Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 103 of 187
Found at i:30380112 original size:35 final size:34
Alignment explanation
Indices: 30380066--30380135 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 34
30380056 GGAAATAATC
30380066 TCACAACTGCTCCTACTAGAATTATTAAAGATAAA
1 TCACAACTGCTCCTACTAGAATTA-TAAAGATAAA
30380101 TCACAACTGCTCCTACTAGAATTATAAAGATAAA
1 TCACAACTGCTCCTACTAGAATTATAAAGATAAA
30380135 T
1 T
30380136 TCATTCCTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 11 0.31
35 24 0.69
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.29
Consensus pattern (34 bp):
TCACAACTGCTCCTACTAGAATTATAAAGATAAA
Found at i:30386615 original size:18 final size:17
Alignment explanation
Indices: 30386571--30386620 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
30386561 CTCGTAGTTC
*
30386571 AATTTCAAAACATTATT
1 AATTTCAAAACGTTATT
* *
30386588 CATTTACAAATCGTTATT
1 AATTT-CAAAACGTTATT
30386606 AAATTTCAAAACGTT
1 -AATTTCAAAACGTT
30386621 TTTTTATTGC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.15
18 18 0.69
19 4 0.15
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.40
Consensus pattern (17 bp):
AATTTCAAAACGTTATT
Found at i:30393979 original size:9 final size:9
Alignment explanation
Indices: 30393965--30394001 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
30393955 TATAGTTTGA
30393965 TATTCGAAT
1 TATTCGAAT
30393974 TATTCGAAT
1 TATTCGAAT
*
30393983 TATTCGAGT
1 TATTCGAAT
30393992 TATTCGAAT
1 TATTCGAAT
30394001 T
1 T
30394002 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:30394078 original size:9 final size:9
Alignment explanation
Indices: 30394054--30394083 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30394044 TCGAGTTGAT
30394054 TCGAATAAC
1 TCGAATAAC
30394063 TCG-ATAAC
1 TCGAATAAC
30394071 TCGAATAAC
1 TCGAATAAC
30394080 TCGA
1 TCGA
30394084 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.40, C:0.23, G:0.13, T:0.23
Consensus pattern (9 bp):
TCGAATAAC
Found at i:30395459 original size:14 final size:14
Alignment explanation
Indices: 30395440--30395467 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30395430 TTGCACTCTG
30395440 TTTCTTTTTTCTTC
1 TTTCTTTTTTCTTC
30395454 TTTCTTTTTTCTTC
1 TTTCTTTTTTCTTC
30395468 ACTTCCCACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTCTTTTTTCTTC
Found at i:30400124 original size:13 final size:12
Alignment explanation
Indices: 30400095--30400123 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
30400085 TCAATCACAC
30400095 AAAAATGAAAAA
1 AAAAATGAAAAA
30400107 AAAAATGAAAAA
1 AAAAATGAAAAA
30400119 AAAAA
1 AAAAA
30400124 AAGAAGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.86, C:0.00, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAAATGAAAAA
Found at i:30406017 original size:21 final size:22
Alignment explanation
Indices: 30405988--30406038 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
30405978 TCTCTCTCGC
*
30405988 TTTCCTTTTCGCCTTTTTCA-T
1 TTTCATTTTCGCCTTTTTCACT
**
30406009 TTTCATTTTCTTCTTTTTCACT
1 TTTCATTTTCGCCTTTTTCACT
30406031 TTT-ATTTT
1 TTTCATTTT
30406039 TCTCTTCTCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.08, C:0.22, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTCATTTTCGCCTTTTTCACT
Found at i:30408388 original size:24 final size:24
Alignment explanation
Indices: 30408364--30408410 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
30408354 AAACTACTTC
30408364 TAAAGAAAACTCAAGAGAGAATTCT
1 TAAAGAAAACTCAA-AGAGAATTCT
**
30408389 TGGAGAAAACTCAAAGAGAATT
1 TAAAGAAAACTCAAAGAGAATT
30408411 TCTACTCAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.51, C:0.11, G:0.19, T:0.19
Consensus pattern (24 bp):
TAAAGAAAACTCAAAGAGAATTCT
Found at i:30420057 original size:3 final size:3
Alignment explanation
Indices: 30420049--30420078 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
30420039 GTAAGGACAA
*
30420049 GTG GTG GTG GTG GTG GTG GTG GTG GCG GTG
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG
30420079 TAAAGCTCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.67, T:0.30
Consensus pattern (3 bp):
GTG
Found at i:30425457 original size:3 final size:3
Alignment explanation
Indices: 30425449--30425508 Score: 52
Period size: 3 Copynumber: 19.3 Consensus size: 3
30425439 ATAAATTTCA
* *
30425449 TAT TAT TAT TAT TAT TGAT CAT TAT TAGT T-T TAT TTT TAT T-T TATT
1 TAT TAT TAT TAT TAT T-AT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T
30425495 TAT TCAT TAT TAT T
1 TAT T-AT TAT TAT T
30425509 GTGATAATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 4 0.09
3 33 0.70
4 10 0.21
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30425872 original size:24 final size:22
Alignment explanation
Indices: 30425830--30425879 Score: 64
Period size: 24 Copynumber: 2.2 Consensus size: 22
30425820 TTTATTGTTA
*
30425830 TTATTTTTTTATGTTCATTTAT
1 TTATTTTTTTATGTCCATTTAT
*
30425852 TTATTTATTTATATGTCCATTTTT
1 TTATTT-TTT-TATGTCCATTTAT
30425876 TTAT
1 TTAT
30425880 GTTGTAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 3 0.12
24 15 0.62
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (22 bp):
TTATTTTTTTATGTCCATTTAT
Found at i:30425991 original size:20 final size:20
Alignment explanation
Indices: 30425968--30426006 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30425958 TTTGCTCATC
30425968 TTATTT-TTAGTCACATTATT
1 TTATTTATTAGTC-CATTATT
*
30425988 TTATTTATTATTCCATTAT
1 TTATTTATTAGTCCATTAT
30426007 GCATATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.10, G:0.03, T:0.62
Consensus pattern (20 bp):
TTATTTATTAGTCCATTATT
Found at i:30426243 original size:110 final size:110
Alignment explanation
Indices: 30426050--30426356 Score: 471
Period size: 110 Copynumber: 2.8 Consensus size: 110
30426040 TTTCTAATTG
* * * *
30426050 AGGCAATGTTTTGCGTTT-AGAAATCTGAGAAAACGTGTCCTAATGTGTTGGGTTTCGATTTTTC
1 AGGCAATGTTTTGCGTTTGGGAATTC-GAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTC
*
30426114 TCGTTCAACCAAATAGCTAAATATCCTTTTAAAAAATTTCAAAATA
65 TCGTTCAACCAAATAGCTAAATATCCTTTCAAAAAATTTCAAAATA
30426160 AGGCAATGTTTTGCGTTTGGGAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
1 AGGCAATGTTTTGCGTTTGGGAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
*
30426225 CGTTCAACCAAATAGCTAAATATCC-TTCCAAAAATTTCAAAATA
66 CGTTCAACCAAATAGCTAAATATCCTTTCAAAAAATTTCAAAATA
* *
30426269 AGGCAATGTTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAATGTGCTGGGTTTCGA--TTTCT
1 AGGCAATGTTTTGCGTTTGGGAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
* * *
30426331 CGTTTAACCAAATTGCCAAATATCCT
66 CGTTCAACCAAATAGCTAAATATCCT
30426357 CTTGAATTTT
Statistics
Matches: 184, Mismatches: 11, Indels: 7
0.91 0.05 0.03
Matches are distributed among these distances:
106 27 0.15
108 27 0.15
109 45 0.24
110 80 0.43
111 5 0.03
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (110 bp):
AGGCAATGTTTTGCGTTTGGGAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTTCT
CGTTCAACCAAATAGCTAAATATCCTTTCAAAAAATTTCAAAATA
Found at i:30429735 original size:9 final size:9
Alignment explanation
Indices: 30429723--30429752 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
30429713 TAAAAAATAT
30429723 TTTTTATAA
1 TTTTTATAA
30429732 -TTTTATAA
1 TTTTTATAA
30429740 TTTTTATAA
1 TTTTTATAA
30429749 TTTT
1 TTTT
30429753 AATACAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (9 bp):
TTTTTATAA
Found at i:30429737 original size:8 final size:8
Alignment explanation
Indices: 30429724--30429753 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
30429714 AAAAAATATT
30429724 TTTTATAA
1 TTTTATAA
30429732 TTTTATAA
1 TTTTATAA
30429740 TTTTTATAA
1 -TTTTATAA
30429749 TTTTA
1 TTTTA
30429754 ATACAATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (8 bp):
TTTTATAA
Found at i:30429898 original size:29 final size:31
Alignment explanation
Indices: 30429838--30429899 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
30429828 TTTATGTTTA
*
30429838 TATAATTTTTTAAATAATGTTTACAACTTTT
1 TATAATTTTTTAAATAATGTTTACAAATTTT
* *
30429869 TATAA-TTTTT-AATAATTTTTAAAATATTTT
1 TATAATTTTTTAAATAATGTTTACAA-ATTTT
30429899 T
1 T
30429900 TTATGCTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
29 12 0.44
30 10 0.37
31 5 0.19
ACGTcount: A:0.37, C:0.03, G:0.02, T:0.58
Consensus pattern (31 bp):
TATAATTTTTTAAATAATGTTTACAAATTTT
Found at i:30429946 original size:20 final size:20
Alignment explanation
Indices: 30429865--30429951 Score: 65
Period size: 19 Copynumber: 4.3 Consensus size: 20
30429855 TGTTTACAAC
30429865 TTTTTATA-ATTTTTAATAA
1 TTTTTATATATTTTTAATAA
* * **
30429884 TTTTTAAAATATTTTTTTATGC
1 TTTTT-ATATA-TTTTTAATAA
*
30429906 TTTTTATGCT-TTTTT--TCAA
1 TTTTTAT-ATATTTTTAAT-AA
30429925 TTTTTATATATTTTTAATAA
1 TTTTTATATATTTTTAATAA
30429945 TTTTTAT
1 TTTTTAT
30429952 TTAAAAAAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
18 2 0.04
19 17 0.33
20 16 0.31
21 3 0.06
22 13 0.25
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTTATATATTTTTAATAA
Found at i:30430171 original size:20 final size:21
Alignment explanation
Indices: 30430133--30430172 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
30430123 ACTTAATAGG
30430133 TTTTGTTTTAATTTATAAGCA
1 TTTTGTTTTAATTTATAAGCA
30430154 TTTT-TTTTATATTT-TAAGC
1 TTTTGTTTTA-ATTTATAAGC
30430173 CCAACGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.62
Consensus pattern (21 bp):
TTTTGTTTTAATTTATAAGCA
Found at i:30434435 original size:24 final size:24
