Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2283
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: 183339
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
File 1 of 2
Found at i:807 original size:20 final size:20
Alignment explanation
Indices: 784--909 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 20
774 AATTACCTAG
784 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
804 ATGTATCGATACATTCTGTCTTTTTACACA
1 ATGTATCGATACA-------TTTTT---CA
*
834 GATGTATCGATACATTTTTTA
1 -ATGTATCGATACATTTTTCA
* * *
855 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
875 ACGTATCGATACATTCTTT-A
1 ATGTATCGATACATT-TTTCA
895 ATGTATCGATACATT
1 ATGTATCGATACATT
910 CTATCTTTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 24
0.73 0.07 0.20
Matches are distributed among these distances:
20 58 0.67
21 3 0.03
24 5 0.06
27 5 0.06
30 2 0.02
31 13 0.15
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:858 original size:51 final size:51
Alignment explanation
Indices: 782--959 Score: 191
Period size: 51 Copynumber: 3.7 Consensus size: 51
772 AAAATTACCT
782 AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACAC
1 AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACAC
* * *
833 AGATGTATCGATACATTTTTTAATGTATCGATACA---TG---TATGA-AC
1 AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACAC
* *
877 ----GTATCGATACATTCTTT-AATGTATCGATACATTCTATCTTTTTACCC
1 AGATGTATCGATACATT-TTTCAATGTATCGATACATTCTGTCTTTTTACAC
* * *
924 AGATGTATCAATATATTTTTCAATATATCGATACAT
1 AGATGTATCGATACATTTTTCAATGTATCGATACAT
960 CTAGTTAAAA
Statistics
Matches: 104, Mismatches: 10, Indels: 26
0.74 0.07 0.19
Matches are distributed among these distances:
40 27 0.26
41 3 0.03
43 1 0.01
44 2 0.02
45 3 0.03
46 3 0.03
47 1 0.01
48 2 0.02
50 3 0.03
51 59 0.57
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (51 bp):
AGATGTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACAC
Found at i:904 original size:91 final size:91
Alignment explanation
Indices: 786--959 Score: 278
Period size: 91 Copynumber: 1.9 Consensus size: 91
776 TTACCTAGAT
* *
786 GTATCGATACATTTTTCAATGTATCGATACATTCTGTCTTTTTACACAGATGTATCGATACATTT
1 GTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACACAGATGTATCAATACATTT
* *
851 TTTAATGTATCGATACATGTATGAAC
66 TTCAATATATCGATACATGTATGAAC
* *
877 GTATCGATACATTCTTT-AATGTATCGATACATTCTATCTTTTTACCCAGATGTATCAATATATT
1 GTATCGATACATT-TTTCAATGTATCGATACATTCTATCTTTTTACACAGATGTATCAATACATT
941 TTTCAATATATCGATACAT
65 TTTCAATATATCGATACAT
960 CTAGTTAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
91 73 0.96
92 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (91 bp):
GTATCGATACATTTTTCAATGTATCGATACATTCTATCTTTTTACACAGATGTATCAATACATTT
TTCAATATATCGATACATGTATGAAC
Found at i:910 original size:20 final size:20
Alignment explanation
Indices: 835--911 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
825 TTTTACACAG
*
835 ATGTATCGATACATTTTTTA
1 ATGTATCGATACATTCTTTA
* *
855 ATGTATCGATACATGT-ATGA
1 ATGTATCGATACAT-TCTTTA
*
875 ACGTATCGATACATTCTTTA
1 ATGTATCGATACATTCTTTA
895 ATGTATCGATACATTCT
1 ATGTATCGATACATTCT
912 ATCTTTTTAC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTCTTTA
Found at i:10173 original size:13 final size:13
Alignment explanation
Indices: 10155--10208 Score: 90
Period size: 13 Copynumber: 4.2 Consensus size: 13
10145 CATTATTCAA
*
10155 TGTATCAATACAT
1 TGTATCGATACAT
10168 TGTATCGATACAT
1 TGTATCGATACAT
*
10181 TGCATCGATACAT
1 TGTATCGATACAT
10194 TGTATCGATACAT
1 TGTATCGATACAT
10207 TG
1 TG
10209 ATCTTTGTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14531 original size:13 final size:13
Alignment explanation
Indices: 14513--14538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
14503 TACACAAAGT
14513 ATGTATCGATACA
1 ATGTATCGATACA
14526 ATGTATCGATACA
1 ATGTATCGATACA
14539 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:14536 original size:32 final size:33
Alignment explanation
Indices: 14495--14558 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
14485 TAGCCAAACT
**
14495 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
