
39081906 AATCTAGAGGGGCAAATTGAAGCCAC
66 AATCCAGAGGGGCAGATTGAAGCCAC
* * * * * * * *
39081932 AATCCAATGTTTTACCCCTAATCCAGAGGGACAGATTGAAGCCACTATCTAATGTTTTACCCCT-
1 CATCCAATCTTTTACCCCTAATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTA
* **
39081996 AATCCAGAGGGACAGATTGAAGTTAC
66 AATCCAGAGGGGCAGATTGAAGCCAC
* * * *
39082022 CATCCAATCTTTCACACCTAAATCTAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT
1 CATCCAATCTTTTACCCCTAATTC-AAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT
*
39082087 -AATCCAGAGGGGCAGATTGAAGCCAT
65 AAATCCAGAGGGGCAGATTGAAGCCAC
* * * * *
39082113 CATCCAATCTTTTACCCCGAAATTCAAATGGGTAAATTGAGGCCACCATCCAATCTTTTACCCCT
1 CATCCAATCTTTTACCCC-TAATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT
* * *
39082178 ATATCTAGAGGGGCAGATTAAAGCCAC
65 AAATCCAGAGGGGCAGATTGAAGCCAC
* * * * *
39082205 CATCTAATCTTTTACCCCTAA-TCTAAAGGGGCATATTGAAGTCA-CATCTAATCTTTTACCCTT
1 CATCCAATCTTTTACCCCTAATTC-AAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT
* * *
39082268 AAATCTAGAGGGACATATTGAAGCCAC
65 AAATCCAGAGGGGCAGATTGAAGCCAC
* ** *
39082295 CATCCAATCTTTTACCCCTAAATCCAAAAAGGCAGATTGAAGCCA-CATCCAATCTTTTACGCCT
1 CATCCAATCTTTTACCCCT-AATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCT
* * *
39082359 AAACCCAAAGGGACAGATTGAAG
65 AAATCCAGAGGGGCAGATTGAAG
39082382 TTACAACACC
Statistics
Matches: 522, Mismatches: 102, Indels: 25
0.80 0.16 0.04
Matches are distributed among these distances:
90 99 0.19
91 273 0.52
92 45 0.09
93 31 0.06
94 5 0.01
95 45 0.09
96 23 0.04
97 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.26
Consensus pattern (91 bp):
CATCCAATCTTTTACCCCTAATTCAAAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTA
AATCCAGAGGGGCAGATTGAAGCCAC
Found at i:39081972 original size:136 final size:136
Alignment explanation
Indices: 39081701--39082381 Score: 699
Period size: 136 Copynumber: 5.0 Consensus size: 136
39081691 AAACTACCAT
* * * * * * *
39081701 ATCCAATCTTATACCCCAAAATTCAAAGGGTCAGATTGAAGCTACCACATCTAATCTTATACCCC
1 ATCCAATCTTTTACCCC-TAATTCAGAGGGACAGATTGAAGCCA-C-CATCCAATCTTTTACCCC
* ** * * * * *
39081766 TAAATCCAGA-TAGAAGATTGAAGCTACCACATCCAATCTTATACCCTTAAATCCAGAAAGG-CA
63 TAAATCTAGAGGGGCAGATTGAAGCCA-CA-ATCCAATCTTTTACCCCT-AATCCAG-AGGGACA
*
39081829 GATTGAAGACACC
124 GATTGAAGCCACC
* ** * *
39081842 ATCCAATATTTTACCCCTAATTGTGAGGGGCAGATTGAAGCCACCATCTAATCTTTTACCCCTAA
1 ATCCAATCTTTTACCCCTAATTCAGAGGGACAGATTGAAGCCACCATCCAATCTTTTACCCCTAA
* *
39081907 ATCTAGAGGGGCAAATTGAAGCCACAATCCAATGTTTTACCCCTAATCCAGAGGGACAGATTGAA
66 ATCTAGAGGGGCAGATTGAAGCCACAATCCAATCTTTTACCCCTAATCCAGAGGGACAGATTGAA
*
39081972 GCCACT
131 GCCACC
* * * ** * *
39081978 ATCTAATGTTTTACCCCTAATCCAGAGGGACAGATTGAAGTTACCATCCAATCTTTCACACCTAA
1 ATCCAATCTTTTACCCCTAATTCAGAGGGACAGATTGAAGCCACCATCCAATCTTTTACCCCTAA
* *
39082043 ATCTAGAGGGGCAGATTGAAGCCACCATCCAATCTTTTACCCCTAATCCAGAGGGGCAGATTGAA
66 ATCTAGAGGGGCAGATTGAAGCCACAATCCAATCTTTTACCCCTAATCCAGAGGGACAGATTGAA
*
39082108 GCCATC
131 GCCACC
* * *
39082114 ATCCAATCTTTTACCCCGAAATTCAAATGGGTA-A-ATTGAGGCCACCATCCAATCTTTTACCCC
1 ATCCAATCTTTTACCCC-TAATTCAGA-GGG-ACAGATTGAAGCCACCATCCAATCTTTTACCCC
* * * * * * * *
39082177 TATATCTAGAGGGGCAGATTAAAGCCACCATCTAATCTTTTACCCCTAATCTAAAGGGGCATATT
63 TAAATCTAGAGGGGCAGATTGAAGCCACAATCCAATCTTTTACCCCTAATCCAGAGGGACAGATT
*
39082242 GAAGTCA-C
128 GAAGCCACC
* * * *
39082250 ATCTAATCTTTTACCCTTAAATCTAGAGGGACATATTGAAGCCACCATCCAATCTTTTACCCCTA
1 ATCCAATCTTTTACCCCTAATTC-AGAGGGACAGATTGAAGCCACCATCCAATCTTTTACCCCTA
* * ** * * *
39082315 AATCCAAAAAGGCAGATTGAAGCCAC-ATCCAATCTTTTACGCCTAAACCCAAAGGGACAGATTG
65 AATCTAGAGGGGCAGATTGAAGCCACAATCCAATCTTTTACCCCT-AATCCAGAGGGACAGATTG
39082379 AAG
129 AAG
39082382 TTACAACACC
Statistics
Matches: 458, Mismatches: 73, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
134 1 0.00
135 27 0.06
136 240 0.52
137 110 0.24
138 32 0.07
139 13 0.03
140 20 0.04
141 15 0.03
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (136 bp):
ATCCAATCTTTTACCCCTAATTCAGAGGGACAGATTGAAGCCACCATCCAATCTTTTACCCCTAA
ATCTAGAGGGGCAGATTGAAGCCACAATCCAATCTTTTACCCCTAATCCAGAGGGACAGATTGAA
GCCACC
Found at i:39083325 original size:11 final size:11
Alignment explanation
Indices: 39083309--39083356 Score: 51
Period size: 11 Copynumber: 4.0 Consensus size: 11
39083299 TTATTTCAGC
39083309 ATTTAATTTTT
1 ATTTAATTTTT
39083320 ATTTAATTTATT
1 ATTTAATTT-TT
*
39083332 ATTATTTATTATTT
1 A-T-TTAATT-TTT
39083346 ATTTAATTTTT
