Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 18 of 120
Found at i:4866570 original size:57 final size:55
Alignment explanation
Indices: 4866498--4866611 Score: 176
Period size: 57 Copynumber: 2.0 Consensus size: 55
4866488 GGAATAATAA
* *
4866498 GAAACATTTGGAAATGATTGT-GATTTTCTCCAAAATGAAAATAAAAATGAAGAAAT
1 GAAACATTTGAAAATGAATGTAG-TTTTCTCCAAAATGAAAATAAAAATGAA-AAAT
4866554 GAAATCATTTGAAAATGAATGTAGTTTTCTCCAAAATGAAAATAAAAATGAAAAAT
1 GAAA-CATTTGAAAATGAATGTAGTTTTCTCCAAAATGAAAATAAAAATGAAAAAT
4866610 GA
1 GA
4866612 CCTAAAAATT
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
56 10 0.19
57 43 0.80
58 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.15, T:0.28
Consensus pattern (55 bp):
GAAACATTTGAAAATGAATGTAGTTTTCTCCAAAATGAAAATAAAAATGAAAAAT
Found at i:4867925 original size:41 final size:41
Alignment explanation
Indices: 4867874--4867961 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
4867864 ACTGAAACAG
4867874 ATAC-CTGAGAATTTAAAGTATGGATATTTGGAAGAGAAGA
1 ATACACTGAGAATTTAAAGTATGGATATTTGGAAGAGAAGA
*
4867914 ATACACTGAGAATTTAAAGTATGGATATTTGGAAGAGAATA
1 ATACACTGAGAATTTAAAGTATGGATATTTGGAAGAGAAGA
4867955 ATACACT
1 ATACACT
4867962 ACCAGTAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 4 0.09
41 42 0.91
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.28
Consensus pattern (41 bp):
ATACACTGAGAATTTAAAGTATGGATATTTGGAAGAGAAGA
Found at i:4870012 original size:13 final size:13
Alignment explanation
Indices: 4869994--4870027 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
4869984 GAGTTTCTGT
4869994 GAGAAAATTTGAA
1 GAGAAAATTTGAA
* *
4870007 GAGAAAGTTTGGA
1 GAGAAAATTTGAA
4870020 GAGAAAAT
1 GAGAAAAT
4870028 ATGATTGCCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.29, T:0.21
Consensus pattern (13 bp):
GAGAAAATTTGAA
Found at i:4874043 original size:17 final size:18
Alignment explanation
Indices: 4874012--4874045 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4874002 AATTTATTTT
4874012 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
4874030 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
4874046 TTATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:4876900 original size:41 final size:38
Alignment explanation
Indices: 4876800--4876903 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
4876790 GTCAAAGCAA
* *
4876800 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** ** * *
4876837 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
4876875 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
4876904 CTCAAGGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:4877221 original size:79 final size:79
Alignment explanation
Indices: 4877131--4877291 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 79
4877121 ATCCACAATT
4877131 TCACCAATTAATCACACAATCAATCTTTATAATTAACCACATAATATTTCACACATATATTTTTC
1 TCACCAATTAATCACACAATCAATCTTTATAATTAACCACATAATATTTCACACATATATTTTTC
*
4877196 TCACATATTGATCA
66 TCACATATTCATCA
4877210 TCACCAATTAATCACACAATCAATCTTTATAATTAACCACATAATATTTCACACATATATTTTTC
1 TCACCAATTAATCACACAATCAATCTTTATAATTAACCACATAATATTTCACACATATATTTTTC
4877275 TCACATATTCATCA
66 TCACATATTCATCA
4877289 TCA
1 TCA
4877292 TATACCTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 81 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.37
Consensus pattern (79 bp):
TCACCAATTAATCACACAATCAATCTTTATAATTAACCACATAATATTTCACACATATATTTTTC
TCACATATTCATCA
Found at i:4880528 original size:98 final size:95
Alignment explanation
Indices: 4880350--4880542 Score: 221
Period size: 98 Copynumber: 2.0 Consensus size: 95
4880340 AACTTTGGAA
* * * * * *
4880350 AAGGATATTCGATTATCTCGTTTTGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTTCAG
1 AAGGATATTCGATTATCTCGATTTGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATATTTCAA
*
4880415 AATCATAGATAAAGAAACATTGCCTCGATTT
66 AATCATAAATAAAG-AACATTGCCTCGATTT
**
4880446 AAGGATATTCGATTAT-TCCGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAA-ATTT
1 AAGGATATTCGATTATCT-CGATTTG-A-AAAAATCGCACCTAGTAAGTTAAGGCACAAATATTT
*
4880509 CAAAATTCA-AAATAAAAGAATATTGCCTCGATTT
63 CAAAA-TCATAAAT-AAAGAACATTGCCTCGATTT
4880543 TAAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
95 1 0.01
96 22 0.27
97 26 0.32
98 33 0.40
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (95 bp):
AAGGATATTCGATTATCTCGATTTGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATATTTCAA
AATCATAAATAAAGAACATTGCCTCGATTT
Found at i:4880545 original size:98 final size:96
Alignment explanation
Indices: 4880350--4880542 Score: 223
Period size: 97 Copynumber: 2.0 Consensus size: 96
4880340 AACTTTGGAA
* * * * * *
4880350 AAGGATATTCGATTATCTCGTTTTGAAAAAGTCGCACCTAGTAAGTTTAGGTACAAATTTTTCAG
1 AAGGATATTCGATTATCTCGATTTGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATATTTCAA
*
4880415 AATCATAGATAAAGAAACATTGCCTCGATTT
66 AATCATAAATAAAGAAACATTGCCTCGATTT
**
4880446 AAGGATATTCGATTAT-TCCGATTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCACAAA-ATTT
1 AAGGATATTCGATTATCT-CGATTTG-A-AAAAATCGCACCTAGTAAGTTAAGGCACAAATATTT
*
4880509 CAAAATTCA-AAATAAA-AGAATATTGCCTCGATTT
63 CAAAA-TCATAAATAAAGA-AACATTGCCTCGATTT
4880543 TAAAAGTTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
95 1 0.01
96 23 0.28
97 29 0.35
98 29 0.35
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGATTTGAAAAAATCGCACCTAGTAAGTTAAGGCACAAATATTTCAA
AATCATAAATAAAGAAACATTGCCTCGATTT
Found at i:4880876 original size:28 final size:28
Alignment explanation
Indices: 4880774--4881052 Score: 121
Period size: 29 Copynumber: 9.6 Consensus size: 28
4880764 GGATACCCGT
* * * *
4880774 GGGTAGAATGGTAATTTTGGGACATTTGG
1 GGGTAAAATGGTAATTTTAGGA-ATTCGA
** * *
4880803 GGGCCAAATGGTAATTTTGGGAAAGTT-TA
1 GGGTAAAATGGTAATTTTAGG-AA-TTCGA
* *
4880832 GGGTTAAAAAT-GAAATTTTAGGTATTCGA
1 GGG-T-AAAATGGTAATTTTAGGAATTCGA
*
4880861 GGGTAAAATGGTAATTTTAGGAAAAATCGA
1 GGGTAAAATGGTAATTTTAGG--AATTCGA
* *
4880891 -GGTCAAAAATGG-AATTTTTGGAAGTT-TA
1 GGGT--AAAATGGTAATTTTAGGAA-TTCGA
*
4880919 GGGGTAAAATGGTAACTTT-GGAAAAATT--A
1 -GGGTAAAATGGTAATTTTAGG---AATTCGA
* **
4880948 GGGTTAAAAAT-GAAATTTTAGGAAGTTTAA
1 GGG-T-AAAATGGTAATTTTAGGAA-TTCGA
*
4880978 GGGTAAAATGGTAATTTT-GGAAAAGTCGA
1 GGGTAAAATGGTAATTTTAGG--AATTCGA
* *
4881007 GGTTAAAATGG-AATTTTTAGAAATTCGA
1 GGGTAAAATGGTAA-TTTTAGGAATTCGA
4881035 GGGTAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
4881053 TGAAAAAATT
Statistics
Matches: 193, Mismatches: 28, Indels: 59
0.69 0.10 0.21
Matches are distributed among these distances:
27 7 0.04
28 59 0.31
29 70 0.36
30 44 0.23
31 13 0.07
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.32
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTAGGAATTCGA
Found at i:4880949 original size:29 final size:29
Alignment explanation
Indices: 4880861--4881170 Score: 176
Period size: 29 Copynumber: 10.6 Consensus size: 29
4880851 AGGTATTCGA
*
4880861 GGGTAAAATGGTAATTTTAGGAAAAA-TCG
1 GGGTAAAATGGTAATTTT-GGAAAAATTAG
* **
4880890 AGGTCAAAAATGG-AATTTTTGG-AAGTTTAG
1 GGGT--AAAATGGTAA-TTTTGGAAAAATTAG
*
4880920 GGGTAAAATGGTAACTTTGGAAAAATTAG
1 GGGTAAAATGGTAATTTTGGAAAAATTAG
* * ** *
4880949 GGTTAAAAAT-GAAATTTTAGG-AAGTTTAA
1 GGGT-AAAATGGTAATTTT-GGAAAAATTAG
* *
4880978 GGGTAAAATGGTAATTTTGG-AAAAGTCG
1 GGGTAAAATGGTAATTTTGGAAAAATTAG
* * * *
4881006 AGGTTAAAATGG-AATTTT-TAGAAATTCG
1 -GGGTAAAATGGTAATTTTGGAAAAATTAG
*
4881034 AGGGTAAAATGGTAATTTTTGAAAAAATT-G
1 -GGGTAAAATGGTAA-TTTTGGAAAAATTAG
** *
4881064 GGGTCAAAAATGG-AATTTTGGAAAGTTTAA
1 GGGT--AAAATGGTAATTTTGGAAAAATTAG
4881094 GGGTAAAATGGTAATTTTTGGAAAAATT-G
1 GGGTAAAATGGTAA-TTTTGGAAAAATTAG
* * * * **
4881123 AGGTTAAAAAGGGAATTTTAGAAAGTTTAG
1 -GGGTAAAATGGTAATTTTGGAAAAATTAG
4881153 GGGTAAAAAT-GTAATTTT
1 GGGT-AAAATGGTAATTTT
4881171 CAAAAAAATC
Statistics
Matches: 215, Mismatches: 44, Indels: 44
0.71 0.15 0.15
Matches are distributed among these distances:
28 52 0.24
29 85 0.40
30 54 0.25
31 24 0.11
ACGTcount: A:0.40, C:0.02, G:0.26, T:0.32
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGAAAAATTAG
Found at i:4880952 original size:116 final size:116
Alignment explanation
Indices: 4880808--4881202 Score: 458
Period size: 116 Copynumber: 3.4 Consensus size: 116
4880798 TTTGGGGGCC
* * ** * **
4880808 AAATGGTAATTTTGGGAAAGTTTAGGGTTAAAAATGAAATTTTAGGTA-TTCGAGGGTAAAATGG
1 AAATGGTAATTTTCGAAAAAATTAGGGTTAAAAATGAAATTTTAGGAAGTTTAAGGGTAAAATGG
4880872 TAATTTTAGGAAAAATCGAGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTA
66 TAATTTT-GGAAAAATCGAGGT-AAAAATGGAATTTTTGGAAGTTTAGGGGTA
* *
4880925 AAATGGTAACTTT-GGAAAAATTAGGGTTAAAAATGAAATTTTAGGAAGTTTAAGGGTAAAATGG
1 AAATGGTAATTTTCGAAAAAATTAGGGTTAAAAATGAAATTTTAGGAAGTTTAAGGGTAAAATGG
* * * * *
4880989 TAATTTTGGAAAAGTCGAGGTTAAAATGGAATTTTTAGAA-ATTCGAGGGTA
66 TAATTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTTAG-GGGTA
* * * *
4881040 AAATGGTAATTTTTGAAAAAATTGGGGTCAAAAATGGAATTTT-GGAAAGTTTAAGGGTAAAATG
1 AAATGGTAATTTTCGAAAAAATTAGGGTTAAAAATGAAATTTTAGG-AAGTTTAAGGGTAAAATG
* * * *
4881104 GTAATTTTTGGAAAAATTGAGGTTAAAAAGGGAATTTTAGAAAGTTTAGGGGTAA
65 GTAA-TTTTGGAAAAATCGAGG-TAAAAATGGAATTTTTGGAAGTTTAGGGGT-A
* * * *
4881159 AAAT-GTAATTTTCAAAAAAATCAAGGTTAAAAATGGAATTTTAG
1 AAATGGTAATTTTCGAAAAAATTAGGGTTAAAAATGAAATTTTAG
4881203 AAAACTTTGG
Statistics
Matches: 238, Mismatches: 31, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
114 3 0.01
115 36 0.15
116 91 0.38
117 48 0.20
118 51 0.21
119 9 0.04
ACGTcount: A:0.41, C:0.02, G:0.25, T:0.32
Consensus pattern (116 bp):
AAATGGTAATTTTCGAAAAAATTAGGGTTAAAAATGAAATTTTAGGAAGTTTAAGGGTAAAATGG
TAATTTTGGAAAAATCGAGGTAAAAATGGAATTTTTGGAAGTTTAGGGGTA
Found at i:4881103 original size:59 final size:59
Alignment explanation
Indices: 4880833--4881205 Score: 409
Period size: 59 Copynumber: 6.4 Consensus size: 59
4880823 GAAAGTTTAG
* ** ** *
4880833 GGTTAAAAATGAAATTTTAGGTA-TTCGAGGGTAAAATGGTAATTTTAGGAAAAATCGA
1 GGTTAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * * * * *
4880891 GGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAATGGTAA-CTTTGGAAAAAT-TA
1 GGTTAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * *
4880948 GGGTTAAAAATGAAATTTTAGGAAGTTTAAGGGTAAAATGGTAA-TTTTGGAAAAGTCGA
1 -GGTTAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATCGA
** * * *
4881007 GGTT-AAAATGGAATTTTTAGAAA-TTCGAGGGTAAAATGGTAATTTTTGAAAAAATTGG
1 GGTTAAAAATGGAA-TTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * *
4881065 GGTCAAAAATGGAATTTTGGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATTGA
1 GGTTAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATCGA
* * *** *
4881124 GGTTAAAAAGGGAATTTTAGAAAGTTTAGGGGTAAAAAT-GTAATTTTCAAAAAAATCAA
1 GGTTAAAAATGGAATTTTAGAAAGTTTAAGGGT-AAAATGGTAATTTTTGGAAAAATCGA
4881183 GGTTAAAAATGGAATTTTAGAAA
1 GGTTAAAAATGGAATTTTAGAAA
4881206 ACTTTGGGTG
Statistics
Matches: 266, Mismatches: 41, Indels: 15
0.83 0.13 0.05
Matches are distributed among these distances:
57 26 0.10
58 112 0.42
59 123 0.46
60 5 0.02
ACGTcount: A:0.42, C:0.02, G:0.24, T:0.31
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTAGAAAGTTTAAGGGTAAAATGGTAATTTTTGGAAAAATCGA
Found at i:4881206 original size:29 final size:29