14527 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
14559 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:18623 original size:15 final size:15
Alignment explanation
Indices: 18600--18630 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18590 TAAAAATGTC
*
18600 CAAATTGAGGAAGCT
1 CAAAATGAGGAAGCT
18615 CAAAATGAGGAAGCT
1 CAAAATGAGGAAGCT
18630 C
1 C
18631 CACAAGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.42, C:0.16, G:0.26, T:0.16
Consensus pattern (15 bp):
CAAAATGAGGAAGCT
Found at i:21997 original size:52 final size:51
Alignment explanation
Indices: 21912--22035 Score: 212
Period size: 52 Copynumber: 2.4 Consensus size: 51
21902 ATATGAAAAG
* *
21912 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAA
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
*
21963 TTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA
1 -TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
22015 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
22036 AAGATCAGTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
51 21 0.30
52 48 0.70
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAA
Found at i:22048 original size:51 final size:51
Alignment explanation
Indices: 21912--22055 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
21902 ATATGAAAAG
*
21912 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
21964 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAA-
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
22015 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
22056 ATGTATCGAT
Statistics
Matches: 84, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
50 2 0.02
51 34 0.40
52 48 0.57
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:22062 original size:13 final size:13
Alignment explanation
Indices: 22044--22068 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22034 CAAAGATCAG
22044 TGTATCGATACAA
1 TGTATCGATACAA
22057 TGTATCGATACA
1 TGTATCGATACA
22069 TTTGCGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:22149 original size:13 final size:13
Alignment explanation
Indices: 22131--22155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22121 TAAAAAAATA
22131 TGTATCGATACAT
1 TGTATCGATACAT
22144 TGTATCGATACA
1 TGTATCGATACA
22156 ACATTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:24311 original size:13 final size:13
Alignment explanation
Indices: 24293--24330 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
24283 CATTTTTCTT
24293 TGTATCGATACAA
1 TGTATCGATACAA
*
24306 TGTATCGATACAC
1 TGTATCGATACAA
24319 TGTATCGATACA
1 TGTATCGATACA
24331 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:24485 original size:20 final size:20
Alignment explanation
Indices: 24442--24487 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
24432 AAATCTTTTG
24442 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
24463 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
24483 CAAAA
1 CAAAA
24488 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:26894 original size:13 final size:13
Alignment explanation
Indices: 26876--26901 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
26866 TACACAAAGT
26876 ATGTATCGATACA
1 ATGTATCGATACA
26889 ATGTATCGATACA
1 ATGTATCGATACA
26902 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:26899 original size:32 final size:33
Alignment explanation
Indices: 26858--26921 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
26848 TAGCCAAACT
**
26858 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
26890 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
26922 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:37064 original size:12 final size:11
Alignment explanation
Indices: 37047--37100 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 11
37037 ATCCTTCGCA
37047 AAAAAAAAAGAC
1 AAAAAAAAA-AC
37059 AAAAAAAAAAC
1 AAAAAAAAAAC
37070 AAAAAAATAAA-
1 AAAAAAA-AAAC
37081 AAGAAAAAAAAC
1 AA-AAAAAAAAC
37093 AACAAAAA
1 AA-AAAAA
37101 GGGTCCGGAT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
11 14 0.37
12 24 0.63