Alignment explanation
Indices: 30434392--30434446 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
30434382 TTTAAAAAAA
*
30434392 TTAATTTAATATAATTATTTTTAT
1 TTAATTTAATATAATAATTTTTAT
30434416 TTAATATTAATATAA-AATTTTTAT
1 TTAAT-TTAATATAATAATTTTTAT
30434440 TTAATTT
1 TTAATTT
30434447 TTACAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 2 0.07
24 18 0.62
25 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TTAATTTAATATAATAATTTTTAT
Found at i:30434462 original size:24 final size:24
Alignment explanation
Indices: 30434408--30434463 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
30434398 TAATATAATT
*
30434408 ATTTTTATTTAATATTAATATAAA
1 ATTTTTATTTAATATTAACATAAA
* *
30434432 ATTTTTATTTAATTTTTACA-AAA
1 ATTTTTATTTAATATTAACATAAA
30434455 ATTGTTTAT
1 ATT-TTTAT
30434464 AAGTTTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 6 0.21
24 22 0.79
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
ATTTTTATTTAATATTAACATAAA
Found at i:30434572 original size:11 final size:10
Alignment explanation
Indices: 30434540--30434574 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
30434530 TTAGAACAAT
30434540 TATTAAAAAA
1 TATTAAAAAA
*
30434550 TATTTAAAAA
1 TATTAAAAAA
30434560 TATTAAAATAA
1 TATTAAAA-AA
30434571 TATT
1 TATT
30434575 TTATTTATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 16 0.73
11 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
TATTAAAAAA
Found at i:30443733 original size:5 final size:5
Alignment explanation
Indices: 30443723--30443769 Score: 60
Period size: 5 Copynumber: 9.4 Consensus size: 5
30443713 ATGATGTGTA
* *
30443723 AATAT AATAT AATA- AATAT AATTAA AATAT AATAT AATAT GATAT AA
1 AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT AATAT AA
30443770 GCAAATAATG
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
4 4 0.11
5 28 0.78
6 4 0.11
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:30444132 original size:25 final size:24
Alignment explanation
Indices: 30444098--30444145 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
30444088 GACGTGGGGT
30444098 GAAGGAAAAAGAGAAAAAGAAAAAC
1 GAAGGAAAAAGAGAAAAA-AAAAAC
*
30444123 GAAGGAAAAAGAGAAGAAAAAAA
1 GAAGGAAAAAGAGAAAAAAAAAA
30444146 GAGAGAGAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (24 bp):
GAAGGAAAAAGAGAAAAAAAAAAC
Found at i:30449709 original size:33 final size:33
Alignment explanation
Indices: 30449672--30449742 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 33
30449662 GAGCCCTTTT
*
30449672 CAGTAATAGAACAATGTGGGCCTTAGCCCAAAA
1 CAGTAAAAGAACAATGTGGGCCTTAGCCCAAAA
*** * * *
30449705 CAGTAAAAGTGTAGTGTGGGCCTTAGCCCCATA
1 CAGTAAAAGAACAATGTGGGCCTTAGCCCAAAA
30449738 CAGTA
1 CAGTA
30449743 TCAGAATCAG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.21
Consensus pattern (33 bp):
CAGTAAAAGAACAATGTGGGCCTTAGCCCAAAA
Found at i:30450181 original size:26 final size:26
Alignment explanation
Indices: 30450129--30450182 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 26
30450119 CATTAGTAGC
* * *
30450129 ATCGCAGCAAAGCTGCCAGCAACAGT
1 ATCGCAACAAAGCTACCAACAACAGT
* *
30450155 ATCGCAACAAAGCTACCAATAATAGT
1 ATCGCAACAAAGCTACCAACAACAGT
30450181 AT
1 AT
30450183 ATATGGTTAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.17
Consensus pattern (26 bp):
ATCGCAACAAAGCTACCAACAACAGT
Found at i:30450367 original size:27 final size:26
Alignment explanation
Indices: 30450337--30450395 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
30450327 TTTTCGATCG
* *
30450337 TTTTACGATACAAGGGTATTACGGTCC
1 TTTTACCATA-AAGGGTATTACGGTCA
* *
30450364 TTTTACCCTATAGGGTATTACGGTCA
1 TTTTACCATAAAGGGTATTACGGTCA
30450390 TTTTAC
1 TTTTAC
30450396 AAATATTAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 20 0.71
27 8 0.29
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (26 bp):
TTTTACCATAAAGGGTATTACGGTCA
Found at i:30476272 original size:13 final size:13
Alignment explanation
Indices: 30476235--30476280 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
30476225 TCATATAATT
*
30476235 ATTTCCATATAACC
1 ATTT-CATATAGCC
*
30476249 AATTCATATAGCC
1 ATTTCATATAGCC
30476262 ATTTCATATAGCC
1 ATTTCATATAGCC
30476275 ATTTCA
1 ATTTCA
30476281 AAGTGTTAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 26 0.90
14 3 0.10
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.37
Consensus pattern (13 bp):
ATTTCATATAGCC
Found at i:30489441 original size:23 final size:23
Alignment explanation
Indices: 30489411--30489457 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
30489401 TAGTGTGATA
30489411 GATCTTCAATGAGCTACCAAACC
1 GATCTTCAATGAGCTACCAAACC
30489434 GATCTTCAATGAGCTACCAAACC
1 GATCTTCAATGAGCTACCAAACC
30489457 G
1 G
30489458 TTCGAGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.30, G:0.15, T:0.21
Consensus pattern (23 bp):
GATCTTCAATGAGCTACCAAACC
Found at i:30490589 original size:19 final size:19
Alignment explanation
Indices: 30490567--30490603 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
30490557 TTTAAAATAC
*
30490567 TTTTAAAATATTTTTTTAT
1 TTTTAAAATAATTTTTTAT
30490586 TTTTAAAATAATTTTTTA
1 TTTTAAAATAATTTTTTA
30490604 ATGTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAAAATAATTTTTTAT
Found at i:30490610 original size:20 final size:19
Alignment explanation
Indices: 30490568--30490610 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
30490558 TTAAAATACT
* *
30490568 TTTAAAATATTTTTTTATT
1 TTTAAAATATTTTTTAATG
30490587 TTTAAAATAATTTTTTAATG
1 TTTAAAAT-ATTTTTTAATG
30490607 TTTA
1 TTTA
30490611 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTAAAATATTTTTTAATG
Found at i:30491435 original size:50 final size:50
Alignment explanation
Indices: 30491367--30491559 Score: 219
Period size: 50 Copynumber: 3.7 Consensus size: 50
30491357 TTTTCTGTAC
* * **
30491367 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
30491417 TGCCCATGCCATGTCCCAGACATGGTCTTAC-GGGGAACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGG-ACCTCTCATATCGG
* *
30491467 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
30491523 TGCCAATGCCATG-CCTCAGACATGGTCTTACATGGGA
1 TGCCAATGCCATGTCC-CAGACATGGTCTTACATGGGA
30491560 TCTCATTCCC
Statistics
Matches: 121, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
49 3 0.02
50 77 0.64
51 3 0.02
53 2 0.02
55 2 0.02
56 34 0.28
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:30492541 original size:20 final size:20
Alignment explanation
Indices: 30492516--30492555 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
30492506 TTTTAAATTT
30492516 CATCAGATAATCGAGAAAGC
1 CATCAGATAATCGAGAAAGC
30492536 CATCAGATAATCGAGAAAGC
1 CATCAGATAATCGAGAAAGC
30492556 TTACACGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (20 bp):
CATCAGATAATCGAGAAAGC
Found at i:30495672 original size:40 final size:40
Alignment explanation
Indices: 30495612--30495888 Score: 311
Period size: 40 Copynumber: 6.9 Consensus size: 40
30495602 TGCATTCAAA
* *
30495612 GTACTGAAGTACAACCAGGGGCACGTATGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* * * *
30495652 GTATCGAAGTACAAATAGGGGTACGTATGTGCATTCAAGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* ** *
30495692 GTACCAAAGTACAAACAGGGGCACGTATGTGCATTTTGGT
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* * *
30495732 GTACCGAAGTACAAACAGGGGCACGTATGTGTATCCAGGA
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* * * * **
30495772 ATACCGAAGTATAAACTGGGGCACATATGTAAATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* ** * *
30495812 GTACCCAAGTATGAATAAGGGCACGTATGTGCATTCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
* * *
30495852 GAATCGAAGTACAAACAAGGGCACGTATGTGCATTCA
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCA
30495889 TACAATAATT
Statistics
Matches: 194, Mismatches: 43, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 194 1.00
ACGTcount: A:0.32, C:0.17, G:0.29, T:0.22
Consensus pattern (40 bp):
GTACCGAAGTACAAACAGGGGCACGTATGTGCATTCAGGG
Found at i:30512013 original size:40 final size:40
Alignment explanation
Indices: 30511916--30512222 Score: 316
Period size: 40 Copynumber: 7.8 Consensus size: 40
30511906 GAGTTATCGG
* * **
30511916 AGTATAAACAGGGGCAC-TAAAGTGCATTCA-AAGTACCG-
1 AGTACAAACAGGGGCACGT-ATGTGCATTCAGGGGTACCGA
* ** *
30511954 AGTACAACCAGGGGCACGTATGTGCATTCAGGGGTGTCAA
1 AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
* * *
30511994 AGTACAAATAGGGGTACGTATGTGCATTCATGGGTACCGA
1 AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
* * * * *
30512034 AGTAGAAACATGGGCATGTATGTGCATTCAAGGGTATCGA
1 AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
* * *
30512074 AGTACAAACA-GGGCATGTATGTGCATTTAGGGATACCGA
1 AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
* * * *
30512113 GGCACAAACAGGGGCACTTATGTGCATTCAGGAGTACCGA
1 AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
* * * * *
30512153 AGTACAAATAAGGGCACGCATGTGCATTTACGGGTACCGA
1 AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
*
30512193 AGTACAAACAGGGGCACGCATGTGCATTCA
1 AGTACAAACAGGGGCACGTATGTGCATTCA
30512223 TACAATAATT
Statistics
Matches: 219, Mismatches: 46, Indels: 6
0.81 0.17 0.02
Matches are distributed among these distances:
38 25 0.11
39 37 0.17
40 157 0.72
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (40 bp):
AGTACAAACAGGGGCACGTATGTGCATTCAGGGGTACCGA
Found at i:30512126 original size:119 final size:120
Alignment explanation
Indices: 30511937--30512220 Score: 324
Period size: 119 Copynumber: 2.4 Consensus size: 120
