Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 41 of 325
Found at i:12239367 original size:17 final size:17
Alignment explanation
Indices: 12239329--12239368 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
12239319 TTTAAACTTA
12239329 TAAAAAAATAGAATTTC
1 TAAAAAAATAGAATTTC
* *
12239346 AAAAAAAATAGAATTTT
1 TAAAAAAATAGAATTTC
12239363 TAAAAA
1 TAAAAA
12239369 TATATGGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (17 bp):
TAAAAAAATAGAATTTC
Found at i:12239480 original size:19 final size:19
Alignment explanation
Indices: 12239458--12239567 Score: 52
Period size: 18 Copynumber: 5.7 Consensus size: 19
12239448 ATAAAAAGGA
12239458 AAAATTATAAAAATATATT
1 AAAATTATAAAAATATATT
* *
12239477 AAAATTTATTTAAAATAATATA
1 AAAA-TTA-TAAAAAT-ATATT
* *
12239499 AAAATGTA-AAAACT-TATA
1 AAAAT-TATAAAAATATATT
** *
12239517 AAAATTGCAAACA-ATATT
1 AAAATTATAAAAATATATT
12239535 AAAA--ATAGAAAAT-TATT
1 AAAATTATA-AAAATATATT
12239552 AAAAATTATATAAAAT
1 -AAAATTATA-AAAAT
12239568 TATGAAAAAG
Statistics
Matches: 68, Mismatches: 12, Indels: 21
0.67 0.12 0.21
Matches are distributed among these distances:
16 1 0.01
17 8 0.12
18 23 0.34
19 4 0.06
20 15 0.22
21 7 0.10
22 10 0.15
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATTATAAAAATATATT
Found at i:12239568 original size:20 final size:19
Alignment explanation
Indices: 12239457--12239576 Score: 79
Period size: 20 Copynumber: 6.3 Consensus size: 19
12239447 TATAAAAAGG
12239457 AAAAATTATAAAAATATATT
1 AAAAATTATAAAAAT-TATT
* * *
12239477 AAAATTTATTTAAAATAATAT
1 AAAAATTA-TAAAAATTAT-T
*
12239498 AAAAATGTA-AAAACTTA-T
1 AAAAAT-TATAAAAATTATT
**
12239516 AAAAATTGCAAACAA-TATT
1 AAAAATTATAAA-AATTATT
*
12239535 AAAAA-TA-GAAAATTATT
1 AAAAATTATAAAAATTATT
*
12239552 AAAAATTATATAAAATTATG
1 AAAAATTATA-AAAATTATT
12239572 AAAAA
1 AAAAA
12239577 GAATCAGCAT
Statistics
Matches: 77, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
16 2 0.03
17 12 0.16
18 15 0.19
19 7 0.09
20 27 0.35
21 12 0.16
22 2 0.03
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
AAAAATTATAAAAATTATT
Found at i:12239798 original size:11 final size:11
Alignment explanation
Indices: 12239778--12239829 Score: 56
Period size: 10 Copynumber: 4.8 Consensus size: 11
12239768 TTATATTTTC
12239778 ATAATTTTTAA
1 ATAATTTTTAA
*
12239789 AT-ATTTTTTA
1 ATAATTTTTAA
12239799 ATAATTTTT--
1 ATAATTTTTAA
12239808 ATAATTTTCTATA
1 ATAATTTT-TA-A
12239821 ATAATTTTT
1 ATAATTTTT
12239830 GAAAAATTAT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
9 8 0.23
10 10 0.29
11 8 0.23
12 1 0.03
13 8 0.23
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
ATAATTTTTAA
Found at i:12239807 original size:22 final size:21
Alignment explanation
Indices: 12239773--12239829 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
12239763 AAAAATTATA
*
12239773 TTTTCATAATTTTTA-AATATT
1 TTTTAATAATTTTTATAAT-TT
12239794 TTTTAATAATTTTTATAATTT
1 TTTTAATAATTTTTATAATTT
*
12239815 TCTATAATAATTTTT
1 T-TTTAATAATTTTT
12239830 GAAAAATTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
21 17 0.53
22 15 0.47
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTAATAATTTTTATAATTT
Found at i:12239872 original size:9 final size:9
Alignment explanation
Indices: 12239858--12239945 Score: 61
Period size: 9 Copynumber: 9.4 Consensus size: 9
12239848 TAGGTGTAAT
12239858 TTTTTAAAA
1 TTTTTAAAA
12239867 TTTTTAAAA
1 TTTTTAAAA
* *
12239876 ATTCTAAAA
1 TTTTTAAAA
12239885 -TTTTAATAA
1 TTTTTAA-AA
* *
12239894 TTTTCTATTAT
1 TTTT-TA-AAA
*
12239905 TTTTTAATA
1 TTTTTAAAA
12239914 TTTTTATAAA
1 TTTTTA-AAA
* *
12239924 TTTGTAAAT
1 TTTTTAAAA
*
12239933 TTTTTATAA
1 TTTTTAAAA
12239942 TTTT
1 TTTT
12239946 ATAACTTTAA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
8 5 0.08
9 36 0.60
10 12 0.20
11 7 0.12
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:12239961 original size:28 final size:28
Alignment explanation
Indices: 12239903--12239958 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
12239893 ATTTTCTATT
* **
12239903 ATTTTTTAATATTTTTATAAATTTGTAA
1 ATTTTTTAATAATTTTATAAATTTAAAA
*
12239931 ATTTTTT-ATAATTTTATAACTTTAAAA
1 ATTTTTTAATAATTTTATAAATTTAAAA
12239958 A
1 A
12239959 ATTCTATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (28 bp):
ATTTTTTAATAATTTTATAAATTTAAAA
Found at i:12240035 original size:19 final size:19
Alignment explanation
Indices: 12239992--12240037 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
12239982 AAGTTCTAAT
*
12239992 TCTTTTATAATTTTAGAAT
1 TCTTTTATAATTTTAGAAA
*
12240011 TCTTTTATAATTTCTATAAA
1 TCTTTTATAATTT-TAGAAA
12240031 T-TTTTAT
1 TCTTTTAT
12240038 GCTTTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.30, C:0.07, G:0.02, T:0.61
Consensus pattern (19 bp):
TCTTTTATAATTTTAGAAA
Found at i:12240919 original size:37 final size:37
Alignment explanation
Indices: 12240878--12240973 Score: 104
Period size: 37 Copynumber: 2.6 Consensus size: 37
12240868 AGAGGGTTGT
* *
12240878 ATCTTAAGGTTTAGGTA-AAAGCCATGAGGGAGTTACA
1 ATCTTAAGGTTTAGGTAGAAA-CCATAAAGGAGTTACA
* * *
12240915 ATCTTAAGGTTTGGGTAGAAACCTTAAAGGAGTTGCA
1 ATCTTAAGGTTTAGGTAGAAACCATAAAGGAGTTACA
**
12240952 ATCTTAAAACTTTAGGTAGAAA
1 ATCTT-AAGGTTTAGGTAGAAA
12240974 TCTTAAAGTA
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 33 0.67
38 16 0.33
ACGTcount: A:0.36, C:0.10, G:0.24, T:0.29
Consensus pattern (37 bp):
ATCTTAAGGTTTAGGTAGAAACCATAAAGGAGTTACA
Found at i:12240979 original size:38 final size:37
Alignment explanation
Indices: 12240906--12240981 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
12240896 AAGCCATGAG
** *
12240906 GGAGTTACAATCTTAAGGTTTGGGTAGAAACCTTAAA
1 GGAGTTACAATCTTAAACTTTAGGTAGAAACCTTAAA
* *
12240943 GGAGTTGCAATCTTAAAACTTTAGGTAGAAATCTTAAA
1 GGAGTTACAATCTT-AAACTTTAGGTAGAAACCTTAAA
12240981 G
1 G
12240982 TAGATTGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
37 13 0.39
38 20 0.61
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (37 bp):
GGAGTTACAATCTTAAACTTTAGGTAGAAACCTTAAA
Found at i:12242458 original size:17 final size:17
Alignment explanation
Indices: 12242438--12242472 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
12242428 ATTTCGAAAC
12242438 TAAAAGATGAAAATAAT
1 TAAAAGATGAAAATAAT
12242455 TAAAAGATGAAAATAAT
1 TAAAAGATGAAAATAAT
12242472 T
1 T
12242473 CACTCTCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
TAAAAGATGAAAATAAT
Found at i:12243429 original size:19 final size:19
Alignment explanation
Indices: 12243382--12243440 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 19
12243372 AAAATGATAA
12243382 AATCAAGTTAAA-ATAGTTTC
1 AATCAAGTTAAACAT--TTTC
**
12243402 AATTGAGTTAAACATTTTC
1 AATCAAGTTAAACATTTTC
12243421 AATCAAGTTGAAACTATTTT
1 AATCAAGTT-AAAC-ATTTT
12243441 AAAAAAAGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 11 0.34
20 14 0.44
21 7 0.22
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (19 bp):
AATCAAGTTAAACATTTTC
Found at i:12245703 original size:22 final size:22
Alignment explanation
Indices: 12245675--12245720 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
12245665 TTCTTTGATT
12245675 CAATGCTAGAATAGTTTATGCA
1 CAATGCTAGAATAGTTTATGCA
12245697 CAATGCTAGAATAGTTTATGCA
1 CAATGCTAGAATAGTTTATGCA
12245719 CA
1 CA
12245721 TACCTATACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.30
Consensus pattern (22 bp):
CAATGCTAGAATAGTTTATGCA
Found at i:12256854 original size:46 final size:48
Alignment explanation
Indices: 12256734--12256859 Score: 130
Period size: 48 Copynumber: 2.7 Consensus size: 48
12256724 GTGATTGTGT
* * * ***
12256734 GCTAGTGTAAGACATGTCTGGGACATGCATTAGCCTCGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACATCGAGATACGGAA
* * * * * *
12256782 GCCAGTGTAGGACATGTCTAGAACATGCATCAACATTGAG-T-CGGGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAACATCGAGATACGGAA
12256828 GCTAGTGTAAGACATGTCTGGGACATGCATCA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCA
12256860 GCCTCGCGGT
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
46 29 0.47
47 1 0.02
48 32 0.52
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAACATCGAGATACGGAA
Found at i:12256895 original size:94 final size:91
Alignment explanation
Indices: 12256734--12256996 Score: 244
Period size: 94 Copynumber: 2.8 Consensus size: 91
12256724 GTGATTGTGT
* * ** * ** *
12256734 GCTAGTGTAAGACATGTCTGGGACATGCATTAGCCTCGAGATATTTAAGCCAGTGTAGGACATGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATA-GAAAGCTAGTGTAAAACCTGT
12256799 CTAGAACAT-GCATCAACATTGAGTCG-GGA
65 CTAG-ACATGGCATCAAC-TT--GTCGTGGA
* *
12256828 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGGTAGACAAGCTAATGTAAAACCTGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGA-AAGCTAGTGTAAAACCTGT
* * * *
12256893 CTAGGCATGGCGTCAGCTTGTCGTGTA
65 CTAGACATGGCATCAACTTGTCGTGGA
* * * *
12256920 TC-AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGCTATATGAAAGCTAGTGTAAAACCAT
1 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGCGATA-GAAAGCTAGTGTAAAACC-T
*
12256984 GTCTGGGACATGG
63 GTCT-AGACATGG
12256997 TTTCGGCATC
Statistics
Matches: 140, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
91 26 0.19
92 32 0.23
93 12 0.09
94 70 0.50
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (91 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGAAAGCTAGTGTAAAACCTGTC
TAGACATGGCATCAACTTGTCGTGGA
Found at i:12260227 original size:45 final size:45
Alignment explanation
Indices: 12260163--12260253 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
12260153 CCTGAAAGAA
12260163 TACTCATTAAGGATTTCAGTCATATAAATTTTAACTCATAATTAT
1 TACTCATTAAGGATTTCAGTCATATAAATTTTAACTCATAATTAT
12260208 TACTCATTAAGGATTTCAGTCATATAAATTTTAACTCATAATTAT
1 TACTCATTAAGGATTTCAGTCATATAAATTTTAACTCATAATTAT
12260253 T
1 T
12260254 TTTGTACAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (45 bp):
TACTCATTAAGGATTTCAGTCATATAAATTTTAACTCATAATTAT
Found at i:12263933 original size:15 final size:15
Alignment explanation
Indices: 12263915--12263958 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
12263905 GAAGCCCAGA
12263915 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
12263930 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
*
12263945 ATAAGGAAATCCAA
1 ATAAAGAAATCCAA
12263959 TTTACAGCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.57, C:0.14, G:0.14, T:0.16
