Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A02
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: 100057689
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3589301 characters in sequence are not A, C, G, or T
File 155 of 295
Found at i:52770300 original size:15 final size:15
Alignment explanation
Indices: 52770252--52770331 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
52770242 CAAAGATAAC
*
52770252 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
52770266 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
52770281 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
52770296 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
52770311 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
52770326 AAGAAA
1 AAGAAA
52770332 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:52770340 original size:15 final size:15
Alignment explanation
Indices: 52770263--52770340 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
52770253 AGAAAACCGA
52770263 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
52770278 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
52770292 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
52770307 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
52770323 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
52770338 ATA
1 ATA
52770341 CGATACTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52773390 original size:93 final size:93
Alignment explanation
Indices: 52773231--52773401 Score: 254
Period size: 93 Copynumber: 1.8 Consensus size: 93
52773221 GCCCATAAGT
*** *
52773231 GAACTCGGACTCAACTCAACAAGCTTGGGTGTTCGCATCCATAATTCAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACAAGCTTGGACATTCGCATCCATAAGTCAACTCGGACTCAACTCAA
52773296 CGAGCTCGGATGCGTAGTTACATCTCTC
66 CGAGCTCGGATGCGTAGTTACATCTCTC
* * *
52773324 GAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCA
1 GAACTCGGACTCAACTCAACAAGCTT-GGACATTCGCATCCATAAGTCAACTCGGACTCAACTCA
*
52773388 ACGAGTTCGGATGC
65 ACGAGCTCGGATGC
52773402 TCAAACATCC
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
92 2 0.03
93 67 0.97
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACAAGCTTGGACATTCGCATCCATAAGTCAACTCGGACTCAACTCAA
CGAGCTCGGATGCGTAGTTACATCTCTC
Found at i:52773391 original size:46 final size:46
Alignment explanation
Indices: 52773223--52773398 Score: 164
Period size: 46 Copynumber: 3.8 Consensus size: 46
52773213 TGTAACCCGC
* *** *
52773223 CCATAAGTGAACTCGGACTCAACTCAACAAGCTT-GGGTGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAG-TTCGGACATTTGCAT
* * * * *
52773269 CCATAATTCAACTCGGACTCAACTCAACGAGCTCGGATGCGTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--C--ATTTGCAT
*
52773319 CTC-T---CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
52773362 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
52773399 TGCTCAAACA
Statistics
Matches: 104, Mismatches: 16, Indels: 20
0.74 0.11 0.14
Matches are distributed among these distances:
42 1 0.01
43 8 0.08
45 2 0.02
46 59 0.57
47 27 0.26
50 6 0.06
51 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCAT
Found at i:52774761 original size:47 final size:48
Alignment explanation
Indices: 52774707--52774834 Score: 147
Period size: 46 Copynumber: 2.7 Consensus size: 48
52774697 CTGTATTAAC
*
52774707 TAGAACACATTAAATAAACTTAAGACATATTAAATGGT-TGAA-CTATT
1 TAGAACACATTAAATAAACTTAAGACATATTAAAT-GTCTGAATCTAAT
* * * * *
52774754 TATAACACATT-AATTAGCTCAAGACATATT-AATTTCTGAATCTAAT
1 TAGAACACATTAAATAAACTTAAGACATATTAAATGTCTGAATCTAAT
* *
52774800 TAGAACATATTAAATAGACTTAAGACATATTAAAT
1 TAGAACACATTAAATAAACTTAAGACATATTAAAT
52774835 ACTTAAACTA
Statistics
Matches: 65, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
44 1 0.02
45 7 0.11
46 29 0.45
47 25 0.38
48 3 0.05
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.34
Consensus pattern (48 bp):
TAGAACACATTAAATAAACTTAAGACATATTAAATGTCTGAATCTAAT
Found at i:52774840 original size:18 final size:19
Alignment explanation
Indices: 52774804--52774840 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
52774794 TCTAATTAGA
52774804 ACATATTAAATAGACTTAAG
1 ACATATTAAATA-ACTTAAG
52774824 ACATATTAAAT-ACTTAA
1 ACATATTAAATAACTTAA
52774841 ACTAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (19 bp):
ACATATTAAATAACTTAAG
Found at i:52778903 original size:40 final size:40
Alignment explanation
Indices: 52778847--52779054 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
52778837 CGGAATTTAA
* * *
52778847 CCGGATATAGCT-ACTCGCTCAAACGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
52778887 CCGGCTATAGTAACTCGCGCAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
52778927 CTGGATTTAGTAACTCGCTCCAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
52778966 CCGGA-ATTAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
52779006 CCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
52779047 CCGGATAT
1 CCGGATAT
52779055 CATTCGAATA
Statistics
Matches: 141, Mismatches: 20, Indels: 13
0.81 0.11 0.07
Matches are distributed among these distances:
38 2 0.01
39 31 0.22
40 77 0.55
41 28 0.20
42 3 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:52778966 original size:79 final size:79
Alignment explanation
Indices: 52778833--52779051 Score: 230
Period size: 79 Copynumber: 2.7 Consensus size: 79
52778823 ACGAAACATA
* *
52778833 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAACGCCTTCGGGACATAGCCCGG-CTATAG
1 CCTTCGGAACTTAACCGGATATAGCTACTCGCTCAAACGCCTTCGGGACATAGCCCGGAAT-TAG
*
52778897 TAACTCGCGCAAATG
65 TAACTCGCACAAATG
* * * * *
52778912 CCTTCGGGACTTAACCTGGATTTAG-TAACTCGCTCCAATGCCTTCGGG-CTTAGCCCGGAATTA
1 CCTTCGGAACTTAACC-GGATATAGCT-ACTCGCTCAAACGCCTTCGGGACATAGCCCGGAATTA
52778975 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
* * * * * *
52778991 CCTTCGGATCTTAGTCCGGATATAG-TCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGAACTTA-ACCGGATATAGCT-AC-TCGCTCAAACGCCTTCGGGACATAGCCCGGA
52779052 TATCATTCGA
Statistics
Matches: 117, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
79 62 0.53
80 44 0.38
81 11 0.09
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (79 bp):
CCTTCGGAACTTAACCGGATATAGCTACTCGCTCAAACGCCTTCGGGACATAGCCCGGAATTAGT
AACTCGCACAAATG
Found at i:52786970 original size:39 final size:38
Alignment explanation
Indices: 52786927--52787109 Score: 147
Period size: 39 Copynumber: 4.6 Consensus size: 38
52786917 ACGAAACATA
52786927 CCTTCGGAATTTAACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGAA-TTAACCGGATATAG-TAACTCGCTCAAATG
* * *
52786966 CCTTCGGACA-TAGCCCGGTTATAGTAACTCGCGCAAATG
1 CCTTCGGA-ATTA-ACCGGATATAGTAACTCGCTCAAATG
* * *
52787005 CCTTCGGGACTTAACCTGGATTTAGTAACTCGCTCCAATG
1 CCTTC-GGAATTAACC-GGATATAGTAACTCGCTCAAATG
** * *
52787045 CCTTCGGGCTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGAATTA-ACCGGATA-TAGTAACTCGCTCAAATG
* *
52787084 CCTTCGGATCTTAGTCCGGATATAGT
1 CCTTCGGA-ATTA-ACCGGATATAGT
52787110 CACTTAGCAC
Statistics
Matches: 118, Mismatches: 16, Indels: 19
0.77 0.10 0.12
Matches are distributed among these distances:
38 3 0.03
39 68 0.58
40 46 0.39
41 1 0.01
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (38 bp):
CCTTCGGAATTAACCGGATATAGTAACTCGCTCAAATG
Found at i:52787059 original size:79 final size:78
Alignment explanation
Indices: 52786927--52787144 Score: 226
Period size: 79 Copynumber: 2.7 Consensus size: 78
52786917 ACGAAACATA
* *
52786927 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGACATAGCCCGG-TTATAGT
1 CCTTCGGAACTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGACATAGCCCGGAAT-TAGT
*
52786991 AACTCGCGCAAATG
65 AACTCGCACAAATG
* * * * *
52787005 CCTTCGGGACTTAACCTGGATTTAG-TAACTCGCTCCAATGCCTTCGGGCTTAGCCCGGAATTAG
1 CCTTCGGAACTTAACC-GGATATAGCT-ACTCGCTCAAATGCCTTCGGACATAGCCCGGAATTAG
52787069 TAACTCGCACAAATG
64 TAACTCGCACAAATG
* * * * * *
52787084 CCTTCGGATCTTAGTCCGGATATAG-TCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGAACTTA-ACCGGATATAGCT-AC-TCGCTCAAATGCCTTC-GGACATAGCCCGGA
52787145 TATCATTCGA
Statistics
Matches: 116, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
78 15 0.13
79 73 0.63
80 15 0.13
81 13 0.11
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (78 bp):
CCTTCGGAACTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGACATAGCCCGGAATTAGTA
ACTCGCACAAATG
Found at i:52789560 original size:35 final size:35
Alignment explanation
Indices: 52789512--52789605 Score: 134
Period size: 35 Copynumber: 2.7 Consensus size: 35
52789502 GGTGTCGCCC
* * *
52789512 TGAATGACCTATATATCATTTACATGGTGTTAACT
1 TGAAGGACCTATATATCATTTACATGATGTCAACT
* * *
52789547 TGAAGGACTTATATACCATTTACATGATGTCACCT
1 TGAAGGACCTATATATCATTTACATGATGTCAACT
52789582 TGAAGGACCTATATATCATTTACA
1 TGAAGGACCTATATATCATTTACA
52789606 CAGTGTCCCC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (35 bp):
TGAAGGACCTATATATCATTTACATGATGTCAACT
Found at i:52793541 original size:22 final size:20
Alignment explanation
Indices: 52793507--52793546 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
52793497 TTCCAATGCC
52793507 TATAATTATAGTGTAATATA
1 TATAATTATAGTGTAATATA
52793527 TATAACTTAGTAGTGTAATA
1 TATAA-TTA-TAGTGTAATA
52793547 ATAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 3 0.17
22 10 0.56
ACGTcount: A:0.42, C:0.03, G:0.12, T:0.42
Consensus pattern (20 bp):
TATAATTATAGTGTAATATA
Found at i:52796798 original size:25 final size:25
Alignment explanation
Indices: 52796633--52796800 Score: 78
Period size: 24 Copynumber: 6.8 Consensus size: 25
52796623 TGGATCTTTG
* *
52796633 TGAGCTTCCTAATTA-ATGGCTCTC-
1 TGAGCTTCCT-GTTATATGGCTCACA
* *
52796657 TGAAGCTTCCCGTTA-ATGTCTCTACA
1 TG-AGCTTCCTGTTATATGGCTC-ACA
* **
52796683 -GAGCTACCTGTTAT-TGGCTTGCA
1 TGAGCTTCCTGTTATATGGCTCACA
* * **
52796706 TGAGCTTCTTGAT-TATGGCTCTTA
1 TGAGCTTCCTGTTATATGGCTCACA
* ** * *
52796730 TGAGCTTCCCGTTATACAGCCCAGA
1 TGAGCTTCCTGTTATATGGCTCACA
* ** *
52796755 TAAGCTTCCCCTTACATGGCTCACA
1 TGAGCTTCCTGTTATATGGCTCACA
*
52796780 TGAGCTTCCTATTATATGGCT
1 TGAGCTTCCTGTTATATGGCT
52796801 TGAGAGAGTG
Statistics
Matches: 103, Mismatches: 34, Indels: 13
0.69 0.23 0.09
Matches are distributed among these distances:
23 3 0.03
24 50 0.49
25 50 0.49
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (25 bp):
TGAGCTTCCTGTTATATGGCTCACA
Found at i:52798825 original size:28 final size:28
Alignment explanation
Indices: 52798785--52798854 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
52798775 GCAATCAAAT
*
52798785 ATGGCACTCAGTGTACGAAATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
52798813 ATGGCACTTAGTGTGCGAGATATTGAGA
1 ATGGCACTTAGTGTACGAAATATTGAGA
* *
52798841 ACGACACTTAGTGT
1 ATGGCACTTAGTGT
52798855 GCAAAAAATC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (28 bp):
ATGGCACTTAGTGTACGAAATATTGAGA
Found at i:52802685 original size:27 final size:27
Alignment explanation
Indices: 52802647--52802704 Score: 107
Period size: 27 Copynumber: 2.1 Consensus size: 27
52802637 GTTAGATCAA
52802647 GAAAACTGAGATTCGGGCTTAAATCGG
1 GAAAACTGAGATTCGGGCTTAAATCGG
*
52802674 GAAAACTGAGATTTGGGCTTAAATCGG
1 GAAAACTGAGATTCGGGCTTAAATCGG
52802701 GAAA
1 GAAA
52802705 GTTCGAGATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.29, T:0.22
