Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold239
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: 1099591
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 28993 characters in sequence are not A, C, G, or T
File 3 of 3
Found at i:813572 original size:190 final size:174
Alignment explanation
Indices: 813265--813944 Score: 1155
Period size: 174 Copynumber: 3.8 Consensus size: 174
813255 GTAAGTTATT
* * *
813265 TAAGTTGTGTAAGTTGTGTATTATGTAAGTTATGTAAGAAATGTATTATGTAAGTTGTGTATAAT
1 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAAT
813330 GTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATT
66 GTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATT
* *
813395 ATGTTATTATGTAACTTATGCAAGTTTATATACAAGTTTATATA
131 ATGTTATTATGTAACTTGTGCAAGTTTATATACAAGTTAATATA
813439 TAAGTTATGTAAGTTGTGCATTATGTAAGTTGTGCATTATGTAAGTTATGTAAAAAATGTATTAT
1 TAAGTTATGT-A-------A-T-T-T--G-TGT--ATTATGTAAGTTATGTAAAAAATGTATTAT
813504 GTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTG
50 GTAAGTTGTGTATAATGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTG
813569 TATTATGTAAGTTATTATGTTATTATGTAACTTGTGCAAGTTTATATACAAGTTAATATA
115 TATTATGTAAGTTATTATGTTATTATGTAACTTGTGCAAGTTTATATACAAGTTAATATA
813629 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATTAA
1 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTA-TAA
813694 -GTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTAT
65 TGTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTAT
813758 TATGTTATTATGTAACTTGTGCAAGTTTATATACAAGTTAATATA
130 TATGTTATTATGTAACTTGTGCAAGTTTATATACAAGTTAATATA
813803 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAAT
1 TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAAT
813868 GTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATT
66 GTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATT
813933 ATGTTATTATGT
131 ATGTTATTATGT
813945 GTAAGTCATG
Statistics
Matches: 483, Mismatches: 5, Indels: 36
0.92 0.01 0.07
Matches are distributed among these distances:
173 3 0.01
174 298 0.62
175 4 0.01
176 3 0.01
177 1 0.00
179 1 0.00
180 1 0.00
181 1 0.00
182 2 0.00
184 1 0.00
185 1 0.00
187 1 0.00
188 3 0.01
189 1 0.00
190 162 0.34
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.46
Consensus pattern (174 bp):
TAAGTTATGTAATTTGTGTATTATGTAAGTTATGTAAAAAATGTATTATGTAAGTTGTGTATAAT
GTTAGTTATCAAAGTTATGTATTATGTAAGTTATTTAAGGTAAGTTGTGTATTATGTAAGTTATT
ATGTTATTATGTAACTTGTGCAAGTTTATATACAAGTTAATATA
Found at i:813724 original size:16 final size:16
Alignment explanation
Indices: 813705--813757 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
813695 TTAGTTATCA
813705 AAGTTATGTATTATGT
1 AAGTTATGTATTATGT
* *
813721 AAGTTAT-T-TAAGGT
1 AAGTTATGTATTATGT
*
813735 AAGTTGTGTATTATGT
1 AAGTTATGTATTATGT
813751 AAGTTAT
1 AAGTTAT
813758 TATGTTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 10 0.34
15 2 0.07
16 17 0.59
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (16 bp):
AAGTTATGTATTATGT
Found at i:813898 original size:16 final size:16
Alignment explanation
Indices: 813879--813931 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
813869 TTAGTTATCA
813879 AAGTTATGTATTATGT
1 AAGTTATGTATTATGT
* *
813895 AAGTTAT-T-TAAGGT
1 AAGTTATGTATTATGT
*
813909 AAGTTGTGTATTATGT
1 AAGTTATGTATTATGT
813925 AAGTTAT
1 AAGTTAT
813932 TATGTTATTA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 10 0.34
15 2 0.07
16 17 0.59
ACGTcount: A:0.32, C:0.00, G:0.21, T:0.47
Consensus pattern (16 bp):
AAGTTATGTATTATGT
Found at i:813971 original size:13 final size:13
Alignment explanation
Indices: 813955--814009 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
813945 GTAAGTCATG
813955 TATTTAAGTAATA
1 TATTTAAGTAATA
813968 TATTTAAGTAA-A
1 TATTTAAGTAATA
* *
813980 TTTTAGTAAGTAATG
1 TATT--TAAGTAATA
*
813995 TGTTTAAGTAATA
1 TATTTAAGTAATA
814008 TA
1 TA
814010 CTATATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 4 0.12
13 20 0.59
14 7 0.21
15 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (13 bp):
TATTTAAGTAATA
Found at i:814034 original size:31 final size:33
Alignment explanation
Indices: 813979--814046 Score: 86
Period size: 31 Copynumber: 2.1 Consensus size: 33
813969 ATTTAAGTAA
*
813979 ATTTTAGTAAGTAATGTGTTTAAGTAATATACTAT
1 ATTTTAGTAAGTAA-GTG-TTAAGTAATATAATAT
*
814014 ATTTTAGTAAGTAA-TG-TAAGTAATGTAATAT
1 ATTTTAGTAAGTAAGTGTTAAGTAATATAATAT
814045 AT
1 AT
814047 ACTTAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 15 0.48
33 2 0.06
35 14 0.45
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (33 bp):
ATTTTAGTAAGTAAGTGTTAAGTAATATAATAT
Found at i:819631 original size:15 final size:14
Alignment explanation
Indices: 819611--819666 Score: 58
Period size: 15 Copynumber: 3.9 Consensus size: 14
819601 CCGACCCCTG
*
819611 AATCCCTAAACCTT
1 AATCCCTAAACCAT
*
819625 AAATCCCTAATCCAT
1 -AATCCCTAAACCAT
*
819640 AATCCTTAAATCCAT
1 AATCCCTAAA-CCAT
*
819655 ATTCCCTAAACC
1 AATCCCTAAACC
819667 TTAAAATATG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
14 10 0.29
15 24 0.71
ACGTcount: A:0.38, C:0.34, G:0.00, T:0.29
Consensus pattern (14 bp):
AATCCCTAAACCAT
Found at i:819637 original size:22 final size:22
Alignment explanation
Indices: 819606--819671 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
819596 CTAACCCGAC
819606 CCCTGAATCCCTAAACCTTAAAT
1 CCCT-AATCCCTAAACCTTAAAT
* *
819629 CCCTAATCCATAATCCTTAAAT
1 CCCTAATCCCTAAACCTTAAAT
* *
819651 CCATATTCCCTAAACCTTAAA
1 CCCTAATCCCTAAACCTTAAA
819672 ATATGAACTC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 33 0.89
23 4 0.11
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.29
Consensus pattern (22 bp):
CCCTAATCCCTAAACCTTAAAT
Found at i:819930 original size:15 final size:14
Alignment explanation
Indices: 819908--819941 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
819898 TCTCAACCCT
819908 TAAACCATAATCCC
1 TAAACCATAATCCC
*
819922 TAAATCCATAATCTC
1 TAAA-CCATAATCCC
819937 TAAAC
1 TAAAC
819942 TTTTAACAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.44, C:0.29, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:820112 original size:41 final size:41
Alignment explanation
Indices: 820055--820337 Score: 395
Period size: 41 Copynumber: 6.9 Consensus size: 41
820045 TTCTATTATT
* * * *
820055 ATTAGTGGCGTTTTTTCAAAAACGCCGCTAAAGGTCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
820096 ATTAGTGGCGCTTTTTCAAAAAAGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
*
820137 ATTAGCGGCGCTTTCTCAAAAACGCTGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
*
820178 ATTAGCGGCGCTTTCTCAAAAACGCTGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
*
820219 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAATGCCCGAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
* * *** *
820260 ATTAGCGGCGCTTTCTCAAAAATGCTGCTAAAGTATCAAGC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
820301 ATTAGCGGTGCTTTTTCAAAAACGCCGCTAAATGCCC
1 ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCC
820338 CCAAAACTAA
Statistics
Matches: 218, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 218 1.00
ACGTcount: A:0.28, C:0.27, G:0.23, T:0.23
Consensus pattern (41 bp):
ATTAGCGGCGCTTTCTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:844388 original size:22 final size:22
Alignment explanation
Indices: 844360--844403 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
844350 CTAATTTCAG
844360 TAGAACTAAGAACTTAGGTAGT
1 TAGAACTAAGAACTTAGGTAGT
844382 TAGAACTAAGAACTTAGGTAGT
1 TAGAACTAAGAACTTAGGTAGT
844404 GACGCCCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (22 bp):
TAGAACTAAGAACTTAGGTAGT
Found at i:851348 original size:18 final size:18
Alignment explanation
Indices: 851325--851371 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
851315 TTTTTATGTG
*
851325 TGTTTATTTTTGTTTTTA
1 TGTTTATTTTTGTGTTTA
*
851343 TGTTTATTTGTGTGTTTA
1 TGTTTATTTTTGTGTTTA
851361 T-TTTAGTTTTT
1 TGTTTA-TTTTT
851372 ATACATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 4 0.16
18 21 0.84
ACGTcount: A:0.11, C:0.00, G:0.15, T:0.74
Consensus pattern (18 bp):
TGTTTATTTTTGTGTTTA
Found at i:851453 original size:42 final size:43
Alignment explanation
Indices: 851392--851475 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
851382 CAAAAAAATT
851392 CAAAAATCCCAAAAATATTTTTCATT-TTTATTTTTAAATTTTC
1 CAAAAATCCCAAAAATATTTTTC-TTCTTTATTTTTAAATTTTC
* * * *
851435 CAAAAAT-GCAAATATATTTTTCTTCTTTGTTTTTAATTTTT
1 CAAAAATCCCAAAAATATTTTTCTTCTTTATTTTTAAATTTT
851476 GTTATTGCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 2 0.06
42 27 0.75
43 7 0.19
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.52
Consensus pattern (43 bp):
CAAAAATCCCAAAAATATTTTTCTTCTTTATTTTTAAATTTTC
Found at i:852922 original size:6 final size:6
Alignment explanation
Indices: 852911--852936 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
