Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 175 of 284
Found at i:58895705 original size:46 final size:46
Alignment explanation
Indices: 58895655--58895830 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
58895645 TGGTTGAGCA
58895655 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * *
58895701 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* * *
58895746 CATCCGAGCTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
58895794 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
58895831 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 63 0.59
47 27 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:58895811 original size:93 final size:93
Alignment explanation
Indices: 58895652--58895823 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
58895642 GGATGGTTGA
* * *
58895652 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58895717 TGAGTCCGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
* *
58895745 GCATCCGAGCTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
58895810 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
58895824 CTTATGGGCG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAATCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:58899072 original size:16 final size:17
Alignment explanation
Indices: 58899051--58899085 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
58899041 AAATTTGCTC
58899051 ATATTT-TATTTAATAA
1 ATATTTATATTTAATAA
*
58899067 ATATTTATTTTTAATAA
1 ATATTTATATTTAATAA
58899084 AT
1 AT
58899086 TAATAGCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
ATATTTATATTTAATAA
Found at i:58900202 original size:19 final size:19
Alignment explanation
Indices: 58900158--58900203 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
58900148 GCCTAATGTA
*
58900158 GTATTTGATATTTAAGTTTG
1 GTATTTAATATTTAAG-TTG
58900178 GT-TTTAATATTTAA-TTG
1 GTATTTAATATTTAAGTTG
58900195 GATATTTAA
1 G-TATTTAA
58900204 GTTTTTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 1 0.04
19 16 0.70
20 2 0.09
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
GTATTTAATATTTAAGTTG
Found at i:58907673 original size:12 final size:12
Alignment explanation
Indices: 58907653--58907690 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
58907643 ACAAAAATAT
58907653 TGAAGTAAATAAG
1 TGAA-TAAATAAG
58907666 TGAATAAATAAG
1 TGAATAAATAAG
*
58907678 TGAGTAAATAAG
1 TGAATAAATAAG
58907690 T
1 T
58907691 AAAAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (12 bp):
TGAATAAATAAG
Found at i:58908087 original size:18 final size:18
Alignment explanation
Indices: 58908064--58908098 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
58908054 ATTCGAGTTG
58908064 ATTCGATTAACTCGATTA
1 ATTCGATTAACTCGATTA
*
58908082 ATTCGATTAACTTGATT
1 ATTCGATTAACTCGATT
58908099 CGAATAATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTCGATTAACTCGATTA
Found at i:58910986 original size:20 final size:22
Alignment explanation
Indices: 58910958--58910997 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
58910948 TTGTAAAAAT
58910958 CTTAAA-TTTTGGG-GGGCCTA
1 CTTAAATTTTTGGGAGGGCCTA
*
58910978 CTTATATTTTTGGGAGGGCC
1 CTTAAATTTTTGGGAGGGCC
58910998 ATAATATATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (22 bp):
CTTAAATTTTTGGGAGGGCCTA
Found at i:58911005 original size:22 final size:21
Alignment explanation
Indices: 58910964--58911006 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
58910954 AAATCTTAAA
*
58910964 TTTTGGGGGGCCTACTTATAT
1 TTTTGGGGGGCCTACATATAT
58910985 TTTTGGGAGGGCCATA-ATATAT
1 TTTTGGG-GGGCC-TACATATAT
58911007 CTACAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 7 0.37
22 10 0.53
23 2 0.11
ACGTcount: A:0.21, C:0.12, G:0.28, T:0.40
Consensus pattern (21 bp):
TTTTGGGGGGCCTACATATAT
Found at i:58912546 original size:101 final size:101
Alignment explanation
Indices: 58912370--58912573 Score: 381
Period size: 101 Copynumber: 2.0 Consensus size: 101
58912360 TTTCATTGGA
*
58912370 TAGGTAGTTCAATGTAACGCGTGTTTTATGCAAGTCTATGCAGTCGTTATCAAGTAATAAGTAAG
1 TAGGTAGTTCAATGTAACGCGTGTTTTATGCAAGTCTACGCAGTCGTTATCAAGTAATAAGTAAG
*
58912435 TAAAAAAGTTATCGTCTCCATAGGGACTGTGTATGT
66 TAAAAAAGTTATCGTCTCCATAGGGACTATGTATGT
58912471 TAGGTAGTTCAATGTAACGCGTGTTTTATGCAAGTCTACGCAGTCGTTATCAAGTAATAAGTAAG
1 TAGGTAGTTCAATGTAACGCGTGTTTTATGCAAGTCTACGCAGTCGTTATCAAGTAATAAGTAAG
*
58912536 TAAAAGAGTTATCGTCTCCATAGGGACTATGTATGT
66 TAAAAAAGTTATCGTCTCCATAGGGACTATGTATGT
58912572 TA
1 TA
58912574 ATCAATTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (101 bp):
TAGGTAGTTCAATGTAACGCGTGTTTTATGCAAGTCTACGCAGTCGTTATCAAGTAATAAGTAAG
TAAAAAAGTTATCGTCTCCATAGGGACTATGTATGT
Found at i:58921142 original size:152 final size:149
Alignment explanation
Indices: 58920983--58921518 Score: 536
Period size: 152 Copynumber: 3.6 Consensus size: 149
58920973 TTTTTTAATC
** *
58920983 ATTTTAAAGGAAA-TTTTAATTTTTTTAAACTATTTCAAAATAAAATCTTTGATATTTAAGAAAA
1 ATTTTAAAACAAAGTTTTAATTTTTTTAAACTATTTCAAAATAAAATCTTTGATCTTTAAGAAAA
*
58921047 ATAGTGTTTTTTTTCCTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAACAAAAATCTATTTTTAA
66 ATAGTGTTTTTTTT--TTAAAAAAAGAGAAAGTTTAGATTTTTAAAAA-AAAAATATATTTTT-A
*
58921112 GTCATTTTAAAGGAAATTTTAAA
127 GTCATTTTAAAGGAAAGTTTAAA
* * * * * *
58921135 ATTTTAAAACAAAGTTTTGATTTTTTTTCAACTATTCCAAAATAAAAACTTTCATCTTTAAGAAG
1 ATTTTAAAACAAAGTTTT-AATTTTTTTAAACTATTTCAAAATAAAATCTTTGATCTTTAAGAAA
* * * * *
58921200 AATAGTGTTTTCCTTTTT--AAAAGGAGAAAGTTTAAATTTTTAAAATAAAAATATGTTTTTTTA
65 AATAGTGTTTT-TTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAA-AAAAA-ATATATTTTTA
58921263 GTCA-TTTAAATGGAAAGTTTAAA
127 GTCATTTTAAA-GGAAAGTTTAAA
* * * * *
58921286 ATTTTTAAAGCAAAATTTTGATTTTTTTAAACATATTTCAAAATAAAACCTTTAATCTTTAAGAA
1 A-TTTTAAAACAAAGTTTTAATTTTTTTAAAC-TATTTCAAAATAAAATCTTTGATCTTTAAGAA
** * * * *
58921351 AAA-A---AATATTGTTTAAAAAAA-A-AGAGTTTAGATTTTTAAAATAAAAATATGATTTTTAG
64 AAATAGTGTTTTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAAAAAAATAT-ATTTTTAG
*
58921410 TCATTTTAAAGGAAAAGTTTAGAT
128 TCATTTTAAAGG-AAAGTTTA-AA
* * * * * * *
58921434 TTTTTAAAACAAAGTTTTGATCTTTTTCAACTATTTGAAAATAAAGT-TTTGATTTTTAAGAAAA
1 ATTTTAAAACAAAGTTTTAATTTTTTTAAACTATTTCAAAATAAAATCTTTGATCTTTAAGAAAA
*
58921498 ATAGTGATGTTTTTTTTAAAA
66 ATAGTG-TTTTTTTTTTAAAA
58921519 GAAAACTTTG
Statistics
Matches: 315, Mismatches: 50, Indels: 40
0.78 0.12 0.10
Matches are distributed among these distances:
145 19 0.06
146 30 0.10
147 61 0.19
148 3 0.01
149 4 0.01
150 16 0.05
151 57 0.18
152 66 0.21
153 6 0.02
154 50 0.16
155 3 0.01
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.42
Consensus pattern (149 bp):
ATTTTAAAACAAAGTTTTAATTTTTTTAAACTATTTCAAAATAAAATCTTTGATCTTTAAGAAAA
ATAGTGTTTTTTTTTTAAAAAAAGAGAAAGTTTAGATTTTTAAAAAAAAAATATATTTTTAGTCA
TTTTAAAGGAAAGTTTAAA
Found at i:58933072 original size:32 final size:32
Alignment explanation
Indices: 58933036--58933100 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
58933026 CCGTACCCTT
58933036 ATGTAGGCAATATTATGACATTGCTAATTATA
1 ATGTAGGCAATATTATGACATTGCTAATTATA
58933068 ATGTAGGCAATATTATGACATTGCTAATTATA
1 ATGTAGGCAATATTATGACATTGCTAATTATA
58933100 A
1 A
58933101 CTTTAGGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.37
Consensus pattern (32 bp):
ATGTAGGCAATATTATGACATTGCTAATTATA
Found at i:58942902 original size:40 final size:40
Alignment explanation
Indices: 58942847--58943028 Score: 305
Period size: 40 Copynumber: 4.6 Consensus size: 40
58942837 TATTCGAATG
*
58942847 ATATCCGGGCTAAGTCCCGAAGGCATTTGTTCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
58942887 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTATTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
58942927 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
*
58942967 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAG-TGACT
*
58943007 ATATCC-GGCTAAATCCCGAAGG
1 ATATCCGGGCTAAGTCCCGAAGG
58943029 TACTTGGGTT
Statistics
Matches: 136, Mismatches: 5, Indels: 3
0.94 0.03 0.02
Matches are distributed among these distances:
39 15 0.11
40 119 0.88
41 2 0.01
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
Found at i:58944517 original size:13 final size:13
Alignment explanation
Indices: 58944499--58944537 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
58944489 GCTCGGCAGG
58944499 GACACGCCCGTGT
1 GACACGCCCGTGT
58944512 GACACGCCCGTGT
1 GACACGCCCGTGT
58944525 GACACGCCCGTGT
1 GACACGCCCGTGT
58944538 ACGAATACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.38, G:0.31, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:58948102 original size:24 final size:24
Alignment explanation
Indices: 58948070--58948122 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
58948060 AGAATAAATG
58948070 TATGAGCATGAATATGGTGAGAAC
1 TATGAGCATGAATATGGTGAGAAC
58948094 TATGAGCATGAATATGGTGAGAAC
1 TATGAGCATGAATATGGTGAGAAC
58948118 TATGA
1 TATGA
58948123 ATATAAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (24 bp):
TATGAGCATGAATATGGTGAGAAC
Found at i:58948131 original size:24 final size:24
Alignment explanation
Indices: 58948070--58948131 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
58948060 AGAATAAATG
* *
58948070 TATGAGCATGAATATGGTGAGAAC
1 TATGAACATAAATATGGTGAGAAC
* *
58948094 TATGAGCATGAATATGGTGAGAAC
1 TATGAACATAAATATGGTGAGAAC
*
58948118 TATGAATATAAATA
1 TATGAACATAAATA
58948132 AAAAAATCTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.24, T:0.27
Consensus pattern (24 bp):
TATGAACATAAATATGGTGAGAAC
Found at i:58948885 original size:16 final size:16
Alignment explanation
Indices: 58948864--58948897 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
58948854 GAGGAGTTTA
58948864 TACTCCTCATTCCTGC
1 TACTCCTCATTCCTGC
58948880 TACTCCTCATTCCTGC
1 TACTCCTCATTCCTGC
58948896 TA
1 TA
58948898 TGAATCCTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.15, C:0.41, G:0.06, T:0.38
Consensus pattern (16 bp):
TACTCCTCATTCCTGC
Found at i:58948995 original size:39 final size:39
Alignment explanation
Indices: 58948940--58949017 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