Consensus pattern (27 bp):
GAAAACTGAGATTCGGGCTTAAATCGG
Found at i:52805852 original size:23 final size:24
Alignment explanation
Indices: 52805820--52805950 Score: 105
Period size: 23 Copynumber: 5.5 Consensus size: 24
52805810 CTGAGCTAAT
*
52805820 AAACAATAAGCT-TTATTGAGCTG
1 AAACAGTAAGCTCTTATTGAGCTG
*
52805843 AAACAGTAAGCTCTT-TTGAGTTG
1 AAACAGTAAGCTCTTATTGAGCTG
*
52805866 -AATAGTAAGCTC--ATTCGAGCTG
1 AAACAGTAAGCTCTTATT-GAGCTG
* **
52805888 AAATAGTAAGCTCCAATT-AGCTG
1 AAACAGTAAGCTCTTATTGAGCTG
*
52805911 AAAACAATAAGCTCTT-TTGAGCTG
1 -AAACAGTAAGCTCTTATTGAGCTG
52805935 ATATATCAGTAAGCTC
1 A-A-A-CAGTAAGCTC
52805951 ATACGAGCTG
Statistics
Matches: 88, Mismatches: 9, Indels: 19
0.76 0.08 0.16
Matches are distributed among these distances:
21 2 0.02
22 16 0.18
23 38 0.43
24 19 0.22
25 4 0.05
26 9 0.10
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (24 bp):
AAACAGTAAGCTCTTATTGAGCTG
Found at i:52810324 original size:15 final size:16
Alignment explanation
Indices: 52810304--52810333 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
52810294 ACACATTTGG
52810304 CTTTTAATTT-TTTTC
1 CTTTTAATTTATTTTC
52810319 CTTTTAATTTATTTT
1 CTTTTAATTTATTTT
52810334 ACCCCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.73
Consensus pattern (16 bp):
CTTTTAATTTATTTTC
Found at i:52812791 original size:46 final size:46
Alignment explanation
Indices: 52812738--52812913 Score: 189
Period size: 46 Copynumber: 3.8 Consensus size: 46
52812728 TGGTTGAGCA
52812738 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * * * * *
52812784 TCTGAACTCGTTGAGTTGAGTCTGAGTTC-GTGA--AATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
52812829 CATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
52812877 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52812914 GCGGGTTACA
Statistics
Matches: 104, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 3 0.03
46 61 0.59
47 26 0.25
48 3 0.03
50 3 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:52812894 original size:93 final size:93
Alignment explanation
Indices: 52812735--52812905 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
52812725 GGATGGTTGA
* * * *
52812735 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCTGAACTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
*
52812800 TGAGTCTGAGTTCGTGAAATGTAACTAG
66 TGAGTCCGAGTTCGTGAAATGTAACTAG
*
52812828 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
52812893 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
52812906 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTAAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAAATGTAACTAG
Found at i:52814759 original size:15 final size:15
Alignment explanation
Indices: 52814735--52814778 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
52814725 GAAGCCCAGA
*
52814735 ATAAATAAATCCAAG
1 ATAAAGAAATCCAAG
*
52814750 ATAAAGAAATCCATG
1 ATAAAGAAATCCAAG
* *
52814765 GTAAGGAAATCCAA
1 ATAAAGAAATCCAA
52814779 ATTATAATAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.18
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:52815315 original size:11 final size:11
Alignment explanation
Indices: 52815299--52815323 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52815289 TTTCACTAAG
52815299 AGAACCAGTTC
1 AGAACCAGTTC
52815310 AGAACCAGTTC
1 AGAACCAGTTC
52815321 AGA
1 AGA
52815324 GGAGATCCTA
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:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (11 bp):
AGAACCAGTTC
Found at i:52825640 original size:22 final size:23
Alignment explanation
Indices: 52825595--52825654 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 23
52825585 TCCATTGAGT
* * *
52825595 TGAAACAGTATGCTCTTTCAAGC
1 TGAAACAGTAAGCTCATACAAGC
*
52825618 T-AAACAGTAAGCTCATACGAGC
1 TGAAACAGTAAGCTCATACAAGC
**
52825640 TGAAATGGTAAGCTC
1 TGAAACAGTAAGCTC
52825655 CAATGAACTA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (23 bp):
TGAAACAGTAAGCTCATACAAGC
Found at i:52828269 original size:43 final size:41
Alignment explanation
Indices: 52828200--52828356 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 41
52828190 TGTGATTTAG
*
52828200 TGTAAGACCATATCT-GGACATTGGCATTGATTTGAGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATTGATTT--GATTACA
* ***
52828242 TGTAAGACCATGTCTGTGACATTGGCATCAT-ATTTGATTTTG
1 TGTAAGACCATGTCTGGGACATTGGCAT--TGATTTGATTACA
* * *
52828284 TGTAAGACCCTGTCTGGGACAATAGCATTGATATTTGATTACA
1 TGTAAGACCATGTCTGGGACATTGGCATTG--ATTTGATTACA
* * *
52828327 TGTAAGACCACGTTTGGGACGTTGGCATTG
1 TGTAAGACCATGTCTGGGACATTGGCATTG
52828357 TACGAGCTTT
Statistics
Matches: 91, Mismatches: 18, Indels: 11
0.76 0.15 0.09
Matches are distributed among these distances:
40 1 0.01
42 42 0.46
43 43 0.47
44 4 0.04
45 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATTGATTTGATTACA
Found at i:52828334 original size:85 final size:84
Alignment explanation
Indices: 52828187--52828354 Score: 212
Period size: 85 Copynumber: 2.0 Consensus size: 84
52828177 AGGATTTCCG
* *
52828187 ATATGTGATTTAGTGTAAGACCATATCTGGACATTGGCATTGATTTGAGATTACATGTAAGACCA
1 ATATGTGATTTAGTGTAAGACCATATCTGGACAATAGCATTGATTTGAGATTACATGTAAGACCA
* *
52828252 TGTCTGTGACATTGGCATC
66 CGTCTGGGACATTGGCATC
* * * * *
52828271 ATATTTGATTTTGTGTAAGACCCTGTCTGGGACAATAGCATTGATATT-TGATTACATGTAAGAC
1 ATATGTGATTTAGTGTAAGACCATATCT-GGACAATAGCATTGAT-TTGAGATTACATGTAAGAC
* *
52828335 CACGTTTGGGACGTTGGCAT
64 CACGTCTGGGACATTGGCAT
52828355 TGTACGAGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
84 24 0.34
85 45 0.63
86 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.35
Consensus pattern (84 bp):
ATATGTGATTTAGTGTAAGACCATATCTGGACAATAGCATTGATTTGAGATTACATGTAAGACCA
CGTCTGGGACATTGGCATC
Found at i:52833768 original size:24 final size:25
Alignment explanation
Indices: 52833718--52833768 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 25
52833708 CTCGCTTGTA
* *
52833718 CTTCCCGATATATGGCTATCCAGAG
1 CTTCCCGATATATGGCTATACAAAG
* *
52833743 CTTCCCGTTA-ATGGCTCTACAAAG
1 CTTCCCGATATATGGCTATACAAAG
52833767 CT
1 CT
52833769 ACTAGTTATT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (25 bp):
CTTCCCGATATATGGCTATACAAAG
Found at i:52834235 original size:17 final size:17
Alignment explanation
Indices: 52834191--52834236 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 17
52834181 GAAATACATG
*
52834191 GAAATG-ATGGTAT-AT
1 GAAATGAATGATATAAT
*
52834206 GAAAT-ATTGATATAAT
1 GAAATGAATGATATAAT
52834222 GAAATGAATGATATA
1 GAAATGAATGATATA
52834237 TGTTTAGGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 10 0.40
16 7 0.28
17 8 0.32
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.33
Consensus pattern (17 bp):
GAAATGAATGATATAAT
Found at i:52843290 original size:40 final size:40
Alignment explanation
Indices: 52843219--52843403 Score: 248
Period size: 40 Copynumber: 4.7 Consensus size: 40
52843209 ATTGTATGAA
* * *
52843219 TGCACATACGTTCCCCTA-TTGTACTTCGGTACTCCTAGT
1 TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAT
* * * * *
52843258 TGCACATACGTGCCTCTGTTTTTACTTCGGTACCCTTGAT
1 TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAT
* *
52843298 TGCACATACGTGTCCCTA-TTGTACTTCAGTACCCCTAAT
1 TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAT
*
52843337 TGCACATATGTGCCCCTATTTGTACTTCGGTACCCCTAAT
1 TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAT
*
52843377 TGCACATACATGCCCCTATTTGTACTT
1 TGCACATACGTGCCCCTATTTGTACTT
52843404 TAGTACTCCT
Statistics
Matches: 124, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
39 48 0.39
40 76 0.61
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (40 bp):
TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCTAAT
Found at i:52843350 original size:79 final size:79
Alignment explanation
Indices: 52843219--52843431 Score: 250
Period size: 79 Copynumber: 2.7 Consensus size: 79
52843209 ATTGTATGAA
* * * * * *
52843219 TGCACATACGT-TCCCCTATTGTACTTCGGTACTCCTAGTTGCACATACGTGCCTCTGTTTTTAC
1 TGCACATACGTGT-CCCTATTGTACTTCAGTACCCCTAATTGCACATACGTGCCCCTATTTGTAC
* *
52843283 TTCGGTACCCTTGAT
65 TTCGGTACCCCTAAT
*
52843298 TGCACATACGTGTCCCTATTGTACTTCAGTACCCCTAATTGCACATATGTGCCCCTATTTGTACT
1 TGCACATACGTGTCCCTATTGTACTTCAGTACCCCTAATTGCACATACGTGCCCCTATTTGTACT
52843363 TCGGTACCCCTAAT
66 TCGGTACCCCTAAT
* * * * * *
52843377 TGCACATACATGCCCCTATTTGTACTTTAGTACTCCTGAA-TGCACTTACATGCCC
1 TGCACATACGTGTCCCTA-TTGTACTTCAGTACCCCT-AATTGCACATACGTGCCC
52843432 TTGATTATAT
Statistics
Matches: 115, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
79 84 0.73
80 29 0.25
81 2 0.02
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.35
Consensus pattern (79 bp):
TGCACATACGTGTCCCTATTGTACTTCAGTACCCCTAATTGCACATACGTGCCCCTATTTGTACT
TCGGTACCCCTAAT
Found at i:52843352 original size:20 final size:20
Alignment explanation
Indices: 52843296--52843394 Score: 69
Period size: 20 Copynumber: 5.0 Consensus size: 20
52843286 GGTACCCTTG
*
52843296 ATTGCACATACGTGTCCCT-
1 ATTGCACATACGTGCCCCTA
* * *
52843315 ATTGTAC-TTCAGTACCCCTA
1 ATTGCACATAC-GTGCCCCTA
*
52843335 ATTGCACATATGTGCCCCTA
1 ATTGCACATACGTGCCCCTA
* * * *
52843355 TTTGTAC-TTCGGTACCCCTA
1 ATTGCACATAC-GTGCCCCTA
*
52843375 ATTGCACATACATGCCCCTA
1 ATTGCACATACGTGCCCCTA
52843395 TTTGTACTTT
Statistics
Matches: 57, Mismatches: 18, Indels: 9
0.68 0.21 0.11
Matches are distributed among these distances:
18 2 0.04
19 13 0.23
20 39 0.68
21 3 0.05
ACGTcount: A:0.23, C:0.31, G:0.13, T:0.32
Consensus pattern (20 bp):
ATTGCACATACGTGCCCCTA
Found at i:52843421 original size:40 final size:39
Alignment explanation
Indices: 52843217--52843431 Score: 218
Period size: 40 Copynumber: 5.4 Consensus size: 39
52843207 CTATTGTATG
* *
52843217 AATGCACATACGTTCCCCTA-TTGTACTTCGGTACTCCT
1 AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
* * * * *
52843255 AGTTGCACATACGTGCCTCTGTTTTTACTTCGGTACCCTT
1 A-ATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
* * *
52843295 GATTGCACATACGTGTCCCTA-TTGTACTTCAGTACCCCT
1 -AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
*
52843334 AATTGCACATATGTGCCCCTATTTGTACTTCGGTACCCCT
1 AA-TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
* ** *
52843374 AATTGCACATACATGCCCCTATTTGTACTTTAGTACTCCT
1 AA-TGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
* *
52843414 GAATGCACTTACATGCCC
1 -AATGCACATACGTGCCC
52843432 TTGATTATAT
Statistics
Matches: 148, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
38 2 0.01
39 46 0.31
40 97 0.66
41 3 0.02
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (39 bp):
AATGCACATACGTGCCCCTATTTGTACTTCGGTACCCCT
Found at i:52845597 original size:29 final size:29
Alignment explanation
Indices: 52845507--52845617 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 29
52845497 ACCCCTACAT
* *
52845507 ACATGCATATAGCCCACTAGGCCCAA-TC
1 ACATTCATATGGCCCACTAGGCCCAATTC
** * * *
52845535 TTATTCAAATGGCCCTTCT--GTCCAATTC
1 ACATTCATATGGCCC-ACTAGGCCCAATTC
* *
52845563 ATATTCTTATGGCCCACTAGGCCCAATTC
1 ACATTCATATGGCCCACTAGGCCCAATTC
*
52845592 ACATTCATATGGCCCATTAGGCCCAA
1 ACATTCATATGGCCCACTAGGCCCAA
52845618 ATCATATTAT
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
27 7 0.11
28 24 0.38
29 33 0.52
ACGTcount: A:0.27, C:0.32, G:0.14, T:0.28
Consensus pattern (29 bp):