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:12269460 original size:79 final size:79
Alignment explanation
Indices: 12269368--12269525 Score: 289
Period size: 79 Copynumber: 2.0 Consensus size: 79
12269358 GGATATTAAA
*
12269368 ATTCCATGATATCCAACATTCATAAAGACATGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
1 ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
12269433 TATACTAGGAGAAT
66 TATACTAGGAGAAT
*
12269447 ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGTAGACATTTGGG
1 ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
*
12269512 TATACTAGTAGAAT
66 TATACTAGGAGAAT
12269526 TTACACATCT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
79 76 1.00
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (79 bp):
ATTCCATGATATCCAACATTCATAAAGACACGAAATCCTATGAATCTGGTGAGGAGACATTTGGG
TATACTAGGAGAAT
Found at i:12288664 original size:28 final size:28
Alignment explanation
Indices: 12288599--12288749 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
12288589 GAGATTGGCG
* * * *
12288599 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
12288628 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
12288656 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
12288684 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
12288712 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
12288739 CTGAGTGTGCG
1 CTAAGTGTGCG
12288750 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.21
28 74 0.65
29 15 0.13
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:12296690 original size:28 final size:28
Alignment explanation
Indices: 12296625--12296775 Score: 214
Period size: 28 Copynumber: 5.4 Consensus size: 28
12296615 GAGATTGGCG
* * * *
12296625 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
12296654 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
* *
12296682 CTAAGTGTGCGAGCTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
12296710 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
12296738 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
12296765 CTGAGTGTGCG
1 CTAAGTGTGCG
12296776 GACTTAATAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.21
28 74 0.65
29 15 0.13
ACGTcount: A:0.26, C:0.13, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:12302073 original size:94 final size:94
Alignment explanation
Indices: 12301912--12302084 Score: 267
Period size: 94 Copynumber: 1.8 Consensus size: 94
12301902 ATTGTATGCT
* **
12301912 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAGTGTAAGACATGTCTGGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCTGGG
*
12301977 ACATGCATCGGCCTTGAGATATTTAAGCC
66 ACATGCATCAGCCTTGAGATATTTAAGCC
* * *
12302006 AGTGTAAGACATGTTTGGGACATGCATCAG-CATTAAGACAAGAGCTAGTGTAAGACATGTCTGG
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCA-CAAGACAAGAGCCAGTGTAAGACATGTCTGG
12302070 GACATGCATCAGCCT
65 GACATGCATCAGCCT
12302085 CGCGATAGAC
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
93 2 0.03
94 69 0.97
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (94 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCTGGG
ACATGCATCAGCCTTGAGATATTTAAGCC
Found at i:12302080 original size:46 final size:46
Alignment explanation
Indices: 12301912--12302082 Score: 211
Period size: 46 Copynumber: 3.7 Consensus size: 46
12301902 ATTGTATGCT
* * *
12301912 AGTGTAAGACATGTCTGGGACATGCATCGGCCA-CAAGATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAG-CATTAAGATAAGAGCC
* * *
12301958 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATTTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGATA---AGAGCC
* * *
12302006 AGTGTAAGACATGTTTGGGACATGCATCAGCATTAAGACAAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGATAAGAGCC
12302052 AGTGTAAGACATGTCTGGGACATGCATCAGC
1 AGTGTAAGACATGTCTGGGACATGCATCAGC
12302083 CTCGCGATAG
Statistics
Matches: 109, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
45 2 0.02
46 67 0.61
48 39 0.36
49 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCATTAAGATAAGAGCC
Found at i:12302106 original size:94 final size:94
Alignment explanation
Indices: 12301909--12302115 Score: 263
Period size: 94 Copynumber: 2.2 Consensus size: 94
12301899 GTGATTGTAT
* **
12301909 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGATGAGAGCCAGTGTAAGACATGTCT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCT
* * ***
12301974 GGGACATGCATCGGCCTTGAGATATTTAA
66 GGGACATGCATCAGCCTCGAGATAGACAA
* * * *
12302003 GCCAGTGTAAGACATGTTTGGGACATGCATCAG-CATTAAGACAAGAGCTAGTGTAAGACATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCA-CAAGACAAGAGCCAGTGTAAGACATGTC
*
12302067 TGGGACATGCATCAGCCTCGCGATAGACAA
65 TGGGACATGCATCAGCCTCGAGATAGACAA
* *
12302097 GCTAATGTAAGACCTGTCT
1 GCTAGTGTAAGACATGTCT
12302116 AGACATGGCG
Statistics
Matches: 95, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
93 2 0.02
94 93 0.98
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (94 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCACAAGACAAGAGCCAGTGTAAGACATGTCT
GGGACATGCATCAGCCTCGAGATAGACAA
Found at i:12302115 original size:48 final size:48
Alignment explanation
Indices: 12301909--12302115 Score: 206
Period size: 46 Copynumber: 4.4 Consensus size: 48
12301899 GTGATTGTAT
* * * *
12301909 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCCACAAGAT-GA-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
* * * ***
12301955 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATATTTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
* * * ** * *
12302003 GCCAGTGTAAGACATGTTTGGGACATGCATCAGCATTAAGACA-A-GA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
*
12302049 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCGATAGACAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
* *
12302097 GCTAATGTAAGACCTGTCT
1 GCTAGTGTAAGACATGTCT
12302116 AGACATGGCG
Statistics
Matches: 133, Mismatches: 24, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
46 75 0.56
47 1 0.01
48 57 0.43
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (48 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATAGACAA
Found at i:12302198 original size:49 final size:49
Alignment explanation
Indices: 12301912--12302267 Score: 201
Period size: 46 Copynumber: 7.5 Consensus size: 49
12301902 ATTGTATGCT
* ** * *
12301912 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCAC-A-AGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAAAGCC
* ** * * * **
12301958 AGTGTAAGACATGTCTGGGACAT-GCATCGGCCTTGAGATATTTAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAAAGCC
* * * * * * *
12302006 AGTGTAAGACATGTTTGGGACAT-GCATCAGCAT-TA-AGA-CAAGAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAA-AGCC
* * * *
12302052 AGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGCGATAGA--CAAGCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCAACCT--CGATAGATGAAAGCC
* * * * * * *
12302100 AATGTAAGACCTGTCT-AGACATGGCGTCAGA--TTG-TCG-TG--TGTC
1 AGTGTAAGACCTGTCTGGGACATGGCATCA-ACCTCGATAGATGAAAGCC
* *
12302143 AGTGTAAGACCTGTCTAGGACATGGCATCAACAC-CGATAGATGAGAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAAC-CTCGATAGATGAAAGCC
* *
12302192 AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGCTATATGAAAGCC
1 AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAAAGCC
*
12302241 AGTGTAAGACCATATCTGGGACATGGC
1 AGTGTAAGACC-TGTCTGGGACATGGC
12302268 GTCGGCATCT
Statistics
Matches: 249, Mismatches: 40, Indels: 38
0.76 0.12 0.12
Matches are distributed among these distances:
43 17 0.07
44 13 0.05
45 3 0.01
46 70 0.28
47 10 0.04
48 61 0.24
49 58 0.23
50 17 0.07
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCAACCTCGATAGATGAAAGCC
Found at i:12304444 original size:34 final size:34
Alignment explanation
Indices: 12304397--12304514 Score: 148
Period size: 34 Copynumber: 3.5 Consensus size: 34
12304387 ACATGGTTAA
* * *
12304397 CCATCTAGCACACCAGATGCTCTTATGAGCCAAT
1 CCATCCAGCACACCAAATGCTCTTATGAGCTAAT
* * * *
12304431 CCATCTAGGACACCAAATGCTCATATGAGCTAAA
1 CCATCCAGCACACCAAATGCTCTTATGAGCTAAT
*
12304465 CTATCCAGCACACCAAATGCT-TATATGAGCTAAT
1 CCATCCAGCACACCAAATGCTCT-TATGAGCTAAT
12304499 CCATCCAGCACACCAA
1 CCATCCAGCACACCAA
12304515 GTAACACTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.35, C:0.31, G:0.13, T:0.21
Consensus pattern (34 bp):
CCATCCAGCACACCAAATGCTCTTATGAGCTAAT
Found at i:12311855 original size:13 final size:13
Alignment explanation
Indices: 12311837--12311862 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12311827 GGTTGTTTAT
12311837 TAAACTAATTAAC
1 TAAACTAATTAAC
12311850 TAAACTAATTAAC
1 TAAACTAATTAAC
12311863 CAATTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12319937 original size:13 final size:13
Alignment explanation
Indices: 12319919--12319947 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
12319909 GGTTGTTTCT
12319919 TAAACTAATTAAC
1 TAAACTAATTAAC
12319932 TAAACTAATTAAC
1 TAAACTAATTAAC
12319945 TAA
1 TAA
12319948 TTAAACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAACTAATTAAC
Found at i:12325164 original size:26 final size:25
Alignment explanation
Indices: 12325112--12325275 Score: 211
Period size: 26 Copynumber: 6.2 Consensus size: 25
12325102 GGGACGAAAT
12325112 AATGACCGAAATACCTCCATAGGGTAA
1 AATGA-CGAAATACC-CCATAGGGTAA
12325139 AATGATCGAAATACCCCATAGGGTAA
1 AATGA-CGAAATACCCCATAGGGTAA
12325165 AATGACCGAAATACCCCATAGGGTAA
1 AATGA-CGAAATACCCCATAGGGTAA
* *
12325191 AATGACTGAAAAACCCCATATGGTAA
1 AATGAC-GAAATACCCCATAGGGTAA
12325217 AATGACTGAAATACCCCCATAGGGTAA
1 AATGAC-GAAATA-CCCCATAGGGTAA
* *
12325244 AATGACTATAATACCCCTATAAGGTAA
1 AATGACGA-AATACCCC-ATAGGGTAA
12325271 AATGA
1 AATGA
12325276 TTATTTTTCC
Statistics
Matches: 125, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
25 1 0.01
26 75 0.60
27 49 0.39
ACGTcount: A:0.43, C:0.20, G:0.17, T:0.20
Consensus pattern (25 bp):
AATGACGAAATACCCCATAGGGTAA
Found at i:12325298 original size:27 final size:25
Alignment explanation
Indices: 12325268--12325397 Score: 102
Period size: 27 Copynumber: 5.0 Consensus size: 25
12325258 CCCTATAAGG
* *
12325268 TAAAATGATTATTTTTCCCTTATGTGT
1 TAAAATGA-CATTTTGCCC-TATGTGT
*
12325295 TAAATTGACAGTTTTGCCCT-TGTGT
1 TAAAATGACA-TTTTGCCCTATGTGT
* * *
12325320 TAAAATGACGATTTTTCCCTTATATGA
1 TAAAATGAC-ATTTTGCCC-TATGTGT