58948930 ATTGTTTACC
* * *
58948940 TTAAAGGTGTCGAATTTGGGATGACTTACCTCGACTGTA
1 TTAAAGGTGCCAAATTTAGGATGACTTACCTCGACTGTA
*
58948979 TTAAAGGTGCCAAATTTAGGATGACTTACCTTGACTGTA
1 TTAAAGGTGCCAAATTTAGGATGACTTACCTCGACTGTA
58949018 CCAAATGGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.33
Consensus pattern (39 bp):
TTAAAGGTGCCAAATTTAGGATGACTTACCTCGACTGTA
Found at i:58952721 original size:15 final size:13
Alignment explanation
Indices: 58952692--58952718 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
58952682 GCTCGGCAGG
58952692 GACACGCCCGTGT
1 GACACGCCCGTGT
58952705 GACACGCCCGTGT
1 GACACGCCCGTGT
58952718 G
1 G
58952719 TGATTGGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:58954423 original size:46 final size:46
Alignment explanation
Indices: 58954363--58954530 Score: 178
Period size: 46 Copynumber: 3.6 Consensus size: 46
58954353 CGAGGCCATT
58954363 GCATGTCCCAGACATGTCTTACACTGGCACTCATAATATGGCTGAA
1 GCATGTCCCAGACATGTCTTACACTGGCACTCATAATATGGCTGAA
* * * * *
58954409 GCATGTCCCAGACATGTCTTACACTAGCCCCCAT-CTGGAT-GCTGATG
1 GCATGTCCCAGACATGTCTTACACTGGCACTCATAAT--ATGGCTGA-A
* * * * * *
58954456 GCATGTCCCAAACATGGTCTTACATTGGCTCTTATAATGTGGCCGAA
1 GCATGTCCCAGACAT-GTCTTACACTGGCACTCATAATATGGCTGAA
*
58954503 GCATGTCCTAGACATGTCTTACACTGGC
1 GCATGTCCCAGACATGTCTTACACTGGC
58954531 GCACAAATCA
Statistics
Matches: 98, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
45 1 0.01
46 48 0.49
47 30 0.31
48 18 0.18
49 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.21, T:0.27
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTGGCACTCATAATATGGCTGAA
Found at i:58954910 original size:30 final size:30
Alignment explanation
Indices: 58954869--58954931 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
58954859 AAATTCACAA
* * *
58954869 CTTTGGTAAAATGACTATTTTGCCCCTAGG
1 CTTTGGCAAAATGACCATTTTACCCCTAGG
*
58954899 CTTTGGCAAAATGACCATTTTACCCCTATG
1 CTTTGGCAAAATGACCATTTTACCCCTAGG
58954929 CTT
1 CTT
58954932 AAAAATCTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.37
Consensus pattern (30 bp):
CTTTGGCAAAATGACCATTTTACCCCTAGG
Found at i:58971864 original size:40 final size:40
Alignment explanation
Indices: 58971757--58971973 Score: 255
Period size: 40 Copynumber: 5.5 Consensus size: 40
58971747 CGGATGATAA
* * *
58971757 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATA-T
* *
58971797 CCGGGCTAAG-CCCGAAGGCAATT-GTGCGAGTTATTATAC
1 CCGGGCTAAGTCCCGAAGGC-ATTCGTGCGAGTTACTATAT
* * *
58971836 CCGGGCTAATTCCCGAAGGCATTCGTGCGAGTTATTATGT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
*
58971876 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
* *
58971916 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTATAT
* *
58971956 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
58971974 TACTTGGCTT
Statistics
Matches: 155, Mismatches: 17, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
39 46 0.30
40 109 0.70
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTATAT
Found at i:58971959 original size:80 final size:80
Alignment explanation
Indices: 58971757--58971973 Score: 250
Period size: 79 Copynumber: 2.7 Consensus size: 80
58971747 CGGATGATAA
* * *
58971757 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGT-GACTA-ATTCCGGGCTAAG-CCCGAAGGCAAT
1 CCGGGCTATGTCCCGAAGGCATTCGTGCGAGTAG-CTATA-TCCGGGCTAAGTCCCGAAGGCAAT
*
58971819 TGTGCGAGTTATTATAC
64 TGTGCGAGTTACTATAC
* *
58971836 CCGGGCTAAT-TCCCGAAGGCATTCGTGCGAGTTA-TTATGTCCGGGCTAAGTCCCGAAGGC-AT
1 CCGGGCT-ATGTCCCGAAGGCATTCGTGCGAG-TAGCTATATCCGGGCTAAGTCCCGAAGGCAAT
*
58971898 TGGTGCGAGTTACTATAT
64 T-GTGCGAGTTACTATAC
* * *
58971916 CCGGGCTATGTCCCGAAGGCATTCGAGCGAGTAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTATGTCCCGAAGGCATTCGTGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGG
58971974 TACTTGGCTT
Statistics
Matches: 118, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
79 60 0.51
80 58 0.49
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (80 bp):
CCGGGCTATGTCCCGAAGGCATTCGTGCGAGTAGCTATATCCGGGCTAAGTCCCGAAGGCAATTG
TGCGAGTTACTATAC
Found at i:58971969 original size:119 final size:119
Alignment explanation
Indices: 58971757--58971973 Score: 289
Period size: 119 Copynumber: 1.8 Consensus size: 119
58971747 CGGATGATAA
* * *
58971757 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGA
* *
58971822 GCGAGTTATTATACCCGGGCTAATTCCCGAAGGCATTCGTGCGAGTTATTATGT
66 GCGAGTTACTATACCCGGGCTAAATCCCGAAGGCATTCGTGCGAGTTATTATGT
* *
58971876 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACT-ATATCCGGGCTATGTCCCGAAGGC-ATT
1 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTGACTAAT-TCCGGGCTAAG-CCCGAAGGCAATT
* *
58971939 CGAGCGAG-TAGCTATATCC-GGTTAAATCCCGAAGG
64 -GAGCGAGTTA-CTATACCCGGGCTAAATCCCGAAGG
58971974 TACTTGGCTT
Statistics
Matches: 85, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
118 2 0.02
119 62 0.73
120 21 0.25
ACGTcount: A:0.23, C:0.24, G:0.29, T:0.25
Consensus pattern (119 bp):
CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGA
GCGAGTTACTATACCCGGGCTAAATCCCGAAGGCATTCGTGCGAGTTATTATGT
Found at i:58979268 original size:40 final size:40
Alignment explanation
Indices: 58979213--58979309 Score: 126
Period size: 40 Copynumber: 2.5 Consensus size: 40
58979203 NNNNNNNNNN
* *
58979213 CGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTA-CTATATC
1 CGGGCTAAGTCCCGAAGGCATTCGAGCGAG-TAGCTATATC
*
58979253 CGGGCTATGTCCCGAAGGCATTCGAGCGAGTAGCTATATC
1 CGGGCTAAGTCCCGAAGGCATTCGAGCGAGTAGCTATATC
* *
58979293 C-GGTTAAATCCCGAAGG
1 CGGGCTAAGTCCCGAAGG
58979310 TACTTGGCTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
39 15 0.30
40 35 0.70
ACGTcount: A:0.24, C:0.24, G:0.30, T:0.23
Consensus pattern (40 bp):
CGGGCTAAGTCCCGAAGGCATTCGAGCGAGTAGCTATATC
Found at i:58991236 original size:64 final size:64
Alignment explanation
Indices: 58991156--58991339 Score: 185
Period size: 67 Copynumber: 2.8 Consensus size: 64
58991146 AGACATTATG
* * *
58991156 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAGGAGAGCTACGGGATAT
1 ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
* * * * * *
58991220 ATGTAGCTAGGTCGCATGCGTGGTTCCAAGTGAAGGACACCATGTAGACAAGAGAGCTACGAGAT
1 ATGTAGCTAGGTCGCATGGGT-GATACTA-TG-TGTACACCATGTAGACAAGAGAGCTACGAGAT
58991285 AA
63 AA
* * * *
58991287 ACTG--GCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 A-TGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
58991340 CGAACTATAT
Statistics
Matches: 97, Mismatches: 18, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
62 1 0.01
63 19 0.20
64 21 0.22
65 8 0.08
66 16 0.16
67 30 0.31
68 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.23
Consensus pattern (64 bp):
ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACGAGATAA
Found at i:58994058 original size:20 final size:19
Alignment explanation
Indices: 58994029--58994083 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
58994019 AGCAGTTTAG
*
58994029 AAAAAATTTTAAATCAATTTT
1 AAAAATTTTTAAA--AATTTT
58994050 -AAAATTTTTAAAAATTTT
1 AAAAATTTTTAAAAATTTT
58994068 AAAAAATTTTTAAAAA
1 -AAAAATTTTTAAAAA
58994084 ATGTATACAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 6 0.19
20 25 0.81
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAAATTTTTAAAAATTTT
Found at i:58994065 original size:10 final size:10
Alignment explanation
Indices: 58994046--58994083 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
58994036 TTTAAATCAA
58994046 TTTT-AAAAT
1 TTTTAAAAAT
58994055 TTTTAAAAAT
1 TTTTAAAAAT
*
58994065 TTTAAAAAAT
1 TTTTAAAAAT
58994075 TTTTAAAAA
1 TTTTAAAAA
58994084 ATGTATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
9 4 0.15
10 22 0.85
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (10 bp):
TTTTAAAAAT
Found at i:58994078 original size:11 final size:11
Alignment explanation
Indices: 58994050--58994100 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
58994040 AATCAATTTT
58994050 AAAATTTTT-A
1 AAAATTTTTAA
58994060 AAAA-TTTTAA
1 AAAATTTTTAA
58994070 AAAATTTTTAA
1 AAAATTTTTAA
* *
58994081 AAAATGTATACA
1 AAAATTTTTA-A
58994093 AAAATTTT
1 AAAATTTT
58994101 ATTTTAATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 4 0.12
10 9 0.26
11 14 0.41
12 7 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (11 bp):
AAAATTTTTAA
Found at i:58997869 original size:45 final size:45
Alignment explanation
Indices: 58997817--58997903 Score: 147
Period size: 45 Copynumber: 1.9 Consensus size: 45
58997807 TATGTAATTT
*
58997817 GAACTCATTGAGTTGTGGTCTGAGTTCATGATATATGTGACATCC
1 GAACTCATTGAGTTGTGGCCTGAGTTCATGATATATGTGACATCC
* *
58997862 GAACTCATTGAGTTGTGGCCTGGGTTCGTGATATATGTGACA
1 GAACTCATTGAGTTGTGGCCTGAGTTCATGATATATGTGACA
58997904 CATGTTTTGG
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.34
Consensus pattern (45 bp):
GAACTCATTGAGTTGTGGCCTGAGTTCATGATATATGTGACATCC
Found at i:59002307 original size:18 final size:19
Alignment explanation
Indices: 59002277--59002313 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
59002267 GCGACAGTTG
59002277 ACTAAGAACATGG-TTTTT
1 ACTAAGAACATGGATTTTT
59002295 ACTAA-AACAATGGATTTTT
1 ACTAAGAAC-ATGGATTTTT
59002314 TGAAAATACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 3 0.18
18 9 0.53
19 5 0.29
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (19 bp):
ACTAAGAACATGGATTTTT
Found at i:59009359 original size:46 final size:46
Alignment explanation
Indices: 59009292--59009467 Score: 180
Period size: 46 Copynumber: 3.8 Consensus size: 46
59009282 TGTAACCCGC
* *
59009292 CCATAAGTGAACTCGGACTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
59009338 CCATAAGTGAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG---GAC--GTTCGCAT
* * * *
59009388 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* *
59009431 CCATAAGTGAACTCGGACTCAACTCAATGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
59009468 TGCCCAAATA
Statistics
Matches: 107, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 3 0.03
45 2 0.02
46 61 0.57
47 25 0.23
48 2 0.02
49 3 0.03
50 3 0.03
51 3 0.03