1 ATTTAATTTTT
39083357 TTACCTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
11 12 0.39
12 8 0.26
13 2 0.06
14 8 0.26
15 1 0.03
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
ATTTAATTTTT
Found at i:39084621 original size:40 final size:40
Alignment explanation
Indices: 39084544--39084634 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 40
39084534 GCCTAAAGCT
* *
39084544 ATTTTGACTTGTTTGAAAAACATTTTGATGTGTTAAAATG
1 ATTTTGACTTGGTTGAAAAACATTTTGATGTGTTAAAATA
**
39084584 ATTTTGACTTGGTTG-AAATTATTTTGACT-TGTCTAAAATA
1 ATTTTGACTTGGTTGAAAAACATTTTGA-TGTGT-TAAAATA
*
39084624 ATTTTAACTTG
1 ATTTTGACTTG
39084635 ATTTTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 13 0.30
40 31 0.70
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.47
Consensus pattern (40 bp):
ATTTTGACTTGGTTGAAAAACATTTTGATGTGTTAAAATA
Found at i:39084622 original size:20 final size:19
Alignment explanation
Indices: 39084543--39084634 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 19
39084533 GGCCTAAAGC
*
39084543 TATTTTGACTTGTTTGAAAAA
1 TATTTTGACTTG-TT-AAAAT
*
39084564 CATTTTGA-TGTGTTAAAAT
1 TATTTTGACT-TGTTAAAAT
* *
39084583 GATTTTGACTTGGTTGAAAT
1 TATTTTGACTT-GTTAAAAT
39084603 TATTTTGACTTGTCTAAAAT
1 TATTTTGACTTGT-TAAAAT
* *
39084623 AATTTTAACTTG
1 TATTTTGACTTG
39084635 ATTTTAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
19 14 0.24
20 36 0.61
21 9 0.15
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (19 bp):
TATTTTGACTTGTTAAAAT
Found at i:39084754 original size:22 final size:23
Alignment explanation
Indices: 39084726--39084776 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
39084716 TACTTTGTCA
39084726 ATTTTAACTTA-TAT-TCTAAAAC
1 ATTTTAACTTATTATATC-AAAAC
* *
39084748 ATTTTAATTTATTATATCAAAAT
1 ATTTTAACTTATTATATCAAAAC
39084771 ATTTTA
1 ATTTTA
39084777 TCAAATAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 13 0.52
24 2 0.08
ACGTcount: A:0.41, C:0.08, G:0.00, T:0.51
Consensus pattern (23 bp):
ATTTTAACTTATTATATCAAAAC
Found at i:39087674 original size:24 final size:23
Alignment explanation
Indices: 39087644--39087722 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 23
39087634 CCTGCAACTT
39087644 CTACCGATACATCAGTACTAAAAA
1 CTACCGATACAT-AGTACTAAAAA
* * **
39087668 CTACCGATAC-TTGTAAT-TCAA
1 CTACCGATACATAGTACTAAAAA
*
39087689 CTACCTATACATTAGTACTAAAAA
1 CTACCGATACA-TAGTACTAAAAA
*
39087713 TTACCGATAC
1 CTACCGATAC
39087723 TTGTAATTCA
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
21 11 0.27
22 4 0.10
23 6 0.15
24 20 0.49
ACGTcount: A:0.41, C:0.24, G:0.08, T:0.28
Consensus pattern (23 bp):
CTACCGATACATAGTACTAAAAA
Found at i:39087692 original size:21 final size:21
Alignment explanation
Indices: 39087666--39087743 Score: 84
Period size: 21 Copynumber: 3.6 Consensus size: 21
39087656 CAGTACTAAA
39087666 AACTACCGATACTTGTAATTC
1 AACTACCGATACTTGTAATTC
* * **
39087687 AACTACCTATACATTAGTACTAAA
1 AACTACCGATAC-TT-GTAAT-TC
*
39087711 AATTACCGATACTTGTAATTC
1 AACTACCGATACTTGTAATTC
39087732 AACTACCGATAC
1 AACTACCGATAC
39087744 AACCCAAGTC
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
21 22 0.50
22 6 0.14
23 6 0.14
24 10 0.23
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (21 bp):
AACTACCGATACTTGTAATTC
Found at i:39087699 original size:45 final size:45
Alignment explanation
Indices: 39087644--39087744 Score: 175
Period size: 45 Copynumber: 2.2 Consensus size: 45
39087634 CCTGCAACTT
39087644 CTACCGATACATCAGTACTAAAAACTACCGATACTTGTAATTCAA
1 CTACCGATACATCAGTACTAAAAACTACCGATACTTGTAATTCAA
* * *
39087689 CTACCTATACATTAGTACTAAAAATTACCGATACTTGTAATTCAA
1 CTACCGATACATCAGTACTAAAAACTACCGATACTTGTAATTCAA
39087734 CTACCGATACA
1 CTACCGATACA
39087745 ACCCAAGTCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.40, C:0.24, G:0.08, T:0.29
Consensus pattern (45 bp):
CTACCGATACATCAGTACTAAAAACTACCGATACTTGTAATTCAA
Found at i:39088339 original size:24 final size:24
Alignment explanation
Indices: 39088312--39088405 Score: 134
Period size: 24 Copynumber: 3.9 Consensus size: 24
39088302 CATAGACAAC
** *
39088312 TTAGCTCACACGAGCCCAGAATTG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
39088336 TTAGCTCTTACGAGTCCTGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
39088360 TTAGCTCTTATGAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
39088384 TTAGCTCTTACGAGCCCAGAAT
1 TTAGCTCTTACGAGCCCAGAAT
