Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
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: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 101 of 205
Found at i:29666602 original size:33 final size:32
Alignment explanation
Indices: 29666553--29666616 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
29666543 CTCGCTGCAA
* *
29666553 TCTGGTGGCTTCGCCACATATATATATATTTGT
1 TCTGGTGGCCTAGCCACA-ATATATATATTTGT
* *
29666586 TCTGGTGGCCTAGCCACAATATCTGTATTTG
1 TCTGGTGGCCTAGCCACAATATATATATTTG
29666617 GTGTCTTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (32 bp):
TCTGGTGGCCTAGCCACAATATATATATTTGT
Found at i:29684821 original size:33 final size:33
Alignment explanation
Indices: 29684778--29684840 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
29684768 CTACAGAGTC
* * * *
29684778 TAATTTGGATTACTAGTCTAGGCTAAATCCAGT
1 TAATTAGGATTACCAATCCAGGCTAAATCCAGT
29684811 TAATTAGGATTACCAATCCAGGCTAAATCC
1 TAATTAGGATTACCAATCCAGGCTAAATCC
29684841 TAATTGAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (33 bp):
TAATTAGGATTACCAATCCAGGCTAAATCCAGT
Found at i:29689210 original size:30 final size:31
Alignment explanation
Indices: 29689175--29689234 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
29689165 ATGGTTATTG
* *
29689175 AACTATTC-AAATTTTTTATTTAAGCCACTA
1 AACTATTCAAAAGTTTTTATTCAAGCCACTA
*
29689205 AACTATTCAAAAGTTTTTATTCAAGTCACT
1 AACTATTCAAAAGTTTTTATTCAAGCCACT
29689235 GGGTTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.42
Consensus pattern (31 bp):
AACTATTCAAAAGTTTTTATTCAAGCCACTA
Found at i:29692560 original size:16 final size:16
Alignment explanation
Indices: 29692539--29692571 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29692529 AAAAATTCAA
*
29692539 GATTTCGGGATTTTTG
1 GATTTCGGGATATTTG
29692555 GATTTCGGGATATTTG
1 GATTTCGGGATATTTG
29692571 G
1 G
29692572 GGCGTTACAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.06, G:0.33, T:0.45
Consensus pattern (16 bp):
GATTTCGGGATATTTG
Found at i:29708158 original size:21 final size:21
Alignment explanation
Indices: 29708133--29708198 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
29708123 TTTCATTAAA
29708133 TATATGAAAATATATTAATTT
1 TATATGAAAATATATTAATTT
* **
29708154 TATATAAATAATA-ATTAAAGT
1 TATATGAA-AATATATTAATTT
**
29708175 T-TATGATCATATATTAAATTT
1 TATATGAAAATATATT-AATTT
29708196 TAT
1 TAT
29708199 TATTATATTT
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
19 3 0.09
20 7 0.21
21 18 0.55
22 5 0.15
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (21 bp):
TATATGAAAATATATTAATTT
Found at i:29708192 original size:20 final size:19
Alignment explanation
Indices: 29708127--29708216 Score: 58
Period size: 20 Copynumber: 4.6 Consensus size: 19
29708117 ATGTAATTTC
* **
29708127 ATTAAATATATGAAAATAT
1 ATTAAATTTATGATCATAT
* *
29708146 ATTAATTTTAT-ATAAATAAT
1 ATTAAATTTATGAT-CAT-AT
29708166 AATTAAAGTTTATGATCATAT
1 -ATTAAA-TTTATGATCATAT
* *
29708187 ATTAAATTTTATTATTATAT
1 ATTAAA-TTTATGATCATAT
29708207 -TTAAATTTAT
1 ATTAAATTTAT
29708217 AGTTATTATA
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
18 6 0.10
19 17 0.29
20 19 0.33
21 7 0.12
22 7 0.12
23 2 0.03
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (19 bp):
ATTAAATTTATGATCATAT
Found at i:29708207 original size:18 final size:20
Alignment explanation
Indices: 29708184--29708227 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
29708174 TTTATGATCA
29708184 TATATTAAATTT-TA-TTAT
1 TATATTAAATTTATAGTTAT
29708202 TATATTTAAATTTATAGTTAT
1 TATA-TTAAATTTATAGTTAT
29708223 TATAT
1 TATAT
29708228 AATATATGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 8 0.35
20 3 0.13
21 8 0.35
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TATATTAAATTTATAGTTAT
Found at i:29708955 original size:26 final size:26
Alignment explanation
Indices: 29708917--29708989 Score: 110
Period size: 26 Copynumber: 2.8 Consensus size: 26
29708907 GGTGCTTTGA
*
29708917 GAGCGTTTAGTGCTCTAGTGCAGGAAG
1 GAGCG-TTGGTGCTCTAGTGCAGGAAG
29708944 GAGCGTTGGTGCTCTAGTGCAGGAAG
1 GAGCGTTGGTGCTCTAGTGCAGGAAG
* *
29708970 GAGCATTGGTGCTCTTGTGC
1 GAGCGTTGGTGCTCTAGTGC
29708990 CTCGCAAGCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
26 38 0.88
27 5 0.12
ACGTcount: A:0.18, C:0.16, G:0.38, T:0.27
Consensus pattern (26 bp):
GAGCGTTGGTGCTCTAGTGCAGGAAG
Found at i:29713029 original size:42 final size:43
Alignment explanation
Indices: 29712916--29713029 Score: 124
Period size: 43 Copynumber: 2.7 Consensus size: 43
29712906 GGAATTTAGA
*
29712916 AATCCGAGCTCGTTGAGCA-GTCCGAGTTCGTGATATATGTGAG
1 AATCCGAGCTCGTTGAG-AGGTCCAAGTTCGTGATATATGTGAG
** * ** * *
29712959 AATCTAAACTTTTTGAGTGGTCCAAGTTCGTGATCTATGTG-G
1 AATCCGAGCTCGTTGAGAGGTCCAAGTTCGTGATATATGTGAG
*
29713001 TATCCGAGCTCGTTGAGAGGTCCAAGTTC
1 AATCCGAGCTCGTTGAGAGGTCCAAGTTC
29713030 ATTATGGATG
Statistics
Matches: 55, Mismatches: 15, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
42 23 0.42
43 32 0.58
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (43 bp):
AATCCGAGCTCGTTGAGAGGTCCAAGTTCGTGATATATGTGAG
Found at i:29714944 original size:125 final size:125
Alignment explanation
Indices: 29714755--29715004 Score: 455
Period size: 125 Copynumber: 2.0 Consensus size: 125
29714745 AATGGTAACA
*
29714755 AAAGGCTGGGAAAATAGCCTAAGTACTAGTCACACGGGCAGAGACACGTCCATGTGTCTCAACCG
1 AAAGGCTGGGAAAATAGCCTAAGTACTAGTCACACGGGCAGAGACACGGCCATGTGTCTCAACCG
* *
29714820 TGTGGAGGACACGGCCTAGCGCACGGGTGTGTGGCCTGACTGTGTGGTTAAATTTGTTTT
66 TGTGGAGGACACGGCCTAGCACACGGGTGTGTGGCCTGACCGTGTGGTTAAATTTGTTTT
*
29714880 AAAGGCTTGGAAAATAGCCTAAGTACTAGTCACACGGGCAGAGACACGGCCATGTGTCTCAACCG
1 AAAGGCTGGGAAAATAGCCTAAGTACTAGTCACACGGGCAGAGACACGGCCATGTGTCTCAACCG
*
29714945 TGTGGAGGACACGGCCTAGCACACGGGTGTGTGGCCTGGCCGTGTGGTTAAATTTGTTTT
66 TGTGGAGGACACGGCCTAGCACACGGGTGTGTGGCCTGACCGTGTGGTTAAATTTGTTTT
29715005 GATGACGTCA
Statistics
Matches: 120, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
125 120 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.24
Consensus pattern (125 bp):
AAAGGCTGGGAAAATAGCCTAAGTACTAGTCACACGGGCAGAGACACGGCCATGTGTCTCAACCG
TGTGGAGGACACGGCCTAGCACACGGGTGTGTGGCCTGACCGTGTGGTTAAATTTGTTTT
Found at i:29720601 original size:44 final size:41
Alignment explanation
Indices: 29720518--29720615 Score: 126
Period size: 44 Copynumber: 2.3 Consensus size: 41
29720508 GTCCTATACA
* *
29720518 GGTCTTACACGAAATCAAATACTATGCCAATGTCTCAGACAT
1 GGTCTTACACGAAATCAAATAC-ATGCCAACGTCCCAGACAT
29720560 GGTCTTACACGTAAATCATAAGTTA-ATGCCAACGTCCCAGACAT
1 GGTCTTACACG-AAATCA-AA--TACATGCCAACGTCCCAGACAT
29720604 GGTCTTACACGA
1 GGTCTTACACGA
29720616 TAACACATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
42 11 0.22
43 7 0.14
44 30 0.60
46 2 0.04
ACGTcount: A:0.34, C:0.24, G:0.16, T:0.26
Consensus pattern (41 bp):
GGTCTTACACGAAATCAAATACATGCCAACGTCCCAGACAT
Found at i:29723575 original size:32 final size:32
Alignment explanation
Indices: 29723539--29723602 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
29723529 TGGATAATCC
*
29723539 ATCGAGACTTTTGAGAAACTCAACGGGATTAA
1 ATCGAGACTTTCGAGAAACTCAACGGGATTAA
29723571 ATCGAGACTTTCGAGAAACTCAACGGGATTAA
1 ATCGAGACTTTCGAGAAACTCAACGGGATTAA
29723603 TATGATATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (32 bp):
ATCGAGACTTTCGAGAAACTCAACGGGATTAA
Found at i:29726235 original size:45 final size:45
Alignment explanation
Indices: 29726184--29726273 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
29726174 TAAACGTTGA
29726184 GTAAATTCAGTCATAATAGGACATAATGAGATGATTTAATAAGAT
1 GTAAATTCAGTCATAATAGGACATAATGAGATGATTTAATAAGAT
29726229 GTAAATTCAGTCATAATAGGACATAATGAGATGATTTAATAAGAT
1 GTAAATTCAGTCATAATAGGACATAATGAGATGATTTAATAAGAT
29726274 ATGATGTGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.44, C:0.07, G:0.18, T:0.31
Consensus pattern (45 bp):
GTAAATTCAGTCATAATAGGACATAATGAGATGATTTAATAAGAT
Found at i:29736434 original size:8 final size:7
Alignment explanation
Indices: 29736417--29736502 Score: 82
Period size: 7 Copynumber: 11.7 Consensus size: 7
29736407 AAACAGAGCA
29736417 AGGGTTT
1 AGGGTTT
29736424 AGGGTTTT
1 AGGG-TTT
*
29736432 AGGATTTT
1 AGG-GTTT
*
29736440 AGGATTT
1 AGGGTTT
*
29736447 AAGGTTT
1 AGGGTTT
29736454 AGGGTTTT
1 AGGG-TTT
29736462 AGGGTTT
1 AGGGTTT
*
29736469 AAGGTTT
1 AGGGTTT
29736476 AGGGTTT
1 AGGGTTT
*
29736483 ATGGTTTT
1 A-GGGTTT
*
29736491 ATGGTTT
1 AGGGTTT
29736498 AGGGT
1 AGGGT
29736503 CCTATATTTT
Statistics
Matches: 64, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
7 39 0.61
8 25 0.39
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (7 bp):
AGGGTTT
Found at i:29736461 original size:22 final size:22
Alignment explanation
Indices: 29736429--29736502 Score: 96
Period size: 22 Copynumber: 3.4 Consensus size: 22
29736419 GGTTTAGGGT
*
29736429 TTTAGGATTTTAGGATTTAAGG
1 TTTAGGGTTTTAGGATTTAAGG
*
29736451 TTTAGGGTTTTAGGGTTTAAGG
1 TTTAGGGTTTTAGGATTTAAGG
* *
29736473 TTTAGGG-TTTATGGTTTTATGG
1 TTTAGGGTTTTA-GGATTTAAGG
29736495 TTTAGGGT
1 TTTAGGGT
29736503 CCTATATTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
21 4 0.09
22 42 0.91
ACGTcount: A:0.19, C:0.00, G:0.32, T:0.49
Consensus pattern (22 bp):
TTTAGGGTTTTAGGATTTAAGG
Found at i:29738799 original size:28 final size:30
Alignment explanation
Indices: 29738735--29738803 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
29738725 ATGGGGCTGA
29738735 CCGTGTGTCACACACGGTCTAGACACACGC
1 CCGTGTGTCACACACGGTCTAGACACACGC
*
29738765 CCGTGTGTCACACACGG-CTTAGACACATGC
1 CCGTGTGTCACACACGGTC-TAGACACACGC
*
29738795 CTGTGTGTC
1 CCGTGTGTC
29738804 TACCCGTGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
29 1 0.03
30 35 0.97
ACGTcount: A:0.20, C:0.33, G:0.25, T:0.22
Consensus pattern (30 bp):
CCGTGTGTCACACACGGTCTAGACACACGC
Found at i:29751575 original size:48 final size:47
Alignment explanation
Indices: 29751375--29751579 Score: 177
Period size: 48 Copynumber: 4.4 Consensus size: 47
29751365 GGTTATGTAC
* *
29751375 GATCCCATGTAAGACCATGTATGAGGCATGGCATTGGCATCGATATGT
1 GATCCCATGTAAGACCATGTCT-AGGCATGGCATTGGCATCGATATAT
* ** * * *
29751423 AATTTCGTGTAAGACCATAG-CTAGGC-T---ATCGGCATCGATATGT
1 GATCCCATGTAAGACCAT-GTCTAGGCATGGCATTGGCATCGATATAT
* * * *
29751466 GATCCCATGTAAGACCATGTCTAGGACATGACATTAGCATCGATCTAC
1 GATCCCATGTAAGACCATGTCTAGG-CATGGCATTGGCATCGATATAT
** * * *
29751514 GATCCCACATAAGACCATGTCTGGGACGTGGCATTGGCATCAATATAT
1 GATCCCATGTAAGACCATGTCTAGG-CATGGCATTGGCATCGATATAT
*
29751562 GATTCCATGTAAGACCAT
1 GATCCCATGTAAGACCAT
29751580 ATTCGGGATA
Statistics
Matches: 123, Mismatches: 27, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
42 1 0.01
43 34 0.28
44 1 0.01
45 1 0.01
46 1 0.01
47 4 0.03
48 80 0.65