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:59015641 original size:4 final size:4
Alignment explanation
Indices: 59015632--59015703 Score: 71
Period size: 4 Copynumber: 18.8 Consensus size: 4
59015622 TAAACACCAA
* *
59015632 AAAG AAAG AAAG AAAG AAA- ACAG AAAG -AAT AAAG AAAG AAAG AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
59015677 ACAG AAAG AATA- AAAA AAAG AAAG AAA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAA
59015704 AAAAAAACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
3 7 0.12
4 48 0.86
5 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:59015652 original size:26 final size:26
Alignment explanation
Indices: 59015623--59015704 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
59015613 AAACAAATCT
59015623 AAACACCAAA-AAGAAAGAAAGAAAGA
1 AAACA-CAAAGAAGAAAGAAAGAAAGA
* *
59015649 AAACAGAAAGAATAAAGAAAGAAAGA
1 AAACACAAAGAAGAAAGAAAGAAAGA
* * *
59015675 AAACAGAAAGAATAAAAAAAAGAAAGA
1 AAACACAAAGAA-GAAAGAAAGAAAGA
59015702 AAA
1 AAA
59015705 AAAAAACAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
25 3 0.06
26 32 0.64
27 15 0.30
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (26 bp):
AAACACAAAGAAGAAAGAAAGAAAGA
Found at i:59015658 original size:11 final size:10
Alignment explanation
Indices: 59015630--59015734 Score: 74
Period size: 11 Copynumber: 10.0 Consensus size: 10
59015620 TCTAAACACC
59015630 AAAAAGAAAG
1 AAAAAGAAAG
59015640 --AAAGAAAG
1 AAAAAGAAAG
59015648 AAAACAGAAAG
1 AAAA-AGAAAG
59015659 AATAAAGAAAG
1 AA-AAAGAAAG
59015670 AAAGAA-AACAG
1 AAA-AAGAA-AG
*
59015681 AAAGAATAAA-
1 AAA-AAGAAAG
59015691 AAAAAGAAAG
1 AAAAAGAAAG
* *
59015701 AAAAAAAAAAC
1 -AAAAAGAAAG
59015712 AAAAAGAATAATG
1 AAAAAG-A-AA-G
59015725 AAAAAGAAAG
1 AAAAAGAAAG
59015735 TGGGAACGTG
Statistics
Matches: 78, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
8 8 0.10
9 5 0.06
10 14 0.18
11 38 0.49
12 7 0.09
13 6 0.08
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:59015668 original size:30 final size:30
Alignment explanation
Indices: 59015632--59015734 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 30
59015622 TAAACACCAA
59015632 AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
1 AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
59015662 ----AAAGAAAGAAAGAAAACAGAAAGAAT
1 AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
* * *
59015688 AAAAAAAAGAAAGAAAAAAAAAACAAAAAGAAT
1 -AAAGAAAGAAAG--AAAGAAAACAGAAAGAAT
*
59015721 AATG-AA-AAAGAAAG
1 AAAGAAAGAAAGAAAG
59015735 TGGGAACGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
26 26 0.43
28 3 0.05
30 4 0.07
31 10 0.16
32 2 0.03
33 16 0.26
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.04
Consensus pattern (30 bp):
AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
Found at i:59015708 original size:15 final size:15
Alignment explanation
Indices: 59015630--59015710 Score: 83
Period size: 15 Copynumber: 5.3 Consensus size: 15
59015620 TCTAAACACC
59015630 AAAAAGAAAGAAAGAA
1 AAAAAGAAAGAAA-AA
* * *
59015646 AGAAA-ACAGAAAGA
1 AAAAAGAAAGAAAAA
* *
59015660 ATAAAGAAAGAAAGA
1 AAAAAGAAAGAAAAA
*
59015675 AAACAGAAAGAATAAA
1 AAAAAGAAAGAA-AAA
59015691 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
59015706 AAAAA
1 AAAAA
59015711 CAAAAAGAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
14 5 0.09
15 32 0.59
16 17 0.31
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAAA
Found at i:59016647 original size:93 final size:93
Alignment explanation
Indices: 59015992--59016633 Score: 1284
Period size: 93 Copynumber: 6.9 Consensus size: 93
59015982 AGCCATTTTC
59015992 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016057 GAACTCGGACTCAACTCAACGAGCTAGA
66 GAACTCGGACTCAACTCAACGAGCTAGA
59016085 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016150 GAACTCGGACTCAACTCAACGAGCTAGA
66 GAACTCGGACTCAACTCAACGAGCTAGA
59016178 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016243 GAACTCGGACTCAACTCAACGAGCTAGA
66 GAACTCGGACTCAACTCAACGAGCTAGA
59016271 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016336 GAACTCGGACTCAACTCAACGAGCTAGA
66 GAACTCGGACTCAACTCAACGAGCTAGA
59016364 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016429 GAACTCGGACTCAACTCAACGAGCTAGA
66 GAACTCGGACTCAACTCAACGAGCTAGA
59016457 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016522 GAACTCGGACTCAACTCAACGAGCTAGA
66 GAACTCGGACTCAACTCAACGAGCTAGA
59016550 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
59016615 GAACTCGGACTCAACTCAA
66 GAACTCGGACTCAACTCAA
59016634 TGAGTTCGGA
Statistics
Matches: 549, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 549 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (93 bp):
ATGCCTAGTTACATCTCACGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
GAACTCGGACTCAACTCAACGAGCTAGA
Found at i:59016662 original size:46 final size:45
Alignment explanation
Indices: 59016011--59016649 Score: 351
Period size: 46 Copynumber: 13.8 Consensus size: 45
59016001 TACATCTCAC
* *
59016011 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* * * * * *
59016057 GAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTTACATCTC--A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCC----CACATC-CAAAGT
* *
59016104 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* * * * * *
59016150 GAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTTACATCTC--A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCC----CACATC-CAAAGT
* *
59016197 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* * * * * *
59016243 GAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTTACATCTC--A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCC----CACATC-CAAAGT
* *
59016290 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* * * * * *
59016336 GAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTTACATCTC--A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCC----CACATC-CAAAGT
* *
59016383 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* * * * * *
59016429 GAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTTACATCTC--A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCC----CACATC-CAAAGT
* *
59016476 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* * * * * *
59016522 GAACTCGGACTCAACTCAACGAGCTAGAATGCCTAGTTACATCTC--A-C
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCC----CACATC-CAAAGT
* *
59016569 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCA-AAGT
* *
59016615 GAACTCGGACTCAACTCAATGAGTTCGGATGCCCA
1 GAACTCGGACTCAACTCAACGAGTTCGGACGCCCA
59016650 AATATCCCAG
Statistics
Matches: 439, Mismatches: 100, Indels: 108
0.68 0.15 0.17
Matches are distributed among these distances:
42 6 0.01
43 24 0.05
45 6 0.01
46 199 0.45
47 168 0.38
48 6 0.01
50 24 0.05
51 6 0.01
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (45 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACGCCCACATCCAAAGT
Found at i:59022817 original size:4 final size:4
Alignment explanation
Indices: 59022808--59022879 Score: 71
Period size: 4 Copynumber: 18.8 Consensus size: 4
59022798 TAAACACCAA
* *
59022808 AAAG AAAG AAAG AAAG AAA- ACAG AAAG -AAT AAAG AAAG AAAG AAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
59022853 ACAG AAAG AATA- AAAA AAAG AAAG AAA
1 AAAG AAAG AA-AG AAAG AAAG AAAG AAA
59022880 AAAAAAACAA
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
3 7 0.12
4 48 0.86
5 1 0.02
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:59022828 original size:26 final size:26
Alignment explanation
Indices: 59022799--59022880 Score: 94
Period size: 26 Copynumber: 3.1 Consensus size: 26
59022789 AAACAAATCT
59022799 AAACACCAAA-AAGAAAGAAAGAAAGA
1 AAACA-CAAAGAAGAAAGAAAGAAAGA
* *
59022825 AAACAGAAAGAATAAAGAAAGAAAGA
1 AAACACAAAGAAGAAAGAAAGAAAGA
* * *
59022851 AAACAGAAAGAATAAAAAAAAGAAAGA
1 AAACACAAAGAA-GAAAGAAAGAAAGA
59022878 AAA
1 AAA
59022881 AAAAAACAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
25 3 0.06
26 32 0.64
27 15 0.30
ACGTcount: A:0.76, C:0.06, G:0.16, T:0.02
Consensus pattern (26 bp):
AAACACAAAGAAGAAAGAAAGAAAGA
Found at i:59022834 original size:11 final size:10
Alignment explanation
Indices: 59022806--59022910 Score: 74
Period size: 11 Copynumber: 10.0 Consensus size: 10
59022796 TCTAAACACC
59022806 AAAAAGAAAG
1 AAAAAGAAAG
59022816 --AAAGAAAG
1 AAAAAGAAAG
59022824 AAAACAGAAAG
1 AAAA-AGAAAG
59022835 AATAAAGAAAG
1 AA-AAAGAAAG
59022846 AAAGAA-AACAG
1 AAA-AAGAA-AG
*
59022857 AAAGAATAAA-
1 AAA-AAGAAAG
59022867 AAAAAGAAAG
1 AAAAAGAAAG
* *
59022877 AAAAAAAAAAC
1 -AAAAAGAAAG
59022888 AAAAAGAATAATG
1 AAAAAG-A-AA-G
59022901 AAAAAGAAAG
1 AAAAAGAAAG
59022911 TGGGAACGTG
Statistics
Matches: 78, Mismatches: 5, Indels: 24
0.73 0.05 0.22
Matches are distributed among these distances:
8 8 0.10
9 5 0.06
10 14 0.18
11 38 0.49
12 7 0.09
13 6 0.08
ACGTcount: A:0.77, C:0.03, G:0.16, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:59022844 original size:30 final size:30
Alignment explanation
Indices: 59022808--59022910 Score: 101
Period size: 26 Copynumber: 3.5 Consensus size: 30
59022798 TAAACACCAA
59022808 AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
1 AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
59022838 ----AAAGAAAGAAAGAAAACAGAAAGAAT
1 AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
* * *
59022864 AAAAAAAAGAAAGAAAAAAAAAACAAAAAGAAT
1 -AAAGAAAGAAAG--AAAGAAAACAGAAAGAAT
*
59022897 AATG-AA-AAAGAAAG
1 AAAGAAAGAAAGAAAG
59022911 TGGGAACGTG
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
26 26 0.43
28 3 0.05
30 4 0.07
31 10 0.16
32 2 0.03
33 16 0.26
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.04
Consensus pattern (30 bp):
AAAGAAAGAAAGAAAGAAAACAGAAAGAAT
Found at i:59022884 original size:15 final size:15
Alignment explanation
Indices: 59022806--59022886 Score: 83
Period size: 15 Copynumber: 5.3 Consensus size: 15
59022796 TCTAAACACC
59022806 AAAAAGAAAGAAAGAA
1 AAAAAGAAAGAAA-AA
* * *
59022822 AGAAA-ACAGAAAGA
1 AAAAAGAAAGAAAAA
* *
59022836 ATAAAGAAAGAAAGA
1 AAAAAGAAAGAAAAA
*
59022851 AAACAGAAAGAATAAA
1 AAAAAGAAAGAA-AAA