30511927 GGGCACTAAA
* * * * * ** * * *
30511937 GTGCATTCAA-AGTACCG-AGTACAACCAGGGGCACGTATGTGCATTCAGGGGTGTCAAAGTACA
1 GTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACGCATGTGCATTTAGGGATACCGAGGCACA
* * * * * *
30512000 AATAGGGGTACGTATGTGCATTCATGG-GTACCGAAGTAGAAACATGGGCATGTAT
66 AACAGGGGCACGTATGTGCATTCA-GGAGTACCGAAGTACAAACAAGGGCACGCAT
* * *
30512055 GTGCATTCAAGGGTATCGAAGTACAAACA-GGGCATGTATGTGCATTTAGGGATACCGAGGCACA
1 GTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACGCATGTGCATTTAGGGATACCGAGGCACA
* *
30512119 AACAGGGGCACTTATGTGCATTCAGGAGTACCGAAGTACAAATAAGGGCACGCAT
66 AACAGGGGCACGTATGTGCATTCAGGAGTACCGAAGTACAAACAAGGGCACGCAT
* *
30512174 GTGCATTTACGGGTACCGAAGTACAAACAGGGGCACGCATGTGCATT
1 GTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACGCATGTGCATT
30512221 CATACAATAA
Statistics
Matches: 138, Mismatches: 24, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
118 12 0.09
119 102 0.74
120 24 0.17
ACGTcount: A:0.31, C:0.18, G:0.29, T:0.21
Consensus pattern (120 bp):
GTGCATTCAAGGGTACCGAAGTACAAACAGGGGCACGCATGTGCATTTAGGGATACCGAGGCACA
AACAGGGGCACGTATGTGCATTCAGGAGTACCGAAGTACAAACAAGGGCACGCAT
Found at i:30516851 original size:21 final size:21
Alignment explanation
Indices: 30516827--30516866 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
30516817 TGTTATTTAT
30516827 TTAATAAAATA-AAATAAAAGG
1 TTAATAAAATACAAA-AAAAGG
30516848 TTAATAAAATACAAAAAAA
1 TTAATAAAATACAAAAAAA
30516867 CAAAATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
TTAATAAAATACAAAAAAAGG
Found at i:30519056 original size:35 final size:35
Alignment explanation
Indices: 30519010--30519085 Score: 97
Period size: 35 Copynumber: 2.2 Consensus size: 35
30519000 AAAATTGGTG
30519010 TATGT-TC-TTAAATGACCAAAATTGGTAT-G-TGT
1 TATGTATCTTTAAATGACCAAAA-TGGTATGGTTGT
*
30519042 TAATGTATCTTTAAATGGCCAAAATGGTATGGTTGT
1 T-ATGTATCTTTAAATGACCAAAATGGTATGGTTGT
30519078 TATGTATC
1 TATGTATC
30519086 AATTATGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 1 0.03
33 4 0.11
34 8 0.21
35 21 0.55
36 4 0.11
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.41
Consensus pattern (35 bp):
TATGTATCTTTAAATGACCAAAATGGTATGGTTGT
Found at i:30525879 original size:23 final size:23
Alignment explanation
Indices: 30525690--30525958 Score: 117
Period size: 23 Copynumber: 11.8 Consensus size: 23
30525680 GGATATGTTC
*
30525690 AAGGGTATA-TTGGTTGTGTTAG
1 AAGGGTATATTTGGTTGTGTTTG
* *
30525712 GAGGTTATATATATGGTTGTGTTTG
1 AAGGGTATAT-T-TGGTTGTGTTTG
* * * *
30525737 GAGGATACATTTGGTTGTGTTCG
1 AAGGGTATATTTGGTTGTGTTTG
** * *
30525760 AAGGGTA-AAATAGTTGT-TTTCA
1 AAGGGTATATTTGGTTGTGTTT-G
* *
30525782 AAGGGTA-ACTTGGCTGTGTTTGG
1 AAGGGTATATTTGGTTGTGTTT-G
* *
30525805 AA-GGTATACTTGGTTGTGTTAG
1 AAGGGTATATTTGGTTGTGTTTG
* * *
30525827 GAGGTTATATATATGGTTATGTTTG
1 AAGGGTATAT-T-TGGTTGTGTTTG
* *
30525852 GAGGGTACATTTGGTTGTGTTTG
1 AAGGGTATATTTGGTTGTGTTTG
** ** *
30525875 AAGGGTA-AAATACTTGT-TTTCA
1 AAGGGTATATTTGGTTGTGTTT-G
*
30525897 AAGGGTA-ACTTGGTTGTGTTT-
1 AAGGGTATATTTGGTTGTGTTTG
* *
30525918 AGAGGCTATGTTTGGTTGTGTTTG
1 A-AGGGTATATTTGGTTGTGTTTG
* * *
30525942 GACGGTA-AATTGGTTGT
1 AAGGGTATATTTGGTTGT
30525959 CTTTAGTGGG
Statistics
Matches: 186, Mismatches: 47, Indels: 28
0.71 0.18 0.11
Matches are distributed among these distances:
21 6 0.03
22 65 0.35
23 74 0.40
24 4 0.02
25 37 0.20
ACGTcount: A:0.22, C:0.04, G:0.32, T:0.41
Consensus pattern (23 bp):
AAGGGTATATTTGGTTGTGTTTG
Found at i:30525901 original size:115 final size:113
Alignment explanation
Indices: 30525693--30525939 Score: 395
Period size: 115 Copynumber: 2.2 Consensus size: 113
30525683 TATGTTCAAG
*
30525693 GGTATATTGGTTGTGTTAGGAGGTTATATATATGGTTGTGTTTGGAGGATACATTTGGTTGTGTT
1 GGTATATTGGTTGTGTTAGGAGGTTATATATATGGTTATGTTTGGAGGATACATTTGGTTGTGTT
* *
30525758 CGAAGGGTAAAATAGTTGTTTTCAAAGGGTAACTTGGCTGTGTTTGGAA
66 CGAAGGGTAAAATACTTGTTTTCAAAGGGTAACTTGGCTGTGTTTAG-A
*
30525807 GGTATACTTGGTTGTGTTAGGAGGTTATATATATGGTTATGTTTGGAGGGTACATTTGGTTGTGT
1 GGTATA-TTGGTTGTGTTAGGAGGTTATATATATGGTTATGTTTGGAGGATACATTTGGTTGTGT
* *
30525872 TTGAAGGGTAAAATACTTGTTTTCAAAGGGTAACTTGGTTGTGTTTAGA
65 TCGAAGGGTAAAATACTTGTTTTCAAAGGGTAACTTGGCTGTGTTTAGA
*
30525921 GGCTATGTTTGGTTGTGTT
1 GG-TAT-ATTGGTTGTGTT
30525940 TGGACGGTAA
Statistics
Matches: 123, Mismatches: 7, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
114 9 0.07
115 114 0.93
ACGTcount: A:0.21, C:0.04, G:0.32, T:0.42
Consensus pattern (113 bp):
GGTATATTGGTTGTGTTAGGAGGTTATATATATGGTTATGTTTGGAGGATACATTTGGTTGTGTT
CGAAGGGTAAAATACTTGTTTTCAAAGGGTAACTTGGCTGTGTTTAGA
Found at i:30533203 original size:21 final size:21
Alignment explanation
Indices: 30533179--30533219 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
30533169 TGTAACTCGA
*
30533179 TCACACGGGCGTGTGTCTCCT
1 TCACACGGGCATGTGTCTCCT
30533200 TCACACGGGCATGTGTCTCC
1 TCACACGGGCATGTGTCTCC
30533220 ACCACACAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.34, G:0.27, T:0.27
Consensus pattern (21 bp):
TCACACGGGCATGTGTCTCCT
Found at i:30533225 original size:21 final size:21
Alignment explanation
Indices: 30533180--30533226 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
30533170 GTAACTCGAT
* **
30533180 CACACGGGCGTGTGTCTCCTT
1 CACACGGGCATGTGTCTCCAC
30533201 CACACGGGCATGTGTCTCCAC
1 CACACGGGCATGTGTCTCCAC
30533222 CACAC
1 CACAC
30533227 AGGTGTGTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.21
Consensus pattern (21 bp):
CACACGGGCATGTGTCTCCAC
Found at i:30537075 original size:71 final size:71
Alignment explanation
Indices: 30536958--30537122 Score: 240
Period size: 71 Copynumber: 2.3 Consensus size: 71
30536948 TGGATAAACA
* * *
30536958 AATCTCCAAAACACACCACACAACTCATTAAGTCGTACACTATCTCCATGTAAGTCTAGCACGTA
1 AATCTCC-AAACACACCACACTACTCATAAAGTCGTACACTATCTCCATGTAAGTCTAGCACATA
30537023 TGCTCAC
65 TGCTCAC
* * * *
30537030 AATCTCCAAGCACACCACACTACTCATAAAGTTGTACGCTATCTCCATGTAAGTGTAGCACATAT
1 AATCTCCAAACACACCACACTACTCATAAAGTCGTACACTATCTCCATGTAAGTCTAGCACATAT
*
30537095 GCTTAC
66 GCTCAC
*
30537101 AATCTCTAAACACACCACACTA
1 AATCTCCAAACACACCACACTA
30537123 TCTATGGTGA
Statistics
Matches: 83, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
71 76 0.92
72 7 0.08
ACGTcount: A:0.35, C:0.31, G:0.10, T:0.24
Consensus pattern (71 bp):
AATCTCCAAACACACCACACTACTCATAAAGTCGTACACTATCTCCATGTAAGTCTAGCACATAT
GCTCAC
Found at i:30540356 original size:42 final size:42
Alignment explanation
Indices: 30540304--30540403 Score: 173
Period size: 42 Copynumber: 2.4 Consensus size: 42
30540294 GCTCTCGGTA
*
30540304 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* *
30540346 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
30540388 TCGCACACTTAGTGCC
1 TCGCACACTTAGTGCC
30540404 GTTCATATAG
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:30542964 original size:23 final size:22
Alignment explanation
Indices: 30542939--30542980 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
30542929 ATCGAATGTT
*
30542939 TTTTTTGGTTTATGCACATTAA
1 TTTTTTGATTTATGCACATTAA
30542961 TTTTTTGATTTATGCACATT
1 TTTTTTGATTTATGCACATT
30542981 CACACTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.10, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTTTTGATTTATGCACATTAA
Found at i:30544364 original size:38 final size:38
Alignment explanation
Indices: 30544285--30544468 Score: 188
Period size: 38 Copynumber: 4.8 Consensus size: 38
30544275 AATGTAATGT
* * * *
30544285 TATTCGGGCTGTGTGCCTAACAGGCTTTGTGCCGATAA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * * *
30544323 TATTTGGGCTCTATGCCTAGCAGGCTTTGTGCCGTTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
** * * * *
30544361 TATTCGAACTATGTGTCTAACAGGATTTGTGCAGGTGA
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* * * *
30544399 TATTCGGGCTATGTGCCTAGCAGGCTGTGTTCTGGTGT
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
* *
30544437 TATTCGGGCTTTGTGCCTAGCAAGCTTTGTGC
1 TATTCGGGCTATGTGCCTAGCAGGCTTTGTGC
30544469 TAGTGTATTA
Statistics
Matches: 117, Mismatches: 29, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
38 117 1.00
ACGTcount: A:0.16, C:0.19, G:0.29, T:0.35
Consensus pattern (38 bp):
TATTCGGGCTATGTGCCTAGCAGGCTTTGTGCCGGTGA
Found at i:30546312 original size:17 final size:17
Alignment explanation
Indices: 30546290--30546323 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30546280 AGAAATACGA
30546290 TATCTACCATTTTCAAG
1 TATCTACCATTTTCAAG
30546307 TATCTACCATTTTCAAG
1 TATCTACCATTTTCAAG
30546324 CCAAAAATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (17 bp):
TATCTACCATTTTCAAG
Found at i:30546761 original size:106 final size:106
Alignment explanation
Indices: 30546576--30546783 Score: 344
Period size: 106 Copynumber: 2.0 Consensus size: 106
30546566 TCACGTTTAT
* * * *
30546576 GCTTATAATTGTGTATGTGTGAAATGTATTATGACTGAATGCCAAGTTATTTGATTAAATGAATT
1 GCTTATAATTGTGAATGTGTCAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGAATT
30546641 GATATAGTCTGGGTTGCTATGATAACATAATGAGACACCAG
66 GATATAGTCTGGGTTGCTATGATAACATAATGAGACACCAG
*
30546682 GCTTATAATTGTGAATGTGTCAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGATTT
1 GCTTATAATTGTGAATGTGTCAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGAATT
* * *
30546747 GATATTGTTTGGGTTGCTATGATAACATAATGTGACA
66 GATATAGTCTGGGTTGCTATGATAACATAATGAGACA
30546784 TAATGCATTT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
106 94 1.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.38
Consensus pattern (106 bp):