Alignment explanation
Indices: 4880865--4881206 Score: 167
Period size: 29 Copynumber: 11.7 Consensus size: 29
4880855 ATTCGAGGGT
** *
4880865 AAAATGGTAATTTTAGGAAAAATCGAGGTCA
1 AAAATGG-AATTTTA-GAAAAATTAAGGTTA
* * ** * *
4880896 AAAATGGAATTTTTGGAAGTTTAGGGGT-
1 AAAATGGAATTTTAGAAAAATTAAGGTTA
* * *
4880924 AAAATGGTAACTTTGGAAAAATTAGGGTTA
1 AAAATGG-AATTTTAGAAAAATTAAGGTTA
* * ** *
4880954 AAAATGAAATTTTAGGAAGTTTAAGGGT-
1 AAAATGGAATTTTAGAAAAATTAAGGTTA
* * **
4880982 AAAATGGTAATTTTGGAAAAGTCGAGGTT-
1 AAAATGG-AATTTTAGAAAAATTAAGGTTA
* *
4881011 AAAATGGAATTTTTAG--AAATTCGAGGGT-
1 AAAATGGAA-TTTTAGAAAAATT-AAGGTTA
* ** *
4881039 AAAATGGTAATTTTTGAAAAAATTGGGGTCA
1 AAAATGG-AATTTTAG-AAAAATTAAGGTTA
* ** *
4881070 AAAATGGAATTTTGGAAAGTTTAAGGGT-
1 AAAATGGAATTTTAGAAAAATTAAGGTTA
* *
4881098 AAAATGGTAATTTTTGGAAAAATTGAGGTTA
1 AAAATGG-AA-TTTTAGAAAAATTAAGGTTA
* ** * *
4881129 AAAAGGGAATTTTAGAAAGTTTAGGGGTA
1 AAAATGGAATTTTAGAAAAATTAAGGTTA
* * *
4881158 AAAATGTAATTTTCAAAAAAATCAAGGTTA
1 AAAATGGAATTTT-AGAAAAATTAAGGTTA
4881188 AAAATGGAATTTTAGAAAA
1 AAAATGGAATTTTAGAAAA
4881207 CTTTGGGTGT
Statistics
Matches: 230, Mismatches: 67, Indels: 30
0.70 0.20 0.09
Matches are distributed among these distances:
27 3 0.01
28 39 0.17
29 102 0.44
30 61 0.27
31 25 0.11
ACGTcount: A:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (29 bp):
AAAATGGAATTTTAGAAAAATTAAGGTTA
Found at i:4882665 original size:17 final size:17
Alignment explanation
Indices: 4882645--4882689 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
4882635 ACCTAAATTT
4882645 AAAATAAATTTATAT-TC
1 AAAATAAATTTA-ATCTC
*
4882662 AAAATAAATTTAATCTT
1 AAAATAAATTTAATCTC
4882679 AAAATAAATTT
1 AAAATAAATTT
4882690 TAAAATGGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 2 0.08
17 24 0.92
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
AAAATAAATTTAATCTC
Found at i:4883458 original size:50 final size:49
Alignment explanation
Indices: 4883388--4883772 Score: 355
Period size: 50 Copynumber: 7.8 Consensus size: 49
4883378 TTGTCTTCAC
* *
4883388 GGTACTAGATCCACCTTTGCGGCTTAAATCTTTCCCTTCATGTCTTTTGA
1 GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTC-TTTGA
* * * * * * *
4883438 GGTACTAGG-TTCGCCATTGCGACTTAAACCTTTCCCTT-GTGTCTTCGT
1 GGTACT-GGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGA
* *
4883486 GGTACTGGATCCACCATTACGGCTTAGATCTTTCCCTTCATGTCTTCTGA
1 GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGA
* * * * * * *
4883536 GGTACTGGATTCATCATTGCGACTTAAACCTTTCCCTT-GTGTCTTCGT
1 GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGA
* * *
4883584 GGTAATAGATCCACCATTGCGGCTTAGATCTTTCCCTTCATGTCTTCTGA
1 GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTT-TGA
* * * * * * * * *
4883634 GGTACTGGGTTCGCCATTGCGACTTAAACCTTTCCCCT-GTGTCTTCGT
1 GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGA
* * * *
4883682 GGTACTGGATCCACCGTTGCGGCTTAGATCTTTCCTTTCATGTCTTTGC
1 GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGA
* * * *
4883731 GGTACTGGATCCGCCATTGCGGTCGTAGATCTTTCCCGTCAT
1 GGTACTGGATCCACCATTGCGG-CTTAAATCTTTCCCTTCAT
4883773 ATTTCATGGT
Statistics
Matches: 261, Mismatches: 66, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
47 2 0.01
48 94 0.36
49 55 0.21
50 109 0.42
51 1 0.00
ACGTcount: A:0.16, C:0.27, G:0.20, T:0.37
Consensus pattern (49 bp):
GGTACTGGATCCACCATTGCGGCTTAAATCTTTCCCTTCATGTCTTTGA
Found at i:4883767 original size:98 final size:98
Alignment explanation
Indices: 4883348--4883751 Score: 587
Period size: 98 Copynumber: 4.1 Consensus size: 98
4883338 AGGTACAAGG
* * * * ** *
4883348 TTCGTCATTGCGACTTAAACCCTTCCTTTTTTGTCTTCACGGTACTAGATCCACCTTTGCGGCTT
1 TTCGCCATTGCGACTTAAACCTTTCC-CTTGTGTCTTCGTGGTACTAGATCCACCATTGCGGCTT
* *
4883413 AAATCTTTCCCTTCATGTCTTTTGAGGTACTAGG-
65 AGATCTTTCCCTTCATGTCTTCTGAGGTACT-GGA
* *
4883447 TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTGGATCCACCATTACGGCTTA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTAGATCCACCATTGCGGCTTA
4883512 GATCTTTCCCTTCATGTCTTCTGAGGTACTGGA
66 GATCTTTCCCTTCATGTCTTCTGAGGTACTGGA
** *
4883545 TTCATCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTAATAGATCCACCATTGCGGCTTA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTAGATCCACCATTGCGGCTTA
*
4883610 GATCTTTCCCTTCATGTCTTCTGAGGTACTGGG
66 GATCTTTCCCTTCATGTCTTCTGAGGTACTGGA
* * *
4883643 TTCGCCATTGCGACTTAAACCTTTCCCCTGTGTCTTCGTGGTACTGGATCCACCGTTGCGGCTTA
1 TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTAGATCCACCATTGCGGCTTA
* *
4883708 GATCTTTCCTTTCATGTCTT-TGCGGTACTGGA
66 GATCTTTCCCTTCATGTCTTCTGAGGTACTGGA
*
4883740 TCCGCCATTGCG
1 TTCGCCATTGCG
4883752 GTCGTAGATC
Statistics
Matches: 277, Mismatches: 27, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
97 23 0.08
98 230 0.83
99 24 0.09
ACGTcount: A:0.16, C:0.27, G:0.19, T:0.38
Consensus pattern (98 bp):
TTCGCCATTGCGACTTAAACCTTTCCCTTGTGTCTTCGTGGTACTAGATCCACCATTGCGGCTTA
GATCTTTCCCTTCATGTCTTCTGAGGTACTGGA
Found at i:4895340 original size:29 final size:28
Alignment explanation
Indices: 4895273--4895539 Score: 99
Period size: 29 Copynumber: 9.1 Consensus size: 28
4895263 CCGGGGGTAG
* ***
4895273 AATGGTAATTTTGGGAAATTTGGGGGCCA
1 AATGG-AATTTTGGGAAATTTAGGGTTAA
4895302 AATGGTAATTTTGGGAAAGTTTAGGGTTAA
1 AATGG-AATTTTGGGAAA-TTTAGGGTTAA
* * ** *
4895332 AATGGAATTTTAGG-CATCCGAAGG-TAA
1 AATGGAATTTTGGGAAAT-TTAGGGTTAA
** *
4895359 AATGGTAATTTTGGGAAAAATCGTGGTTAAA
1 AATGG-AATTTTGGGAAATTTAG-GGTT-AA
** * * *
4895390 AATGGAATTTTTTGAAGTTTGGGGGTAA
1 AATGGAATTTTGGGAAATTTAGGGTTAA
* ** *
4895418 AATGGTAATTTTTGGAAAAATCGAGGTTAA
1 AATGG-AATTTTGGGAAATTTAG-GGTTAA
* *
4895448 AATGGAATTTT-GGAAAGTTTGGGGGTAA
1 AATGGAATTTTGGGAAA-TTTAGGGTTAA
* * * * * *
4895476 AATAGTAATTTTTGGAAAAATCAAGGTCAAA
1 AAT-GGAA-TTTTGGGAAATTTAGGGT-TAA
* *
4895507 AATGGAATTTTGGAAAAGTTTGAGGGTCAA
1 AATGGAATTTTGGGAAA-TTT-AGGGTTAA
4895537 AAT
1 AAT
4895540 ATAATTTTTA
Statistics
Matches: 176, Mismatches: 46, Indels: 31
0.70 0.18 0.12
Matches are distributed among these distances:
27 9 0.05
28 32 0.18
29 65 0.37
30 50 0.28
31 20 0.11
ACGTcount: A:0.36, C:0.04, G:0.28, T:0.32
Consensus pattern (28 bp):
AATGGAATTTTGGGAAATTTAGGGTTAA
Found at i:4895399 original size:58 final size:57
Alignment explanation
Indices: 4895273--4895547 Score: 250
Period size: 58 Copynumber: 4.7 Consensus size: 57
4895263 CCGGGGGTAG
* ** * **
4895273 AATGGTAATTTTGGGAAATTTGGGGGCCAAATGGTAATTTTGGG-AAAGTTTAGGGTTAA
1 AATGG-AATTTT-GGAAGTTTGGGGGTAAAATGGTAATTTTGGGAAAAATCGA-GGTTAA
* ** ** *
4895332 AATGGAATTTTAGGCA-TCCGAAGGTAAAATGGTAATTTTGGGAAAAATCGTGGTTAAA
1 AATGGAATTTT-GGAAGTTTGGGGGTAAAATGGTAATTTTGGGAAAAATCGAGGTT-AA
* *
4895390 AATGGAATTTTTTGAAGTTTGGGGGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAA
1 AATGGAA-TTTTGGAAGTTTGGGGGTAAAATGGTAATTTTGGGAAAAATCGAGGTTAA
* * * *
4895448 AATGGAATTTTGGAAAGTTTGGGGGTAAAATAGTAATTTTTGGAAAAATCAAGGTCAAA
1 AATGGAATTTTGG-AAGTTTGGGGGTAAAATGGTAATTTTGGGAAAAATCGAGGT-TAA
* *
4895507 AATGGAATTTTGGAAAAGTTTGAGGGTCAAAAT-ATAATTTT
1 AATGGAATTTTGG--AAGTTTGGGGGT-AAAATGGTAATTTT
4895548 TAGACAGTTT
Statistics
Matches: 182, Mismatches: 26, Indels: 15
0.82 0.12 0.07
Matches are distributed among these distances:
57 29 0.16
58 72 0.40
59 57 0.31
60 19 0.10
61 5 0.03
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (57 bp):
AATGGAATTTTGGAAGTTTGGGGGTAAAATGGTAATTTTGGGAAAAATCGAGGTTAA
Found at i:4895435 original size:59 final size:60
Alignment explanation
Indices: 4895354--4895548 Score: 265
Period size: 58 Copynumber: 3.3 Consensus size: 60
4895344 GGCATCCGAA
* * *
4895354 GGTAAAATGGTAATTTTGGGAAAAATCGTGGTTAAAAATGGAATTTTTTG-AAGTTTGGG
1 GGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAAGTTTGGG
4895413 GGTAAAATGGTAATTTTTGGAAAAATCGAGGTT-AAAATGGAA-TTTTGGAAAGTTTGGG
1 GGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAAGTTTGGG
* * * *
4895471 GGTAAAATAGTAATTTTTGGAAAAATCAAGGTCAAAAATGGAA-TTTTGGAAAAGTTTGAG
1 GGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGG-AAAGTTTGGG
*
4895531 GGTCAAAAT-ATAATTTTT
1 GGT-AAAATGGTAATTTTT
4895549 AGACAGTTTA
Statistics
Matches: 124, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
57 5 0.04
58 48 0.39
59 46 0.37
60 20 0.16
61 5 0.04
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.34
Consensus pattern (60 bp):
GGTAAAATGGTAATTTTTGGAAAAATCGAGGTTAAAAATGGAATTTTTGGAAAGTTTGGG
Found at i:4895546 original size:30 final size:30
Alignment explanation
Indices: 4895453--4895547 Score: 83
Period size: 30 Copynumber: 3.2 Consensus size: 30
4895443 GTTAAAATGG
*
4895453 AATTTTGG-AAAGTTTGGGGGT-AAAATAGT
1 AATTTTGGAAAAGTTTGAGGGTCAAAATA-T
* * *
4895482 AATTTTTGGAAAA--ATCAAGGTCAAAA-AT
1 AA-TTTTGGAAAAGTTTGAGGGTCAAAATAT
4895510 GGAATTTTGGAAAAGTTTGAGGGTCAAAATAT
1 --AATTTTGGAAAAGTTTGAGGGTCAAAATAT
4895542 AATTTT
1 AATTTT
4895548 TAGACAGTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 15
0.70 0.10 0.21
Matches are distributed among these distances:
28 1 0.02
29 17 0.33
30 18 0.35
31 13 0.25
32 2 0.04
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (30 bp):
AATTTTGGAAAAGTTTGAGGGTCAAAATAT
Found at i:4896325 original size:15 final size:15
Alignment explanation
Indices: 4896302--4896340 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
4896292 AAGGTAAAGC
*
4896302 TCTTGCCTTTTCTTT
1 TCTTTCCTTTTCTTT
*
4896317 TCTTTCCTTTTGTTT
1 TCTTTCCTTTTCTTT
*
4896332 TTTTTCCTT
1 TCTTTCCTT
4896341 AAAAAGGTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (15 bp):
TCTTTCCTTTTCTTT
Found at i:4897567 original size:17 final size:17
Alignment explanation
Indices: 4897511--4897601 Score: 85
Period size: 17 Copynumber: 5.2 Consensus size: 17
4897501 TATAATAAGT
4897511 TTTAAATTTAAATATAAA
1 TTTAAATTTAAA-ATAAA
** *
4897529 CCTAAATTTTAAAACAAAA
1 TTTAAA-TTTAAAA-TAAA
4897548 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* * *
4897565 TTTATATTCAAAATATA
1 TTTAAATTTAAAATAAA
4897582 TTT-AATCTTAAAATAAA
1 TTTAAAT-TTAAAATAAA
4897599 TTT
1 TTT
4897602 TAAAATGAGT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
16 2 0.03
17 31 0.53
18 12 0.21
19 13 0.22
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:4900810 original size:21 final size:21
Alignment explanation
Indices: 4900784--4900832 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
4900774 ATAAGTAGAA
4900784 CTACCGATACTTATCTTGAAT
1 CTACCGATACTTATCTTGAAT
*
4900805 CTACCGATACTTATCTTGCAT
1 CTACCGATACTTATCTTGAAT
4900826 CTACCGA
1 CTACCGA
4900833 AACAACACAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.35
Consensus pattern (21 bp):
CTACCGATACTTATCTTGAAT
Found at i:4901641 original size:13 final size:13
Alignment explanation
Indices: 4901623--4901650 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4901613 TCATGATGAC
4901623 ACATAGTCATCGG
1 ACATAGTCATCGG
4901636 ACATAGTCATCGG
1 ACATAGTCATCGG
4901649 AC
1 AC
4901651 CTCATAATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (13 bp):
ACATAGTCATCGG
Found at i:4901651 original size:65 final size:65
Alignment explanation
Indices: 4901571--4901702 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
4901561 TCATGTTGAC
* *
4901571 ACATAGTCATTGGACCTCATAATCCGAAAAGGATTCATATACTCATGATGACACATAGTCATCGG