59022867 AAAAAGAAAGAAAAA
1 AAAAAGAAAGAAAAA
59022882 AAAAA
1 AAAAA
59022887 CAAAAAGAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
14 5 0.09
15 32 0.59
16 17 0.31
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.02
Consensus pattern (15 bp):
AAAAAGAAAGAAAAA
Found at i:59026721 original size:47 final size:47
Alignment explanation
Indices: 59026667--59026804 Score: 213
Period size: 47 Copynumber: 2.9 Consensus size: 47
59026657 GACTTTATGA
** * * *
59026667 GATGAATGTGAATGTGTATATATGAGATAAGGCCTAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAATGT
*
59026714 GATGAATGTGAACATGCATATGTGTGATAAGGCCAAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAATGT
*
59026761 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAA
1 GATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAA
59026805 ATGACAGACG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 83 1.00
ACGTcount: A:0.35, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCAAATGGCCAATGT
Found at i:59026740 original size:25 final size:24
Alignment explanation
Indices: 59026711--59026788 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 24
59026701 TAATGGCCAA
59026711 TGTGATGAATGTGAACATGCATAT
1 TGTGATGAATGTGAACATGCATAT
* **
59026735 GTGTGAT-AAGGCCAA-ATGGCCA-A-
1 -TGTGATGAATGTGAACAT-G-CATAT
59026758 TGTGATGAATGTGAACATGCATAT
1 TGTGATGAATGTGAACATGCATAT
59026782 ATGTGAT
1 -TGTGAT
59026789 AAGGCCGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 14
0.67 0.10 0.23
Matches are distributed among these distances:
22 8 0.20
23 9 0.22
24 9 0.22
25 14 0.35
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.29
Consensus pattern (24 bp):
TGTGATGAATGTGAACATGCATAT
Found at i:59030895 original size:20 final size:19
Alignment explanation
Indices: 59030867--59030917 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
59030857 AAAATGATAA
59030867 AATCAAGTTAAA-ATGGTTTC
1 AATCAAGTTAAACAT--TTTC
*
59030887 AATCGAGTTAAACATTTTC
1 AATCAAGTTAAACATTTTC
59030906 AATCAAGTTAAA
1 AATCAAGTTAAA
59030918 TCTATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 15 0.54
20 11 0.39
21 2 0.07
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (19 bp):
AATCAAGTTAAACATTTTC
Found at i:59030933 original size:21 final size:19
Alignment explanation
Indices: 59030892--59030934 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
59030882 GTTTCAATCG
* *
59030892 AGTTAAACATTTTCAATCA
1 AGTTAAACATTTTAAAACA
59030911 AGTTAAATCTATTTTAAAACA
1 AGTTAAA-C-ATTTTAAAACA
59030932 AGT
1 AGT
59030935 CAGTATTGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (19 bp):
AGTTAAACATTTTAAAACA
Found at i:59031405 original size:15 final size:15
Alignment explanation
Indices: 59031385--59031421 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
59031375 TAATATTTCT
59031385 TACTTTTCTTGCACA
1 TACTTTTCTTGCACA
*
59031400 TACTTTTCTTGTACA
1 TACTTTTCTTGCACA
*
59031415 CACTTTT
1 TACTTTT
59031422 GAGTTTTCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.24, G:0.05, T:0.51
Consensus pattern (15 bp):
TACTTTTCTTGCACA
Found at i:59036200 original size:30 final size:30
Alignment explanation
Indices: 59036166--59036225 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
59036156 CCTTAAGCCG
59036166 AAAATCGTTGTTTGCTTTACGAGCGATGAA
1 AAAATCGTTGTTTGCTTTACGAGCGATGAA
59036196 AAAATCGTTGTTTGCTTTACGAGCGATGAA
1 AAAATCGTTGTTTGCTTTACGAGCGATGAA
59036226 TGTGCACTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAATCGTTGTTTGCTTTACGAGCGATGAA
Found at i:59046039 original size:12 final size:12
Alignment explanation
Indices: 59046022--59046047 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59046012 TGAGATTGCA
59046022 TTTTCATAACAT
1 TTTTCATAACAT
59046034 TTTTCATAACAT
1 TTTTCATAACAT
59046046 TT
1 TT
59046048 GCACTATTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.00, T:0.54
Consensus pattern (12 bp):
TTTTCATAACAT
Found at i:59055472 original size:50 final size:49
Alignment explanation
Indices: 59055392--59055546 Score: 152
Period size: 50 Copynumber: 3.1 Consensus size: 49
59055382 CATTAGGGAT
* *
59055392 TACCAATTCTTAGCTCGTATGAGCTTACCGATATT-CAGCTCGTAAGAGCT-
1 TACCGATTC-TAGCTCGTATGAGATTACCGAT-TTACAGCTCGTAAGAG-TA
* * *
59055442 TGCCGATTCTCAGCTCGTATAAGATTACCGATTTACAGCTCGTGAGAGTA
1 TACCGATTCT-AGCTCGTATGAGATTACCGATTTACAGCTCGTAAGAGTA
* * * *
59055492 TACCGATTCATAGCTCGTATGAGCATATACCGATTCATAGCTCGTATGAGCA
1 TACCGATTC-TAGCTCGTATGAG-AT-TACCGATTTACAGCTCGTAAGAGTA
59055544 TAC
1 TAC
59055547 ATGTACAAGA
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
49 4 0.05
50 57 0.66
51 3 0.03
52 23 0.26
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (49 bp):
TACCGATTCTAGCTCGTATGAGATTACCGATTTACAGCTCGTAAGAGTA
Found at i:59055545 original size:27 final size:26
Alignment explanation
Indices: 59055390--59055544 Score: 137
Period size: 25 Copynumber: 6.1 Consensus size: 26
59055380 GTCATTAGGG
* *
59055390 ATTACCAATTCTTAGCTCGTATGAGC
1 ATTACCGATTCATAGCTCGTATGAGC
*
59055416 -TTACCGA-T-ATTCAGCTCGTAAGAGC
1 ATTACCGATTCA-T-AGCTCGTATGAGC
* *
59055441 -TTGCCGATTC-TCAGCTCGTATAAG-
1 ATTACCGATTCAT-AGCTCGTATGAGC
* * *
59055465 ATTACCGATTTACAGCTCGTGA-GAGT
1 ATTACCGATTCATAGCTCGT-ATGAGC
59055491 A-TACCGATTCATAGCTCGTATGAGC
1 ATTACCGATTCATAGCTCGTATGAGC
59055516 ATATACCGATTCATAGCTCGTATGAGC
1 AT-TACCGATTCATAGCTCGTATGAGC
59055543 AT
1 AT
59055545 ACATGTACAA
Statistics
Matches: 105, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
24 3 0.03
25 73 0.70
26 3 0.03
27 26 0.25
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (26 bp):
ATTACCGATTCATAGCTCGTATGAGC
Found at i:59057727 original size:28 final size:28
Alignment explanation
Indices: 59057683--59057773 Score: 114
Period size: 28 Copynumber: 3.3 Consensus size: 28
59057673 GGAGGAAGCG
59057683 TTCTGGTGGCTATGCCACAAATATCTGT
1 TTCTGGTGGCTATGCCACAAATATCTGT
* *
59057711 TTCTGGTGGCTAAGCCACAAATATCT-A
1 TTCTGGTGGCTATGCCACAAATATCTGT
* *
59057738 TTCAGGGTGGCTCTGCCAC-AATATCTGT
1 TTC-TGGTGGCTATGCCACAAATATCTGT
*
59057766 ATCTGGTG
1 TTCTGGTG
59057774 ACTCTGTTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 14 0.26
28 39 0.74
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (28 bp):
TTCTGGTGGCTATGCCACAAATATCTGT
Found at i:59060458 original size:27 final size:27
Alignment explanation
Indices: 59060428--59060544 Score: 85
Period size: 27 Copynumber: 4.4 Consensus size: 27
59060418 TAATACCATG
* *
59060428 CAGGGGTATTACGGTCATTTTTCTCTA
1 CAGGGGTATTACGGTCATTTTACACTA
* ** *
59060455 CAGGGGT-TTTCAATAATTTTACACTA
1 CAGGGGTATTACGGTCATTTTACACTA
* * * *
59060481 TAAGGGTATTTCGGTCATTTTACCCTA
1 CAGGGGTATTACGGTCATTTTACACTA
* * * *
59060508 CATGGGCATTACGGTTATTTTACA-AA
1 CAGGGGTATTACGGTCATTTTACACTA
59060534 CTAGGGGTATT
1 C-AGGGGTATT
59060545 TTGATAATTT
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
26 20 0.30
27 47 0.70
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (27 bp):
CAGGGGTATTACGGTCATTTTACACTA
Found at i:59060554 original size:27 final size:27
Alignment explanation
Indices: 59060524--59060582 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
59060514 CATTACGGTT
59060524 ATTTTACAAACTAG-GGGTATTTTGATA
1 ATTTTACAAAC-AGAGGGTATTTTGATA
** *
59060551 ATTTTGTAAACCGAGGGTATTTTGATA
1 ATTTTACAAACAGAGGGTATTTTGATA
59060578 ATTTT
1 ATTTT
59060583 GTAAATCGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 1 0.04
27 27 0.96
ACGTcount: A:0.31, C:0.07, G:0.19, T:0.44
Consensus pattern (27 bp):
ATTTTACAAACAGAGGGTATTTTGATA
Found at i:59060583 original size:27 final size:27
Alignment explanation
Indices: 59060538--59060599 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
59060528 TACAAACTAG
59060538 GGGTATTTTGATAATTTTGTAAACCGA
1 GGGTATTTTGATAATTTTGTAAACCGA
* *
59060565 GGGTATTTTGATAATTTTGTAAATCGG
1 GGGTATTTTGATAATTTTGTAAACCGA
59060592 GGGTATTT
1 GGGTATTT
59060600 ATGACCCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTGTAAACCGA
Found at i:59070434 original size:25 final size:25
Alignment explanation
Indices: 59070385--59070436 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
59070375 TCTAAGACAT
*
59070385 GGGTTCTCACATGGCCCTAGGACAC
1 GGGTTCTCACATGGCCCTAGAACAC
*
59070410 GGGTTGTCACATGG-CCTAGCAACAC
1 GGGTTCTCACATGGCCCTAG-AACAC
59070435 GG
1 GG
59070437 TCGTGTGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 5 0.21
25 19 0.79
ACGTcount: A:0.21, C:0.29, G:0.31, T:0.19
Consensus pattern (25 bp):
GGGTTCTCACATGGCCCTAGAACAC
Found at i:59073306 original size:20 final size:21
Alignment explanation
Indices: 59073275--59073315 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
59073265 CCACATACAT
59073275 TCAAATATATAAGC-TCATATA
1 TCAAATATATAA-CTTCATATA
59073296 TCAAA-ATATAACTTCATATA
1 TCAAATATATAACTTCATATA
59073316 CACTAGTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 13 0.68
21 5 0.26
ACGTcount: A:0.49, C:0.15, G:0.02, T:0.34
Consensus pattern (21 bp):
TCAAATATATAACTTCATATA
Found at i:59077542 original size:47 final size:47
Alignment explanation
Indices: 59077466--59077699 Score: 369
Period size: 47 Copynumber: 5.0 Consensus size: 47
59077456 CTTCGGGACT
* * * * * *
59077466 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
59077513 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
59077560 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* *
59077607 TATCACATATATACACCTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
59077654 TATCACATATATACACCTTCACATTCATCACATCGGCCATTAGGCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCC
59077700 ATACTATCAT
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 177 1.00
ACGTcount: A:0.28, C:0.32, G:0.09, T:0.30
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:59081030 original size:28 final size:27
Alignment explanation
Indices: 59080999--59081089 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 27
59080989 CTGACTGATT
*
59080999 TCGCACACATAGCGCTCGATTAAAGAAC
1 TCGCACACATAGTGCTC-ATTAAAGAAC
* *
59081027 TCGCACACATAGTGCCTCAATTACCA-ATC
1 TCGCACACATAGTG-CTC-ATTA-AAGAAC
*
59081056 TCGCACACATAGTGCTCAGTTGAAGAAC
1 TCGCACACATAGTGCTCA-TTAAAGAAC