852901 ATATTTTAGC
852911 TTAGTT TTAGTT TTAGTT TTAGTT TT
1 TTAGTT TTAGTT TTAGTT TTAGTT TT
852937 CTTTAGGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTAGTT
Found at i:854751 original size:23 final size:22
Alignment explanation
Indices: 854708--854751 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
854698 TTCTAAATCG
854708 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
854731 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
854752 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:854868 original size:45 final size:45
Alignment explanation
Indices: 854799--854889 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
854789 AAATACTCGA
* * *
854799 TGGATTCAGCATATAGCAACCACCTTATTAATCAATGATGTCCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
*
854844 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTTCGG
1 TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
854889 T
1 T
854890 TCATATGGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (45 bp):
TGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCCGG
Found at i:855072 original size:50 final size:51
Alignment explanation
Indices: 854940--855079 Score: 160
Period size: 50 Copynumber: 2.8 Consensus size: 51
854930 TACCATCCGA
* *
854940 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAACTATCCAG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGCGACCGAAACTATCCAG
* * * * * *
854991 TACGCAG-AGTAGCCTGCACATAGTACTACACATGCGACC-TATC-ATTTCGG
1 TACAC-GTAGTAGCCTGCACATAGTACTACACACGCGACCGAAACTA-TCCAG
*
855041 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACC
1 TACACGTAGTAGCCTGCACATAGTACTACACACGCGACC
855080 ATCACTTTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
49 2 0.03
50 39 0.52
51 33 0.44
52 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGCGACCGAAACTATCCAG
Found at i:856572 original size:174 final size:178
Alignment explanation
Indices: 856275--856637 Score: 583
Period size: 174 Copynumber: 2.0 Consensus size: 178
856265 TTTAGTTTAA
856275 TGTATTTTAGTTTATTTTACTTCAAATATGTTAAAGCTTGTTCCTTGCATGTTTCCTGCTTTAGA
1 TGTATTTTAGTTTATTTTACTTCAAATATGTTAAAGCTTGTTCCTT--ATGTTT-CTGCTTTAGA
* *
856340 TTTCTTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTT
63 TTTATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTC
* *
856405 ATATTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
128 ACACTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
*
856456 TGTATTTTAGTTTATTTTA-TGTCAAATATGTTAAAGTTTGTTCCTT-T-TTT-T-CTTTAGATT
1 TGTATTTTAGTTTATTTTACT-TCAAATATGTTAAAGCTTGTTCCTTATGTTTCTGCTTTAGATT
*
856516 TATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTGCATAAAAATCTCAACTTTCAC
65 TATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTCAC
*
856581 ACTTTTCTTAAGCTTTACTTTCATGGCTTCTTTGTTTCCTATTGTTATG
130 ACTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
*
856630 TTTATTTT
1 TGTATTTT
856638 CTTAACTTTG
Statistics
Matches: 173, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
174 124 0.72
175 1 0.01
177 3 0.02
178 1 0.01
180 1 0.01
181 43 0.25
ACGTcount: A:0.21, C:0.13, G:0.11, T:0.55
Consensus pattern (178 bp):
TGTATTTTAGTTTATTTTACTTCAAATATGTTAAAGCTTGTTCCTTATGTTTCTGCTTTAGATTT
ATTTGTTAAATGCTTTTGGTTTCATGTTATTTAAGTTTTCTTACATAAAAATCTCAACTTTCACA
CTTTTCTTAAGCTTTACTTTCATAGCTTCTTTGTTTCCTATTGTTATG
Found at i:860175 original size:19 final size:20
Alignment explanation
Indices: 860148--860187 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
860138 ATCATGGAAA
860148 TGCAAATTTCAT-AAAACGG
1 TGCAAATTTCATGAAAACGG
* *
860167 TGCAGATTTTATGAAAACGG
1 TGCAAATTTCATGAAAACGG
860187 T
1 T
860188 CCTACTCATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (20 bp):
TGCAAATTTCATGAAAACGG
Found at i:863877 original size:21 final size:19
Alignment explanation
Indices: 863851--863891 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
863841 AGTCCACCCA
*
863851 AATTACTGAATATACATGAAT
1 AATTACTCAAT-TAC-TGAAT
863872 AATTACTCAATTACTGAAT
1 AATTACTCAATTACTGAAT
863891 A
1 A
863892 TACATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 3 0.16
21 10 0.53
ACGTcount: A:0.46, C:0.12, G:0.07, T:0.34
Consensus pattern (19 bp):
AATTACTCAATTACTGAAT
Found at i:863893 original size:29 final size:29
Alignment explanation
Indices: 863851--863913 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
863841 AGTCCACCCA
863851 AATTACTGAATATACATGAATAATTACTC
1 AATTACTGAATATACATGAATAATTACTC
863880 AATTACTGAATATACATGAATAATTACTC
1 AATTACTGAATATACATGAATAATTACTC
863909 AATTA
1 AATTA
863914 TTACTCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.46, C:0.13, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTACTGAATATACATGAATAATTACTC
Found at i:863918 original size:11 final size:11
Alignment explanation
Indices: 863902--863926 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
863892 TACATGAATA
863902 ATTACTCAATT
1 ATTACTCAATT
863913 ATTACTCAATT
1 ATTACTCAATT
863924 ATT
1 ATT
863927 GGGCAGGTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTACTCAATT
Found at i:879512 original size:25 final size:26
Alignment explanation
Indices: 879459--879512 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
879449 TTCTCCTAAA
* *
879459 TTTCAATTTTCTTTAATTATTTAATT
1 TTTCAATTTTATTGAATTATTTAATT
879485 TTTCAA-TTTATTGAATTA-TTAATAT
1 TTTCAATTTTATTGAATTATTTAAT-T
879510 TTT
1 TTT
879513 ATATTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 5 0.20
25 14 0.56
26 6 0.24
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTTAATT
Found at i:879526 original size:25 final size:25
Alignment explanation
Indices: 879473--879526 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
879463 AATTTTCTTT
* *
879473 AATTATTTAATTTTTCAATTTATTG
1 AATTATTTAATTTTTCAATTAATTA
879498 AATTA-TTAATATTTT-ATATTAATTA
1 AATTATTTAAT-TTTTCA-ATTAATTA
879523 AATT
1 AATT
879527 TTTGAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 6 0.24
25 19 0.76
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTATTTAATTTTTCAATTAATTA
Found at i:885695 original size:35 final size:37
Alignment explanation
Indices: 885656--885751 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 37
885646 ATATTTTATT
*
885656 ATTTTTATTCGCATGTTAAGCATGCT-ATTA-TTCTG
1 ATTTTGATTCGCATGTTAAGCATGCTCATTATTTCTG
* *
885691 ATTTTGACTCACATGTTAAGCATG-TCATTATTTCTG
1 ATTTTGATTCGCATGTTAAGCATGCTCATTATTTCTG
*
885727 ATTCTGATTCGCATGTTAAGCATGC
1 ATTTTGATTCGCATGTTAAGCATGC
885752 CACTATATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
34 1 0.02
35 25 0.48
36 26 0.50
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.44
Consensus pattern (37 bp):
ATTTTGATTCGCATGTTAAGCATGCTCATTATTTCTG
Found at i:888250 original size:8 final size:8
Alignment explanation
Indices: 888232--888275 Score: 81
Period size: 8 Copynumber: 5.6 Consensus size: 8
888222 AAAATATTTT
888232 AAAAT-AA
1 AAAATAAA
888239 AAAATAAA
1 AAAATAAA
888247 AAAATAAA
1 AAAATAAA
888255 AAAATAAA
1 AAAATAAA
888263 AAAATAAA
1 AAAATAAA
888271 AAAAT
1 AAAAT
888276 NNNNNNNNNN
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 5 0.14
8 31 0.86
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (8 bp):
AAAATAAA
Found at i:894623 original size:22 final size:20
Alignment explanation
Indices: 894586--894636 Score: 77
Period size: 22 Copynumber: 2.5 Consensus size: 20
894576 AGTACAAATA
894586 TAATAAATTTATATATTTAT
1 TAATAAATTTATATATTTAT
894606 TAATAAATATATATATATTTAT
1 TAATAAAT-T-TATATATTTAT
894628 T-ATAAATTT
1 TAATAAATTT
894637 TAGTTAACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 1 0.03
20 9 0.31
21 7 0.24
22 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATAAATTTATATATTTAT
Found at i:896732 original size:22 final size:21
Alignment explanation
Indices: 896676--896732 Score: 51
Period size: 22 Copynumber: 2.6 Consensus size: 21
896666 ATACACAAAC
*
896676 AATAACAACAAAATAGTAGCAA
1 AATAA-AAGAAAATAGTAGCAA
* * *
896698 CATAATAGTAAAATGGTAGCAA
1 AATAAAAG-AAAATAGTAGCAA
896720 AATAAGAAGAAAA
1 AATAA-AAGAAAA
896733 CAACAAGAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
21 1 0.04
22 24 0.89
23 2 0.07
ACGTcount: A:0.61, C:0.09, G:0.14, T:0.16
Consensus pattern (21 bp):
AATAAAAGAAAATAGTAGCAA
Found at i:897223 original size:71 final size:72
Alignment explanation
Indices: 897133--897275 Score: 279
Period size: 71 Copynumber: 2.0 Consensus size: 72
897123 AGATATAGGC
897133 TATTAAAATAATAAAATTGTATTTTTACGATAATTTAATTTCGATCTCTCCTACAAATTTTTTTT
1 TATTAAAATAATAAAATTGTATTTTTACGATAATTTAATTTCGATCTCTCCTACAAATTTTTTTT
897198 GACTTGG
66 GACTTGG
897205 TATTAAAAT-ATAAAATTGTATTTTTACGATAATTTAATTTCGATCTCTCCTACAAATTTTTTTT
1 TATTAAAATAATAAAATTGTATTTTTACGATAATTTAATTTCGATCTCTCCTACAAATTTTTTTT
897269 GACTTGG
66 GACTTGG
897276 CCTATAATCT
Statistics
Matches: 71, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
71 62 0.87
72 9 0.13
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (72 bp):