1 ACATAGTCATCGGACCTCATAATCCGAAAAGGATTCATATACTCACGATGACACATAGTCATCGG
* * *
4901636 ACATAGTCATCGGACCTCATAATCCGTAAAGGATTCATATACTTACGATGACACATTGTCATCGG
1 ACATAGTCATCGGACCTCATAATCCGAAAAGGATTCATATACTCACGATGACACATAGTCATCGG
4901701 AC
1 AC
4901703 CTTTTGCATT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.27
Consensus pattern (65 bp):
ACATAGTCATCGGACCTCATAATCCGAAAAGGATTCATATACTCACGATGACACATAGTCATCGG
Found at i:4902716 original size:16 final size:16
Alignment explanation
Indices: 4902692--4902724 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
4902682 TCCTTACAAA
*
4902692 TTTATTCCTTTAACAT
1 TTTAATCCTTTAACAT
4902708 TTTAATCCTTTAACAT
1 TTTAATCCTTTAACAT
4902724 T
1 T
4902725 AAAATCATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAATCCTTTAACAT
Found at i:4902730 original size:16 final size:16
Alignment explanation
Indices: 4902697--4902730 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
4902687 ACAAATTTAT
**
4902697 TCCTTTAACATTTTAA
1 TCCTTTAACATTAAAA
4902713 TCCTTTAACATTAAAA
1 TCCTTTAACATTAAAA
4902729 TC
1 TC
4902731 ATCAAAAAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.21, G:0.00, T:0.44
Consensus pattern (16 bp):
TCCTTTAACATTAAAA
Found at i:4906491 original size:30 final size:30
Alignment explanation
Indices: 4906423--4906493 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 30
4906413 GATGATCTGT
* *
4906423 ATAAAAATAAAAAATAATAGAATTAAATTTG
1 ATAAAAAT-AAAAATAATAGAAATAAATTTA
* *
4906454 ATTAAAATAAAAATGATAGAAAT-AATTATA
1 ATAAAAATAAAAATAATAGAAATAAATT-TA
4906484 ATAAAAATAA
1 ATAAAAATAA
4906494 TTAAGTCGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 4 0.12
30 23 0.68
31 7 0.21
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (30 bp):
ATAAAAATAAAAATAATAGAAATAAATTTA
Found at i:4914332 original size:13 final size:14
Alignment explanation
Indices: 4914311--4914347 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
4914301 ATATATACAC
*
4914311 ATATACATATTA-G
1 ATATCCATATTAGG
4914324 ATATCCATATTAGG
1 ATATCCATATTAGG
4914338 ATATCC-TATT
1 ATATCCATATT
4914348 TTAGGTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (14 bp):
ATATCCATATTAGG
Found at i:4916161 original size:3 final size:3
Alignment explanation
Indices: 4916153--4916177 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
4916143 ATCATTCGAC
4916153 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
4916178 CGATTTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:4917932 original size:24 final size:23
Alignment explanation
Indices: 4917904--4917949 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
4917894 TGATAATTAA
4917904 ATCCACTTTAATATTTGTATTTTT
1 ATCCACTTTAATATTTG-ATTTTT
*
4917928 ATCCACTTTGATATTTGATTTT
1 ATCCACTTTAATATTTGATTTT
4917950 GACAATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.57
Consensus pattern (23 bp):
ATCCACTTTAATATTTGATTTTT
Found at i:4918752 original size:26 final size:26
Alignment explanation
Indices: 4918712--4918787 Score: 107
Period size: 26 Copynumber: 2.9 Consensus size: 26
4918702 TTGAATAGCA
* *
4918712 TGCGAGCATTGTCGATGAGCTCTCCT
1 TGCGAGCCTTATCGATGAGCTCTCCT
*
4918738 TGCGAGCCTTATCGATGAGCTCTCTT
1 TGCGAGCCTTATCGATGAGCTCTCCT
* *
4918764 TGCGAACCTTATCGGTGAGCTCTC
1 TGCGAGCCTTATCGATGAGCTCTC
4918788 TTCGCCATCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.32
Consensus pattern (26 bp):
TGCGAGCCTTATCGATGAGCTCTCCT
Found at i:4922609 original size:23 final size:24
Alignment explanation
Indices: 4922583--4922627 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
4922573 ATCTCATTCC
4922583 CTCTCACC-TCCTTATT-TCTCCTT
1 CTCTCACCTTCCTT-TTCTCTCCTT
4922606 CTCTCACCTTCCTTTTCTCTCC
1 CTCTCACCTTCCTTTTCTCTCC
4922628 ACTTAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.07, C:0.47, G:0.00, T:0.47
Consensus pattern (24 bp):
CTCTCACCTTCCTTTTCTCTCCTT
Found at i:4923267 original size:15 final size:14
Alignment explanation
Indices: 4923247--4923281 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
4923237 TTTAATAAAT
*
4923247 AATATTAAATTATTA
1 AATATTAAATT-TAA
4923262 AATATTAAATTTAA
1 AATATTAAATTTAA
4923276 AATATT
1 AATATT
4923282 TTTAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
AATATTAAATTTAA
Found at i:4928034 original size:17 final size:17
Alignment explanation
Indices: 4928012--4928051 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
4928002 AGGTGGAGAA
*
4928012 CTTGTTCGTTA-AGAGTT
1 CTTGTTCG-TAGAGAATT
4928029 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
4928046 CTTGTT
1 CTTGTT
4928052 AATGTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 2 0.10
17 19 0.90
ACGTcount: A:0.17, C:0.12, G:0.23, T:0.47
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:4928085 original size:41 final size:41
Alignment explanation
Indices: 4928040--4928135 Score: 156
Period size: 41 Copynumber: 2.3 Consensus size: 41
4928030 TTGTTCGTAG
* *
4928040 AGAATTCTTGTTAATGTGGAAATTGTTAAAATTGGGTGACT
1 AGAATTCTTGTTAAGGTGGAAATTGTTAAAATTGAGTGACT
* *
4928081 AGAATTCTTGTTAAGGTGGATATTGTTAGAATTGAGTGACT
1 AGAATTCTTGTTAAGGTGGAAATTGTTAAAATTGAGTGACT
4928122 AGAATTCTTGTTAA
1 AGAATTCTTGTTAA
4928136 AATAAAATTC
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (41 bp):
AGAATTCTTGTTAAGGTGGAAATTGTTAAAATTGAGTGACT
Found at i:4929190 original size:16 final size:16
Alignment explanation
Indices: 4929157--4929187 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
4929147 TAATGTATTT
4929157 TATTTTCTAAATAAAA
1 TATTTTCTAAATAAAA
4929173 TATTTT-TAAATAAAA
1 TATTTTCTAAATAAAA
4929188 ATAATCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTTCTAAATAAAA
Found at i:4931680 original size:24 final size:24
Alignment explanation
Indices: 4931653--4931715 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
4931643 AAAAATAATT
*
4931653 TTTCAGTTAAACTT-TATTTATTTG
1 TTTCAATTAAA-TTCTATTTATTTG
*
4931677 TTTCAATTAAATTCTGTTTATTTG
1 TTTCAATTAAATTCTATTTATTTG
* *
4931701 TTTGAATCAAATTCT
1 TTTCAATTAAATTCT
4931716 TATTAGTATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 2 0.06
24 32 0.94
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.56
Consensus pattern (24 bp):
TTTCAATTAAATTCTATTTATTTG
Found at i:4933643 original size:24 final size:24
Alignment explanation
Indices: 4933615--4933665 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
4933605 AGAAATAATC
* * *
4933615 TTTCAGTTAAACTTTATTTATTTG
1 TTTCAATTAAACTCTATTTATATG
*
4933639 TTTCAATTAAACTCTGTTTATATG
1 TTTCAATTAAACTCTATTTATATG
4933663 TTT
1 TTT
4933666 GAGTCAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.25, C:0.10, G:0.08, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATATG
Found at i:4934717 original size:20 final size:19
Alignment explanation
Indices: 4934683--4934730 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
4934673 AAGTGTTGGA
*
4934683 TATATAATTTAATTTAAAT
1 TATATATTTTAATTTAAAT
* *
4934702 GTATATATTTTTATTTTAAT
1 -TATATATTTTAATTTAAAT
4934722 TAATATATT
1 T-ATATATT
4934731 CTATTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TATATATTTTAATTTAAAT
Found at i:4935586 original size:21 final size:21
Alignment explanation
Indices: 4935543--4935586 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
4935533 AGTAAAAAAT
*
4935543 AATAAAAATAAATAAGATCGA
1 AATAAAAATAAATAAGATAGA
*
4935564 AATAACAATAAAATAA-ATAGA
1 AATAAAAAT-AAATAAGATAGA
4935585 AA
1 AA
4935587 GGAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.70, C:0.05, G:0.07, T:0.18
Consensus pattern (21 bp):
AATAAAAATAAATAAGATAGA
Found at i:4935939 original size:40 final size:40
Alignment explanation
Indices: 4935832--4935939 Score: 126
Period size: 40 Copynumber: 2.7 Consensus size: 40
4935822 TCGAAAACGT
* **
4935832 CGCAAAAAGTAAAGCAATAGTGACGTTTTTTAATAAACAC
1 CGCAAAAAGTAAAGCAATAGCGACGTTTTCCAATAAACAC
* * * * *
4935872 CGCAAAAGGTAAATCAATAGCAACGTTTTCCCATAAACGC
1 CGCAAAAAGTAAAGCAATAGCGACGTTTTCCAATAAACAC
* *
4935912 TGCAAAAAGTAAAGCAATAGCGGCGTTT
1 CGCAAAAAGTAAAGCAATAGCGACGTTT
4935940 ATGGGAAAAA
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 55 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.22
Consensus pattern (40 bp):
CGCAAAAAGTAAAGCAATAGCGACGTTTTCCAATAAACAC
Found at i:4935958 original size:41 final size:41
Alignment explanation
Indices: 4935913--4936075 Score: 161
Period size: 41 Copynumber: 4.0 Consensus size: 41
4935903 CATAAACGCT
* * *
4935913 GCAAAAAGTAA-AGCAATAGCGGCGTTTATGGGAAAAATGCC
1 GCAAAAAGTAAGAGCATTAACGGCGTTTATGAGAAAAA-GCC
* * *
4935954 GCAAAATGTAAGAGCATTAATGGTGTTTATGAGAAAACA-CC
1 GCAAAAAGTAAGAGCATTAACGGCGTTTATGAGAAAA-AGCC
* * *
4935995 GC-AAAAGTTAAGAGCATTAATGGCATTTATGAGAAAACGCC
1 GCAAAAAG-TAAGAGCATTAACGGCGTTTATGAGAAAAAGCC
* * * *
4936036 ACAAAAGGTAAGAGCATTAGCGGCGTTTATGACAAAAAGC
1 GCAAAAAGTAAGAGCATTAACGGCGTTTATGAGAAAAAGC
4936076 AGCTAAAGGT
Statistics
Matches: 100, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
40 4 0.04
41 71 0.71
42 24 0.24
43 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.24, T:0.20
Consensus pattern (41 bp):
GCAAAAAGTAAGAGCATTAACGGCGTTTATGAGAAAAAGCC
Found at i:4936712 original size:21 final size:20
Alignment explanation
Indices: 4936683--4936721 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
4936673 TGCTCCATGC
*
4936683 TAATTTTTTGTGAACTTTTTA
1 TAATATTTTGTGAA-TTTTTA
*
4936704 TAATATTTTTTGAATTTT
1 TAATATTTTGTGAATTTT
4936722 AAATTTTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TAATATTTTGTGAATTTTTA
Found at i:4938374 original size:58 final size:59
Alignment explanation
Indices: 4938264--4938379 Score: 162
Period size: 58 Copynumber: 2.0 Consensus size: 59
4938254 GTCGTAATAC
* * * * *
4938264 GTAAAGAGCATTAGCGGCTTTTATGAGAAAAACGCTACTAAAAATTAAGCAATAGTGAG
1 GTAAAAAGCATTAACGACGTTTATGAGAAAAACGCCACTAAAAATTAAGCAATAGTGAG
**
4938323 GTAAAAAGCATTAACGACGTTTATGA-AAAAACGCCACTAAAAATTTTGCAATAGTGA
1 GTAAAAAGCATTAACGACGTTTATGAGAAAAACGCCACTAAAAATTAAGCAATAGTGA
4938380 CGTTTACTCT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 28 0.56
59 22 0.44
ACGTcount: A:0.44, C:0.13, G:0.19, T:0.24
Consensus pattern (59 bp):
GTAAAAAGCATTAACGACGTTTATGAGAAAAACGCCACTAAAAATTAAGCAATAGTGAG
Found at i:4946282 original size:9 final size:9
Alignment explanation
Indices: 4946249--4946282 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
4946239 AAAACAAAAC
*
4946249 TTGAGAAAG
1 TTGAGAGAG
*
4946258 TTGAGAGAA
1 TTGAGAGAG
4946267 TTGAGAGAG
1 TTGAGAGAG
4946276 TTGAGAG
1 TTGAGAG
4946283 TTTAGAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (9 bp):
TTGAGAGAG
Found at i:4949382 original size:16 final size:15
Alignment explanation
Indices: 4949345--4949390 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 15
4949335 ACTTAAATTT
4949345 AATACTTATTTTTTC
1 AATACTTATTTTTTC
*
4949360 AAAACTTATTTTTTAC
1 AATACTTATTTTTT-C
*
4949376 ATTACTTAATTTTTT
1 AATACTT-ATTTTTT
4949391 TAGTTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 13 0.50
16 6 0.23
17 7 0.27
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.59
Consensus pattern (15 bp):
AATACTTATTTTTTC
Found at i:4956211 original size:36 final size:36