GCTTATAATTGTGAATGTGTCAAATGTATTATGACTAAATGCCAAGTTATTTGATTAAACGAATT
GATATAGTCTGGGTTGCTATGATAACATAATGAGACACCAG
Found at i:30557681 original size:22 final size:23
Alignment explanation
Indices: 30557534--30557682 Score: 115
Period size: 23 Copynumber: 6.5 Consensus size: 23
30557524 TATTGTTTAC
*
30557534 GTTTGGAGGGTATACTTGGTTGT
1 GTTTGGAGGGTATAATTGGTTGT
** *
30557557 GTTCAGAGGTTATATATATGGTTGT
1 GTTTGGAGGGTATA-AT-TGGTTGT
* * *
30557582 GTTTGAAGAGTATATTTGGTTGT
1 GTTTGGAGGGTATAATTGGTTGT
*
30557605 GTTTGGAGGGTA-AATTAGTTGT
1 GTTTGGAGGGTATAATTGGTTGT
*** **
30557627 GTTTGGCA-ACCATGTTTGGTTGT
1 GTTTGG-AGGGTATAATTGGTTGT
**
30557650 GTTTCTAGGGTA-AATTGGTTGT
1 GTTTGGAGGGTATAATTGGTTGT
30557672 GTTTGGAGGGT
1 GTTTGGAGGGT
30557683 GATAGCTTTA
Statistics
Matches: 92, Mismatches: 29, Indels: 11
0.70 0.22 0.08
Matches are distributed among these distances:
22 33 0.36
23 41 0.45
24 2 0.02
25 16 0.17
ACGTcount: A:0.18, C:0.04, G:0.34, T:0.44
Consensus pattern (23 bp):
GTTTGGAGGGTATAATTGGTTGT
Found at i:30572892 original size:69 final size:69
Alignment explanation
Indices: 30572811--30572950 Score: 235
Period size: 69 Copynumber: 2.0 Consensus size: 69
30572801 CCTATAAGTC
* *
30572811 CTCCCCTATTCTCCCTTGTTCTAATAGCTCCTCTTTTAATCACTAGTTTTTAATTTACACATTTA
1 CTCCCCTATTCTCCCTTGTTCTAATAGCTCCCCTTTTAACCACTAGTTTTTAATTTACACATTTA
30572876 ACCT
66 ACCT
* * *
30572880 CTCCCCTATTCTCCTTTGTTCTAATAGCTCCCCTTTTAACCCCTAGTTTTTGATTTACACATTTA
1 CTCCCCTATTCTCCCTTGTTCTAATAGCTCCCCTTTTAACCACTAGTTTTTAATTTACACATTTA
30572945 ACCT
66 ACCT
30572949 CT
1 CT
30572951 ACTTTAACCA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 66 1.00
ACGTcount: A:0.20, C:0.31, G:0.05, T:0.44
Consensus pattern (69 bp):
CTCCCCTATTCTCCCTTGTTCTAATAGCTCCCCTTTTAACCACTAGTTTTTAATTTACACATTTA
ACCT
Found at i:30577393 original size:6 final size:6
Alignment explanation
Indices: 30577382--30577414 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
30577372 AGGTTTCCAA
*
30577382 AAATGG AAATGG AAATGG AAATGA AAATGG AAA
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAA
30577415 CTTAAAATCC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.58, C:0.00, G:0.27, T:0.15
Consensus pattern (6 bp):
AAATGG
Found at i:30587294 original size:27 final size:27
Alignment explanation
Indices: 30586965--30587296 Score: 209
Period size: 27 Copynumber: 12.3 Consensus size: 27
30586955 TAGACCTTTT
* *
30586965 AAATGATCGAAATACCCTCG-ATGGGTA
1 AAATGACCGAAATACCCTCGTA-AGGTA
* * *
30586992 AAATTATCGAAATACCCTC-AAAGGGTA
1 AAATGACCGAAATACCCTCGTAA-GGTA
* * *
30587019 AAATTATCGGAATACCCTC-TATAGGTA
1 AAATGACCGAAATACCCTCGTA-AGGTA
30587046 AAATGACCGAAATACCCTCG-ATAGGTA
1 AAATGACCGAAATACCCTCGTA-AGGTA
*
30587073 AAATGACCTAAATACCCTCG-ATAGGTA
1 AAATGACCGAAATACCCTCGTA-AGGTA
* * * *
30587100 AAATGACCGAAGTACTCTCATAGGGTA
1 AAATGACCGAAATACCCTCGTAAGGTA
* * *
30587127 AAATGATCGTAATGCCC-CTGTAAGGTA
1 AAATGACCGAAATACCCTC-GTAAGGTA
* *
30587154 AAATGATCGTAATACTCCT-GTAAGGT-
1 AAATGACCGAAATAC-CCTCGTAAGGTA
* * * * *
30587180 -AATGACAGAAAAACCCCCCATAGGGTA
1 AAATGACCGAAATA-CCCTCGTAAGGTA
* * * *
30587207 AAATGACCGTAATGCCC-CTGTAGGGAA
1 AAATGACCGAAATACCCTC-GTAAGGTA
* * * *
30587234 AAATGACCGTAATACCCTCATAGGGTT
1 AAATGACCGAAATACCCTCGTAAGGTA
*
30587261 AAATGACTC-AAATACCCTTGTAAGGTA
1 AAATGAC-CGAAATACCCTCGTAAGGTA
30587288 AAATGACCG
1 AAATGACCG
30587297 TAATGCCTCT
Statistics
Matches: 246, Mismatches: 43, Indels: 32
0.77 0.13 0.10
Matches are distributed among these distances:
25 11 0.04
26 9 0.04
27 211 0.86
28 15 0.06
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
AAATGACCGAAATACCCTCGTAAGGTA
Found at i:30587294 original size:54 final size:55
Alignment explanation
Indices: 30586965--30587320 Score: 245
Period size: 54 Copynumber: 6.6 Consensus size: 55
30586955 TAGACCTTTT
* * * * * **
30586965 AAATGATCGAAATACCCTCGAT-GGGTAAAATTATCGAAATACCC-TCAAAGGGTA
1 AAATGACCGTAATACCCTCTATAGGGTAAAATGACCGAAATACCCTTGTAA-GGTA
* * * *
30587019 AAATTATCGGAATACCCTCTATA-GGTAAAATGACCGAAATACCCTCG-ATAGGTA
1 AAATGACCGTAATACCCTCTATAGGGTAAAATGACCGAAATACCCTTGTA-AGGTA
* * * ** *
30587073 AAATGACC-TAAATACCCTCGATA-GGTAAAATGACCGAAGTACTCTCATAGGGTA
1 AAATGACCGT-AATACCCTCTATAGGGTAAAATGACCGAAATACCCTTGTAAGGTA
* * * * * *
30587127 AAATGATCGTAATGCCC-CTGTAAGGTAAAATGATCGTAATACTCC-TGTAAGGT-
1 AAATGACCGTAATACCCTCTATAGGGTAAAATGACCGAAATAC-CCTTGTAAGGTA
* * * * * * * * * *
30587180 -AATGACAGAAAAACCCCCCATAGGGTAAAATGACCGTAATGCCCCTGTAGGGAA
1 AAATGACCGTAATACCCTCTATAGGGTAAAATGACCGAAATACCCTTGTAAGGTA
*
30587234 AAATGACCGTAATACCCTC-ATAGGGTTAAATGACTC-AAATACCCTTGTAAGGTA
1 AAATGACCGTAATACCCTCTATAGGGTAAAATGAC-CGAAATACCCTTGTAAGGTA
* *
30587288 AAATGACCGTAAT-GCCTCTAGAGGGT-AAATGAC
1 AAATGACCGTAATACCCTCTATAGGGTAAAATGAC
30587321 TATTTTGCCC
Statistics
Matches: 238, Mismatches: 50, Indels: 29
0.75 0.16 0.09
Matches are distributed among these distances:
52 13 0.05
53 40 0.17
54 166 0.70
55 19 0.08
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (55 bp):
AAATGACCGTAATACCCTCTATAGGGTAAAATGACCGAAATACCCTTGTAAGGTA
Found at i:30587329 original size:26 final size:26
Alignment explanation
Indices: 30587300--30587353 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
30587290 ATGACCGTAA
*
30587300 TGCCTCTAGAGGGTAAATGACTA-TTT
1 TGCCCCTAGAGGGTAAATGA-TAGTTT
* *
30587326 TGCCCCTTGAGTGTAAATGATAGTTT
1 TGCCCCTAGAGGGTAAATGATAGTTT
30587352 TG
1 TG
30587354 TCTGTGATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (26 bp):
TGCCCCTAGAGGGTAAATGATAGTTT
Found at i:30587377 original size:24 final size:24
Alignment explanation
Indices: 30587350--30587399 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
30587340 AAATGATAGT
30587350 TTTGTCTGTGATTTAAATGACTGA
1 TTTGTCTGTGATTTAAATGACTGA
**
30587374 TTTGTCTGTGATTTGTATGACTGA
1 TTTGTCTGTGATTTAAATGACTGA
30587398 TT
1 TT
30587400 CTAAGCATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.08, G:0.22, T:0.50
Consensus pattern (24 bp):
TTTGTCTGTGATTTAAATGACTGA
Found at i:30587591 original size:32 final size:32
Alignment explanation
Indices: 30587545--30587693 Score: 151
Period size: 32 Copynumber: 4.7 Consensus size: 32
30587535 GCTGCAATGC
*
30587545 TACTGATGGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCAATCATATTACCAT
*
30587577 TACTAATGGCTTTGTGCCAATCATATTACCAT
1 TACTGATGGCTTTGTGCCAATCATATTACCAT
* * * * * ***
30587609 TACTGATGACTGTGTACCGATCATATCACTGC
1 TACTGATGGCTTTGTGCCAATCATATTACCAT
*
30587641 TACTGATGGCTTTCTGCCAATCATATTA-C-T
1 TACTGATGGCTTTGTGCCAATCATATTACCAT
*
30587671 GTACTTATGGC-TTGTAGCCAATC
1 -TACTGATGGCTTTGT-GCCAATC
30587694 TGTTTATAGC
Statistics
Matches: 94, Mismatches: 21, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
30 3 0.03
31 16 0.17
32 75 0.80
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCAATCATATTACCAT
Found at i:30587632 original size:64 final size:64
Alignment explanation
Indices: 30587545--30587669 Score: 169
Period size: 64 Copynumber: 2.0 Consensus size: 64
30587535 GCTGCAATGC
* * * * * *
30587545 TACTGATGGCTTTGTGCCGATCATATTACCATTACTAATGGCTTTGTGCCAATCATATTACCAT
1 TACTGATGACTGTGTACCGATCATATCACCACTACTAATGGCTTTCTGCCAATCATATTACCAT
** *
30587609 TACTGATGACTGTGTACCGATCATATCACTGCTACTGATGGCTTTCTGCCAATCATATTAC
1 TACTGATGACTGTGTACCGATCATATCACCACTACTAATGGCTTTCTGCCAATCATATTAC
30587670 TGTACTTATG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (64 bp):
TACTGATGACTGTGTACCGATCATATCACCACTACTAATGGCTTTCTGCCAATCATATTACCAT
Found at i:30600656 original size:24 final size:23
Alignment explanation
Indices: 30600608--30600659 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
30600598 GGCGATTTAT
*
30600608 TGCATTTTCACTGGTAGCTTGTC
1 TGCATTTTCACTGGTAGATTGTC
* *
30600631 TGCATTTTTACTGGTAGAATTTTC
1 TGCATTTTCACTGGTAG-ATTGTC
30600655 TGCAT
1 TGCAT
30600660 ATTGTTATCG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.46
Consensus pattern (23 bp):
TGCATTTTCACTGGTAGATTGTC
Found at i:30603116 original size:26 final size:26
Alignment explanation
Indices: 30603075--30603141 Score: 89
Period size: 26 Copynumber: 2.6 Consensus size: 26
30603065 TTTCTTGAAA
* *
30603075 TTTACCAGGGGCAAAATCATCAAAAT
1 TTTACCAAGGGTAAAATCATCAAAAT
** *
30603101 TTTATTAAGGGTAAAATCTTCAAAAT
1 TTTACCAAGGGTAAAATCATCAAAAT
30603127 TTTACCAAGGGTAAA
1 TTTACCAAGGGTAAA
30603142 CTTGGGATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (26 bp):
TTTACCAAGGGTAAAATCATCAAAAT
Found at i:30614595 original size:110 final size:110
Alignment explanation
Indices: 30614391--30614595 Score: 383
Period size: 111 Copynumber: 1.9 Consensus size: 110
30614381 AATCAAGATC
*
30614391 AAAAACCCTTTAATTAGATCAAAATGAGTTAGAATTAAATTTAAAACAAAAGCTTGGCTAAGAAA
1 AAAAACCCTTTAATTAGATCAAAATGAGTTAGAATTAAATTTAAAAAAAAAGCTTGGCTAAGAAA
30614456 TATGATATCTACCATTTTCAAGCCAAAAAACAAAATGATCTAATT
66 TATGATATCTACCATTTTCAAGCCAAAAAACAAAATGATCTAATT
*
30614501 AAAAACCCTTTAATTAGATCAAAATGAGTTGGAATTAAATTTTAAAAAAAAAGCTTGGCTAAGAA
1 AAAAACCCTTTAATTAGATCAAAATGAGTTAGAATTAAA-TTTAAAAAAAAAGCTTGGCTAAGAA
30614566 ATATGATATCTACCATTTTCAAGCCAAAAA
65 ATATGATATCTACCATTTTCAAGCCAAAAA
30614596 TCAAGTTAAA
Statistics
Matches: 92, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 38 0.41
111 54 0.59
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (110 bp):
AAAAACCCTTTAATTAGATCAAAATGAGTTAGAATTAAATTTAAAAAAAAAGCTTGGCTAAGAAA
TATGATATCTACCATTTTCAAGCCAAAAAACAAAATGATCTAATT
Found at i:30629310 original size:49 final size:50
Alignment explanation
Indices: 30629206--30629350 Score: 166