39088406 CAGAATAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:39088436 original size:27 final size:27
Alignment explanation
Indices: 39088399--39088463 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
39088389 TCTTACGAGC
39088399 CCAGAATCAGAATAATGCTCTTTTGAG
1 CCAGAATCAGAATAATGCTCTTTTGAG
39088426 CCAGAATCAGAATAATGCTCTTTTGAG
1 CCAGAATCAGAATAATGCTCTTTTGAG
39088453 CCAGAATCAGA
1 CCAGAATCAGA
39088464 TTACTCCTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (27 bp):
CCAGAATCAGAATAATGCTCTTTTGAG
Found at i:39089198 original size:8 final size:8
Alignment explanation
Indices: 39089185--39089213 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
39089175 CGGCTTGAAG
39089185 AAGAAGAA
1 AAGAAGAA
39089193 AAGAAGAA
1 AAGAAGAA
39089201 AAGAAGAA
1 AAGAAGAA
39089209 AAGAA
1 AAGAA
39089214 ATTGAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AAGAAGAA
Found at i:39090933 original size:30 final size:30
Alignment explanation
Indices: 39090899--39090969 Score: 92
Period size: 30 Copynumber: 2.4 Consensus size: 30
39090889 GCTTCTGTCG
* *
39090899 ATTTGAGGTGTGTTTCT-TACTGTGCTACAT
1 ATTTGATGTGTGTTTCTGT-CTATGCTACAT
*
39090929 ATTTGTTGTGTGTTTCTGTCTATGCTACAT
1 ATTTGATGTGTGTTTCTGTCTATGCTACAT
39090959 -TTTGATGTGTG
1 ATTTGATGTGTG
39090970 ACGGTGTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 10 0.28
30 25 0.69
31 1 0.03
ACGTcount: A:0.14, C:0.11, G:0.24, T:0.51
Consensus pattern (30 bp):
ATTTGATGTGTGTTTCTGTCTATGCTACAT
Found at i:39094266 original size:3 final size:3
Alignment explanation
Indices: 39094254--39094292 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
39094244 ACTTATTCGA
39094254 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
39094293 TTAAAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:39095653 original size:22 final size:22
Alignment explanation
Indices: 39095606--39095661 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
39095596 ATTTTTTTTT
* *
39095606 TTTTTTAAATCAAAAGTTTTCTC
1 TTTTTTAAAACAAAAG-TTACTC
39095629 TTTTTTAAAACAAAA-TTACTAC
1 TTTTTTAAAACAAAAGTTACT-C
39095651 TTTTCTTAAAA
1 TTTT-TTAAAA
39095662 AATAAAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 4 0.14
22 5 0.17
23 20 0.69
ACGTcount: A:0.38, C:0.12, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTTAAAACAAAAGTTACTC
Found at i:39095819 original size:145 final size:145
Alignment explanation
Indices: 39095646--39095911 Score: 412
Period size: 145 Copynumber: 1.8 Consensus size: 145
39095636 AAACAAAATT
* * * *
39095646 ACTACTTTTCTTAAAAAATAAAATTTTTATTTCGAACTAGTTAAAAAGA-ATCAAATTTTATTTA
1 ACTACTTTACTTAAAAAATAAAACTTTTATTTCGAAATAGTTAAAAA-ATATCAAACTTTATTTA
39095710 AAAATTTAAACTTTTCTCTTT-AAAATGACTAAAAACAGATTTTTATTTTTAAAAATCTAAACTT
65 AAAATTTAAACTTTT-TCTTTAAAAATGACTAAAAACAGATTTTTATTTTTAAAAATCTAAACTT
39095774 TCTTTTTTTTTTTAAAA
129 TCTTTTTTTTTTTAAAA
*
39095791 ACTACTTTACTT-AAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAATATCAAACTTTGTTTA
1 ACTACTTTACTTAAAAAAT-AAAACTTTTATTTCGAAATAGTTAAAAAATATCAAACTTTATTTA
* * *
39095855 AAAATTTAAACTTTTTCTTTAAAAATGCCTAAAAATATATTTTTATTTTTAAAAATC
65 AAAATTTAAACTTTTTCTTTAAAAATGACTAAAAACAGATTTTTATTTTTAAAAATC
39095912 AAATATTTTT
Statistics
Matches: 110, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
144 12 0.11
145 98 0.89
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.44
Consensus pattern (145 bp):
ACTACTTTACTTAAAAAATAAAACTTTTATTTCGAAATAGTTAAAAAATATCAAACTTTATTTAA
AAATTTAAACTTTTTCTTTAAAAATGACTAAAAACAGATTTTTATTTTTAAAAATCTAAACTTTC
TTTTTTTTTTTAAAA
Found at i:39095856 original size:51 final size:49
Alignment explanation
Indices: 39095801--39095957 Score: 126
Period size: 51 Copynumber: 3.2 Consensus size: 49
39095791 ACTACTTTAC
39095801 TTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAATATCAAACTTTGT
1 TTAAAAATC-AAACTTTT-TTTCGAAATAGTTAAAAAATATCAAACTTTGT
* * * * *** *
39095852 TTAAAAATTTAAACTTTTTCTT-TAAAAATGCCT-AAAAATAT-ATTTTTATTT
1 TTAAAAA-TCAAACTTTTT-TTCGAAATA-G-TTAAAAAATATCAAACTT-TGT
* *
39095903 TTAAAAATCAAA-TATTTTTCGAAATAATTAAAAAA-ATCAAACTTTGT
1 TTAAAAATCAAACTTTTTTTCGAAATAGTTAAAAAATATCAAACTTTGT
39095950 TTAAAAAT
1 TTAAAAAT
39095958 TTAGATTTTT
Statistics
Matches: 80, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
47 13 0.16
48 10 0.12
49 8 0.10
50 12 0.15
51 35 0.44
52 2 0.03
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (49 bp):
TTAAAAATCAAACTTTTTTTCGAAATAGTTAAAAAATATCAAACTTTGT