Alignment explanation
Indices: 4956162--4956262 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
4956152 TGGTAATAGG
* *
4956162 CATGAGCTTTGGGTCAATAGGGGGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
*
4956198 CATGACCTCTGGGTCAATAGGGAGTAAAACGAGCAT
1 CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
* * *
4956234 TATGACTTTTGGGTCAACAGGGAGTAAAA
1 CATGACCTTTGGGTCAATAGGGAGTAAAA
4956263 TGAATAACGA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.23
Consensus pattern (36 bp):
CATGACCTTTGGGTCAATAGGGAGTAAAACGAGCAT
Found at i:4956981 original size:21 final size:21
Alignment explanation
Indices: 4956932--4957003 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
4956922 GTTTTAGGTG
*
4956932 TCGATAGAAGTAAGACTTGTAT
1 TCGATAGAAGTGAGACTTGT-T
4956954 T-GATAGAAGTGAGACTTGTT
1 TCGATAGAAGTGAGACTTGTT
* * * *
4956974 TCGTTAGAACTGACACTTGTA
1 TCGATAGAAGTGAGACTTGTT
*
4956995 TCGGTAGAA
1 TCGATAGAA
4957004 AATTGTACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
20 2 0.05
21 40 0.93
22 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (21 bp):
TCGATAGAAGTGAGACTTGTT
Found at i:4964785 original size:21 final size:21
Alignment explanation
Indices: 4964759--4964830 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
4964749 GTTTTTGGTG
*
4964759 TCGGTAGAAGTAAGACTTGTA
1 TCGGTAGAAGTGAGACTTGTA
* *
4964780 TCGGTAAAAGTGAGACTTGTT
1 TCGGTAGAAGTGAGACTTGTA
* * * *
4964801 TCGATAGAACTGACACTTATA
1 TCGGTAGAAGTGAGACTTGTA
4964822 TCGGTAGAA
1 TCGGTAGAA
4964831 AATTATACTA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.29
Consensus pattern (21 bp):
TCGGTAGAAGTGAGACTTGTA
Found at i:4968114 original size:19 final size:18
Alignment explanation
Indices: 4968090--4968125 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
4968080 GGATTGTTAT
4968090 TTCTAGAAAATAGAATTTA
1 TTCTAGAAAATA-AATTTA
4968109 TTCTAGAAAATAAATTT
1 TTCTAGAAAATAAATTT
4968126 TCACCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.47, C:0.06, G:0.08, T:0.39
Consensus pattern (18 bp):
TTCTAGAAAATAAATTTA
Found at i:4970025 original size:23 final size:22
Alignment explanation
Indices: 4969994--4970037 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
4969984 AAAGAAATAA
*
4969994 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
4970016 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
4970038 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:4973255 original size:19 final size:19
Alignment explanation
Indices: 4973219--4973289 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
4973209 AAGGATGGTA
* * *
4973219 CGACAACAACAACAATGTG
1 CGACAGCAACGACGATGTG
*
4973238 CGACAGCAACGATGATGTGTGG
1 CGACAGCAACGACGA--TGT-G
* *
4973260 CGACAACAATGACGATGTG
1 CGACAGCAACGACGATGTG
*
4973279 CGACGGCAACG
1 CGACAGCAACG
4973290 TTGGTGCTTC
Statistics
Matches: 39, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 20 0.51
20 3 0.08
21 3 0.08
22 13 0.33
ACGTcount: A:0.35, C:0.24, G:0.28, T:0.13
Consensus pattern (19 bp):
CGACAGCAACGACGATGTG
Found at i:4973262 original size:22 final size:22
Alignment explanation
Indices: 4973237--4973278 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
4973227 ACAACAATGT
* *
4973237 GCGACAGCAACGATGATGTGTG
1 GCGACAACAACGACGATGTGTG
*
4973259 GCGACAACAATGACGATGTG
1 GCGACAACAACGACGATGTG
4973279 CGACGGCAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.31, C:0.19, G:0.33, T:0.17
Consensus pattern (22 bp):
GCGACAACAACGACGATGTGTG
Found at i:4973288 original size:22 final size:22
Alignment explanation
Indices: 4973233--4973288 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 22
4973223 AACAACAACA
* * *
4973233 ATGTGCGACAGCAACGATGATG
1 ATGTGCGACGGCAACAATGACG
*
4973255 -TGTG-G-CGACAACAATGACG
1 ATGTGCGACGGCAACAATGACG
4973274 ATGTGCGACGGCAAC
1 ATGTGCGACGGCAAC
4973289 GTTGGTGCTT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
19 10 0.38
20 5 0.19
21 5 0.19
22 6 0.23
ACGTcount: A:0.30, C:0.21, G:0.32, T:0.16
Consensus pattern (22 bp):
ATGTGCGACGGCAACAATGACG
Found at i:4987832 original size:30 final size:29
Alignment explanation
Indices: 4987795--4987871 Score: 138
Period size: 29 Copynumber: 2.7 Consensus size: 29
4987785 AATAATTTTA
4987795 AAATTATTAAAATTATTTTTTTAAAATAT
1 AAATTATTAAAATTATTTTTTTAAAATAT
4987824 AATATTATTAAAATTA-TTTTTTAAAATAT
1 AA-ATTATTAAAATTATTTTTTTAAAATAT
4987853 AAATTATTAAAATTATTTT
1 AAATTATTAAAATTATTTT
4987872 AAAATTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
28 13 0.28
29 20 0.43
30 13 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AAATTATTAAAATTATTTTTTTAAAATAT
Found at i:4987858 original size:28 final size:28
Alignment explanation
Indices: 4987795--4987871 Score: 136
Period size: 28 Copynumber: 2.7 Consensus size: 28
4987785 AATAATTTTA
4987795 AAATTATTAAAATTATTTTTTTAAAATAT
1 AAATTATTAAAATTA-TTTTTTAAAATAT
4987824 AATATTATTAAAATTATTTTTTAAAATAT
1 AA-ATTATTAAAATTATTTTTTAAAATAT
4987853 AAATTATTAAAATTATTTT
1 AAATTATTAAAATTATTTT
4987872 AAAATTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
28 17 0.36
29 17 0.36
30 13 0.28
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
AAATTATTAAAATTATTTTTTAAAATAT
Found at i:4989189 original size:29 final size:29
Alignment explanation
Indices: 4989157--4989233 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
4989147 GAGTTTCGTA
4989157 GAATTTGGGATTAAAA-CGTAA-TTTTTGAG
1 GAATTTGGGATTAAAATCG-AAGTTTTTG-G
*
4989186 GAATTTAGGGATCAAAATCGAAGTTTTTGG
1 GAATTT-GGGATTAAAATCGAAGTTTTTGG
* *
4989216 AAAATTGGGATTAAAATC
1 GAATTTGGGATTAAAATC
4989234 AAACTTTTGG
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
29 17 0.41
30 16 0.39
31 8 0.20
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (29 bp):
GAATTTGGGATTAAAATCGAAGTTTTTGG
Found at i:4989338 original size:31 final size:30
Alignment explanation
Indices: 4989294--4989419 Score: 121
Period size: 30 Copynumber: 4.2 Consensus size: 30
4989284 GGTAAAATGG
*
4989294 TAATTTTTG-GAAGTTTAGGGGTAAAAAATG
1 TAATTTTTGAGAAGTTTAGGGGT-AAAAATA
* * *
4989324 TAATTTTTGAGAAGTTCAAGGGCAAAAATA
1 TAATTTTTGAGAAGTTTAGGGGTAAAAATA
* *
4989354 TAATTTTTGAGAAG-TTCGAGGGTTAAAATA
1 TAATTTTTGAGAAGTTTAG-GGGTAAAAATA
* * * *
4989384 TAATTTTGGAAAAGTTTAGGGATTAAAATA
1 TAATTTTTGAGAAGTTTAGGGGTAAAAATA
*
4989414 TGATTT
1 TAATTT
4989420 CTAAACAGTT
Statistics
Matches: 79, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
29 1 0.01
30 65 0.82
31 13 0.16
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.37
Consensus pattern (30 bp):
TAATTTTTGAGAAGTTTAGGGGTAAAAATA
Found at i:4989410 original size:30 final size:29
Alignment explanation
Indices: 4989348--4989435 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 29
4989338 TTCAAGGGCA
* *
4989348 AAAATATAATTTTTGAGAAGTTCGAGGG-TT
1 AAAATATAA-TTTTGAAAAGTT-TAGGGATT
4989378 AAAATATAATTTTGGAAAAGTTTAGGGATT
1 AAAATATAATTTT-GAAAAGTTTAGGGATT
*
4989408 AAAATATGATTTCT-AAACAGTTTAGGGA
1 AAAATATAATTT-TGAAA-AGTTTAGGGA
4989436 CCTTCTTGGC
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
29 11 0.22
30 39 0.76
31 1 0.02
ACGTcount: A:0.41, C:0.03, G:0.20, T:0.35
Consensus pattern (29 bp):
AAAATATAATTTTGAAAAGTTTAGGGATT
Found at i:4989877 original size:17 final size:17
Alignment explanation
Indices: 4989854--4989983 Score: 82
Period size: 17 Copynumber: 8.1 Consensus size: 17
4989844 ATCGAGCCCC
4989854 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
4989872 -TTAAATTTGA-TTTAAA
1 TTTAAATTT-ATTTTAAA
* *
4989888 TTTAGACTTATTTTAAA
1 TTTAAATTTATTTTAAA
4989905 TTTAAATTTA----AAA
1 TTTAAATTTATTTTAAA
* *
4989918 -TTCAA---ACTTTAAA
1 TTTAAATTTATTTTAAA
* * *
4989931 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
4989948 TCTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
4989965 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
4989982 TT
1 TT
4989984 GAAACCCAAT
Statistics
Matches: 86, Mismatches: 15, Indels: 23
0.69 0.12 0.19
Matches are distributed among these distances:
9 1 0.01
12 4 0.05
13 6 0.07
14 4 0.05
16 2 0.02
17 68 0.79
18 1 0.01
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:4989890 original size:6 final size:6
Alignment explanation
Indices: 4989854--4989970 Score: 75
Period size: 6 Copynumber: 20.0 Consensus size: 6
4989844 ATCGAGCCCC
* * * * *
4989854 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-GA TTTAAA TTTAGA CTT-AT
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
4989899 TTTAAA TTTAAA TTTAAAA TTCAAA CTTTAAA TTTGAA TTT-AA TTTAAG
1 TTTAAA TTTAAA TTT-AAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* *
4989948 TCTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
4989971 ATTATTATAA
Statistics
Matches: 83, Mismatches: 19, Indels: 18
0.69 0.16 0.15
Matches are distributed among these distances:
5 20 0.24
6 53 0.64
7 10 0.12
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:4990794 original size:33 final size:31
Alignment explanation
Indices: 4990738--4990817 Score: 81
Period size: 33 Copynumber: 2.5 Consensus size: 31
4990728 AATAAACGTT
* * *
4990738 TTAATAA-TAATTATTATTGTTTTAAAAACA
1 TTAATAATTAATAATAACTGTTTTAAAAACA
* *
4990768 TTAATGACATTAATAATAACTGTTTTAATAATA
1 TTAAT-A-ATTAATAATAACTGTTTTAAAAACA
*
4990801 TTAATATTTAATAATAA
1 TTAATAATTAATAATAA
4990818 ATAATTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 5 0.12
31 11 0.27
32 2 0.05
33 23 0.56
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (31 bp):
TTAATAATTAATAATAACTGTTTTAAAAACA
Found at i:4991676 original size:33 final size:31
Alignment explanation
Indices: 4991610--4991676 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 31
4991600 ATATTTTGCG
* *
4991610 TTTAATCCTTTCGTATTTTTGATTATTTCAA
1 TTTAATCCTTTCGTACTTTTAATTATTTCAA
* *
4991641 TTTAATCCTTTTGGTACTTTTAATTTATTTTAA
1 TTTAATCC-TTTCGTACTTTTAA-TTATTTCAA
4991674 TTT
1 TTT
4991677 TGCCCAGTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 8 0.27
32 11 0.37
33 11 0.37
ACGTcount: A:0.22, C:0.10, G:0.06, T:0.61
Consensus pattern (31 bp):
TTTAATCCTTTCGTACTTTTAATTATTTCAA
Found at i:4992000 original size:30 final size:30
Alignment explanation
Indices: 4991954--4992205 Score: 195
Period size: 30 Copynumber: 8.6 Consensus size: 30
4991944 TAAACTGTTT
* * *
4991954 AAAAATTACA-TTTTGACCCCCGAACTTCT
1 AAAAATTCCATTTTTGACCCTCGAACTTCC
*
4991983 AAAAATTCCATTTTTGA-CCTTGAAACTTCC
1 AAAAATTCCATTTTTGACCCTCG-AACTTCC
* * * *
4992013 AAAAATTAC-TTTTTTACCCTCAAAATTCC
1 AAAAATTCCATTTTTGACCCTCGAACTTCC
*
4992042 AAAAATTCTATTTTTGA-CCTCGAAACTTCC
1 AAAAATTCCATTTTTGACCCTCG-AACTTCC
* * * *
4992072 AAAAATT--ATGTTTTTACCCCCAAACTTCT
1 AAAAATTCCAT-TTTTGACCCTCGAACTTCC
*
4992101 AAAAATTCCATTTTTAACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCCTCGAACTTCC
*
4992131 AAAAATTCTATTTTTGACCC-CGAAAC-TCC
1 AAAAATTCCATTTTTGACCCTCG-AACTTCC
* * *
4992160 TAAAATTATCA-TTTT-ACCCTCGAA-TATTC
1 AAAAATT-CCATTTTTGACCCTCGAACT-TCC
4992189 AAAAA-TCTCATTTTTGA
1 AAAAATTC-CATTTTTGA
4992206 TCCTGATTTT
Statistics
Matches: 176, Mismatches: 30, Indels: 33
0.74 0.13 0.14
Matches are distributed among these distances:
28 11 0.06
29 80 0.45
30 83 0.47
31 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAAATTCCATTTTTGACCCTCGAACTTCC