TATTAAAATAATAAAATTGTATTTTTACGATAATTTAATTTCGATCTCTCCTACAAATTTTTTTT
GACTTGG
Found at i:899968 original size:17 final size:19
Alignment explanation
Indices: 899934--899975 Score: 52
Period size: 17 Copynumber: 2.3 Consensus size: 19
899924 ATAATTTTTT
*
899934 AAAATATATATAATACATC
1 AAAATATATATAAAACATC
*
899953 AAAATAT-TA-AAAACATT
1 AAAATATATATAAAACATC
899970 AAAATA
1 AAAATA
899976 AATGTTTCCC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 12 0.57
18 2 0.10
19 7 0.33
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATATATATAAAACATC
Found at i:904686 original size:26 final size:26
Alignment explanation
Indices: 904657--904708 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
904647 ATATAATTTT
904657 CAAATCATGTATC-TATATATCATGTA
1 CAAATCAT-TATCATATATATCATGTA
* *
904683 CAAATCATTTTCATATATCTCATGTA
1 CAAATCATTATCATATATATCATGTA
904709 AATACCTATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (26 bp):
CAAATCATTATCATATATATCATGTA
Found at i:911130 original size:22 final size:22
Alignment explanation
Indices: 911078--911132 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
911068 AATGTGCAGG
**
911078 TCTTGAGACAATTTACCATATG
1 TCTTGAGACAATTTACCATACA
** *
911100 TCTCAAGACAATTTATCATACA
1 TCTTGAGACAATTTACCATACA
911122 TCTTGAGACAA
1 TCTTGAGACAA
911133 GGCTCTCTTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.33
Consensus pattern (22 bp):
TCTTGAGACAATTTACCATACA
Found at i:916700 original size:6 final size:6
Alignment explanation
Indices: 916687--916722 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
916677 CATTTTCATT
916687 ATTT-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
916723 ATAACTATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:921353 original size:24 final size:24
Alignment explanation
Indices: 921326--921382 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
921316 AAACCTAATT
*
921326 CTAATCAATGTCAAATATATTATG
1 CTAATAAATGTCAAATATATTATG
** **
921350 CTAATAAATGTTGAATATATTACA
1 CTAATAAATGTCAAATATATTATG
921374 CTAATAAAT
1 CTAATAAAT
921383 ACTAAATCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.46, C:0.11, G:0.07, T:0.37
Consensus pattern (24 bp):
CTAATAAATGTCAAATATATTATG
Found at i:924206 original size:2 final size:2
Alignment explanation
Indices: 924199--924227 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
924189 AAACAAGCAA
924199 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
924228 ATTTATAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:939914 original size:60 final size:61
Alignment explanation
Indices: 939787--939913 Score: 254
Period size: 61 Copynumber: 2.1 Consensus size: 61
939777 GGGAGAGGTT
939787 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
1 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
939848 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
1 TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
939909 TTTTT
1 TTTTT
939914 GGCTTAATAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.33, C:0.02, G:0.22, T:0.43
Consensus pattern (61 bp):
TTTTTTGAAAGGTTTCTGTTTTTTAAAAAAGAAGGAAAGGGAGAATGAATTTTTTGAGTTA
Found at i:945116 original size:10 final size:10
Alignment explanation
Indices: 945099--945171 Score: 71
Period size: 10 Copynumber: 7.3 Consensus size: 10
945089 AAAAAAATTT
945099 AAAA-TTAAA
1 AAAATTTAAA
945108 AAAATTTAAA
1 AAAATTTAAA
945118 AAAGTATTTTAAA
1 AAA--A-TTTAAA
945131 AAAATTTAAA
1 AAAATTTAAA
**
945141 AAAATTT-TT
1 AAAATTTAAA
945150 AAAA-TTAAA
1 AAAATTTAAA
*
945159 AAATTTTAAA
1 AAAATTTAAA
945169 AAA
1 AAA
945172 GTATTTTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
8 2 0.04
9 11 0.21
10 29 0.55
11 1 0.02
12 1 0.02
13 9 0.17
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:945151 original size:51 final size:51
Alignment explanation
Indices: 945085--945222 Score: 190
Period size: 51 Copynumber: 2.7 Consensus size: 51
945075 AAAAAAGTAT
*
945085 TTTAAAAAAA-ATTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAAA
1 TTTAAAAAAATTTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAAA
* **
945135 TTTAAAAAAATTTTTAAAATTAAAAAATTTTAAAAAAGTATTTTAAAAGTA
1 TTTAAAAAAATTTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAAA
* * *
945186 TTT-TAAAAGTATTTTAAAATTAAAAAAATTAAAAAAA
1 TTTAAAAAAAT-TTTTAAAATTAAAAAAATTTAAAAAA
945223 TAAAAATATT
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
50 15 0.19
51 63 0.81
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (51 bp):
TTTAAAAAAATTTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAAAA
Found at i:945170 original size:11 final size:11
Alignment explanation
Indices: 945103--945204 Score: 74
Period size: 11 Copynumber: 9.5 Consensus size: 11
945093 AAATTTAAAA
945103 TTAAAAAAA-T
1 TTAAAAAAATT
945113 TTAAAAAAGTATT
1 TTAAAAAA--ATT
945126 TTAAAAAAA-T
1 TTAAAAAAATT
945136 TTAAAAAAATT
1 TTAAAAAAATT
*
945147 TT--TAAAA--
1 TTAAAAAAATT
945154 TT-AAAAAATT
1 TTAAAAAAATT
945164 TTAAAAAAGTATT
1 TTAAAAAA--ATT
**
945177 TTAAAAGTATT
1 TTAAAAAAATT
**
945188 TTAAAAGTATT
1 TTAAAAAAATT
945199 TTAAAA
1 TTAAAA
945205 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 4, Indels: 19
0.77 0.04 0.19
Matches are distributed among these distances:
7 2 0.03
8 4 0.05
9 4 0.05
10 20 0.26
11 29 0.37
12 1 0.01
13 18 0.23
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:953308 original size:44 final size:44
Alignment explanation
Indices: 953249--953939 Score: 553
Period size: 44 Copynumber: 15.6 Consensus size: 44
953239 GGCTAAAAAG
* *
953249 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGGCGCGAAGTAGATCGAAGA
* * * *
953293 AAGCAGATCTTGTCTTCCTATATTGGTAGCAAAGTGGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
* ** *
953338 TA-CAGATCTTGTCTTCCCATACTGATG-GCGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTG--GCGCGAAGTAGATCGAAGA
* * *
953382 AAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGGCGCGAAGTAGATCGAAGA
* * * * *
953426 TAA-CATATCCTGTCTTCCTATATTGGTAGCGAAGTGGATCGAAGA
1 -AAGCAGATCTTGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
* ** * *
953471 TA-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
* * *
953515 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGGCGCGAAGTAGATCGAAGA
* * * *
953559 TAA-CAGAT-TCTGTCTTCCTATATTGGTAGCAAAGTGGATCGAAGA
1 -AAGCAGATCT-TGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
* ** *
953604 TA-CAGATCTTGTCTTCCCATACTGATG-GCGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTG--GCGCGAAGTAGATCGAAGA
* * *
953648 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGGCGCGAAGTAGATCGAAGA
* * * *
953692 TAA-CAGAT-TCTGTCTTCCTATATTGGTAGCAAAGTGGATCGAAGA
1 -AAGCAGATCT-TGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
* * ** * *
953737 CA-TAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
* * * * * *
953781 AAGCAGATCTCGTCTTCATGTATTAGCGTGAAGTAGATCAAAGG
1 AAGCAGATCTTGTCTTCATATATTGGCGCGAAGTAGATCGAAGA
* * * *** *
953825 TAGCAGATCCTGTCTTCCTATATTCATAG-GAAGTGGATCGAAG-
1 AAGCAGATCTTGTCTTCATATATT-GGCGCGAAGTAGATCGAAGA
* ** *
953868 ATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGA
1 AAGCAGATCTTGTCTTCATATATTGG-CGCGAAGTAGATCGAAGA
*
953913 AAGCAGATCTTGTCTTCATGTATTGGC
1 AAGCAGATCTTGTCTTCATATATTGGC
953940 ATTAAGTGGA
Statistics
Matches: 516, Mismatches: 106, Indels: 50
0.77 0.16 0.07
Matches are distributed among these distances:
43 25 0.05
44 330 0.64
45 159 0.31
46 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (44 bp):
AAGCAGATCTTGTCTTCATATATTGGCGCGAAGTAGATCGAAGA
Found at i:953487 original size:133 final size:133
Alignment explanation
Indices: 953249--953982 Score: 1184
Period size: 133 Copynumber: 5.5 Consensus size: 133
953239 GGCTAAAAAG
*
953249 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGA-AAGCAGATCTTGTCTTCCTA
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAA-CAGATCCTGTCTTCCTA
*
953313 TATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCG
65 TATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
953378 AAGA
130 AAGA
* *
953382 AAGCAGATCTTGTCTTCATGTATTGGTGTGAAGTAGATCGAAGATAACATATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
*
953447 ATTGGTAGCGAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
953512 AGA
131 AGA
* *
953515 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATTCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
*
953580 ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGATGGCGAAGTAGATCGA
66 ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
953645 AGA
131 AGA
* *
953648 AAGCAGATCTTGCCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATTCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
* *
953713 ATTGGTAGCAAAGTGGATCGAAGACATAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
953778 AGA
131 AGA
* * * * *
953781 AAGCAGATCTCGTCTTCATGTATTAGCGTGAAGTAGATCAAAGGTAGCAGATCCTGTCTTCCTAT
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