ACATTCATATGGCCCACTAGGCCCAATTC
Found at i:52849102 original size:45 final size:46
Alignment explanation
Indices: 52848939--52849167 Score: 223
Period size: 50 Copynumber: 4.8 Consensus size: 46
52848929 ATCAAAGTCA
* * * *
52848939 ATGCCATGTCCCAGACATGGTCTTATACTGACTCTCATATATCGAGGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGA----CACATATCGATGCCG
* * * *
52848989 ATGCCATGTCCCAAACATGGTCTTACACTGGCTC-TCATCTGTTGGTGTCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACACAT-ATC----GATGCCG
* *
52849039 ATGCCATGTCCCAGACATGGTCTTACACTGACACATATC-AAGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACACATATCGATGCCG
*
52849084 ATGCCATGTCCCAAACATGCTCTTACACTGACACATATC-ATGCCG
1 ATGCCATGTCCCAAACATGGTCTTACACTGACACATATCGATGCCG
*
52849129 ATGCCATGTTCCAAACAT-GTCTTACACTAGCACACATAT
1 ATGCCATGTCCCAAACATGGTCTTACACT-G-ACACATAT
52849168 TACCAAAATG
Statistics
Matches: 152, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
44 9 0.06
45 64 0.42
46 12 0.08
50 66 0.43
51 1 0.01
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (46 bp):
ATGCCATGTCCCAAACATGGTCTTACACTGACACATATCGATGCCG
Found at i:52851000 original size:23 final size:23
Alignment explanation
Indices: 52850973--52851030 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
52850963 ACATATTTGA
52850973 TTATTTGA-TTTCTCGTTTCTCAT
1 TTATTT-ACTTTCTCGTTTCTCAT
**
52850996 TTATTTACTTTTCTTTTTTCTCAT
1 TTATTTAC-TTTCTCGTTTCTCAT
52851020 TTATTTACTTT
1 TTATTTACTTT
52851031 TCTTTTATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
22 1 0.03
23 9 0.29
24 21 0.68
ACGTcount: A:0.14, C:0.16, G:0.03, T:0.67
Consensus pattern (23 bp):
TTATTTACTTTCTCGTTTCTCAT
Found at i:52851015 original size:24 final size:24
Alignment explanation
Indices: 52850988--52851036 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
52850978 TGATTTCTCG
52850988 TTTCTCATTTATTTACTTTTCTTT
1 TTTCTCATTTATTTACTTTTCTTT
52851012 TTTCTCATTTATTTACTTTTCTTT
1 TTTCTCATTTATTTACTTTTCTTT
52851036 T
1 T
52851037 ATTTCCTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.71
Consensus pattern (24 bp):
TTTCTCATTTATTTACTTTTCTTT
Found at i:52852300 original size:50 final size:52
Alignment explanation
Indices: 52852236--52852354 Score: 163
Period size: 50 Copynumber: 2.3 Consensus size: 52
52852226 TTAATAAAGC
* * * *
52852236 CATGCCTTATGTAACTCTCATGTTAGTT-AGGTTTGCATCA-TAAATTATGA-
1 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATTA-CAT
52852286 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATTACAT
1 CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATTACAT
*
52852338 CATGCATTAAGTAACTC
1 CATGCATTATGTAACTC
52852355 ATTTGTTCAT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
50 26 0.43
51 12 0.20
52 23 0.38
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (52 bp):
CATGCATTATGTAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATTACAT
Found at i:52854193 original size:16 final size:16
Alignment explanation
Indices: 52854174--52854209 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
52854164 CTTAAAAAAT
52854174 ATAAAAATTAAAAT-TA
1 ATAAAAA-TAAAATATA
52854190 ATAAAAATAAAATATA
1 ATAAAAATAAAATATA
52854206 ATAA
1 ATAA
52854210 TTAAATTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
ATAAAAATAAAATATA
Found at i:52854199 original size:22 final size:23
Alignment explanation
Indices: 52854158--52854201 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
52854148 GACTAAAATT
52854158 TTAAAACTTAAAAAATATAAAAA
1 TTAAAACTTAAAAAATATAAAAA
52854181 TTAAAA-TTAATAAAA-ATAAAA
1 TTAAAACTTAA-AAAATATAAAA
52854202 TATAATAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (23 bp):
TTAAAACTTAAAAAATATAAAAA
Found at i:52855245 original size:26 final size:31
Alignment explanation
Indices: 52855213--52855277 Score: 77
Period size: 29 Copynumber: 2.2 Consensus size: 31
52855203 GTTAGTGATT
52855213 TAATATA-AAT-ATATAATTAT-TATT-TAA
1 TAATATAGAATAATATAATTATCTATTATAA
*
52855240 -AATATATGATTAATATAATTATCTATTATAA
1 TAATATA-GAATAATATAATTATCTATTATAA
52855271 TAATATA
1 TAATATA
52855278 TTCGAGTCGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 6 0.19
28 2 0.06
29 10 0.32
30 4 0.13
31 3 0.10
32 6 0.19
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (31 bp):
TAATATAGAATAATATAATTATCTATTATAA
Found at i:52855915 original size:37 final size:38
Alignment explanation
Indices: 52855873--52855951 Score: 108
Period size: 37 Copynumber: 2.1 Consensus size: 38
52855863 ATTGACACAC
* *
52855873 TTTTAAATAATAAAAATTTAATATAAA-TCCTTAATT-T
1 TTTTAAATAACAAAAATTCAATATAAATTCC-TAATTCT
*
52855910 TTTTAAATAACAAAAATTCAATCTAAATTCCTAATTCT
1 TTTTAAATAACAAAAATTCAATATAAATTCCTAATTCT
52855948 TTTT
1 TTTT
52855952 CTTCTTGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 29 0.78
38 8 0.22
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (38 bp):
TTTTAAATAACAAAAATTCAATATAAATTCCTAATTCT
Found at i:52864746 original size:20 final size:19
Alignment explanation
Indices: 52864683--52864767 Score: 75
Period size: 20 Copynumber: 4.4 Consensus size: 19
52864673 AGTTCAAAAC
*
52864683 TAAAAAA-ATTATAAATTA
1 TAAAAAATATTAAAAATTA
*
52864701 TAAAAAATATTAAAATTTA
1 TAAAAAATATTAAAAATTA
* * *
52864720 TTTAAAATTATTAAAAATCA
1 -TAAAAAATATTAAAAATTA
52864740 TAAAAAATCA-TAAGAAATTA
1 TAAAAAAT-ATTAA-AAATTA
52864760 TTAAAAAA
1 -TAAAAAA
52864768 AAGAATAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
18 7 0.13
19 18 0.34
20 21 0.40
21 7 0.13
ACGTcount: A:0.64, C:0.02, G:0.01, T:0.33
Consensus pattern (19 bp):
TAAAAAATATTAAAAATTA
Found at i:52864764 original size:39 final size:39
Alignment explanation
Indices: 52864690--52864766 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
52864680 AACTAAAAAA
* * *
52864690 ATTATAAATTATAAAAAATATTAAAATTTATTTAAAATT
1 ATTAAAAATCATAAAAAATATTAAAAATTATTTAAAATT
*
52864729 ATTAAAAATCATAAAAAATCA-TAAGAAATTATTAAAAA
1 ATTAAAAATCATAAAAAAT-ATTAA-AAATTATTTAAAA
52864767 AAAGAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 20 0.62
40 12 0.38
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (39 bp):
ATTAAAAATCATAAAAAATATTAAAAATTATTTAAAATT
Found at i:52866179 original size:25 final size:25
Alignment explanation
Indices: 52866107--52866183 Score: 77
Period size: 25 Copynumber: 3.1 Consensus size: 25
52866097 GGACTCACCA
*
52866107 CAACTCGTATGAGCTTACCGAT-TT
1 CAACTCGTATGAGCTTACCGATACT
* * * *
52866131 ACAGCTCATGA-GAGCCTACTGATACT
1 -CAACTCGT-ATGAGCTTACCGATACT
52866157 CAACTCGTATGAGCTTACCGATACT
1 CAACTCGTATGAGCTTACCGATACT
52866182 CA
1 CA
52866184 GCTCAGAAGT
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
24 1 0.03
25 37 0.93
26 2 0.05
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (25 bp):
CAACTCGTATGAGCTTACCGATACT
Found at i:52871368 original size:29 final size:29
Alignment explanation
Indices: 52871269--52871398 Score: 116
Period size: 30 Copynumber: 4.4 Consensus size: 29
52871259 CGTATAAGTG
* * * * *
52871269 AGCCTTTGTGGCAATCTTTGTTAAAATGGA
1 AGCCTTTGTGGCGATATTTATTATAA-GAA
* *
52871299 AGCCTTAGTGGCTATATTTATTATAATGAA
1 AGCCTTTGTGGCGATATTTATTATAA-GAA
* * *
52871329 AGTCTTTGTGGCGAAATCTATTATAAGAA
1 AGCCTTTGTGGCGATATTTATTATAAGAA
* *
52871358 AGCCTTTGTGGCGATCTTTGTTATAAGAA
1 AGCCTTTGTGGCGATATTTATTATAAGAA
* *
52871387 AACCTTTATGGC
1 AGCCTTTGTGGC
52871399 TATCTCTGTC
Statistics
Matches: 82, Mismatches: 18, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
29 37 0.45
30 45 0.55
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (29 bp):
AGCCTTTGTGGCGATATTTATTATAAGAA
Found at i:52871421 original size:29 final size:29
Alignment explanation
Indices: 52871389--52871478 Score: 110
Period size: 29 Copynumber: 3.1 Consensus size: 29
52871379 TATAAGAAAA
* *
52871389 CCTTTATGGCTATCTCTGTCAAAAGGATT
1 CCTTTATGGCTATCTCTATCAAAAGGATG
* *
52871418 CCTTTATGGTTATATCTATCAAAAGGATG
1 CCTTTATGGCTATCTCTATCAAAAGGATG
* *
52871447 CCTTTATGGCTATCGCTAT-TAAAGGAATG
1 CCTTTATGGCTATCTCTATCAAAAGG-ATG
52871476 CCT
1 CCT
52871479 GGTGGCAAAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 5 0.10
29 47 0.90
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.37
Consensus pattern (29 bp):
CCTTTATGGCTATCTCTATCAAAAGGATG
Found at i:52874937 original size:27 final size:27
Alignment explanation
Indices: 52874907--52875073 Score: 237
Period size: 27 Copynumber: 6.2 Consensus size: 27
52874897 TTAGTTTACC
52874907 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* **
52874934 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCCTGGTTTGTA
52874961 AAATTACCAAAATACCCCTGGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
* * *
52874988 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCCTGGTTTGTA
*
52875015 AAA-TACCAAAATACCCCTAGTTTGTA
1 AAATTACCAAAATACCCCTGGTTTGTA
** *
52875041 AAATTACCAAAATACCCCTAATTTGTG
1 AAATTACCAAAATACCCCTGGTTTGTA
52875068 AAATTA
1 AAATTA
52875074 TTGAAATACC
Statistics
Matches: 124, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
26 22 0.18
27 102 0.82
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGGTTTGTA
Found at i:52875045 original size:53 final size:54
Alignment explanation
Indices: 52874900--52875057 Score: 273
Period size: 54 Copynumber: 2.9 Consensus size: 54
52874890 GAATACTTTA
*
52874900 GTTTACCAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
*
52874954 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTTG
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
* *
52875008 GTTTATAAAA-TACCAAAATACCCCTAGTTTGTAAAATTACCAAAATACCC
1 GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCC
52875058 CTAATTTGTG
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
53 38 0.38
54 61 0.62
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (54 bp):
GTTTACAAAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTG
Found at i:52875049 original size:80 final size:81
Alignment explanation
Indices: 52874907--52875085 Score: 243
Period size: 80 Copynumber: 2.2 Consensus size: 81
52874897 TTAGTTTACC
* * * * *
52874907 AAATTACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCTTGGTTTACAAAATTACCAAA
1 AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAA
**
52874972 ATACCCCTGGTTTGTA
66 ATACCCCTAATTTGTA
**
52874988 AAATTACTAAAATACCCTTGGTTTATAAAA-TACCAAAATACCCCTAGTTTGTAAAATTACCAAA
1 AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAA
*
52875052 ATACCCCTAATTTGTG
66 ATACCCCTAATTTGTA
* *
52875068 AAATTATTGAAATACCCT
1 AAATTACTAAAATACCCT
52875086 CGACCTATAA
Statistics
Matches: 86, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
80 59 0.69
81 27 0.31
ACGTcount: A:0.40, C:0.21, G:0.08, T:0.31
Consensus pattern (81 bp):
AAATTACTAAAATACCCTTGGTTTATAAAATTACCAAAATACCCCTAGTTTACAAAATTACCAAA
ATACCCCTAATTTGTA
Found at i:52875191 original size:27 final size:27
Alignment explanation
Indices: 52874907--52875193 Score: 170
Period size: 27 Copynumber: 10.7 Consensus size: 27
52874897 TTAGTTTACC
* *
52874907 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
52874934 AAATTACCAAAATACCCTTGGTTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* *
52874961 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTATA
* * *
52874988 AAATTACTAAAATACCCTTGGTTTATA
1 AAATTACCAAAATACCCTCGATTTATA
* *
52875015 AAA-TACCAAAATACCC-CTAGTTTGTA