Found at i:39095944 original size:98 final size:102
Alignment explanation
Indices: 39095801--39096015 Score: 330
Period size: 98 Copynumber: 2.1 Consensus size: 102
39095791 ACTACTTTAC
* *
39095801 TTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAATATCAAACTTTGTTTAAAAATTTAAAC
1 TTAAAAATCAAAACTATTATTTCGAAATAATTAAAAAATATCAAACTTTGTTTAAAAATTTAAAC
*
39095866 TTTTTCTTTAAAAATGCCTAAAAATATATTTTTATTT
66 TTTTTCTTTAAAAATGCCTAAAAATAAATTTTTATTT
* *
39095903 TTAAAAATC-AAA-TATT-TTTCGAAATAATTAAAAAA-ATCAAACTTTGTTTAAAAATTTAGAT
1 TTAAAAATCAAAACTATTATTTCGAAATAATTAAAAAATATCAAACTTTGTTTAAAAATTTAAAC
* *
39095964 TTTTTCTTTTAAAATGCTTAAAAATAAATTTTTATTT
66 TTTTTCTTTAAAAATGCCTAAAAATAAATTTTTATTT
*
39096001 TTAAAAATCTAAACT
1 TTAAAAATCAAAACT
39096016 TTCTTTTTTT
Statistics
Matches: 104, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
98 67 0.64
99 21 0.20
100 4 0.04
101 3 0.03
102 9 0.09
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.43
Consensus pattern (102 bp):
TTAAAAATCAAAACTATTATTTCGAAATAATTAAAAAATATCAAACTTTGTTTAAAAATTTAAAC
TTTTTCTTTAAAAATGCCTAAAAATAAATTTTTATTT
Found at i:39096013 original size:22 final size:22
Alignment explanation
Indices: 39095981--39096031 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 22
39095971 TTTAAAATGC
39095981 TTAAAAATAAA-TTT-TTATTT
1 TTAAAAATAAACTTTCTTATTT
*
39096001 TTAAAAATCTAAACTTTCTTTTTT
1 TTAAAAA--TAAACTTTCTTATTT
39096025 TTAAAAA
1 TTAAAAA
39096032 AAAATCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 7 0.27
22 4 0.15
23 3 0.12
24 12 0.46
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAAAAATAAACTTTCTTATTT
Found at i:39096402 original size:3 final size:3
Alignment explanation
Indices: 39096394--39096445 Score: 59
Period size: 3 Copynumber: 17.3 Consensus size: 3
39096384 CATGAAACCC
* * * * *
39096394 TAA TAA TAA TAA TAA TAG TAA TAG TAA TAG TAA TAG TAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39096442 TAA T
1 TAA T
39096446 TTAAGCTCTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:39098871 original size:14 final size:14
Alignment explanation
Indices: 39098852--39098879 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39098842 GCTGCTTCAA
39098852 AAGAATGTTTGTCT
1 AAGAATGTTTGTCT
39098866 AAGAATGTTTGTCT
1 AAGAATGTTTGTCT
39098880 GCTTTCAAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.43
Consensus pattern (14 bp):
AAGAATGTTTGTCT
Found at i:39103343 original size:27 final size:27
Alignment explanation
Indices: 39103313--39103371 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
39103303 ATTGTTATTG
* *
39103313 AATTAGCGATTTAATATA-AATTTATGT
1 AATTA-CGATTTAATATATAATATATAT
**
39103340 AATTATTATTTAATATATAATATATAT
1 AATTACGATTTAATATATAATATATAT
39103367 AATTA
1 AATTA
39103372 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 10 0.37
27 17 0.63
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
AATTACGATTTAATATATAATATATAT
Found at i:39103378 original size:27 final size:27
Alignment explanation
Indices: 39103321--39103391 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
39103311 TGAATTAGCG
* *
39103321 ATTTAATATA-AATTTATGTAATTATT
1 ATTTAATATATAATATATATAATTATT
39103347 ATTTAATATATAATATATATAATTATT
1 ATTTAATATATAATATATATAATTATT
* *
39103374 -TTTTATAACATAATATAT
1 ATTTAAT-ATATAATATAT
39103392 TTAAGGTTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
26 15 0.38
27 24 0.62
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (27 bp):
ATTTAATATATAATATATATAATTATT
Found at i:39103579 original size:24 final size:23
Alignment explanation
Indices: 39103543--39103591 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
39103533 TGTAAAATTT
* *
39103543 TTAAAATATATATTAAAAATAAA
1 TTAAAAAATATATAAAAAATAAA
*
39103566 TTAAAAAATCATATAAAAAATCAA
1 TTAAAAAAT-ATATAAAAAATAAA
39103590 TT
1 TT
39103592 TCAGTAAGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
TTAAAAAATATATAAAAAATAAA
Found at i:39104590 original size:30 final size:33
Alignment explanation
Indices: 39104540--39104603 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 33
39104530 TAATAAAATT
*
39104540 AAAATTACATTTTAAATTTTTTTAAAATGATAA
1 AAAATTACATTTTAAATTTTTTAAAAATGATAA
*
39104573 AAAATTA-A-TTT-AATTTTTTAAAAATTATAA
1 AAAATTACATTTTAAATTTTTTAAAAATGATAA
39104603 A
1 A
39104604 GGTAATAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 18 0.62
31 3 0.10
32 1 0.03
33 7 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