59081084 TCGCAC
1 TCGCAC
59081090 TCTCAGTGCC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
27 2 0.04
28 26 0.50
29 23 0.44
30 1 0.02
ACGTcount: A:0.32, C:0.31, G:0.16, T:0.21
Consensus pattern (27 bp):
TCGCACACATAGTGCTCATTAAAGAAC
Found at i:59081356 original size:40 final size:40
Alignment explanation
Indices: 59081296--59082296 Score: 1705
Period size: 40 Copynumber: 25.0 Consensus size: 40
59081286 GTCCGAATAC
* * * * *
59081296 ACATCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGTT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * * * **
59081336 ATAACACCAGGACGAATGCTCTTCGGGACTTAACCCTAAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
** * * * * *
59081376 GTAACTCTAGCACAAATGCTCTTTGAGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * *
59081416 ATAACACCAGCACAAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * *
59081456 ATAACACCAGCACAAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* *
59081496 ACATCACTAGCATGAATGCTCTTCGGGACTTAGCCCGAAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
* * * *
59081536 ATAACACCAGCACAAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081576 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081616 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081656 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081696 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081736 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081776 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081816 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081856 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081896 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081936 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59081976 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082016 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082056 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082096 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082136 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082176 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082216 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082256 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
1 ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
59082296 A
1 A
59082297 TATATAACTC
Statistics
Matches: 920, Mismatches: 41, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 920 1.00
ACGTcount: A:0.26, C:0.30, G:0.22, T:0.23
Consensus pattern (40 bp):
ACATCACTAGCACGAATGCTCTTCGGGACTTAGCCCGGAT
Found at i:59082499 original size:38 final size:37
Alignment explanation
Indices: 59082446--59082522 Score: 136
Period size: 38 Copynumber: 2.1 Consensus size: 37
59082436 ATAGTCATAA
*
59082446 CACTCTTTAAAATTGCATCACTTATACCCTTATAATT
1 CACTCTTTAAAATTGCATCACTTATACCATTATAATT
59082483 CACTCTTTCAAAATTGCATCACTTATACCATTATAATT
1 CACTCTTT-AAAATTGCATCACTTATACCATTATAATT
59082521 CA
1 CA
59082523 ATACAAATCA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 8 0.21
38 30 0.79
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.39
Consensus pattern (37 bp):
CACTCTTTAAAATTGCATCACTTATACCATTATAATT
Found at i:59083612 original size:40 final size:40
Alignment explanation
Indices: 59083527--59083664 Score: 159
Period size: 40 Copynumber: 3.5 Consensus size: 40
59083517 CTCGATAATA
* * ** *
59083527 TAAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCT
1 TAAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAACT
* *
59083567 CAAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAATT
1 TAAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAACT
* * * *
59083607 TAAAGTGAATAGGATTTATTCTTAATTCACTACGGTAACT
1 TAAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAACT
* *
59083647 TAAGGCGGATAGGATTTG
1 TAAAGTGGATAGGATTTG
59083665 ACCTGAAAAG
Statistics
Matches: 81, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 81 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (40 bp):
TAAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAACT
Found at i:59085767 original size:28 final size:28
Alignment explanation
Indices: 59085727--59085783 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
59085717 TACTTAATTG
59085727 AGTGACATTTAGAATGGGCTTCACATCC
1 AGTGACATTTAGAATGGGCTTCACATCC
59085755 AGTGACATTTAGAATGGGCTTCACATCC
1 AGTGACATTTAGAATGGGCTTCACATCC
59085783 A
1 A
59085784 CTAACTCAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (28 bp):
AGTGACATTTAGAATGGGCTTCACATCC
Found at i:59086601 original size:24 final size:25
Alignment explanation
Indices: 59086557--59086604 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
59086547 GACATACTGA
59086557 TGGCACCCATTAAAAAAAATTTCTG
1 TGGCACCCATTAAAAAAAATTTCTG
59086582 TGGCACCCATT-AAAAAAATTTCT
1 TGGCACCCATTAAAAAAAATTTCT
59086605 AACAATCTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 12 0.52
25 11 0.48
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.29
Consensus pattern (25 bp):
TGGCACCCATTAAAAAAAATTTCTG
Found at i:59086789 original size:33 final size:33
Alignment explanation
Indices: 59086744--59086809 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
59086734 TTTTTCACTT
59086744 TCACTAAAATATGACCGTGTAATGATTAGGAAA
1 TCACTAAAATATGACCGTGTAATGATTAGGAAA
* *
59086777 TCACTAATATATGACTGTGTAATGATTAGGAAA
1 TCACTAAAATATGACCGTGTAATGATTAGGAAA
59086810 AAAAAGACGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.41, C:0.11, G:0.18, T:0.30
Consensus pattern (33 bp):
TCACTAAAATATGACCGTGTAATGATTAGGAAA
Found at i:59087042 original size:17 final size:17
Alignment explanation
Indices: 59087017--59087055 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
59087007 CTTTCACTTT
* *
59087017 TCCAATCTTTCCTTACA
1 TCCATTCTTGCCTTACA
*
59087034 TCCATTCTTGCCTTTCA
1 TCCATTCTTGCCTTACA
59087051 TCCAT
1 TCCAT
59087056 CTACTTTTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.36, G:0.03, T:0.44
Consensus pattern (17 bp):
TCCATTCTTGCCTTACA
Found at i:59089363 original size:24 final size:24
Alignment explanation
Indices: 59089336--59089419 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
59089326 TTCACCCAAT
*
59089336 ACTATTATAATTCGATTCCCCTGA
1 ACTATCATAATTCGATTCCCCTGA
* *
59089360 ACTATCATAA-TAGATTTCACCC-AA
1 ACTATCATAATTCGA-TTC-CCCTGA
*
59089384 TACTATTATAATTCGATTCCCCTGA
1 -ACTATCATAATTCGATTCCCCTGA
59089409 ACTATCATAAT
1 ACTATCATAAT
59089420 AGTTGTTGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
23 3 0.06
24 26 0.54
25 16 0.33
26 3 0.06
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.36
Consensus pattern (24 bp):
ACTATCATAATTCGATTCCCCTGA
Found at i:59089389 original size:25 final size:25
Alignment explanation
Indices: 59089323--59089395 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
59089313 CCATTACACC
*
59089323 GATTTCACCCAATACTATTATAATTC
1 GATTTCACCCAATACTATTATAA-TA
* *
59089349 GA-TTC-CCCTGA-ACTATCATAATA
1 GATTTCACCC-AATACTATTATAATA
59089372 GATTTCACCCAATACTATTATAAT
1 GATTTCACCCAATACTATTATAAT
59089396 TCGATTCCCC
Statistics
Matches: 38, Mismatches: 5, Indels: 9
0.73 0.10 0.17
Matches are distributed among these distances:
23 3 0.08
24 16 0.42
25 17 0.45
26 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.05, T:0.36
Consensus pattern (25 bp):
GATTTCACCCAATACTATTATAATA
Found at i:59089395 original size:49 final size:49
Alignment explanation
Indices: 59089323--59089421 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
59089313 CCATTACACC
59089323 GATTTCACCCAATACTATTATAATTCGATTCCCCTGAACTATCATAATA
1 GATTTCACCCAATACTATTATAATTCGATTCCCCTGAACTATCATAATA
59089372 GATTTCACCCAATACTATTATAATTCGATTCCCCTGAACTATCATAATA
1 GATTTCACCCAATACTATTATAATTCGATTCCCCTGAACTATCATAATA
59089421 G
1 G
59089422 TTGTTGAAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.34, C:0.24, G:0.07, T:0.34
Consensus pattern (49 bp):
GATTTCACCCAATACTATTATAATTCGATTCCCCTGAACTATCATAATA
Found at i:59089555 original size:64 final size:64
Alignment explanation
Indices: 59089476--59089600 Score: 225
Period size: 64 Copynumber: 2.0 Consensus size: 64
59089466 ACTAGTTAAT
*
59089476 TTTCTTTTTTATTTTAAATTCAAATAGACTTGGCTTTATTAAAGCATAAACTAGAATACATTTC
1 TTTCTTTTTTATTTTAAATTCAAATAGACTTGGCTTTATTAAAACATAAACTAGAATACATTTC
59089540 TTTCTCTTTTT-TTTTAAATTCAAATAGACTTGGCTTTATTAAAACATAAACTAGAATACAT
1 TTTCT-TTTTTATTTTAAATTCAAATAGACTTGGCTTTATTAAAACATAAACTAGAATACAT
59089601 ATCACTAAGC
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
64 54 0.92
65 5 0.08
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (64 bp):
TTTCTTTTTTATTTTAAATTCAAATAGACTTGGCTTTATTAAAACATAAACTAGAATACATTTC
Found at i:59091540 original size:59 final size:59
Alignment explanation
Indices: 59091474--59091656 Score: 357
Period size: 59 Copynumber: 3.1 Consensus size: 59
59091464 ACGATAAATA
59091474 AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
1 AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
59091533 AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
1 AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
59091592 AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
1 AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
*
59091651 AGTAAA
1 AATAAA
59091657 CATATAACTT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
59 123 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.37
Consensus pattern (59 bp):
AATAAATAAAGTTAATTAATAAAATAGGTTTCCCTTGTTAGGAAATGTGCCCATATTTT
Found at i:59103446 original size:11 final size:11
Alignment explanation
Indices: 59103430--59103459 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
59103420 TTACCAAAGT
59103430 TCGATCACATA
1 TCGATCACATA
59103441 TCGATCACATA
1 TCGATCACATA
59103452 TCGATCAC
1 TCGATCAC
59103460 GTTGCTCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.27
Consensus pattern (11 bp):
TCGATCACATA
Found at i:59103532 original size:19 final size:20
Alignment explanation
Indices: 59103494--59103533 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
59103484 AACCTTCACT
59103494 TATTCATCATCACATAGTCA
1 TATTCATCATCACATAGTCA