12325347 TAAAATGACAGTTTTGCCCT-TGTGT
1 TAAAATGACA-TTTTGCCCTATGTGT
**
12325372 TAAAATGATTGTTTTGCCCCTATGTG
1 TAAAATGA-CATTTTG-CCCTATGTG
12325398 ACGTATGTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
25 36 0.43
26 10 0.12
27 37 0.45
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (25 bp):
TAAAATGACATTTTGCCCTATGTGT
Found at i:12325328 original size:25 final size:25
Alignment explanation
Indices: 12325290--12325390 Score: 114
Period size: 25 Copynumber: 4.0 Consensus size: 25
12325280 TTTTCCCTTA
*
12325290 TGTGTTAAATTGACAGTTTTGCCCT
1 TGTGTTAAAATGACAGTTTTGCCCT
*
12325315 TGTGTTAAAATGAC-GATTTTTCCCTT
1 TGTGTTAAAATGACAG-TTTTGCCC-T
* *
12325341 ATATGATAAAATGACAGTTTTGCCCT
1 -TGTGTTAAAATGACAGTTTTGCCCT
**
12325367 TGTGTTAAAATGATTGTTTTGCCC
1 TGTGTTAAAATGACAGTTTTGCCC
12325391 CTATGTGACG
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
24 1 0.02
25 40 0.63
26 2 0.03
27 19 0.30
28 1 0.02
ACGTcount: A:0.25, C:0.15, G:0.18, T:0.43
Consensus pattern (25 bp):
TGTGTTAAAATGACAGTTTTGCCCT
Found at i:12325356 original size:52 final size:52
Alignment explanation
Indices: 12325268--12325379 Score: 179
Period size: 52 Copynumber: 2.2 Consensus size: 52
12325258 CCCTATAAGG
** * * *
12325268 TAAAATGATTATTTTTCCCTTATGTGTTAAATTGACAGTTTTGCCCTTGTGT
1 TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
12325320 TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
1 TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
12325372 TAAAATGA
1 TAAAATGA
12325380 TTGTTTTGCC
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (52 bp):
TAAAATGACGATTTTTCCCTTATATGATAAAATGACAGTTTTGCCCTTGTGT
Found at i:12326901 original size:53 final size:53
Alignment explanation
Indices: 12326821--12326926 Score: 212
Period size: 53 Copynumber: 2.0 Consensus size: 53
12326811 TTTCCAATCT
12326821 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
1 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
12326874 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
1 CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
12326927 TATTGTTCTA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 53 1.00
ACGTcount: A:0.26, C:0.19, G:0.17, T:0.38
Consensus pattern (53 bp):
CTTAAGGCACCACATACGCATTTGGGTAGTTTTTATACCTAGTATTGTTCTAA
Found at i:12327733 original size:12 final size:14
Alignment explanation
Indices: 12327716--12327751 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 14
12327706 TTAGGTTTCC
12327716 AAAAATGGAAA-T-
1 AAAAATGGAAATTA
12327728 AAAAAT-GAAATTA
1 AAAAATGGAAATTA
12327741 AAAAATGGAAA
1 AAAAATGGAAA
12327752 CTTGCAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 4 0.19
12 7 0.33
13 6 0.29
14 4 0.19
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (14 bp):
AAAAATGGAAATTA
Found at i:12327928 original size:26 final size:25
Alignment explanation
Indices: 12327892--12327975 Score: 105
Period size: 26 Copynumber: 3.2 Consensus size: 25
12327882 ATGAATTTTC
*
12327892 TCAAAACTTTATCGGGGCTAAAATCG
1 TCAAAATTTTATCGGGG-TAAAATCG
*
12327918 TCAAAATTTTATTGGGGGTAAAATCG
1 TCAAAATTTTA-TCGGGGTAAAATCG
* *
12327944 TCAAAATTTTACCGAGGGTAAAATTG
1 TCAAAATTTTATCG-GGGTAAAATCG
12327970 TCAAAA
1 TCAAAA
12327976 AATTTATTGG
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
25 1 0.02
26 45 0.88
27 5 0.10
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (25 bp):
TCAAAATTTTATCGGGGTAAAATCG
Found at i:12327991 original size:26 final size:25
Alignment explanation
Indices: 12327892--12327991 Score: 101
Period size: 26 Copynumber: 3.8 Consensus size: 25
12327882 ATGAATTTTC
* *
12327892 TCAAAACTTTATCGGGGCTAAAATCG
1 TCAAAATTTTATTGGGG-TAAAATCG
12327918 TCAAAATTTTATTGGGGGTAAAATCG
1 TCAAAATTTTATT-GGGGTAAAATCG
** *
12327944 TCAAAATTTTACCGAGGGTAAAATTG
1 TCAAAATTTTATTG-GGGTAAAATCG
* *
12327970 TCAAAAAATTTATTGGGTTAAA
1 TC-AAAATTTTATTGGGGTAAA
12327992 TTTGGGATGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
25 1 0.02
26 48 0.77
27 13 0.21
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (25 bp):
TCAAAATTTTATTGGGGTAAAATCG
Found at i:12338769 original size:28 final size:28
Alignment explanation
Indices: 12338737--12338792 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
12338727 ATTTAAGGAT
12338737 TAAAT-TGAGAAA-TGTGAAAATTGTATGG
1 TAAATATGAGAAATTGTG-AAA-TGTATGG
*
12338765 TAAATATGTGAAATTGTGAAATGTATGG
1 TAAATATGAGAAATTGTGAAATGTATGG
12338793 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 12 0.48
29 9 0.36
30 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.25, T:0.34
Consensus pattern (28 bp):
TAAATATGAGAAATTGTGAAATGTATGG
Found at i:12345323 original size:13 final size:13
Alignment explanation
Indices: 12345301--12345333 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12345291 AAGGGTTTGT
12345301 TTAT-TAAACTAA
1 TTATCTAAACTAA
12345313 TTATCTAAACTAA
1 TTATCTAAACTAA
*
12345326 TTAACTAA
1 TTATCTAA
12345334 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:12348255 original size:22 final size:23
Alignment explanation
Indices: 12348228--12348328 Score: 104
Period size: 22 Copynumber: 4.5 Consensus size: 23
12348218 TATGTCTTTC
*
12348228 AAAATAAGAA-AATTGAAAAATA
1 AAAATAAGAATAAATGAAAAATA
* *
12348250 AAAATAAAAATCAAAAGAAAAATA
1 AAAATAAGAAT-AAATGAAAAATA
*
12348274 AGAATAAGAATAAA--ATAAAATA
1 AAAATAAGAATAAATGA-AAAATA
*
12348296 AGAATAAGAATAAAT-AAAAATA
1 AAAATAAGAATAAATGAAAAATA
12348318 AAAATAA-AATA
1 AAAATAAGAATA
12348329 GGAGGATTCG
Statistics
Matches: 69, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
21 5 0.07
22 41 0.59
23 4 0.06
24 19 0.28
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (23 bp):
AAAATAAGAATAAATGAAAAATA
Found at i:12348265 original size:7 final size:6
Alignment explanation
Indices: 12348243--12348326 Score: 86
Period size: 6 Copynumber: 14.7 Consensus size: 6
12348233 AAGAAAATTG
* * * *
12348243 AAAAAT AAAAAT AAAAAT CAAAAG AAAAAT AAGAAT AAGAAT -AAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* *
12348290 -AAAAT AAGAAT AAGAAT --AAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
12348327 TAGGAGGATT
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
4 3 0.04
5 9 0.13
6 55 0.82
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:12348297 original size:16 final size:16
Alignment explanation
Indices: 12348268--12348328 Score: 79
Period size: 16 Copynumber: 3.7 Consensus size: 16
12348258 AATCAAAAGA
12348268 AAAATAAGAATAAGAAT
1 AAAATAA-AATAAGAAT
12348285 AAAATAAAATAAGAAT
1 AAAATAAAATAAGAAT
*
12348301 AAGAAT-AAATAAAAAT
1 AA-AATAAAATAAGAAT
12348317 AAAAATAAAATA
1 -AAAATAAAATA
12348329 GGAGGATTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 23 0.57
17 17 0.43
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (16 bp):
AAAATAAAATAAGAAT
Found at i:12353227 original size:9 final size:9
Alignment explanation
Indices: 12353213--12353240 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
12353203 AAATCAGAAT
12353213 ATAAAAATA
1 ATAAAAATA
12353222 ATAAAAATA
1 ATAAAAATA
12353231 ATAAAAATA
1 ATAAAAATA
12353240 A
1 A
12353241 CTAACTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAAAAATA
Found at i:12353759 original size:27 final size:26
Alignment explanation
Indices: 12353712--12353762 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
12353702 CGAGGCTGCT
*
12353712 AGATATTGTGACGAAGTCACCAGAAC
1 AGATATTGTGACGAAGCCACCAGAAC
* *
12353738 AGATATATGTGGCGACGCCACCAGA
1 AGATAT-TGTGACGAAGCCACCAGA
12353763 TTGCAGCGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.18
Consensus pattern (26 bp):
AGATATTGTGACGAAGCCACCAGAAC
Found at i:12354121 original size:28 final size:28
Alignment explanation
Indices: 12354090--12354144 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
12354080 ATGCACACTC
12354090 TGCACTCTAATCATCCAAATACACCATT
1 TGCACTCTAATCATCCAAATACACCATT
*
12354118 TGCACTCTAATCATCCAAATGCACCAT
1 TGCACTCTAATCATCCAAATACACCAT
12354145 ATTCATTAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.35, C:0.33, G:0.05, T:0.27
Consensus pattern (28 bp):
TGCACTCTAATCATCCAAATACACCATT
Found at i:12356158 original size:13 final size:13
Alignment explanation
Indices: 12356136--12356168 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
12356126 AAGGGTTTGT
12356136 TTAT-TAAACTAA
1 TTATCTAAACTAA
12356148 TTATCTAAACTAA
1 TTATCTAAACTAA
*
12356161 TTAACTAA
1 TTATCTAA
12356169 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:12361831 original size:27 final size:26
Alignment explanation
Indices: 12361796--12361906 Score: 141
Period size: 27 Copynumber: 4.1 Consensus size: 26
12361786 AGCATGGTTG
* *
12361796 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
12361822 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
*
12361850 CCAGAACAAATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
12361877 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
12361904 CCA
1 CCA
12361907 AGACTCTTCC
Statistics
Matches: 75, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 52 0.69
28 17 0.23
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:12361890 original size:54 final size:54
Alignment explanation
Indices: 12361796--12361906 Score: 161
Period size: 54 Copynumber: 2.1 Consensus size: 54
12361786 AGCATGGTTG
* *
12361796 CCAGAACAGATAATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAAATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
* * *
12361850 CCAGAACAAATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCA
1 CCAGAACAAATA-ATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
12361904 CCA
1 CCA
12361907 AGACTCTTCC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAAATAATGTGACAGAGCCACCAGATACAGATAATCGTGGCAGAGCCA
Found at i:12367098 original size:56 final size:57
Alignment explanation
Indices: 12366970--12367123 Score: 220
Period size: 56 Copynumber: 2.7 Consensus size: 57
12366960 ATGTATATGA
* * * * * *
12366970 GGCATTGATATGTGATTCCGATATATGAGTGTGAGTAAGACCACATTTTTATATGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAACAGTTTTATATGTT
*
12367027 GGCATCGATATGTGACTCCGATATATGTGTACGAGTAAGACAAC-GTTTTATATGTT
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAACAGTTTTATATGTT
* *
12367083 GGCATCGATATGTGACTCTGATATATTTGTGCGAGTAAGAC
1 GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGAC
12367124 CTTGCCTGGG