49 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (47 bp):
GATCCCATGTAAGACCATGTCTAGGCATGGCATTGGCATCGATATAT
Found at i:29751813 original size:26 final size:26
Alignment explanation
Indices: 29751751--29751804 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
29751741 ATTGAGATTA
** *
29751751 TGAATCGATGAGACCTTGGTAGGATG
1 TGAATCGATGAGACCTCAGTAAGATG
29751777 TGAATCGATGAGACCTCAGTAAGATG
1 TGAATCGATGAGACCTCAGTAAGATG
29751803 TG
1 TG
29751805 GATGAATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (26 bp):
TGAATCGATGAGACCTCAGTAAGATG
Found at i:29751935 original size:23 final size:21
Alignment explanation
Indices: 29751902--29751948 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
29751892 ATAAATATTA
29751902 TTATGTTATG-TGTATAATAAT
1 TTATGTTATGTTGT-TAATAAT
*
29751923 TTATGGTTAATGTTGTTAATCAT
1 TTAT-GTT-ATGTTGTTAATAAT
29751946 TTA
1 TTA
29751949 CATGCAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 4 0.18
22 3 0.14
23 12 0.55
24 3 0.14
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (21 bp):
TTATGTTATGTTGTTAATAAT
Found at i:29756967 original size:47 final size:47
Alignment explanation
Indices: 29756898--29757120 Score: 161
Period size: 47 Copynumber: 4.7 Consensus size: 47
29756888 TATAATGCCA
* *
29756898 ATGCCTTGTCCCAGGCATGGTCTTACACTGGCTCGTC-TATCAAGTCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCATATCAAGTCG
* ** *
29756945 ATGCCATGTCCCAGACATGGTCTTACACTGACTCTCACATATCCGTGTGG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCT--CATAT-CAAGTCG
* * * * * ** *
29756995 ATGCCATTTCCCAGACATGGTCTTAGACTGAC-AT-ATTTTGTAGCCG
1 ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-TATCAAGTCG
* * * *
29757041 ATG-CATGTCCCAGACATGTGTTCTTACACTAGCTCTCGTCTCAA-TGCTA
1 ATGCCATGTCCCAGACATG-G-TCTTACACTGGCTCTCATATCAAGT-C-G
29757090 ATGCCATGTCCCAGACAT-GTCTTACACTGGC
1 ATGCCATGTCCCAGACATGGTCTTACACTGGC
29757121 ACACAAATAA
Statistics
Matches: 137, Mismatches: 27, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
45 14 0.10
46 8 0.06
47 53 0.39
48 7 0.05
49 7 0.05
50 48 0.35
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.30
Consensus pattern (47 bp):
ATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATATCAAGTCG
Found at i:29757842 original size:13 final size:13
Alignment explanation
Indices: 29757824--29757848 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29757814 CTAAAAATGC
29757824 AAAAATCATCAAG
1 AAAAATCATCAAG
29757837 AAAAATCATCAA
1 AAAAATCATCAA
29757849 AATCACTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAATCATCAAG
Found at i:29764830 original size:23 final size:23
Alignment explanation
Indices: 29764804--29764882 Score: 86
Period size: 23 Copynumber: 3.4 Consensus size: 23
29764794 TACCGTAGCC
29764804 CAACTTTTGGCTTTTCGGCATTT
1 CAACTTTTGGCTTTTCGGCATTT
*
29764827 CAACTTTTCGGCTTTTCGACATTT
1 CAACTTTT-GGCTTTTCGGCATTT
*** * *
29764851 TGGCTTTCGGCTTTTTGGCATTT
1 CAACTTTTGGCTTTTCGGCATTT
*
29764874 CAGCTTTTG
1 CAACTTTTG
29764883 TCGATTCATT
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
23 27 0.60
24 18 0.40
ACGTcount: A:0.11, C:0.22, G:0.19, T:0.48
Consensus pattern (23 bp):
CAACTTTTGGCTTTTCGGCATTT
Found at i:29764841 original size:8 final size:8
Alignment explanation
Indices: 29764807--29764881 Score: 57
Period size: 8 Copynumber: 9.6 Consensus size: 8
29764797 CGTAGCCCAA
29764807 CTTTT-GG
1 CTTTTCGG
29764814 CTTTTCGG
1 CTTTTCGG
* **
29764822 CATTTCAA
1 CTTTTCGG
29764830 CTTTTCGG
1 CTTTTCGG
*
29764838 CTTTTCGA
1 CTTTTCGG
29764846 CATTTT-GG
1 C-TTTTCGG
29764854 C-TTTCGG
1 CTTTTCGG
*
29764861 CTTTTTGG
1 CTTTTCGG
* *
29764869 CATTTCAG
1 CTTTTCGG
29764877 CTTTT
1 CTTTT
29764882 GTCGATTCAT
Statistics
Matches: 51, Mismatches: 13, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
6 3 0.06
7 8 0.16
8 36 0.71
9 4 0.08
ACGTcount: A:0.09, C:0.21, G:0.19, T:0.51
Consensus pattern (8 bp):
CTTTTCGG
Found at i:29769091 original size:29 final size:29
Alignment explanation
Indices: 29769024--29769101 Score: 92
Period size: 29 Copynumber: 2.8 Consensus size: 29
29769014 TACATACATG
*
29769024 CATATGGCCCA-CTAGGCCCAATATTATT
1 CATATGGCCCATCTAGGCCCAATATTACT
*
29769052 CAAATGGCCCATCT-GGCCCAAT-TCTCACT
1 CATATGGCCCATCTAGGCCCAATAT-T-ACT
29769081 CATATGGCCCAT-TAGGCCCAA
1 CATATGGCCCATCTAGGCCCAA
29769102 ATCATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 1 0.02
28 20 0.47
29 22 0.51
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.24
Consensus pattern (29 bp):
CATATGGCCCATCTAGGCCCAATATTACT
Found at i:29769214 original size:10 final size:9
Alignment explanation
Indices: 29769183--29769222 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
29769173 GGGCCCAACA
*
29769183 GCCCATTAG
1 GCCCATTTG
*
29769192 GCCCATTTA
1 GCCCATTTG
29769201 GCCCATTTTG
1 GCCCA-TTTG
29769211 GCCCATTTG
1 GCCCATTTG
29769220 GCC
1 GCC
29769223 AATTCTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.35, G:0.20, T:0.30
Consensus pattern (9 bp):
GCCCATTTG
Found at i:29769215 original size:19 final size:18
Alignment explanation
Indices: 29769182--29769218 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
29769172 TGGGCCCAAC
29769182 AGCCCATTAGGCCCATTT
1 AGCCCATTAGGCCCATTT
*
29769200 AGCCCATTTTGGCCCATTT
1 AGCCCA-TTAGGCCCATTT
29769219 GGCCAATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (18 bp):
AGCCCATTAGGCCCATTT
Found at i:29771069 original size:40 final size:39
Alignment explanation
Indices: 29771038--29771247 Score: 233
Period size: 40 Copynumber: 5.3 Consensus size: 39
29771028 GGACTAAGAT
* *
29771038 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
29771078 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
29771118 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* ** *
29771158 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGAT-ACAAATCCGGGTTAAGTC
* * * * *
29771198 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
29771237 CCGAAGGCATT
1 CCGAAGGCATT
29771248 TGAACGAGGA
Statistics
Matches: 153, Mismatches: 13, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
39 33 0.22
40 117 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:29771201 original size:120 final size:120
Alignment explanation
Indices: 29770985--29771247 Score: 300
Period size: 120 Copynumber: 2.2 Consensus size: 120
29770975 TTGAATGCTG
* *
29770985 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
29771049 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
29771105 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* ** * * * *
29771168 TCGTGCGAGTTGTTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
29771224 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
29771248 TGAACGAGGA
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
119 38 0.32
120 73 0.61
121 9 0.08
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:29771267 original size:79 final size:80
Alignment explanation
Indices: 29771038--29771282 Score: 228
Period size: 80 Copynumber: 3.1 Consensus size: 80
29771028 GGACTAAGAT
* * * * * * * ** *
29771038 CCGAAGGCATTTGTGCGAGATAC-AAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGA-GATAC
1 CCGAAGGCATTCGTGCGAGTTACTAAA-ACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGA-GC
29771101 TAAATCCGGGTTAAGTC
64 TAAATCCGGGTTAAGTC
* * * ** ** *
29771118 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
*
29771183 AATCCGGGTTATGTC
66 AATCCGGGTTAAGTC
* * *
29771198 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTGAACGAGGAGCTA
1 CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
* *
29771262 TATCC-GGTTAAATC
66 AATCCGGGTTAAGTC
29771276 CCGAAGG
1 CCGAAGG
29771283 TACGTGATTT
Statistics
Matches: 138, Mismatches: 25, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
78 14 0.10
79 46 0.33
80 75 0.54
81 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGAAGGCATTCGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGAACGAGGAGCTA
AATCCGGGTTAAGTC
Found at i:29774786 original size:46 final size:46
Alignment explanation
Indices: 29774736--29774909 Score: 210
Period size: 46 Copynumber: 3.7 Consensus size: 46
29774726 ACATTTTATA
29774736 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAG
* * * *
29774782 GCCGATGCATGTCCCAGACATGTCATACACTAGC-TATCGTCTCAAT
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTA-CATCTCGAG
* * * *
29774828 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCT-CATAAT-GTG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTAGCT-TACAT-CTCGAG
29774876 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
29774910 ACACAAATAA
Statistics
Matches: 108, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.02
46 57 0.53
47 28 0.26
48 19 0.18
49 1 0.01
50 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (46 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTAGCTTACATCTCGAG
Found at i:29774855 original size:94 final size:92
Alignment explanation
Indices: 29774594--29774909 Score: 256
Period size: 94 Copynumber: 3.4 Consensus size: 92
29774584 AGGGTATAAT
* * * * *
29774594 GCCGATGTAATGTCCC-GACATGGTCCTACACTAGCTCATC-TATCAA-GTTGATACCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCATACACTAGCT-ATCGTCTCAATGCTGAT-GCATGTCCC
* *
29774656 AGACATGGTCTTACACT-GACTCTCATAGATCTAT
62 AGACAT-GTCTTACACTAG-CTCTCATA-AT-GAG
* * * * ** *
29774690 GCCGATGCCATGTCCTAGACATGGTCTTACA-TTGAC-A-CAT-TTTATAGCCGATGCATGTCCC
1 GCCGATG-CATGTCCCAGACAT-GTCATACACTAG-CTATCGTCTCAAT-GCTGATGCATGTCCC
*
29774751 AGACATGTCTTACACTAGCT-TACAT-CTCGAG
62 AGACATGTCTTACACTAGCTCT-CATAAT-GAG
29774782 GCCGATGCATGTCCCAGACATGTCATACACTAGCTATCGTCTCAATGCTGATGCCATGTCCCAGA
1 GCCGATGCATGTCCCAGACATGTCATACACTAGCTATCGTCTCAATGCTGATG-CATGTCCCAGA
* *
29774847 CATGGTCTTACACTGGCTCTCATAATGTG
65 CAT-GTCTTACACTAGCTCTCATAATGAG
*
29774876 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAGACATGTCATACACTAGC
29774910 ACACAAATAA
Statistics
Matches: 181, Mismatches: 24, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
90 8 0.04
91 16 0.09
92 18 0.10
93 18 0.10
94 69 0.38
95 19 0.10
96 19 0.10
97 14 0.08
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCATACACTAGCTATCGTCTCAATGCTGATGCATGTCCCAGAC
ATGTCTTACACTAGCTCTCATAATGAG
Found at i:29780547 original size:28 final size:28
Alignment explanation
Indices: 29780515--29780614 Score: 89
Period size: 28 Copynumber: 3.6 Consensus size: 28
29780505 ACATACCTAT
29780515 ATATGGCCCACTAGGCCCAATCTCTTTC
1 ATATGGCCCACTAGGCCCAATCTCTTTC
* * * *
29780543 ATATGGCCCATTAAGCCCATTCATATTT-
1 ATATGGCCCACTAGGCCCAATC-TCTTTC
* * * *
29780571 ATATGGCCTATTAGGCCCAAATCACATTC
1 ATATGGCCCACTAGGCCC-AATCTCTTTC
29780600 ATATGG--CACTAGGCC
1 ATATGGCCCACTAGGCC