1 AAATTACCAAAATACCCTCGA-TTTATA
* * *
52875041 AAATTACCAAAATACCC-CTAATTTGTG
1 AAATTACCAAAATACCCTC-GATTTATA
*** **
52875068 AAATTATTGAAATACCCTCGACCTATA
1 AAATTACCAAAATACCCTCGATTTATA
*** * * *
52875095 AAATTATTGAAATACCATCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTATA
* ** *
52875122 AAATTACCAAAGTACCCTTAATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
* **** *
52875149 GAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTATA
*
52875176 AAATTACCGAAATACCCT
1 AAATTACCAAAATACCCT
52875194 TGTAGGGAGA
Statistics
Matches: 205, Mismatches: 48, Indels: 14
0.77 0.18 0.05
Matches are distributed among these distances:
26 20 0.10
27 183 0.89
28 2 0.01
ACGTcount: A:0.39, C:0.22, G:0.08, T:0.31
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTATA
Found at i:52875206 original size:27 final size:27
Alignment explanation
Indices: 52875176--52875425 Score: 173
Period size: 27 Copynumber: 9.3 Consensus size: 27
52875166 TCGATTTACA
52875176 AAATTACCGAAATACCCTTGTAGGGAG
1 AAATTACCGAAATACCCTTGTAGGGAG
52875203 AAATGT--CGAAATACCCTTGTAGGGTAG
1 AAAT-TACCGAAATACCCTTGTAGGG-AG
** * *
52875230 AAA-TACTAAAATACCCCTGTAGGATAG
1 AAATTACCGAAATACCCTTGTAGG-GAG
* *
52875257 AAA-TACCGAAATACCCCTGTAAGGTAG
1 AAATTACCGAAATACCCTTGT-AGGGAG
** * *
52875284 -AATTACTAAAATACCTTTGTAGTGTAG
1 AAATTACCGAAATACCCTTGTAG-GGAG
*
52875311 -AATTACCGAAATACCATTGTAGGGTAG
1 AAATTACCGAAATACCCTTGTAGGG-AG
* *
52875338 AAA-TATCGAAATACCCCTGTAGGGTAG
1 AAATTACCGAAATACCCTTGTAGGG-AG
* *
52875365 -AATTACTGAAATACTCC-TGTAAGGTAG
1 AAATTACCGAAATAC-CCTTGT-AGGGAG
*
52875392 -AATTACC-AATATACCCTTGTGGGGTA-
1 AAATTACCGAA-ATACCCTTGTAGGG-AG
52875418 AAATTACC
1 AAATTACC
52875426 ATTTTACCCC
Statistics
Matches: 183, Mismatches: 23, Indels: 34
0.76 0.10 0.14
Matches are distributed among these distances:
25 1 0.01
26 31 0.17
27 140 0.77
28 11 0.06
ACGTcount: A:0.38, C:0.17, G:0.19, T:0.26
Consensus pattern (27 bp):
AAATTACCGAAATACCCTTGTAGGGAG
Found at i:52875417 original size:54 final size:52
Alignment explanation
Indices: 52875177--52875425 Score: 230
Period size: 54 Copynumber: 4.6 Consensus size: 52
52875167 CGATTTACAA
* ** *
52875177 AATTACCGAAATACCCTTGTAGGG-AGAAATGTCGAAATACCCTTGTAGGGTAG
1 AATTACC-AAATACCCTTGTAGGGTAGAATTACCGAAATACCC-TGTAAGGTAG
* * * * *
52875230 AAATACTAAAATACCCCTGTAGGATAGAAATACCGAAATACCCCTGTAAGGTAG
1 AATTAC-CAAATACCCTTGTAGGGTAGAATTACCGAAATA-CCCTGTAAGGTAG
* * * * *
52875284 AATTACTAAAATACCTTTGTAGTGTAGAATTACCGAAATACCATTGTAGGGTAG
1 AATTAC-CAAATACCCTTGTAGGGTAGAATTACCGAAATACC-CTGTAAGGTAG
* * * *
52875338 AAATATCGAAATACCCCTGTAGGGTAGAATTACTGAAATACTCCTGTAAGGTAG
1 AATTA-CCAAATACCCTTGTAGGGTAGAATTACCGAAATAC-CCTGTAAGGTAG
* *
52875392 AATTACCAATATACCCTTGTGGGGTAAAATTACC
1 AATTACCAA-ATACCCTTGTAGGGTAGAATTACC
52875426 ATTTTACCCC
Statistics
Matches: 160, Mismatches: 29, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
53 24 0.15
54 131 0.82
55 5 0.03
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.26
Consensus pattern (52 bp):
AATTACCAAATACCCTTGTAGGGTAGAATTACCGAAATACCCTGTAAGGTAG
Found at i:52875417 original size:81 final size:79
Alignment explanation
Indices: 52875180--52875421 Score: 260
Period size: 81 Copynumber: 3.0 Consensus size: 79
52875170 TTTACAAAAT
* * * *
52875180 TACCGAAATACCCTTGTAGGG-AGAAATGT-C-GAAATACCCTTGTAGGGTAGAAATACTAAAAT
1 TACCGAAATACCCCTGTAGGGTAG-AAT-TACTGAAATACCC-TGTAAGGTAGAATTAC-CAAAT
* *
52875242 ACCCCTGTAGGATAGAAA
62 ACCCTTGTAGGGTAGAAA
* * *
52875260 TACCGAAATACCCCTGTAAGGTAGAATTACTAAAATACCTTTGT-AGTGTAGAATTACCGAAATA
1 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACC-CTGTAAG-GTAGAATTACC-AAATA
*
52875324 CCATTGTAGGGTAGAAA
63 CCCTTGTAGGGTAGAAA
*
52875341 TATCGAAATACCCCTGTAGGGTAGAATTACTGAAATACTCCTGTAAGGTAGAATTACCAATATAC
1 TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATAC-CCTGTAAGGTAGAATTACCAA-ATAC
*
52875406 CCTTGTGGGGTA-AAA
64 CCTTGTAGGGTAGAAA
52875421 T
1 T
52875422 TACCATTTTA
Statistics
Matches: 137, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
79 1 0.01
80 30 0.22
81 103 0.75
82 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (79 bp):
TACCGAAATACCCCTGTAGGGTAGAATTACTGAAATACCCTGTAAGGTAGAATTACCAAATACCC
TTGTAGGGTAGAAA
Found at i:52875849 original size:6 final size:6
Alignment explanation
Indices: 52875840--52876032 Score: 128
Period size: 6 Copynumber: 31.3 Consensus size: 6
52875830 TTGCATTCAC
* * *
52875840 ATTCTG ATTCTA ATTCTG ATTCTG -TTACCTG ATACTA ATTCTG ATTCTG
1 ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG
* * * * *
52875889 -TGACCTA ATTTTG ATTCTG GTTCTG ATTCTG ATTCTG -TTACCTG ATACTG
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG
* *
52875939 ATTCTG ATTCTG -TTACCTA ATTTTG ATTCTG ATTCTG ATTCTG ATTCTG
1 ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG
* * *
52875988 -TCACCTG ATTCTG ATTCTG ATTCTC ATTTTG ATTCT- AGTTCTG AT
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
52876033 AATGTTTCTT
Statistics
Matches: 144, Mismatches: 26, Indels: 34
0.71 0.13 0.17
Matches are distributed among these distances:
5 9 0.06
6 115 0.80
7 14 0.10
8 6 0.04
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (6 bp):
ATTCTG
Found at i:52875871 original size:25 final size:24
Alignment explanation
Indices: 52875840--52876032 Score: 128
Period size: 25 Copynumber: 7.8 Consensus size: 24
52875830 TTGCATTCAC
*
52875840 ATTCTGATTCTAATTCTGATTCTG
1 ATTCTGATTCTGATTCTGATTCTG
* *
52875864 -TTACCTGATACTAATTCTGATTCTG
1 ATT--CTGATTCTGATTCTGATTCTG
* * * *
52875889 -TGACCTAATTTTGATTCTGGTTCTG
1 AT--TCTGATTCTGATTCTGATTCTG
*
52875914 ATTCTGATTCTG-TTACCTGATACTG
1 ATTCTGATTCTGATT--CTGATTCTG
* *
52875939 ATTCTGATTCTG-TTACCTAATTTTG
1 ATTCTGATTCTGATT--CTGATTCTG
52875964 ATTCTGATTCTGATTCTGATTCTG
1 ATTCTGATTCTGATTCTGATTCTG
* *
52875988 -TCACCTGATTCTGATTCTGATTCTC
1 AT--TCTGATTCTGATTCTGATTCTG
*
52876013 ATTTTGATTCT-AGTTCTGAT
1 ATTCTGATTCTGA-TTCTGAT
52876033 AATGTTTCTT
Statistics
Matches: 136, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
23 6 0.04
24 28 0.21
25 98 0.72
26 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.15, T:0.48
Consensus pattern (24 bp):
ATTCTGATTCTGATTCTGATTCTG
Found at i:52875918 original size:37 final size:37
Alignment explanation
Indices: 52875868--52875950 Score: 103
Period size: 37 Copynumber: 2.2 Consensus size: 37
52875858 ATTCTGTTAC
* * **
52875868 CTGATACTAATTCTGATTCTGTGACCTAATTTTGATT
1 CTGATTCTGATTCTGATTCTGTGACCTAATACTGATT
* * *
52875905 CTGGTTCTGATTCTGATTCTGTTACCTGATACTGATT
1 CTGATTCTGATTCTGATTCTGTGACCTAATACTGATT
52875942 CTGATTCTG
1 CTGATTCTG
52875951 TTACCTAATT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.19, C:0.18, G:0.17, T:0.46
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTGACCTAATACTGATT
Found at i:52875937 original size:62 final size:62
Alignment explanation
Indices: 52875840--52876011 Score: 290
Period size: 62 Copynumber: 2.8 Consensus size: 62
52875830 TTGCATTCAC
* *
52875840 ATTCTGATTCTAATTCTGATTCTGTTACCTGATACTAATTCTGATTCTGTGACCTAATTTTG
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTGACCTAATTTTG
* *
52875902 ATTCTGGTTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTTACCTAATTTTG
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTGACCTAATTTTG
* *
52875964 ATTCTGATTCTGATTCTGATTCTGTCACCTGATTCTGATTCTGATTCT
1 ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCT
52876012 CATTTTGATT
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 103 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (62 bp):
ATTCTGATTCTGATTCTGATTCTGTTACCTGATACTGATTCTGATTCTGTGACCTAATTTTG
Found at i:52875971 original size:37 final size:37
Alignment explanation
Indices: 52875930--52876023 Score: 134
Period size: 37 Copynumber: 2.5 Consensus size: 37
52875920 ATTCTGTTAC
* * *
52875930 CTGATACTGATTCTGATTCTGTTACCTAATTTTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
*
52875967 CTGATTCTGATTCTGATTCTGTCACCTGATTCTGATT
1 CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
* *
52876004 CTGATTCTCATTTTGATTCT
1 CTGATTCTGATTCTGATTCT
52876024 AGTTCTGATA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.18, C:0.19, G:0.14, T:0.49
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTCACCTAATTCTGATT
Found at i:52877528 original size:23 final size:23
Alignment explanation
Indices: 52877491--52877577 Score: 115
Period size: 23 Copynumber: 3.8 Consensus size: 23
52877481 TGATGGACAA
*
52877491 TAAGCTC-TACTGAGCTGAAACGG
1 TAAGCTCTTAC-GAGCTGAAACAG
*
52877514 TAAGCT-TTGACGAGCTGAATCAG
1 TAAGCTCTT-ACGAGCTGAAACAG
52877537 TAAGCTCTTACGAGCTGAAACAG
1 TAAGCTCTTACGAGCTGAAACAG
*
52877560 TAAGCTCTTATGAGCTGA
1 TAAGCTCTTACGAGCTGA
52877578 TATATCGGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
23 53 0.93
24 4 0.07
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (23 bp):
TAAGCTCTTACGAGCTGAAACAG
Found at i:52881869 original size:25 final size:25
Alignment explanation
Indices: 52881851--52881901 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
52881841 TTGCACATAT
*
52881851 ATATATACTCATACATTGCTATTAC
1 ATATATACTCATACATTGCTAATAC
* *
52881876 ATATATACTCATGCATTGCTATTAC
1 ATATATACTCATACATTGCTAATAC
52881901 A
1 A
52881902 ACCGAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (25 bp):
ATATATACTCATACATTGCTAATAC
Found at i:52885419 original size:13 final size:13
Alignment explanation
Indices: 52885401--52885425 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52885391 GTAAGTGATT
52885401 TTGATGATTTTTC
1 TTGATGATTTTTC
52885414 TTGATGATTTTT
1 TTGATGATTTTT
52885426 GTACTTTTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.04, G:0.16, T:0.64
Consensus pattern (13 bp):
TTGATGATTTTTC
Found at i:52886417 original size:26 final size:26
Alignment explanation
Indices: 52886383--52886435 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
52886373 AGCTCTTAGG
52886383 AGTAAACTATCCATGTATCCATTGGT
1 AGTAAACTATCCATGTATCCATTGGT
*
52886409 AGTATACTATCCATGTATCCATTGGT
1 AGTAAACTATCCATGTATCCATTGGT
52886435 A
1 A
52886436 TTTCCGAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.36
Consensus pattern (26 bp):
AGTAAACTATCCATGTATCCATTGGT
Found at i:52887598 original size:21 final size:21
Alignment explanation
Indices: 52887567--52887622 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
52887557 GTTATAATGA
*
52887567 CCACACAGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
52887588 CCGCACGGGCGTGTTGCCCTT
1 CCACACGGGCGTGTTGCCCTT
*
52887609 CTACACGGGCGTGT
1 CCACACGGGCGTGT
52887623 GCCTTGTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.11, C:0.36, G:0.30, T:0.23
Consensus pattern (21 bp):
CCACACGGGCGTGTTGCCCTT
Found at i:52903871 original size:68 final size:65
Alignment explanation
Indices: 52903663--52903908 Score: 205
Period size: 68 Copynumber: 3.7 Consensus size: 65
52903653 CCTAGCTCGA
* * * * *
52903663 TTGTACACATGGTGAACACATAGTATCACCCATGTGACCTAGCCAC-TTTA-TCTCGTAGCTCTC
1 TTGTACACATGGTGTACACATAGTACCACACATGTGACCTAGCTACATCTATTCTCGTAGCTCTC
** * * * * ** *
52903726 TTGTTTACATGGTGTCCTTCACCTGGAACCACACATGCAACCTAGCTACATCTA-TCTCTTAGCT
1 TTGTACACATGGTG---TACACATAGTACCACACATGTGACCTAGCTACATCTATTCTCGTAGCT
52903790 CTC
63 CTC
* *
52903793 TTGT-CTACATGGTGTACACATAGTATCACCCATGTGACCTAGCTACATCGTAATGTCTCGTAGC