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:37065 original size:14 final size:13
Alignment explanation
Indices: 37046--37091 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
37036 CATCCTTCGC
*
37046 AAAAAAAAAAGAC
1 AAAAAAAAAAGAA
*
37059 AAAAAAAAAACAA
1 AAAAAAAAAAGAA
37072 AAAAATAAAAAGAA
1 AAAAA-AAAAAGAA
37086 AAAAAA
1 AAAAAA
37092 CAACAAAAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 17 0.59
14 12 0.41
ACGTcount: A:0.89, C:0.04, G:0.04, T:0.02
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:37075 original size:26 final size:26
Alignment explanation
Indices: 37046--37100 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 26
37036 CATCCTTCGC
37046 AAAAA-AAAAAGACAAAAAAAAAACAA
1 AAAAATAAAAAGA-AAAAAAAAAACAA
*
37072 AAAAATAAAAAGAAAAAAAACAACAA
1 AAAAATAAAAAGAAAAAAAAAAACAA
37098 AAA
1 AAA
37101 GGGTCCGGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 20 0.74
27 7 0.26
ACGTcount: A:0.87, C:0.07, G:0.04, T:0.02
Consensus pattern (26 bp):
AAAAATAAAAAGAAAAAAAAAAACAA
Found at i:38164 original size:37 final size:37
Alignment explanation
Indices: 38123--38204 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
38113 TGCCACAATC
* *
38123 ATGCATTTCTGACATTCATAACATTTCATTTTGCATG
1 ATGCATTTATGACATTCACAACATTTCATTTTGCATG
38160 ATGCATTTATGACATTCACAACATTTCATTTTGCATG
1 ATGCATTTATGACATTCACAACATTTCATTTTGCATG
38197 ATGCATTT
1 ATGCATTT
38205 GTGCTTCATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.28, C:0.18, G:0.11, T:0.43
Consensus pattern (37 bp):
ATGCATTTATGACATTCACAACATTTCATTTTGCATG
Found at i:38604 original size:29 final size:28
Alignment explanation
Indices: 38572--38870 Score: 350
Period size: 29 Copynumber: 10.5 Consensus size: 28
38562 CCTCATCTTC
*
38572 CAAAGCCCACAAGTCAGTGTCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCATCTTTT
*
38600 CCAAAGCCCACAAGTCAGTGCCATCTTTT
1 -CAAAGCCCACAAGTCAGTGGCATCTTTT
* * *
38629 CAAAAGCCCATAAGTTAGTGTCATCTTTT
1 C-AAAGCCCACAAGTCAGTGGCATCTTTT
* * *
38658 CAAAAGCCCATAAGTTAGTGGCACCCTTTT
1 C-AAAGCCCACAAGTCAGTGGCA-TCTTTT
* * *
38688 CAAAGCCCACAATTCAGTGGCAAC-CTT
1 CAAAGCCCACAAGTCAGTGGCATCTTTT
* *
38715 CAGAAGCCCACTAGTCGGTGGCACTCTTTT
1 CA-AAGCCCACAAGTCAGTGGCA-TCTTTT
*
38745 CAAAGCCCACAAGTCAGTGGCACCCTTTT
1 CAAAGCCCACAAGTCAGTGGCA-TCTTTT
38774 CAAAGCCCACAAGTCAGTGGCATCTTTT
1 CAAAGCCCACAAGTCAGTGGCATCTTTT
*
38802 CAAAAGCCCACAAGTCAGTGGCACCTTTT
1 C-AAAGCCCACAAGTCAGTGGCATCTTTT
* * *
38831 CAAAGCCCATAAGTCAGTGGCAAC-CTT
1 CAAAGCCCACAAGTCAGTGGCATCTTTT
38858 CAAAGCCCACAAG
1 CAAAGCCCACAAG
38871 GTAGCGGCAA
Statistics
Matches: 239, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
27 18 0.08
28 46 0.19
29 165 0.69
30 10 0.04
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
CAAAGCCCACAAGTCAGTGGCATCTTTT
Found at i:38772 original size:86 final size:87
Alignment explanation
Indices: 38572--38891 Score: 379
Period size: 86 Copynumber: 3.7 Consensus size: 87
38562 CCTCATCTTC
* * * * *
38572 CAAAGCCCACAAGTCAGTGTCA-TCTTTTCCAAAGCCCACAAGTCAGTGCCATCTTTTCAAAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTT-CAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGC
* *
38636 CCA-TAAGTTAGTGTCA-TCTTTT
65 CCACT-AGTCAGTGGCACTCTTTT
* * * *
38658 CAAAAGCCCATAAGTTAGTGGCACCCTTTTCAAAGCCCACAATTCAGTGGCAAC-CTTCAGAAGC
1 C-AAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGC
*
38722 CCACTAGTCGGTGGCACTCTTTT
65 CCACTAGTCAGTGGCACTCTTTT
* *
38745 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCTTTTCAAAAGCC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGCC
*
38810 CACAAGTCAGTGGCAC-CTTTT
66 CACTAGTCAGTGGCACTCTTTT
* * *
38831 CAAAGCCCATAAGTCAGTGGCAACC--TTCAAAGCCCACAAGGT-AGCGGCAAC-CTTCAAAAGC
1 CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAA-GTCAGTGGCAACTCTTCAAAAGC
38892 ACATAAGTTG
Statistics
Matches: 203, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
83 9 0.04
84 21 0.10
85 2 0.01
86 96 0.47
87 70 0.34
88 5 0.02
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (87 bp):
CAAAGCCCACAAGTCAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCAACTCTTCAAAAGCC
CACTAGTCAGTGGCACTCTTTT
Found at i:38907 original size:27 final size:28