29780615 AAAATTGAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
27 7 0.12
28 37 0.65
29 13 0.23
ACGTcount: A:0.27, C:0.29, G:0.15, T:0.29
Consensus pattern (28 bp):
ATATGGCCCACTAGGCCCAATCTCTTTC
Found at i:29780898 original size:8 final size:8
Alignment explanation
Indices: 29780839--29780900 Score: 52
Period size: 8 Copynumber: 7.8 Consensus size: 8
29780829 GTAGCCAAAC
*
29780839 TTTCAGCT
1 TTTCGGCT
*
29780847 TTTCAGCT
1 TTTCGGCT
*
29780855 TTTCGACT
1 TTTCGGCT
* *
29780863 TTTAGACT
1 TTTCGGCT
*
29780871 TTTTGGCT
1 TTTCGGCT
* *
29780879 TTTTGGCA
1 TTTCGGCT
29780887 TTTCGGCT
1 TTTCGGCT
29780895 TTTCGG
1 TTTCGG
29780901 GATTTGCCGA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 46 1.00
ACGTcount: A:0.10, C:0.19, G:0.19, T:0.52
Consensus pattern (8 bp):
TTTCGGCT
Found at i:29782160 original size:16 final size:16
Alignment explanation
Indices: 29782135--29782166 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29782125 AAATTTGAGA
*
29782135 TTTCAGGATTTTTGGG
1 TTTCAAGATTTTTGGG
29782151 TTTCAAGATTTTTGGG
1 TTTCAAGATTTTTGGG
29782167 ACGTTACAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.06, G:0.28, T:0.50
Consensus pattern (16 bp):
TTTCAAGATTTTTGGG
Found at i:29786585 original size:66 final size:69
Alignment explanation
Indices: 29786455--29786585 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 69
29786445 GGGATGTATC
* * *
29786455 CCATGTAGACAAGAGAGATACGGGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATTCCAAGTG
1 CCATGTAGACAAGAGAGATAC--G-GAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
29786520 AAGGACA
63 AAGGACA
* * * *
29786527 CCATGTAGACAAGAGAGCTAC-GA-GATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTG
1 CCATGTAGACAAGAGAGATACGGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTG
29786586 TTCACCATGT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
66 23 0.44
67 7 0.13
68 2 0.04
72 20 0.38
ACGTcount: A:0.34, C:0.15, G:0.31, T:0.21
Consensus pattern (69 bp):
CCATGTAGACAAGAGAGATACGGAGGATAAATGTAGCTAGGTCACATGGGTGATACCAAGTGAAG
GACA
Found at i:29789338 original size:205 final size:205
Alignment explanation
Indices: 29788986--29789395 Score: 802
Period size: 205 Copynumber: 2.0 Consensus size: 205
29788976 TATGGCCGAA
29788986 TCTGGCGTGTCACATTGAAGTGTTTTAGCGAAAACTTTGTTTTCATTGAAAACCCTTCCTTAAAA
1 TCTGGCGTGTCACATTGAAGTGTTTTAGCGAAAACTTTGTTTTCATTGAAAACCCTTCCTTAAAA
*
29789051 AGTTACATCTCAATTACTTAGTAAAATCTCCTTTTTTGTTGCAAGGCTTTCCTTAAACCATTTGA
66 AGTTACATCTCAATTACTTAGTAAAATCTCCTTTTTTGTTGCAAGGCTTTCCTTAAAACATTTGA
29789116 CTTAAGAAAACTTATCCTTTAAAACTTTAGTTGCGAAAATGTAGTATTAAAGGAAAACCATAGCT
131 CTTAAGAAAACTTATCCTTTAAAACTTTAGTTGCGAAAATGTAGTATTAAAGGAAAACCATAGCT
29789181 TAGAAAATCC
196 TAGAAAATCC
29789191 TCTGGCGTGTCACATTGAAGTGTTTTAGCGAAAACTTTGTTTTCATTGAAAACCCTTCCTTAAAA
1 TCTGGCGTGTCACATTGAAGTGTTTTAGCGAAAACTTTGTTTTCATTGAAAACCCTTCCTTAAAA
*
29789256 AGTTACATCTCAATTACTTAGTAAAATCTCCTTTTTTGTTGCAAGGCTTTGCTTAAAACATTTGA
66 AGTTACATCTCAATTACTTAGTAAAATCTCCTTTTTTGTTGCAAGGCTTTCCTTAAAACATTTGA
29789321 CTTAAGAAAACTTATCCTTTAAAACTTTAGTTGCGAAAATGTAGTATTAAAGGAAAACCATAGCT
131 CTTAAGAAAACTTATCCTTTAAAACTTTAGTTGCGAAAATGTAGTATTAAAGGAAAACCATAGCT
29789386 TAGAAAATCC
196 TAGAAAATCC
29789396 AGGTTCCACT
Statistics
Matches: 203, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
205 203 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (205 bp):
TCTGGCGTGTCACATTGAAGTGTTTTAGCGAAAACTTTGTTTTCATTGAAAACCCTTCCTTAAAA
AGTTACATCTCAATTACTTAGTAAAATCTCCTTTTTTGTTGCAAGGCTTTCCTTAAAACATTTGA
CTTAAGAAAACTTATCCTTTAAAACTTTAGTTGCGAAAATGTAGTATTAAAGGAAAACCATAGCT
TAGAAAATCC
Found at i:29790424 original size:29 final size:27
Alignment explanation
Indices: 29790390--29790447 Score: 71
Period size: 29 Copynumber: 2.1 Consensus size: 27
29790380 TATGGCCCAT
* *
29790390 TCACATTTATGTAGCCCATTAGGCCCAAA
1 TCACATTCATATAGCCC--TAGGCCCAAA
*
29790419 TCACATTCATATGGCCCTAGGCCCAAA
1 TCACATTCATATAGCCCTAGGCCCAAA
29790446 TC
1 TC
29790448 GGATTTACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 12 0.46
29 14 0.54
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (27 bp):
TCACATTCATATAGCCCTAGGCCCAAA
Found at i:29791293 original size:122 final size:122
Alignment explanation
Indices: 29791072--29791316 Score: 463
Period size: 122 Copynumber: 2.0 Consensus size: 122
29791062 TCCAAAGACT
*
29791072 GAGATTCGATACCTATTCCTACCAAAGACTGATTAGAAGAAGTGGGGGACAATAATTGATACTTA
1 GAGATTCGATACCTATTCCTACCAAAGACCGATTAGAAGAAGTGGGGGACAATAATTGATACTTA
*
29791137 GCAAAACAAGCCGATTGGAAGAGCGAACACTTAAACTAGAATCGACTGAGTGGAAAG
66 GCAAAACAAACCGATTGGAAGAGCGAACACTTAAACTAGAATCGACTGAGTGGAAAG
29791194 GAGATTCGATACCTATTCCTACCAAAGACCGATTAGAAGAAGTGGGGGACAATAATTGATACTTA
1 GAGATTCGATACCTATTCCTACCAAAGACCGATTAGAAGAAGTGGGGGACAATAATTGATACTTA
*
29791259 GCAAAACAAACCGATTGGAAGAGCGAACAGTTAAACTAGAATCGACTGAGTGGAAAG
66 GCAAAACAAACCGATTGGAAGAGCGAACACTTAAACTAGAATCGACTGAGTGGAAAG
29791316 G
1 G
29791317 GTAGTGGCGG
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
122 120 1.00
ACGTcount: A:0.40, C:0.16, G:0.24, T:0.20
Consensus pattern (122 bp):
GAGATTCGATACCTATTCCTACCAAAGACCGATTAGAAGAAGTGGGGGACAATAATTGATACTTA
GCAAAACAAACCGATTGGAAGAGCGAACACTTAAACTAGAATCGACTGAGTGGAAAG
Found at i:29799307 original size:6 final size:6
Alignment explanation
Indices: 29799296--29799326 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29799286 GCATTGATGT
29799296 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
1 AAAGGA AAAGGA AAAGGA AAAGGA AAAGGA A
29799327 TGGTTTCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAGGA
Found at i:29817890 original size:57 final size:57
Alignment explanation
Indices: 29817794--29817949 Score: 260
Period size: 57 Copynumber: 2.7 Consensus size: 57
29817784 ATCGTATAAC
* *
29817794 AGGATTACCAGTCCAGGCTAAATCCATTAT-ATAACGTATGCTCAGAGGGGCTCGATT
1 AGGATTACCAGTCCAGGCTAAA-CCCTAATCATAACGTATGCTCAGAGGGGCTCGATT
*
29817851 AGGATTACCAGTCCAGGCTAAACCCTAATCATAATGTATGCTCAGAGGGGCTCGATT
1 AGGATTACCAGTCCAGGCTAAACCCTAATCATAACGTATGCTCAGAGGGGCTCGATT
*
29817908 AGGATTACCAGTCCAGGCTAAACCCTAATCACAACGTATGCT
1 AGGATTACCAGTCCAGGCTAAACCCTAATCATAACGTATGCT
29817950 TGAGAGGTAT
Statistics
Matches: 93, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
56 5 0.05
57 88 0.95
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.24
Consensus pattern (57 bp):
AGGATTACCAGTCCAGGCTAAACCCTAATCATAACGTATGCTCAGAGGGGCTCGATT
Found at i:29818479 original size:20 final size:20
Alignment explanation
Indices: 29818454--29818500 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
29818444 TTAGCACATG
* *
29818454 TTTTCATAAAATTTTAGAAT
1 TTTTCATAAAATTTTACAAC
*
29818474 TTTTCATCAAATTTTACAAC
1 TTTTCATAAAATTTTACAAC
29818494 TTTTCAT
1 TTTTCAT
29818501 TTTAGTCCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.13, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTCATAAAATTTTACAAC
Found at i:29830070 original size:47 final size:47
Alignment explanation
Indices: 29830017--29830378 Score: 620
Period size: 47 Copynumber: 7.7 Consensus size: 47
29830007 TTAGGATTCT
29830017 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29830064 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
*
29830111 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCTTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29830158 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29830205 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
29830252 ATGTGATGAATGTGAAAGTG--TATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
29830297 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * *
29830344 ACGTGGTGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
29830379 TCCCGAAGGG
Statistics
Matches: 300, Mismatches: 13, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
45 45 0.15
47 255 0.85
ACGTcount: A:0.32, C:0.08, G:0.31, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:29830258 original size:22 final size:22
Alignment explanation
Indices: 29830230--29830303 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
29830220 AAGTGTATAT
29830230 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* * ***
29830252 ATGTGATGAATG--TGAAAGTGTAT
1 ATGTGAT-AAGGCCT-AATG-GCCG
29830275 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
29830297 ATGTGAT
1 ATGTGAT
29830304 GAATGTGAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
21 1 0.03
22 21 0.57
23 14 0.38
24 1 0.03
ACGTcount: A:0.30, C:0.11, G:0.31, T:0.28
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:29830553 original size:37 final size:37
Alignment explanation
Indices: 29830497--29830575 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
29830487 CCGAGCTCTA
* * *
29830497 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
29830534 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
29830571 AAGAC
1 AAGAC
29830576 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:29836493 original size:16 final size:16
Alignment explanation
Indices: 29836472--29836506 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
29836462 CACAAAGGTA
29836472 ACTATATTCACTGATC
1 ACTATATTCACTGATC
29836488 ACTATATTCACTGATC
1 ACTATATTCACTGATC
29836504 ACT
1 ACT
29836507 CGATGTTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (16 bp):
ACTATATTCACTGATC
Found at i:29836725 original size:15 final size:15
Alignment explanation
Indices: 29836705--29836735 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
29836695 CCAAATGAAA
29836705 AGTTATTTGCTATAG
1 AGTTATTTGCTATAG
29836720 AGTTATTTGCTATAG
1 AGTTATTTGCTATAG
29836735 A
1 A
29836736 TGCAACTCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (15 bp):
AGTTATTTGCTATAG
Found at i:29841401 original size:34 final size:34
Alignment explanation
Indices: 29841335--29841401 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
29841325 TCGAAAAATA
** *
29841335 TTAAGTTTTGTTTGAAGGATGAATTTTAATGGAG
1 TTAAGTTCCGTTTGAAGGATGAATTTCAATGGAG
* *
29841369 TTAAGTTCCGTTTGAATGATGAATTTCGATGGA
1 TTAAGTTCCGTTTGAAGGATGAATTTCAATGGA
29841402 TATATGTGAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.28, C:0.04, G:0.25, T:0.42
Consensus pattern (34 bp):
TTAAGTTCCGTTTGAAGGATGAATTTCAATGGAG
Found at i:29849703 original size:334 final size:334
Alignment explanation
Indices: 29849094--29849762 Score: 1338
Period size: 334 Copynumber: 2.0 Consensus size: 334
29849084 TGATTTTTGT
29849094 TTATATATCTTGAATTAAAACATAGGCATTTATGCATTGATTGTTTAAACCTCAACACATTAGAG
1 TTATATATCTTGAATTAAAACATAGGCATTTATGCATTGATTGTTTAAACCTCAACACATTAGAG
29849159 AATCAAGTATGATAAGTTGATTTTTAAGAATTTAAAATCTTAGGTTGTTTCCCCAAAGTTTAAGT
66 AATCAAGTATGATAAGTTGATTTTTAAGAATTTAAAATCTTAGGTTGTTTCCCCAAAGTTTAAGT