1 TTGTAC-ACATGGTGTACACATAGTACCACACATGTGACCTAGCTACATC-T-AT-TCTCGTAGC
52903857 TCTC
62 TCTC
* * * *
52903861 TTGTACACATGATGTGCAC-TCAGCACCATACATGTGACCTAGCTACAT
1 TTGTACACATGGTGTACACAT-AGTACCACACATGTGACCTAGCTACAT
52903909 ACCATCTGTA
Statistics
Matches: 142, Mismatches: 30, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
63 12 0.08
64 27 0.19
65 1 0.01
66 23 0.16
67 28 0.20
68 50 0.35
69 1 0.01
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.31
Consensus pattern (65 bp):
TTGTACACATGGTGTACACATAGTACCACACATGTGACCTAGCTACATCTATTCTCGTAGCTCTC
Found at i:52909341 original size:21 final size:22
Alignment explanation
Indices: 52909298--52909341 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
52909288 TTCGTATTAG
*
52909298 TGACTTTATATTTTAATGCAAA
1 TGACTTTATATTTGAATGCAAA
* *
52909320 TGACTTTA-ATTTGGATGGAAA
1 TGACTTTATATTTGAATGCAAA
52909341 T
1 T
52909342 TTATGACTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (22 bp):
TGACTTTATATTTGAATGCAAA
Found at i:52913655 original size:6 final size:6
Alignment explanation
Indices: 52913637--52913787 Score: 98
Period size: 6 Copynumber: 24.3 Consensus size: 6
52913627 AAGAAACATT
*
52913637 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
52913686 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATTAGA ATCA-A TATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA -ATCA-G-A
* * *
52913737 A-CAGA ATCAAA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAAA ATCAGA
1 ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATC-AGA ATCAGA
52913786 AT
1 AT
52913788 GTGAATGCAG
Statistics
Matches: 114, Mismatches: 14, Indels: 34
0.70 0.09 0.21
Matches are distributed among these distances:
5 9 0.08
6 83 0.73
7 17 0.15
8 4 0.04
9 1 0.01
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:52913658 original size:18 final size:18
Alignment explanation
Indices: 52913637--52913787 Score: 98
Period size: 19 Copynumber: 8.1 Consensus size: 18
52913627 AAGAAACATT
52913637 ATCAGAA-CTAGAATCAGA
1 ATCAGAATC-AGAATCAGA
52913655 ATCAGAATCAGAATCAG-
1 ATCAGAATCAGAATCAGA
*
52913672 GTGACAGAATCAGAATCAGA
1 AT--CAGAATCAGAATCAGA
*
52913692 ATCAGTATCAGGTAA-CAGA
1 ATCAGAATCA-G-AATCAGA
* *
52913711 ATCAAAATTAGAATCA-A
1 ATCAGAATCAGAATCAGA
*
52913728 TATCAGGTAA-CAGAATCAAA
1 -ATCA-G-AATCAGAATCAGA
*
52913748 ATCAGAATCAGTATCAGGTA
1 ATCAGAATCAGAATCA-G-A
*
52913768 A-CAGAATCAAAAATCAGA
1 ATCAGAATC-AGAATCAGA
52913786 AT
1 AT
52913788 GTGAATGCAG
Statistics
Matches: 105, Mismatches: 12, Indels: 31
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.06
18 39 0.37
19 47 0.45
20 13 0.12
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (18 bp):
ATCAGAATCAGAATCAGA
Found at i:52913684 original size:31 final size:31
Alignment explanation
Indices: 52913646--52913787 Score: 205
Period size: 31 Copynumber: 4.5 Consensus size: 31
52913636 TATCAGAACT
* *
52913646 AGAATCAGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
* *
52913677 AGAATCAGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
*
52913708 AGAATCAAAATTAGAATCA-ATATCAGGTAAC
1 AGAATCAAAATCAGAATCAGA-ATCAGGTAAC
*
52913739 AGAATCAAAATCAGAATCAGTATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
52913770 AGAATCAAAAATCAGAAT
1 AGAATC-AAAATCAGAAT
52913788 GTGAATGCAG
Statistics
Matches: 101, Mismatches: 7, Indels: 5
0.89 0.06 0.04
Matches are distributed among these distances:
31 90 0.89
32 11 0.11
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAAC
Found at i:52913724 original size:62 final size:62
Alignment explanation
Indices: 52913621--52913787 Score: 223
Period size: 62 Copynumber: 2.7 Consensus size: 62
52913611 TAACCCATTA
* * * * *
52913621 CAGAATAAGAAACATTATCA-G-AACTAGAATCAGAATCAGAATCAGA-ATCAGGTGACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAAC-AGAATCAAAATCAGAATCA-ATATCAGGTAACAGAAT
*
52913682 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATTAGAATCAATATCAGGTAACAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAATATCAGGTAACAGAAT
*
52913744 CAAAATCAGAATCAGTATCAGGTAACAGAATCAAAAATCAGAAT
1 CAGAATCAGAATCAGTATCAGGTAACAGAATC-AAAATCAGAAT
52913788 GTGAATGCAG
Statistics
Matches: 94, Mismatches: 8, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
61 18 0.19
62 63 0.67
63 13 0.14
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (62 bp):
CAGAATCAGAATCAGTATCAGGTAACAGAATCAAAATCAGAATCAATATCAGGTAACAGAAT
Found at i:52913966 original size:27 final size:27
Alignment explanation
Indices: 52913936--52914024 Score: 99
Period size: 27 Copynumber: 3.3 Consensus size: 27
52913926 GAATTGTGAT
* *
52913936 AGAGTCACCAGAAATAGATATTGTGGC
1 AGAGCCACCAGAAACAGATATTGTGGC
*
52913963 AGAGCCACCAG-AACAGATATTTGTGGT
1 AGAGCCACCAGAAACAGATA-TTGTGGC
* * *
52913990 ATAGCCACTAGAAACAGATAATGTGGC
1 AGAGCCACCAGAAACAGATATTGTGGC
*
52914017 AAAGCCAC
1 AGAGCCAC
52914025 TTAACAGAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
26 7 0.13
27 37 0.71
28 8 0.15
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (27 bp):
AGAGCCACCAGAAACAGATATTGTGGC
Found at i:52914210 original size:22 final size:22
Alignment explanation
Indices: 52914182--52914246 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
52914172 GCAAATACGT
*
52914182 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
*
52914204 TTGGCACAAAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
52914226 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
52914247 AAGGCTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.05
22 33 0.89
23 2 0.05
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:52914780 original size:52 final size:52
Alignment explanation
Indices: 52914630--52914788 Score: 133
Period size: 52 Copynumber: 3.0 Consensus size: 52
52914620 AGTCACTTGG
* * * *
52914630 CCACCAGGGCAAAACAATCATTTAACACCTTAGAGGCAAAATGGTAATTTTA
1 CCACCAGGGTAAAACAGTCATTTAACACCTTAGGGGAAAAATGGTAATTTTA
* * *** * * * *** *
52914682 CCCCACAAGGTATCTCAGTAATTCT-AC-CCTACAGGGGTATTTTGGTAATTCTA
1 CCAC-CAGGGTAAAACAGTCATT-TAACACCT-TAGGGGAAAAATGGTAATTTTA
52914735 CCACCAGGGTAAAACAGTCATTTAACACCTTAGGGGAAAAATGGTAATTTTA
1 CCACCAGGGTAAAACAGTCATTTAACACCTTAGGGGAAAAATGGTAATTTTA
52914787 CC
1 CC
52914789 CCACAAGGTA
Statistics
Matches: 75, Mismatches: 27, Indels: 10
0.67 0.24 0.09
Matches are distributed among these distances:
51 1 0.01
52 39 0.52
53 34 0.45
54 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (52 bp):
CCACCAGGGTAAAACAGTCATTTAACACCTTAGGGGAAAAATGGTAATTTTA
Found at i:52914787 original size:105 final size:105
Alignment explanation
Indices: 52914630--52914841 Score: 379
Period size: 105 Copynumber: 2.0 Consensus size: 105
52914620 AGTCACTTGG
*
52914630 CCACCAGGGCAAAACAATCATTTAACACCTTAGAGGCAAAATGGTAATTTTACCCCACAAGGTAT
1 CCACCAGGGCAAAACAATCATTTAACACCTTAGAGGAAAAATGGTAATTTTACCCCACAAGGTAT
52914695 CTCAGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTA
66 CTCAGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTA
* * *
52914735 CCACCAGGGTAAAACAGTCATTTAACACCTTAGGGGAAAAATGGTAATTTTACCCCACAAGGTAT
1 CCACCAGGGCAAAACAATCATTTAACACCTTAGAGGAAAAATGGTAATTTTACCCCACAAGGTAT
*
52914800 CTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTA
66 CTCAGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTA
52914840 CC
1 CC
52914842 CTATAGGGGT
Statistics
Matches: 102, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
105 102 1.00
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (105 bp):
CCACCAGGGCAAAACAATCATTTAACACCTTAGAGGAAAAATGGTAATTTTACCCCACAAGGTAT
CTCAGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTA
Found at i:52914833 original size:27 final size:27
Alignment explanation
Indices: 52914777--52914952 Score: 237
Period size: 27 Copynumber: 6.6 Consensus size: 27
52914767 GGGGAAAAAT
* * * *
52914777 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
52914803 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
*
52914830 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
52914857 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52914884 GGCAATTCTACCCTACAGGGGTATTGC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
52914911 GATAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
52914938 AGTAATTCTACCCTA
1 GGTAATTCTACCCTA
52914953 TATTTTAGTA
Statistics
Matches: 131, Mismatches: 18, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
26 15 0.11
27 116 0.89
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:52915020 original size:27 final size:27
Alignment explanation
Indices: 52914953--52915452 Score: 232
Period size: 27 Copynumber: 18.5 Consensus size: 27
52914943 TTCTACCCTA
* **
52914953 TATTTTAGTAATTCCACAAATCAGGGG
1 TATTTTGGTAATTTTACAAATCAGGGG
*
52914980 TATTTTGGTAATTTTACAAACCAGGGG
1 TATTTTGGTAATTTTACAAATCAGGGG
***
52915007 TATTTTGGTAATTTTATTGATC-GAGGG
1 TATTTTGGTAATTTTACAAATCAG-GGG
** * **
52915034 TATTTTGGTAATTTTGTAAACCAATGG
1 TATTTTGGTAATTTTACAAATCAGGGG
** *
52915061 TATTTCT-GTAATTTTGTAAATCAAGGG
1 TATTT-TGGTAATTTTACAAATCAGGGG
*** * *
52915088 TAAAATGGTAATTCTATAAATC-GAGGG
1 TATTTTGGTAATTTTACAAATCAG-GGG
**** * *
52915115 TAAAACGGTAATTCTATAAATC-GAGGG
1 TATTTTGGTAATTTTACAAATCAG-GGG
*** * ** * *
52915142 TAAAATGGTAATTCTATCTTA-CAAGAG
1 TATTTTGGTAATTTTA-CAAATCAGGGG
**
52915169 TATTTCAGTAATTTTACAAATC-GAGGG
1 TATTTTGGTAATTTTACAAATCAG-GGG
*** * *
52915196 TATTTCAATAATTTTGCAAAT-TGAGGG
1 TATTTTGGTAATTTTACAAATCAG-GGG
* *
52915223 TATTTCGGTAATTTTACAAATC-GAGGA
1 TATTTTGGTAATTTTACAAATCAG-GGG
* * **
52915250 TATTTAGGTAATTTTATAAATTGGGGG
1 TATTTTGGTAATTTTACAAATCAGGGG
* * *
52915277 TACTTTGGTAATTTTACAAGTC-GAGAG
1 TATTTTGGTAATTTTACAAATCAG-GGG
*** **
52915304 TATTTCAATAATTTTACAGGTC-GAGGG
1 TATTTTGGTAATTTTACAAATCAG-GGG
* * **
52915331 TATTTTAGTAATTTCACAAATCAATGG
1 TATTTTGGTAATTTTACAAATCAGGGG
52915358 TATTTTGGTAATTTTACAAA-CTAGGGG
1 TATTTTGGTAATTTTACAAATC-AGGGG
* *
52915385 TATTTTGATAATTTTACAAACCAGGGG
1 TATTTTGGTAATTTTACAAATCAGGGG
* *
52915412 TATTTTGCTAATTTTACAAA-CTAGAGG
1 TATTTTGGTAATTTTACAAATC-AGGGG
*
52915439 TATTTTAGTAATTT
1 TATTTTGGTAATTT
52915453 GGTAAACTAA
Statistics
Matches: 379, Mismatches: 77, Indels: 34
0.77 0.16 0.07
Matches are distributed among these distances:
26 7 0.02
27 368 0.97
28 4 0.01
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (27 bp):
TATTTTGGTAATTTTACAAATCAGGGG
Found at i:52915035 original size:54 final size:54
Alignment explanation
Indices: 52914953--52915452 Score: 276
Period size: 54 Copynumber: 9.3 Consensus size: 54
52914943 TTCTACCCTA
* **
52914953 TATTTTAGTAATTCCACAAATC-AGGGGTATTTTGGTAATTTTACAAACCAGGGG
1 TATTTTGGTAATTTTACAAATCGA-GGGTATTTTGGTAATTTTACAAACCAGGGG
*** ** **
52915007 TATTTTGGTAATTTTATTGATCGAGGGTATTTTGGTAATTTTGTAAACCAATGG
1 TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAGGGG
** * *** * * *
52915061 TATTTCT-GTAATTTTGTAAATCAAGGGTAAAATGGTAATTCTATAAATC-GAGGG
1 TATTT-TGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAG-GGG
**** * * *** * ** * *
52915115 TAAAACGGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATCTTA-CAAGAG
1 TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTA-CAAACCAGGGG
** *** * **
52915169 TATTTCAGTAATTTTACAAATCGAGGGTATTTCAATAATTTTGCAAA-TTGAGGG
1 TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAG-GGG