Alignment explanation
Indices: 38849--38925 Score: 77
Period size: 27 Copynumber: 2.8 Consensus size: 28
38839 ATAAGTCAGT
*
38849 GGCAACCTTC-AAAGCCCACAAGGTAGC
1 GGCAACCTTCAAAAGCACACAAGGTAGC
* *
38876 GGCAACCTTCAAAAGCACATAA-GTTGC
1 GGCAACCTTCAAAAGCACACAAGGTAGC
* *
38903 TGCAACCCTTTCAAAAGCCCACA
1 GGCAA-CC-TTCAAAAGCACACA
38926 CAAGTTGGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
27 18 0.44
28 11 0.27
29 12 0.29
ACGTcount: A:0.35, C:0.32, G:0.17, T:0.16
Consensus pattern (28 bp):
GGCAACCTTCAAAAGCACACAAGGTAGC
Found at i:39059 original size:49 final size:49
Alignment explanation
Indices: 39004--39334 Score: 209
Period size: 52 Copynumber: 6.5 Consensus size: 49
38994 TTTAATGTTG
*
39004 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATTA
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * * * *
39053 CTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTCAAGTCCAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTTAAGTCCAATATCA
** ** * *
39105 CTGGTTTTGAATCAGCACATTACCACCTTCACCTTTAAGTCCAAAATCA
1 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
* * * * ** * *
39154 CTAGCCTTGAATCAGCATATTGGCATCTGTAACAT-TCCTAAACCCAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCT-T--CATCT-TTAAGTCCAATATCA
* * * * * *
39206 TTGGCCTTGAATCAGGACATTGGCATTCTTC-TCATATTCAAGTCTAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCA-CCTTCATC-T-TT-AAGTCCAATATCA
* * * * *
39258 CTGACCGTGAATCAGCACATTGACATTCTTTACATCTTTAAGCCCAATATCA
1 CTGGCCTTGAATCAGCACATTGGCA--CCTT-CATCTTTAAGTCCAATATCA
* *
39310 TTGGTCC-TGAATCAGCATATTGGCA
1 CTGG-CCTTGAATCAGCACATTGGCA
39335 TCTTTATCAT
Statistics
Matches: 212, Mismatches: 55, Indels: 27
0.72 0.19 0.09
Matches are distributed among these distances:
49 63 0.30
50 3 0.01
51 4 0.02
52 128 0.60
53 10 0.05
54 2 0.01
55 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.16, T:0.32
Consensus pattern (49 bp):
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATCA
Found at i:39201 original size:101 final size:101
Alignment explanation
Indices: 38997--39226 Score: 273
Period size: 101 Copynumber: 2.3 Consensus size: 101
38987 CTTTAAGTTT
* ** * * * *
38997 AATGTTGCTGGCCTTGAATCAGCACATTGGCACCTTCATCTTTAAGTCCAATATTACTGGCCTTG
1 AATGTCGCTGGCCTTGAATCAGCACATTACCACCTTCACCTTTAAGTCCAAAATCACTAGCCTTG
* * ** * **
39062 AATCAGCATATTGGCGCCTTTGTCATCTTCAAGTCC
66 AATCAGCATATTGGCACCTGTAACATCCTCAAACCC
**
39098 AATGTCGCTGGTTTTGAATCAGCACATTACCACCTTCACCTTTAAGTCCAAAATCACTAGCCTTG
1 AATGTCGCTGGCCTTGAATCAGCACATTACCACCTTCACCTTTAAGTCCAAAATCACTAGCCTTG
*
39163 AATCAGCATATTGGCATCTGTAACATTCCT-AAACCC
66 AATCAGCATATTGGCACCTGTAACA-TCCTCAAACCC
* *
39199 AATGTCGTTGGCCTTGAATCAGGACATT
1 AATGTCGCTGGCCTTGAATCAGCACATT
39227 GGCATTCTTC
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
101 104 0.97
102 3 0.03
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.32
Consensus pattern (101 bp):
AATGTCGCTGGCCTTGAATCAGCACATTACCACCTTCACCTTTAAGTCCAAAATCACTAGCCTTG
AATCAGCATATTGGCACCTGTAACATCCTCAAACCC
Found at i:39980 original size:19 final size:21
Alignment explanation
Indices: 39934--39988 Score: 78
Period size: 19 Copynumber: 2.7 Consensus size: 21
39924 TTTCAACAAT
39934 TTGTATCGATACAAATAGTAA
1 TTGTATCGATACAAATAGTAA
* *
39955 ATGTATCGATACATA-AGT-A
1 TTGTATCGATACAAATAGTAA
39974 TTGTATCGATACAAA
1 TTGTATCGATACAAA
39989 GCTACCCTAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 14 0.47
20 3 0.10
21 13 0.43
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.33
Consensus pattern (21 bp):
TTGTATCGATACAAATAGTAA
Found at i:40052 original size:13 final size:13
Alignment explanation
Indices: 40034--40061 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40024 CATTATTCAA
40034 TGTATCGATACAT
1 TGTATCGATACAT
40047 TGTATCGATACAT
1 TGTATCGATACAT
40060 TG
1 TG
40062 ATCTTCGCAT
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:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:45232 original size:34 final size:34
Alignment explanation
Indices: 45191--45258 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
45181 ATGGCAAAGT
*
45191 ATGAATGTGTGTGGACTCTCGAGATCTGAATCGA