* *
59103514 TATTCATTA-CACCTAGTCA
1 TATTCATCATCACATAGTCA
59103533 T
1 T
59103534 TTCCCGTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.38
Consensus pattern (20 bp):
TATTCATCATCACATAGTCA
Found at i:59103711 original size:51 final size:51
Alignment explanation
Indices: 59103571--59103749 Score: 182
Period size: 51 Copynumber: 3.5 Consensus size: 51
59103561 CGGATGCCCG
* * * * *
59103571 GTGGCCTGCACATAGTACAACCCTTGT-AGTCAAAGCTACCTTCTT-CACAAA
1 GTGGCCTGCACATAGTACCACACATGTGA-TCAAAGCTATCTT-TTACACATA
* * *
59103622 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCTTTTACACATA
1 GTGGCCTGCACATAGTACCACACATGTGATCAAAGCTATCTTTTACACATA
* *** *
59103673 GTGGCCTGCACTTAGTACCACACATGTGATCAAAGCTATCGGGTACGCATA
1 GTGGCCTGCACATAGTACCACACATGTGATCAAAGCTATCTTTTACACATA
* * *
59103724 GTAGCCTGCACTTAGTACTACACATG
1 GTGGCCTGCACATAGTACCACACATG
59103750 CGACCTAACC
Statistics
Matches: 110, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
50 2 0.02
51 107 0.97
52 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.26
Consensus pattern (51 bp):
GTGGCCTGCACATAGTACCACACATGTGATCAAAGCTATCTTTTACACATA
Found at i:59103792 original size:50 final size:51
Alignment explanation
Indices: 59103665--59103797 Score: 151
Period size: 51 Copynumber: 2.6 Consensus size: 51
59103655 AGCTATCTTT
** * * * *
59103665 TACACATAGTGGCCTGCACTTAGTACCACACATGTGATCAAAGCTATCGGG
1 TACACATAGAAGCCTGCACTTAGTACTACACATGCGACCAAAGCCATCGGG
* * * *
59103716 TACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAA-CCATCTGG
1 TACACATAGAAGCCTGCACTTAGTACTACACATGCGACCAAAGCCATCGGG
* *
59103766 TGCACGTAGAAGCCTGCACTTAGTACTACACA
1 TACACATAGAAGCCTGCACTTAGTACTACACA
59103798 CGTGACATAA
Statistics
Matches: 70, Mismatches: 12, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
50 34 0.49
51 36 0.51
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (51 bp):
TACACATAGAAGCCTGCACTTAGTACTACACATGCGACCAAAGCCATCGGG
Found at i:59111638 original size:3 final size:3
Alignment explanation
Indices: 59111564--59111589 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59111554 TAATTTTTGT
59111564 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
59111590 TATTTCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59113927 original size:27 final size:26
Alignment explanation
Indices: 59113896--59114073 Score: 178
Period size: 27 Copynumber: 6.6 Consensus size: 26
59113886 TAAATTGTAC
59113896 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
59113923 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
59113949 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
59113977 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA--TTGACTATGT
* *
59114005 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* *
59114032 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
59114059 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59114074 GGCTCAATAT
Statistics
Matches: 129, Mismatches: 17, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
26 1 0.01
27 103 0.80
28 25 0.19
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:59114012 original size:82 final size:81
Alignment explanation
Indices: 59113897--59114052 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
59113887 AAATTGTACA
* *
59113897 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
59113961 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
* ** *
59113978 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
59114043 TGCGAGTTGA
65 TGCGAATTGA
59114053 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 15 0.23
82 50 0.76
83 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:59114064 original size:82 final size:81
Alignment explanation
Indices: 59113893--59114073 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
59113883 GATTAAATTG
* *
59113893 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59113958 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * * ** *
59113974 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
59114038 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
59114056 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59114074 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 18 0.22
82 65 0.78
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59114084 original size:27 final size:27
Alignment explanation
Indices: 59113978--59114084 Score: 70
Period size: 27 Copynumber: 3.9 Consensus size: 27
59113968 TGACCATGCG
* * * *
59113978 GCACTAAGTGTGCGAGTTTGACTATGTA
1 GCACTAAGTGTGCGAG-CTCAATATATA
** * * **
59114006 GCACTAAGTGTGCGATTTGATTACGTA
1 GCACTAAGTGTGCGAGCTCAATATATA
* * *
59114033 GCACTAAGTGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGCTCAATATATA
* *
59114060 GCACTGAGTGTGCGGGCTCAATATA
1 GCACTAAGTGTGCGAGCTCAATATA
59114085 CATTCGTGAA
Statistics
Matches: 68, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
27 53 0.78
28 15 0.22
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGCTCAATATATA
Found at i:59121622 original size:27 final size:27
Alignment explanation
Indices: 59121591--59121768 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
59121581 TAAATTGTAC
59121591 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
59121618 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59121644 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
59121672 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
59121700 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59121727 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59121754 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59121769 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:59121705 original size:82 final size:81
Alignment explanation
Indices: 59121592--59121747 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
59121582 AAATTGTACA
* *
59121592 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
59121656 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
59121673 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
59121738 TGCGAGTTGA
65 TGCGAATTGA
59121748 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:59121759 original size:82 final size:81
Alignment explanation
Indices: 59121588--59121768 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
59121578 GATTAAATTG
* *
59121588 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59121653 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
59121669 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
59121733 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
59121751 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59121769 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59124258 original size:6 final size:6
Alignment explanation
Indices: 59124237--59124299 Score: 74
Period size: 6 Copynumber: 10.7 Consensus size: 6
59124227 AGTCCATTTG
* * * *
59124237 TTTTTA TGTCTA TTTTTA -TTTTA TTTTTA TTTTTC TGTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
*
59124284 TTTTTA TGTTTA TTTT
1 TTTTTA TTTTTA TTTT
59124300 GTCTTTATAC
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
5 5 0.11
6 41 0.89
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:59128658 original size:21 final size:19
Alignment explanation
Indices: 59128620--59128655 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
59128610 CTCTGGGCTT
59128620 TCTTTTTTTGTGATTATTC
1 TCTTTTTTTGTGATTATTC
*
59128639 TCTTGTTTTGTG-TTATT
1 TCTTTTTTTGTGATTATT
59128656 ATTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.08, C:0.08, G:0.14, T:0.69
Consensus pattern (19 bp):
TCTTTTTTTGTGATTATTC
Found at i:59141658 original size:51 final size:51
Alignment explanation
Indices: 59141582--59141682 Score: 159
Period size: 51 Copynumber: 2.0 Consensus size: 51
59141572 TATTTTACCT
*
59141582 AAAAGGGAGAGGCCAAGGTGAAAACCCACAAAGGGCGCTTTGAGACCAAAA
1 AAAAGGGAGAGGCCAAGCTGAAAACCCACAAAGGGCGCTTTGAGACCAAAA
* *
59141633 AAAAGGGAGAGGCCAAAGCT-AAAACCCGCAAAGGGCGCTTTGAGGCCAAA
1 AAAAGGGAGAGGCC-AAGCTGAAAACCCACAAAGGGCGCTTTGAGACCAAA
59141683 GGGGTTTTTG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.91
52 4 0.09
ACGTcount: A:0.42, C:0.21, G:0.30, T:0.08
Consensus pattern (51 bp):
AAAAGGGAGAGGCCAAGCTGAAAACCCACAAAGGGCGCTTTGAGACCAAAA
Found at i:59142522 original size:45 final size:45
Alignment explanation
Indices: 59142453--59142845 Score: 189
Period size: 45 Copynumber: 8.8 Consensus size: 45
59142443 GATTCTACAG
*
59142453 ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGACGGTAA
1 ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTAA
* * * ** *
59142498 ATCTCGTCTTCCTGAAGTTGCAGTGAAGCAGATT-TA-A-GCCACC
1 ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTA-A
* * * * * * * * * *
59142541 ACCCTATCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAGATTGTAG
1 ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTAA
* * * **
59142586 ATCTTGT-TTCCCTGAAATTGCAGTGGAGCAGATCGAAGATTGCGA
1 ATCTTGTCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTAA
* * * * * * * ** *
59142631 ATCTCGCCTTTCTAAAGTTGTAGTGAAGCAGATT-TA-A-GCCACC
1 ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTA-A
* * * * * * * * *
59142674 ACCCTATC-TCCTTAAAGTTGTAGTGGAGTAGACTGAAGATTGTAG
1 ATCTTGTCTTCC-TGAAGTTGCAGTGGAGCAGATTGAAGATGGTAA
*
59142719 ATCTTGT-TTCCCTGAAGTTG-AGTGGAGCAGATCGAAGATGGTAA
1 ATCTTGTCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTAA
* * *
59142763 ATCTCG-CATTCCTGAAGTTGCAGTGGAGCAGATCGAAGA-GTGTAG
1 ATCTTGTC-TTCCTGAAGTTGCAGTGGAGCAGATTGAAGATG-GTAA
* * ** *
59142808 ATCTTATCTCCCTGAAGTTATAGTGGAGCAGATCGAAG
1 ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAG
59142846 TCACAATCCT
Statistics
Matches: 253, Mismatches: 77, Indels: 36
0.69 0.21 0.10
Matches are distributed among these distances:
42 5 0.02
43 48 0.19
44 40 0.16
45 153 0.60
46 7 0.03
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (45 bp):
ATCTTGTCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGATGGTAA
Found at i:59142690 original size:133 final size:133
Alignment explanation