Period size: 49 Copynumber: 2.9 Consensus size: 50
30629196 TTATTGAGGT
* * * * *
30629206 TATGAGTGGTCCCACGTAAGACTATGTCTAGGACATGGCGTTGGCATCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
* * *
30629256 GATGAGAGGTCCCCCGTAAGACCATGT-TGGGACATGGCATGGGCACCGA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
** * * *
30629305 TATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
30629351 GTACAGGAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
49 39 0.50
50 39 0.50
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.23
Consensus pattern (50 bp):
TATGAGAGGTCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGA
Found at i:30637236 original size:7 final size:7
Alignment explanation
Indices: 30637224--30637253 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
30637214 AGCTGAGGAC
30637224 AACGGAG
1 AACGGAG
30637231 AACGGAG
1 AACGGAG
*
30637238 AACGAAG
1 AACGGAG
30637245 AACGGAG
1 AACGGAG
30637252 AA
1 AA
30637254 ATCAGTCAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.50, C:0.13, G:0.37, T:0.00
Consensus pattern (7 bp):
AACGGAG
Found at i:30644876 original size:10 final size:10
Alignment explanation
Indices: 30644833--30644877 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
30644823 AATATGAACA
*
30644833 TGATGAATTT
1 TGATTAATTT
*
30644843 TAATTAATTT
1 TGATTAATTT
30644853 TGTAGTTAATTT
1 TG-A-TTAATTT
30644865 TGATTAATTT
1 TGATTAATTT
30644875 TGA
1 TGA
30644878 CTATTTTCGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 19 0.63
11 2 0.07
12 9 0.30
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (10 bp):
TGATTAATTT
Found at i:30646702 original size:20 final size:20
Alignment explanation
Indices: 30646677--30646725 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
30646667 TGAGTTATTT
30646677 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
30646697 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
30646717 AAG-AAGCAA
1 AAGTAAGCAA
30646726 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:30649525 original size:55 final size:55
Alignment explanation
Indices: 30649415--30649766 Score: 301
Period size: 55 Copynumber: 6.4 Consensus size: 55
30649405 ATCAAAGAGA
* * ** * * *
30649415 TATTTTAATCA-TTTCACAAA-CTGAGGGTATTTTAATCATTTCACAAATCGAGGG
1 TATTTTAATAATTTTTACAAATC-GAGGGTATTTCGATAATTTTACAAATCGGGGG
* * * *
30649469 TATTTTGATAATTTTTACATATCGAAGGTATTTCGATAATTTTGCAAA-CTGGGGG
1 TATTTTAATAATTTTTACAAATCGAGGGTATTTCGATAATTTTACAAATC-GGGGG
* * * * *
30649524 TATTTTAGTAATTTTTACAAATCGAGGGTATTTTGAAAATTTTGCAAATCGAGGG
1 TATTTTAATAATTTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGGGGG
* * *
30649579 TATTTCAATAATTTTGA-AAA-CTGAGGGTATTTC-AGTAATTTTTACAAATCGAGGG
1 TATTTTAATAATTTTTACAAATC-GAGGGTATTTCGA-TAA-TTTTACAAATCGGGGG
* * *
30649634 TATTTCAGTAATTTTTTGCAAATCG-GGGATATTTCGATAATTTTACAAATCGGGGG
1 TATTTTAATAA-TTTTTACAAATCGAGGG-TATTTCGATAATTTTACAAATCGGGGG
* * * * *
30649690 TATTTTGATAA-TTTTGCAAAT-TAGGGGTATTTCGGTAATTTTACAAA-CTGGGGC
1 TATTTTAATAATTTTTACAAATCGA-GGGTATTTCGATAATTTTACAAATC-GGGGG
*
30649744 TATTTTAATAATTTTTCCAAATC
1 TATTTTAATAATTTTTACAAATC
30649767 AGGATAATTT
Statistics
Matches: 245, Mismatches: 36, Indels: 32
0.78 0.12 0.10
Matches are distributed among these distances:
53 3 0.01
54 68 0.28
55 127 0.52
56 32 0.13
57 13 0.05
58 2 0.01
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.40
Consensus pattern (55 bp):
TATTTTAATAATTTTTACAAATCGAGGGTATTTCGATAATTTTACAAATCGGGGG
Found at i:30649575 original size:82 final size:82
Alignment explanation
Indices: 30649431--30649704 Score: 331
Period size: 82 Copynumber: 3.3 Consensus size: 82
30649421 AATCATTTCA
* * * * * *
30649431 CAAACTGAGGGTATTTTAATCA-TTTCACAAATCGAGGGTATTTTGATAATTTTTACATATCGAA
1 CAAACTGAGGGTATTTTAGTAATTTTTACAAATCGAGGGTATTTTGA-AATTTTTGCAAATCGAG
30649495 GGTATTTCGATAATTTTG
65 GGTATTTCGATAATTTTG
* *
30649513 CAAACTGGGGGTATTTTAGTAATTTTTACAAATCGAGGGTATTTTGAAAATTTTGCAAATCGAGG
1 CAAACTGAGGGTATTTTAGTAATTTTTACAAATCGAGGGTATTTTGAAATTTTTGCAAATCGAGG
*
30649578 GTATTTCAATAATTTTG
66 GTATTTCGATAATTTTG
* * * *
30649595 AAAACTGAGGGTATTTCAGTAATTTTTACAAATCGAGGGTATTTCAGTAATTTTTTGCAAATCG-
1 CAAACTGAGGGTATTTTAGTAATTTTTACAAATCGAGGGTATTT-TG-AAATTTTTGCAAATCGA
*
30649659 GGGATATTTCGATAATTTTA
64 GGG-TATTTCGATAATTTTG
*
30649679 CAAA-TCGGGGGTATTTT-GATAATTTT
1 CAAACT-GAGGGTATTTTAG-TAATTTT
30649705 GCAAATTAGG
Statistics
Matches: 166, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
82 90 0.54
83 29 0.17
84 47 0.28
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.40
Consensus pattern (82 bp):
CAAACTGAGGGTATTTTAGTAATTTTTACAAATCGAGGGTATTTTGAAATTTTTGCAAATCGAGG
GTATTTCGATAATTTTG
Found at i:30649685 original size:27 final size:27
Alignment explanation
Indices: 30649437--30649736 Score: 247
Period size: 27 Copynumber: 10.9 Consensus size: 27
30649427 TTCACAAACT
** * *
30649437 GAGGGTATTTTAATCATTTCACAAATC
1 GAGGGTATTTCGATAATTTTACAAATC
* *
30649464 GAGGGTATTTTGATAATTTTTACATATC
1 GAGGGTATTTCGATAA-TTTTACAAATC
* *
30649492 GAAGGTATTTCGATAATTTTGCAAA-C
1 GAGGGTATTTCGATAATTTTACAAATC
* *
30649518 TGGGGGTATTT-TAGTAATTTTTACAAATC
1 -GAGGGTATTTCGA-TAA-TTTTACAAATC
* * *
30649547 GAGGGTATTTTGAAAATTTTGCAAATC
1 GAGGGTATTTCGATAATTTTACAAATC
*
30649574 GAGGGTATTTCAATAATTTTGA-AAA-C
1 GAGGGTATTTCGATAATTTT-ACAAATC
30649600 TGAGGGTATTTC-AGTAATTTTTACAAATC
1 -GAGGGTATTTCGA-TAA-TTTTACAAATC
*
30649629 GAGGGTATTTC-AGTAATTTTTTGCAAATC
1 GAGGGTATTTCGA-TAA--TTTTACAAATC
30649658 G-GGGATATTTCGATAATTTTACAAATC
1 GAGGG-TATTTCGATAATTTTACAAATC
* * *
30649685 GGGGGTATTTTGATAATTTTGCAAAT-
1 GAGGGTATTTCGATAATTTTACAAATC
* *
30649711 TAGGGGTATTTCGGTAATTTTACAAA
1 GA-GGGTATTTCGATAATTTTACAAA
30649737 CTGGGGCTAT
Statistics
Matches: 227, Mismatches: 29, Indels: 34
0.78 0.10 0.12
Matches are distributed among these distances:
26 4 0.02
27 127 0.56
28 71 0.31
29 24 0.11
30 1 0.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (27 bp):
GAGGGTATTTCGATAATTTTACAAATC
Found at i:30649782 original size:18 final size:19
Alignment explanation
Indices: 30649751--30649787 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
30649741 GGCTATTTTA
30649751 ATAATTTTTCCAAATCAGG
1 ATAATTTTTCCAAATCAGG
*
30649770 ATAA-TTTTGCAAATCAGG
1 ATAATTTTTCCAAATCAGG
30649788 CGTATTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (19 bp):
ATAATTTTTCCAAATCAGG
Found at i:30649821 original size:73 final size:73
Alignment explanation
Indices: 30649696--30649842 Score: 197
Period size: 73 Copynumber: 2.0 Consensus size: 73
30649686 GGGGTATTTT
* * * *
30649696 GATAATTTTGCAAATTAGGGGTATTTCGGTAATTTTACAAACTGGGGCTATTTTAATAATTTTTC
1 GATAATTTTGCAAATCAGGCGTATTTCAGTAATTTTACAAACTGGGGCTATTTCAATAATTTTTC
30649761 CAAATCAG
66 CAAATCAG
* * *
30649769 GATAATTTTGCAAATCAGGCGTATTTTAGTAATTTTGCAAATTTGGGG-TATTTCAATAATTTTT
1 GATAATTTTGCAAATCAGGCGTATTTCAGTAATTTTACAAA-CTGGGGCTATTTCAATAATTTTT
* *
30649833 TCAAGTCAG
65 CCAAATCAG
30649842 G
1 G
30649843 GGTATTTCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
73 59 0.92
74 5 0.08
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (73 bp):
GATAATTTTGCAAATCAGGCGTATTTCAGTAATTTTACAAACTGGGGCTATTTCAATAATTTTTC
CAAATCAG
Found at i:30649865 original size:100 final size:100
Alignment explanation
Indices: 30649669--30649866 Score: 240
Period size: 100 Copynumber: 2.0 Consensus size: 100
30649659 GGGATATTTC
* * **
30649669 GATAATTTTACAAATCGGGGGTATTTTGATAATTTTGCAAATTAGGGGTATTTCGGTAATTTTAC
1 GATAATTTTACAAATCAGGCGTATTTTGATAATTTTGCAAATTAGGGGTATTTCAATAATTTTAC
* * *
30649734 AAACTGGGGCTATTTTAATAATTTTTCCAAATCAG
66 AAACAGGGGCTATTTCAATAATTTTTACAAATCAG
* *
30649769 GATAATTTTGCAAATCAGGCGTATTTT-AGTAATTTTGCAAATTTGGGGTATTTCAATAATTTTT
1 GATAATTTTACAAATCAGGCGTATTTTGA-TAATTTTGCAAATTAGGGGTATTTCAATAA-TTTT
* * *
30649833 TCAAGTCAGGGG-TATTTCGATAA-TTTTACAAATC
64 ACAA-ACAGGGGCTATTTCAATAATTTTTACAAATC
30649867 GGGGGTCTCG
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
99 1 0.01
100 61 0.73
101 16 0.19
102 5 0.06
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (100 bp):
GATAATTTTACAAATCAGGCGTATTTTGATAATTTTGCAAATTAGGGGTATTTCAATAATTTTAC
AAACAGGGGCTATTTCAATAATTTTTACAAATCAG
Found at i:30649871 original size:27 final size:27
Alignment explanation
Indices: 30649769--30649872 Score: 102
Period size: 27 Copynumber: 3.8 Consensus size: 27
30649759 TCCAAATCAG
*
30649769 GATAATTTTGCAAATCAGGCGTATTT-
1 GATAATTTTGCAAATCAGGGGTATTTC
* **
30649795 TAGTAATTTTGCAAATTTGGGGTATTTC
1 GA-TAATTTTGCAAATCAGGGGTATTTC
* * *
30649823 AATAATTTTTTCAAGTCAGGGGTATTTC
1 GATAA-TTTTGCAAATCAGGGGTATTTC
* *
30649851 GATAATTTTACAAATCGGGGGT
1 GATAATTTTGCAAATCAGGGGT
30649873 CTCGGTGACC
Statistics
Matches: 62, Mismatches: 13, Indels: 5
0.77 0.16 0.06
Matches are distributed among these distances:
26 1 0.02
27 38 0.61
28 23 0.37
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (27 bp):
GATAATTTTGCAAATCAGGGGTATTTC
Found at i:30653874 original size:17 final size:16
Alignment explanation
Indices: 30653852--30653890 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
30653842 CCCTCATCCG
30653852 TCATCTCATCATCCCTC
1 TCATCTCATCAT-CCTC
30653869 TCATCTC-TCATCCTC
1 TCATCTCATCATCCTC
30653884 TC-TCTCA
1 TCATCTCA
30653891 ACTCTCTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 4 0.19
15 6 0.29
16 4 0.19
17 7 0.33
ACGTcount: A:0.15, C:0.46, G:0.00, T:0.38
Consensus pattern (16 bp):
TCATCTCATCATCCTC
Found at i:30653879 original size:19 final size:19
Alignment explanation