1 ATGAATGTGTGTGGACTATCGAGATCTGAATCGA
45225 ATGAATGTGTGTGGACTATCGAGATCTGAATCGA
1 ATGAATGTGTGTGGACTATCGAGATCTGAATCGA
45259 GCTAGTCCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (34 bp):
ATGAATGTGTGTGGACTATCGAGATCTGAATCGA
Found at i:48125 original size:8 final size:8
Alignment explanation
Indices: 48104--48179 Score: 57
Period size: 8 Copynumber: 9.2 Consensus size: 8
48094 CCTTTATACC
48104 CAAAAAAA
1 CAAAAAAA
*
48112 TAAAAAAAA
1 -CAAAAAAA
48121 CAAAAAAAA
1 C-AAAAAAA
*
48130 GAAAAAAA
1 CAAAAAAA
48138 CCAAAAAAAA
1 -C-AAAAAAA
48148 CAAAAAAA
1 CAAAAAAA
* *
48156 C-CAAGAA
1 CAAAAAAA
*
48163 -AAAATAA
1 CAAAAAAA
48170 CAAAAAAA
1 CAAAAAAA
48178 CA
1 CA
48180 GAAAGGGGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 11
0.73 0.12 0.15
Matches are distributed among these distances:
7 8 0.15
8 23 0.43
9 15 0.28
10 7 0.13
ACGTcount: A:0.83, C:0.12, G:0.03, T:0.03
Consensus pattern (8 bp):
CAAAAAAA
Found at i:48128 original size:18 final size:18
Alignment explanation
Indices: 48105--48176 Score: 90
Period size: 18 Copynumber: 3.9 Consensus size: 18
48095 CTTTATACCC
48105 AAAAAAATAAAAAAAACA
1 AAAAAAATAAAAAAAACA
* *
48123 AAAAAAAGAAAAAAACCA
1 AAAAAAATAAAAAAAACA
* *
48141 AAAAAAACAAAAAAACCA
1 AAAAAAATAAAAAAAACA
48159 AGAAAAAATAACAAAAAA
1 A-AAAAAATAA-AAAAAA
48177 ACAGAAAGGG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
18 34 0.72
19 8 0.17
20 5 0.11
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (18 bp):
AAAAAAATAAAAAAAACA
Found at i:48174 original size:10 final size:9
Alignment explanation
Indices: 48105--48176 Score: 81
Period size: 9 Copynumber: 7.8 Consensus size: 9
48095 CTTTATACCC
*
48105 AAAAAAATA
1 AAAAAAACA
48114 AAAAAAACA
1 AAAAAAACA
*
48123 AAAAAAAGA
1 AAAAAAACA
*
48132 AAAAAACCA
1 AAAAAAACA
48141 AAAAAAACA
1 AAAAAAACA
*
48150 AAAAAACCA
1 AAAAAAACA
*
48159 AGAAAAAATA
1 A-AAAAAACA
48169 ACAAAAAA
1 A-AAAAAA
48177 ACAGAAAGGG
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
9 40 0.75
10 13 0.25
ACGTcount: A:0.85, C:0.10, G:0.03, T:0.03
Consensus pattern (9 bp):
AAAAAAACA
Found at i:49444 original size:57 final size:58
Alignment explanation
Indices: 49375--50175 Score: 952
Period size: 57 Copynumber: 13.9 Consensus size: 58
49365 CGTCCATCTC
* * **
49375 TTCAAAGCCCACAAGTCAATGGCA-TCCTTCCAAAGCCCACAAGTCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* ** *
49432 TTCAAAGCCCACAAGTCAGTGTCACTTTTTTCAAAGCCCACAAGTCAGTGG-AATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
49489 TTCAAAGCCCACATGTCAATAGCAC-CCTTTCAAAGCCCACAAGTCAGTGTCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
** * * * *
49546 TTCAAAGCCCATGAGTCGGTGGTAACTCTTTTCAAAGCCCACAAGTCAATGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGG-CACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
49604 TTCAAAGCCCACAAGTCAGTGGCATTCTTTTCAAACCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
49661 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAACCCCACATGAG-CCGATGGAAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACA--AGTCAG-TGG-CACTCCT
**
49722 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
49779 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTCAAAGCTCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
49836 TTTAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCTCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * * *
49893 TTCAAAGCCCACACGAGCCGGTGGCAATTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACA--AGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
*
49953 TTCAAAGCCCACAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
50009 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
50065 TTCAAATCCCACAAGTCAGTGGCATTCTTTTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
50122 TTCAAAACCCACAAGTCAATGGCAC-CCTTT-ATAAGCCCACGCAAGTCAGTGGCA
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCA-AAGCCCA--CAAGTCAGTGGCA
50176 ACCCTTTTCA
Statistics
Matches: 646, Mismatches: 75, Indels: 45
0.84 0.10 0.06
Matches are distributed among these distances:
55 1 0.00
56 166 0.26
57 258 0.40
58 98 0.15
59 39 0.06
60 33 0.05
61 51 0.08