* * * * ***
52915223 TATTTCGGTAATTTTACAAATCGAGGATATTTAGGTAATTTTATAAATTGGGGG
1 TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAGGGG
* * * *** ***
52915277 TACTTTGGTAATTTTACAAGTCGAGAGTATTTCAATAATTTTACAGGTC-GAGGG
1 TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAG-GGG
* * * * *
52915331 TATTTTAGTAATTTCACAAATCAATGGTATTTTGGTAATTTTACAAACTAGGGG
1 TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAGGGG
* * * * *
52915385 TATTTTGATAATTTTACAAA-CCAGGGGTATTTTGCTAATTTTACAAACTAGAGG
1 TATTTTGGTAATTTTACAAATCGA-GGGTATTTTGGTAATTTTACAAACCAGGGG
*
52915439 TATTTTAGTAATTT
1 TATTTTGGTAATTT
52915453 GGTAAACTAA
Statistics
Matches: 338, Mismatches: 97, Indels: 22
0.74 0.21 0.05
Matches are distributed among these distances:
53 5 0.01
54 327 0.97
55 6 0.02
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.39
Consensus pattern (54 bp):
TATTTTGGTAATTTTACAAATCGAGGGTATTTTGGTAATTTTACAAACCAGGGG
Found at i:52917414 original size:6 final size:6
Alignment explanation
Indices: 52917396--52917534 Score: 65
Period size: 6 Copynumber: 22.3 Consensus size: 6
52917386 AAGAAACATT
* *
52917396 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAG- GTGACAGA ATCAGA ATCAGT
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA ATCAGA
* * * *
52917445 ATCAGGTA A-CAGA ATCAAA ATTAGA ATCA-A TATTAGGTA A-CAGA ATCAAA
1 ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA -ATCA-G-A ATCAGA ATCAGA
* *
52917495 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAAA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATC-AGA ATCAGA AT
52917535 GTGAATGCAG
Statistics
Matches: 100, Mismatches: 16, Indels: 34
0.67 0.11 0.23
Matches are distributed among these distances:
5 9 0.09
6 70 0.70
7 16 0.16
8 4 0.04
9 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.17, T:0.20
Consensus pattern (6 bp):
ATCAGA
Found at i:52917438 original size:25 final size:25
Alignment explanation
Indices: 52917405--52917505 Score: 103
Period size: 25 Copynumber: 3.8 Consensus size: 25
52917395 TATCAGAACT
*
52917405 AGAATCAGAATCAGAATCAGGTGAC
1 AGAATCAGAATCAGAATCAGGTAAC
*
52917430 AGAATCAGAATCAGTATCAGGTAAC
1 AGAATCAGAATCAGAATCAGGTAAC
* *
52917455 AGAATCAAAATTAGAATCAATATTAGGTAAC
1 AGAATCAGAATCAGAATC------AGGTAAC
*
52917486 AGAATCAAAATCAGAATCAG
1 AGAATCAGAATCAGAATCAG
52917506 TATCAGGTAA
Statistics
Matches: 64, Mismatches: 6, Indels: 12
0.78 0.07 0.15
Matches are distributed among these distances:
25 40 0.62
31 24 0.38
ACGTcount: A:0.49, C:0.14, G:0.18, T:0.20
Consensus pattern (25 bp):
AGAATCAGAATCAGAATCAGGTAAC
Found at i:52917440 original size:31 final size:30
Alignment explanation
Indices: 52917407--52917534 Score: 140
Period size: 31 Copynumber: 4.3 Consensus size: 30
52917397 TCAGAACTAG
* *
52917407 AATCAGAATCAGAATCAGGTGACAGAATCAG
1 AATCAGAATCA-AATCAGGTAACAGAATCAA
52917438 AATCAG--T---ATCAGGTAACAGAATCAA
1 AATCAGAATCAAATCAGGTAACAGAATCAA
* *
52917463 AATTAGAATCAATATTAGGTAACAGAATCAA
1 AATCAGAATCAA-ATCAGGTAACAGAATCAA
*
52917494 AATCAGAATCAGTATCAGGTAACAGAATCAAA
1 AATCAGAATCA-AATCAGGTAACAGAATC-AA
52917526 AATCAGAAT
1 AATCAGAAT
52917535 GTGAATGCAG
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
25 21 0.26
27 1 0.01
29 1 0.01
31 48 0.59
32 11 0.13
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.20
Consensus pattern (30 bp):
AATCAGAATCAAATCAGGTAACAGAATCAA
Found at i:52917713 original size:27 final size:26
Alignment explanation
Indices: 52917683--52917771 Score: 97
Period size: 27 Copynumber: 3.3 Consensus size: 26
52917673 GAATTGTGAT
*
52917683 AGAGTCACCAGATACAGATATTGTGGC
1 AGAGCCACCAGA-ACAGATATTGTGGC
*
52917710 AGAGCCACCAGAACAAATATTTGTGGC
1 AGAGCCACCAGAACAGATA-TTGTGGC
* * *
52917737 ATAGCCACTAGAAACAGATAATGTGGC
1 AGAGCCACCAG-AACAGATATTGTGGC
*
52917764 AAAGCCAC
1 AGAGCCAC
52917772 TTAATAGAAT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
26 6 0.11
27 40 0.75
28 7 0.13
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.18
Consensus pattern (26 bp):
AGAGCCACCAGAACAGATATTGTGGC
Found at i:52917958 original size:22 final size:22
Alignment explanation
Indices: 52917930--52917994 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
52917920 GCAAATACGT
*
52917930 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
52917952 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
52917974 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
52917995 AAGGCTTTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:52918450 original size:26 final size:26
Alignment explanation
Indices: 52918421--52918618 Score: 189
Period size: 27 Copynumber: 7.5 Consensus size: 26
52918411 AAGGCAAAAT
* * * *
52918421 GGTAATTTTACCCCATAAGGTATCTC
1 GGTAATTCTACCCTACAGGGTATCTC
* * *
52918447 GGTAATTCTACACTACAGGGGTATTTT
1 GGTAATTCTACCCTACA-GGGTATCTC
* * *
52918474 TGCAATTCTACCCTACAGGGGTATGTC
1 GGTAATTCTACCCTACA-GGGTATCTC
* * *
52918501 GATAATTCTACCCTATAGGGTATTTC
1 GGTAATTCTACCCTACAGGGTATCTC
* * *
52918527 GGTAATTTTACCCCACAAGGTATCTC
1 GGTAATTCTACCCTACAGGGTATCTC
* *
52918553 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACA-GGGTATCTC
*
52918580 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACA-GGGTATCTC
52918607 GGTAATTCTACC
1 GGTAATTCTACC
52918619 TTATATTTCG
Statistics
Matches: 141, Mismatches: 29, Indels: 3
0.82 0.17 0.02
Matches are distributed among these distances:
26 56 0.40
27 85 0.60
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (26 bp):
GGTAATTCTACCCTACAGGGTATCTC
Found at i:52918480 original size:27 final size:27
Alignment explanation
Indices: 52918447--52918618 Score: 204
Period size: 27 Copynumber: 6.4 Consensus size: 27
52918437 AAGGTATCTC
*
52918447 GGTAATTCTACACTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTT
* * * *
52918474 TGCAATTCTACCCTACAGGGGTATGTC
1 GGTAATTCTACCCTACAGGGGTATTTT
* * *
52918501 GATAATTCTACCCTATA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
* * * * *
52918527 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTT
52918553 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTT
*
52918580 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
52918607 GGTAATTCTACC
1 GGTAATTCTACC
52918619 TTATATTTCG
Statistics
Matches: 122, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
26 43 0.35
27 79 0.65
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTT
Found at i:52918510 original size:54 final size:54
Alignment explanation
Indices: 52918439--52918618 Score: 247
Period size: 53 Copynumber: 3.4 Consensus size: 54
52918429 TACCCCATAA
* * *
52918439 GGTATCTCGGTAATTCTACACTACAGGGGTATTTTTGCAATTCTACCCTACAGG
1 GGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAGG
* * * * * * *
52918493 GGTATGTCGATAATTCTACCCTATA-GGGTATTTCGGTAATTTTACCCCACA-A
1 GGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAGG
52918545 GGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAGG
1 GGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAGG
*
52918599 GGTATTTCGGTAATTCTACC
1 GGTATCTCGGTAATTCTACC
52918619 TTATATTTCG
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
52 22 0.21
53 44 0.42
54 40 0.38
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (54 bp):
GGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACCCTACAGG
Found at i:52918569 original size:106 final size:106
Alignment explanation
Indices: 52918421--52918623 Score: 343
Period size: 106 Copynumber: 1.9 Consensus size: 106
52918411 AAGGCAAAAT
* *
52918421 GGTAATTTTACCCCATAAGGTATCTCGGTAATTCTACACTACAGGGGTATTTTTGCAATTCTACC
1 GGTAATTTTACCCCACAAGGTATCTCGGTAATTCTACACTACAGGGGTATTTTGGCAATTCTACC
52918486 CTACAGGGGTATGTCGATAATTCTACCCTATAGGGTATTTC
66 CTACAGGGGTATGTCGATAATTCTACCCTATAGGGTATTTC
* *
52918527 GGTAATTTTACCCCACAAGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGTAATTCTACC
1 GGTAATTTTACCCCACAAGGTATCTCGGTAATTCTACACTACAGGGGTATTTTGGCAATTCTACC
* * *
52918592 CTACAGGGGTATTTCGGTAATTCTACCTTATA
66 CTACAGGGGTATGTCGATAATTCTACCCTATA
52918624 TTTCGATAAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 90 1.00
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (106 bp):
GGTAATTTTACCCCACAAGGTATCTCGGTAATTCTACACTACAGGGGTATTTTGGCAATTCTACC
CTACAGGGGTATGTCGATAATTCTACCCTATAGGGTATTTC
Found at i:52918660 original size:27 final size:27
Alignment explanation
Indices: 52918630--52918688 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
52918620 TATATTTCGA
*
52918630 TAATTCCACAAA-TCAGGTGTATTTTGG
1 TAATTCCACAAACT-AGGGGTATTTTGG
** *
52918657 TAATTTTATAAACTAGGGGTATTTTGG
1 TAATTCCACAAACTAGGGGTATTTTGG
52918684 TAATT
1 TAATT
52918689 TTATTGATCG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (27 bp):
TAATTCCACAAACTAGGGGTATTTTGG
Found at i:52918689 original size:27 final size:27
Alignment explanation
Indices: 52918648--52919127 Score: 151
Period size: 27 Copynumber: 17.9 Consensus size: 27
52918638 CAAATCAGGT
52918648 GTATTTTGGTAATTTTATAAACTAGGG
1 GTATTTTGGTAATTTTATAAACTAGGG
** * *
52918675 GTATTTTGGTAATTTTATTGA-TCGAGT
1 GTATTTTGGTAATTTTATAAACTAG-GG
* * *
52918702 GTATTTTGGTAATTTTGTAAACCAAGG
1 GTATTTTGGTAATTTTATAAACTAGGG
* * * *
52918729 GTATTTCGATAATTTTGTAAA-TTGAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
*** * *
52918756 GTAAAATGGTAATTCTATAAA-TCAAGG
1 GTATTTTGGTAATTTTATAAACT-AGGG
**** * * *
52918783 GTAAAACGATAATTCTATAAA-TCGAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
*** * ** *
52918810 GTAAAATGGTAATTCTATCTTAC-AGGA
1 GTATTTTGGTAATTTTAT-AAACTAGGG
** * *
52918837 G--TTTCAGTAATTTTACAAA-TCGAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
* * **
52918862 GTGTTTAGGTAATTTTGCAAACT-GAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
* * *
52918889 GTATTTCGGTAATTTTACAAA-TCGAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
* *
52918916 ATATTTAGGTAATTTTATAAA-TCAGGG
1 GTATTTTGGTAATTTTATAAACT-AGGG
* * * *
52918943 GTACTTTGGTAATTTTA-CAAGTCGAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
*** * ** *
52918970 GTATTTCAATAATTTTA-CAGGTTGAGG
1 GTATTTTGGTAATTTTATAAACTAG-GG
** * * *
52918997 GTATTTCAGTAATTTCACAAATTAGGG
1 GTATTTTGGTAATTTTATAAACTAGGG
*
52919024 GTATTTTGGTAATTTTACAAACTAGGG
1 GTATTTTGGTAATTTTATAAACTAGGG
* * * *
52919051 GTATTTTGATAATTTTACAGACCAGGG
1 GTATTTTGGTAATTTTATAAACTAGGG
* *
52919078 GTATTTTGGTAATTTTACAAACTA-AG
1 GTATTTTGGTAATTTTATAAACTAGGG
**
52919104 GTATTTTGGTAATTTCGTAAACTA
1 GTATTTTGGTAATTTTATAAACTA
52919128 AAGTATTCTA
Statistics
Matches: 349, Mismatches: 87, Indels: 35
0.74 0.18 0.07
Matches are distributed among these distances:
24 2 0.01
25 10 0.03
26 28 0.08
27 302 0.87
28 7 0.02
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (27 bp):
GTATTTTGGTAATTTTATAAACTAGGG
Found at i:52918914 original size:54 final size:53
Alignment explanation
Indices: 52918622--52919118 Score: 269
Period size: 54 Copynumber: 9.3 Consensus size: 53
52918612 TTCTACCTTA
* ** * *
52918622 TATTTCGATAATTCCACAAATC-AGGTGTATTTTGGTAATTTTATAAACTAGGGG
1 TATTTCGGTAATTTTACAAATCGAGG-GTATTTAGGTAATTTTACAAACTA-GGG
* *** * * ** *
52918676 TATTTTGGTAATTTTATTGATCGAGTGTATTTTGGTAATTTTGTAAACCAAGGG
1 TATTTCGGTAATTTTACAAATCGAGGGTATTTAGGTAATTTTACAAA-CTAGGG
* ** * ** * * *
52918730 TATTTCGATAATTTTGTAAATTGAGGGTA-AAATGGTAATTCTATAAATCAAGGG