29849224 ATTACTTTGAGTTGGAATTCACAAGTTTTAACATCAAAAAGCCATAATTTTTGTGATATTTTTTG
131 ATTACTTTGAGTTGGAATTCACAAGTTTTAACATCAAAAAGCCATAATTTTTGTGATATTTTTTG
29849289 AGCCTTTTGAGCATCTATTAATTCTTTCATGCTAACTTTTATTATTGCTTTAAGTGCATCAGTAT
196 AGCCTTTTGAGCATCTATTAATTCTTTCATGCTAACTTTTATTATTGCTTTAAGTGCATCAGTAT
29849354 TGAACTGTTATTCTAGAACTTGCTTGATTATGCATGTTGAGACCACACCATTTGATTTTATATGT
261 TGAACTGTTATTCTAGAACTTGCTTGATTATGCATGTTGAGACCACACCATTTGATTTTATATGT
29849419 CAAAATGAA
326 CAAAATGAA
29849428 TTATATATCTTGAATTAAAACATAGGCATTTATGCATTGATTGTTTAAACCTCAACACATTAGAG
1 TTATATATCTTGAATTAAAACATAGGCATTTATGCATTGATTGTTTAAACCTCAACACATTAGAG
29849493 AATCAAGTATGATAAGTTGATTTTTAAGAATTTAAAATCTTAGGTTGTTTCCCCAAAGTTTAAGT
66 AATCAAGTATGATAAGTTGATTTTTAAGAATTTAAAATCTTAGGTTGTTTCCCCAAAGTTTAAGT
29849558 ATTACTTTGAGTTGGAATTCACAAGTTTTAACATCAAAAAGCCATAATTTTTGTGATATTTTTTG
131 ATTACTTTGAGTTGGAATTCACAAGTTTTAACATCAAAAAGCCATAATTTTTGTGATATTTTTTG
29849623 AGCCTTTTGAGCATCTATTAATTCTTTCATGCTAACTTTTATTATTGCTTTAAGTGCATCAGTAT
196 AGCCTTTTGAGCATCTATTAATTCTTTCATGCTAACTTTTATTATTGCTTTAAGTGCATCAGTAT
29849688 TGAACTGTTATTCTAGAACTTGCTTGATTATGCATGTTGAGACCACACCATTTGATTTTATATGT
261 TGAACTGTTATTCTAGAACTTGCTTGATTATGCATGTTGAGACCACACCATTTGATTTTATATGT
29849753 CAAAATGAA
326 CAAAATGAA
29849762 T
1 T
29849763 AAGGCACTTA
Statistics
Matches: 335, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
334 335 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (334 bp):
TTATATATCTTGAATTAAAACATAGGCATTTATGCATTGATTGTTTAAACCTCAACACATTAGAG
AATCAAGTATGATAAGTTGATTTTTAAGAATTTAAAATCTTAGGTTGTTTCCCCAAAGTTTAAGT
ATTACTTTGAGTTGGAATTCACAAGTTTTAACATCAAAAAGCCATAATTTTTGTGATATTTTTTG
AGCCTTTTGAGCATCTATTAATTCTTTCATGCTAACTTTTATTATTGCTTTAAGTGCATCAGTAT
TGAACTGTTATTCTAGAACTTGCTTGATTATGCATGTTGAGACCACACCATTTGATTTTATATGT
CAAAATGAA
Found at i:29854328 original size:40 final size:40
Alignment explanation
Indices: 29854219--29854329 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
29854209 TTCACAGCTG
** *
29854219 AAGCTATCTCGATCTCGCACACTAAGTGCCATATATAACCA
1 AAGCTATCTCGA-AACGCACACTAAGTGCTATATATAACCA
** * *
29854260 AAATTAT-TCTAATACGCACACTAAGTGCTATATATAGCCA
1 AAGCTATCTCGAA-ACGCACACTAAGTGCTATATATAACCA
29854300 AAGCTATCTCGAAACGCACACTAAGTGCTA
1 AAGCTATCTCGAAACGCACACTAAGTGCTA
29854330 AACATAGTCG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
40 49 0.84
41 9 0.16
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (40 bp):
AAGCTATCTCGAAACGCACACTAAGTGCTATATATAACCA
Found at i:29856190 original size:48 final size:48
Alignment explanation
Indices: 29856128--29856280 Score: 200
Period size: 48 Copynumber: 3.2 Consensus size: 48
29856118 TAGCTGGGTT
*
29856128 ATTGGCATCGATCTATGATCCCATGTAAGTCCATGTCT-AGGATATGGC
1 ATTGGCATCGATCTATGATCCCATGTAAGACCATGTCTGA-GATATGGC
* * * * **
29856176 ATTAGCATCTATCTACGATCCTATGTAAGACCATGTCTGAGACGTGGC
1 ATTGGCATCGATCTATGATCCCATGTAAGACCATGTCTGAGATATGGC
* * *
29856224 ATTGGCATCGATATGTGATCCCATGTAAGACCATATCTGAGATATGGC
1 ATTGGCATCGATCTATGATCCCATGTAAGACCATGTCTGAGATATGGC
29856272 ATTGGCATC
1 ATTGGCATC
29856281 CTACTATGTG
Statistics
Matches: 88, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
48 87 0.99
49 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (48 bp):
ATTGGCATCGATCTATGATCCCATGTAAGACCATGTCTGAGATATGGC
Found at i:29858149 original size:23 final size:24
Alignment explanation
Indices: 29858119--29858167 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 24
29858109 GGGAAAATGG
29858119 AGGAAACAACT-AAACTAAGCATA
1 AGGAAACAACTAAAACTAAGCATA
*
29858142 AGGAAACATCTAAAAACTAAGCATA
1 AGGAAACAACT-AAAACTAAGCATA
29858167 A
1 A
29858168 TTAAAGATGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 10 0.43
25 13 0.57
ACGTcount: A:0.57, C:0.16, G:0.12, T:0.14
Consensus pattern (24 bp):
AGGAAACAACTAAAACTAAGCATA
Found at i:29862010 original size:23 final size:23
Alignment explanation
Indices: 29861983--29862034 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
29861973 ATGTGCCCAA
*
29861983 GGCCCATAATACGGGCCCATGTG
1 GGCCCATAATACAGGCCCATGTG
29862006 GGCCCATAATACAGGCCCATGTG
1 GGCCCATAATACAGGCCCATGTG
29862029 GGCCCA
1 GGCCCA
29862035 CACATCCCCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.23, C:0.33, G:0.29, T:0.15
Consensus pattern (23 bp):
GGCCCATAATACAGGCCCATGTG
Found at i:29874704 original size:24 final size:23
Alignment explanation
Indices: 29874671--29874728 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
29874661 AGTTGAAAAG
29874671 TATAA-AATAAAATAAATAATGATA
1 TATAATAATAAAAT-AAT-ATGATA
*
29874695 -ATAATAATAAAATGATATGATA
1 TATAATAATAAAATAATATGATA
29874717 TATATATAATAA
1 TATA-ATAATAA
29874729 TGTTTGATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 6 0.20
23 9 0.30
24 15 0.50
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (23 bp):
TATAATAATAAAATAATATGATA
Found at i:29877121 original size:26 final size:27
Alignment explanation
Indices: 29877090--29877141 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
29877080 GCTCAAGTAT
*
29877090 AATCA-TACATCTCACAGGGGCATAAC
1 AATCATTACATCACACAGGGGCATAAC
**
29877116 AATCATTTTATCACACAGGGGCATAA
1 AATCATTACATCACACAGGGGCATAA
29877142 TAGTCATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (27 bp):
AATCATTACATCACACAGGGGCATAAC
Found at i:29877134 original size:27 final size:27
Alignment explanation
Indices: 29877102--29877154 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
29877092 TCATACATCT
29877102 CACAGGGGCATAACAATCATTTTATCA
1 CACAGGGGCATAACAATCATTTTATCA
* *
29877129 CACAGGGGCATAATAGTCATTTTATC
1 CACAGGGGCATAACAATCATTTTATC
29877155 GATTAGGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (27 bp):
CACAGGGGCATAACAATCATTTTATCA
Found at i:29883215 original size:17 final size:17
Alignment explanation
Indices: 29883160--29883225 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 17
29883150 ATTTTGTTTC
29883160 TTGTTTATTAT-TATTA
1 TTGTTTATTATCTATTA
*
29883176 GTTATTTTATTATCTTTATTTA
1 -TT-GTTTATTATC--TA-TTA
29883198 TTGTTTATTATCTATTA
1 TTGTTTATTATCTATTA
29883215 TT-TTCTATTAT
1 TTGTT-TATTAT
29883226 TAGTTATATT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
16 2 0.05
17 13 0.32
18 10 0.24
20 9 0.22
21 4 0.10
22 3 0.07
ACGTcount: A:0.23, C:0.05, G:0.05, T:0.68
Consensus pattern (17 bp):
TTGTTTATTATCTATTA
Found at i:29883232 original size:17 final size:17
Alignment explanation
Indices: 29883168--29883241 Score: 57
Period size: 17 Copynumber: 4.4 Consensus size: 17
29883158 TCTTGTTTAT
*
29883168 TATTATTAGTTATTTTAT
1 TATTATTAGTTATTTT-C
*
29883186 TATCT-TTATTTATTGTT-
1 TAT-TATTAGTTATT-TTC
29883203 TATTATCTA-TTATTTTC
1 TATTAT-TAGTTATTTTC
*
29883220 TATTATTAGTTATATTC
1 TATTATTAGTTATTTTC
29883237 T-TTAT
1 TATTAT
29883242 GTTTTTAGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
16 9 0.19
17 23 0.48
18 13 0.27
19 3 0.06
ACGTcount: A:0.24, C:0.05, G:0.04, T:0.66
Consensus pattern (17 bp):
TATTATTAGTTATTTTC
Found at i:29886177 original size:43 final size:42
Alignment explanation
Indices: 29886129--29886286 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 42
29886119 ATATATGTTC
*
29886129 TCGTGTAAGACCACATCTGGGACGTTGGCATCGATATGTGAT
1 TCGTGTAAGACCACATCTGGGACATTGGCATCGATATGTGAT
* ** *
29886171 TACGTGTAAGAACATGTCTGGGACATTGGCATCG-TATTTGAT
1 T-CGTGTAAGACCACATCTGGGACATTGGCATCGATATGTGAT
* *
29886213 TCGTGTAAGACC-CAGACTGGGACAGTGGCATCGATATGTGAT
1 TCGTGTAAGACCACA-TCTGGGACATTGGCATCGATATGTGAT
* * **
29886255 GGCATGTAAGACCATGTCTGGGACATTGGCAT
1 -TCGTGTAAGACCACATCTGGGACATTGGCAT
29886287 TGTATGATAT
Statistics
Matches: 94, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
41 26 0.28
42 16 0.17
43 52 0.55
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (42 bp):
TCGTGTAAGACCACATCTGGGACATTGGCATCGATATGTGAT
Found at i:29886271 original size:84 final size:84
Alignment explanation
Indices: 29886129--29886291 Score: 240
Period size: 84 Copynumber: 1.9 Consensus size: 84
29886119 ATATATGTTC
* * *
29886129 TCGTGTAAGACCACATCTGGGACGTTGGCATCGATATGTGATTACGTGTAAGAACATGTCTGGGA
1 TCGTGTAAGACCACAACTGGGACGTTGGCATCGATATGTGATGACATGTAAGAACATGTCTGGGA
29886194 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
* *
29886213 TCGTGTAAGACC-CAGACTGGGACAG-TGGCATCGATATGTGATGGCATGTAAGACCATGTCTGG
1 TCGTGTAAGACCACA-ACTGGGAC-GTTGGCATCGATATGTGATGACATGTAAGAACATGTCTGG
*
29886276 GACATTGGCATTGTAT
64 GACATTGGCATCGTAT
29886292 GATATGTGTG
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
83 2 0.03
84 68 0.96
85 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (84 bp):
TCGTGTAAGACCACAACTGGGACGTTGGCATCGATATGTGATGACATGTAAGAACATGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:29888091 original size:6 final size:6
Alignment explanation
Indices: 29888080--29888119 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
29888070 AGTCTATTTG
* *
29888080 TTTTTA TTTTTA TTTTTA TTTTTA TGTTTA TTGTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
29888120 CTTAGACTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.00, G:0.05, T:0.80
Consensus pattern (6 bp):
TTTTTA
Found at i:29889119 original size:18 final size:17
Alignment explanation
Indices: 29889096--29889130 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29889086 AATAATAATT
29889096 GAAAAAAAAAGAAAGAAA
1 GAAAAAAAAAG-AAGAAA
*
29889114 GAAAAAAAGAGAAGAAA
1 GAAAAAAAAAGAAGAAA
29889131 ATCGAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (17 bp):
GAAAAAAAAAGAAGAAA
Found at i:29889120 original size:17 final size:17
Alignment explanation
Indices: 29889099--29889130 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
29889089 AATAATTGAA
29889099 AAAAAAAGA-AAGAAAG
1 AAAAAAAGAGAAGAAAG
29889115 AAAAAAAGAGAAGAAA
1 AAAAAAAGAGAAGAAA
29889131 ATCGAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAAGAGAAGAAAG
Found at i:29890741 original size:14 final size:14
Alignment explanation
Indices: 29890722--29890751 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
29890712 ATTGTGTTCG
29890722 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
29890736 TAGTTAAATTAGAT
1 TAGTTAAATTAGAT
29890750 TA
1 TA
29890752 AAAACAATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (14 bp):
TAGTTAAATTAGAT
Found at i:29896472 original size:20 final size:20
Alignment explanation
Indices: 29896435--29896474 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
29896425 TATATATATT
*
29896435 AAGAAAAACCATCGATACTA
1 AAGAAAAACCATCAATACTA
**
29896455 AAGAAAAAGGATCAATACTA
1 AAGAAAAACCATCAATACTA
29896475 TCAGGTATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.57, C:0.15, G:0.12, T:0.15
Consensus pattern (20 bp):
AAGAAAAACCATCAATACTA
Found at i:29904081 original size:27 final size:27
Alignment explanation