** * * *
953846 ATTCATAG-GAAGTGGATCGAAGATGCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGA
66 ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
953910 AGA
131 AGA
* * * * * * *
953913 AAGCAGATCTTGTCTTCATGTATTGGCATTAAGTGGATCGAAAATAACAGATTCTGTCTTCTTAA
1 AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
953978 ATTGG
66 ATTGG
953983 CAGTAAGGCA
Statistics
Matches: 558, Mismatches: 42, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
132 110 0.20
133 446 0.80
134 2 0.00
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (133 bp):
AAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAACAGATCCTGTCTTCCTAT
ATTGGTAGCAAAGTGGATCGAAGATACAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGA
AGA
Found at i:954062 original size:44 final size:44
Alignment explanation
Indices: 954007--954123 Score: 198
Period size: 44 Copynumber: 2.7 Consensus size: 44
953997 GACGTGGGCG
*
954007 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAGGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
* * *
954051 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCGAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
954095 AATCTTATCTCCCTGAAGTTGCAGTGGAG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG
954124 TAGACATAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 68 1.00
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGAAGATTAAAGCCAAT
Found at i:955861 original size:13 final size:13
Alignment explanation
Indices: 955824--955862 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
955814 TTATTTTGTT
955824 TATATAAACTTTTA
1 TATATAAA-TTTTA
*
955838 TAATCTAAATTTTA
1 T-ATATAAATTTTA
955852 TATATAAATTT
1 TATATAAATTT
955863 ATGTGTATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 7 0.32
15 6 0.27
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATAAATTTTA
Found at i:956054 original size:17 final size:17
Alignment explanation
Indices: 956034--956068 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
956024 CCCTTATGTA
956034 TATTTGTTTCAT-TTATT
1 TATTTGTTT-ATATTATT
956051 TATTTGTTTATATTATT
1 TATTTGTTTATATTATT
956068 T
1 T
956069 CTATGCTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 15 0.88
ACGTcount: A:0.20, C:0.03, G:0.06, T:0.71
Consensus pattern (17 bp):
TATTTGTTTATATTATT
Found at i:958384 original size:41 final size:41
Alignment explanation
Indices: 958299--958386 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 41
958289 TGAATCCATG
*
958299 AAATGGTTGAAAAGGAAGTTATTCAAAAAGGATAACAAATGA
1 AAAT-GTTGAAAAGGAAGTTATCCAAAAAGGATAACAAATGA
* **
958341 AAATGTTGAAAAGGATGTTATCCGGAAAGGATAACAAATGA
1 AAATGTTGAAAAGGAAGTTATCCAAAAAGGATAACAAATGA
958382 AAATG
1 AAATG
958387 ATGTGTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 38 0.90
42 4 0.10
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.22
Consensus pattern (41 bp):
AAATGTTGAAAAGGAAGTTATCCAAAAAGGATAACAAATGA
Found at i:976549 original size:52 final size:53
Alignment explanation
Indices: 976477--976581 Score: 203
Period size: 52 Copynumber: 2.0 Consensus size: 53
976467 AATGAAATTA
976477 TTTATTAAGACTTCTCTTTTTGAAAAGAAAAATATCACACCCAATGCGTTAGG
1 TTTATTAAGACTTCTCTTTTTGAAAAGAAAAATATCACACCCAATGCGTTAGG
976530 TTTATTAAGA-TTCTCTTTTTGAAAAGAAAAATATCACACCCAATGCGTTAGG
1 TTTATTAAGACTTCTCTTTTTGAAAAGAAAAATATCACACCCAATGCGTTAGG
976582 GCACAACATT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 42 0.81
53 10 0.19
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.34
Consensus pattern (53 bp):
TTTATTAAGACTTCTCTTTTTGAAAAGAAAAATATCACACCCAATGCGTTAGG
Found at i:978817 original size:44 final size:44
Alignment explanation
Indices: 978768--978977 Score: 262
Period size: 44 Copynumber: 4.8 Consensus size: 44
978758 ATCTGCTATT
* * *
978768 TTCAACCTACTCCACTGCTG-CTGAGGGAGATAGGATTCATAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
** *
978812 TTCAACCTATTCCACTGCTGACCAGGGAGATA-GAACCTACAACC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATC
* * * * *
978856 TTCAATCTATTCCACTGCTGCCCAGAGAGATAGAATTCTCAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
978900 TTCAACCCATTCCACTACTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
978944 TTTAACCTATTCCACTGCTGACCAGGGAGATAGG
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGG
978978 GCTGGGGTCA
Statistics
Matches: 139, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
43 3 0.02
44 133 0.96
45 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.25
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:979114 original size:88 final size:88
Alignment explanation
Indices: 978977--979294 Score: 555
Period size: 88 Copynumber: 3.6 Consensus size: 88
978967 AGGGAGATAG
* * * *
978977 GGCTGGGGTCATCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
979042 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
979065 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
** *
979130 TCTACTGTAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
979153 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
979218 TCCGCTGCAACCCAGGGAGGCAA
66 TCCGCTGCAACCCAGGGAGGCAA
* *
979241 GGCTGGTGTCTTCGATCTGCTTTGTTGTCAGTGCAGGAAGGCAAGATCTGCTAT
1 GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTAT
979295 CTTCGATCTA
Statistics
Matches: 218, Mismatches: 12, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 218 1.00
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAGCCTGC
TCCGCTGCAACCCAGGGAGGCAA
Found at i:979283 original size:44 final size:45
Alignment explanation
Indices: 978988--979308 Score: 142
Period size: 44 Copynumber: 7.3 Consensus size: 45
978978 GCTGGGGTCA
* * * *
978988 TCGATCTGCTTTGCTGTCGGTGCAGGAAGGCAAGATCTGCTAT-T
1 TCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
** * * * *** * * *
979032 TTTAGCCTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCT
1 TCGA-TCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
* *
979076 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTAT-T
1 TCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
** * *** * * *
979120 TTTAGCCTGC-TC-TACTGT-AACCCAGGGAGGCAAG-GCTGGTGTCT
1 TCGA-TCTGCTTCGT--TGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
* *
979164 TCGATCTGCTTCGTTGTCGGTGCAGGAAGGCAAGATCTGCTAT-T
1 TCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
** * * * *** * * *
979208 TTTAGCCTGCTCCGCTG-CAACCCAGGGAGGCAAG-GCTGGTGTCT
1 TCGA-TCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
* *
979252 TCGATCTGCTTTGTTGTCAGTGCAGGAAGGCAAGATCTGCTATCT
1 TCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
*
979297 TCGATCTACTTC
1 TCGATCTGCTTC
979309 ACGCCAATAC
Statistics
Matches: 185, Mismatches: 76, Indels: 31
0.63 0.26 0.11
Matches are distributed among these distances:
43 40 0.22
44 92 0.50
45 53 0.29
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (45 bp):
TCGATCTGCTTCGTTGTCAGTGCAGGAAGGCAAGAGCTGCTATCT
Found at i:979347 original size:44 final size:43
Alignment explanation
Indices: 979277--979827 Score: 418
Period size: 44 Copynumber: 12.5 Consensus size: 43
979267 GTCAGTGCAG
*
979277 GAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-CGCCAATACAT
* * * * *
979321 GAAGACAGGATATGCTTTCTTCGATCTACTT-CGCCACTAGTAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCCGCCAATA-CAT
* * * *
979364 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAA
1 --GAAGACAAGATCTGCTATCTTCGATCTACTTCC-GCCAATACAT
* *
979409 GAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-CGCCAATACAT
* * * * *
979453 GAAGACAGGATATGCTTTCTTCGATCTACTT-CGCCACTAGTAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCCGCCAATA-CAT
* * * *
979496 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAG
1 --GAAGACAAGATCTGCTATCTTCGATCTACTTC-C-GCCAATACAT
* *
979542 GAAGACAGGATCTTCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTC-CGCCAATACAT
* * *
979586 GAAGACAAGATCTGCTTTCTTCGATCTACTCTGCCACCAATATC-G
1 GAAGACAAGATCTGCTATCTTCGATCTACT-T-CCGCCAATA-CAT
* * * *
979631 GAAGACAAGATCTGC-ATCTTCGATCCACTTCCTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCC-GCCAATACAT
* **
979674 GAAGACAGGA-CTTGCTATCTTCGATCTACTTAATGCCAATACAT
1 GAAGACAAGATC-TGCTATCTTCGATCTACTT-CCGCCAATACAT
* * * * ***
979718 GAAGACAAGATCTGCTTTATTCGATCTACTCAACCACCAATATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACT--TCCGCCAATACAT
* * * * *
979763 GAAGACAAGATATGC-ATCTTCGATCCATTTCCTACCAATATA-
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCC-GCCAATACAT
* *
979805 GAAAGACAGGACCTGCTATCTTC
1 G-AAGACAAGATCTGCTATCTTC
979828 AATGATCTGC
Statistics
Matches: 406, Mismatches: 73, Indels: 56
0.76 0.14 0.10
Matches are distributed among these distances:
42 20 0.05
43 57 0.14
44 224 0.55
45 90 0.22
46 10 0.02
47 5 0.01
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (43 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCCGCCAATACAT
Found at i:979525 original size:132 final size:132
Alignment explanation