Found at i:4992046 original size:59 final size:60
Alignment explanation
Indices: 4991954--4992164 Score: 270
Period size: 59 Copynumber: 3.6 Consensus size: 60
4991944 TAAACTGTTT
* * *
4991954 AAAAATTAC-ATTTTGACCCCCGAACTTCTAAAAATTCCATTTTTGACCTTGAAACTTCC
1 AAAAATTACTATTTTTACCCCCAAACTTCTAAAAATTCCATTTTTGACCTCGAAACTTCC
* * * *
4992013 AAAAATTACT-TTTTTACCCTCAAAATTCCAAAAATTCTATTTTTGACCTCGAAACTTCC
1 AAAAATTACTATTTTTACCCCCAAACTTCTAAAAATTCCATTTTTGACCTCGAAACTTCC
* *
4992072 AAAAATTA-TGTTTTTACCCCCAAACTTCTAAAAATTCCATTTTTAACCCTCG-AACTTCC
1 AAAAATTACTATTTTTACCCCCAAACTTCTAAAAATTCCATTTTTGA-CCTCGAAACTTCC
* *
4992131 AAAAATT-CTATTTTTGACCCCGAAACTCCTAAAA
1 AAAAATTACTATTTTT-ACCCCCAAACTTCTAAAA
4992165 TTATCATTTT
Statistics
Matches: 132, Mismatches: 15, Indels: 9
0.85 0.10 0.06
Matches are distributed among these distances:
58 1 0.01
59 110 0.83
60 21 0.16
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.35
Consensus pattern (60 bp):
AAAAATTACTATTTTTACCCCCAAACTTCTAAAAATTCCATTTTTGACCTCGAAACTTCC
Found at i:4992203 original size:58 final size:60
Alignment explanation
Indices: 4991964--4992205 Score: 218
Period size: 59 Copynumber: 4.1 Consensus size: 60
4991954 AAAAATTACA
* * * *
4991964 TTTTGACCCCCGAACTTCTAAAAATTCCATTTTTGA-CCTTGAAACTTCCAAAAATTACT-T
1 TTTTGACCCCCAAACTCCTAAAAATTCCATTTTTAACCCTCG-AACTTCCAAAAATT-CTAT
* * * * * *
4992024 TTTT-ACCCTCAAAATTCC-AAAAATTCTATTTTTGA-CCTCGAAACTTCCAAAAATTATGT
1 TTTTGACCC-CCAAACTCCTAAAAATTCCATTTTTAACCCTCG-AACTTCCAAAAATTCTAT
*
4992083 TTTT-ACCCCCAAACTTCTAAAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTCTAT
1 TTTTGACCCCCAAACTCCTAAAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTCTAT
* * *
4992142 TTTTGACCCCGAAACTCCT-AAAATTATCA-TTTT-ACCCTCGAA-TATTCAAAAA-TCTCAT
1 TTTTGACCCCCAAACTCCTAAAAATT-CCATTTTTAACCCTCGAACT-TCCAAAAATTCT-AT
4992200 TTTTGA
1 TTTTGA
4992206 TCCTGATTTT
Statistics
Matches: 156, Mismatches: 18, Indels: 18
0.81 0.09 0.09
Matches are distributed among these distances:
57 4 0.03
58 31 0.20
59 93 0.60
60 28 0.18
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (60 bp):
TTTTGACCCCCAAACTCCTAAAAATTCCATTTTTAACCCTCGAACTTCCAAAAATTCTAT
Found at i:4994818 original size:6 final size:6
Alignment explanation
Indices: 4994807--4994834 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
4994797 TGATCAAAAT
4994807 TGAAAG TGAAAG TGAAAG TGAAAG TGAA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAA
4994835 GTTGAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.32, T:0.18
Consensus pattern (6 bp):
TGAAAG
Found at i:4994840 original size:18 final size:17
Alignment explanation
Indices: 4994807--4994851 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 17
4994797 TGATCAAAAT
4994807 TGAAAGTGAAAGTGAAAG
1 TGAAAGTG-AAGTGAAAG
*
4994825 TGAAAGTGAAGTTGAAAT
1 TGAAAGTGAAG-TGAAAG
*
4994843 TAAAAGTGA
1 TGAAAGTGA
4994852 TATGAATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.49, C:0.00, G:0.29, T:0.22
Consensus pattern (17 bp):
TGAAAGTGAAGTGAAAG
Found at i:4995001 original size:41 final size:40
Alignment explanation
Indices: 4994953--4995053 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
4994943 TCGACCTCGA
** *
4994953 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
4994993 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
4995031 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
4995054 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:5003346 original size:98 final size:98
Alignment explanation
Indices: 5003199--5003425 Score: 311
Period size: 98 Copynumber: 2.3 Consensus size: 98
5003189 AACACGACGG
* * * *
5003199 GAAAGATCTAAGATCGCAATGGTGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTTTAAGTC
1 GAAAGATCTAAGACCGCAAT-G-GCATCCAGTACCGCAAAGATAAAAAAGGGAAAGGTCTAAGTC
*
5003264 ACAATGGCAGA-TCGTGTACCTCAGAAGCATGAAGA
64 ACAACGGCAGACT-GTGTACCTCAGAAGCATGAAGA
* * *
5003299 GAAAGATCTAAGACCGCAATGGCATCCAGTACTGCAAAGATAAAAAAGGGCAAGGTCTAAGTCGC
1 GAAAGATCTAAGACCGCAATGGCATCCAGTACCGCAAAGATAAAAAAGGGAAAGGTCTAAGTCAC
*
5003364 AACGGCGGACTGTGTACCTCAGAAGCATGAAGA
66 AACGGCAGACTGTGTACCTCAGAAGCATGAAGA
5003397 G--A-A-CTAAGACCGCAATGGCATCCAGTACC
1 GAAAGATCTAAGACCGCAATGGCATCCAGTACC
5003426 ACGAAGATTC
Statistics
Matches: 116, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
94 25 0.22
95 1 0.01
96 1 0.01
98 68 0.59
99 2 0.02
100 19 0.16
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (98 bp):
GAAAGATCTAAGACCGCAATGGCATCCAGTACCGCAAAGATAAAAAAGGGAAAGGTCTAAGTCAC
AACGGCAGACTGTGTACCTCAGAAGCATGAAGA
Found at i:5003483 original size:93 final size:97
Alignment explanation
Indices: 5003201--5003487 Score: 262
Period size: 98 Copynumber: 3.0 Consensus size: 97
5003191 CACGACGGGA
* * * * * *
5003201 AAGATCTAAGATCGCAATGGTGGATCCAGTACCGCAAAGATACAAAAGGGAAAGGTTTAAGTCAC
1 AAGATCTAAGACCGCAAT-G-GCATCCAGTACCACAAAGATAAAAAAGGGAAAGGTCTAAGTCGC
* * * *
5003266 AATGGC-AGATCGTGTACCTCAGAAGCATGAAGAG
64 AACGACGA-ACCGTATACCTCAGAAGCATGAAGAG
** *
5003300 AAAGATCTAAGACCGCAATGGCATCCAGTACTGCAAAGATAAAAAAGGGCAAGGTCTAAGTCGCA
1 -AAGATCTAAGACCGCAATGGCATCCAGTACCACAAAGATAAAAAAGGGAAAGGTCTAAGTCGCA
* * * *
5003365 ACGGCGGACTGTGTACCTCAGAAGCATGAAGAG
65 ACGACGAACCGTATACCTCAGAAGCATGAAGAG
* *** * *
5003398 -A-A-CTAAGACCGCAATGGCATCCAGTACCACGAAGAT-TCGAAGGGAAAGGTTTAAGTCGCGA
1 AAGATCTAAGACCGCAATGGCATCCAGTACCACAAAGATAAAAAAGGGAAAGGTCTAAGTCGCAA
* *
5003459 TGACGAACCCG-ATACCTTAGAAGCATGAA
66 CGACGAA-CCGTATACCTCAGAAGCATGAA
5003488 AGGTCGAATC
Statistics
Matches: 159, Mismatches: 26, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
93 39 0.25
94 33 0.21
95 1 0.01
96 1 0.01
98 67 0.42
99 1 0.01
100 17 0.11
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.17
Consensus pattern (97 bp):
AAGATCTAAGACCGCAATGGCATCCAGTACCACAAAGATAAAAAAGGGAAAGGTCTAAGTCGCAA
CGACGAACCGTATACCTCAGAAGCATGAAGAG
Found at i:5003706 original size:92 final size:92
Alignment explanation
Indices: 5003549--5004419 Score: 1521
Period size: 92 Copynumber: 9.5 Consensus size: 92
5003539 ATCAAAATAT
*
5003549 CAAGTCTTTATCTCTCTAAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
* * * *
5003614 TCTTGAAGTTGTAGTAGAGCTGGACAC
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
5003641 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
5003706 TCTTGAAGTTGTAGTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
*
5003733 CAAGTCTTTATCTCTTTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
* *
5003798 TCTTGAAGTTGTATTAAAGCTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
5003825 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
*
5003890 TCTTGAAGTTGTAGTAGAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
*
5003917 CAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
5003982 TCTTGAAGTTGTAGTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
*
5004009 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGAAGAAGCATCAAACATCAA-TCTCTATC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTC-CTATC
*
5004073 CTCTTGAAGTTGTAGTAAAGTTGGATAA
65 CTCTTGAAGTTGTAGTAAAGTTGGATAG
* * *
5004101 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAAATGAAACATCAAACGTCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
*
5004166 TCTTGAAGTTGTAGTAGAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* *
5004193 CAAATCTTTATCTCTCTGAAGTTGTAGTAAGAACAAGATGAAGCATCAAACATCAATTCCTATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
*
5004258 TCTTGAAGTTGTATTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
* *
5004285 CAAGTCTTTATCTCTCTGAAGTTATAGTAAGAGCAAGATGAAGCATCAAACATCAATTCATATCC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
5004350 TCTTGAAGTTGTAGTAAAGTTGGATAG
66 TCTTGAAGTTGTAGTAAAGTTGGATAG
*
5004377 CAAGTCTTTATCTCTCTGAA-TTGTAGTAAGAGCAAGATAAAGC
1 CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGC
5004420 TTCGACACCA
Statistics
Matches: 740, Mismatches: 37, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
91 23 0.03
92 715 0.97
93 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (92 bp):
CAAGTCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCATCAAACATCAATTCCTATCC
TCTTGAAGTTGTAGTAAAGTTGGATAG
Found at i:5005080 original size:13 final size:12
Alignment explanation
Indices: 5005018--5005166 Score: 105
Period size: 13 Copynumber: 12.5 Consensus size: 12
5005008 ACTGGGCCCC
*
5005018 TTTAAATTT-AT
1 TTTAAATTTAAA
5005029 TTTAAGA-TTAAA
1 TTTAA-ATTTAAA
*
5005041 TTT-CATTTAAA
1 TTTAAATTTAAA
* *
5005052 TTTAGACTTT--T
1 TTTA-AATTTAAA
5005063 TTTAAATTTAAA
1 TTTAAATTTAAA
5005075 TTTTAAATTTAAA
1 -TTTAAATTTAAA
*
5005088 CTTTAAATTTGAA
1 -TTTAAATTTAAA
*
5005101 TTTAATTTTTAAA
1 TTTAA-ATTTAAA
5005114 TTTAAACTTTAAA
1 TTTAAA-TTTAAA
*
5005127 TTTGAATTT-AA
1 TTTAAATTTAAA
* *
5005138 TTTAAGTCTAAA
1 TTTAAATTTAAA
*
5005150 TTT-ATTTTAAA
1 TTTAAATTTAAA
5005161 TTTAAA
1 TTTAAA
5005167 ATTATTATAA
Statistics
Matches: 107, Mismatches: 19, Indels: 23
0.72 0.13 0.15
Matches are distributed among these distances:
10 5 0.05
11 36 0.34
12 19 0.18
13 47 0.44
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:5005081 original size:7 final size:6
Alignment explanation
Indices: 5005018--5005166 Score: 105
Period size: 6 Copynumber: 25.0 Consensus size: 6
5005008 ACTGGGCCCC
* * * *
5005018 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-CA TTTAAA TTTAGAC TTT--T
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA
* *
5005063 TTTAAA TTTAAA TTTTAAA TTTAAA CTTTAAA TTTGAA TTTAATT TTTAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA -TTTAAA TTTAAA TTTAA-A TTTAAA
* * * *
5005114 TTTAAA CTTTAAA TTTGAA TTT-AA TTTAAG TCTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5005161 TTTAAA
1 TTTAAA
5005167 ATTATTATAA
Statistics
Matches: 112, Mismatches: 18, Indels: 26
0.72 0.12 0.17
Matches are distributed among these distances:
4 3 0.03
5 18 0.16
6 64 0.57
7 27 0.24
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
TTTAAA
Found at i:5005111 original size:32 final size:32
Alignment explanation
Indices: 5005046--5005140 Score: 140
Period size: 32 Copynumber: 3.0 Consensus size: 32
5005036 TTAAATTTCA
* * * *
5005046 TTTAAATTTAGACTTT--TTTTAAATTTAAAT
1 TTTAAATTTAAACTTTAAATTTGAATTTAATT
5005076 TTTAAATTTAAACTTTAAATTTGAATTTAATT
1 TTTAAATTTAAACTTTAAATTTGAATTTAATT
5005108 TTTAAATTTAAACTTTAAATTTGAATTTAATT
1 TTTAAATTTAAACTTTAAATTTGAATTTAATT
5005140 T
1 T
5005141 AAGTCTAAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
30 15 0.25
32 44 0.75
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (32 bp):
TTTAAATTTAAACTTTAAATTTGAATTTAATT
Found at i:5005166 original size:17 final size:17
Alignment explanation
Indices: 5005018--5005179 Score: 114
Period size: 17 Copynumber: 9.1 Consensus size: 17
5005008 ACTGGGCCCC
5005018 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
5005036 -TTAAATTTCA-TTTAAA
1 TTTAAATTT-ATTTTAAA
*
5005052 TTTAGACTTT-TTTTAAA
1 TTTA-AATTTATTTTAAA
*
5005069 TTTAAATTTTAAATTTAAA
1 TTTAAA-TTT-ATTTTAAA
* *
5005088 CTTTAAATTTGAATTTAATT
1 -TTTAAATTT-ATTTTAA-A
*
5005108 TTTAAATTTAAACTTTAAA
1 TTTAAATTT--ATTTTAAA
* * *