Indices: 29904051--29904172 Score: 183
Period size: 27 Copynumber: 4.5 Consensus size: 27
29904041 TTTTGACCTT
*
29904051 ATAGGGTAAAATGATCGAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCTC
*
29904078 ATAGGGTAAAATGACCGAAATACCCCC
1 ATAGGGTAAAATGACCGAAATACCCTC
* *
29904105 ATCGGGTAAAATGACCAAAATACCCTC
1 ATAGGGTAAAATGACCGAAATACCCTC
29904132 ATAGGGTAAAATGACCGAAATACCC-C
1 ATAGGGTAAAATGACCGAAATACCCTC
*
29904158 AGTAAGGTAAAATGA
1 A-TAGGGTAAAATGA
29904173 TAGAATTTCT
Statistics
Matches: 86, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
26 2 0.02
27 84 0.98
ACGTcount: A:0.43, C:0.20, G:0.19, T:0.18
Consensus pattern (27 bp):
ATAGGGTAAAATGACCGAAATACCCTC
Found at i:29904614 original size:34 final size:34
Alignment explanation
Indices: 29904568--29904662 Score: 145
Period size: 34 Copynumber: 2.8 Consensus size: 34
29904558 CACTAATTAA
* *
29904568 TGTTACTGAAATGGGCTAAAGCCCAGACCGCTAC
1 TGTTACTGAAATGGGCTAAGGCCCAGACAGCTAC
*
29904602 TGTTACTAAAATGGGCTAAGGCCCAGACAGCTAC
1 TGTTACTGAAATGGGCTAAGGCCCAGACAGCTAC
* *
29904636 TGTTACTGATATGGGCTTAGGCCCAGA
1 TGTTACTGAAATGGGCTAAGGCCCAGA
29904663 ATGTATTCGC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (34 bp):
TGTTACTGAAATGGGCTAAGGCCCAGACAGCTAC
Found at i:29909975 original size:21 final size:21
Alignment explanation
Indices: 29909924--29909977 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
29909914 CAAAATGTGA
*
29909924 TGTCACGACATTGAGGGTCGG
1 TGTCACGACACTGAGGGTCGG
* ** *
29909945 TTTCGTGACACTGAGGGTTGG
1 TGTCACGACACTGAGGGTCGG
29909966 TGTCACGACACT
1 TGTCACGACACT
29909978 ACATCAAATC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (21 bp):
TGTCACGACACTGAGGGTCGG
Found at i:29911708 original size:14 final size:15
Alignment explanation
Indices: 29911684--29911715 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
29911674 ATTTTCTGTG
29911684 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
29911699 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
29911713 TTT
1 TTT
29911716 TTTGTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:29913539 original size:40 final size:40
Alignment explanation
Indices: 29913484--29913625 Score: 187
Period size: 40 Copynumber: 3.5 Consensus size: 40
29913474 CGGATGATAA
29913484 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* * *
29913524 CCGGGCTATGTCCCGAAGGCATTTGTGCGAGTTACCAAAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
* * * *
29913564 CCGGGCTAAGTCTCGAAGCCATTGGTGCGAGTTACT-ATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-T
* *
29913604 CCGGGCTATGTCCCAAAGGCAT
1 CCGGGCTAAGTCCCGAAGGCAT
29913626 CTGACGAGTA
Statistics
Matches: 87, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 86 0.99
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAATT
Found at i:29917445 original size:69 final size:69
Alignment explanation
Indices: 29917334--29917557 Score: 448
Period size: 69 Copynumber: 3.2 Consensus size: 69
29917324 ACATAGCTTG
29917334 GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
1 GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
29917399 CGTA
66 CGTA
29917403 GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
1 GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
29917468 CGTA
66 CGTA
29917472 GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
1 GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
29917537 CGTA
66 CGTA
29917541 GCTCTCTTGTACACATG
1 GCTCTCTTGTACACATG
29917558 ATGTGCACTT
Statistics
Matches: 155, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 155 1.00
ACGTcount: A:0.25, C:0.26, G:0.16, T:0.32
Consensus pattern (69 bp):
GCTCTCTTGTACACATGGTGAACATGAATACTTAGTACCATCCATGTGACCTAGCCACTTTATCT
CGTA
Found at i:29920399 original size:46 final size:45
Alignment explanation
Indices: 29920349--29920524 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
29920339 TGGTTGAGCA
29920349 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
29920395 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
29920442 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
29920488 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
29920525 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:29920505 original size:93 final size:93
Alignment explanation
Indices: 29920346--29920516 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
29920336 GGATGGTTGA
* *
29920346 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29920411 TGAGTCCGAGTTCGAGAGATGTAACTAG
66 TGAGTCCGAGTTCGAGAGATGTAACTAG
* *
29920439 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
29920504 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
29920517 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGAGAGATGTAACTAG
Found at i:29923231 original size:22 final size:23
Alignment explanation
Indices: 29923188--29923231 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 23
29923178 TACCAATCAA
* *
29923188 ATCACAACATATAGCATACATTT
1 ATCACAACATAAAACATACATTT
*
29923211 ATCA-AACATAAAACATTCATT
1 ATCACAACATAAAACATACATT
29923232 CTCATAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.48, C:0.20, G:0.02, T:0.30
Consensus pattern (23 bp):
ATCACAACATAAAACATACATTT
Found at i:29930604 original size:27 final size:27
Alignment explanation
Indices: 29930585--29930757 Score: 213
Period size: 27 Copynumber: 6.4 Consensus size: 27
29930575 ATTACCAAAG
* *
29930585 TACCCTCGATTTACAGAATTACTAATT
1 TACCCTCGATTTACAGAATTACCATTT
* * *
29930612 CACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
29930639 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* *
29930666 TACCCTCAATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCATTT
*
29930693 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACCATTT
* * * *
29930720 TACACTTTG-TTTACAAAATTACCGTTT
1 TAC-CCTCGATTTACAGAATTACCATTT
29930747 TACCCTCGATT
1 TACCCTCGATT
29930758 GTGAAATTAC
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 3 0.02
27 120 0.95
28 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.06, T:0.39
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCATTT
Found at i:29930678 original size:81 final size:81
Alignment explanation
Indices: 29930585--29930753 Score: 241
Period size: 81 Copynumber: 2.1 Consensus size: 81
29930575 ATTACCAAAG
* *
29930585 TACCCTCGATTTACAGAATTACTAATTCACCCTCGATTTACAAAATTACTATTTTAC-CCTCGAT
1 TACCCTCAATTTACAGAATTACTAATTCACCCTCGATTTACAAAATTACCATTTTACACCTCG-T
* *
29930649 TTATAGAATTACCATTT
65 TTACAAAATTACCATTT
* * * *
29930666 TACCCTCAATTTACAGAATTACTATTTTACCCTCGATTTACAAAATTACCATTTTACACTTTGTT
1 TACCCTCAATTTACAGAATTACTAATTCACCCTCGATTTACAAAATTACCATTTTACACCTCGTT
*
29930731 TACAAAATTACCGTTT
66 TACAAAATTACCATTT
29930747 TACCCTC
1 TACCCTC
29930754 GATTGTGAAA
Statistics
Matches: 78, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 75 0.96
82 3 0.04
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.39
Consensus pattern (81 bp):
TACCCTCAATTTACAGAATTACTAATTCACCCTCGATTTACAAAATTACCATTTTACACCTCGTT
TACAAAATTACCATTT
Found at i:29930819 original size:27 final size:27
Alignment explanation
Indices: 29930789--29930939 Score: 189
Period size: 27 Copynumber: 5.6 Consensus size: 27
29930779 TATAGGATAG
*
29930789 AATTATCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
29930816 AATTACCAAAATACCCCTAGTTTGTAA
1 AATTACCAAAATACCCCTAGTTTGTAA
* * * *
29930843 AATTACCGAAATACCACTATTTTGTGA
1 AATTACCAAAATACCCCTAGTTTGTAA
*
29930870 AATTACCAAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-AGTTTGTAA
**
29930897 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCCTAG-TTTGTAA
*
29930924 AATTACAAAAATACCC
1 AATTACCAAAATACCC
29930940 TTGACTTTCT
Statistics
Matches: 108, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
26 3 0.03
27 101 0.94
28 4 0.04
ACGTcount: A:0.43, C:0.22, G:0.06, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCCTAGTTTGTAA
Found at i:29930828 original size:54 final size:53
Alignment explanation
Indices: 29930756--29930939 Score: 190
Period size: 54 Copynumber: 3.4 Consensus size: 53
29930746 TTACCCTCGA
* ** ** * *
29930756 TTGTGAAATTACTGAAATACCCCTATAGGATAGAATTATCAAAATACCCCTAGT
1 TTGTAAAATTACCAAAATACCCCTATTTG-TAAAATTACCAAAATACCCCTAGT
* * *
29930810 TTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAATACCACTATT
1 TTGTAAAATTACCAAAATACCCCTA-TTTGTAAAATTACCAAAATACCCCTAGT
* *
29930864 TTGTGAAATTACCAAAATACCCTCAATTTGTAAAATTACCAAAATACCCCT-GAT
1 TTGTAAAATTACCAAAATACCC-CTATTTGTAAAATTACCAAAATACCCCTAG-T
** *
29930918 TTACAAAATTACAAAAATACCC
1 TTGTAAAATTACCAAAATACCC
29930940 TTGACTTTCT
Statistics
Matches: 108, Mismatches: 19, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
54 104 0.96
55 4 0.04
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (53 bp):
TTGTAAAATTACCAAAATACCCCTATTTGTAAAATTACCAAAATACCCCTAGT
Found at i:29930926 original size:81 final size:81
Alignment explanation
Indices: 29930789--29930938 Score: 214
Period size: 81 Copynumber: 1.9 Consensus size: 81
29930779 TATAGGATAG
* * ** **
29930789 AATTATCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTACCGAAA
1 AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAAAAA
29930854 TACCACTATTTTGTGA
66 TACCACTATTTTGTGA
29930870 AATTACCAAAATA-CCCTCAATTTGTAAAATTACCAAAATACCCCT-GATTTACAAAATTACAAA
1 AATTACCAAAATACCCCT-AATTTGTAAAATTACCAAAATACCCCTAG-TTTACAAAATTACAAA
29930933 AATACC
64 AATACC
29930939 CTTGACTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
80 5 0.08
81 56 0.92
ACGTcount: A:0.43, C:0.21, G:0.06, T:0.29
Consensus pattern (81 bp):
AATTACCAAAATACCCCTAATTTGTAAAATTACCAAAATACCCCTAGTTTACAAAATTACAAAAA
TACCACTATTTTGTGA
Found at i:29930990 original size:27 final size:27
Alignment explanation
Indices: 29930951--29931002 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
29930941 TGACTTTCTA
29930951 AAAATTATAGAAATACCATTGGTTTAC
1 AAAATTATAGAAATACCATTGGTTTAC
*
29930978 AAAATTACT-GAAATACCCTTGGTTT
1 AAAATTA-TAGAAATACCATTGGTTT
29931003 GTAGATTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (27 bp):
AAAATTATAGAAATACCATTGGTTTAC
Found at i:29931108 original size:27 final size:27
Alignment explanation
Indices: 29931074--29931625 Score: 570
Period size: 27 Copynumber: 20.7 Consensus size: 27
29931064 GACTGTAAAG
*
29931074 CCCCTGTAGGGTAGAATTA-TCGCAATA
1 CCCCTGTAGGGTAGAATTACT-GAAATA
* * *
29931101 CCCTTGTAAGGTAGAATTACCG-AATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
*
29931127 CCCCTGTAGTGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931154 CCCCTTATAAGGTAGAATTACCGAAATA
1 CCCC-TGTAGGGTAGAATTACTGAAATA
* * *
29931182 CCGCTGTAGGGTAAAATTACTAAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931209 CCCCTGTAAGATAGAATTACCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* *