Indices: 979288--979827 Score: 834
Period size: 132 Copynumber: 4.1 Consensus size: 132
979278 AAGGCAAGAT
*
979288 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAGGATATGCTTTCTTCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTAC-TC
* *
979353 -GCCACTAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAG
65 AGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAG
979417 GAC
130 GAC
*
979420 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAGGATATGCTTTCTTCGATCTACTTC
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTAC-TC
* * *
979485 -GCCACTAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGACA
65 AGCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAAGAAGACA
*
979549 GGAT
129 GGAC
* * *
979553 CTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTCT
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTACTCA
* *
979618 GCCACCAATATCGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAGG
979683 AC
131 AC
* * * * *
979685 TTGCTATCTTCGATCTACTTAATGCCAATACATGAAGACAAGATCTGCTTTATTCGATCTACTCA
1 CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTACTCA
* * *
979750 ACCACCAATATGGGAAGACAAGATATGCATCTTCGATCCATTTCCTACCAATAT-AGAAAGACAG
66 GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAG-AAGACAG
979814 GAC
130 GAC
979817 CTGCTATCTTC
1 CTGCTATCTTC
979828 AATGATCTGC
Statistics
Matches: 384, Mismatches: 21, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
131 1 0.00
132 262 0.68
133 121 0.32
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
CTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTCTTCGATCTACTCA
GCCACCAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAAGAAGACAGG
AC
Found at i:979604 original size:265 final size:264
Alignment explanation
Indices: 979275--979827 Score: 867
Period size: 265 Copynumber: 2.1 Consensus size: 264
979265 TTGTCAGTGC
* * *
979275 AGGAAGGCAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAGGATATGCTTTC
1 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTC
* * *
979340 TTCGATCTACT-TCGCCACTAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAA
66 TTCGATCTACTCT-GCCACCAATATCGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAA
* *
979404 TATAAGAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAGGATATGCT
130 TATAAGAAGACAGGACCTGCTATCTTCGATCTACTTAACGCCAATACATGAAGACAAGATATGCT
* * * * *
979469 TTCTTCGATCTACTTC-GCCACTAGTATGGGAAGACAAGATCTGCATCTTCGATCCACTTCGCTA
195 TTATTCGATCTAC-TCAACCACCAATATGGGAAGACAAGATATGCATCTTCGATCCACTTC-CTA
979533 CCAATAT
258 CCAATAT
* *
979540 AGGAAGACAGGATCTTCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTC
1 AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTC
979605 TTCGATCTACTCTGCCACCAATATCGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
66 TTCGATCTACTCTGCCACCAATATCGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
* * * *
979670 ATAGGAAGACAGGACTTGCTATCTTCGATCTACTTAATGCCAATACATGAAGACAAGATCTGCTT
131 ATAAGAAGACAGGACCTGCTATCTTCGATCTACTTAACGCCAATACATGAAGACAAGATATGCTT
*
979735 TATTCGATCTACTCAACCACCAATATGGGAAGACAAGATATGCATCTTCGATCCATTTCCTACCA
196 TATTCGATCTACTCAACCACCAATATGGGAAGACAAGATATGCATCTTCGATCCACTTCCTACCA
979800 ATAT
261 ATAT
* *
979804 AGAAAGACAGGACCTGCTATCTTC
1 AGGAAGACAGGATCTGCTATCTTC
979828 AATGATCTGC
Statistics
Matches: 263, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
264 33 0.13
265 229 0.87
266 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (264 bp):
AGGAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATATGCTTTC
TTCGATCTACTCTGCCACCAATATCGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAAT
ATAAGAAGACAGGACCTGCTATCTTCGATCTACTTAACGCCAATACATGAAGACAAGATATGCTT
TATTCGATCTACTCAACCACCAATATGGGAAGACAAGATATGCATCTTCGATCCACTTCCTACCA
ATAT
Found at i:979801 original size:88 final size:89
Alignment explanation
Indices: 979274--979827 Score: 468
Period size: 88 Copynumber: 6.3 Consensus size: 89
979264 GTTGTCAGTG
* * * * * * *
979274 CAGGAAGGCAAGATCTGCTATCTTCGATCTACTTCA-CGCCAATACATGAAGACAGGATATGCTT
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGCTA
* * * *
979338 TCTTCGATCTACTTCGCCACTAGTA
66 TCTTCGATCCACTTC-CTACCAATA
** * * * * *
979363 TGGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAAGAAGACAGGACCTGCTA
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGCTA
* *
979426 TCTTCGATCTACTTCAC-GCCAATA
66 TCTTCGATCCACTTC-CTACCAATA
* * * * * * * *
979450 CATGAAGACAGGATATGCTTTCTTCGATCTACTTCGCCACTAGTATGGGAAGACAAGATCTGC-A
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGCTA
979514 TCTTCGATCCACTTCGCTACCAATA
66 TCTTCGATCCACTTC-CTACCAATA
* * * * * * *
979539 TAGGAAGACAGGATCTTCTATCTTCGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGCTT
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGCTA
*
979603 TCTTCGATCTACTCTGCC-ACCAATA
66 TCTTCGATCCACT-T-CCTACCAATA
* * *
979628 TC-GGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAGGAAGACAGGA-CTTGC
1 -CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATC-TGC
* ** *
979689 TATCTTCGATCTACTTAATGCCAATA
64 TATCTTCGATCCACTTCCTACCAATA
* * * * *
979715 CATGAAGACAAGATCTGCTTTATTCGATCTAC-TCAACCACCAATATGGGAAGACAAGATATGC-
1 CAGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACCACCAATATAGGAAGACAAGATCTGCT
*
979778 ATCTTCGATCCATTTCCTACCAATA
65 ATCTTCGATCCACTTCCTACCAATA
* * * *
979803 TAGAAAGACAGGACCTGCTATCTTC
1 CAGGAAGACAAGATCTGCTATCTTC
979828 AATGATCTGC
Statistics
Matches: 370, Mismatches: 79, Indels: 33
0.77 0.16 0.07
Matches are distributed among these distances:
86 1 0.00
87 42 0.11
88 198 0.54
89 126 0.34
90 2 0.01
91 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (89 bp):
CAGGAAGACAAGATCTGCTATCTTCGATCTACTTCACCACCAATATAGGAAGACAAGATCTGCTA
TCTTCGATCCACTTCCTACCAATA
Found at i:985278 original size:3 final size:3
Alignment explanation
Indices: 985270--985308 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
985260 GTATATATAG
* *
985270 TAA TAA TAA TAA TCA TAA TAA TAA CAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
985309 GTTAATAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:985694 original size:14 final size:12
Alignment explanation
Indices: 985661--985686 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
985651 GATTGCATAT
985661 ATCATATCTAAG
1 ATCATATCTAAG
985673 ATCATATCTAAG
1 ATCATATCTAAG
985685 AT
1 AT
985687 TGCATATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (12 bp):
ATCATATCTAAG
Found at i:988568 original size:48 final size:48
Alignment explanation
Indices: 988498--988671 Score: 204
Period size: 48 Copynumber: 3.6 Consensus size: 48
988488 AGAACAAATT
* * * *
988498 TCTCGGTGGCCTACACACAGTCCGTACCACCTTTGTGTAATAACAGAC
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * **
988546 TCTCGGTGGCCTGCACATAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * **
988594 TATTGGTGGCCTACACACAGTCCGTGCCACCCTTGTATCTTAACAGAA
1 TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
* * * *
988642 TATTGGTGGCTTTCACACAGTCCGTGCCAC
1 TCTCGGTGGCCTACACACAGTCCGTGCCAC
988672 ATATGCGACC
Statistics
Matches: 112, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 112 1.00
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (48 bp):
TCTCGGTGGCCTACACACAGTCCGTGCCACCCTTGTATAATAACAGAA
Found at i:997123 original size:33 final size:32
Alignment explanation
Indices: 997050--997127 Score: 84
Period size: 33 Copynumber: 2.4 Consensus size: 32
997040 CAATGTTCAT
* * * **
997050 ATGTAAGACCATAGCTGGGCTATGGCATTCTG
1 ATGTAAGACCATAACTAGGCTATGGCATACAA
*
997082 ATGATAAGACCATAACTAGGTTATGGCACTACAA
1 ATG-TAAGACCATAACTAGGCTATGGCA-TACAA
997116 ATGTAAGACCAT
1 ATGTAAGACCAT
997128 GGCAGAGTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
32 3 0.08
33 30 0.79
34 5 0.13
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.26
Consensus pattern (32 bp):
ATGTAAGACCATAACTAGGCTATGGCATACAA
Found at i:1001152 original size:18 final size:18
Alignment explanation
Indices: 1001131--1001168 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
1001121 TCTTCTTTTT
1001131 CTTTTTCATCTTCAGCAA
1 CTTTTTCATCTTCAGCAA
*
1001149 CTTTTTCTTCTTCAGCAA
1 CTTTTTCATCTTCAGCAA
1001167 CT
1 CT
1001169 ACTTCGTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.18, C:0.29, G:0.05, T:0.47
Consensus pattern (18 bp):
CTTTTTCATCTTCAGCAA
Found at i:1010100 original size:924 final size:926
Alignment explanation
Indices: 1007427--1010469 Score: 4556
Period size: 924 Copynumber: 3.3 Consensus size: 926
1007417 TGGATTATAC
* * *
1007427 TTGCTCTAAGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTGGCATTCTAAGTTCC
1 TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
* * * * * *
1007492 CCAAAATTGTTGGTTGCGTGCAGAGTTGTTGTAGGAGTTGCCATAAGAATTTTTGCGGATGTAAT
66 CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
* * * *
1007557 AATATAACATGCATTCTCTGCATGTTGTGGTCAATCTTCATAGCTATGGTTCTGACTACAAATCT
131 AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