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
56 49 0.56
57 38 0.44
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (57 bp):
GGCATCGATATGTGACTCCGATATATGTGTGCGAGTAAGACAACAGTTTTATATGTT
Found at i:12371203 original size:26 final size:26
Alignment explanation
Indices: 12371173--12371254 Score: 146
Period size: 26 Copynumber: 3.2 Consensus size: 26
12371163 TGAAATTCCC
12371173 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12371199 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
12371225 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
12371251 ATCA
1 ATCA
12371255 ATTTGTATCA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:12376035 original size:41 final size:41
Alignment explanation
Indices: 12375979--12376198 Score: 289
Period size: 41 Copynumber: 5.4 Consensus size: 41
12375969 ATTTTACTCA
* *
12375979 AAAATGCCGCT-AAAACCAAAGCATTAGCGGCGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
* * * **
12376019 AAAAGGACGCTAAAAACCAGAGCATTAGCGGTGCTTTCCGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
* *
12376060 AAAACGCCGCAAAAAACCAGAGCATTAGCGACGCTTTAGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
* * *
12376101 AAAACGCCGCTAAAAACTAGAGCATTAGCGGCGGTTTTGGT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
* ***
12376142 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGGTTTTTCT
1 AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
12376183 AAAACGCCGCTAAAAA
1 AAAACGCCGCTAAAAA
12376199 TCCCATAACC
Statistics
Matches: 158, Mismatches: 21, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
40 9 0.06
41 149 0.94
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.19
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCAGAGCATTAGCGGCGCTTTAGGT
Found at i:12376049 original size:82 final size:80
Alignment explanation
Indices: 12375948--12376198 Score: 247
Period size: 82 Copynumber: 3.1 Consensus size: 80
12375938 AAAACGCCAG
** * * *
12375948 TAAAAA-CAGAGCAACAGCGGCATTTTACTCAAAAATGCCGCTAAAACCAAAGCATTAGCGGCGC
1 TAAAAACCAGAGCATTAGCGGCGTTTT-CTC-AAAACGCCGCTAAAACCAGAGCATTAGCGGCGC
*
12376012 TTTAGGTAAAAGGACGC
64 TTTAGGTAAAACGACGC
* * * *
12376029 TAAAAACCAGAGCATTAGCGGTGCTTTC-CGTAAAACGCCGCAAAAAACCAGAGCATTAGCGACG
1 TAAAAACCAGAGCATTAGCGGCGTTTTCTC--AAAACGCCGC-TAAAACCAGAGCATTAGCGGCG
*
12376093 CTTTAGGTAAAACGCCGC
63 CTTTAGGTAAAACGACGC
* *
12376111 TAAAAACTAGAGCATTAGCGGCGGTTTTGGT-AAAACGCCGCTAAAAACCAGAGCATTAGCGGCG
1 TAAAAACCAGAGCATTAGCGGC-GTTTT-CTCAAAACGCCGCT-AAAACCAGAGCATTAGCGGCG
* *** *
12376175 GTTTTTCTAAAACGCCGC
63 CTTTAGGTAAAACGACGC
12376193 TAAAAA
1 TAAAAA
12376199 TCCCATAACC
Statistics
Matches: 141, Mismatches: 22, Indels: 13
0.80 0.12 0.07
Matches are distributed among these distances:
80 1 0.01
81 16 0.11
82 120 0.85
83 4 0.03
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (80 bp):
TAAAAACCAGAGCATTAGCGGCGTTTTCTCAAAACGCCGCTAAAACCAGAGCATTAGCGGCGCTT
TAGGTAAAACGACGC
Found at i:12376364 original size:14 final size:14
Alignment explanation
Indices: 12376342--12376381 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
12376332 TTAATTATCA
* *
12376342 TTATAGTTTAAGGT
1 TTATGGTTTAAGAT
12376356 TTATGGTTTAAGAT
1 TTATGGTTTAAGAT
*
12376370 ATATGGTTTAAG
1 TTATGGTTTAAG
12376382 CAGGTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTATGGTTTAAGAT
Found at i:12376426 original size:25 final size:26
Alignment explanation
Indices: 12376396--12376444 Score: 75
Period size: 25 Copynumber: 1.9 Consensus size: 26
12376386 TTTAATTATA
12376396 AGTTAACTA-TAGTTT-AAGGTTTAGG
1 AGTTAACTAGTA-TTTGAAGGTTTAGG
12376421 AGTTAACTAGTATTTGAAGGTTTA
1 AGTTAACTAGTATTTGAAGGTTTA
12376445 TGATGAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.33, C:0.04, G:0.22, T:0.41
Consensus pattern (26 bp):
AGTTAACTAGTATTTGAAGGTTTAGG
Found at i:12377277 original size:10 final size:10
Alignment explanation
Indices: 12377259--12377312 Score: 54
Period size: 10 Copynumber: 4.9 Consensus size: 10
12377249 AGATAAATGT
12377259 ATATAATATAA
1 ATAT-ATATAA
12377270 ATATATATAAA
1 ATATATAT-AA
*
12377281 ATATTATTTTAAA
1 ATA-TA-TAT-AA
12377294 ATATATATAA
1 ATATATATAA
12377304 ATATATATA
1 ATATATATA
12377313 TGAAAAGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
10 15 0.39
11 11 0.29
12 4 0.11
13 8 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATATATATAA
Found at i:12377318 original size:24 final size:23
Alignment explanation
Indices: 12377251--12377318 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 23
12377241 AATTTAGAAG
*
12377251 ATAAATGTATATAATATAAATATAT
1 ATAAATATATAT-ATA-AAATATAT
*
12377276 ATAAA-ATATTATTTTAAAATATAT
1 ATAAATATA-TA-TATAAAATATAT
12377300 ATAAATATATATATGAAAA
1 ATAAATATATATAT-AAAA
12377319 GTGGTTTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
23 2 0.06
24 21 0.58
25 12 0.33
26 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (23 bp):
ATAAATATATATATAAAATATAT
Found at i:12378895 original size:18 final size:17
Alignment explanation
Indices: 12378874--12378916 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 17
12378864 ATCTTAATGA
12378874 TGATGATGATGTTGATAC
1 TGATGATGATGTTGAT-C
*
12378892 TGATGTTGATGTTGATC
1 TGATGATGATGTTGATC
12378909 TCGATGAT
1 T-GATGAT
12378917 TATACCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.09
18 20 0.91
ACGTcount: A:0.23, C:0.07, G:0.28, T:0.42
Consensus pattern (17 bp):
TGATGATGATGTTGATC
Found at i:12379994 original size:23 final size:23
Alignment explanation
Indices: 12379968--12380011 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
12379958 CTTGGTCCTA
12379968 TTTCTCCTGTTAATGGTATACTG
1 TTTCTCCTGTTAATGGTATACTG
*
12379991 TTTCTCCTGTTAATGTTATAC
1 TTTCTCCTGTTAATGGTATAC
12380012 CAAATTGCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.14, T:0.50
Consensus pattern (23 bp):
TTTCTCCTGTTAATGGTATACTG
Found at i:12382865 original size:467 final size:467
Alignment explanation
Indices: 12381992--12383270 Score: 2409
Period size: 467 Copynumber: 2.7 Consensus size: 467
12381982 TTCTCTCCAA
*
12381992 CCTTATTTTAAATATTTTAAATATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
12382057 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
*
12382122 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTCATATAACCTTAATTTATTTCCA
131 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
12382187 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
196 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
*
12382252 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTATATATCTTTAAAAGTTATAACTAATT
261 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
12382317 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
326 TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
*
12382382 GTTCAACTTAAGTATTATTTGACTCAACTTAATTATGAATTAATTTTATTACCATATATGTAGCT
391 GTTCAACTTAAGTATTATTTGACTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
12382447 TGCTTGTCCATT
456 TGCTTGTCCATT
12382459 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
12382524 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
*
12382589 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTAAATATTTATATAACCTTAATTTATTTCCA
131 ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
12382654 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
196 ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
*
12382719 TATATTAAACATATTTGATTTTAATATTTAATATTTTTAAAT-TCCTTTAAAAGTTATAACTAAT
261 TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATAT-CTTTAAAAGTTATAACTAAT
12382783 TTTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTT
325 TTTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTT
*
12382848 GGTTCAACTTAAGTATTATTTGATTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGC
390 GGTTCAACTTAAGTATTATTTGACTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGC
12382913 TTGCTTGTCCATT
455 TTGCTTGTCCATT
12382926 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
1 CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
* *
12382991 AGAGCTGCAAGATATAATGGATCCTCCCTGGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
66 CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
* *
12383056 ATTCAAAAAGAATTAAAAAAATTTCTAGT-GCTATTGAATATTTATATAACCTTAATTTATTTCC
131 ATTCAAAAAGAATTGAAAAAAGTTCTA-TCGCTATTGAATATTTATATAACCTTAATTTATTTCC
12383120 AATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTG
195 AATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTG
*
12383185 TTATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATGTCTTTAAAAGTTATAACTAAT
260 TTATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAAT
*
12383250 TTTTATTAAAATAGTATTAAT
325 TTTTATCAAAATAGTATTAAT
12383271 ATTGATCATT
Statistics
Matches: 795, Mismatches: 14, Indels: 6
0.98 0.02 0.01
Matches are distributed among these distances:
466 1 0.00
467 792 1.00
468 2 0.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (467 bp):
CCTTATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGACGGGTTGCCTTATAT
CGAGCTGCAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAA
ATTCAAAAAGAATTGAAAAAAGTTCTATCGCTATTGAATATTTATATAACCTTAATTTATTTCCA
ATTTACTTATAAAAATTAAACTACGATTCTTTCTTGATATTATTATATTCAAATTACTATTTTGT
TATATTAAACATGTTTGATTTTAATATTTAATATTTTTAAATATCTTTAAAAGTTATAACTAATT
TTTATCAAAATAGTATTAATTATTATTTGAAGTATGAATAAGTATGAATAAGTTTTTATATTTTG
GTTCAACTTAAGTATTATTTGACTCAACTTAAGTATGAATTAATTTTATTACCATATATGTAGCT
TGCTTGTCCATT
Found at i:12382874 original size:21 final size:21
Alignment explanation
Indices: 12382845--12382884 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
12382835 GTTTTTATAT
*
12382845 TTTGGTTCAACTTAAGTATTA
1 TTTGATTCAACTTAAGTATTA
12382866 TTTGATTCAACTTAAGTAT
1 TTTGATTCAACTTAAGTAT
12382885 GAATTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.47
Consensus pattern (21 bp):
TTTGATTCAACTTAAGTATTA
Found at i:12388909 original size:21 final size:21
Alignment explanation
Indices: 12388883--12388927 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
12388873 ACTTAGAGCA
*
12388883 GAGGCAGCATCGAGGGAGGCG
1 GAGGCAGCAGCGAGGGAGGCG
12388904 GAGGCAGCAGCGAGGGAGGCG
1 GAGGCAGCAGCGAGGGAGGCG
12388925 GAG
1 GAG
12388928 CAGAACAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.18, G:0.56, T:0.02
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCG
Found at i:12389289 original size:43 final size:43