29931236 CCCCTGTAGGGTAAAATTACTAAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931263 ---CT-TAAGATAGAATTACCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* *
29931286 CCCCTGTAGGGTAAAATTACTAAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931313 CTCCTATAAGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* *
29931340 CCCCTATATGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931367 CCCCTATATGGTAGAATTACTAAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* *
29931394 CCCCTATATGGT---ATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* *
29931418 CCCTTATAGGGTAGAATTA-TCGAAATA
1 CCCCTGTAGGGTAGAATTACT-GAAATA
* * *
29931445 TCCCTGTAAGGTAGAATTACCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
29931472 CCCCTGTAGGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
*
29931499 CCCCTGTAGGGTAGAATTA-TCGCAATA
1 CCCCTGTAGGGTAGAATTACT-GAAATA
* *
29931526 CCCTTGTAAGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
*
29931553 CCCCTGTAGGGTAGAATTACTAAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931580 CCCCTGTAAGGTAGAATTACCGAGATA
1 CCCCTGTAGGGTAGAATTACTGAAATA
* * *
29931607 -CCTTGTGGGGTAAAATTAC
1 CCCCTGTAGGGTAGAATTAC
29931626 CATTTTGCCC
Statistics
Matches: 439, Mismatches: 72, Indels: 29
0.81 0.13 0.05
Matches are distributed among these distances:
23 16 0.04
24 23 0.05
26 41 0.09
27 336 0.77
28 23 0.05
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (27 bp):
CCCCTGTAGGGTAGAATTACTGAAATA
Found at i:29931166 original size:54 final size:54
Alignment explanation
Indices: 29931074--29931625 Score: 631
Period size: 54 Copynumber: 10.4 Consensus size: 54
29931064 GACTGTAAAG
* *
29931074 CCCCTGTAGGGTAGAATTA-TCGCAATACCCTTGTAAGGTAGAATTACCG-AATA
1 CCCCTGTAGGGTAGAATTACT-GAAATACCCCTGTAAGGTAGAATTACCGAAATA
* *
29931127 CCCCTGTAGTGTAGAATTACTGAAATACCCCTTATAAGGTAGAATTACCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCC-TGTAAGGTAGAATTACCGAAATA
* * * *
29931182 CCGCTGTAGGGTAAAATTACTAAAATACCCCTGTAAGATAGAATTACCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * *
29931236 CCCCTGTAGGGTAAAATTACTAAAATA---CT-TAAGATAGAATTACCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * * * *
29931286 CCCCTGTAGGGTAAAATTACTAAAATACTCCTATAAGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * * * **
29931340 CCCCTATATGGTAGAATTACTGAAATACCCCTATATGGTAGAATTACTAAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * * * * *
29931394 CCCCTATATGGT---ATTACTGAAATACCCTTATAGGGTAGAATTATCGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * * * *
29931445 TCCCTGTAAGGTAGAATTACCGAAATACCCCTGTAGGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * *
29931499 CCCCTGTAGGGTAGAATTA-TCGCAATACCCTTGTAAGGTAGAATTACTGAAATA
1 CCCCTGTAGGGTAGAATTACT-GAAATACCCCTGTAAGGTAGAATTACCGAAATA
* *
29931553 CCCCTGTAGGGTAGAATTACTAAAATACCCCTGTAAGGTAGAATTACCGAGATA
1 CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
* * *
29931607 -CCTTGTGGGGTAAAATTAC
1 CCCCTGTAGGGTAGAATTAC
29931626 CATTTTGCCC
Statistics
Matches: 440, Mismatches: 47, Indels: 24
0.86 0.09 0.05
Matches are distributed among these distances:
50 48 0.11
51 45 0.10
53 44 0.10
54 271 0.62
55 32 0.07
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (54 bp):
CCCCTGTAGGGTAGAATTACTGAAATACCCCTGTAAGGTAGAATTACCGAAATA
Found at i:29933167 original size:39 final size:39
Alignment explanation
Indices: 29933045--29933267 Score: 231
Period size: 39 Copynumber: 5.6 Consensus size: 39
29933035 GCTCCTCGTT
* *
29933045 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCA
1 CAAATGCCTTCGGG-CTTAGCCCGGAAT-TAGT-ATCTCGCA
* * * * *
29933085 CAAATGCCTTCGAGACTTAACCCGGATTTAGTAACTCGTA
1 CAAATGCCTTCG-GGCTTAGCCCGGAATTAGTATCTCGCA
29933125 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
29933164 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
* * ** *
29933203 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCCCTTAGCA
1 CAAATGCCTTCGG-GCTTAGCCCGGA-ATTAGTATC-TCGCA
29933244 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGG-CTTAGCCCGGA
29933268 CATCATTCAA
Statistics
Matches: 159, Mismatches: 17, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
39 93 0.58
40 55 0.35
41 11 0.07
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCA
Found at i:29933222 original size:79 final size:78
Alignment explanation
Indices: 29933045--29933267 Score: 231
Period size: 79 Copynumber: 2.8 Consensus size: 78
29933035 GCTCCTCGTT
* * * *
29933045 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAAT-TCGCACAAATGCCTTCGAGACTTAACCC
1 CAAATGCCTTC-GGACTTAGCCCGGAAT-TAGT-ATCTCGCACAAATGCCTTCG-GGCTTAGCCC
* *
29933108 GGATTTAGTAACTCGTA
62 GGAATTAGTAACTCGCA
*
29933125 CAAATGCCTTCGGGCTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
1 CAAATGCCTTCGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
*
29933190 TTAGTATCTCGCA
66 TTAGTAACTCGCA
* ** *
29933203 CAAATGCCTTCGGATCTTAGTCCGGATATT-GTCCCTTAGCAC-AA-GCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGA-CTTAGCCCGGA-ATTAGTATC-TCGCACAAATGCCTTCGGG-CTTAGCCC
29933265 GGA
62 GGA
29933268 CATCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
78 46 0.37
79 58 0.47
80 20 0.16
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGGCTTAGCCCGGAA
TTAGTAACTCGCA
Found at i:29941175 original size:40 final size:40
Alignment explanation
Indices: 29941075--29941246 Score: 213
Period size: 40 Copynumber: 4.3 Consensus size: 40
29941065 GCTCCTCGTT
* * *
29941075 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
29941115 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29941154 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
29941194 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
29941234 CAAATGCCTTCGG
1 CAAATGCCTTCGG
29941247 ATCTTAGTCC
Statistics
Matches: 117, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 35 0.30
40 78 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:29941259 original size:80 final size:78
Alignment explanation
Indices: 29941075--29941299 Score: 220
Period size: 80 Copynumber: 2.8 Consensus size: 78
29941065 GCTCCTCGTT
* * * * *
29941075 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTC-GGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
29941139 ATTTAATAACTCGCA
64 ATTTAATAACTCGCA
* * * *
29941154 CGAATGCCTTTGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCC-TTCGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
29941219 AATTT-GTATCTCGCA
63 AATTTAATAACTCGCA
* * * * *
29941234 CAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCGG
29941299 A
63 A
29941300 CAGCATTCAA
Statistics
Matches: 119, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
78 1 0.01
79 37 0.31
80 68 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (78 bp):
CAAATGCCTTCGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAAT
TTAATAACTCGCA
Found at i:29941308 original size:41 final size:41
Alignment explanation
Indices: 29941231--29941308 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
29941221 TTTGTATCTC
* * *
29941231 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
29941272 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
29941309 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:29942566 original size:203 final size:202
Alignment explanation
Indices: 29942217--29942619 Score: 779
Period size: 203 Copynumber: 2.0 Consensus size: 202
29942207 ATGCATGGCC
29942217 GAATCTCTTCACCTTTCTTCTTCTTTCCTCCTTAAAATTTTTGGCCAAGGATGAACCAAAGGATG
1 GAATCTCTTCACCTTTCTTCTTCTTTCCTCCTTAAAATTTTTGGCCAAGGATGAACCAAAGGATG
29942282 AGAAAATTTTTTCTTTGTTTTTCTTTCTAATTTAGGCTAAATGAAGGTGAGAAAAGGATGAACAA
66 AGAAAATTTTTTCTTTGTTTTTCTTTCTAATTTAGGCTAAATGAAGGTGAGAAAAGGATGAACAA
29942347 AGATCTTCTCCTCTCTTTTCTTTAGCTCACGGCAATGGGGGGGGAAAGAATCAACTACACACTTT
131 AGATCTTCTCCTCTCTTTTCTTTAGCTCACGGCAAT-GGGGGGGAAAGAATCAACTACACACTTT
29942412 TTTTTTTT
195 TTTTTTTT
29942420 GAATCTCTTCACCTTTCTTCTTCTTTCCTCCTTAAAATTTTTGGCCAAGGATGAACCAAAGGATG
1 GAATCTCTTCACCTTTCTTCTTCTTTCCTCCTTAAAATTTTTGGCCAAGGATGAACCAAAGGATG
*
29942485 AGAAAATTTTTTCTTTGTTTTTCTTTCTAATTTAGGGTAAATGAAGGTGAGAAAAGGATGAACAA
66 AGAAAATTTTTTCTTTGTTTTTCTTTCTAATTTAGGCTAAATGAAGGTGAGAAAAGGATGAACAA
*
29942550 AGATCTTCTCCTCTCTTTTCTTTAGCTCACGGCAATGGGGGGGAAAGAATTAACTACACACTTTT
131 AGATCTTCTCCTCTCTTTTCTTTAGCTCACGGCAATGGGGGGGAAAGAATCAACTACACACTTTT
29942615 TTTTT
196 TTTTT
29942620 GTGTATTCAT
Statistics
Matches: 198, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
202 33 0.17
203 165 0.83
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (202 bp):
GAATCTCTTCACCTTTCTTCTTCTTTCCTCCTTAAAATTTTTGGCCAAGGATGAACCAAAGGATG
AGAAAATTTTTTCTTTGTTTTTCTTTCTAATTTAGGCTAAATGAAGGTGAGAAAAGGATGAACAA
AGATCTTCTCCTCTCTTTTCTTTAGCTCACGGCAATGGGGGGGAAAGAATCAACTACACACTTTT
TTTTTTT
Found at i:29944763 original size:20 final size:21
Alignment explanation
Indices: 29944723--29944763 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29944713 AACTAGAACT
*
29944723 AAATATTTTGTCTCCTTATTTG
1 AAATATTTTG-CTCATTATTTG
29944745 AAATATTTTG-TCATTATTT
1 AAATATTTTGCTCATTATTT
29944764 TAGTTGAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.27, C:0.10, G:0.07, T:0.56
Consensus pattern (21 bp):
AAATATTTTGCTCATTATTTG
Found at i:29948870 original size:39 final size:36
Alignment explanation
Indices: 29948781--29948870 Score: 92
Period size: 36 Copynumber: 2.4 Consensus size: 36
29948771 AGTTTAAGTC
* *
29948781 TTTAATTATGTCATAACTTGAACATCATTAATATGT
1 TTTAATTATGTCATAACTTAAACATCATTAATAGGT
* * *
29948817 TTTAATTTTATCATAA-TCTAAACATCTTTAATAAAGGTT
1 TTTAATTATGTCATAACT-TAAACATCATTAAT--AGG-T
29948856 TTTAATTATGTCATA
1 TTTAATTATGTCATA
29948871 GTGTAGGACA
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
35 1 0.02
36 26 0.60
38 2 0.05
39 14 0.33
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.47
Consensus pattern (36 bp):
TTTAATTATGTCATAACTTAAACATCATTAATAGGT
Found at i:29948898 original size:39 final size:38
Alignment explanation
Indices: 29948855--29948937 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
29948845 TAATAAAGGT
* *
29948855 TTTTAATTATGTCATAGTGTAGGACATCATAAATATATA
1 TTTTAAATATGTCATAGTGTA-GACATCATAAATACATA
* * *
29948894 TTTTAAATATGTCCTAGTTTAGACATCATTAATACATA
1 TTTTAAATATGTCATAGTGTAGACATCATAAATACATA
29948932 TCTTTA
1 T-TTTA
29948938 GTTCAGACAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
38 16 0.42
39 22 0.58
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (38 bp):
TTTTAAATATGTCATAGTGTAGACATCATAAATACATA
Found at i:29960813 original size:26 final size:24
Alignment explanation
Indices: 29960798--29960841 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