5005127 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
5005144 TCTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
5005161 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
5005178 TT
1 TT
5005180 GAAACCCAAT
Statistics
Matches: 116, Mismatches: 18, Indels: 21
0.75 0.12 0.14
Matches are distributed among these distances:
16 2 0.02
17 64 0.55
18 5 0.04
19 33 0.28
20 12 0.10
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:5007213 original size:30 final size:30
Alignment explanation
Indices: 5007160--5007393 Score: 187
Period size: 30 Copynumber: 8.0 Consensus size: 30
5007150 AAAGGTCCCT
**
5007160 AAACTATCCAAAAATTAGA-TTTTGACCCCC
1 AAACT-TCCAAAAATTCCATTTTTGACCCCC
* * *
5007190 AAACTTTCAAAAATTCCATTTTTGACCTCG
1 AAACTTCCAAAAATTCCATTTTTGACCCCC
*
5007220 AAACTTCCAAAAATT--ATGTTTTTACCCCC
1 AAACTTCCAAAAATTCCAT-TTTTGACCCCC
* * *
5007249 GAACTTCCAAAAATTCCATTGTTGACCCTC
1 AAACTTCCAAAAATTCCATTTTTGACCCCC
* * * * *
5007279 GAACTTCCAAAAATTCTATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTGACCCCC
* * * *
5007309 AAACTTCTAAAAATTACA-TTTT-AACCTC
1 AAACTTCCAAAAATTCCATTTTTGACCCCC
* * *
5007337 --ACTTTCAAAAATTACATTTTT-TCCCCC
1 AAACTTCCAAAAATTCCATTTTTGACCCCC
*
5007364 AAACTTCCCAAAAATTCCATTTTCGACCCC
1 AAACTT-CCAAAAATTCCATTTTTGACCCC
5007394 AGAACTCCTG
Statistics
Matches: 159, Mismatches: 36, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
26 14 0.09
27 7 0.04
28 4 0.03
29 40 0.25
30 88 0.55
31 6 0.04
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (30 bp):
AAACTTCCAAAAATTCCATTTTTGACCCCC
Found at i:5007260 original size:59 final size:58
Alignment explanation
Indices: 5007161--5007391 Score: 252
Period size: 59 Copynumber: 3.9 Consensus size: 58
5007151 AAGGTCCCTA
* * *
5007161 AACTATCCAAAAATTAGATTTTGACCCCCAAACTTTCAAAAATTCCATTTTTGACCTCG
1 AACT-TCCAAAAATTATATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCG
* * *
5007220 AAACTTCCAAAAATTATGTTTTTACCCCCGAACTTCCAAAAATTCCATTGTTGACCCTCG
1 -AACTTCCAAAAATTATATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGA-CCTCG
* * * * * *
5007280 AACTTCCAAAAATTCTATTTTTAACCTCAAAACTTCTAAAAATTACA-TTTTAACCTC-
1 AACTTCCAAAAATTATATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCG
* * * *
5007337 -ACTTTCAAAAATTACATTTTTTCCCCCAAACTTCCCAAAAATTCCATTTTCGACC
1 AACTTCCAAAAATTATATTTTTACCCCCAAACTT-CCAAAAATTCCATTTTTGACC
5007392 CCAGAACTCC
Statistics
Matches: 142, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
55 9 0.06
56 28 0.20
57 6 0.04
58 4 0.03
59 67 0.47
60 28 0.20
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (58 bp):
AACTTCCAAAAATTATATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCG
Found at i:5007552 original size:144 final size:144
Alignment explanation
Indices: 5007404--5007677 Score: 324
Period size: 144 Copynumber: 1.9 Consensus size: 144
5007394 AGAACTCCTG
** * ** * *
5007404 AAATTACCATTTTACTCC-C-GAATGTTAAAAAATCTCATTTTTGATCTTGATTTTTCTAAAAAT
1 AAATTACCATTTTAC-CCTCGGAAT-CCAAAAAATCTC-GTTTTGATCCCGATTCTTCGAAAAAT
* **
5007467 TACCGTTTTAACCTCGATTGTCTAAAATATCAT-TTTAA-CCTAAAATTTTTCC-AAAATTACCA
63 TACCGTTTTAACCCCGATCATCTAAAATATCATCTTTAACCCT-AAA-TTTTCCTAAAATTACCA
5007529 TTTTACCCCTTAGAGTCTA
126 TTTTACCCCTTAGAGTCTA
* * *
5007548 AAATTACCATTTTGCCCTCGGGCATCCAAAAAGTCTCGTTTTGATCCCGATTCTTCGAAAAATTA
1 AAATTACCATTTTACCCTC-GGAATCCAAAAAATCTCGTTTTGATCCCGATTCTTCGAAAAATTA
* *
5007613 CCGTTTTACCCCCGATCATCTAAAATGTCATCTTTAACCCTAAATTTTCCTAAAATTACCATTTT
65 CCGTTTTAACCCCGATCATCTAAAATATCATCTTTAACCCTAAATTTTCCTAAAATTACCATTTT
5007678 GCCCTCGAGT
Statistics
Matches: 109, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
143 2 0.02
144 70 0.64
145 31 0.28
146 6 0.06
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (144 bp):
AAATTACCATTTTACCCTCGGAATCCAAAAAATCTCGTTTTGATCCCGATTCTTCGAAAAATTAC
CGTTTTAACCCCGATCATCTAAAATATCATCTTTAACCCTAAATTTTCCTAAAATTACCATTTTA
CCCCTTAGAGTCTA
Found at i:5008958 original size:3 final size:3
Alignment explanation
Indices: 5008940--5008980 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
5008930 TTTTATTTAT
* * *
5008940 TTA TTA TTC TTT TTA TTA TTA TTA CTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
5008981 TTAAAAAACT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:5009218 original size:4 final size:4
Alignment explanation
Indices: 5009211--5009256 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
5009201 TTTTTTTACC
*
5009211 TTAT TTA- TTA- TTAC TTA- TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
5009256 T
1 T
5009257 AAAATGTTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 9 0.22
4 31 0.77
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:5010532 original size:11 final size:11
Alignment explanation
Indices: 5010514--5010582 Score: 74
Period size: 11 Copynumber: 6.6 Consensus size: 11
5010504 GATGATAATT
5010514 ATAATTTTAAA
1 ATAATTTTAAA
*
5010525 ACAATTTT--A
1 ATAATTTTAAA
5010534 ATAATTTTAAA
1 ATAATTTTAAA
*
5010545 TTAATTTTAAA
1 ATAATTTTAAA
5010556 ATAATTTT--A
1 ATAATTTTAAA
*
5010565 ATAATTTTGAA
1 ATAATTTTAAA
*
5010576 ATTATTT
1 ATAATTT
5010583 GCTGATGTGG
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
9 17 0.35
11 32 0.65
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:5010550 original size:31 final size:32
Alignment explanation
Indices: 5010515--5010579 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 32
5010505 ATGATAATTA
5010515 TAATTTTAAAACAATTTTAATAATTTT-AAAT
1 TAATTTTAAAACAATTTTAATAATTTTGAAAT
*
5010546 TAATTTTAAAATAATTTTAATAATTTTGAAAT
1 TAATTTTAAAACAATTTTAATAATTTTGAAAT
5010578 TA
1 TA
5010580 TTTGCTGATG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 26 0.81
32 6 0.19
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (32 bp):
TAATTTTAAAACAATTTTAATAATTTTGAAAT
Found at i:5010577 original size:20 final size:22
Alignment explanation
Indices: 5010514--5010582 Score: 74
Period size: 20 Copynumber: 3.3 Consensus size: 22
5010504 GATGATAATT
**
5010514 ATAATTTTAAAACAATTTT--A
1 ATAATTTTAAATTAATTTTAAA
5010534 ATAATTTTAAATTAATTTTAAA
1 ATAATTTTAAATTAATTTTAAA
*
5010556 ATAATTTT-AA-TAATTTTGAA
1 ATAATTTTAAATTAATTTTAAA
*
5010576 ATTATTT
1 ATAATTT
5010583 GCTGATGTGG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 32 0.74
21 2 0.05
22 9 0.21
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (22 bp):
ATAATTTTAAATTAATTTTAAA
Found at i:5011885 original size:95 final size:95
Alignment explanation
Indices: 5011779--5011971 Score: 368
Period size: 95 Copynumber: 2.0 Consensus size: 95
5011769 GACTAAATAC
*
5011779 AATAAGTGACCTTATTTCTATCACTCCCTAGTATAGAATCCTTACTTTTCCTTCTAAATAACATC
1 AATAAGTGACCTTAGTTCTATCACTCCCTAGTATAGAATCCTTACTTTTCCTTCTAAATAACATC
*
5011844 TAAAATAGATCAATATAATTATAATAAGCA
66 TAAAATAGATCAATATAATTATAACAAGCA
5011874 AATAAGTGACCTTAGTTCTATCACTCCCTAGTATAGAATCCTTACTTTTCCTTCTAAATAACATC
1 AATAAGTGACCTTAGTTCTATCACTCCCTAGTATAGAATCCTTACTTTTCCTTCTAAATAACATC
5011939 TAAAATAGATCAATATAATTATAACAAGCA
66 TAAAATAGATCAATATAATTATAACAAGCA
5011969 AAT
1 AAT
5011972 TAACGTGGAC
Statistics
Matches: 96, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (95 bp):
AATAAGTGACCTTAGTTCTATCACTCCCTAGTATAGAATCCTTACTTTTCCTTCTAAATAACATC
TAAAATAGATCAATATAATTATAACAAGCA
Found at i:5013335 original size:23 final size:23
Alignment explanation
Indices: 5013309--5013387 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
5013299 AATTTTTTAA
*
5013309 TACATTTATTTCTATGTTCACAG
1 TACATCTATTTCTATGTTCACAG
**
5013332 TACATCTATTTCTAACCTTCACA-
1 TACATCTATTTCT-ATGTTCACAG
5013355 T---T-TATTTCTATGTTCACAG
1 TACATCTATTTCTATGTTCACAG
5013374 TACATCTATTTCTA
1 TACATCTATTTCTA
5013388 ACCTTCACAT
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
18 7 0.16
19 8 0.18
20 1 0.02
22 1 0.02
23 21 0.47
24 7 0.16
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.47
Consensus pattern (23 bp):
TACATCTATTTCTATGTTCACAG
Found at i:5013360 original size:19 final size:19
Alignment explanation
Indices: 5013333--5013405 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 19
5013323 TGTTCACAGT
*
5013333 ACATCTATTTCTAACCTTC
1 ACATTTATTTCTAACCTTC
**
5013352 ACATTTATTTCT-ATGTTC
1 ACATTTATTTCTAACCTTC
5013370 ACAGTACATCTATTTCTAACCTTC
1 ACA-T---T-TATTTCTAACCTTC
5013394 ACATTTATTTCT
1 ACATTTATTTCT
5013406 CATTCTGATT
Statistics
Matches: 43, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
18 7 0.16
19 19 0.44
20 1 0.02
22 1 0.02
23 8 0.19
24 7 0.16
ACGTcount: A:0.26, C:0.25, G:0.03, T:0.47
Consensus pattern (19 bp):
ACATTTATTTCTAACCTTC
Found at i:5013369 original size:42 final size:42
Alignment explanation
Indices: 5013310--5013405 Score: 192
Period size: 42 Copynumber: 2.3 Consensus size: 42
5013300 ATTTTTTAAT
5013310 ACATTTATTTCTATGTTCACAGTACATCTATTTCTAACCTTC
1 ACATTTATTTCTATGTTCACAGTACATCTATTTCTAACCTTC
5013352 ACATTTATTTCTATGTTCACAGTACATCTATTTCTAACCTTC
1 ACATTTATTTCTATGTTCACAGTACATCTATTTCTAACCTTC
5013394 ACATTTATTTCT
1 ACATTTATTTCT
5013406 CATTCTGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (42 bp):
ACATTTATTTCTATGTTCACAGTACATCTATTTCTAACCTTC
Found at i:5014725 original size:7 final size:7
Alignment explanation
Indices: 5014713--5014748 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
5014703 TTTCTTGAGC
5014713 GATGTGG
1 GATGTGG
5014720 GATGTGG
1 GATGTGG
*
5014727 GATGTGA
1 GATGTGG
5014734 GATGTGG
1 GATGTGG
*
5014741 GATATGG
1 GATGTGG
5014748 G
1 G
5014749 TATATATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.53, T:0.28
Consensus pattern (7 bp):
GATGTGG
Found at i:5015059 original size:18 final size:18
Alignment explanation
Indices: 5015036--5015095 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
5015026 GTTTTACAAA
5015036 AACTAAATTTAAATATCT
1 AACTAAATTTAAATATCT
* *
5015054 AACTAAA--AAAATATAT
1 AACTAAATTTAAATATCT
*
5015070 AATTTAAATTTAAATATCT
1 AA-CTAAATTTAAATATCT
*
5015089 AATTAAA
1 AACTAAA
5015096 AAATATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 9 0.26
17 4 0.12
18 12 0.35
19 9 0.26
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (18 bp):
AACTAAATTTAAATATCT
Found at i:5015086 original size:19 final size:16
Alignment explanation
Indices: 5015059--5015108 Score: 57
Period size: 15 Copynumber: 3.0 Consensus size: 16
5015049 TATCTAACTA
5015059 AAAAAATATATAATTT
1 AAAAAATATATAATTT
*
5015075 AAATTTAAATATCTAA-TT
1 AAA---AAATATATAATTT
5015093 AAAAAATATATAATTT
1 AAAAAATATATAATTT
5015109 GAAGGTTGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 9 0.32
16 5 0.18
18 5 0.18
19 9 0.32
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAAATATATAATTT
Found at i:5015101 original size:15 final size:16
Alignment explanation
Indices: 5015046--5015105 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
5015036 AACTAAATTT
* *
5015046 AAATATCTAACTAAAA
1 AAATATATAACTTAAA
*
5015062 AAATATATAATTTAAA
1 AAATATATAACTTAAA
*
5015078 TTTAAATATCTAA-TTAAA
1 ---AAATATATAACTTAAA
5015096 AAATATATAA
1 AAATATATAA
5015106 TTTGAAGGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 9 0.25
16 13 0.36
18 5 0.14
19 9 0.25
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATATATAACTTAAA
Found at i:5015102 original size:34 final size:35