1 TATTTCGGTAATTTTACAAATCGAGGGTATTTA-GGTAATTTTACAAA-CTAGGG
*** * * * ** * **
52918784 TAAAACGATAATTCTATAAATCGAGGGTA-AAATGGTAATTCTATCTTAC-A-GG
1 TATTTCGGTAATTTTACAAATCGAGGGTATTTA-GGTAATTTTA-CAAACTAGGG
* * *
52918836 -AGTTTCAGTAATTTTACAAATCGAGGGTGTTTAGGTAATTTTGCAAACTGAGGG
1 TA-TTTCGGTAATTTTACAAATCGAGGGTATTTAGGTAATTTTACAAACT-AGGG
* *
52918890 TATTTCGGTAATTTTACAAATCGAGGATATTTAGGTAATTTTATAAA-TCAGGGG
1 TATTTCGGTAATTTTACAAATCGAGGGTATTTAGGTAATTTTACAAACT-A-GGG
* * ***
52918944 TACTTT-GGTAATTTTACAAGTCGAGGGTATTTCA-ATAATTTTACAGGTTGAGGG
1 TA-TTTCGGTAATTTTACAAATCGAGGGTATTT-AGGTAATTTTACAAACT-AGGG
* * * *
52918998 TATTTCAGTAATTTCACAAAT-TAGGGGTATTTTGGTAATTTTACAAACTAGGGG
1 TATTTCGGTAATTTTACAAATCGA-GGGTATTTAGGTAATTTTACAAACTA-GGG
* * * * * *
52919052 TATTTTGATAATTTTACAGA-CCAGGGGTATTTTGGTAATTTTACAAACTAAGG
1 TATTTCGGTAATTTTACAAATCGA-GGGTATTTAGGTAATTTTACAAACTAGGG
*
52919105 TATTTTGGTAATTT
1 TATTTCGGTAATTT
52919119 CGTAAACTAA
Statistics
Matches: 348, Mismatches: 76, Indels: 39
0.75 0.16 0.08
Matches are distributed among these distances:
51 4 0.01
52 29 0.08
53 25 0.07
54 278 0.80
55 12 0.03
ACGTcount: A:0.32, C:0.08, G:0.21, T:0.39
Consensus pattern (53 bp):
TATTTCGGTAATTTTACAAATCGAGGGTATTTAGGTAATTTTACAAACTAGGG
Found at i:52919070 original size:81 final size:80
Alignment explanation
Indices: 52918838--52919118 Score: 275
Period size: 81 Copynumber: 3.5 Consensus size: 80
52918828 CTTACAGGAG
* * * * *
52918838 TTTCAGTAATTTTACAAA-TCGAGGGTGTTTAGGTAATTTTGCAAACTGAGGGTATTTCGGTAAT
1 TTTCAGTAATTTTACAAATTAG-GGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCGATAAT
* *
52918902 TTTACAAATCGAGGATA
65 TTTAC-AGTCGAGGGTA
* * * * *
52918919 TTT-AGGTAATTTTATAAATCAGGGGTACTTTGGTAATTTTAC-AAGTCGAGGGTATTTCAATAA
1 TTTCA-GTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAACT-GAGGGTATTTCGATAA
*
52918982 TTTTACAGGTTGAGGGTA
64 TTTTACA-GTCGAGGGTA
* *
52919000 TTTCAGTAATTTCACAAATTAGGGGTATTTTGGTAATTTTACAAACT-AGGGGTATTTTGATAAT
1 TTTCAGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAACTGA-GGGTATTTCGATAAT
* *
52919064 TTTACAGACCAGGGGTA
65 TTTACAGTCGA-GGGTA
** * *
52919081 TTTTGGTAATTTTACAAACTA-AGGTATTTTGGTAATTT
1 TTTCAGTAATTTTACAAATTAGGGGTATTTTGGTAATTT
52919119 CGTAAACTAA
Statistics
Matches: 164, Mismatches: 28, Indels: 17
0.78 0.13 0.08
Matches are distributed among these distances:
80 24 0.15
81 135 0.82
82 5 0.03
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (80 bp):
TTTCAGTAATTTTACAAATTAGGGGTATTTTGGTAATTTTACAAACTGAGGGTATTTCGATAATT
TTACAGTCGAGGGTA
Found at i:52920555 original size:14 final size:15
Alignment explanation
Indices: 52920538--52920569 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
52920528 ATTACTCCCC
52920538 AAAAATA-GCATGG-
1 AAAAATATGCATGGT
52920551 AAAAATATGCATGGT
1 AAAAATATGCATGGT
52920566 AAAA
1 AAAA
52920570 CTAATAGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 6 0.35
15 4 0.24
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (15 bp):
AAAAATATGCATGGT
Found at i:52921144 original size:13 final size:13
Alignment explanation
Indices: 52921126--52921150 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
52921116 TATTGGTGCC
52921126 CACGACCGTGTCA
1 CACGACCGTGTCA
52921139 CACGACCGTGTC
1 CACGACCGTGTC
52921151 CTACTTTGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.40, G:0.24, T:0.16
Consensus pattern (13 bp):
CACGACCGTGTCA
Found at i:52925754 original size:63 final size:62
Alignment explanation
Indices: 52925616--52925754 Score: 140
Period size: 63 Copynumber: 2.2 Consensus size: 62
52925606 AAGATGGTTT
* * * * * *
52925616 TAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACATGTACCAGATTGTTGGTTACATGTG
1 TAGGTAACATGTGTAGTACTAAATGCAGGCTACTACATGTACCAGATAGTTGGTTACAAGGG
*
52925678 TAGGGTCACATGTGTAGTACTAAATGCAGGCTACT--ATGCTTACCAGATAGCTTCGGTTACAAG
1 TA-GGTAACATGTGTAGTACTAAATGCAGGCTACTACATG--TACCAGATAG-TT-GGTTACAAG
52925741 GG
61 GG
*
52925743 T-GGTAATATGTG
1 TAGGTAACATGTG
52925755 CAGGCAACCG
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
61 3 0.05
62 2 0.03
63 48 0.74
64 2 0.03
65 10 0.15
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (62 bp):
TAGGTAACATGTGTAGTACTAAATGCAGGCTACTACATGTACCAGATAGTTGGTTACAAGGG
Found at i:52925946 original size:16 final size:15
Alignment explanation
Indices: 52925925--52925954 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
52925915 GAATGGAGTA
52925925 AGTGAAATTATGTAAG
1 AGTGAAATT-TGTAAG
52925941 AGTGAAATTTGTAA
1 AGTGAAATTTGTAA
52925955 TAAAACAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.43, C:0.00, G:0.23, T:0.33
Consensus pattern (15 bp):
AGTGAAATTTGTAAG
Found at i:52927782 original size:15 final size:15
Alignment explanation
Indices: 52927762--52927790 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52927752 CATTAAATTC
52927762 TTACTCTATTTTATT
1 TTACTCTATTTTATT
52927777 TTACTCTATTTTAT
1 TTACTCTATTTTAT
52927791 AGTATTGGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.66
Consensus pattern (15 bp):
TTACTCTATTTTATT
Found at i:52931810 original size:31 final size:31
Alignment explanation
Indices: 52931769--52931832 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
52931759 CCTTTTCATA
* *
52931769 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTAGGCCGAAGCCT
**
52931800 TTTCAAATTTCATATTACTAGGCCGAAGCCT
1 TTTCAAATTTCATAACACTAGGCCGAAGCCT
52931831 TT
1 TT
52931833 ACTGTAAACG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTAGGCCGAAGCCT
Found at i:52932078 original size:24 final size:24
Alignment explanation
Indices: 52932040--52932214 Score: 284
Period size: 24 Copynumber: 7.4 Consensus size: 24
52932030 CTAGAGGCCT
*
52932040 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
*
52932065 AGCCCTTTTTATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
52932089 AGCCC-TTTAATAACTGGGGCGTA
1 AGCCCTTTTAATAACTGGGGCATA
52932112 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
52932136 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
52932160 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
52932183 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
52932206 AGCCCTTTT
1 AGCCCTTTT
52932215 GCACTTCCTC
Statistics
Matches: 141, Mismatches: 7, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
23 66 0.47
24 71 0.50
25 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:52932100 original size:47 final size:47
Alignment explanation
Indices: 52932047--52932214 Score: 284
Period size: 47 Copynumber: 3.6 Consensus size: 47
52932037 CCTAGCCTCT
* *
52932047 TTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
*
52932094 TTTAATAACTGGGGCGTAAGCCCTTTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
*
52932141 TTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
52932188 TTTAATAACTGGGGCATAAGCCCTTTT
1 TTTAATAACTGGGGCATAAGCCCTTTT
52932215 GCACTTCCTC
Statistics
Matches: 113, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
46 22 0.19
47 70 0.62
48 21 0.19
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (47 bp):
TTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCC
Found at i:52932105 original size:23 final size:23
Alignment explanation
Indices: 52932047--52932213 Score: 271
Period size: 23 Copynumber: 7.1 Consensus size: 23
52932037 CCTAGCCTCT
*
52932047 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
52932070 TTTTTATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
52932094 TTTAATAACTGGGGCGTAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52932117 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
52932141 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
52932165 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52932188 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
52932211 TTT
1 TTT
52932214 TGCACTTCCT
Statistics
Matches: 135, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
23 69 0.51
24 66 0.49
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:52932286 original size:9 final size:9
Alignment explanation
Indices: 52932272--52932328 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
52932262 ATCTCATGTG
52932272 CATATCATA
1 CATATCATA
*
52932281 CATATCATGTG
1 CATATCA--TA
52932292 CATATCATA
1 CATATCATA
* *
52932301 CATGTCATGTG
1 CATATCA--TA
52932312 CATATCATA
1 CATATCATA
52932321 CATATCAT
1 CATATCAT
52932329 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:52932288 original size:20 final size:20
Alignment explanation
Indices: 52932260--52932330 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
52932250 GCATTTATGA
*
52932260 ACATCTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
52932280 ACATATCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
*
52932300 ACATGTCATGTGCATATCAT
1 ACATATCATGTGCATATCAT
52932320 ACATATCATGT
1 ACATATCATGT
52932331 TTATCAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.35
Consensus pattern (20 bp):
ACATATCATGTGCATATCAT
Found at i:52932295 original size:11 final size:11
Alignment explanation
Indices: 52932265--52932319 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
52932255 TATGAACATC
52932265 TCATGTGCATA
1 TCATGTGCATA
*
52932276 TCA--TACATA
1 TCATGTGCATA
52932285 TCATGTGCATA
1 TCATGTGCATA
* *
52932296 TCA--TACATG
1 TCATGTGCATA
52932305 TCATGTGCATA
1 TCATGTGCATA
52932316 TCAT
1 TCAT
52932320 ACATATCATG
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (11 bp):
TCATGTGCATA
Found at i:52942536 original size:42 final size:42
Alignment explanation
Indices: 52942489--52942602 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 42
52942479 AACCATACCA
* * *
52942489 ATGCCATATCCCAGATATGGTCTTACATG-AGATCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACACGAAG-TATCATATCG
*
52942531 ATGCCAATAGCCCA-ACTATGGTCTTACACGAAGTATCATATCG
1 ATGCC-ATATCCCAGA-TATGGTCTTACACGAAGTATCATATCG
*
52942574 ATGCCATATCCTAGATATGGTCTTACACG
1 ATGCCATATCCCAGATATGGTCTTACACG
52942603 TAATCTCAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
42 26 0.42
43 34 0.55
44 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACACGAAGTATCATATCG
Found at i:52946922 original size:12 final size:12
Alignment explanation
Indices: 52946905--52946930 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
52946895 GAACATAGTA
52946905 TATCATTTAATC
1 TATCATTTAATC
52946917 TATCATTTAATC
1 TATCATTTAATC
52946929 TA
1 TA
52946931 ACAATAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (12 bp):
TATCATTTAATC
Found at i:52946962 original size:37 final size:37
Alignment explanation
Indices: 52946921--52946997 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
52946911 TTAATCTATC
52946921 ATTTAATCTAACAATAATTGATTATGATTTATATATT
1 ATTTAATCTAACAATAATTGATTATGATTTATATATT
52946958 ATTTAATCTAACAATAATTGATTATGATTTATATATT
1 ATTTAATCTAACAATAATTGATTATGATTTATATATT
52946995 ATT
1 ATT
52946998 CAATTCAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.49
Consensus pattern (37 bp):
ATTTAATCTAACAATAATTGATTATGATTTATATATT
Found at i:52948865 original size:16 final size:16
Alignment explanation
Indices: 52948844--52948876 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52948834 CCAATAATCG
52948844 TCTTTAATTCAAGTAT
1 TCTTTAATTCAAGTAT
52948860 TCTTTAATTCAAGTAT
1 TCTTTAATTCAAGTAT
52948876 T
1 T