29960788 ACAAAAAGAA
29960798 AAAATTGAAAAAGAAAAAGAAAAG
1 AAAATTGAAAAAGAAAAAGAAAAG
29960822 AAAATTG-AAAA-AAAAAGAAA
1 AAAATTGAAAAAGAAAAAGAAA
29960842 GCAAGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 9 0.45
23 4 0.20
24 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (24 bp):
AAAATTGAAAAAGAAAAAGAAAAG
Found at i:29960837 original size:12 final size:12
Alignment explanation
Indices: 29960796--29960837 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
29960786 AAACAAAAAG
29960796 AAAAAATTGAAA
1 AAAAAATTGAAA
*
29960808 AAGAAAA-AGAAA
1 AA-AAAATTGAAA
*
29960820 AGAAAATTGAAA
1 AAAAAATTGAAA
29960832 AAAAAA
1 AAAAAA
29960838 GAAAGCAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (12 bp):
AAAAAATTGAAA
Found at i:29960842 original size:21 final size:22
Alignment explanation
Indices: 29960784--29960842 Score: 70
Period size: 21 Copynumber: 2.7 Consensus size: 22
29960774 TTGAGAGCAA
29960784 GAAAACAAAAAG-AA-AAAATT
1 GAAAACAAAAAGAAAGAAAATT
*
29960804 GAAAAAGAAAAAGAAAAGAAAATT
1 G-AAAACAAAAAG-AAAGAAAATT
29960828 GAAAA-AAAAAGAAAG
1 GAAAACAAAAAGAAAG
29960843 CAAGAGGGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 6 0.18
23 6 0.18
24 7 0.21
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (22 bp):
GAAAACAAAAAGAAAGAAAATT
Found at i:29960973 original size:49 final size:49
Alignment explanation
Indices: 29960907--29961005 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
29960897 GAAAAAGAAA
29960907 GAAAAGACAAAAAAAAGATTGAAAAATTAAGTTTGTATGCAGAAGAGCG
1 GAAAAGACAAAAAAAAGATTGAAAAATTAAGTTTGTATGCAGAAGAGCG
*
29960956 GAAAAGACAAAAAAAAGATTGAAAAATTAAGTTTGTATGCAGAATAGCG
1 GAAAAGACAAAAAAAAGATTGAAAAATTAAGTTTGTATGCAGAAGAGCG
29961005 G
1 G
29961006 TAGATTCGAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.53, C:0.06, G:0.22, T:0.19
Consensus pattern (49 bp):
GAAAAGACAAAAAAAAGATTGAAAAATTAAGTTTGTATGCAGAAGAGCG
Found at i:29964046 original size:38 final size:39
Alignment explanation
Indices: 29963997--29964071 Score: 125
Period size: 38 Copynumber: 1.9 Consensus size: 39
29963987 TAAATTAGTT
*
29963997 TAAGTCTTTAATTATGTCATAATTTGAACATCATTAAAA
1 TAAGTCTTTAATTATGTCATAATCTGAACATCATTAAAA
*
29964036 TAAGT-TTTAATTATGTCATAATCTGAACATCTTTAA
1 TAAGTCTTTAATTATGTCATAATCTGAACATCATTAA
29964072 TAACGGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
38 29 0.85
39 5 0.15
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.43
Consensus pattern (39 bp):
TAAGTCTTTAATTATGTCATAATCTGAACATCATTAAAA
Found at i:29964081 original size:38 final size:39
Alignment explanation
Indices: 29963997--29964094 Score: 121
Period size: 38 Copynumber: 2.5 Consensus size: 39
29963987 TAAATTAGTT
* *
29963997 TAAGTCTTTAATTATGTCATAATTTGAACATCATTAAAA
1 TAAGTTTTTAATTATGTCATAATCTGAACATCATTAAAA
*
29964036 TAAG-TTTTAATTATGTCATAATCTGAACATC-TT-TAA
1 TAAGTTTTTAATTATGTCATAATCTGAACATCATTAAAA
*
29964072 TAACGGTTTTTAGTTATGTCATA
1 TAA--GTTTTTAATTATGTCATA
29964095 GTTTAGGACA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
36 5 0.10
37 2 0.04
38 26 0.50
39 19 0.37
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (39 bp):
TAAGTTTTTAATTATGTCATAATCTGAACATCATTAAAA
Found at i:29964122 original size:39 final size:39
Alignment explanation
Indices: 29964079--29964164 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
29964069 TAATAACGGT
29964079 TTTTAGTTATGTCATAGTTTAGGACATCTTCAATATAT-A
1 TTTTAGTTATGTCATAGTTTA-GACATCTTCAATATATGA
** * * *
29964118 TTTTAAATATGTCTTAGTTTAGACATCTTTAATATATGT
1 TTTTAGTTATGTCATAGTTTAGACATCTTCAATATATGA
29964157 TTTTAGTT
1 TTTTAGTT
29964165 CAGACAAATT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
38 15 0.38
39 24 0.62
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (39 bp):
TTTTAGTTATGTCATAGTTTAGACATCTTCAATATATGA
Found at i:29964152 original size:38 final size:39
Alignment explanation
Indices: 29964086--29964159 Score: 114
Period size: 38 Copynumber: 1.9 Consensus size: 39
29964076 GGTTTTTAGT
29964086 TATGTCATAGTTTAGGACATCTTCAATATATATTTTAAA
1 TATGTCATAGTTTAGGACATCTTCAATATATATTTTAAA
* * *
29964125 TATGTCTTAGTTTA-GACATCTTTAATATATGTTTT
1 TATGTCATAGTTTAGGACATCTTCAATATATATTTT
29964160 TAGTTCAGAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 19 0.59
39 13 0.41
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (39 bp):
TATGTCATAGTTTAGGACATCTTCAATATATATTTTAAA
Found at i:29964155 original size:27 final size:27
Alignment explanation
Indices: 29964119--29964170 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
29964109 CAATATATAT
*
29964119 TTTAAATATG-TCTTAGTTTAGACATC
1 TTTAAATATGTTCTTAGTTCAGACATC
*
29964145 TTTAATATATGTTTTTAGTTCAGACA
1 TTTAA-ATATGTTCTTAGTTCAGACA
29964171 AATTAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 5 0.23
28 12 0.55
ACGTcount: A:0.31, C:0.10, G:0.12, T:0.48
Consensus pattern (27 bp):
TTTAAATATGTTCTTAGTTCAGACATC
Found at i:29967262 original size:44 final size:44
Alignment explanation
Indices: 29967199--29967285 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
29967189 CTTTAATTCC
29967199 CCTTTGTTGAACAATTTCTCAATCCAATAACTTAATAGTCATGA
1 CCTTTGTTGAACAATTTCTCAATCCAATAACTTAATAGTCATGA
29967243 CCTTTGTTGAACAATTTCTCAATCCAATAACTTAATAGTCATG
1 CCTTTGTTGAACAATTTCTCAATCCAATAACTTAATAGTCATG
29967286 TTTATCTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (44 bp):
CCTTTGTTGAACAATTTCTCAATCCAATAACTTAATAGTCATGA
Found at i:29973405 original size:45 final size:45
Alignment explanation
Indices: 29973342--29973432 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
29973332 CTGCGAAGTA
* * *
29973342 AGAGAGGAGTGGGTGAGCTCATTGCGAACTCAATGAATAATTAGG
1 AGAGAGGAGTGGGTGAGCTCATTCCAAACTCAATGAATAATCAGG
*
29973387 AGAGAGGAGTGGGTGAGCTCATTCCAAACTCAGTGAATAATCAGG
1 AGAGAGGAGTGGGTGAGCTCATTCCAAACTCAATGAATAATCAGG
29973432 A
1 A
29973433 ATTAGCAGAG
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:0.34, C:0.13, G:0.32, T:0.21
Consensus pattern (45 bp):
AGAGAGGAGTGGGTGAGCTCATTCCAAACTCAATGAATAATCAGG
Found at i:29976587 original size:36 final size:33
Alignment explanation
Indices: 29976497--29976588 Score: 98
Period size: 33 Copynumber: 2.7 Consensus size: 33
29976487 AAAAATGTAC
29976497 AAGACCATGGTTGGACCATGGCAATGTTTACGT
1 AAGACCATGGTTGGACCATGGCAATGTTTACGT
* * *
29976530 AAGACCATAGCG-AGG-CTATGGCAATTTTTCAAACGT
1 AAGACCAT-G-GTTGGACCATGGCAATGTTT---ACGT
29976566 AAGACCATGGTTGGACCATGGCA
1 AAGACCATGGTTGGACCATGGCA
29976589 GTGTATATAT
Statistics
Matches: 47, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
33 20 0.43
34 4 0.09
35 4 0.09
36 19 0.40
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.24
Consensus pattern (33 bp):
AAGACCATGGTTGGACCATGGCAATGTTTACGT
Found at i:29981813 original size:104 final size:104
Alignment explanation
Indices: 29981633--29981960 Score: 586
Period size: 104 Copynumber: 3.2 Consensus size: 104
29981623 TGTATATAAA
** * * * *
29981633 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
29981697 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29981737 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
29981802 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29981841 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
29981906 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29981945 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
29981961 GATATCCATT
Statistics
Matches: 217, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
104 216 1.00
105 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:29982012 original size:71 final size:71
Alignment explanation
Indices: 29981879--29982101 Score: 392
Period size: 71 Copynumber: 3.1 Consensus size: 71
29981869 TCATTGGTGG
*** * *
29981879 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
29981944 GAGGGGT
65 GAGGGGT
29981951 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29982016 AGGGGT
66 AGGGGT
29982022 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
29982087 AGGGGT
66 AGGGGT
29982093 TGCTAAGTG
1 TGCTAAGTG
29982102 ATGATTCCCC
Statistics
Matches: 146, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
71 116 0.79
72 30 0.21
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (71 bp):
TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGT
Found at i:29992104 original size:17 final size:17
Alignment explanation
Indices: 29992079--29992118 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
29992069 TGAGGTGGAG
*
29992079 GTTGTGATGGAAAATAA
1 GTTGCGATGGAAAATAA
* *
29992096 GTTGCGATGGTAATTAA
1 GTTGCGATGGAAAATAA
29992113 GTTGCG
1 GTTGCG
29992119 GTGCTGAAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.33
Consensus pattern (17 bp):
GTTGCGATGGAAAATAA
Found at i:29996485 original size:14 final size:14
Alignment explanation
Indices: 29996448--29996487 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
29996438 TTCTTATTTC
29996448 CTTTTCTTTCTTTT
1 CTTTTCTTTCTTTT
*
29996462 -TATTTTTTTCTTTT
1 CT-TTTCTTTCTTTT
29996476 CTTTTCTTTCTT
1 CTTTTCTTTCTT
29996488 CTTTTAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
CTTTTCTTTCTTTT
Found at i:29996492 original size:23 final size:23
Alignment explanation
Indices: 29996438--29996492 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
29996428 TCCTGACATG
29996438 TTCTTATTTCCTTTTCTTTCTTT-
1 TTCTT-TTTCCTTTTCTTTCTTTC
* *
29996461 TTATTTTTTTCTTTTCTTTTCTTTC
1 TT-CTTTTTCCTTTTC-TTTCTTTC
29996486 TTCTTTT
1 TTCTTTT
29996493 AACTCCTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
23 11 0.42
24 13 0.50
25 2 0.08
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (23 bp):
TTCTTTTTCCTTTTCTTTCTTTC
Found at i:30006952 original size:23 final size:23
Alignment explanation
Indices: 30006924--30007320 Score: 551
Period size: 23 Copynumber: 17.1 Consensus size: 23
30006914 TTGGACAGTG
* *
30006924 TTATACATCAAATCGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
30006947 TTATACACCCAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* *
30006970 ATATATACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
30006993 ATATACACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
30007016 TTATACACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
30007039 TTATACACCAAATTGGACAACAT
1 TTATACACCAAATTGGACAGCAT
* * *
30007062 ATATACACTAAATTGGACAACAT
1 TTATACACCAAATTGGACAGCAT
30007085 TTATACACCAAATTGGACAGCATT
1 TTATACACCAAATTGGACAGCA-T
30007109 TTATACACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* * * * *
30007132 ATATACACTATATTGGATAACAT
1 TTATACACCAAATTGGACAGCAT
*
30007155 TTATACACCAAATTGGATAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
30007178 ATATACACTAATTTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