Indices: 59142451--59142795 Score: 532
Period size: 133 Copynumber: 2.6 Consensus size: 133
59142441 CCGATTCTAC
* * *
59142451 AGATCTTGTCTT-CCTGAAGTTGCAGTGGAGCAGATTGAAGACGGTAAATCTCGTCTTCCTGAAG
1 AGATCTTGT-TTCCCTGAAGTTGCAGTGGAGCAGATCGAAGATGGTAAATCTCGCCTTCCTGAAG
**
59142515 TTGCAGTGAAGCAGATTTAAGCCACCACCCTATCTCCCTAAAGTTGTAGTGGAGTAGGTTGAAGA
65 TTGCAGTGAAGCAGATTTAAGCCACCACCCTATCTCCCTAAAGTTGTAGTGGAGTAGACTGAAGA
59142580 TTGT
130 TTGT
* * ** * *
59142584 AGATCTTGTTTCCCTGAAATTGCAGTGGAGCAGATCGAAGATTGCGAATCTCGCCTTTCTAAAGT
1 AGATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGATGGTAAATCTCGCCTTCCTGAAGT
* *
59142649 TGTAGTGAAGCAGATTTAAGCCACCACCCTATCTCCTTAAAGTTGTAGTGGAGTAGACTGAAGAT
66 TGCAGTGAAGCAGATTTAAGCCACCACCCTATCTCCCTAAAGTTGTAGTGGAGTAGACTGAAGAT
59142714 TGT
131 TGT
*
59142717 AGATCTTGTTTCCCTGAAGTTG-AGTGGAGCAGATCGAAGATGGTAAATCTCGCATTCCTGAAGT
1 AGATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGATGGTAAATCTCGCCTTCCTGAAGT
*
59142781 TGCAGTGGAGCAGAT
66 TGCAGTGAAGCAGAT
59142796 CGAAGAGTGT
Statistics
Matches: 189, Mismatches: 22, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
132 51 0.27
133 138 0.73
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (133 bp):
AGATCTTGTTTCCCTGAAGTTGCAGTGGAGCAGATCGAAGATGGTAAATCTCGCCTTCCTGAAGT
TGCAGTGAAGCAGATTTAAGCCACCACCCTATCTCCCTAAAGTTGTAGTGGAGTAGACTGAAGAT
TGT
Found at i:59142881 original size:89 final size:88
Alignment explanation
Indices: 59142708--59142882 Score: 194
Period size: 89 Copynumber: 2.0 Consensus size: 88
59142698 GGAGTAGACT
* * * *
59142708 GAAGATTGTAGATCTTGTTTCCCTGAAGTTGAGTGGAGCAGATCGAAGATGGTAAATCTCGCATT
1 GAAGAGTGTAGATCTTATCTCCCTGAAGTTGAGTGGAGCAGATCGAAGAT-GCAAATCTCGCATT
* **
59142773 CCTGAAGTTGCAGTGGAGCAGATC
65 CCTGAAGGTGCAGCAGAGCAGATC
* **
59142797 GAAGAGTGTAGATCTTATCTCCCTGAAGTTATAGTGGAGCAGATCGAAG-T-CACAATC-CTTAT
1 GAAGAGTGTAGATCTTATCTCCCTGAAGTT-GAGTGGAGCAGATCGAAGATGCA-AATCTCGCAT
59142859 CTCTCTGAAGGTGCAGCAGAGCAG
64 -TC-CTGAAGGTGCAGCAGAGCAG
59142883 GATAAAAACA
Statistics
Matches: 72, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
87 4 0.06
88 6 0.08
89 45 0.62
90 17 0.24
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (88 bp):
GAAGAGTGTAGATCTTATCTCCCTGAAGTTGAGTGGAGCAGATCGAAGATGCAAATCTCGCATTC
CTGAAGGTGCAGCAGAGCAGATC
Found at i:59143236 original size:12 final size:12
Alignment explanation
Indices: 59143219--59143248 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
59143209 AACCCAATGG
59143219 CCCAAACTTAAA
1 CCCAAACTTAAA
59143231 CCCAAACTTAAA
1 CCCAAACTTAAA
59143243 CCCAAA
1 CCCAAA
59143249 ACCCAATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.37, G:0.00, T:0.13
Consensus pattern (12 bp):
CCCAAACTTAAA
Found at i:59143628 original size:19 final size:18
Alignment explanation
Indices: 59143601--59143636 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
59143591 CTCTAGGCTT
*
59143601 TCTTTTTTTGTGATTATTC
1 TCTTGTTTTGTG-TTATTC
59143620 TCTTGTTTTGTGTTATT
1 TCTTGTTTTGTGTTATT
59143637 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.08, C:0.08, G:0.14, T:0.69
Consensus pattern (18 bp):
TCTTGTTTTGTGTTATTC
Found at i:59144858 original size:30 final size:31
Alignment explanation
Indices: 59144799--59144858 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
59144789 ATATATTTTG
* *
59144799 TATTAAAGTTAATTTTATTTCATATATATAT
1 TATTAAAGTTAATATTATTTCATACATATAT
* *
59144830 TATTAAA-TTTATATTATTTTATACATATA
1 TATTAAAGTTAATATTATTTCATACATATA
59144859 ATTCCTTCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (31 bp):
TATTAAAGTTAATATTATTTCATACATATAT
Found at i:59145466 original size:198 final size:198
Alignment explanation
Indices: 59145128--59145526 Score: 798
Period size: 198 Copynumber: 2.0 Consensus size: 198
59145118 TGTATATATG
59145128 TTTTGTAAATCTATCGTCTATATTTCCTAGGATTATATTTTATCATACATTCTTGCTATTCTTTC
1 TTTTGTAAATCTATCGTCTATATTTCCTAGGATTATATTTTATCATACATTCTTGCTATTCTTTC
59145193 ATATTACATATATTATTTAAGTTTTATTTTATTGTGTGTATTTTAGCAAATATTTTAATACTTTG
66 ATATTACATATATTATTTAAGTTTTATTTTATTGTGTGTATTTTAGCAAATATTTTAATACTTTG
59145258 TATATTATGTATTTTAAAAAATATTCATTCTATAACACATATTTTAATGATTGCATGTATATATT
131 TATATTATGTATTTTAAAAAATATTCATTCTATAACACATATTTTAATGATTGCATGTATATATT
59145323 AAA
196 AAA
59145326 TTTTGTAAATCTATCGTCTATATTTCCTAGGATTATATTTTATCATACATTCTTGCTATTCTTTC
1 TTTTGTAAATCTATCGTCTATATTTCCTAGGATTATATTTTATCATACATTCTTGCTATTCTTTC
59145391 ATATTACATATATTATTTAAGTTTTATTTTATTGTGTGTATTTTAGCAAATATTTTAATACTTTG
66 ATATTACATATATTATTTAAGTTTTATTTTATTGTGTGTATTTTAGCAAATATTTTAATACTTTG
59145456 TATATTATGTATTTTAAAAAATATTCATTCTATAACACATATTTTAATGATTGCATGTATATATT
131 TATATTATGTATTTTAAAAAATATTCATTCTATAACACATATTTTAATGATTGCATGTATATATT
59145521 AAA
196 AAA
59145524 TTT
1 TTT
59145527 GCCTTTGCAA
Statistics
Matches: 201, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
198 201 1.00
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.51
Consensus pattern (198 bp):
TTTTGTAAATCTATCGTCTATATTTCCTAGGATTATATTTTATCATACATTCTTGCTATTCTTTC
ATATTACATATATTATTTAAGTTTTATTTTATTGTGTGTATTTTAGCAAATATTTTAATACTTTG
TATATTATGTATTTTAAAAAATATTCATTCTATAACACATATTTTAATGATTGCATGTATATATT
AAA
Found at i:59151838 original size:4 final size:4
Alignment explanation
Indices: 59151829--59151882 Score: 62
Period size: 4 Copynumber: 14.2 Consensus size: 4
59151819 TAGCAAAAGA
*
59151829 TAAT TAAT TAAT TATAT T-AT TAAT T-AT TAAT TAAT TAAT TAA- -AAA
1 TAAT TAAT TAAT TA-AT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
59151874 TAAT TAAT T
1 TAAT TAAT T
59151883 TCTTTTAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
2 2 0.05
3 6 0.14
4 33 0.75
5 3 0.07
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:59159524 original size:13 final size:13
Alignment explanation
Indices: 59159506--59159530 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59159496 GTTAATTTTA
59159506 TAAAATAAAATTT
1 TAAAATAAAATTT
59159519 TAAAATAAAATT
1 TAAAATAAAATT
59159531 AGGATGAAAA
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:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAATAAAATTT
Found at i:59160260 original size:22 final size:23
Alignment explanation
Indices: 59160218--59160260 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
59160208 GCATTCTCTT
**
59160218 AAAATCACAAAAGTTGTATAATA
1 AAAATCACAAAAGGAGTATAATA
59160241 AAAATCACAAAAGGAG-ATAA
1 AAAATCACAAAAGGAGTATAA
59160261 AGATTTAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (23 bp):
AAAATCACAAAAGGAGTATAATA
Found at i:59165079 original size:31 final size:31
Alignment explanation
Indices: 59165044--59165106 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
59165034 ATCAATTAAA
59165044 AAAACATTAAGGCATACACAAGCTTGGCACC
1 AAAACATTAAGGCATACACAAGCTTGGCACC
59165075 AAAACATTAAGGCATACACAAGCTTGGCACC
1 AAAACATTAAGGCATACACAAGCTTGGCACC
59165106 A
1 A
59165107 TTCAAACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.43, C:0.25, G:0.16, T:0.16
Consensus pattern (31 bp):
AAAACATTAAGGCATACACAAGCTTGGCACC
Found at i:59166776 original size:42 final size:43
Alignment explanation
Indices: 59166676--59166823 Score: 126
Period size: 42 Copynumber: 3.4 Consensus size: 43
59166666 TGTGATATTG
* * *
59166676 TGTAAGACCACGTCTGGGAC-GTTGGCATCGACTTGATAT--TTACG
1 TGTAAGACCATGTCTGGGACAG-TGACATCG--TT-ATATGATTACA
*
59166720 TGTAAGACCATGTCTGGGACA-TCGACATCG-TATATGATTTCA
1 TGTAAGACCATGTCTGGGACAGT-GACATCGTTATATGATTACA
* * * *
59166762 TGTAAGACCTTGTCTGAGACAGTGGCATCGTTATTTGATTACA
1 TGTAAGACCATGTCTGGGACAGTGACATCGTTATATGATTACA
* *
59166805 TGTAATACCACGTCTGGGA
1 TGTAAGACCATGTCTGGGA
59166824 TGTTGGCATT
Statistics
Matches: 85, Mismatches: 13, Indels: 13
0.77 0.12 0.12
Matches are distributed among these distances:
40 4 0.05
41 1 0.01
42 28 0.33
43 27 0.32
44 25 0.29
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (43 bp):
TGTAAGACCATGTCTGGGACAGTGACATCGTTATATGATTACA
Found at i:59176504 original size:24 final size:24
Alignment explanation
Indices: 59176475--59176523 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
59176465 AAGTTAAACA
59176475 AAGCATAACCTTAGTTAATAATTC
1 AAGCATAACCTTAGTTAATAATTC
59176499 AAGCATAACCTTAGTTAATAATTC
1 AAGCATAACCTTAGTTAATAATTC
59176523 A
1 A
59176524 TCCAAAATAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.33
Consensus pattern (24 bp):
AAGCATAACCTTAGTTAATAATTC
Found at i:59178169 original size:83 final size:83
Alignment explanation
Indices: 59178052--59178220 Score: 293
Period size: 83 Copynumber: 2.0 Consensus size: 83
59178042 AATTAATATA
* *
59178052 AAGCCTGAAAGAGAAAGTGGCCCAGTGTGCTAAGCATTGAAGACTGATCCAACAAGCAAATTGGC
1 AAGCCTAAAAGAGAAAGTGACCCAGTGTGCTAAGCATTGAAGACTGATCCAACAAGCAAATTGGC
*
59178117 AGCCCAAAACCATCCAAC
66 AGCCCAAAAACATCCAAC
* *
59178135 AAGCCTAAAAGAGAAAGTGACCCAGTGTGTTAAGCATTGAAGATTGATCCAACAAGCAAATTGGC
1 AAGCCTAAAAGAGAAAGTGACCCAGTGTGCTAAGCATTGAAGACTGATCCAACAAGCAAATTGGC
59178200 AGCCCAAAAACATCCAAC
66 AGCCCAAAAACATCCAAC
59178218 AAG
1 AAG
59178221 TTGACCCAAT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 81 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (83 bp):
AAGCCTAAAAGAGAAAGTGACCCAGTGTGCTAAGCATTGAAGACTGATCCAACAAGCAAATTGGC
AGCCCAAAAACATCCAAC
Found at i:59179544 original size:25 final size:25
Alignment explanation
Indices: 59179515--59179566 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
59179505 CGACATTTAC
59179515 TTGTCACTTTATTACTTGATAACGA
1 TTGTCACTTTATTACTTGATAACGA
59179540 TTGTCACTTTATTACTTGATAACGA
1 TTGTCACTTTATTACTTGATAACGA
59179565 TT
1 TT
59179567 ATGCACACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (25 bp):
TTGTCACTTTATTACTTGATAACGA
Found at i:59185698 original size:28 final size:28
Alignment explanation
Indices: 59185667--59185724 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
59185657 TTAATTACAT
*
59185667 TCCTAATATTTTTAGTTAATTTTCAAAC
1 TCCTAATATTTTTAGTGAATTTTCAAAC
*
59185695 TCCTACTATTTTTAGTGAATTTTCAAAC
1 TCCTAATATTTTTAGTGAATTTTCAAAC
59185723 TC
1 TC
59185725 ACATCACTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.48
Consensus pattern (28 bp):
TCCTAATATTTTTAGTGAATTTTCAAAC
Found at i:59186532 original size:40 final size:40