*
1007622 CACAACAAAAAGTAGGAACATCAACTTGTTGAGTGACTTG--TA--T--AACGCCACTAGTCTAT
196 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
1007681 TGCATATTTTTAATCATG-TTTGTGATAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCA
261 TGCATATTTTTAATCATGTTTTGTG--AGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCA
*
1007745 ATTCAATAACTCCTGGAGTAGTTTTTGCTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTC
324 ATTCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTC
*
1007810 TGAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGC
389 TGAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCTAACAGAGGTCCATTGGC
* ** *
1007875 AGATGTTTTGACAAGTTTCCTTGTATATGAATTCAACCCATTATAAAAATCTCAATTTGTGTTTC
454 TGATGCATCGACAAGTTTCC---T-TATG-A-TC-ACCCATTATAAAAATCTCAATTTGTGTTTC
* * *
1007940 TAGTTGAATGTCGTGCATGGGACAAAGTCGAAGTAAAGATTTATAATTTTCCCATGTGCTGTGAA
512 TGGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAA
* * *
1008005 GATTTTGATCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGATGAGCATTCATTGTTGGC
577 GATTTTCATCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAACATTCATTGTTGGC
* * *
1008070 GGGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAAAAGTAATTGATTCAGTAGGTAG
642 GGGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAG
* * *
1008135 CCCAAAAAACGAAGTACTGGCTCTTCTCTCTAAGGAATAAGGAAATAATTGCATCTTCAAGGCAT
707 CCCAAAAAACCAAGTACGGGCTCTTC-CTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCAT
* * *
1008200 CATCAAGATATCATAAGGAATAAGGATATATCAATCCTACAGGGATGCTTGTCTTTTTT-TCTAT
771 CATCAAGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTCTA-
*
1008264 TAGTGTCGATGCAATAACTAGATAAAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAAC
835 -AGTGTCGATGCAATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAAC
*
1008329 TTGAAAACAATAAAATAAAATTTGATAA
899 TTGAAAACAATAAAATAAAATATGATAA
* * *
1008357 TTGCCCTAGGTAGATGAATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTGACTTCC
1 TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
* * * *
1008422 CCAAAATGGTTGGTTGCATGCAAAGTTGTTGTAAGAGTTACCATAAGAATTTTTGCGGATGTACT
66 CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
1008487 AATATAACAGGCA---T-T-C---TT-T-G---------ATAGCTATGGTTGTCACTACAAATCT
131 AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
* *
1008533 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGCATAGGTGCAATGCCACTAGTCTAT
196 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
1008598 TGCATATTTTTAATCATGTTTGTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAA
261 TGCATATTTTTAATCATGTTT-TGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAA
* *
1008663 TTCAATAACTCCTGGACTAGTTTTTACTTGTGCAACTATGGAGATAAGGTATTGATAATCATTCT
325 TTCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCT
* * * *
1008728 GTGCAATTCTCTCGAGAATTCTCACAGCATCATTATAAGTACAAT-TCAACAGAAGTCCATTGGT
390 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCT-AACAGAGGTCCATTGGC
*
1008792 TGATGCATCGACAAGTTTCCCTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTT
454 TGATGCATCGACAAGTTT-CC--T-TATG-A-TCA-CCCATTATAAAAATCTCAATTTGTGTTTC
* * *
1008857 TGGTTAAATGTCGTGCAGGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAA
512 TGGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAA
* *
1008922 GATTTTCATCCA-GCAGCTGATGGTAAGTAGTAATATCATTTTCAAGAC-AAGCATTCATTGTTG
577 GATTTTCAT-CATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAA-CATTCATTGTTG
* *
1008985 GCGAGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGATAGGT
640 GCGGGTTAAATCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGT
1009050 AGCCCAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGC
705 AGCCCAAAAAACCAAGTACGGGCTCTT-CCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGC
* * * * *
1009115 ATCATCATGATATCATAAGGATTAATGATATATCGATCCCACAGGGATGGTTGTTTTTTTTCTCG
769 ATCATCAAGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTCT
*
1009180 AAGTGTCGATGCAATAACTAGATAGAAACAAGATAAATTGTGAGGATAGTTGTCAGAGCAACAAC
834 AAGTGTCGATGCAATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAAC
*
1009245 TTGAGAACAATAAAATAAAATATGATAA
899 TTGAAAACAATAAAATAAAATATGATAA
* * * *
1009273 TTGCCATAGGTAGATGTATTCCCATATATGAATGTCGCAGCTTTTTGTCTAGCATTCTGAGTTCC
1 TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
* * *
1009338 CCAAAATAGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGTGAATGTACT
66 CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
* *
1009403 AATATAATAGGCATTCTTTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
131 AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
*
1009468 CACAACAAAAAGTAGGAACATGAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
196 CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
*
1009533 TGCATATTTTTAATCATGATTTTGTGAGAAGAAACTTGAGCACTTAGTGCAGTTATTGCATCCAA
261 TGCATATTTTTAATCATG-TTTTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAA
* * *
1009598 TTCAATAACTCCGGGAGTAGTTTTTCCTTGTGCAGCTCTGGAGATAAGGTATTGATAATCATTCT
325 TTCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCT
*
1009663 GAGCAATTCTCTCAAGAATTCTCACAGCATCATCATAAGTACAATCTAACAGAGGTCCATTGGCT
390 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCTAACAGAGGTCCATTGGCT
* * *
1009728 GATGCGTCGACAAGTTTCC-T-TG-T-ACCCGTTATAGAAATCTCAATTTGTGTTTCTGGTTGAA
455 GATGCATCGACAAGTTTCCTTATGATCACCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAA
* *
1009789 TGCCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTTTGAAGATTTTCA
520 TGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAAGATTTTCA
* * * * *
1009854 TAATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAACATTCATTATTGGCGGGTTAAA
585 TCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAACATTCATTGTTGGCGGGTTAAA
* * * *
1009919 TTGCAAAACAAACTTTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGATAGCCTAAAAA
650 TCGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAA
* *
1009984 ACCAAGTACGGGCTCTTCCGTATAAGGAATAAGGAAATAATTACATCTTCAAGGCATCATCAGGA
715 ACCAAGTACGGGCTCTTCC-TATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAAGA
* * * *
1010049 TATCATAAGGAATAAGGATATATCGATCCCACAGCGATGGTTGCCTTTTTTCTATTAGTGTCGAT
779 TATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTCTAAGTGTCGAT
* *
1010114 GCAATAACTAGATAGGAACGAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAA
844 GCAATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAA
1010179 TAAAATAAAATATGATAA
909 TAAAATAAAATATGATAA
* * *
1010197 TTGCCCT-GAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATCCTAAGTTC
1 TTGCCCTAG-GTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTC
* *
1010261 CCCAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGC-AGATGTA
65 CCCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGA-ATGTA
* * *
1010325 ATAATATAACAGACATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAAT
129 ATAATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAAT
* *
1010390 CTCACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCT
194 CTCACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCT
1010455 ATTGCATATTTTTAA
259 ATTGCATATTTTTAA
1010470 CCATATGGGA
Statistics
Matches: 1930, Mismatches: 142, Indels: 88
0.89 0.07 0.04
Matches are distributed among these distances:
911 63 0.03
913 2 0.00
915 1 0.00
916 222 0.12
917 533 0.28
918 10 0.01
919 5 0.00
920 2 0.00
921 2 0.00
922 2 0.00
923 5 0.00
924 653 0.34
925 5 0.00
926 3 0.00
927 1 0.00
929 2 0.00
930 131 0.07
934 2 0.00
935 282 0.15
936 4 0.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (926 bp):
TTGCCCTAGGTAGATGTATTCCCATATCTGAATGTCGCAGCATTTTGTCTAGCATTCTAAGTTCC
CCAAAATGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCGAATGTAAT
AATATAACAGGCATTCTCTGCATATTGTGGTCAATCTTCATAGCTATGGTTGTCACTACAAATCT
CACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGTATAGGTGCAACGCCACTAGTCTAT
TGCATATTTTTAATCATGTTTTGTGAGAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAAT
TCAATAACTCCTGGAGTAGTTTTTACTTGTGCAGCTATGGAGATAAGGTATTGATAATCATTCTG
AGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCTAACAGAGGTCCATTGGCTG
ATGCATCGACAAGTTTCCTTATGATCACCCATTATAAAAATCTCAATTTGTGTTTCTGGTTGAAT
GTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATTTTCCCATGTGGTGTGAAGATTTTCAT
CATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACGAACATTCATTGTTGGCGGGTTAAAT
CGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGGTAGCCCAAAAAA
CCAAGTACGGGCTCTTCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCATCAAGATA
TCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGTCTTTTTTCTCTAAGTGTCGATGC
AATAACTAGATAGAAACGAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACTTGAAAACAATA
AAATAAAATATGATAA
Found at i:1012101 original size:19 final size:19
Alignment explanation
Indices: 1012073--1012112 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
1012063 TCAAAATATG
1012073 GTTTTGGGGGATGGAATTT
1 GTTTTGGGGGATGGAATTT
*
1012092 GTTTTTGGGGATGGAATTT