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (58 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACTCCT
Found at i:49447 original size:29 final size:29
Alignment explanation
Indices: 49375--50175 Score: 952
Period size: 28 Copynumber: 27.8 Consensus size: 29
49365 CGTCCATCTC
*
49375 TTCAAAGCCCACAAGTCAATGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* **
49403 TCCAAAGCCCACAAGTCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* **
49432 TTCAAAGCCCACAAGTCAGTGTCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
*
49461 TTCAAAGCCCACAAGTCAGTGG-AATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
49489 TTCAAAGCCCACATGTCAATAGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
49517 TTCAAAGCCCACAAGTCAGTGTCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
** * * *
49546 TTCAAAGCCCATGAGTCGGTGGTAACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CACTCCT
*
49576 TTCAAAGCCCACAAGTCAATGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
49604 TTCAAAGCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
*
49633 TTCAAACCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
*
49661 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
49690 TTCAAACCCCACATGAG-CCGATGGAAACTCTT
1 TTCAAAGCCCACA--AGTCAG-TGG-CACTCCT
49722 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
**
49750 TTCAAAGCCCACAAGTCAGTGGCACTTTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
49779 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
*
49808 TTCAAAGCTCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
49836 TTTAAAGCCCACAAGTTAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
49864 TTCAAAGCTCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* * * *
49893 TTCAAAGCCCACACGAGCCGGTGGCAATTCTT
1 TTCAAAGCCCACA--AGTCAGTGGC-ACTCCT
*
49925 TTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
*
49953 TTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
49981 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
50009 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
50037 TTCAAAGCCCACAAGTCAGTGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* * *
50065 TTCAAATCCCACAAGTCAGTGGCATTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
*
50094 TTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
* *
50122 TTCAAAACCCACAAGTCAATGGCAC-CCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCT
50150 TT-ATAAGCCCACGCAAGTCAGTGGCA
1 TTCA-AAGCCCA--CAAGTCAGTGGCA
50176 ACCCTTTTCA
Statistics
Matches: 672, Mismatches: 78, Indels: 44
0.85 0.10 0.06
Matches are distributed among these distances:
27 1 0.00
28 366 0.54
29 204 0.30
30 50 0.07
31 15 0.02
32 36 0.05
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (29 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCT
Found at i:51049 original size:20 final size:20
Alignment explanation
Indices: 51027--51138 Score: 147
Period size: 20 Copynumber: 5.6 Consensus size: 20
51017 TACCCAGATA
*
51027 TATCGATACATTCTTCAATA
1 TATCGATACATTCTTCAATG
* *
51047 TATCGATACATGT-ATGAATG
1 TATCGATACAT-TCTTCAATG
51067 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
* *
51087 TATCGATACATGT-ATGAATG
1 TATCGATACAT-TCTTCAATG
51107 TATCGATACATTCTTCAATG
1 TATCGATACATTCTTCAATG
51127 TATCGATACATT
1 TATCGATACATT
51139 GTATCTTTTT
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
19 2 0.03
20 75 0.95
21 2 0.03
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.38
Consensus pattern (20 bp):
TATCGATACATTCTTCAATG
Found at i:51082 original size:40 final size:40
Alignment explanation
Indices: 51027--51142 Score: 214
Period size: 40 Copynumber: 2.9 Consensus size: 40
51017 TACCCAGATA
*
51027 TATCGATACATTCTTCAATATATCGATACATGTATGAATG
1 TATCGATACATTCTTCAATGTATCGATACATGTATGAATG
51067 TATCGATACATTCTTCAATGTATCGATACATGTATGAATG
1 TATCGATACATTCTTCAATGTATCGATACATGTATGAATG
51107 TATCGATACATTCTTCAATGTATCGATACATTGTAT
1 TATCGATACATTCTTCAATGTATCGATACA-TGTAT
51143 CTTTTTACCT
Statistics
Matches: 74, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
40 69 0.93
41 5 0.07
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (40 bp):