Indices: 30653855--30653896 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
30653845 TCATCCGTCA
*
30653855 TCTCATCATCCCTCTCATC
1 TCTCATCATCCCTCTCAAC
* *
30653874 TCTCATCCTCTCTCTCAAC
1 TCTCATCATCCCTCTCAAC
30653893 TCTC
1 TCTC
30653897 TTAGCTCTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.14, C:0.48, G:0.00, T:0.38
Consensus pattern (19 bp):
TCTCATCATCCCTCTCAAC
Found at i:30662047 original size:11 final size:11
Alignment explanation
Indices: 30662033--30662061 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
30662023 AAATGATATT
30662033 TTATTATTTTA
1 TTATTATTTTA
30662044 TTATTATTTTA
1 TTATTATTTTA
30662055 TTATTAT
1 TTATTAT
30662062 ATATATAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTATTTTA
Found at i:30662796 original size:15 final size:15
Alignment explanation
Indices: 30662771--30662805 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
30662761 GACTCTATTT
*
30662771 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
30662785 TAATTAATATTAAGA
1 TAATTAATATTAAGA
30662800 TAATTA
1 TAATTA
30662806 TTAAGAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:30675580 original size:30 final size:30
Alignment explanation
Indices: 30675527--30675599 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
30675517 ACGCTTAAAA
* * * **
30675527 TATTTGCACTATTAGTCCTTCAAATTTTTTG
1 TATTTACACT-TTAATCCCTCAAATTTTGAG
30675558 TATTTACACTTTAATCCCTCAAATTTTGAG
1 TATTTACACTTTAATCCCTCAAATTTTGAG
*
30675588 TATTTACTCTTT
1 TATTTACACTTT
30675600 GGCAACAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.51
Consensus pattern (30 bp):
TATTTACACTTTAATCCCTCAAATTTTGAG
Found at i:30677345 original size:50 final size:50
Alignment explanation
Indices: 30677288--30677564 Score: 362
Period size: 50 Copynumber: 5.5 Consensus size: 50
30677278 TACTGCTAAT
*
30677288 GCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGATGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAC
*
30677338 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAC
* *
30677388 GCCATGTCCCAGACATGGTCTTACATGGGACCCCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAC
*
30677438 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GATGCCAAC
* * * * * * *
30677494 GCAATATCCCAGACATGGTCTTACACT-GG--CTCACATATCGATGTCGAT
1 GCCATGTCCCAGACATGGTCTTACA-TGGGACCTCTCATCTCGATGCCAAC
30677542 GCCATGTCCCAGACATGGTCTTA
1 GCCATGTCCCAGACATGGTCTTA
30677565 TACGAGATTG
Statistics
Matches: 206, Mismatches: 14, Indels: 16
0.87 0.06 0.07
Matches are distributed among these distances:
48 28 0.14
50 132 0.64
51 4 0.02
53 5 0.02
54 4 0.02
56 32 0.16
57 1 0.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.25
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAAC
Found at i:30681373 original size:16 final size:17
Alignment explanation
Indices: 30681348--30681382 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
30681338 ACTTTATCCA
30681348 TCATCCCTCAT-CTCTC
1 TCATCCCTCATCCTCTC
*
30681364 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
30681381 TC
1 TC
30681383 TCAAATCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.11, C:0.49, G:0.00, T:0.40
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:30684032 original size:50 final size:50
Alignment explanation
Indices: 30683978--30684171 Score: 192
Period size: 50 Copynumber: 3.9 Consensus size: 50
30683968 CATTGAGATT
* * *
30683978 ATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACTGAG
1 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACTGAC
** * * * * * *
30684028 ATGAGAGGTCCCCCGTAAGACCATGTCTGGAACATAGCATGGGCACCGAT
1 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACTGAC
** * * *
30684078 ATGAGAACTCCCATGTAAGACCATATATGGGATATGGCATTGGCAGT-AC
1 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACTGAC
* * ** *
30684127 AAGAAATATCCCATGTAAGACCATGTATGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCA
30684172 TGTTATTATC
Statistics
Matches: 115, Mismatches: 29, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
49 39 0.34
50 76 0.66
ACGTcount: A:0.29, C:0.20, G:0.28, T:0.23
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCATTGGCACTGAC
Found at i:30684412 original size:14 final size:12
Alignment explanation
Indices: 30684383--30684416 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 12
30684373 TCTAAATAGG
30684383 TAAGTAAATAAA
1 TAAGTAAATAAA
30684395 TAAGTAAATGAGAA
1 TAAGTAAAT-A-AA
30684409 TAAGTAAA
1 TAAGTAAA
30684417 GAGGAAACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 1 0.05
14 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.24
Consensus pattern (12 bp):
TAAGTAAATAAA
Found at i:30690950 original size:50 final size:50
Alignment explanation
Indices: 30690825--30691071 Score: 210
Period size: 50 Copynumber: 4.8 Consensus size: 50
30690815 ATTTGGGTAA
* * *
30690825 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTGAGATTATT
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--CGAG---ATG
*
30690881 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
30690931 AGAGGTCCCTTGTAAGACCATGTCTGGAACATAGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * * * * * * *
30690981 AGAACTCCCATGTAAGACCATATATCGGATATGGCATTGG-A-AGTACAAG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATG
* ** * *
30691030 AAACATCCCATGTAAGACCATGTATGGGACATGGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
30691072 TGTTATTATC
Statistics
Matches: 159, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 37 0.23
50 77 0.48
53 3 0.02
55 1 0.01
56 40 0.25
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:30705295 original size:15 final size:15
Alignment explanation
Indices: 30705275--30705305 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
30705265 TGAGTGAGTT
30705275 AGAGATTTTTTTTAA
1 AGAGATTTTTTTTAA
30705290 AGAGATTTTTTTTAA
1 AGAGATTTTTTTTAA
30705305 A
1 A
30705306 AAAAACCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (15 bp):
AGAGATTTTTTTTAA
Found at i:30709890 original size:5 final size:5
Alignment explanation
Indices: 30709880--30709921 Score: 66
Period size: 5 Copynumber: 8.2 Consensus size: 5
30709870 ATGATGCGTA
*
30709880 AATAT AATAT AATAT AATAT AATAT AATAA ACATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT A
30709922 GTAAGATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 30 0.88
6 4 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:30711117 original size:26 final size:26
Alignment explanation
Indices: 30711088--30711141 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
30711078 AATGCTTAAC
30711088 AAATATTACATTTTATTTATTTCTTT
1 AAATATTACATTTTATTTATTTCTTT
30711114 AAATATTACATTTTATTTATTTCTTT
1 AAATATTACATTTTATTTATTTCTTT
30711140 AA
1 AA
30711142 CTAGAGGACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.59
Consensus pattern (26 bp):
AAATATTACATTTTATTTATTTCTTT
Found at i:30713485 original size:19 final size:17
Alignment explanation
Indices: 30713461--30713509 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
30713451 GCCTAATATT
30713461 CCCACACGCCCATGTAGGG
1 CCCACACGCCCATGTA--G
*
30713480 CCCACAAGCCCATGTAG
1 CCCACACGCCCATGTAG
30713497 CCCACACGGCCCA
1 CCCACAC-GCCCA
30713510 ATTCGACCTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 5 0.19
19 15 0.56
ACGTcount: A:0.24, C:0.47, G:0.20, T:0.08
Consensus pattern (17 bp):
CCCACACGCCCATGTAG
Found at i:30714084 original size:15 final size:15
Alignment explanation
Indices: 30714064--30714097 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
30714054 GAGGAGAGGA
30714064 AATTGAAAAGAAAAC
1 AATTGAAAAGAAAAC
*
30714079 AATTGAAAAGAACAC
1 AATTGAAAAGAAAAC
30714094 AATT
1 AATT
30714098 AATTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.09, G:0.12, T:0.18
Consensus pattern (15 bp):
AATTGAAAAGAAAAC
Found at i:30714500 original size:21 final size:20
Alignment explanation
Indices: 30714466--30714512 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
30714456 GATTTTTTTG
30714466 AAAA-AAAATCATAATAATC
1 AAAATAAAATCATAATAATC
30714485 AAAATAAAATCAATAATAATC
1 AAAATAAAATC-ATAATAATC
*
30714506 TAAATAA
1 AAAATAA
30714513 TATGAGAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 15 0.60
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (20 bp):
AAAATAAAATCATAATAATC
Found at i:30720742 original size:20 final size:20
Alignment explanation
Indices: 30720717--30720754 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
30720707 ACCCCCTTTA
30720717 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
30720737 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
30720755 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:30727455 original size:17 final size:17
Alignment explanation
Indices: 30727433--30727470 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
30727423 ACGATAGGCG
30727433 TGAGAGAGGATGA-GAGA
1 TGAGAG-GGATGATGAGA
30727450 TGAGAGGGATGATGAGA
1 TGAGAGGGATGATGAGA
30727467 TGAG
1 TGAG
30727471 GGATGAGGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.37, C:0.00, G:0.47, T:0.16
Consensus pattern (17 bp):
TGAGAGGGATGATGAGA
Found at i:30727456 original size:15 final size:15
Alignment explanation
Indices: 30727436--30727477 Score: 59
Period size: 15 Copynumber: 2.7 Consensus size: 15
30727426 ATAGGCGTGA
30727436 GAGAGGATGAGAGAT
1 GAGAGGATGAGAGAT
30727451 GAGAGGGATGATGAGAT
1 GAGA-GGATGA-GAGAT
30727468 GAG-GGATGAG
1 GAGAGGATGAG
30727478 GGATAAAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 10 0.40