*
30007201 TTATACACCAAACTGGACAGCATT
1 TTATACACCAAATTGGACAGCA-T
30007225 TTATACACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
* * *
30007248 ATATACACTAAATTGGATAGCAT
1 TTATACACCAAATTGGACAGCAT
*
30007271 TTATACACCAAAGTGGACAGCATT
1 TTATACACCAAATTGGACAGCA-T
30007295 TTATACACCAAATTGGACAGCAT
1 TTATACACCAAATTGGACAGCAT
30007318 TTA
1 TTA
30007321 ATATACCCAA
Statistics
Matches: 331, Mismatches: 40, Indels: 6
0.88 0.11 0.02
Matches are distributed among these distances:
23 264 0.80
24 67 0.20
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (23 bp):
TTATACACCAAATTGGACAGCAT
Found at i:30007160 original size:116 final size:116
Alignment explanation
Indices: 30006924--30007320 Score: 589
Period size: 116 Copynumber: 3.4 Consensus size: 116
30006914 TTGGACAGTG
* * * * * *
30006924 TTATACATCAAATCGGACAGCATTTATACACCCAATTGGACAGCATATATATACCAAATTGGACA
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAATTGGACA
* * * *
30006989 GCA-TATATACACCAAATTGGACAGCATTTATACACCAAATTGGACAGCAT
66 GCATTTTATACACCAAATTGGACAGCATATATACACTAAATTGGATAGCAT
* * *
30007039 TTATACACCAAATTGGACAACATATATACACTAAATTGGACAACATTTATACACCAAATTGGACA
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAATTGGACA
* *
30007104 GCATTTTATACACCAAATTGGACAGCATATATACACTATATTGGATAACAT
66 GCATTTTATACACCAAATTGGACAGCATATATACACTAAATTGGATAGCAT
* * * *
30007155 TTATACACCAAATTGGATAGCATATATACACTAATTTGGACAGCATTTATACACCAAACTGGACA
1 TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAATTGGACA
30007220 GCATTTTATACACCAAATTGGACAGCATATATACACTAAATTGGATAGCAT
66 GCATTTTATACACCAAATTGGACAGCATATATACACTAAATTGGATAGCAT
* *
30007271 TTATACACCAAAGTGGACAGCATTTTATACACCAAATTGGACAGCATTTA
1 TTATACACCAAATTGGACAGCA-TATATACACCAAATTGGACAGCATTTA
30007321 ATATACCCAA
Statistics
Matches: 253, Mismatches: 27, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
115 59 0.23
116 170 0.67
117 24 0.09
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (116 bp):
TTATACACCAAATTGGACAGCATATATACACCAAATTGGACAGCATTTATACACCAAATTGGACA
GCATTTTATACACCAAATTGGACAGCATATATACACTAAATTGGATAGCAT
Found at i:30008366 original size:43 final size:42
Alignment explanation
Indices: 30008296--30008422 Score: 134
Period size: 43 Copynumber: 3.0 Consensus size: 42
30008286 ATATCGTACA
* * *
30008296 ATGCCAACGTCCTAGACGTGGTTTTACATGTAATCACATAATG
1 ATGCCAACGTCCCAGACGTGGTCTTACAAGTAA-CACATAATG
* *
30008339 ATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACA-AGTTG
1 ATGCCAAC-GTCCCAGAC-GTGGTCTTACAAGT-AACACATA-ATG
30008382 ATGCCAACGTCCCAGACGTGGTCTTACAAGATAACACATAA
1 ATGCCAACGTCCCAGACGTGGTCTTACAAG-TAACACATAA
30008423 CGCAATCCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
42 4 0.06
43 59 0.84
44 7 0.10
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
ATGCCAACGTCCCAGACGTGGTCTTACAAGTAACACATAATG
Found at i:30013207 original size:174 final size:174
Alignment explanation
Indices: 30012916--30013243 Score: 593
Period size: 174 Copynumber: 1.9 Consensus size: 174
30012906 AACTCAAGGT
* *
30012916 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
30012981 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGC
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
30013046 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTTGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTTGCAC
* *
30013090 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAGGTCTCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
30013155 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGT
66 GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
*
30013220 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
30013244 TGTACAATTT
Statistics
Matches: 147, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
174 147 1.00
ACGTcount: A:0.31, C:0.24, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGGGTTCGCACACATAGTGCTTAATAATCAACCACGCACACTTAGTGCCATGC
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTTGCAC
Found at i:30013235 original size:29 final size:30
Alignment explanation
Indices: 30013196--30013274 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
30013186 CTTAATAATC
30013196 AACCACGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
30013226 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
30013255 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
30013275 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:30015361 original size:52 final size:52
Alignment explanation
Indices: 30015291--30015394 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
30015281 ACTTTATCTC
* * *
30015291 CCACCTGATATTCAATGTCCTTTCGTTTCAAGTCCGCATACGATTTCTGACG
1 CCACCTGATACTCAATGTCCTTTCGTTTCAAATCCGCATACGACTTCTGACG
* * * *
30015343 CCACCTGATACTCGATGTCTTTTCGTTTCAAATCTGCGTACGACTTCTGACG
1 CCACCTGATACTCAATGTCCTTTCGTTTCAAATCCGCATACGACTTCTGACG
30015395 ATCCGTGGCT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (52 bp):
CCACCTGATACTCAATGTCCTTTCGTTTCAAATCCGCATACGACTTCTGACG
Found at i:30023260 original size:29 final size:29
Alignment explanation
Indices: 30023197--30023264 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
30023187 TAATCAACCG
*
30023197 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
30023226 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
30023255 CGCACACTTA
1 CGCACACTTA
30023265 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:30025358 original size:102 final size:103
Alignment explanation
Indices: 30025025--30025393 Score: 623
Period size: 103 Copynumber: 3.6 Consensus size: 103
30025015 ATTGCATATA
*
30025025 AAGGGGTTGTTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
30025090 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
30025128 AAGGGGTTGCTGTGTGTTGATTCCCCGATTCATTGGTGGTTGCTAAGTGTTGATTCCACCGTATT
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
30025193 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* ** * * *
30025231 GAGGGGTTGCTAAGTGCTGATTCCCCTATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGCATC
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
*
30025296 TAAAATGTG-AAGGGGGTTGCTAAGTGCTGATTCCCCC
66 TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
* *
30025333 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCGGAATCCACCG
1 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCG
30025394 ATAACGGTTA
Statistics
Matches: 248, Mismatches: 18, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
102 83 0.33
103 165 0.67
ACGTcount: A:0.18, C:0.20, G:0.30, T:0.33
Consensus pattern (103 bp):
AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATT
TTAAATGTGAAAGGGGGTTGCTAAGTGCTGATTCCCCC
Found at i:30029741 original size:5 final size:5
Alignment explanation
Indices: 30029731--30029755 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
30029721 TTTAACTAAG
30029731 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
30029756 GCTCTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:30031610 original size:13 final size:13
Alignment explanation
Indices: 30031592--30031619 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
30031582 CTAGATTGGC
30031592 TAGGAAATCGTCA
1 TAGGAAATCGTCA
30031605 TAGGAAATCGTCA
1 TAGGAAATCGTCA
30031618 TA
1 TA
30031620 TGTATCTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (13 bp):
TAGGAAATCGTCA
Found at i:30046923 original size:41 final size:41
Alignment explanation
Indices: 30046874--30047186 Score: 335
Period size: 41 Copynumber: 7.6 Consensus size: 41
30046864 ACTAGAGTGT
* ** *
30046874 AAATAGGGGCACGTATGTGCTATTCAGGGGTACTGGAGTAT
1 AAATAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
* * *
30046915 AAACAGGGGCACGTGTGTGCAATTCAAGGGTAAC-AAAGTAC
1 AAATAGGGGCACGTATGTGCAATTCAGGGGT-ACTAAAGTAC
* * *
30046956 AAATAGGGGCACGCATGTGCAATTCAGGGGCACCAAAGTAC
1 AAATAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
** * *
30046997 AACCAGGTGCACGTATGTGCAATTCAGGGGTACTGAAGTAC
1 AAATAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
* * * *
30047038 AAATAGGGGCACCTTTGTGCAATTCAGGGG-AATCGAAGTAC
1 AAATAGGGGCACGTATGTGCAATTCAGGGGTACT-AAAGTAC
* * **
30047079 AAATAGGGGCACATATGTGCAATTTAGGGGTACCGAAGTAC
1 AAATAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
* ** *
30047120 AAATATGGGCATC-TATACGCAATTCAGGGGTACCAAAGTAC
1 AAATAGGGGCA-CGTATGTGCAATTCAGGGGTACTAAAGTAC
*
30047161 AAATAGGGGCATGTATGTGCAATTCA
1 AAATAGGGGCACGTATGTGCAATTCA
30047187 AGAGTTAACT
Statistics
Matches: 227, Mismatches: 39, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
40 4 0.02
41 219 0.96
42 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.29, T:0.21
Consensus pattern (41 bp):
AAATAGGGGCACGTATGTGCAATTCAGGGGTACTAAAGTAC
Found at i:30046986 original size:21 final size:21
Alignment explanation
Indices: 30046960--30047026 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
30046950 AAGTACAAAT
30046960 AGGGGCACGCATGTGCAATTC
1 AGGGGCACGCATGTGCAATTC
* * *
30046981 AGGGGCAC-CAAAGTACAA-CC
1 AGGGGCACGC-ATGTGCAATTC
* *
30047001 AGGTGCACGTATGTGCAATTC
1 AGGGGCACGCATGTGCAATTC
30047022 AGGGG
1 AGGGG
30047027 TACTGAAGTA
Statistics
Matches: 34, Mismatches: 9, Indels: 6
0.69 0.18 0.12
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.28, C:0.22, G:0.33, T:0.16
Consensus pattern (21 bp):
AGGGGCACGCATGTGCAATTC
Found at i:30047077 original size:123 final size:122
Alignment explanation
Indices: 30046880--30047186 Score: 375
Period size: 123 Copynumber: 2.5 Consensus size: 122
30046870 GTGTAAATAG
* * * * *
30046880 GGGCACGTATGTGCTATTCAGGGGTACTGGAGTATAAACAGGGGCACGTGTGTGCAATTCAAGGG
1 GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATTC-AGGG
* * *
30046945 TAACAAAGTACAAATAGGGGCACGCATGTGCAATTCAGGGGCACCAAAGTACAACCA-
65 GAACAAAGTACAAATAGGGGCACACATGTGCAATTCAGGGGCACCAAAGTACAAACAT
* *
30047002 GGTGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAATAGGGGCACCTTTGTGCAATTCAGGG
1 GG-GCACGTATGTGCAATTCAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATTCAGGG
* * * * * *
30047067 GAATCGAAGTACAAATAGGGGCACATATGTGCAATTTAGGGGTACCGAAGTACAAATAT
65 GAA-CAAAGTACAAATAGGGGCACACATGTGCAATTCAGGGGCACCAAAGTACAAACAT
** ** *
30047126 GGGCATC-TATACGCAATTCAGGGGTACCAAAGTACAAATAGGGGCATGTATGTGCAATTCA
1 GGGCA-CGTATGTGCAATTCAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATTCA
30047187 AGAGTTAACT
Statistics
Matches: 159, Mismatches: 22, Indels: 7
0.85 0.12 0.04
Matches are distributed among these distances:
122 8 0.05
123 148 0.93
124 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.21
Consensus pattern (122 bp):
GGGCACGTATGTGCAATTCAGGGGTACTGAAGTACAAATAGGGGCACGTATGTGCAATTCAGGGG
AACAAAGTACAAATAGGGGCACACATGTGCAATTCAGGGGCACCAAAGTACAAACAT
Done.