TATCGATACATTCTTCAATGTATCGATACATGTATGAATG
Found at i:54540 original size:31 final size:31
Alignment explanation
Indices: 54504--54565 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
54494 TACTATTTTG
54504 TTGGTTTTCAACTTTTAAATGAATTTTATTT
1 TTGGTTTTCAACTTTTAAATGAATTTTATTT
*
54535 TTGGTTTTCAACTTTTAAGTGAATTTTATTT
1 TTGGTTTTCAACTTTTAAATGAATTTTATTT
54566 ACTTTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.24, C:0.06, G:0.11, T:0.58
Consensus pattern (31 bp):
TTGGTTTTCAACTTTTAAATGAATTTTATTT
Found at i:56269 original size:13 final size:13
Alignment explanation
Indices: 56251--56307 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
56241 TTCAACAATT
56251 TGTATCGATACAA
1 TGTATCGATACAA
*
56264 TGTATCGATGCATAA
1 TGTATCGAT--ACAA
56279 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
56296 TGTATCGATACA
1 TGTATCGATACA
56308 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 21 0.58
15 3 0.08
17 3 0.08
19 9 0.25
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:56291 original size:32 final size:32
Alignment explanation
Indices: 56250--56332 Score: 148
Period size: 32 Copynumber: 2.6 Consensus size: 32
56240 TTTCAACAAT
*
56250 TTGTATCGATACAATGTATCGATGCATAAGTG
1 TTGTATCGATACAATGTATCGATACATAAGTG
*
56282 TTGTATCGATACAATGTATCGATACATAAGTT
1 TTGTATCGATACAATGTATCGATACATAAGTG
56314 TTGTATCGATACAATGTAT
1 TTGTATCGATACAATGTAT
56333 TGCTACGAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
TTGTATCGATACAATGTATCGATACATAAGTG
Found at i:56320 original size:19 final size:18
Alignment explanation
Indices: 56264--56326 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
56254 ATCGATACAA
*
56264 TGTATCGATGCATAAGTGT
1 TGTATCGATACATAAGT-T
56283 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
56296 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
56315 TGTATCGATACA
1 TGTATCGATACA
56327 ATGTATTGCT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
17 2 0.05
19 22 0.59
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:60911 original size:27 final size:27
Alignment explanation
Indices: 60881--60951 Score: 124
Period size: 27 Copynumber: 2.6 Consensus size: 27
60871 GATTGAAAAC
* *
60881 GGGGTTGGAGTGTCTCCTCGGAGGAAT
1 GGGGTTGGAGTGTCCCCTCAGAGGAAT
60908 GGGGTTGGAGTGTCCCCTCAGAGGAAT
1 GGGGTTGGAGTGTCCCCTCAGAGGAAT
60935 GGGGTTGGAGTGTCCCC
1 GGGGTTGGAGTGTCCCC
60952 GATGAATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.14, C:0.18, G:0.44, T:0.24
Consensus pattern (27 bp):
GGGGTTGGAGTGTCCCCTCAGAGGAAT
Found at i:63240 original size:52 final size:52
Alignment explanation
Indices: 63092--63220 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
63082 CGAAATATGA
*
63092 AAATTTGCCTGCATGTATCGATACATTTCATAGTATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
63144 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
63196 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
63221 AAGATCAATG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:63244 original size:13 final size:13
Alignment explanation
Indices: 63226--63253 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
63216 ATACAAAGAT
63226 CAATGTATCGATA
1 CAATGTATCGATA
63239 CAATGTATCGATA
1 CAATGTATCGATA
63252 CA
1 CA
63254 TTTGAGTAAT
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:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:63899 original size:15 final size:14
Alignment explanation
Indices: 63871--63905 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
63861 GGCAAAAAGG
*
63871 AAAAAATAATTTAA
1 AAAAAATAAATTAA
63885 AAAAAATTAAATTAA
1 AAAAAA-TAAATTAA
63900 AAAAAA
1 AAAAAA
63906 ATCACATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
AAAAAATAAATTAA
Found at i:64040 original size:19 final size:18
Alignment explanation
Indices: 64016--64078 Score: 64
Period size: 19 Copynumber: 3.7 Consensus size: 18
64006 AAACAGAAAA
64016 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
64035 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
*
64048 TGTATCAATACATAAGTTT
1 TGTATCGATACATAAG-TT
64067 TGTATCGATACA
1 TGTATCGATACA