Alignment explanation
Indices: 5015039--5015108 Score: 124
Period size: 34 Copynumber: 2.0 Consensus size: 35
5015029 TTACAAAAAC
5015039 TAAATTTAAATATCTAACTAAAAAAATATATAATT
1 TAAATTTAAATATCTAACTAAAAAAATATATAATT
*
5015074 TAAATTTAAATATCTAA-TTAAAAAATATATAATT
1 TAAATTTAAATATCTAACTAAAAAAATATATAATT
5015108 T
1 T
5015109 GAAGGTTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.50
35 17 0.50
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (35 bp):
TAAATTTAAATATCTAACTAAAAAAATATATAATT
Found at i:5020969 original size:9 final size:9
Alignment explanation
Indices: 5020951--5021014 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
5020941 GTCAGTAAAT
5020951 AATT-TTAA
1 AATTATTAA
5020959 AATTATTAA
1 AATTATTAA
5020968 AATTATT--
1 AATTATTAA
*
5020975 --TTTTTAA
1 AATTATTAA
5020982 AA-TA-TAA
1 AATTATTAA
5020989 AATTATTAA
1 AATTATTAA
5020998 AATTATTTTAA
1 AATTA--TTAA
5021009 AATTAT
1 AATTAT
5021015 AATTATCATT
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
5 4 0.09
7 5 0.11
8 7 0.16
9 20 0.44
11 9 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AATTATTAA
Found at i:5021733 original size:11 final size:11
Alignment explanation
Indices: 5021717--5021754 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
5021707 GATGATGATT
5021717 ATAATTTTAAA
1 ATAATTTTAAA
5021728 ATAATTTT--A
1 ATAATTTTAAA
5021737 ATAATTTTAAA
1 ATAATTTTAAA
*
5021748 ATTATTT
1 ATAATTT
5021755 GCTAATGTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 9 0.38
11 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
ATAATTTTAAA
Found at i:5021742 original size:20 final size:20
Alignment explanation
Indices: 5021717--5021754 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5021707 GATGATGATT
5021717 ATAATTTTAAAATAATTTTA
1 ATAATTTTAAAATAATTTTA
*
5021737 ATAATTTTAAAATTATTT
1 ATAATTTTAAAATAATTT
5021755 GCTAATGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAATTTTAAAATAATTTTA
Found at i:5023129 original size:2 final size:2
Alignment explanation
Indices: 5023122--5023148 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5023112 TTTTATTCTT
5023122 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5023149 GCAAACATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5023303 original size:8 final size:8
Alignment explanation
Indices: 5023252--5023305 Score: 54
Period size: 8 Copynumber: 6.2 Consensus size: 8
5023242 TTTTTATAAG
*
5023252 TAAAAAAG
1 TAAAAAAA
5023260 TAAAAATAA
1 TAAAAA-AA
5023269 TATAAAACAGA
1 TA-AAAA-A-A
*
5023280 TTAAAAAA
1 TAAAAAAA
5023288 TAAAAAAA
1 TAAAAAAA
5023296 TAAAAAAA
1 TAAAAAAA
5023304 TA
1 TA
5023306 TTCAAAACGT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 24 0.62
9 4 0.10
10 9 0.23
11 2 0.05
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:5025455 original size:32 final size:32
Alignment explanation
Indices: 5025390--5025455 Score: 96
Period size: 32 Copynumber: 2.1 Consensus size: 32
5025380 TATATATATG
* ** *
5025390 ATCCTTTGCATTTTCTATTAAATATTATGATA
1 ATCCTTTGCATTTTCTATGAAATACCATAATA
5025422 ATCCTTTGCATTTTCTATGAAATACCATAATA
1 ATCCTTTGCATTTTCTATGAAATACCATAATA
5025454 AT
1 AT
5025456 ATTATTGCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (32 bp):
ATCCTTTGCATTTTCTATGAAATACCATAATA
Found at i:5028716 original size:3 final size:3
Alignment explanation
Indices: 5028703--5028782 Score: 101
Period size: 3 Copynumber: 27.3 Consensus size: 3
5028693 CTATTAAAAG
* * * *
5028703 AGA AAA AGA AGA AGA AAA AGA AGA AGA AGA AGC AGA AGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
5028751 AGA AGA AGA AGA AGA GGA AGA A-A AGA A-A AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
5028783 AGAAAAGGTC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
2 4 0.06
3 61 0.94
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5028723 original size:9 final size:9
Alignment explanation
Indices: 5028698--5028788 Score: 73
Period size: 9 Copynumber: 10.3 Consensus size: 9
5028688 ACACACTATT
5028698 AAAAG-AGA
1 AAAAGAAGA
5028706 AAAAGAAGA
1 AAAAGAAGA
5028715 AGAAA-AAGA
1 A-AAAGAAGA
*
5028724 AGAAGAAGA
1 AAAAGAAGA
**
5028733 AGCAGAAGA
1 AAAAGAAGA
5028742 AAAAGAAGA
1 AAAAGAAGA
*
5028751 AGAAGAAGA
1 AAAAGAAGA
* *
5028760 AGAAGAGGA
1 AAAAGAAGA
*
5028769 AGAA-AAG-
1 AAAAGAAGA
5028776 AAAAGAAAGA
1 AAAAG-AAGA
5028786 AAA
1 AAA
5028789 GGTCAAGATG
Statistics
Matches: 69, Mismatches: 8, Indels: 10
0.79 0.09 0.11
Matches are distributed among these distances:
7 3 0.04
8 9 0.13
9 51 0.74
10 6 0.09
ACGTcount: A:0.71, C:0.01, G:0.27, T:0.00
Consensus pattern (9 bp):
AAAAGAAGA
Found at i:5030573 original size:49 final size:49
Alignment explanation
Indices: 5030506--5030919 Score: 289
Period size: 49 Copynumber: 8.5 Consensus size: 49
5030496 TACCAAGAAG
* * *
5030506 CATGAAGGGAAAGATTTAAGCCGTAACTGCGAATCCAGTACCACGAGGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCGAGGA
* * * * * * *
5030555 CATGGAGGGAATGGTTTAAGTCGCAACGGTGAA-CCTTGTACCTC-AGAAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTCGAG-GA
* * *
5030604 CATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCAT-GAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACC-TCGAGGA
* * * * *
5030653 TATGGAGGGAAA-AGTTTAAGTCGCAACGGCGAA-CCTTGTACCTC-AGAA
1 CATGAAGGGAAAGA-TTTAAGCCGCAACGGCGAATCC-AGTACCTCGAGGA
* *
5030701 GCATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCTCGAGGA
1 -CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCGAGGA
* * * * * * *
5030751 CATGGACGGAATGGTTTAAGTCGCAACGGCGAA-CCTTGTACCTC-AGAAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCTCGAG-GA
* * * * *
5030800 TATGAAGGGAAAGATTTAAGTCGCAACGGCAAATCCAGTACCACGAAGA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCGAGGA
* * * * * **
5030849 TAT--AGGGAAAGGTTTAAG--TCAACGGTGAA-CCTTA-TACCTCAAAAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC--AGTACCTCGAGGA
5030894 CATGAAGGGAAAGATTTAAGCCGCAA
1 CATGAAGGGAAAGATTTAAGCCGCAA
5030920 TGACAAATCT
Statistics
Matches: 279, Mismatches: 64, Indels: 44
0.72 0.17 0.11
Matches are distributed among these distances:
44 2 0.01
45 18 0.06
46 1 0.00
47 28 0.10
48 13 0.05
49 205 0.73
50 12 0.04
ACGTcount: A:0.36, C:0.19, G:0.26, T:0.19
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCTCGAGGA
Found at i:5030675 original size:98 final size:98
Alignment explanation
Indices: 5030501--5031141 Score: 680
Period size: 98 Copynumber: 6.7 Consensus size: 98
5030491 TTCATTACCA
* * * *
5030501 AGAAGCATGAAGGGAAAGATTTAAGCCGTAACTG-CGAATCCAGTACCACGAGGACATGGAGGGA
1 AGAAACATGAAGGGAAAGATTTAAGCCGCAAC-GACGAATCCAGTACCACGAAGATATGGAGGGA
* *
5030565 ATGGTTTAAGTCGCAACGGTGAACCTTGTACCTC
65 AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
* *
5030599 AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCTAGTACCATGAAGATATGGAGGGAA
1 AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGATATGGAGGGAA
*
5030664 AAGTTTAAGTCGCAACGGCGAACCTTGTACCTC
66 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
* * * * * *
5030697 AGAAGCATGAAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCTCGAGGACATGGACGGAA
1 AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGATATGGAGGGAA
*
5030762 TGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
66 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
* * * *
5030795 AGAAATATGAAGGGAAAGATTTAAGTCGCAACGGCAAATCCAGTACCACGAAGATAT--AGGGAA
1 AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGATATGGAGGGAA
* *
5030858 AGGTTTAAGT--CAACGGTGAACCTTATACCTC
66 AGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
* * * * *
5030889 AAAAACATGAAGGGAAAGATTTAAGCCGCAATGACAAATCTA-TAACCACGAAGATATAGAGGGA
1 AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGT-ACCACGAAGATATGGAGGGA
* *
5030953 AAGGTTTAAGTCGCAACGACGAACCTTGCACCTC
65 AAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
* * * * *
5030987 A-AAAGATGAGATGGGAAAGATTTAAGCCTCAAC-AGTGAATCTAGTA--AC------A-CGA-G
1 AGAAACATGA-A-GGGAAAGATTTAAGCCGCAACGA-CGAATCCAGTACCACGAAGATATGGAGG
* *
5031040 G--A--TATAAGTCGCAATGGCGAACCTTGTACCTC
63 GAAAGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
* * * * * * *
5031072 AGAAACATGAAGGGAAAGATTGAAGCCGCAACGGCGAGTTCGGTACCATGAAGACT-TGAAGGGA
1 AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGA-TATGGAGGGA
5031136 AAGGTT
65 AAGGTT
5031142 ATGACCGCGA
Statistics
Matches: 451, Mismatches: 65, Indels: 54
0.79 0.11 0.09
Matches are distributed among these distances:
84 25 0.06
85 28 0.06
86 8 0.02
87 1 0.00
89 2 0.00
90 2 0.00
91 1 0.00
93 2 0.00
94 70 0.16
96 31 0.07
97 10 0.02
98 244 0.54
99 26 0.06
100 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.19
Consensus pattern (98 bp):
AGAAACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACGAAGATATGGAGGGAA
AGGTTTAAGTCGCAACGGCGAACCTTGTACCTC
Found at i:5031418 original size:90 final size:91
Alignment explanation
Indices: 5031244--5031525 Score: 282
Period size: 90 Copynumber: 3.0 Consensus size: 91
5031234 ACTATAATAG
*
5031244 CAAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAGATAAAGCTTCAACGTCAAATCCTATCCT
1 CAAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT
* *
5031309 CTTGAAATTGCGGTAAAGTTGGATAA
66 CCTGAAATTGCAGTAAAGTTGGATAA
* * * *
5031335 CAAGTCTTTATCTCTTTGAAGTTGCAGTAA-AGCAAGATGAAGCTTCAACATCAAATCCTATCTT
1 CAAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT
* *
5031399 CCTGAAGTTGCAGTGAAGTTGGATTAAAAA
66 CCTGAAATTGCAGTAAAGTTGGA-T---AA
* * * *
5031429 CAAAAATAACAGGTCTT-TATCTCTCTGAAGTTGCAATAAGAGCAAGATGAAGCTTTAACATCAA
1 C--AAGT--C---T-TTATCTCTC--TGAAGTTGCAATAAGAGCAAGATAAAGCTTCAACATCAA
* *
5031493 ATCCTAT-CTTCTGAAGTTGCAGTAAAGTTGGAT
56 ATCCTATCCTCCTGAAATTGCAGTAAAGTTGGAT
5031526 TAAAAACAAA
Statistics
Matches: 159, Mismatches: 17, Indels: 19
0.82 0.09 0.10
Matches are distributed among these distances:
90 50 0.31
91 29 0.18
94 3 0.02
96 3 0.02
98 1 0.01
101 5 0.03
102 3 0.02
103 35 0.22
104 30 0.19
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (91 bp):
CAAGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAGATAAAGCTTCAACATCAAATCCTATCCT
CCTGAAATTGCAGTAAAGTTGGATAA
Found at i:5031666 original size:103 final size:104
Alignment explanation
Indices: 5031331--5031634 Score: 495
Period size: 103 Copynumber: 2.9 Consensus size: 104
5031321 GTAAAGTTGG
* * *
5031331 ATAACAAGTCTTTATCTCTTTGAAGTTGCAGTAA-AGCAAGATGAAGCTTCAACATCAAATCCTA
1 ATAACAGGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACATCAAATCCTA
5031395 TCTTCCTGAAGTTGCAGTGAAGTTGGATTAAAAACAAAA
66 TCTTCCTGAAGTTGCAGTGAAGTTGGATTAAAAACAAAA
*
5031434 ATAACAGGTCTTTATCTCTCTGAAGTTGCAATAAGAGCAAGATGAAGCTTTAACATCAAATCCTA
1 ATAACAGGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACATCAAATCCTA
*
5031499 TCTT-CTGAAGTTGCAGTAAAGTTGGATTAAAAACAAAA
66 TCTTCCTGAAGTTGCAGTGAAGTTGGATTAAAAACAAAA
* *
5031537 ATAACAGGGCTTTATCTCTCTGAAGTTGTAGTAAGAGCAAGATGAAGCTTTAACATCAAATCCTA
1 ATAACAGGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACATCAAATCCTA
* * * *
5031602 TCTTCCTGAAGTTACGGCGAAGTTGGATCAAAA
66 TCTTCCTGAAGTTGCAGTGAAGTTGGATTAAAA
5031635 CCACAGTAGC
Statistics
Matches: 186, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
103 130 0.70