Alignment explanation
Indices: 12389226--12389428 Score: 239
Period size: 43 Copynumber: 4.7 Consensus size: 43
12389216 CTGGGCAAAT
*
12389226 TAGCGGCATTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
* * * *
12389269 TAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAGGTCCTGGTC-A
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
* * *
12389311 TTAGCGGCCTTTTTTTATAAAAGCGCCACTAAAAGTACAAGTCTA
1 -TAGCGG-CGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
* * * * * *
12389356 GAGCGGCGTTTTTTAAAAAAACGCCGCTAAAGGTCCAGGTCTT
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
*
12389399 TAGCGGCG-TTTTTATAAGAGCGCCGCTAAA
1 TAGCGGCGTTTTTTATAAAAGCGCCGCTAAA
12389429 GGTCAACGCC
Statistics
Matches: 132, Mismatches: 25, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
42 20 0.15
43 78 0.59
44 33 0.25
45 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (43 bp):
TAGCGGCGTTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTA
Found at i:12389369 original size:87 final size:85
Alignment explanation
Indices: 12389224--12389428 Score: 311
Period size: 87 Copynumber: 2.4 Consensus size: 85
12389214 AACTGGGCAA
* *
12389224 ATTAGCGGCATTTTTTATAAAAGCGCCGCTAAAAGTACAGGTCTATAGCGGCGTTTTTTAAAAAA
1 ATTAGCGGC-TTTTTTATAAAAGCGCCGCTAAAAGTACAAGTCTAGAGCGGCGTTTTTTAAAAAA
* *
12389289 GCGCCGCTAAAGGTCCTGGTC
65 ACGCCGCTAAAGGTCCAGGTC
*
12389310 ATTAGCGGCCTTTTTTTATAAAAGCGCCACTAAAAGTACAAGTCTAGAGCGGCGTTTTTTAAAAA
1 ATTAGCGG-C-TTTTTTATAAAAGCGCCGCTAAAAGTACAAGTCTAGAGCGGCGTTTTTTAAAAA
12389375 AACGCCGCTAAAGGTCCAGGTC
64 AACGCCGCTAAAGGTCCAGGTC
* * *
12389397 TTTAGCGGCGTTTTTATAAGAGCGCCGCTAAA
1 ATTAGCGGCTTTTTTATAAAAGCGCCGCTAAA
12389429 GGTCAACGCC
Statistics
Matches: 108, Mismatches: 10, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
85 20 0.19
86 9 0.08
87 79 0.73
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (85 bp):
ATTAGCGGCTTTTTTATAAAAGCGCCGCTAAAAGTACAAGTCTAGAGCGGCGTTTTTTAAAAAAA
CGCCGCTAAAGGTCCAGGTC
Found at i:12400991 original size:77 final size:76
Alignment explanation
Indices: 12400864--12401011 Score: 208
Period size: 77 Copynumber: 1.9 Consensus size: 76
12400854 AAACTAGGAT
* * *
12400864 TATTCCCTTATTAATAGAAAAGGCAAATGAAAAGTTAAAAAAAAGGAATTATATT-TTTTTACAA
1 TATTCCCTTATTAATAGAAAAGGCAAAGGAAAAGTTAAAAAAAAGAAATTATATTCTTTCT--AA
12400928 AAGAATATAAGAC
64 AAGAATATAAGAC
* * * *
12400941 TATTCCCTTATTAATAGAGAAGGCAAAGGGAAAGTTAGAAAAAATAAATTATATTCTTTCTAAAA
1 TATTCCCTTATTAATAGAAAAGGCAAAGGAAAAGTTAAAAAAAAGAAATTATATTCTTTCTAAAA
12401006 GAATAT
66 GAATAT
12401012 TAATTTCCAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
76 10 0.16
77 49 0.78
78 4 0.06
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (76 bp):
TATTCCCTTATTAATAGAAAAGGCAAAGGAAAAGTTAAAAAAAAGAAATTATATTCTTTCTAAAA
GAATATAAGAC
Found at i:12413562 original size:22 final size:23
Alignment explanation
Indices: 12413472--12413580 Score: 84
Period size: 23 Copynumber: 4.7 Consensus size: 23
12413462 CCAATATATT
* *
12413472 AGCTCG-TAAGAGCTTACTGTTGTC
1 AGCTCGAT-AGAGCTTACCGAT-TC
*
12413496 AGCTC-ATTAGAGCTTACCGTTTC
1 AGCTCGA-TAGAGCTTACCGATTC
*
12413519 AGCTCG-TATGAGCTT-CCTATTC
1 AGCTCGATA-GAGCTTACCGATTC
*
12413541 AACTCGATAGAGCTTACC-ATTC
1 AGCTCGATAGAGCTTACCGATTC
*
12413563 TAGCTCAATAGAGCTTAC
1 -AGCTCGATAGAGCTTAC
12413581 TGTTCATCAG
Statistics
Matches: 72, Mismatches: 6, Indels: 15
0.77 0.06 0.16
Matches are distributed among these distances:
22 22 0.31
23 32 0.44
24 17 0.24
25 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (23 bp):
AGCTCGATAGAGCTTACCGATTC
Found at i:12420902 original size:23 final size:25
Alignment explanation
Indices: 12420870--12420919 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
12420860 ATTCTTATTT
12420870 AATTAAG-AAATATA-TACTTTAAA
1 AATTAAGAAAATATATTACTTTAAA
* *
12420893 AATTATGAAAATATATTATTTTAAA
1 AATTAAGAAAATATATTACTTTAAA
12420918 AA
1 AA
12420920 ATAAATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 6 0.26
24 7 0.30
25 10 0.43
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
AATTAAGAAAATATATTACTTTAAA
Found at i:12421939 original size:10 final size:10
Alignment explanation
Indices: 12421881--12421971 Score: 55
Period size: 10 Copynumber: 9.0 Consensus size: 10
12421871 ATTTTTTTTG
12421881 TAATTTTTAA
1 TAATTTTTAA
12421891 -AATTTATTAA
1 TAATTT-TTAA
* *
12421901 TCATTATTT-G
1 TAATT-TTTAA
12421911 TAATTTTT-A
1 TAATTTTTAA
* *
12421920 TAACTCTTAA
1 TAATTTTTAA
12421930 TAATTTTTAAA
1 TAATTTTT-AA
12421941 TAATTTTCT-A
1 TAATTTT-TAA
*
12421951 TAATTATGTAA
1 TAATT-TTTAA
*
12421962 TAATTGTTAA
1 TAATTTTTAA
12421972 AGAAACTACT
Statistics
Matches: 62, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
9 14 0.23
10 25 0.40
11 21 0.34
12 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.54
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:12421966 original size:32 final size:30
Alignment explanation
Indices: 12421911--12421972 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
12421901 TCATTATTTG
* *
12421911 TAATTTTTATAACTCTTAATAATTTTTAAA
1 TAATTTTTATAACTATTAATAATTGTTAAA
*
12421941 TAATTTTCTATAATTATGTAATAATTGTTAAA
1 TAATTTT-TATAACTAT-TAATAATTGTTAAA
12421973 GAAACTACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 7 0.26
32 13 0.48
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.52
Consensus pattern (30 bp):
TAATTTTTATAACTATTAATAATTGTTAAA
Found at i:12423444 original size:29 final size:28
Alignment explanation
Indices: 12423413--12423468 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 28
12423403 TTAGTATTTT
*
12423413 AAAT-AATATATTTTTTATTATAACTTTATA
1 AAATAAATA-ATTATTT-TTATAA-TTTATA
12423443 AAATAAATAATTATTTTTATAATTTA
1 AAATAAATAATTATTTTTATAATTTA
12423469 ATTTTTTACG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 6 0.25
30 10 0.42
31 4 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATAAATAATTATTTTTATAATTTATA
Found at i:12427681 original size:15 final size:15
Alignment explanation
Indices: 12427638--12427701 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 15
12427628 ATTCAAACTG
*
12427638 TATATGTGCGAACCC
1 TATATGTACGAACCC
* * *
12427653 TATATATGCAAACCC
1 TATATGTACGAACCC
* *
12427668 TATATGTATGAACCA
1 TATATGTACGAACCC
* *
12427683 TGTATGTGCGAACCC
1 TATATGTACGAACCC
12427698 TATA
1 TATA
12427702 AGTGTGACCT
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
15 37 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (15 bp):
TATATGTACGAACCC
Found at i:12427681 original size:30 final size:30
Alignment explanation
Indices: 12427638--12427701 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
12427628 ATTCAAACTG
* *
12427638 TATATGTGCGAACCCTATATATGCAAACCC
1 TATATGTACGAACCATATATATGCAAACCC
* * * *
12427668 TATATGTATGAACCATGTATGTGCGAACCC
1 TATATGTACGAACCATATATATGCAAACCC
12427698 TATA
1 TATA
12427702 AGTGTGACCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.30
Consensus pattern (30 bp):
TATATGTACGAACCATATATATGCAAACCC
Found at i:12432131 original size:21 final size:20
Alignment explanation
Indices: 12432094--12432133 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
12432084 GCCTAGAATG
*
12432094 TGAATTGAATTGAATTAAAC
1 TGAATTGAAATGAATTAAAC
*
12432114 TGAATATGAAATGGATTAAA
1 TGAAT-TGAAATGAATTAAA
12432134 TTGACGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (20 bp):
TGAATTGAAATGAATTAAAC
Found at i:12432471 original size:24 final size:25
Alignment explanation
Indices: 12432444--12432502 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
12432434 TAACTTGAAA
*
12432444 GAGCATCCTGTTATAAGCCCTCT-C
1 GAGCATCCTATTATAAGCCCTCTGC
* * * *
12432468 GAGCTTCCTATTATATGGCTTCTGC
1 GAGCATCCTATTATAAGCCCTCTGC
12432493 GAGCATCCTA
1 GAGCATCCTA
12432503 ATCAGTAGTG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
24 18 0.64
25 10 0.36
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (25 bp):
GAGCATCCTATTATAAGCCCTCTGC
Found at i:12444827 original size:19 final size:19
Alignment explanation
Indices: 12444792--12444852 Score: 70
Period size: 19 Copynumber: 3.3 Consensus size: 19
12444782 GTGGATAGGC
*
12444792 CGTGTGG-TCACACACGCT
1 CGTGTGGCTCAAACACGCT
* *
12444810 CGTTTGGTTCAAACACGCT
1 CGTGTGGCTCAAACACGCT
* *
12444829 CGTGTGGCTCAGACATGCT
1 CGTGTGGCTCAAACACGCT
12444848 CGTGT
1 CGTGT
12444853 CCTCAGCTCG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
18 6 0.17
19 30 0.83
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (19 bp):
CGTGTGGCTCAAACACGCT
Found at i:12454162 original size:13 final size:13
Alignment explanation
Indices: 12454144--12454174 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
12454134 AACATTTGAC
12454144 TTGTTCTTAATTA
1 TTGTTCTTAATTA
*
12454157 TTGTTCTTAATTC
1 TTGTTCTTAATTA
12454170 TTGTT
1 TTGTT
12454175 TTGATATTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (13 bp):
TTGTTCTTAATTA
Found at i:12455286 original size:48 final size:48
Alignment explanation
Indices: 12455232--12455607 Score: 443
Period size: 48 Copynumber: 7.9 Consensus size: 48
12455222 TACGAAGTCT
* * *
12455232 CATATCAGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * *
12455280 CTTATC-ATCACCGATGCCATGTCCCAAACATGGTCTTACACT-GCACA
1 CATATCAAT-GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* *
12455327 CATATCAATGCTGATGCCATGTCCCAAACATGGTCTTACACTGGCACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * * *
12455375 CAAATCAATGCCGATGCAATGTCCCACACATGGTCTTACACT-ACACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* ** *
12455422 CATGTCAACACCGATGCCATGTCCCAGACATGGTCTTACATTGGCACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
** **
12455470 CATATCAACACCGATGCCATGTCTTAGACATGGTCTTACACTGGCACA
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * ***
12455518 CATATCAACGCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTTT
1 CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
* * * * *
12455566 CATCTCGGACGCCAATGTCATGTCCCAGACATGGTCTTACAC
1 CATATC-AATGCCGATGCCATGTCCCAGACATGGTCTTACAC
12455608 GGGATCTCAT
Statistics
Matches: 286, Mismatches: 37, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
47 80 0.28
48 175 0.61
49 31 0.11
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.24
Consensus pattern (48 bp):
CATATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACA
Found at i:12455358 original size:95 final size:95