16 6 0.24
17 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.50, T:0.14
Consensus pattern (15 bp):
GAGAGGATGAGAGAT
Found at i:30755676 original size:26 final size:26
Alignment explanation
Indices: 30755647--30755697 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
30755637 AGATAAAAAA
30755647 GGGTCACCAAGTGCAGATTCCCCGAG
1 GGGTCACCAAGTGCAGATTCCCCGAG
** * *
30755673 GGGTTGCTAAGTGCTGATTCCCCGA
1 GGGTCACCAAGTGCAGATTCCCCGA
30755698 ATTATTGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.20, C:0.27, G:0.31, T:0.22
Consensus pattern (26 bp):
GGGTCACCAAGTGCAGATTCCCCGAG
Found at i:30755818 original size:85 final size:85
Alignment explanation
Indices: 30755671--30756078 Score: 597
Period size: 85 Copynumber: 4.8 Consensus size: 85
30755661 AGATTCCCCG
* * * * * * *
30755671 AGGGGTTGCTAAGTGCTGATTCCCCGAATTATTGATTCTAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTGCTGATTCC
30755736 ACCGTATATTTGATTGTGAA
66 ACCGTATATTTGATTGTGAA
* *
30755756 AGGGGTTGTTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTGATGATTCC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTGCTGATTCC
*
30755821 ACTGTATATTTGATTGTGAA
66 ACCGTATATTTGATTGTGAA
*
30755841 AGGGGTTGCTATGTACTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTGAC-GATTC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTG-CTGATTC
30755905 CACCGTATATTTGATTGTGAA
65 CACCGTATATTTGATTGTGAA
* * * *
30755926 AGGGGTTGCTATGTCCTGATTCCCCATATCATTGAATATAAAGGTGGTTGCTAAGTGCTGATTCC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTGCTGATTCC
*
30755991 ACCGTATCTTTGATTGTGAA
66 ACCGTATATTTGATTGTGAA
* * * *
30756011 AGGGGTTGCTATGTGCTGGTTCCACGTATCACTGAAT-TTAAGGTGG-GTGCTAAGTGCTGAATC
1 AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTG-GCTAAGTGCTGATTC
30756074 CACCG
65 CACCG
30756079 AGTAACGGAT
Statistics
Matches: 293, Mismatches: 27, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
84 28 0.10
85 265 0.90
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (85 bp):
AGGGGTTGCTATGTGCTGATTCCCCGTATCACTGAATATAAAGGTGGTGGCTAAGTGCTGATTCC
ACCGTATATTTGATTGTGAA
Found at i:30756076 original size:41 final size:41
Alignment explanation
Indices: 30755674--30756076 Score: 247
Period size: 43 Copynumber: 9.5 Consensus size: 41
30755664 TTCCCCGAGG
* * *
30755674 GGTTGCTAAGTGCTGATTCCCCGAATTATTG-ATTCTAAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCATTGAATT-T-AAGGT
30755716 GGTTGCTAAGTGCTGATTCCACCGTAT-ATTTG-ATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCA-CGTATCA-TTGAATT-T--AAGGT
* * * * *
30755759 GGTTGTTATGTGCTGATTCCCCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCATTGAAT-TTAAGGT
* *
30755801 GGTGGCTAAGTGATGATTCCACTGTAT-ATTTG-ATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCAC-GTATCA-TTGAATT-T--AAGGT
* * * * *
30755844 GGTTGCTATGTACTGATTCCCCGTATCACTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCATTGAAT-TTAAGGT
*
30755886 GGTGGCTAAGTGAC-GATTCCACCGTAT-ATTTG-ATTGTGAAAGG-
1 GGTTGCTAAGTG-CTGATTCCA-CGTATCA-TTGAATT-T--AAGGT
* * * * *
30755929 GGTTGCTATGTCCTGATTCCCCATATCATTGAATATAAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCATTGAAT-TTAAGGT
*
30755971 GGTTGCTAAGTGCTGATTCCACCGTATCTTTG-ATTGTGAAAGG-
1 GGTTGCTAAGTGCTGATTCCA-CGTATCATTGAATT-T--AAGGT
* * *
30756014 GGTTGCTATGTGCTGGTTCCACGTATCACTGAATTTAAGGT
1 GGTTGCTAAGTGCTGATTCCACGTATCATTGAATTTAAGGT
* *
30756055 GGGTGCTAAGTGCTGAATCCAC
1 GGTTGCTAAGTGCTGATTCCAC
30756077 CGAGTAACGG
Statistics
Matches: 280, Mismatches: 48, Indels: 67
0.71 0.12 0.17
Matches are distributed among these distances:
40 4 0.01
41 33 0.12
42 109 0.39
43 114 0.41
44 20 0.07
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACGTATCATTGAATTTAAGGT
Found at i:30763312 original size:12 final size:12
Alignment explanation
Indices: 30763287--30763319 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30763277 CACTGTTTTT
30763287 GAAAAAAA-AAA
1 GAAAAAAAGAAA
*
30763298 GAAAATAAGAAA
1 GAAAAAAAGAAA
30763310 GAAAAAAAGA
1 GAAAAAAAGA
30763320 CCCCAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 7 0.37
12 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (12 bp):
GAAAAAAAGAAA
Found at i:30765952 original size:29 final size:29
Alignment explanation
Indices: 30765920--30765980 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
30765910 TCTAGGTCAC
* *
30765920 GTGTCACACACGATCTGTCACACGGTCGT
1 GTGTCACACACGACCTGGCACACGGTCGT
*
30765949 GTGTCACACACGGCCTGGCACACGGTCGT
1 GTGTCACACACGACCTGGCACACGGTCGT
30765978 GTG
1 GTG
30765981 GCATCAACAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.18, C:0.31, G:0.30, T:0.21
Consensus pattern (29 bp):
GTGTCACACACGACCTGGCACACGGTCGT
Found at i:30770278 original size:12 final size:11
Alignment explanation
Indices: 30770251--30770288 Score: 53
Period size: 10 Copynumber: 3.5 Consensus size: 11
30770241 GAAAATAGTC
30770251 AAAATTAATA-
1 AAAATTAATAT
30770261 AAAATTAACTAT
1 AAAATTAA-TAT
30770273 AAAATTAAT-T
1 AAAATTAATAT
30770283 AAAATT
1 AAAATT
30770289 CATCATGTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 15 0.58
11 3 0.12
12 8 0.31
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.34
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:30777964 original size:14 final size:14
Alignment explanation
Indices: 30777945--30777972 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30777935 GTTTAAAGAT
30777945 GATTAAAAACTAAG
1 GATTAAAAACTAAG
30777959 GATTAAAAACTAAG
1 GATTAAAAACTAAG
30777973 TAAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.07, G:0.14, T:0.21
Consensus pattern (14 bp):
GATTAAAAACTAAG
Found at i:30778569 original size:9 final size:9
Alignment explanation
Indices: 30778555--30778581 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
30778545 CGGTAAAACC
30778555 ACATGATCA
1 ACATGATCA
30778564 ACATGATCA
1 ACATGATCA
30778573 ACATGATCA
1 ACATGATCA
30778582 GTCTCAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (9 bp):
ACATGATCA
Found at i:30781251 original size:21 final size:21
Alignment explanation
Indices: 30781205--30781253 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
30781195 GTGAGGGTCT
*
30781205 CACACGCCCGTGTGCCAACCA
1 CACACGCCCGTGTGCCAACAA
* *
30781226 GACACGGCCGTGTGTCCAA-AA
1 CACACGCCCGTGTG-CCAACAA
30781247 CACACGC
1 CACACGC
30781254 ACATGTAGGA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.27, C:0.41, G:0.22, T:0.10
Consensus pattern (21 bp):
CACACGCCCGTGTGCCAACAA
Found at i:30788303 original size:15 final size:15
Alignment explanation
Indices: 30788283--30788324 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
30788273 AAATCTAAAC
*
30788283 TAAATACATATTTAA
1 TAAATAAATATTTAA
*
30788298 TAAATAAATATTTAG
1 TAAATAAATATTTAA
30788313 TAAATAAATATT
1 TAAATAAATATT
30788325 AAACATTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
TAAATAAATATTTAA
Found at i:30792340 original size:3 final size:3
Alignment explanation
Indices: 30792332--30792360 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
30792322 CTCTGTGGGA
30792332 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
30792361 GGGATCCTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:30803999 original size:53 final size:53
Alignment explanation
Indices: 30803917--30804056 Score: 199
Period size: 53 Copynumber: 2.6 Consensus size: 53
30803907 AGAGGTCAAT
*
30803917 AAATGACCGAAATACCTCTATAGGGTAAAATGACCAAAATACCGCCATAGGATA
1 AAATGACCGAAATACCTC-ATAGGGTAAAATGACCAAAATACCCCCATAGGATA
* * * *
30803971 AAATGACCGAAATACCTCATAGGGTAAAATTATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCTCATAGGGTAAAATGACCAAAATACCCCCATAGGATA
* *
30804024 AAATGATCGAAATACCCCCATAGGGTAAAATGA
1 AAATGACCGAAATA-CCTCATAGGGTAAAATGA
30804057 TTGATATACC
Statistics
Matches: 77, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
53 43 0.56
54 34 0.44
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (53 bp):
AAATGACCGAAATACCTCATAGGGTAAAATGACCAAAATACCCCCATAGGATA
Found at i:30804057 original size:27 final size:27
Alignment explanation
Indices: 30803917--30804056 Score: 192
Period size: 27 Copynumber: 5.2 Consensus size: 27
30803907 AGAGGTCAAT
* *
30803917 AAATGACCGAAATACCTCTATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* * *
30803944 AAATGACCAAAATACCGCCATAGGATA
1 AAATGACCGAAATACCCCCATAGGGTA
*
30803971 AAATGACCGAAATA-CCTCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
* *
30803997 AAATTATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
*
30804024 AAATGATCGAAATACCCCCATAGGGTA
1 AAATGACCGAAATACCCCCATAGGGTA
30804051 AAATGA
1 AAATGA
30804057 TTGATATACC
Statistics
Matches: 100, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
26 21 0.21
27 79 0.79
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCCCATAGGGTA
Found at i:30804082 original size:54 final size:53
Alignment explanation
Indices: 30803917--30804084 Score: 171
Period size: 53 Copynumber: 3.1 Consensus size: 53
30803907 AGAGGTCAAT
* * * *
30803917 AAATGACCGAAATACCTCTATAGGGTAAAATGACCAAAATACCGCCATAG-GATA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACC-CC-TAGAGATA
* * *
30803971 AAATGACCGAAATA-CCTCATAGGGTAAAATTATCGAAATACCCCCATAG-GGTA
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATA-CCCC-TAGAGATA
* * * *
30804024 AAATGATCGAAATACCCCCATAGGGTAAAATGATTGATATACCCCTAGAAGATG
1 AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTAG-AGATA
30804078 AAATGAC
1 AAATGAC
30804085 TGATATGGCC
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
52 3 0.03