AAAATTACATTTTAAATTTTTTAAAAATGATAA
Found at i:39105743 original size:59 final size:60
Alignment explanation
Indices: 39105676--39105789 Score: 144
Period size: 59 Copynumber: 1.9 Consensus size: 60
39105666 TTGGAGACCA
* * *
39105676 ATAATTAAA-TTATA-TATTTTTATGATAGTAAAAATATGATTTTATTATT-TTAATAATTT
1 ATAATTAAATTTATATTATTTTTA--AAAATAAAAATATAATTTTATTATTATTAATAATTT
* *
39105735 ATAATTAAATTTTTATTATTTTTAAAAATTAAAATATAATTTTATTATTATTAAT
1 ATAATTAAATTTATATTATTTTTAAAAATAAAAATATAATTTTATTATTATTAAT
39105790 TTAAAAATCA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
59 30 0.64
60 9 0.19
61 8 0.17
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (60 bp):
ATAATTAAATTTATATTATTTTTAAAAATAAAAATATAATTTTATTATTATTAATAATTT
Found at i:39105788 original size:29 final size:29
Alignment explanation
Indices: 39105706--39105789 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 29
39105696 TATGATAGTA
* *
39105706 AAAATATGATTTTATTATTTTAATAATTT
1 AAAATATAATTTTATTATTTTAATAAATT
*
39105735 ATAAT-TAAATTTTTATTATTTTTAA-AAATT
1 AAAATAT-AA-TTTTATTA-TTTTAATAAATT
39105765 AAAATATAATTTTATTATTATTAAT
1 AAAATATAATTTTATTATT-TTAAT
39105790 TTAAAAATCA
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
28 3 0.07
29 17 0.38
30 18 0.40
31 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (29 bp):
AAAATATAATTTTATTATTTTAATAAATT
Found at i:39105994 original size:18 final size:16
Alignment explanation
Indices: 39105963--39105996 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
39105953 TTTCCAATAA
39105963 AAATTTCTAAATTTCC
1 AAATTTCTAAATTTCC
39105979 AAATTTCCTAAAATTTCC
1 AAATTT-CT-AAATTTCC
39105997 CCTTCCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 2 0.12
18 8 0.50
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (16 bp):
AAATTTCTAAATTTCC
Found at i:39121033 original size:6 final size:5
Alignment explanation
Indices: 39120969--39121018 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
39120959 AAGGGCATTT
*
39120969 AAAA- AAAAG AAAAG AAAAG AAAAG AAAAC AAGAAG AAGAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG AAAA
39121019 AGGAAGAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
4 4 0.10
5 28 0.67
6 10 0.24
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:39122998 original size:49 final size:49
Alignment explanation
Indices: 39122878--39123254 Score: 305
Period size: 49 Copynumber: 7.6 Consensus size: 49
39122868 GGAAACATAG
* * * * *
39122878 AGATATGAATGGAAAGGTTGAGGCCGCAATGGT-ATACCCGGTACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGA-ATCTGGTACCAT-GA
* * *
39122928 AGATATGACGAG-AAGGATTGAGGCCGCAACGATGAATCTGGTACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAATCTGGTACCATGA
* *
39122977 AGATATGAAGGGAAAGGTTGAGGACGCAACGGGGAATCTGGTACCATGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCTGGTACCATGA
** * * * * *
39123026 AGATATGAAGGGAAAGGTTGAGGTTGAAACGATGAACCCGGTACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCTGGTACCAT-GA
* ** * * *
39123076 AGATGTGATTGG-AAGGATTGAGGTCGTAACGGGGAATCTGGTACCATGA
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAATCTGGTACCATGA
* * * * * ** *
39123125 AGATATGAAGGGAAAGGTTGAGGTCGTAACTGCGAACCAAGTACCTTAGA
1 AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCTGGTACCAT-GA
* * * *
39123175 AGATGTGATGGG-AAGGATTGAGGCCGCAACGGCGAATCTTGTACCAT-A
1 AGATATGAAGGGAAAGG-TTGAGGCCGCAACGGTGAATCTGGTACCATGA
* * *
39123223 GAGATACGGAGGGAAAGGTTGAAGCCGCAACG
1 -AGATATGAAGGGAAAGGTTGAGGCCGCAACG
39123255 ACAAACTTTA
Statistics
Matches: 263, Mismatches: 54, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.00
49 148 0.56
50 113 0.43
51 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.19
Consensus pattern (49 bp):
AGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAATCTGGTACCATGA
Found at i:39123078 original size:99 final size:99
Alignment explanation
Indices: 39122878--39123301 Score: 360
Period size: 99 Copynumber: 4.3 Consensus size: 99
39122868 GGAAACATAG
* * * * * * * *
39122878 AGATATGAATGGAAAGG-TTGAGGCCGCAA-TGGTATACCCGGTACCTTAGAAGATATGACGAG-
1 AGATATGAA-GGGAAGGATTGAGGCCGCAACGGGGA-ATCTGGTACCAT-GAAGATATGAAGGGA
* * * * *
39122940 AAGGATTGAGGCCGCAACGATGAATCTGGTACCAT-GA
63 AAGG-TTGAGGTCGAAACGATGAACCAGGTACCTTAGA
*
39122977 AGATATGAAGGGAAAGG-TTGAGGACGCAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAA
1 AGATATGAAGGG-AAGGATTGAGGCCGCAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAA
* *
39123041 GGTTGAGGTTGAAACGATGAACCCGGTACCTTAGA
65 GGTTGAGGTCGAAACGATGAACCAGGTACCTTAGA
* ** * *
39123076 AGATGTGATTGGAAGGATTGAGGTCGTAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAAG
1 AGATATGAAGGGAAGGATTGAGGCCGCAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAAG
* * *
39123141 GTTGAGGTCGTAACTG-CGAACCAAGTACCTTAGA
66 GTTGAGGTCGAAAC-GATGAACCAGGTACCTTAGA
* * * * * *
39123175 AGATGTGATGGGAAGGATTGAGGCCGCAACGGCGAATCTTGTACCAT-AGAGATACGGAGGGAAA
1 AGATATGAAGGGAAGGATTGAGGCCGCAACGGGGAATCTGGTACCATGA-AGATATGAAGGGAAA
* * * ** ****
39123239 GGTTGAAGCCGCAACGACAAACTTTATACCTTAG-
65 GGTTGAGGTCGAAACGATGAACCAGGTACCTTAGA
* *
39123273 AGATATGAAGGGAAAGATTGAGGCTGCAA
1 AGATATGAAGGGAAGGATTGAGGCCGCAA
39123302 TGACGAATCT
Statistics
Matches: 273, Mismatches: 44, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
98 69 0.25
99 200 0.73
100 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (99 bp):
AGATATGAAGGGAAGGATTGAGGCCGCAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAAG
GTTGAGGTCGAAACGATGAACCAGGTACCTTAGA
Found at i:39123146 original size:148 final size:148
Alignment explanation
Indices: 39122878--39123147 Score: 400
Period size: 148 Copynumber: 1.8 Consensus size: 148
39122868 GGAAACATAG
* * * *
39122878 AGATATGAATGGAAAGGTTGAGGCCGCAATGGTATACCCGGTACCTTAGAAGATATGACGAGAAG
1 AGATATGAAGGGAAAGGTTGAGGCCGAAACGATATACCCGGTACCTTAGAAGATATGACGAGAAG
*
39122943 GATTGAGGCCGCAACGATGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGACGCAACG
66 GATTGAGGCCGCAACGAGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGACGCAACG
39123008 GGGAATCTGGTACCATGA
131 GGGAATCTGGTACCATGA
** * *
39123026 AGATATGAAGGGAAAGGTTGAGGTTGAAACGATGA-ACCCGGTACCTTAGAAGATGTGATTG-GA
1 AGATATGAAGGGAAAGGTTGAGGCCGAAACGAT-ATACCCGGTACCTTAGAAGATATGA-CGAGA
* * *
39123089 AGGATTGAGGTCGTAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGG
64 AGGATTGAGGCCGCAACGAGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGG
39123148 TCGTAACTGC
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
148 106 0.98
149 2 0.02
ACGTcount: A:0.34, C:0.12, G:0.34, T:0.20
Consensus pattern (148 bp):
AGATATGAAGGGAAAGGTTGAGGCCGAAACGATATACCCGGTACCTTAGAAGATATGACGAGAAG
GATTGAGGCCGCAACGAGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGACGCAACG
GGGAATCTGGTACCATGA
Found at i:39123169 original size:148 final size:149
Alignment explanation
Indices: 39122873--39123205 Score: 397
Period size: 148 Copynumber: 2.2 Consensus size: 149
39122863 ACTGAGGAAA
* * * *
39122873 CATAG-AGATATGAATGGAAAGGTTGAGGCCGCAATGGTATACCCGGTACCTTAGAAGATATGAC
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGAAACGATATACCCGGTACCTTAGAAGATATGAC
*
39122937 GAGAAGGATTGAGGCCGCAACGATGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGAC
66 GAGAAGGATTGAGGCCGCAACGAGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGAC
* * **
39123002 GCAACGGGGAATCTGGTAC
131 GCAACGGCGAACCAAGTAC
** *
39123021 CAT-GAAGATATGAAGGGAAAGGTTGAGGTTGAAACGATGA-ACCCGGTACCTTAGAAGATGTGA
1 CATAGAAGATATGAAGGGAAAGGTTGAGGCCGAAACGAT-ATACCCGGTACCTTAGAAGATATGA
* * * *
39123084 TTG-GAAGGATTGAGGTCGTAACGGGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGG
65 -CGAGAAGGATTGAGGCCGCAACGAGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGG
* * *
39123148 TCGTAACTGCGAACCAAGTAC
129 ACGCAACGGCGAACCAAGTAC
* * * *
39123169 CTTAGAAGATGTGATGGG-AAGGATTGAGGCCGCAACG
1 CATAGAAGATATGAAGGGAAAGG-TTGAGGCCGAAACG
39123206 GCGAATCTTG
Statistics
Matches: 155, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
147 1 0.01
148 129 0.83
149 25 0.16
ACGTcount: A:0.33, C:0.14, G:0.33, T:0.20
Consensus pattern (149 bp):
CATAGAAGATATGAAGGGAAAGGTTGAGGCCGAAACGATATACCCGGTACCTTAGAAGATATGAC
GAGAAGGATTGAGGCCGCAACGAGGAATCTGGTACCATGAAGATATGAAGGGAAAGGTTGAGGAC
GCAACGGCGAACCAAGTAC
Found at i:39123317 original size:49 final size:49
Alignment explanation
Indices: 39122875--39123317 Score: 195
Period size: 49 Copynumber: 9.0 Consensus size: 49
39122865 TGAGGAAACA
* * * * * *
39122875 TAGAGATATGAATGGAAAGGTTGAGGCCGCAATG--GTATACCCGGTACCT
1 TAGAGATATGAAGGGAAAGATTGAGGCCGCAACGACGAAT-CTC-ATACCT
* * * * ** *
39122924 TAGAAGATATGACGAGAAGGATTGAGGCCGCAACGATGAATCTGGTACCA
1 TAG-AGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTCATACCT
* * ** ** *
39122974 T-GAAGATATGAAGGGAAAGGTTGAGGACGCAACGGGGAATCTGGTACCA
1 TAG-AGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTCATACCT
* ** * * * *
39123023 T-GAAGATATGAAGGGAAAGGTTGAGGTTGAAACGATGAA-CCCGGTACCT
1 TAG-AGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTC-ATACCT
* ** * * * ** ** *
39123072 TAGAAGATGTGATTGGAAGGATTGAGGTCGTAACGGGGAATCTGGTACCA
1 TAG-AGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTCATACCT
* * *
39123122 T-GAAGATATGAAGGGAAAGGTTGAGGTCGTAACTG-CGAA-C-CAAGTACCT
1 TAG-AGATATGAAGGGAAAGATTGAGGCCGCAAC-GACGAATCTC-A-TACCT
* * * * ** *
39123171 TAGAAGATGTGATGGGAAGGATTGAGGCCGCAACGGCGAATCTTGTACCA
1 TAG-AGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTCATACCT
* * * * * *
39123221 TAGAGATACGGAGGGAAAGGTTGAAGCCGCAACGAC-AAACTTTATACCT
1 TAGAGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATC-TCATACCT
* *
39123270 TAGAGATATGAAGGGAAAGATTGAGGCTGCAATGACGAATCTCATACC
1 TAGAGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTCATACC
39123318 CTAAAGATGA
Statistics
Matches: 305, Mismatches: 74, Indels: 30
0.75 0.18 0.07
Matches are distributed among these distances:
48 5 0.02
49 187 0.61
50 107 0.35
51 3 0.01
52 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.20
Consensus pattern (49 bp):
TAGAGATATGAAGGGAAAGATTGAGGCCGCAACGACGAATCTCATACCT
Found at i:39123673 original size:39 final size:39
Alignment explanation
Indices: 39123550--39123723 Score: 138
Period size: 42 Copynumber: 4.2 Consensus size: 39
39123540 CACCAATATC
* * * *
39123550 TTACCCCAATCATGGGGCAGATTGAAG-CATCCAGTCTT
1 TTACCCCTATTATGAGGCAGATTGAAGCCATCCAATCTT
* *
39123588 TTA-CCCTAATTA-GAGGGCAGATTGAAAACATCATCCAATCTC
1 TTACCCCT-ATTATGA-GGCAGATTG-AAGC--CATCCAATCTT
39123630 TTACCCCTATTATGAGGCAGATTGAAGCCATCCAATCTT
1 TTACCCCTATTATGAGGCAGATTGAAGCCATCCAATCTT
* *
39123669 TTACCCCTAAGTCAAGAGAGGCAGATTGAAGCCACCATCCAATCTT
1 TTACCCCT-A-T-TA-TGAGGCAGATTGAAG---CCATCCAATCTT
*
39123715 TTACTCCTA
1 TTACCCCTA
39123724 GGTCAAGAGA
Statistics
Matches: 110, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
37 4 0.04
38 15 0.14
39 20 0.18
40 1 0.01
41 4 0.04
42 26 0.24
43 20 0.18
45 1 0.01
46 19 0.17
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (39 bp):
TTACCCCTATTATGAGGCAGATTGAAGCCATCCAATCTT
Found at i:39123729 original size:46 final size:45
Alignment explanation
Indices: 39123577--39123799 Score: 205
Period size: 46 Copynumber: 5.1 Consensus size: 45
39123567 CAGATTGAAG
* * ** *
39123577 CATCCAGTCTTTTACCCTAA-T-TAGAG-GGCAGATTGAAAACAT
1 CATCCAATCTTTTACCCTAAGTCAAGAGAGGCAGATTGAAGCCAC
* * *
39123619 CATCCAATCTCTTACCCCT-A-T-TA-TGAGGCAGATTGAAG---C
1 CATCCAATCTTTTA-CCCTAAGTCAAGAGAGGCAGATTGAAGCCAC
39123658 CATCCAATCTTTTACCCCTAAGTCAAGAGAGGCAGATTGAAGCCAC
1 CATCCAATCTTTTA-CCCTAAGTCAAGAGAGGCAGATTGAAGCCAC
* *
39123704 CATCCAATCTTTTACTCCTAGGTCAAGAGAGGCAGATTAAAGCCAC
1 CATCCAATCTTTTAC-CCTAAGTCAAGAGAGGCAGATTGAAGCCAC
* * * *
39123750 TATCCAATCTTTTACCCTTAAAATCAAGAGGGGCAGATTGAAGCTAC
1 CATCCAATCTTTTACCC-T-AAGTCAAGAGAGGCAGATTGAAGCCAC
39123797 CAT
1 CAT
39123800 ATCACAGAAG
Statistics
Matches: 152, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
39 18 0.12
40 1 0.01
41 2 0.01
42 28 0.18
43 18 0.12
45 3 0.02
46 58 0.38
47 24 0.16
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (45 bp):
CATCCAATCTTTTACCCTAAGTCAAGAGAGGCAGATTGAAGCCAC
Found at i:39124510 original size:429 final size:431
Alignment explanation
Indices: 39123956--39124769 Score: 1282
Period size: 429 Copynumber: 1.9 Consensus size: 431
39123946 AGTGAAGCTA
*
39123956 CAACAATAAATTTTATCTTTTTGAAGTTGCTATAGGGTAAGAAAAATCACGACACTAAATCCTAT
1 CAACAATAAATTTTATCTTTTTGAAGTTGCAATAGGGTAAGAAAAATCACGACACTAAATCCTAT
*
39124021 CTTCCTAAAGTTTAGAGAAGCAGATATAGTGAAATGAGTAACCAATAAAGCGAAAGAGCGGGCTA
66 CTTCCTAAAGTTTAGAGAAGCAGATACAGTGAAATGAGTAACCAATAAAGCGAAAGAGCGGGCTA
* * * * *
39124086 TTGAAGAAAGGAATCACCAAAAAAGTCAAGATTCGGTAGGACCGGACAAAATTGGCCTCCATGGA
131 TTGAAGAAAAGAAGCACCAAAAAAGTCAAGATTCGGTAAGACCAGACAAAATTGGCCTCCATAGA
* *
39124151 ATCTTTGCTCTATTCCCATTTCAC-GACAATGAGCAAACAGGGGCAGCTGTAGAGGTCCATTTTT
196 ATCTTTGCTCTATTCCCATTTC-CTGACAATGAGCAAACAGGGGCAACTGTAGAGGCCCATTTTT
* *
39124215 GTCCGGCCCAAAATC-A-AATAA-AA-AAATAAATAAAAACAACATCCAAAATCAATTTTAATTA
260 GTCCGACCCAAAATCAATAATAATAATAAATAAATAAAAACAACATCCAAAAACAATTTTAATTA
* *
39124276 AAATTTCCAAATTTCAAATTAAAACC-ATTTACCCTTAACCAAAACCAACTAAACCCAATCCTAA
325 AAA-GTCCAAATTACAAATTAAAACCAATTTACCCTTAACCAAAACCAACTAAACCCAATCCTAA
39124340 TCCATACCCAAACATCACCCACTTAACCCAAACACTCCCAAAC