Alignment explanation
Indices: 12455232--12455562 Score: 448
Period size: 95 Copynumber: 3.5 Consensus size: 95
12455222 TACGAAGTCT
** * * *
12455232 CATATCAGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACTTATCATCACCGATGC
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
12455297 CATGTCCCAAACATGGTCTTACACTGCACA
66 CATGTCCCAAACATGGTCTTACACTGCACA
* * * * *
12455327 CATATCAATGCTGATGCCATGTCCCAAACATGGTCTTACACTGGCACACAAATCAAT-GCCGATG
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATC-ATCACCGATG
* * *
12455391 CAATGTCCCACACATGGTCTTACACTACACA
65 CCATGTCCCAAACATGGTCTTACACTGCACA
* * * *
12455422 CATGTCAACACCGATGCCATGTCCCAGACATGGTCTTACATTGGCACACATATCAACACCGATGC
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
** *
12455487 CATGTCTTAGACATGGTCTTACACTGGCACA
66 CATGTCCCAAACATGGTCTTACACT-GCACA
*
12455518 CATATCAACGCTGATGCCATGTCCCAGACATGGTCTTACACTGGC
1 CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGC
12455563 TTTCATCTCG
Statistics
Matches: 204, Mismatches: 29, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
94 1 0.00
95 156 0.76
96 47 0.23
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (95 bp):
CATATCAACGCCGATGCCATGTCCCAGACATGGTCTTACACTGGCACACATATCATCACCGATGC
CATGTCCCAAACATGGTCTTACACTGCACA
Found at i:12455410 original size:143 final size:143
Alignment explanation
Indices: 12455235--12455559 Score: 472
Period size: 143 Copynumber: 2.3 Consensus size: 143
12455225 GAAGTCTCAT
* * * *
12455235 ATCAGTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCGCACTTATCATCACCGATGCCAT
1 ATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTA-CACACATATCAACACCGATGCCAT
** *
12455300 GTCCCAAACATGGTCTTACACT-GCACACATATCAATGCTGATGCCATGTCCCAAACATGGTCTT
65 GTCCCAAACATGGTCTTACACTGGCACACATATCAACACCGATGCCATGTCCCAAACATGGTCTT
12455364 ACACTGGCACACAA
130 ACACTGGCACACAA
* * *
12455378 ATCAATGCCGATGCAATGTCCCACACATGGTCTTACACTACACACATGTCAACACCGATGCCATG
1 ATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTACACACATATCAACACCGATGCCATG
* * ** *
12455443 TCCCAGACATGGTCTTACATTGGCACACATATCAACACCGATGCCATGTCTTAGACATGGTCTTA
66 TCCCAAACATGGTCTTACACTGGCACACATATCAACACCGATGCCATGTCCCAAACATGGTCTTA
*
12455508 CACTGGCACACAT
131 CACTGGCACACAA
* *
12455521 ATCAACGCTGATGCCATGTCCCAGACATGGTCTTACACT
1 ATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACT
12455560 GGCTTTCATC
Statistics
Matches: 161, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
142 40 0.25
143 121 0.75
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (143 bp):
ATCAATGCCGATGCCATGTCCCAGACATGGTCTTACACTACACACATATCAACACCGATGCCATG
TCCCAAACATGGTCTTACACTGGCACACATATCAACACCGATGCCATGTCCCAAACATGGTCTTA
CACTGGCACACAA
Found at i:12461571 original size:48 final size:47
Alignment explanation
Indices: 12461529--12461890 Score: 332
Period size: 48 Copynumber: 7.6 Consensus size: 47
12461519 TATCAATTTT
*
12461529 GATGCCATGTCCCAGACATGGTCTTACACTAGCACACTTATC-ATCACC
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCACACATATCAAT-ACC
* * * ***
12461577 AATTCCATGTCCCAAACATGGTCTTACACTGCACACATATCAATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGCACACATATCAATACC
* * ** *
12461624 GATGCCATGTCCCAGATATGGTCTTACACTAGTACACATATCAACGCA
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCACACATATCAATACC
* ** * *
12461672 AATGCCATGTCTTAAACATGGTCTTACACTGCACACATATCAACACC
1 GATGCCATGTCCCAGACATGGTCTTACACTGCACACATATCAATACC
* * *
12461719 GATG-CATGTCCTAGACATGGTCTTACACTGGCACACATATCAATGCT
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCACACATATCAATACC
* * * *
12461766 AATGCCATGTCCCAAACATCGTCTTACACTGGCACACATATCAACACC
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCACACATATCAATACC
* * * *** * ** *
12461814 GACGCCATGTCCTAGACATGGTATTACACTGGCTTTCATCTTGGATGCC
1 GATGCCATGTCCCAGACATGGTCTTACACT-GCACACAT-ATCAATACC
*
12461863 AATGCCATGTCCCAGACATGGTCTTACA
1 GATGCCATGTCCCAGACATGGTCTTACA
12461891 GGGGATCTCA
Statistics
Matches: 255, Mismatches: 54, Indels: 9
0.80 0.17 0.03
Matches are distributed among these distances:
46 23 0.09
47 70 0.27
48 134 0.53
49 28 0.11
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (47 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGCACACATATCAATACC
Found at i:12461635 original size:95 final size:95
Alignment explanation
Indices: 12461529--12461843 Score: 418
Period size: 95 Copynumber: 3.3 Consensus size: 95
12461519 TATCAATTTT
* * * *
12461529 GATGCCATGTCCCAGACATGGTCTTACACTAGCACACTTATCATCACCAATTCCATGTCCCAAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCAAATGCCATGTCCCAAAC
****
12461594 ATGGTCTTACACTGCACACATATCAATGTT
66 ATGGTCTTACACTGCACACATATCAACACC
* * * **
12461624 GATGCCATGTCCCAGATATGGTCTTACACTAGTACACATATCAACGCAAATGCCATGTCTTAAAC
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCAAATGCCATGTCCCAAAC
12461689 ATGGTCTTACACTGCACACATATCAACACC
66 ATGGTCTTACACTGCACACATATCAACACC
* * *
12461719 GATG-CATGTCCTAGACATGGTCTTACACTGGCACACATATCAAT-GCTAATGCCATGTCCCAAA
1 GATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATC-ATCGCAAATGCCATGTCCCAAA
*
12461782 CATCGTCTTACACTGGCACACATATCAACACC
65 CATGGTCTTACACT-GCACACATATCAACACC
* * *
12461814 GACGCCATGTCCTAGACATGGTATTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
12461844 GGCTTTCATC
Statistics
Matches: 193, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
94 62 0.32
95 107 0.55
96 24 0.12
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (95 bp):
GATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCATCGCAAATGCCATGTCCCAAAC
ATGGTCTTACACTGCACACATATCAACACC
Found at i:12461790 original size:142 final size:142
Alignment explanation
Indices: 12461530--12461844 Score: 416
Period size: 142 Copynumber: 2.2 Consensus size: 142
12461520 ATCAATTTTG
* * *
12461530 ATGCCATGTCCCAGACATGGTCTTACACTAGCACACTTATCATCACCAATTCCATGTCCCAAACA
1 ATGCCATGTCCTAGACATGGTCTTACACT-GCACACATATCAACACCAATTCCATGTCCCAAACA
* * * * * *
12461595 TGGTCTTACACTGCACACATATCAATGTTGATGCCATGTCCCAGATATGGTCTTACACTAGTACA
65 TGGTCTTACACTGCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTAGCACA
*
12461660 CATATCAACGCAA
130 CATATCAACACAA
* * * * * *
12461673 ATGCCATGTCTTAAACATGGTCTTACACTGCACACATATCAACACCGA-TGCATGTCCTAGACAT
1 ATGCCATGTCCTAGACATGGTCTTACACTGCACACATATCAACACCAATTCCATGTCCCAAACAT
*
12461737 GGTCTTACACTGGCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTGGCACA
66 GGTCTTACACT-GCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTAGCACA
**
12461802 CATATCAACACCG
130 CATATCAACACAA
* *
12461815 ACGCCATGTCCTAGACATGGTATTACACTG
1 ATGCCATGTCCTAGACATGGTCTTACACTG
12461845 GCTTTCATCT
Statistics
Matches: 148, Mismatches: 23, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
141 24 0.16
142 98 0.66
143 26 0.18
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (142 bp):
ATGCCATGTCCTAGACATGGTCTTACACTGCACACATATCAACACCAATTCCATGTCCCAAACAT
GGTCTTACACTGCACACATATCAATGCTAATGCCATGTCCCAAACATCGTCTTACACTAGCACAC
ATATCAACACAA
Found at i:12467113 original size:15 final size:14
Alignment explanation
Indices: 12467076--12467113 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
12467066 GTCCATTTAC
12467076 AAAAAAATAAAAGA
1 AAAAAAATAAAAGA
12467090 AAATAAAATAAAAGA
1 AAA-AAAATAAAAGA
12467105 AAAACAAAT
1 AAAA-AAAT
12467114 CATACAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.18
15 18 0.82
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.11
Consensus pattern (14 bp):
AAAAAAATAAAAGA
Found at i:12473430 original size:11 final size:11
Alignment explanation
Indices: 12473414--12473438 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
12473404 CCACAATTAA
12473414 ACTCACATTTT
1 ACTCACATTTT
12473425 ACTCACATTTT
1 ACTCACATTTT
12473436 ACT
1 ACT
12473439 TACCGTTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.00, T:0.44
Consensus pattern (11 bp):
ACTCACATTTT
Found at i:12474761 original size:23 final size:23
Alignment explanation
Indices: 12474729--12474782 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
12474719 AAACAAAGAC
12474729 ATTTTCGATTTACCATGCTTCAA
1 ATTTTCGATTTACCATGCTTCAA
* *
12474752 ATTTTTGATTTACCATGCTTTAA
1 ATTTTCGATTTACCATGCTTCAA
12474775 ATTTTCGA
1 ATTTTCGA
12474783 ACACATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.26, C:0.17, G:0.09, T:0.48
Consensus pattern (23 bp):
ATTTTCGATTTACCATGCTTCAA
Found at i:12484774 original size:23 final size:23
Alignment explanation
Indices: 12484748--12484793 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
12484738 TATTAAATAA
12484748 ATAAAACAAAACAATTTTTTTAT
1 ATAAAACAAAACAATTTTTTTAT
*
12484771 ATAAAACAAAATAATTTTTTTAT
1 ATAAAACAAAACAATTTTTTTAT
12484794 CCCTTATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (23 bp):
ATAAAACAAAACAATTTTTTTAT
Found at i:12491871 original size:21 final size:21
Alignment explanation
Indices: 12491826--12491880 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
12491816 TTCTATATGC
*
12491826 ATATTTTAATTATTTTTTAAAAA
1 ATATTTT-ATT-TTTTGTAAAAA
*
12491849 ATATTTTATTTTTTGTAAGAA
1 ATATTTTATTTTTTGTAAAAA
12491870 ATATTTT-TTTT
1 ATATTTTATTTT
12491881 GGTGACATGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 4 0.13
21 16 0.53
22 3 0.10
23 7 0.23
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (21 bp):
ATATTTTATTTTTTGTAAAAA
Found at i:12493482 original size:15 final size:15
Alignment explanation
Indices: 12493452--12493480 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12493442 ACTATTAGTA
12493452 ATTTTTTACATATTT
1 ATTTTTTACATATTT
12493467 ATTTTTTA-ATATTT
1 ATTTTTTACATATTT
12493481 TACCATACCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
ATTTTTTACATATTT
Found at i:12496328 original size:21 final size:21
Alignment explanation
Indices: 12496287--12496328 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
12496277 AAAAATACTC
*
12496287 TTTTAAAAATGTGATAATTAAT
1 TTTTAAAAAAGT-ATAATTAAT
12496309 TTTTAAAAAAGT-TAAGTTAA
1 TTTTAAAAAAGTATAA-TTAA
12496329 AACCAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 4 0.22
22 11 0.61
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.43
Consensus pattern (21 bp):
TTTTAAAAAAGTATAATTAAT
Found at i:12496557 original size:48 final size:48
Alignment explanation
Indices: 12496502--12496646 Score: 290
Period size: 48 Copynumber: 3.0 Consensus size: 48
12496492 ATCTAATTTA