1 GTTTTGGGGGATGGAATTT
1012111 GT
1 GT
1012113 GGCGTCAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (19 bp):
GTTTTGGGGGATGGAATTT
Found at i:1014404 original size:935 final size:934
Alignment explanation
Indices: 1012595--1015468 Score: 4978
Period size: 935 Copynumber: 3.1 Consensus size: 934
1012585 AAAAGAATAT
1012595 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
* *
1012660 TACCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTAAGTTCCC
66 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
* *
1012725 CAAAATGGTTGGTTGCGTGTAAAGTTGTTATAAGAGTTACCATAAGAATTGTTGCAGATGTAATA
131 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCA-ATGTAATA
1012790 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
195 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
1012855 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
260 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
*
1012920 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTACATCCAAT
325 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAAT
1012985 TCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTG
390 TCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTG
* *
1013050 ACCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTA
455 AGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTG
*
1013115 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCGTTATAGAAATCTCAATTTGTGTTTCTG
520 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCTG
1013180 GTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGA
585 GTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGA
* *
1013245 TTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAACATTCATTATTGGCGG
650 TTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCGG
* *
1013310 GTTAAATTGCAAAACAAACTTTGTTACTAGTGCATCCCAAGAAGTAATTGATCCGGTAGATAGCC
715 GTTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGCC
* * * *
1013375 TAAAAAACCAAGTACGGGCTCTTCCGTATAAGAAATAAGGAAATAATTACATCTTCTAGGCATCA
780 TAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCA
1013440 TCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGT
845 TCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGT
1013505 GTCGATGCAATAACTAGATAGGAAC
910 GTCGATGCAATAACTAGATAGGAAC
1013530 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1013595 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
66 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
1013660 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCATATGTAATA
131 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCA-ATGTAATA
*
1013725 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCGATGGTTATCACTACAAATCTC
195 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
1013790 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
260 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
*
1013855 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTACGAG-TATTGCATCCAA
325 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCG-GTTATTGCATCCAA
1013919 TTCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCT
389 TTCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCT
1013984 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCT
454 GAGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCT
* *
1014049 GATGCGTCGACAAGTTTCCTTGTATATGAATTAAGCCCATTATAGAAATCTCAATTTGTGTTTCT
519 GATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCT
*
1014114 GGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATATATAATGTTCCCATGTGGTTTGAAG
584 GGTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAG
*
1014179 ATTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGACG
649 ATTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCG
*
1014244 GGTTAAATTGCAAAACAAACTGTGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGC
714 GGTTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGC
* *
1014309 CTAAAAACCCAAGTACGGGCTCTTCCCTATATGGAATAAGGAAATAATTGCATCTTCAAGGCATC
779 CTAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATC
*
1014374 ATCAGGTTATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAG
844 ATCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAG
1014439 TG-CGGATGCAATAACTAGATAGGAAC
909 TGTC-GATGCAATAACTAGATAGGAAC
*
1014465 GAGATAAATTGTGAGGATATTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
* * * *
1014530 TGCCCTAAGTAGATGTATTCCCATATCTAAATGTCACAGTATTTTGTCTAGCATTCTGAGCTCCA
66 TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
* *
1014595 CAAAACGGTTGGTTGCGTGCAAAGTTGTTGTAAGAGTTAACATAAGAATTGTTGCGAATGTAATA
131 CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGC-AATGTAATA
* *
1014660 ATATAACAGGCATTCTCTGCAGATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
195 ATATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTC
* * * *
1014725 ACAACAAAAAGTAGGAACATCAACTTGTTGAGCGACTTGCATAGGTGCAATGCCACTAGTCTATT
260 ACAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATT
* * *
1014790 ACATATTTTTAATCATGTTTGTGAGAGAAGAAACTTGAGCACTTACTGCGGTTATTGCATCCAAT
325 GCATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAAT
* * * *
1014855 TCAATAACTCCTGGACTAGTTTTTGCTTGTGCAACTATGGAGATAAGGTATTGATAATCATTATG
390 TCAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTG
* * * *
1014920 AGCAATTCTCTCGAGAATTCTCACAGCATCATTATAAGTGCAATTCAACAGAGGTCCATTGGCCG
455 AGCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTG
* *
1014985 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAAAAATCTCAATTTGTGTTTTTG
520 ATGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCTG
* * *
1015050 GTTGAATGTCGTGCAGGGGACAAAGTTAAAGTAAAGATTTATAATGTTCCCATGTGGTGTGAAGA
585 GTTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGA
* * * * * **
1015115 TTTTCATCATCCAGCTGATGGTAAGTAGTAATATCATTTTGAAGACAAGCATTTATTGTTGGCAA
650 TTTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCGG
* *
1015180 GTTAAATCGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGGTAGCC
715 GTTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGCC
*
1015245 CAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCA
780 TAAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCA
* ** *
1015310 TCATGATATCATAAGGAATAAGGATATATCGATCCCACAGGTCTGGTTGTGTTCTTTCTTTCTAT
845 TCAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGG-T-TG-CCTTT-TTTCTAT
*
1015375 TAGTGTCGATGCAATAACTAGATAGAAAC
906 TAGTGTCGATGCAATAACTAGATAGGAAC
* * * * *
1015404 AAGATAAATTGTGAGGATAGTTGTCAGAGCAACAACATGAAAATAATGAAATAAAATATGATAAT
1 GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
1015469 GAAAAATTGG
Statistics
Matches: 1844, Mismatches: 86, Indels: 14
0.95 0.04 0.01
Matches are distributed among these distances:
934 2 0.00
935 1740 0.94
936 3 0.00
937 2 0.00
938 4 0.00
939 92 0.05
940 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.31
Consensus pattern (934 bp):
GAGATAAATTGTGAGGATAGTTGTTAGAGCAACAACTTGAAAACAATAAAATAAAATATGATAAT
TGCCCTGAGTAGATGTATTCCCATATCTAAATGTCGCAGTATTTTGTCTAGCATTCTGAGTTCCC
CAAAACGGTTGGTTGCGTGTAAAGTTGTTGTAAGAGTTACCATAAGAATTGTTGCAATGTAATAA
TATAACAGGCATTCTCTACATATTGTGGTCAATCTTCATAGCTATGGTTATCACTACAAATCTCA
CAACAAAAAGTAGGAAAATCAACTTGTTGAGCAACTTGTATAGGTGCAACGCCACTAGTCTATTG
CATATTTTTAATCATGTTTGTGAGATAAGAAACTTGAGCACTTAGTGCGGTTATTGCATCCAATT
CAATAACTCCTGGAGTAGCTTTTGCTTGTGCAACTATGGATATAAGGTATTGATAATCATTCTGA
GCAATTCTCTCAAGAATTCTCACAGCATCATTATAAGTACAATCCAACAGAGGTCCATTGGCTGA
TGCATCGACAAGTTTCCTTGTATATGAATTCAGCCCATTATAGAAATCTCAATTTGTGTTTCTGG
TTGAATGTCGTGCATGGGACAAAGTCAAAGTAAAGATTTATAATGTTCCCATGTGGTTTGAAGAT
TTTCATCATCCAACTGATGGTAAGCAATAATATCATTTTGAAGACGAGCATTCATTGTTGGCGGG
TTAAATTGCAAAACAAACTATGTTACTAGTGCATCCCAAGAAGTAATTGATCTGGTAGATAGCCT
AAAAAACCAAGTACGGGCTCTTCCCTATAAGGAATAAGGAAATAATTGCATCTTCAAGGCATCAT
CAGGATATCATAAGGAATAAGGATATATCGATCCCACAGGGATGGTTGCCTTTTTTCTATTAGTG
TCGATGCAATAACTAGATAGGAAC
Found at i:1016705 original size:23 final size:24
Alignment explanation
Indices: 1016643--1016717 Score: 116
Period size: 24 Copynumber: 3.2 Consensus size: 24
1016633 TAAACACGTG
* *
1016643 ATTCTGTAAGTTCCTTTGTGGCAT
1 ATTCTATAAGTTCCTTTGTGGCGT
1016667 ATTCTATAAGTTCCTTTGTGGCGT
1 ATTCTATAAGTTCCTTTGTGGCGT
*
1016691 ATT-TATAAGTGCCTTTGTGGCGT
1 ATTCTATAAGTTCCTTTGTGGCGT
1016714 ATTC
1 ATTC
1016718 GAGGTTGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 22 0.47
24 25 0.53
ACGTcount: A:0.17, C:0.16, G:0.21, T:0.45
Consensus pattern (24 bp):
ATTCTATAAGTTCCTTTGTGGCGT
Found at i:1024048 original size:12 final size:13
Alignment explanation
Indices: 1024023--1024052 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
1024013 AGGGCTATAA
1024023 TTATTGCATTTAT
1 TTATTGCATTTAT
1024036 TTATTGC-TTTAT
1 TTATTGCATTTAT
1024048 TTATT
1 TTATT
1024053 CATGTATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:1030451 original size:213 final size:213
Alignment explanation
Indices: 1030084--1030515 Score: 864
Period size: 213 Copynumber: 2.0 Consensus size: 213