389 TCCATACCCAAACATCACCCACTTAACCCAAACACTCCCAAAC
*
39124383 CAACAATAAATTTTATCTTTTTGAAGTTGCAATGGGGTAAGATAAAATCACGACACTAAATCCTA
1 CAACAATAAATTTTATCTTTTTGAAGTTGCAATAGGGTAAGA-AAAATCACGACACTAAATCCTA
*
39124448 TCTTCCTAATGTTGTAGAGAAGCAGATACAGTGAAATGAGT-ACCTAATAAAGCGAAAGAGCGGG
65 TCTTCCTAAAGTT-TAGAGAAGCAGATACAGTGAAATGAGTAACC-AATAAAGCGAAAGAGCGGG
* *
39124512 CTATTGAAGAAAAGAAGCACCAAAGAAGTCAAGATTCGGTAAGACCAGACAAAATTGGCCTCCTT
128 CTATTGAAGAAAAGAAGCACCAAAAAAGTCAAGATTCGGTAAGACCAGACAAAATTGGCCTCCAT
* * *
39124577 AGAATCTTTGCTCTATTCCCGTTTCCTGACAATGTGCAAAGAGGGGCAACTGTAGAGGCCCATTT
193 AGAATCTTTGCTCTATTCCCATTTCCTGACAATGAGCAAACAGGGGCAACTGTAGAGGCCCATTT
* *
39124642 TTGTTCGACCCAAAATCAAAAAATAATAATAATAAATAAATAAAAACAACATCCAAAAACCATTT
258 TTGTCCGACCCAAAATC----AATAATAATAATAAATAAATAAAAACAACATCCAAAAACAATTT
* *
39124707 TATTTAAAAGTCCAAATTACAAATTAAAACCAATTTACCCTTAACCCAAACCAACTAAACCCA
319 TAATTAAAAGTCCAAATTACAAATTAAAACCAATTTACCCTTAACCAAAACCAACTAAACCCA
39124770 CTAAACCCAA
Statistics
Matches: 350, Mismatches: 24, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
427 40 0.11
428 38 0.11
429 176 0.50
434 1 0.00
435 5 0.01
436 22 0.06
437 68 0.19
ACGTcount: A:0.41, C:0.21, G:0.14, T:0.24
Consensus pattern (431 bp):
CAACAATAAATTTTATCTTTTTGAAGTTGCAATAGGGTAAGAAAAATCACGACACTAAATCCTAT
CTTCCTAAAGTTTAGAGAAGCAGATACAGTGAAATGAGTAACCAATAAAGCGAAAGAGCGGGCTA
TTGAAGAAAAGAAGCACCAAAAAAGTCAAGATTCGGTAAGACCAGACAAAATTGGCCTCCATAGA
ATCTTTGCTCTATTCCCATTTCCTGACAATGAGCAAACAGGGGCAACTGTAGAGGCCCATTTTTG
TCCGACCCAAAATCAATAATAATAATAAATAAATAAAAACAACATCCAAAAACAATTTTAATTAA
AAGTCCAAATTACAAATTAAAACCAATTTACCCTTAACCAAAACCAACTAAACCCAATCCTAATC
CATACCCAAACATCACCCACTTAACCCAAACACTCCCAAAC
Found at i:39130402 original size:5 final size:5
Alignment explanation
Indices: 39130388--39130440 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
39130378 AAGGGCATTT
*
39130388 AAAA- AAAAG AAAAG AAAAG AAAAG -AAA- ACAAG AAGAAG AAGAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AA-AAG AAAAG
39130437 AAAA
1 AAAA
39130441 AGGAAGAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
4 9 0.21
5 23 0.53
6 11 0.26
ACGTcount: A:0.79, C:0.02, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:39130428 original size:6 final size:6
Alignment explanation
Indices: 39130394--39130454 Score: 51
Period size: 5 Copynumber: 10.8 Consensus size: 6
39130384 ATTTAAAAAA
*
39130394 AAGAA- AAGAA- AAGAA- AAGAA- AACAAG AAGAAG AAGAAG AA-AAG
1 AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG AAGAAG
* *
39130437 AAAAAGG AAGAAA AAGAA
1 AAGAA-G AAGAAG AAGAA
39130455 AGTCAAGATG
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
5 24 0.49
6 20 0.41
7 5 0.10
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (6 bp):
AAGAAG
Found at i:39131360 original size:13 final size:12
Alignment explanation
Indices: 39131342--39131408 Score: 71
Period size: 13 Copynumber: 5.3 Consensus size: 12
39131332 AAGGAGAGAG
39131342 AAAGAAAAGAAAA
1 AAAGAAAA-AAAA
39131355 AAAGAAAAAAAAA
1 AAAG-AAAAAAAA
*
39131368 AAAGAAAAAGAA
1 AAAGAAAAAAAA
*
39131380 GAAGAAGAAAAAA
1 AAAGAA-AAAAAA
* *
39131393 AAGGAAAAAGAA
1 AAAGAAAAAAAA
39131405 AAAG
1 AAAG
39131409 GAGAGGTCAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
12 20 0.44
13 21 0.47
14 4 0.09
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:39131362 original size:6 final size:6
Alignment explanation
Indices: 39131342--39131408 Score: 64
Period size: 6 Copynumber: 10.7 Consensus size: 6
39131332 AAGGAGAGAG
* * *
39131342 AAAGAA AAGAAAA AAAGAAA AAAAAA AAAGAA AAAGAA GAAGAA GAAA-AA
1 AAAGAA AA-AGAA AAAG-AA AAAGAA AAAGAA AAAGAA AAAGAA -AAAGAA
39131392 AAAGGAA AAAGAA AAAG
1 AAA-GAA AAAGAA AAAG
39131409 GAGAGGTCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 3 0.06
6 30 0.60
7 17 0.34
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:39131363 original size:9 final size:9
Alignment explanation
Indices: 39131340--39131401 Score: 63
Period size: 9 Copynumber: 6.9 Consensus size: 9
39131330 AAAAGGAGAG
*
39131340 AGAAAGAAA
1 AGAAAAAAA
39131349 AG-AAAAAA
1 AGAAAAAAA
39131357 AGAAAAAAA
1 AGAAAAAAA
*
39131366 AAAAAGAAAA
1 AGAAA-AAAA
* *
39131376 AGAAGAAGA
1 AGAAAAAAA
39131385 AGAAAAAAA
1 AGAAAAAAA
*
39131394 AGGAAAAA
1 AGAAAAAA
39131402 GAAAAAGGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
8 7 0.16
9 29 0.67
10 7 0.16
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (9 bp):
AGAAAAAAA
Done.