52948877 GATAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.06, T:0.52
Consensus pattern (16 bp):
TCTTTAATTCAAGTAT
Found at i:52949211 original size:19 final size:18
Alignment explanation
Indices: 52949176--52949221 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
52949166 ACAATAACTA
*
52949176 CAAAGTCCAAAAGAAAGTC
1 CAAA-TCCAAAACAAAGTC
52949195 CAAATCCAAAACCAAAGTC
1 CAAATCCAAAA-CAAAGTC
52949214 CAAATCCA
1 CAAATCCA
52949222 TTAAACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.52, C:0.28, G:0.09, T:0.11
Consensus pattern (18 bp):
CAAATCCAAAACAAAGTC
Found at i:52950432 original size:27 final size:27
Alignment explanation
Indices: 52950388--52950461 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
52950378 TACTGAAATG
* * *
52950388 CCCTCAACTTGTAAAATTACCAAAGTA
1 CCCTCAATTTATAGAATTACCAAAGTA
* * ***
52950415 CCCTCGATTTATAGAATTACTATTTTA
1 CCCTCAATTTATAGAATTACCAAAGTA
52950442 CCCTCAATTTATAGAATTAC
1 CCCTCAATTTATAGAATTAC
52950462 TGTTTTACCC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (27 bp):
CCCTCAATTTATAGAATTACCAAAGTA
Found at i:52950460 original size:54 final size:54
Alignment explanation
Indices: 52950388--52950500 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 54
52950378 TACTGAAATG
* *
52950388 CCCTCAACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTA-CTATTTTA
1 CCCTCAACTTATAAAATTACCAAAGTACCCTCGATTTACAGAATTATC-ATTTTA
* * *****
52950442 CCCTCAATTTATAGAATTACTGTTTTACCCTCGATTTACAGAATTATCATTTTA
1 CCCTCAACTTATAAAATTACCAAAGTACCCTCGATTTACAGAATTATCATTTTA
52950496 CCCTC
1 CCCTC
52950501 GATTGTGAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 48 0.98
55 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (54 bp):
CCCTCAACTTATAAAATTACCAAAGTACCCTCGATTTACAGAATTATCATTTTA
Found at i:52950462 original size:27 final size:27
Alignment explanation
Indices: 52950413--52950504 Score: 141
Period size: 27 Copynumber: 3.4 Consensus size: 27
52950403 ATTACCAAAG
52950413 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTATAGAATTACTATTT
* *
52950440 TACCCTCAATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTATTT
*
52950467 TACCCTCGATTTACAGAATTA-TCATTT
1 TACCCTCGATTTATAGAATTACT-ATTT
52950494 TACCCTCGATT
1 TACCCTCGATT
52950505 GTGAAATTAC
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.02
27 58 0.98
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTATTT
Found at i:52950526 original size:27 final size:26
Alignment explanation
Indices: 52950496--52950659 Score: 93
Period size: 27 Copynumber: 6.1 Consensus size: 26
52950486 TATCATTTTA
**
52950496 CCCTCGATTGTGAAATTACTGAAATAC
1 CCCT-GATTGTGAAATTACCAAAATAC
* * *
52950523 CCCT-ATAGGGTAGAATTACCAAAATAT
1 CCCTGATTGTG-A-AATTACCAAAATAC
* *
52950550 CCCTAGTTTGTAAAATTACCAAAATAC
1 CCCT-GATTGTGAAATTACCAAAATAC
* * *
52950577 CACTGGTTTGTGAAATTACCGAAATA-
1 CCCT-GATTGTGAAATTACCAAAATAC
* * *
52950603 CCCTCAATTTGTAAAATTACTAAAATAC
1 CCCT-GA-TTGTGAAATTACCAAAATAC
52950631 CCCTGATT-TAGAAAATTA-CAGAAATAC
1 CCCTGATTGT-G-AAATTACCA-AAATAC
52950658 CC
1 CC
52950660 TTCACTTTCT
Statistics
Matches: 104, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
25 5 0.05
26 7 0.07
27 85 0.82
28 5 0.05
29 2 0.02
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.29
Consensus pattern (26 bp):
CCCTGATTGTGAAATTACCAAAATAC
Found at i:52950575 original size:54 final size:54
Alignment explanation
Indices: 52950494--52950637 Score: 143
Period size: 54 Copynumber: 2.7 Consensus size: 54
52950484 ATTATCATTT
* * *
52950494 TACCCTCGA-TTGTGAAATTACTGAAATACCCCT-ATAGGGT-AGAATTACCAAAA
1 TACCCTCAATTTGTAAAATTACTAAAATACCCCTGAT-GGGTGA-AATTACCAAAA
* * * * ** *
52950547 TATCCCT-AGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAA
1 TA-CCCTCAATTTGTAAAATTACTAAAATACCCCTGATGGGTGAAATTACCAAAA
52950601 TACCCTCAATTTGTAAAATTACTAAAATACCCCTGAT
1 TACCCTCAATTTGTAAAATTACTAAAATACCCCTGAT
52950638 TTAGAAAATT
Statistics
Matches: 72, Mismatches: 14, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
53 6 0.08
54 64 0.89
55 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.30
Consensus pattern (54 bp):
TACCCTCAATTTGTAAAATTACTAAAATACCCCTGATGGGTGAAATTACCAAAA
Found at i:52950646 original size:81 final size:81
Alignment explanation
Indices: 52950503--52950658 Score: 185
Period size: 81 Copynumber: 1.9 Consensus size: 81
52950493 TTACCCTCGA
* * * *
52950503 TTGTGAAATTACTGAAATACCCCTATAGGGTAGAATTACCAAAATATCCCTAGTTTGTAAAATTA
1 TTGTGAAATTACCGAAATACCCCAATAGGGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTA
52950568 CCA-AAATACCACTGGT
66 -CAGAAATACCACTGGT
** *
52950584 TTGTGAAATTACCGAAATACCCTCAAT-TTGTAAAATTACTAAAATACCCCT-GATTTAG-AAAA
1 TTGTGAAATTACCGAAATACCC-CAATAGGGTAAAATTACCAAAATACCCCTAG-TTT-GTAAAA
52950646 TTACAGAAATACC
63 TTACAGAAATACC
52950659 CTTCACTTTC
Statistics
Matches: 64, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
80 3 0.05
81 57 0.89
82 4 0.06
ACGTcount: A:0.40, C:0.19, G:0.12, T:0.29
Consensus pattern (81 bp):
TTGTGAAATTACCGAAATACCCCAATAGGGTAAAATTACCAAAATACCCCTAGTTTGTAAAATTA
CAGAAATACCACTGGT
Found at i:52950647 original size:54 final size:54
Alignment explanation
Indices: 52950536--52950716 Score: 172
Period size: 54 Copynumber: 3.3 Consensus size: 54
52950526 TATAGGGTAG
* * * * *
52950536 AATTACCAAAATATCCCT-AGTTTGTAAAATTACCAAAATACCACTGGTTT-GTGA
1 AATTACCGAAATA-CCCTCAATTTGTAAAATTACTAAAATACCCCTGGTTTAG-AA
*
52950590 AATTACCGAAATACCCTCAATTTGTAAAATTACTAAAATACCCCTGATTTAGAA
1 AATTACCGAAATACCCTCAATTTGTAAAATTACTAAAATACCCCTGGTTTAGAA
* * * * *
52950644 AATTACAGAAATACCCTTCACTTTCTAAAAATTA-TAGAAATA-CCATCGGTTTACAA
1 AATTACCGAAATACCC-TCAATTTGT-AAAATTACTA-AAATACCCCT-GGTTTAGAA
*
52950700 AATTACTGAAATACCCT
1 AATTACCGAAATACCCT
52950717 TGGTTTGTAG
Statistics
Matches: 108, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
53 4 0.04
54 56 0.52
55 14 0.13
56 34 0.31
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.30
Consensus pattern (54 bp):
AATTACCGAAATACCCTCAATTTGTAAAATTACTAAAATACCCCTGGTTTAGAA
Found at i:52950721 original size:27 final size:27
Alignment explanation
Indices: 52950615--52950722 Score: 85
Period size: 27 Copynumber: 3.9 Consensus size: 27
52950605 CTCAATTTGT
* * * *
52950615 AAAATTACTAAAATACCCCTGATTTAG
1 AAAATTACTGAAATACCCTTGGTTTAC
* **
52950642 AAAATTACAGAAATACCCTTCACTTT-C
1 AAAATTACTGAAATACCCTT-GGTTTAC
* *
52950669 TAAAAATTA-TAGAAATACCATCGGTTTAC
1 --AAAATTACT-GAAATACCCTTGGTTTAC
52950698 AAAATTACTGAAATACCCTTGGTTT
1 AAAATTACTGAAATACCCTTGGTTT
52950723 GTAGATTTAC
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
27 38 0.61
28 7 0.11
29 17 0.27
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.31
Consensus pattern (27 bp):
AAAATTACTGAAATACCCTTGGTTTAC
Found at i:52950814 original size:27 final size:27
Alignment explanation
Indices: 52950767--52950851 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
52950757 GACTAAAATA
** *
52950767 CCCCTAATA-GGTAAAAAGACCATAAAG
1 CCCCT-ATAGGGTAAAGTGACCGTAAAG
*
52950794 CCCTTATAGGGTAAAGTGACCGTAAAG
1 CCCCTATAGGGTAAAGTGACCGTAAAG
*
52950821 CCCCTGTAGGGTAAAGTGACCGTAAAG
1 CCCCTATAGGGTAAAGTGACCGTAAAG
52950848 CCCC
1 CCCC
52950852 CTGTATGGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
26 3 0.06
27 48 0.94
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.18
Consensus pattern (27 bp):
CCCCTATAGGGTAAAGTGACCGTAAAG
Found at i:52950861 original size:28 final size:27
Alignment explanation
Indices: 52950784--52950863 Score: 115
Period size: 27 Copynumber: 2.9 Consensus size: 27
52950774 TAGGTAAAAA
* * *
52950784 GACCATAAAGCCCTTATAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
52950811 GACCGTAAAGCCCCTGTAGGGTAAAGT
1 GACCGTAAAGCCCCTGTAGGGTAAAGT
*
52950838 GACCGTAAAGCCCCCTGTATGGTAAA
1 GACCGTAAAG-CCCCTGTAGGGTAAA
52950864 ATGTCAAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
27 34 0.71
28 14 0.29
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.20
Consensus pattern (27 bp):
GACCGTAAAGCCCCTGTAGGGTAAAGT
Found at i:52951599 original size:10 final size:10
Alignment explanation
Indices: 52951584--52951644 Score: 61
Period size: 10 Copynumber: 5.9 Consensus size: 10
52951574 ATATTGTTAT
52951584 ACATGATATG
1 ACATGATATG
52951594 ACATGATATG
1 ACATGATATG
52951604 CACATGATATG
1 -ACATGATATG
** *
52951615 TTATGAGATG
1 ACATGATATG
52951625 CACATGATATG
1 -ACATGATATG
52951636 -CTATGATAT
1 AC-ATGATAT
52951645 ACTTATTTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 1 0.02
10 24 0.57
11 17 0.40
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (10 bp):
ACATGATATG
Found at i:52951609 original size:21 final size:20
Alignment explanation
Indices: 52951584--52951644 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 20
52951574 ATATTGTTAT
52951584 ACATGATATGACATGATATGC
1 ACATGATATG-CATGATATGC
* *
52951605 ACATGATATGTTATGAGATGC
1 ACATGATATG-CATGATATGC
52951626 ACATGATATGCTATGATAT
1 ACATGATATGC-ATGATAT
52951645 ACTTATTTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (20 bp):
ACATGATATGCATGATATGC
Found at i:52951610 original size:11 final size:11
Alignment explanation
Indices: 52951584--52951636 Score: 65
Period size: 11 Copynumber: 5.0 Consensus size: 11
52951574 ATATTGTTAT
52951584 ACATGATATG-
1 ACATGATATGC
52951594 ACATGATATGC
1 ACATGATATGC
52951605 ACATGATATG-
1 ACATGATATGC
** *
52951615 TTATGAGATGC
1 ACATGATATGC
52951626 ACATGATATGC
1 ACATGATATGC
52951637 TATGATATAC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
10 17 0.49
11 18 0.51
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (11 bp):
ACATGATATGC
Found at i:52953303 original size:35 final size:36
Alignment explanation
Indices: 52953217--52953313 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 36
52953207 TTATAACTAT
*
52953217 GGCATGCTTAACATGCGAATCAGAATAAAAAAATAA
1 GGCATGCTTAACATGCGAATCATAATAAAAAAATAA
* * *
52953253 GGGTATGCTTAACATGTGAATCATAGATAGAAAAAT-A
1 -GGCATGCTTAACATGCGAATCATA-ATAAAAAAATAA
52953290 -GCATGCTTAACATGCGAATCATAA
1 GGCATGCTTAACATGCGAATCATAA
52953314 CCAGAATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 1 0.02
35 21 0.40
37 22 0.42
38 9 0.17
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (36 bp):
GGCATGCTTAACATGCGAATCATAATAAAAAAATAA
Found at i:52953668 original size:45 final size:45
Alignment explanation
Indices: 52953616--52953707 Score: 166
Period size: 45 Copynumber: 2.0 Consensus size: 45
52953606 AATCATCATC
52953616 TTCTTCCTTCTCTACTGCTTGTTTAAGAAAGGAAAGAAATAAATT
1 TTCTTCCTTCTCTACTGCTTGTTTAAGAAAGGAAAGAAATAAATT
* *
52953661 TTCTTCCTTCTTTACTGCTTGTTTGAGAAAGGAAAGAAATAAATT
1 TTCTTCCTTCTCTACTGCTTGTTTAAGAAAGGAAAGAAATAAATT
52953706 TT
1 TT
52953708 AAGTTTGCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (45 bp):
TTCTTCCTTCTCTACTGCTTGTTTAAGAAAGGAAAGAAATAAATT
Found at i:52955152 original size:33 final size:34
Alignment explanation
Indices: 52955091--52955157 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 34
52955081 CAGATCGGTA
* *
52955091 ACAGTCTGGGCCAAAAGCCCTATTCAGTATCAGT
1 ACAGTCTGGGCCAAAAGCCCTATACAGTAACAGT
**
52955125 ACAGTCTGGGCC-TTAGCCCTATACAGTAACAGT
1 ACAGTCTGGGCCAAAAGCCCTATACAGTAACAGT
52955158 GTGGGCCTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (34 bp):
ACAGTCTGGGCCAAAAGCCCTATACAGTAACAGT
Done.