53 46 0.48
54 46 0.48
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (53 bp):
AAATGACCGAAATACCCCCATAGGGTAAAATGATCGAAATACCCCTAGAGATA
Found at i:30804266 original size:25 final size:26
Alignment explanation
Indices: 30804216--30804295 Score: 135
Period size: 26 Copynumber: 3.1 Consensus size: 26
30804206 TGGAGGAAGT
30804216 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
* *
30804242 ATACTGTTACT-GCAGCTTTGTTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
30804267 ATACTATTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTGCG
30804293 ATA
1 ATA
30804296 TTGGTGTGTT
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 23 0.47
26 26 0.53
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTGCG
Found at i:30804446 original size:28 final size:27
Alignment explanation
Indices: 30804406--30804468 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
30804396 GTACTAATTT
*
30804406 TGTACTGGGCTAAGGCCTACACTGTTAC
1 TGTACTGGGCTAAGGCCCACACTG-TAC
*
30804434 TGTATTGGGCTAAGGCCCACACTGTAC
1 TGTACTGGGCTAAGGCCCACACTGTAC
30804461 TGTTACTG
1 TG-TACTG
30804469 AATAGGGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.30
Consensus pattern (27 bp):
TGTACTGGGCTAAGGCCCACACTGTAC
Found at i:30804506 original size:14 final size:14
Alignment explanation
Indices: 30804487--30804522 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
30804477 TCGAGCCTAG
30804487 ACTGACTGTTGTTT
1 ACTGACTGTTGTTT
30804501 ACTGACTGTTGTTT
1 ACTGACTGTTGTTT
30804515 ACTGACTG
1 ACTGACTG
30804523 ACTGATAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.17, C:0.17, G:0.22, T:0.44
Consensus pattern (14 bp):
ACTGACTGTTGTTT
Found at i:30816415 original size:23 final size:23
Alignment explanation
Indices: 30816383--30816433 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
30816373 GCATATACTC
* * *
30816383 TTGAG-ATGATAACTCTAATGGT
1 TTGAGTATGATAACTATAACGAT
30816405 TTGAGTATGATAACTATAACGAT
1 TTGAGTATGATAACTATAACGAT
30816428 TTGAGT
1 TTGAGT
30816434 GGAACTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (23 bp):
TTGAGTATGATAACTATAACGAT
Found at i:30823316 original size:21 final size:21
Alignment explanation
Indices: 30823277--30823316 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
30823267 TTTTGCTTGG
*
30823277 TTTAATAAGTTTTTCTTAAGA
1 TTTAATAAATTTTTCTTAAGA
30823298 TTTAATAAATTATTT-TTAA
1 TTTAATAAATT-TTTCTTAA
30823317 TTGGACTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTAATAAATTTTTCTTAAGA
Found at i:30827445 original size:19 final size:19
Alignment explanation
Indices: 30827407--30827445 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
30827397 ATTTTATCTT
30827407 AATTTAACAAATCCTGAATG
1 AATTTAACAAAT-CTGAATG
30827427 AATTTAAGCAAAT-TGAATG
1 AATTTAA-CAAATCTGAATG
30827446 TTTTCCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 7 0.39
21 5 0.28
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.31
Consensus pattern (19 bp):
AATTTAACAAATCTGAATG
Found at i:30839048 original size:10 final size:10
Alignment explanation
Indices: 30839033--30839075 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
30839023 CTTTTTGCCA
30839033 ACACACAAAC
1 ACACACAAAC
30839043 ACACACAAAC
1 ACACACAAAC
***
30839053 ACACACGTGC
1 ACACACAAAC
30839063 ACACACAAAC
1 ACACACAAAC
30839073 ACA
1 ACA
30839076 TTCCATAATA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.53, C:0.40, G:0.05, T:0.02
Consensus pattern (10 bp):
ACACACAAAC
Found at i:30841465 original size:23 final size:23
Alignment explanation
Indices: 30841438--30841559 Score: 156
Period size: 23 Copynumber: 5.3 Consensus size: 23
30841428 AGTGTTATTG
30841438 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* *
30841461 TTCAGTGGTAGCTACAGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
*
30841484 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
* * * *
30841507 TTTAGTGGTAGCTAC-GCCTACGT
1 ATCAGTGGTAGCTTCAG-CTACAT
*
30841530 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCAGCTACAT
30841553 ATCAGTG
1 ATCAGTG
30841560 TGGCACTTAT
Statistics
Matches: 84, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
22 1 0.01
23 82 0.98
24 1 0.01
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCAGCTACAT
Found at i:30841490 original size:46 final size:46
Alignment explanation
Indices: 30841438--30841559 Score: 192
Period size: 46 Copynumber: 2.7 Consensus size: 46
30841428 AGTGTTATTG
*
30841438 ATCAGTGGTAGCTTCAGCTACATTTCAGTGGTAGCTACAG-CTACAT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTAC-GCCTACAT
* *
30841484 ATCAGTGGTAGCTTCGGCTACATTTTAGTGGTAGCTACGCCTACGT
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGCCTACAT
*
30841530 ATCAGTGGTAGCTTCGGCTACATATCAGTG
1 ATCAGTGGTAGCTTCGGCTACATTTCAGTG
30841560 TGGCACTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
45 1 0.01
46 69 0.99
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (46 bp):
ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTACGCCTACAT
Found at i:30846361 original size:31 final size:30
Alignment explanation
Indices: 30846323--30846404 Score: 112
Period size: 30 Copynumber: 2.7 Consensus size: 30
30846313 AACTTTTCAA
*
30846323 AAATTACATTTTGACCCCTAAATTTTTTCT
1 AAATTACATTTTGACCCCTAAATATTTTCT
*
30846353 AAATTTACATTTTGACCCCT-AATATTTTGT
1 AAA-TTACATTTTGACCCCTAAATATTTTCT
* *
30846383 AAATTACATTTAGGCCCCTAAA
1 AAATTACATTTTGACCCCTAAA
30846405 CTTTCTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 14 0.30
30 16 0.35
31 16 0.35
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (30 bp):
AAATTACATTTTGACCCCTAAATATTTTCT
Found at i:30847035 original size:13 final size:13
Alignment explanation
Indices: 30846997--30847052 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
30846987 AAGAGAGGAG
*
30846997 AAAGAAAGAAA-A
1 AAAGAGAGAAAGA
30847009 AAAG-GA-AAAGGA
1 AAAGAGAGAAA-GA
30847021 AAAGAGAGAAAGA
1 AAAGAGAGAAAGA
* *
30847034 AAAGAGAAAAAAA
1 AAAGAGAGAAAGA
30847047 AAAGAG
1 AAAGAG
30847053 TAGATGAGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
10 3 0.08
11 1 0.03
12 9 0.24
13 21 0.57
14 3 0.08
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (13 bp):
AAAGAGAGAAAGA
Found at i:30847045 original size:28 final size:27
Alignment explanation
Indices: 30846981--30847052 Score: 64
Period size: 24 Copynumber: 2.7 Consensus size: 27
30846971 GTCGAAATAG
* *
30846981 AAGAGAAAGAGAGGAGAAAGAAAGAAAAA
1 AAGAGAAA-AAAGGA-AAAGAGAGAAAAA
30847010 AAG-G--AAAAGGAAAAGAGAGAAAGAA
1 AAGAGAAAAAAGGAAAAGAGAGAAA-AA
30847035 AAGAGAAAAAA--AAAAGAG
1 AAGAGAAAAAAGGAAAAGAG
30847053 TAGATGAGAG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
24 10 0.27
25 10 0.27
26 9 0.24
28 5 0.14
29 3 0.08
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (27 bp):
AAGAGAAAAAAGGAAAAGAGAGAAAAA
Found at i:30847169 original size:7 final size:7
Alignment explanation
Indices: 30847147--30847208 Score: 63
Period size: 7 Copynumber: 8.3 Consensus size: 7
30847137 GAGGAAGAAG
30847147 AAGAAAGA
1 AAGAAA-A
30847155 AAGAAAA
1 AAGAAAA
30847162 AA-AGAAA
1 AAGA-AAA
30847169 AAGAAAAA
1 AAG-AAAA
30847177 ATAGAAAA
1 A-AGAAAA
*
30847185 TAGAAAAA
1 AAG-AAAA
30847193 AAGAAAA
1 AAGAAAA
30847200 AAGAAAA
1 AAGAAAA
30847207 AA
1 AA
30847209 TTTTAAAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
6 1 0.02
7 23 0.49
8 20 0.43
9 3 0.06
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (7 bp):
AAGAAAA
Found at i:30847172 original size:22 final size:21
Alignment explanation
Indices: 30847141--30847208 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 21
30847131 AAAGAGGAGG
*
30847141 AAGAAGAAGAAAGAAAGAAAAA
1 AAGAAAAAGAAA-AAAGAAAAA
30847163 AAGAAAAAGAAAAAATAGAAAATA
1 AAGAAAAAG-AAAAA-AGAAAA-A
30847187 GAA-AAAAAGAAAAAAGAAAAA
1 -AAGAAAAAGAAAAAAGAAAAA
30847208 A
1 A
30847209 TTTTAAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.39
23 14 0.34
24 7 0.17
25 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (21 bp):
AAGAAAAAGAAAAAAGAAAAA
Found at i:30847182 original size:15 final size:14
Alignment explanation
Indices: 30847154--30847208 Score: 83
Period size: 15 Copynumber: 3.7 Consensus size: 14
30847144 AAGAAGAAAG
30847154 AAAGAAAAAAAGAA
1 AAAGAAAAAAAGAA
30847168 AAAGAAAAAATAGAA
1 AAAGAAAAAA-AGAA
30847183 AATAGAAAAAAAGAAA
1 AA-AGAAAAAAAG-AA
30847199 AAAGAAAAAA
1 AAAGAAAAAA
30847209 TTTTAAAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.26
15 16 0.42
16 12 0.32
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.04
Consensus pattern (14 bp):
AAAGAAAAAAAGAA
Found at i:30847183 original size:31 final size:31
Alignment explanation
Indices: 30847148--30847209 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
30847138 AGGAAGAAGA
30847148 AGAAAGAAAGAAAAAAAG-AAAAAGAAAAAAT
1 AGAAA-AAAGAAAAAAAGAAAAAAGAAAAAAT
*
30847179 AGAAAATAGAAAAAAAGAAAAAAGAAAAAAT
1 AGAAAAAAGAAAAAAAGAAAAAAGAAAAAAT
30847210 TTTAAAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 11 0.38
31 18 0.62
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.05
Consensus pattern (31 bp):
AGAAAAAAGAAAAAAAGAAAAAAGAAAAAAT
Found at i:30847591 original size:16 final size:15
Alignment explanation
Indices: 30847571--30847609 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
30847561 AAAAAGAGAG
30847571 AGAAAAAGGAAGAAAA
1 AGAAAAAGG-AGAAAA
* *
30847587 GGAAAAAAGAGAAAA
1 AGAAAAAGGAGAAAA
30847602 AGAAAAAG
1 AGAAAAAG
30847610 AAACAAAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (15 bp):
AGAAAAAGGAGAAAA
Done.