Alignment explanation
Indices: 59186454--59186637 Score: 232
Period size: 40 Copynumber: 4.5 Consensus size: 40
59186444 ACCCAAGTAT
* *
59186454 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
* **
59186493 CTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
59186533 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAG-CAACTAGCACAAATGC
*
59186573 CTTTGGGACTTAGCCCGTG-TATAGCAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCG-GATATAGCAACTA---GCACAAATGC
59186616 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
59186638 CATCCGAATA
Statistics
Matches: 127, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 12 0.09
40 83 0.65
41 2 0.02
42 1 0.01
43 29 0.23
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGCAACTAGCACAAATGC
Found at i:59196203 original size:284 final size:284
Alignment explanation
Indices: 59195693--59196222 Score: 907
Period size: 284 Copynumber: 1.9 Consensus size: 284
59195683 AGTATAAGTC
* * *
59195693 TTGAGATAATGGAACTTTTGTCTTCAAACAAAGCCATGTATGTCTTGAGACAAGTACCTATTGCT
1 TTGAGATAATGGAACTTTTGTCTTCAAACAAAGCCATGTATGTATTGAGACAAGGACCTATTGAT
*
59195758 GTAGAATTTTACCTTTGAAGTTTTTATGTCTCGAGACCCAAGAAAATAGACCTAAAAAATATGCT
66 GTAGAATTTTACCTTCGAAGTTTTTATGTCTCGAGACCCAAGAAAATAGACCTAAAAAATATGCT
* * *
59195823 TTTAAACACTCTTAAATCATACTAAATTGTCCACAATGATTTCAATCATTGACCAAAACACCTAA
131 TTAAAACACTCTTAAACCATACTAAATTGTCCACAATGACTTCAATCATTGACCAAAACACCTAA
* * *
59195888 AATCAAGTCAAAACCATTACCAATCATTTTCTTATGTTTCATTAAAAACTTCCTTCGAAGTTTTA
196 AATCAAGTCAAAACCATTACCAATAATTTTCTTAGGGTTCATTAAAAACTTCCTTCGAAGTTTTA
59195953 AGGTAAGGACCTATTGCTGTAGAA
261 AGGTAAGGACCTATTGCTGTAGAA
* * *
59195977 TTGAGATAATGGAAGTTTTGTCTTCAAACAAAGTCATGTATGTATTGAGACAAGGATCTATTGAT
1 TTGAGATAATGGAACTTTTGTCTTCAAACAAAGCCATGTATGTATTGAGACAAGGACCTATTGAT
* ** *
59196042 GTAGAATTTTAGCTTCGAAGTTTTTATGTCTCGAGACCCGGGAAAATAGACCTGAAAAATATGCT
66 GTAGAATTTTACCTTCGAAGTTTTTATGTCTCGAGACCCAAGAAAATAGACCTAAAAAATATGCT
59196107 TTAAAACACTCTTAAACCATACTAAATTGTCCACAATGACTTCAATCATTGACCAAAACACCTAA
131 TTAAAACACTCTTAAACCATACTAAATTGTCCACAATGACTTCAATCATTGACCAAAACACCTAA
59196172 AATCAAGTCAAAACCATTACCAATAATTTTCTTAGGGTTCATTAAAAACTT
196 AATCAAGTCAAAACCATTACCAATAATTTTCTTAGGGTTCATTAAAAACTT
59196223 GCATGCTATT
Statistics
Matches: 229, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
284 229 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (284 bp):
TTGAGATAATGGAACTTTTGTCTTCAAACAAAGCCATGTATGTATTGAGACAAGGACCTATTGAT
GTAGAATTTTACCTTCGAAGTTTTTATGTCTCGAGACCCAAGAAAATAGACCTAAAAAATATGCT
TTAAAACACTCTTAAACCATACTAAATTGTCCACAATGACTTCAATCATTGACCAAAACACCTAA
AATCAAGTCAAAACCATTACCAATAATTTTCTTAGGGTTCATTAAAAACTTCCTTCGAAGTTTTA
AGGTAAGGACCTATTGCTGTAGAA
Found at i:59204493 original size:23 final size:23
Alignment explanation
Indices: 59204467--59204511 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
59204457 TAATCCCCAC
59204467 ATGGTGTGTAGA-GCTGGATGGGG
1 ATGGTGTGTAGAGGCTGG-TGGGG
59204490 ATGGTGTGTAGAGGCTGGTGGG
1 ATGGTGTGTAGAGGCTGGTGGG
59204512 TAGGATTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.16, C:0.04, G:0.53, T:0.27
Consensus pattern (23 bp):
ATGGTGTGTAGAGGCTGGTGGGG
Found at i:59210027 original size:20 final size:20
Alignment explanation
Indices: 59210002--59210048 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
59209992 AATCATAACG
59210002 TTGAGGAGGCTAGTGGGAGC
1 TTGAGGAGGCTAGTGGGAGC
59210022 TTGAGGAGGCTAGTGGGAGC
1 TTGAGGAGGCTAGTGGGAGC
*
59210042 CTGAGGA
1 TTGAGGA
59210049 TGCGAGTGTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.49, T:0.19
Consensus pattern (20 bp):
TTGAGGAGGCTAGTGGGAGC
Found at i:59218231 original size:27 final size:27
Alignment explanation
Indices: 59218200--59218377 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
59218190 TAAATTGTAC
59218200 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
59218227 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59218253 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
59218281 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
59218309 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59218336 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59218363 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59218378 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:59218314 original size:82 final size:81
Alignment explanation
Indices: 59218201--59218356 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
59218191 AAATTGTACA
* *
59218201 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
59218265 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
59218282 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
59218347 TGCGAGTTGA
65 TGCGAATTGA
59218357 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:59218368 original size:82 final size:81
Alignment explanation
Indices: 59218197--59218377 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
59218187 GATTAAATTG
* *
59218197 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59218262 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
59218278 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
59218342 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
59218360 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59218378 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59226418 original size:27 final size:27
Alignment explanation
Indices: 59226387--59226564 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
59226377 TAAATTGTAC
59226387 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
59226414 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59226440 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
59226468 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
59226496 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
59226523 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
59226550 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
59226565 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:59226501 original size:82 final size:81
Alignment explanation
Indices: 59226388--59226543 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
59226378 AAATTGTACA
* *
59226388 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
59226452 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
59226469 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
59226534 TGCGAGTTGA
65 TGCGAATTGA
59226544 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:59226555 original size:82 final size:81
Alignment explanation
Indices: 59226384--59226564 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
59226374 GATTAAATTG
* *
59226384 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
59226449 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
59226465 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
59226529 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
59226547 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
59226565 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:59229889 original size:23 final size:24
Alignment explanation
Indices: 59229851--59229895 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
59229841 TATGGCAAGA
59229851 AATTAAGTAGAAAAAG-AAGTATG
1 AATTAAGTAGAAAAAGTAAGTATG
59229874 AATTAAGTTAG-AAAAGTAAGTA
1 AATTAAG-TAGAAAAAGTAAGTA
59229896 AACTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (24 bp):
AATTAAGTAGAAAAAGTAAGTATG
Found at i:59230378 original size:25 final size:25
Alignment explanation
Indices: 59230331--59230378 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
59230321 GTATTGATTT
* *
59230331 TGAAAATGGATTTTTGAAATGAAAG
1 TGAAAATGGATTGTGGAAATGAAAG
* *
59230356 TGAAATTGGATTGTGGAATTGAA
1 TGAAAATGGATTGTGGAAATGAA
59230379 TTGCATATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (25 bp):
TGAAAATGGATTGTGGAAATGAAAG
Found at i:59234670 original size:22 final size:22
Alignment explanation
Indices: 59234644--59234689 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
59234634 ATTATGTGTA
59234644 TTAATTCATAATATAA-TTAATT
1 TTAATTC-TAATATAATTTAATT
*
59234666 TTAATTCTAATCTAATTTAATT
1 TTAATTCTAATATAATTTAATT
59234688 TT
1 TT
59234690 GGTTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAATTCTAATATAATTTAATT
Found at i:59238442 original size:8 final size:8
Alignment explanation
Indices: 59238400--59238424 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
59238390 ATATAGAATA
59238400 AATAAAAT
1 AATAAAAT
59238408 AATAAAAT
1 AATAAAAT
59238416 AATAAAAT
1 AATAAAAT
59238424 A
1 A
59238425 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:59238448 original size:29 final size:31
Alignment explanation
Indices: 59238402--59238469 Score: 81
Period size: 29 Copynumber: 2.3 Consensus size: 31
59238392 ATAGAATAAA
*
59238402 TAAAATAATAAAATAATAA-AA-TATCTTAT
1 TAAAATAATAAAATAATAACAATTATCTAAT
*
59238431 TAAAAT-ATTAAATAAATAACAATTATCTAAT
1 TAAAATAATAAAAT-AATAACAATTATCTAAT
59238462 T-AAATAAT
1 TAAAATAAT
59238470 TATAAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 6 0.18
29 11 0.33
30 6 0.18
31 10 0.30
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (31 bp):
TAAAATAATAAAATAATAACAATTATCTAAT
Found at i:59239051 original size:18 final size:18
Alignment explanation
Indices: 59239028--59239065 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59239018 AATATATATT
59239028 AACCCAAGTACCCAACCC
1 AACCCAAGTACCCAACCC
**
59239046 AACCCATTTACCCAACCC
1 AACCCAAGTACCCAACCC
59239064 AA
1 AA
59239066 TCATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.47, G:0.03, T:0.11
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:59239125 original size:20 final size:21
Alignment explanation
Indices: 59239083--59239125 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
59239073 AATTACAAAT
*
59239083 AATTTAATAAATAAAAATGAA
1 AATTTAATAAATAAAAATAAA
*
59239104 AATTTAA-AACTAAAAATAAA
1 AATTTAATAAATAAAAATAAA
59239124 AA
1 AA
59239126 CAAAAATCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (21 bp):
AATTTAATAAATAAAAATAAA
Done.