104 56 0.30
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (104 bp):
ATAACAGGTCTTTATCTCTCTGAAGTTGCAGTAAGAGCAAGATGAAGCTTTAACATCAAATCCTA
TCTTCCTGAAGTTGCAGTGAAGTTGGATTAAAAACAAAA
Found at i:5032783 original size:48 final size:46
Alignment explanation
Indices: 5032714--5032808 Score: 111
Period size: 48 Copynumber: 2.0 Consensus size: 46
5032704 TATGCAGGCT
* * * *
5032714 TATATATGTATATATAGACATATAT-TATGATTTTATTCTTTATTTA
1 TATATATATATATATAAACATACATAT-TGATTTCATTCTTTATTTA
*
5032760 TATATATATATATATGCAAACATACATATTGATTTCATTTTTTATTTA
1 TATATATATATATAT--AAACATACATATTGATTTCATTCTTTATTTA
5032808 T
1 T
5032809 CTCATATACA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
46 14 0.34
48 26 0.63
49 1 0.02
ACGTcount: A:0.36, C:0.06, G:0.05, T:0.53
Consensus pattern (46 bp):
TATATATATATATATAAACATACATATTGATTTCATTCTTTATTTA
Found at i:5035821 original size:18 final size:19
Alignment explanation
Indices: 5035798--5035835 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
5035788 GGGTTTGTAT
5035798 CCTAACCCTTATAT-TTTC
1 CCTAACCCTTATATGTTTC
5035816 CCTAACCCTTATATGTTTC
1 CCTAACCCTTATATGTTTC
5035835 C
1 C
5035836 ATTTTCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.21, C:0.34, G:0.03, T:0.42
Consensus pattern (19 bp):
CCTAACCCTTATATGTTTC
Found at i:5036908 original size:142 final size:145
Alignment explanation
Indices: 5036638--5036929 Score: 421
Period size: 142 Copynumber: 2.0 Consensus size: 145
5036628 AATAAAGGCT
*
5036638 ATTTAACAATAAATAATAAATATTTATAAAAATAATTGAATAAATTGAATAAAAATAAAACAGAA
1 ATTTAACAATAAATAATAAATATTCATAAAAATAATTGAATAAATTGAATAAAAATAAAACAG-A
* *
5036703 AAAAATAAAAAAAAAATTAATTCTTTCAATTTGTTATGGGTTTTTTTACCTAAAATATATAAAAT
65 AAAAACAAAAAAAAAATTAATTCTTTCAATTTGTTATGGATTTTTTTACCTAAAATATATAAAAT
* * *
5036768 AAATATTAAAATTTTA
130 AAATACTAAAACTCTA
* * *
5036784 ATTTAACAATAAATAATAAAT-TTCCA-ATAAATAATTGAATAATTTGAATAAAAATAAAATAG-
1 ATTTAACAATAAATAATAAATATT-CATAAAAATAATTGAATAAATTGAATAAAAATAAAACAGA
* * * *
5036846 TAAAACAAAAATAAATTTAATTCTTTCAATTTGTTAT-GATTTTTTTACCTAAAATATTTAAAAT
65 AAAAACAAAAAAAAAATTAATTCTTTCAATTTGTTATGGATTTTTTTACCTAAAATATATAAAAT
5036910 AAATACTAAAACTCTA
130 AAATACTAAAACTCTA
5036926 ATTT
1 ATTT
5036930 TAAAAACCTA
Statistics
Matches: 132, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
142 42 0.32
143 33 0.25
145 35 0.27
146 22 0.17
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (145 bp):
ATTTAACAATAAATAATAAATATTCATAAAAATAATTGAATAAATTGAATAAAAATAAAACAGAA
AAAACAAAAAAAAAATTAATTCTTTCAATTTGTTATGGATTTTTTTACCTAAAATATATAAAATA
AATACTAAAACTCTA
Found at i:5038009 original size:21 final size:22
Alignment explanation
Indices: 5037975--5038015 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
5037965 AAACAGTGAG
5037975 AAAGCAGTAAAAAAA-AACAAC
1 AAAGCAGTAAAAAAAGAACAAC
**
5037996 AAAGCAGTGGAAAAAGAACA
1 AAAGCAGTAAAAAAAGAACA
5038016 GTAGAGCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.66, C:0.12, G:0.17, T:0.05
Consensus pattern (22 bp):
AAAGCAGTAAAAAAAGAACAAC
Found at i:5044032 original size:159 final size:159
Alignment explanation
Indices: 5043733--5044052 Score: 451
Period size: 159 Copynumber: 2.0 Consensus size: 159
5043723 TTGTAACTTC
* *
5043733 ACTCCATTCCACGGTAACCTCAAGGACATTGAGATCCGTTACTCATTTTAATCCAATCCACTGCA
1 ACTCCATTCCACGGCAACCTCAAGGACATTGAGATCCGTTACTCATTTTAATCCAATCCACTACA
* * * * * * ** * *
5043798 ACTTTAAGGATATTGGGTTTGGTTCTTCACTCCATTCCATTGTAATTTTAGGGACATTGAGATCT
66 ACTTCAAGGATATTAGATTTGGTGCTTCACTACATTCCACTGTAACCTCAGGGACATTAAGATCT
**
5043863 ACTTCATTGTTTTAATTTGACCCACTACA
131 ACTTCATTGTTTTAATTCAACCCACTACA
* * * **
5043892 ACTCTATTCCACTGCAACCTCAAGGACATTGAGATTCGTTACTCATTTTAATCCAATCTGCTACA
1 ACTCCATTCCACGGCAACCTCAAGGACATTGAGATCCGTTACTCATTTTAATCCAATCCACTACA
*
5043957 ACTTCAAGGATATTAGATTTGGTGCTTCACTACATTTCACTGTAACCTCAGGGACATTAAGATCT
66 ACTTCAAGGATATTAGATTTGGTGCTTCACTACATTCCACTGTAACCTCAGGGACATTAAGATCT
*
5044022 ACTTCTTTGTTTTAATTCAACCCACTACA
131 ACTTCATTGTTTTAATTCAACCCACTACA
5044051 AC
1 AC
5044053 CCAGGGGCAT
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
159 140 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (159 bp):
ACTCCATTCCACGGCAACCTCAAGGACATTGAGATCCGTTACTCATTTTAATCCAATCCACTACA
ACTTCAAGGATATTAGATTTGGTGCTTCACTACATTCCACTGTAACCTCAGGGACATTAAGATCT
ACTTCATTGTTTTAATTCAACCCACTACA
Found at i:5044068 original size:93 final size:94
Alignment explanation
Indices: 5043892--5044363 Score: 343
Period size: 98 Copynumber: 4.9 Consensus size: 94
5043882 ACCCACTACA
* * * * * **
5043892 ACTCTATTCCACTGCAACCTCAAGGACATTGAGAT-T-CGTTACTCATTTTAATCCAATCTGCTA
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGC-TT-CTTATTTTAATCCAACCCACTA
* * *
5043955 CAACTTCAAGGATATTAGATTTGG-TG-CTTC
64 CAAC-TCAGGGGTATGAGATTTGGTTGACTTC
* * * * * *
5043985 ACTACATTTCACTGTAACCTCAGGGACATTAAGATCTACTTCTTTGTTTTAATTCAACCCACTAC
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTC-TTATTTTAATCCAACCCACTAC
* *
5044050 AACCCAGGGGCATGAGATTTGGTATTGTAACTTC
65 AACTCAGGGGTATGAGATTTGG--TTG--ACTTC
* * * *** *
5044084 TCTCCATTCCACTGTAACCTCAGGGACATTGA-ATATGCTTCGTTGTTTTAATTTGACCCACTGC
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTC-TTATTTTAATCCAACCCACTAC
*
5044148 AACTCAGGGGTATGGGATTTAGTGTTGTAACTTC
65 AACTCAGGGGTATGAGATTT-G-GTTG--ACTTC
* * * * * * *
5044182 TCTCTATTCCACTGTAACCTTAGGGACATTGAGATCCG-TTACTAATTTTAATCCAATCCACTGC
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTT-CTTATTTTAATCCAACCCACTAC
* *
5044246 AACTTCAAGGATATTGA-ATTTGG-TG-CTTC
65 AAC-TCAGGGGTA-TGAGATTTGGTTGACTTC
* * * *
5044275 ACTCCATTCTACTGTAACCTTAGGGACATTGAGATCTGCTTCATTATTTTAATCCGACCTACTAC
1 ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTC-TTATTTTAATCCAACCCACTAC
* *
5044340 AACTTAGAGGTAT-AGGATTTGGTT
65 AACTCAGGGGTATGA-GATTTGGTT
5044364 TTAATGAAAA
Statistics
Matches: 303, Mismatches: 56, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
91 1 0.00
92 1 0.00
93 94 0.31
94 45 0.15
95 1 0.00
96 4 0.01
97 1 0.00
98 105 0.35
99 48 0.16
100 3 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.35
Consensus pattern (94 bp):
ACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGCTTCTTATTTTAATCCAACCCACTACA
ACTCAGGGGTATGAGATTTGGTTGACTTC
Found at i:5055499 original size:29 final size:30
Alignment explanation
Indices: 5055467--5055536 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 30
5055457 TAAATAATAG
5055467 AAAAAGGATTAAATTCTAAAAA-AA-AAAA
1 AAAAAGGATTAAATTCTAAAAAGAATAAAA
* *
5055495 TAAAAAGGGA-AAAATTTTAAAAAGAATAAAA
1 -AAAAA-GGATTAAATTCTAAAAAGAATAAAA
5055526 ATAAAAGGATT
1 A-AAAAGGATT
5055537 TTAATTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
29 16 0.48
30 9 0.27
31 8 0.24
ACGTcount: A:0.67, C:0.01, G:0.11, T:0.20
Consensus pattern (30 bp):
AAAAAGGATTAAATTCTAAAAAGAATAAAA
Found at i:5055579 original size:30 final size:30
Alignment explanation
Indices: 5055468--5055579 Score: 81
Period size: 30 Copynumber: 3.8 Consensus size: 30
5055458 AAATAATAGA
* *
5055468 AAAAGGA-TTAAATTCTAAAAAA-AAAAAT
1 AAAAGGAGTTTAATTTTAAAAAATAAAAAT
***
5055496 AAAAAGG-GAAAAATTTTAAAAAGAATAAAAAT
1 -AAAAGGAGTTTAATTTT-AAAA-AATAAAAAT
* * *
5055528 AAAAGGATTTTAA-TTTGAAAAATGAGAAAT
1 AAAAGGAGTTTAATTTTAAAAAAT-AAAAAT
5055558 AAAAGG-GTTTAATTTTAAAAAA
1 AAAAGGAGTTTAATTTTAAAAAA
5055580 CTGAATAAAG
Statistics
Matches: 65, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
29 20 0.31
30 26 0.40
31 11 0.17
32 8 0.12
ACGTcount: A:0.62, C:0.01, G:0.12, T:0.25
Consensus pattern (30 bp):
AAAAGGAGTTTAATTTTAAAAAATAAAAAT
Found at i:5064286 original size:27 final size:27
Alignment explanation
Indices: 5064245--5064297 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
5064235 TAATTCTATA
*
5064245 ATTTTTAAAATAAAAAAT-TCAATATC
1 ATTTTTTAAATAAAAAATATCAATATC
5064271 ATTTTTTATAA-AAAAAATATCAATATC
1 ATTTTTTA-AATAAAAAATATCAATATC
5064298 TTACTCATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.40
Consensus pattern (27 bp):
ATTTTTTAAATAAAAAATATCAATATC
Found at i:5064612 original size:3 final size:3
Alignment explanation
Indices: 5064604--5064631 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5064594 TATATAACTT
5064604 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
5064632 GTAGTGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5065272 original size:40 final size:40
Alignment explanation
Indices: 5065179--5065301 Score: 151
Period size: 40 Copynumber: 3.1 Consensus size: 40
5065169 ATCCGTTTGG
* * *
5065179 TTTCAAGATACCCTTTGCGGGTTTTTATCTTGA-CCTTTT
1 TTTCGAGACACCCTTTGCGGGTTTTTATCTCGATCCTTTT
* * *
5065218 TTT-GTAGACGCCCTTTGCGGGTTTTCATCTCAATCCTTTT
1 TTTCG-AGACACCCTTTGCGGGTTTTTATCTCGATCCTTTT
*
5065258 TTTCGAGACACCCTTTACGGGTTTTTATCTCGATCCTTCTT
1 TTTCGAGACACCCTTTGCGGGTTTTTATCTCGATCCTT-TT
5065299 TTT
1 TTT
5065302 TTTTAGGCGA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
39 26 0.37
40 38 0.54
41 6 0.09
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.47
Consensus pattern (40 bp):
TTTCGAGACACCCTTTGCGGGTTTTTATCTCGATCCTTTT
Found at i:5072512 original size:15 final size:15
Alignment explanation
Indices: 5072492--5072521 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5072482 GAAATGTGAT
5072492 GCTTATGAATCCATA
1 GCTTATGAATCCATA
5072507 GCTTATGAATCCATA
1 GCTTATGAATCCATA
5072522 CATGCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (15 bp):
GCTTATGAATCCATA
Found at i:5076285 original size:30 final size:30
Alignment explanation
Indices: 5076239--5076433 Score: 127
Period size: 30 Copynumber: 6.6 Consensus size: 30
5076229 AAAAATGAAA
*
5076239 TTTTGGAAAG-TTGGGGGCTAAA-CTTGAAT
1 TTTTGGAAAGTTTGGGGGCTAAATC-TAAAT
*
5076268 TTTTAGG-AAGTTTGGGGGTTAAATCTAAAT
1 TTTT-GGAAAGTTTGGGGGCTAAATCTAAAT
* *
5076298 TTTTGGAAAGTTTGAGGG-TCAAATCTAAGT
1 TTTTGGAAAGTTTGGGGGCT-AAATCTAAAT
* *
5076328 TTTTGGGAAGTTTGAGGG-TCAAATCTAAA-
1 TTTTGGAAAGTTTGGGGGCT-AAATCTAAAT
* * * * *
5076357 TGTTAGAAAGTTTGAGGG-TCAAAACTCAAT
1 TTTTGGAAAGTTTGGGGGCT-AAATCTAAAT
** * *
5076387 TTTTCAAAAGTTTAGGGG-TCAAATCTAGAT
1 TTTTGGAAAGTTTGGGGGCT-AAATCTAAAT
* *
5076417 TTTTAGAAAATTTGGGG
1 TTTTGGAAAGTTTGGGG
5076434 TCAAAACATA
Statistics
Matches: 137, Mismatches: 23, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
29 34 0.25
30 102 0.74
31 1 0.01
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTTGGGGGCTAAATCTAAAT
Found at i:5076398 original size:59 final size:58
Alignment explanation
Indices: 5076275--5076448 Score: 190
Period size: 59 Copynumber: 2.9 Consensus size: 58
5076265 AATTTTTAGG
* * * * ***
5076275 AAGTTTGGGGGTTAAATCTAAATTTTTGGAAAGTTTGAGGGTCAAATCTAAGTTTTTGGG
1 AAGTTTGAGGGTCAAATCTAAA-TTTTAGAAAGTTTGAGGGTCAAAACTAA-TTTTTCAA
*
5076335 AAGTTTGAGGGTCAAATCTAAATGTTAGAAAGTTTGAGGGTCAAAACTCAATTTTTCAA
1 AAGTTTGAGGGTCAAATCTAAATTTTAGAAAGTTTGAGGGTCAAAACT-AATTTTTCAA
* *
5076394 AAGTTT-AGGGGTCAAATCTAGATTTTTAGAAAATTTG-GGGTCAAAACATAATTTT
1 AAGTTTGA-GGGTCAAATCTA-AATTTTAGAAAGTTTGAGGGTCAAAAC-TAATTTT
5076449 GGATAGTTTA
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
58 1 0.01
59 62 0.63
60 36 0.36
ACGTcount: A:0.34, C:0.07, G:0.23, T:0.36
Consensus pattern (58 bp):
AAGTTTGAGGGTCAAATCTAAATTTTAGAAAGTTTGAGGGTCAAAACTAATTTTTCAA
Done.