12496502 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
1 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
12496550 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
1 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
12496598 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
1 ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
12496646 A
1 A
12496647 AATATTGTTT
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 97 1.00
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (48 bp):
ATTTAATAATGTTAAATATATTTTAATTTATCTAATTAACAATTTTTT
Found at i:12496645 original size:24 final size:24
Alignment explanation
Indices: 12496522--12496647 Score: 120
Period size: 24 Copynumber: 5.2 Consensus size: 24
12496512 GTTAAATATA
12496522 TTTTAATTTATCTAATTAACAATT
1 TTTTAATTTATCTAATTAACAATT
* *
12496546 TTTT-ATTTA-ATAATGTTAA-ATATA
1 TTTTAATTTATCTAA--TTAACA-ATT
12496570 TTTTAATTTATCTAATTAACAATT
1 TTTTAATTTATCTAATTAACAATT
* *
12496594 TTTT-ATTTA-ATAATGTTAA-ATATA
1 TTTTAATTTATCTAA--TTAACA-ATT
12496618 TTTTAATTTATCTAATTAACAATT
1 TTTTAATTTATCTAATTAACAATT
12496642 TTTTAA
1 TTTTAA
12496648 ATATTGTTTA
Statistics
Matches: 82, Mismatches: 8, Indels: 24
0.72 0.07 0.21
Matches are distributed among these distances:
22 6 0.07
23 12 0.15
24 46 0.56
25 12 0.15
26 6 0.07
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.55
Consensus pattern (24 bp):
TTTTAATTTATCTAATTAACAATT
Found at i:12517173 original size:25 final size:24
Alignment explanation
Indices: 12517121--12517196 Score: 67
Period size: 20 Copynumber: 3.4 Consensus size: 24
12517111 CTTATTTTAT
* *
12517121 TAAATAAA-AAATTTAAAATATAA
1 TAAATAAATACATTTAAAACATAA
12517144 TAAATGAAATACATTTAAAAACATAA
1 TAAAT-AAATACATTT-AAAACATAA
12517170 -AAATAAAT--A-TTAAAACA-AA
1 TAAATAAATACATTTAAAACATAA
12517189 TAAA-AAAT
1 TAAATAAAT
12517197 GATATTAAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
19 6 0.13
20 9 0.19
21 2 0.04
22 1 0.02
23 5 0.11
24 7 0.15
25 9 0.19
26 8 0.17
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAATAAATACATTTAAAACATAA
Found at i:12517194 original size:22 final size:22
Alignment explanation
Indices: 12517150--12517209 Score: 63
Period size: 22 Copynumber: 2.8 Consensus size: 22
12517140 ATAATAAATG
* *
12517150 AAATACAT-TTAAAA-ACATAA
1 AAATAAATATTAAAACAAATAA
12517170 AAATAAATATTAAAACAAATAA
1 AAATAAATATTAAAACAAATAA
*
12517192 AAA-ATGATATTAAAACAA
1 AAATA-AATATTAAAACAA
12517210 TACACAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 7 0.21
21 7 0.21
22 20 0.59
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATAAATATTAAAACAAATAA
Found at i:12519644 original size:56 final size:56
Alignment explanation
Indices: 12519583--12519724 Score: 205
Period size: 56 Copynumber: 2.5 Consensus size: 56
12519573 AACGTGGAAT
**
12519583 CGATATATCTGTGGGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
1 CGATATATCTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
* *
12519639 CGATATATGTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATGTGATTC
1 CGATATATCTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
*
12519695 CGATATATGTGATTAC-ATGTAAGACCACGT
1 CGATATATCTG--TACGA-GTAAGACCACGT
12519725 CTGGGACGTT
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
56 63 0.80
57 1 0.01
58 15 0.19
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.32
Consensus pattern (56 bp):
CGATATATCTGTACGAGTAAGACCACGTTTAATACGTTGGCATCGATATATGATTC
Found at i:12519924 original size:97 final size:97
Alignment explanation
Indices: 12519815--12520009 Score: 318
Period size: 97 Copynumber: 2.0 Consensus size: 97
12519805 GTTGTGATCG
* * * *
12519815 AATGTGTAATCGAGCTAAAGTGATCAGGTATGTGATAGTTAATTTCCTATTTGAAATTAAGGTAA
1 AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAA
12519880 GTTGGCTGTTTGGTATGTGATACAAAATGTAT
66 GTTGGCTGTTTGGTATGTGATACAAAATGTAT
* *
12519912 AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCTTATTTAAAAGTAAGGTAG
1 AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAA
* *
12519977 GTTGGTTGTTTGGTATGTGATACAAATTGTAT
66 GTTGGCTGTTTGGTATGTGATACAAAATGTAT
12520009 A
1 A
12520010 TGATAAAGTG
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
97 90 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (97 bp):
AATGTGTAATCGAGCTAAAGCGATCAAGTATGTGATAGTTAATTTCCTATTTAAAAGTAAGGTAA
GTTGGCTGTTTGGTATGTGATACAAAATGTAT
Found at i:12522917 original size:216 final size:216
Alignment explanation
Indices: 12522543--12522977 Score: 870
Period size: 216 Copynumber: 2.0 Consensus size: 216
12522533 ATAATAATAT
12522543 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
1 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
12522608 TTGCGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
66 TTGCGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
12522673 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
131 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
12522738 TTCATAGATAAATCCTTTATA
196 TTCATAGATAAATCCTTTATA
12522759 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
1 ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
12522824 TTGCGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
66 TTGCGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
12522889 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
131 AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
12522954 TTCATAGATAAATCCTTTATA
196 TTCATAGATAAATCCTTTATA
12522975 ACT
1 ACT
12522978 CAATTAATTC
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 219 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (216 bp):
ACTTTTCCACTTAGAGTTTGGGATTGGCCTGGGATGTTGATCCAACGATCTGATTTTAACTTATC
TTGCGCACAGAAACAAACCGTACGCTGAGTATGAACTCAATGGTATTTCTATAATCCGAACACTT
AATAATATGAAAATATAACATTCATTTAAAAATCATATAACAATTACAATTATATAATTGTTCAA
TTCATAGATAAATCCTTTATA
Found at i:12523248 original size:18 final size:18
Alignment explanation
Indices: 12523225--12523289 Score: 94
Period size: 18 Copynumber: 3.6 Consensus size: 18
12523215 TATCAGTATC
12523225 ATTCAGTAACAATCAATT
1 ATTCAGTAACAATCAATT
* * *
12523243 ATTCAGTAGCAACCAGTT
1 ATTCAGTAACAATCAATT
*
12523261 ATTCAGTAACAATCAATA
1 ATTCAGTAACAATCAATT
12523279 ATTCAGTAACA
1 ATTCAGTAACA
12523290 GTTAGTCATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.29
Consensus pattern (18 bp):
ATTCAGTAACAATCAATT
Found at i:12523259 original size:28 final size:28
Alignment explanation
Indices: 12523206--12523259 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
12523196 TTTTCAATAT
* **
12523206 CAATCAACTTATCAGTATCATTCAGTAA
1 CAATCAACTTATCAGTAGCAACCAGTAA
12523234 CAATCAA-TTATTCAGTAGCAACCAGT
1 CAATCAACTTA-TCAGTAGCAACCAGT
12523260 TATTCAGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 3 0.14
28 19 0.86
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (28 bp):
CAATCAACTTATCAGTAGCAACCAGTAA
Found at i:12523301 original size:36 final size:36
Alignment explanation
Indices: 12523223--12523304 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
12523213 CTTATCAGTA
* *
12523223 TCATTCAGTAACAATCAATTATTCAGTAGCAACCAG
1 TCATTCAGTAACAATCAATAATTCAGTAACAACCAG
* ***
12523259 TTATTCAGTAACAATCAATAATTCAGTAACAGTTAG
1 TCATTCAGTAACAATCAATAATTCAGTAACAACCAG
12523295 TCATTCAGTA
1 TCATTCAGTA
12523305 CCTTTATCCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (36 bp):
TCATTCAGTAACAATCAATAATTCAGTAACAACCAG
Found at i:12524087 original size:13 final size:13
Alignment explanation
Indices: 12524069--12524094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12524059 TAGAAATACA
12524069 AACCGTAATTTCC
1 AACCGTAATTTCC
12524082 AACCGTAATTTCC
1 AACCGTAATTTCC
12524095 GAGCTAACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.31, G:0.08, T:0.31
Consensus pattern (13 bp):
AACCGTAATTTCC
Found at i:12524243 original size:11 final size:11
Alignment explanation
Indices: 12524220--12524249 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
12524210 TTAATATTTA
12524220 AATTTCTTATTC
1 AATTTC-TATTC
12524232 AATTTCTATTC
1 AATTTCTATTC
12524243 AATTTCT
1 AATTTCT
12524250 GCTTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.57
Consensus pattern (11 bp):
AATTTCTATTC
Found at i:12524825 original size:19 final size:19
Alignment explanation
Indices: 12524801--12524850 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
12524791 TAATAACAAT
* **
12524801 ATAATTTAATATTAATTTA
1 ATAATTTAATATAAAACTA
12524820 ATAATTTAATATAAAACTA
1 ATAATTTAATATAAAACTA
12524839 ATAATTATAATA
1 ATAATT-TAATA
12524851 AATATCTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
ATAATTTAATATAAAACTA
Found at i:12525175 original size:13 final size:13
Alignment explanation
Indices: 12525153--12525192 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12525143 GAAAACCATG
12525153 ATAATAATTAATA
1 ATAATAATTAATA
*
12525166 ATAATTATT-ATA
1 ATAATAATTAATA
12525178 ATAATAGATTAATA
1 ATAATA-ATTAATA
12525192 A
1 A
12525193 CAAAACCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 8 0.35
13 11 0.48
14 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (13 bp):
ATAATAATTAATA
Found at i:12525370 original size:20 final size:19
Alignment explanation
Indices: 12525324--12525370 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
12525314 AATCATTTTT
*
12525324 CCTAATTTCTCTTAATTAAG
1 CCTAA-TTCACTTAATTAAG
12525344 -CTAAATTCACTTAATTAAAG
1 CCT-AATTCACTTAATT-AAG
12525364 CCTAATT
1 CCTAATT
12525371 AAACACACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (19 bp):
CCTAATTCACTTAATTAAG
Found at i:12537586 original size:23 final size:23
Alignment explanation
Indices: 12537518--12537592 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 23
12537508 CCTGATCAGT
** *
12537518 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACGAGGTGCCTGAA
12537540 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACGAGGTGCCTGAA
*
12537560 ATACAACACACGAGGTGCCTGAA
1 ATACGACACACGAGGTGCCTGAA
12537583 ATACGACACA
1 ATACGACACA
12537593 TAAAGTGCCT
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 1 0.02
21 33 0.75
22 1 0.02
23 9 0.20
ACGTcount: A:0.40, C:0.27, G:0.20, T:0.13
Consensus pattern (23 bp):
ATACGACACACGAGGTGCCTGAA
Found at i:12537600 original size:23 final size:23
Alignment explanation
Indices: 12537518--12537604 Score: 83
Period size: 21 Copynumber: 4.0 Consensus size: 23
12537508 CCTGATCAGT