1030074 GGCTTGGTTC
1030084 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
1 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
1030149 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
66 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
1030214 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
131 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
1030279 ATAATTTACCCCATCTCA
196 ATAATTTACCCCATCTCA
1030297 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
1 GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
1030362 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
66 TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
1030427 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
131 TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
1030492 ATAATTTACCCCATCTCA
196 ATAATTTACCCCATCTCA
1030510 GATAGT
1 GATAGT
1030516 TCATGGGTAA
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 219 1.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (213 bp):
GATAGTAGATCAGACTTCTCAATGCCGAGGCGTCGCTGTCTACTCAAATTGAAGTTTCAGTAATT
TCTAAACCATTATTTCGCCCCGATTCGTTCCTCACACATGGATCCATGAGTTGAATTGCCAGAAT
TATATTTTTTTATTAATTTTTGTTGCGCAATGGGGGTACCAGCTTTCCAACAGTTAGATGCGGGT
ATAATTTACCCCATCTCA
Found at i:1047378 original size:26 final size:26
Alignment explanation
Indices: 1047341--1047576 Score: 357
Period size: 26 Copynumber: 9.1 Consensus size: 26
1047331 GTAATAGGCC
* *
1047341 TAAATTATCGAAATACCCTCTATGGG
1 TAAATTACCGAAATACCCTCGATGGG
1047367 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
1047393 TAAATTACTGAAATACTCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
1047419 TAAATTATCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
1047445 TAAATTACCAAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
1047471 TAAATTATCGAATTACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
1047497 TAAATTACCGAAATACCCTCGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
*
1047523 TAAATTACCGAAATACCCTTGATGGG
1 TAAATTACCGAAATACCCTCGATGGG
* *
1047549 TAAATTATCGAAATAGCCC-CGAAGGG
1 TAAATTACCGAAATA-CCCTCGATGGG
1047575 TA
1 TA
1047577 GAATGACTGT
Statistics
Matches: 191, Mismatches: 18, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
26 188 0.98
27 3 0.02
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (26 bp):
TAAATTACCGAAATACCCTCGATGGG
Found at i:1047807 original size:26 final size:26
Alignment explanation
Indices: 1047778--1047827 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1047768 GCATATAGTG
* *
1047778 TACTGGCAACTCTGCTGCGATATTAT
1 TACTGGCAACTATGCTGCAATATTAT
*
1047804 TACTGGCAGCTATGCTGCAATATT
1 TACTGGCAACTATGCTGCAATATT
1047828 GGTGTGTGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (26 bp):
TACTGGCAACTATGCTGCAATATTAT
Found at i:1049140 original size:15 final size:14
Alignment explanation
Indices: 1049115--1049162 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
1049105 AATTTGAGAG
*
1049115 AAGAAAAAAAGAAA
1 AAGAGAAAAAGAAA
*
1049129 TGAGAGAAAAAGAAA
1 -AAGAGAAAAAGAAA
1049144 AAGAGATAAAAGAAA
1 AAGAGA-AAAAGAAA
1049159 AAGA
1 AAGA
1049163 AATTGAGAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 5 0.17
15 24 0.83
ACGTcount: A:0.75, C:0.00, G:0.21, T:0.04
Consensus pattern (14 bp):
AAGAGAAAAAGAAA
Found at i:1049146 original size:21 final size:21
Alignment explanation
Indices: 1049109--1049164 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
1049099 TGAATGAATT
*
1049109 TGAGAGAAGAA-AAAAAGAAA
1 TGAGAGAAAAAGAAAAAGAAA
*
1049129 TGAGAGAAAAAGAAAAAGAGA
1 TGAGAGAAAAAGAAAAAGAAA
* *
1049150 TAAAAGAAAAAGAAA
1 TGAGAGAAAAAGAAA
1049165 TTGAGAGTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 10 0.32
21 21 0.68
ACGTcount: A:0.71, C:0.00, G:0.23, T:0.05
Consensus pattern (21 bp):
TGAGAGAAAAAGAAAAAGAAA
Found at i:1055107 original size:15 final size:14
Alignment explanation
Indices: 1055084--1055142 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 14
1055074 TGCATAATAA
1055084 AATAAAATAAAAATCT
1 AATAAAATAAAAA--T
1055100 AA-AAAATAAAAAT
1 AATAAAATAAAAAT
1055113 AATAACAATAAAAATT
1 AATAA-AATAAAAA-T
1055129 AATAAAATATAAAA
1 AATAAAATA-AAAA
1055143 CTAAATGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.08
14 2 0.05
15 22 0.56
16 12 0.31
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAAATAAAAAT
Found at i:1064547 original size:25 final size:25
Alignment explanation
Indices: 1064513--1064565 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
1064503 ATTGCATGGG
1064513 GTTCAAGATGATTTCAAATGAGGGA
1 GTTCAAGATGATTTCAAATGAGGGA
*
1064538 GTTCAAGATGATTTGAAATGAGGGA
1 GTTCAAGATGATTTCAAATGAGGGA
1064563 GTT
1 GTT
1064566 TCTGATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.34, C:0.06, G:0.30, T:0.30
Consensus pattern (25 bp):
GTTCAAGATGATTTCAAATGAGGGA
Found at i:1068588 original size:7 final size:7
Alignment explanation
Indices: 1068576--1068604 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
1068566 TATATTACTA
1068576 TTGTTCT
1 TTGTTCT
1068583 TTGTTCT
1 TTGTTCT
1068590 TTGTTCT
1 TTGTTCT
1068597 TTGTTCT
1 TTGTTCT
1068604 T
1 T
1068605 AGTATTCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.00, C:0.14, G:0.14, T:0.72
Consensus pattern (7 bp):
TTGTTCT
Found at i:1078114 original size:23 final size:23
Alignment explanation
Indices: 1078066--1078119 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
1078056 AGATTTATCA
*
1078066 ATTTAAG--TTTTAAAATCAATG
1 ATTTAAGCATTTTAAAATCAAAG
1078087 ATTTAAGCATTTTAAAATCCAAAG
1 ATTTAAGCATTTTAAAAT-CAAAG
*
1078111 -TTTATGCAT
1 ATTTAAGCAT
1078120 GTCTTTGGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 7 0.25
23 17 0.61
24 4 0.14
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (23 bp):
ATTTAAGCATTTTAAAATCAAAG
Found at i:1085415 original size:33 final size:33
Alignment explanation
Indices: 1085373--1085439 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
1085363 TCAAAACTTA
1085373 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1085406 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1 TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
1085439 T
1 T
1085440 TAAAAGTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (33 bp):
TAGCAAAAGTATCAATCAAACAGAATCTAGGAT
Found at i:1089385 original size:40 final size:40
Alignment explanation
Indices: 1089314--1089402 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
1089304 AAATATATAA
* * *
1089314 ATTTCGATTAATTCGGTTATCAAACCAAATTAACTGAAAT
1 ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
** *
1089354 ATTTCGATTAATTCAGTTAACGGACCGAATTAACCGAAAT
1 ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
1089394 ATTTCGATT
1 ATTTCGATT
1089403 CAACTAATGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (40 bp):
ATTTCGATTAATTCAGTTAACAAACCAAATTAACCGAAAT
Found at i:1096831 original size:17 final size:19
Alignment explanation
Indices: 1096798--1096836 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1096788 ATAGATTTTG
1096798 AAACAAATAACTGTAAAAC
1 AAACAAATAACTGTAAAAC
*
1096817 AAACAAA-AA-TGTAAATC
1 AAACAAATAACTGTAAAAC
1096834 AAA
1 AAA
1096837 GGCAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 2 0.11
19 7 0.37
ACGTcount: A:0.67, C:0.13, G:0.05, T:0.15
Consensus pattern (19 bp):
AAACAAATAACTGTAAAAC
Found at i:1099105 original size:26 final size:26
Alignment explanation
Indices: 1099073--1099139 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
1099063 ATAAAAAATA
* *
1099073 ACCAAAATGTTAT-TTTTTTTTCATTT
1 ACCAAAATATTATAATTTTTTT-ATTT
*
1099099 ACTAAAATATTATAAATTTTTTTATTT
1 ACCAAAATATTAT-AATTTTTTTATTT
1099126 ACCAAAATA-TATAA
1 ACCAAAATATTATAA
1099140 AAAAAAATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.06
26 14 0.40
27 12 0.34
28 7 0.20
ACGTcount: A:0.40, C:0.09, G:0.01, T:0.49
Consensus pattern (26 bp):
ACCAAAATATTATAATTTTTTTATTT
Found at i:1099140 original size:26 final size:28
Alignment explanation
Indices: 1099087--1099140 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1099077 AAATGTTATT
*
1099087 TTTTTTTCATTTACTAAAATATTATAAA
1 TTTTTTTCATTTACCAAAATATTATAAA
1099115 TTTTTTT-ATTTACCAAAATA-TATAAA
1 TTTTTTTCATTTACCAAAATATTATAAA
1099141 AAAAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 6 0.24
27 12 0.48
28 7 0.28
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (28 bp):
TTTTTTTCATTTACCAAAATATTATAAA
Found at i:1099202 original size:27 final size:27
Alignment explanation
Indices: 1099172--1099234 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
1099162 AAAAAACTTG
* *
1099172 TGGCGGCACCAAAGGTGTCAAAGTGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
* *
1099199 TGGCAGCACTAAAGGTGCCAAAGAGAT
1 TGGCGGCACCAAAGGTGCCAAAGAGAT
1099226 TGGCGGCAC
1 TGGCGGCAC
1099235 AGGACTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.30, C:0.21, G:0.33, T:0.16
Consensus pattern (27 bp):
TGGCGGCACCAAAGGTGCCAAAGAGAT
Done.