*
12537518 ATACGACACATAAAGTGCCT-AA
1 ATACGACACACAAAGTGCCTGAA
* *
12537540 A-ACGACACACGAGGTGCCTG--
1 ATACGACACACAAAGTGCCTGAA
* * *
12537560 ATACAACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTGAA
*
12537583 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
12537605 TCGATAAAGC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 1 0.02
21 33 0.62
22 1 0.02
23 18 0.34
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.15
Consensus pattern (23 bp):
ATACGACACACAAAGTGCCTGAA
Found at i:12538001 original size:15 final size:15
Alignment explanation
Indices: 12537976--12538033 Score: 89
Period size: 15 Copynumber: 3.8 Consensus size: 15
12537966 TCATATATAT
12537976 TATATAATTCAATCAA
1 TATA-AATTCAATCAA
12537992 TATAAATTCAATCAA
1 TATAAATTCAATCAA
* *
12538007 AATAATTTCAATCAA
1 TATAAATTCAATCAA
12538022 TATAAATTCAAT
1 TATAAATTCAAT
12538034 AAATTCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
15 34 0.89
16 4 0.11
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAAATTCAATCAA
Found at i:12539290 original size:5 final size:5
Alignment explanation
Indices: 12539282--12539316 Score: 70
Period size: 5 Copynumber: 7.0 Consensus size: 5
12539272 TCTTTAGTTT
12539282 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA
12539317 TTTAAAACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:12539359 original size:13 final size:13
Alignment explanation
Indices: 12539341--12539366 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12539331 TATCTTTATT
12539341 ATATAATAATATA
1 ATATAATAATATA
12539354 ATATAATAATATA
1 ATATAATAATATA
12539367 CTAAACATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
ATATAATAATATA
Found at i:12540303 original size:17 final size:17
Alignment explanation
Indices: 12540283--12540340 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
12540273 AAAATTAATG
12540283 ATAATTATACATTTAAA
1 ATAATTATACATTTAAA
*
12540300 ATAATTATA-ATTTAAT
1 ATAATTATACATTTAAA
* * *
12540316 AGAAGTACACATTTAAA
1 ATAATTATACATTTAAA
12540333 ACTAATTA
1 A-TAATTA
12540341 AAATTATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 12 0.38
17 16 0.50
18 4 0.12
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAATTATACATTTAAA
Found at i:12541196 original size:25 final size:25
Alignment explanation
Indices: 12541154--12541202 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
12541144 AAAATTAAGG
*
12541154 TAAAAAATTTATGCTAATTTTATTT
1 TAAAAAAGTTATGCTAATTTTATTT
* *
12541179 TAAAAAAGTTGTGTTAATTTTATT
1 TAAAAAAGTTATGCTAATTTTATT
12541203 GATGTAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.08, T:0.51
Consensus pattern (25 bp):
TAAAAAAGTTATGCTAATTTTATTT
Found at i:12547107 original size:17 final size:17
Alignment explanation
Indices: 12547085--12547117 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12547075 AGGCGTTGCC
12547085 TCATCA-CATCACACAAA
1 TCATCATCATCA-ACAAA
12547102 TCATCATCATCAACAA
1 TCATCATCATCAACAA
12547118 GGGTAACAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.45, C:0.33, G:0.00, T:0.21
Consensus pattern (17 bp):
TCATCATCATCAACAAA
Found at i:12553509 original size:14 final size:14
Alignment explanation
Indices: 12553486--12553515 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12553476 ATTGTCTCCT
12553486 AGAAACTTTTTTGG
1 AGAAACTTTTTTGG
*
12553500 AGAAAGTTTTTTGG
1 AGAAACTTTTTTGG
12553514 AG
1 AG
12553516 GTTTATCTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.40
Consensus pattern (14 bp):
AGAAACTTTTTTGG
Found at i:12574856 original size:20 final size:22
Alignment explanation
Indices: 12574817--12574858 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
12574807 TGTGATTGGA
12574817 TCACTTAATAAAACATTTTGTT
1 TCACTTAATAAAACATTTTGTT
*
12574839 TCACTTAA-AATA-ATTTTGTT
1 TCACTTAATAAAACATTTTGTT
12574859 CTACGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 3 0.16
22 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.48
Consensus pattern (22 bp):
TCACTTAATAAAACATTTTGTT
Found at i:12583165 original size:20 final size:20
Alignment explanation
Indices: 12583142--12583180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12583132 GTTCTAAGTT
*
12583142 AATACCAAAATTTCTAATGC
1 AATAACAAAATTTCTAATGC
*
12583162 AATAACAATATTTCTAATG
1 AATAACAAAATTTCTAATG
12583181 GAAACCATTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.15, G:0.05, T:0.33
Consensus pattern (20 bp):
AATAACAAAATTTCTAATGC
Found at i:12583511 original size:19 final size:20
Alignment explanation
Indices: 12583471--12583517 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
12583461 AGCATGTACT
* *
12583471 AATTTTTAATACGATACTAA
1 AATTTCTAATACGATACCAA
12583491 AATTTCTAATA-GATACCAA
1 AATTTCTAATACGATACCAA
12583510 AATTTCTA
1 AATTTCTA
12583518 GCCAAATACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.45, C:0.13, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTTCTAATACGATACCAA
Found at i:12585241 original size:48 final size:48
Alignment explanation
Indices: 12585145--12585316 Score: 166
Period size: 48 Copynumber: 3.6 Consensus size: 48
12585135 ATAATTTACT
*
12585145 GATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATGTCGAGGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATATCGAGGCC
* * *
12585193 GATGCTATGTCCTAGACATGGTCTTACACTGGCTTTCATAAT-GTGGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTTACAT-ATCGAGGCC
* * * * * ** * * * *
12585241 GTTGCCATGTCCCAGGCATTGTCTTACACTAGCGCACCTAACAATGCC
1 GATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATATCGAGGCC
* * *
12585289 GATGTCATGTCCCAGGCATGGTCTTACA
1 GATGCCATGTCCTAGACATGGTCTTACA
12585317 TTAGCTCTTA
Statistics
Matches: 101, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 99 0.98
49 1 0.01
ACGTcount: A:0.22, C:0.27, G:0.23, T:0.28
Consensus pattern (48 bp):
GATGCCATGTCCTAGACATGGTCTTACACTGGCTTACATATCGAGGCC
Found at i:12585331 original size:48 final size:48
Alignment explanation
Indices: 12585246--12585346 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
12585236 TGGCCGTTGC
* * *
12585246 CATGTCCCAGGCATTGTCTTACACTAGCGCACCTAACAATGCCGATGT
1 CATGTCCCAGGCATGGTCTTACACTAGCGCACATAACAATGCCAATGT
* * ** *
12585294 CATGTCCCAGGCATGGTCTTACATTAGCTCTTATAACATTGCCAATGT
1 CATGTCCCAGGCATGGTCTTACACTAGCGCACATAACAATGCCAATGT
12585342 CATGT
1 CATGT
12585347 TCCAAACATG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.30
Consensus pattern (48 bp):
CATGTCCCAGGCATGGTCTTACACTAGCGCACATAACAATGCCAATGT
Found at i:12592858 original size:48 final size:47
Alignment explanation
Indices: 12592709--12592987 Score: 164
Period size: 48 Copynumber: 5.8 Consensus size: 47
12592699 TAAATTACCG
* *
12592709 ATGCCATGTCCC-AGACATGGTTTTACACTGG--CTCA-CATGTCGAGACC
1 ATGCCATGTCCCGA-ACATGGTCTTACACTGGCTCTCATAATGTC--G-CC
* * * *
12592756 GATGCCATGTTCC-AGACATGGTATTACACTAGCTCTTGTCTTAATGTCG--
1 -ATGCCATGTCCCGA-ACATGGTCTTACACTGGCTC---TCATAATGTCGCC
*
12592805 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAATGTGGCC
1 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAATGTCGCC
* * * * * **
12592852 ATTGCCATGTCCC-AGACATGTTCTTACACTAGCGCACCTAATAACGCC
1 A-TGCCATGTCCCGA-ACATGGTCTTACACTGGCTCTCATAATGTCGCC
* * * *
12592900 GATGCCGTATCCCGAACATTGTCTTACACTGGCTCTCATAACATTGTTG--
1 -ATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCAT-A-A-TGTCGCC
* * *
12592949 ATGCCATGTTCCAAACATGGTCTTATACTGGCTCTCATA
1 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATA
12592988 TCGTGTTTGA
Statistics
Matches: 180, Mismatches: 35, Indels: 33
0.73 0.14 0.13
Matches are distributed among these distances:
45 9 0.05
47 3 0.02
48 152 0.84
49 4 0.02
50 2 0.01
51 2 0.01
52 1 0.01
53 2 0.01
54 5 0.03
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.30
Consensus pattern (47 bp):
ATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAATGTCGCC
Found at i:12592871 original size:96 final size:97
Alignment explanation
Indices: 12592706--12592940 Score: 253
Period size: 96 Copynumber: 2.4 Consensus size: 97
12592696 GGGTAAATTA
* * * *
12592706 CCGATGCCATGTCCC-AGACATGGTTTTACACTGGCTCACAT-GTCGAGACCGATGCCATGTTCC
1 CCGATGCCATGTCCCGA-ACATGGTCTTACACTGGCTCTCATAATCGAGACCGATGCCATGTCCC
* *** ** *
12592769 AGACATGGTATTACACTAGCTCTTGTCTTAATG
65 AGACATGGTATTACACTAGCGCACCTAATAACG
* * *
12592802 TCGATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAAT-GTGGCC-ATTGCCATGTCCC
1 CCGATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAATCGAGACCGA-TGCCATGTCCC
* *
12592865 AGACATGTTCTTACACTAGCGCACCTAATAACG
65 AGACATGGTATTACACTAGCGCACCTAATAACG
* * *
12592898 CCGATGCCGTATCCCGAACATTGTCTTACACTGGCTCTCATAA
1 CCGATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAA
12592941 CATTGTTGAT
Statistics
Matches: 116, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
95 1 0.01
96 113 0.97
97 2 0.02
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.28
Consensus pattern (97 bp):
CCGATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCATAATCGAGACCGATGCCATGTCCCA
GACATGGTATTACACTAGCGCACCTAATAACG
Found at i:12593003 original size:48 final size:48
Alignment explanation
Indices: 12592914--12593025 Score: 138
Period size: 48 Copynumber: 2.3 Consensus size: 48
12592904 CCGTATCCCG
* * *
12592914 AACATTGTCTTACACTGGCTCTCATAACATTGTTGATGCCATGTTCC-A
1 AACATGGTCTTATACTGGCTCTCATAACATTGTTGACGCCATG-TCCGA
* *
12592962 AACATGGTCTTATACTGGCTCTCATATC-GTGTTTGACGCCATGTCCGA
1 AACATGGTCTTATACTGGCTCTCATAACATTG-TTGACGCCATGTCCGA
*
12593010 GACATGGTCTTATACT
1 AACATGGTCTTATACT
12593026 AGTACACATA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 5 0.09
48 51 0.91
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (48 bp):
AACATGGTCTTATACTGGCTCTCATAACATTGTTGACGCCATGTCCGA
Found at i:12593036 original size:48 final size:48
Alignment explanation
Indices: 12592946--12593037 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
12592936 CATAACATTG
* * *
12592946 TTGATGCCATGTTCCAAACATGGTCTTATACTGGCTCTCATATCGTGT
1 TTGACGCCATGTTCCAAACATGGTCTTATACTAGCTCACATATCGTGT
*
12592994 TTGACGCCATG-TCCGAGACATGGTCTTATACTAG-TACACATATC
1 TTGACGCCATGTTCC-AAACATGGTCTTATACTAGCT-CACATATC
12593038 ACCCAAATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
47 4 0.11
48 34 0.89
ACGTcount: A:0.24, C:0.24, G:0.18, T:0.34
Consensus pattern (48 bp):
TTGACGCCATGTTCCAAACATGGTCTTATACTAGCTCACATATCGTGT
Done.