64079 ATGTATCGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 10 0.28
15 2 0.06
17 2 0.06
19 22 0.61
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:64059 original size:32 final size:32
Alignment explanation
Indices: 64014--64085 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
64004 ACAAACAGAA
*
64014 AATGTATCGATACATAAGTGTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
*
64046 AATGTATCAATACATAAGTTTTGTATCGATAC
1 AATGTATCAATACATAAGTGTTGTATCGATAC
64078 AATGTATC
1 AATGTATC
64086 GCTACGAAGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (32 bp):
AATGTATCAATACATAAGTGTTGTATCGATAC
Found at i:64149 original size:13 final size:13
Alignment explanation
Indices: 64131--64156 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
64121 ATTAAGGAAA
64131 TGTATCGATACAT
1 TGTATCGATACAT
64144 TGTATCGATACAT
1 TGTATCGATACAT
64157 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:66585 original size:52 final size:53
Alignment explanation
Indices: 66523--66907 Score: 169
Period size: 52 Copynumber: 7.4 Consensus size: 53
66513 CAATTGTTCA
* *
66523 TAATCGGGGATACTCCAA-TCCCGATTTTATTTTC-AAAACACCAATTTTTCTT
1 TAATCAGGGATACTCCAACT-CCGATTTTATTTCCAAAAACACCAATTTTTCTT
* *
66575 TAATCAGGGATACTCGAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
1 TAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCTT
* ** * * **
66627 CAATC-GAGGATACTCCAA--CC--TTGTTATTTCATCGGGGATACTCCAA---CCCTAT
1 TAATCAG-GGATACTCCAACTCCGATT-TTATTTC--C--AAAAACACCAATTTTTCT-T
* ** * * *** * *
66679 TACCTCCGAGGGGATACTCCAAC-CTCGGCTTTA-TTCCCAAAATATTGATTTCTC-A
1 TA-AT-C-A-GGGATACTCCAACTC-CGATTTTATTTCCAAAAACACCAATTTTTCTT
* * * * **
66734 TAATCGGGGATACTCCAAC-CCTAGTTTTATTT-CTAAAACACTAA-TTTTCCA
1 TAATCAGGGATACTCCAACTCCGA-TTTTATTTCCAAAAACACCAATTTTTCTT
* * * * * * *
66785 CAATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAATTTTCCTG
1 TAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCTT
* *
66837 TAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-A
1 TAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCTT
* *
66889 CAATCAAGGATACTCCAAC
1 TAATCAGGGATACTCCAAC
66908 CTCGTTATTT
Statistics
Matches: 252, Mismatches: 52, Indels: 58
0.70 0.14 0.16
Matches are distributed among these distances:
48 2 0.01
49 7 0.03
50 8 0.03
51 64 0.25
52 99 0.39
53 41 0.16
54 5 0.02
55 2 0.01
56 12 0.05
57 4 0.02
58 4 0.02
59 3 0.01
60 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (53 bp):
TAATCAGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCTT
Found at i:66752 original size:51 final size:50
Alignment explanation
Indices: 66688--66908 Score: 201
Period size: 51 Copynumber: 4.3 Consensus size: 50
66678 TTACCTCCGA
* * * * *
66688 GGGGATACTCCAACCTCGGCTTTATTCCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACC-CGGTTTTATTCCCAAAACACTAATTTTC-CACAATC
* * *
66739 GGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCC-GGTTTTATTCCCAAAACACTAATTTTCCACAATC
** * **
66790 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTGTAATC
1 GGGGATACTCCAA-CCCGGTTTTATTCCCAAAACACTAATTTTCC-ACAATC
* * * *
66842 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATC
1 GGGGATACTCCAAC-CCGGTTTTA-TTCCCAAAACACTAATTTTCCACAATC
**
66894 AAGGATACTCCAACC
1 GGGGATACTCCAACC
66909 TCGTTATTTC
Statistics
Matches: 141, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
50 1 0.01
51 75 0.53
52 48 0.34
53 17 0.12
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (50 bp):
GGGGATACTCCAACCCGGTTTTATTCCCAAAACACTAATTTTCCACAATC
Found at i:66953 original size:28 final size:28
Alignment explanation
Indices: 66895--66967 Score: 92
Period size: 28 Copynumber: 2.6 Consensus size: 28
66885 TTCACAATCA
* ** **
66895 AGGATACTCCAACCTCGTTATTTCATCG
1 AGGATACTCCAACCCCGTTACCTCAGAG
*
66923 AGGATACTCCAACCCCGTTACCTCCGAG
1 AGGATACTCCAACCCCGTTACCTCAGAG
66951 AGGATACTCCAACCCCG
1 AGGATACTCCAACCCCG
66968 GCTTTATTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.22
Consensus pattern (28 bp):
AGGATACTCCAACCCCGTTACCTCAGAG
Found at i:66989 original size:262 final size:262
Alignment explanation
Indices: 66524--67015 Score: 858
Period size: 262 Copynumber: 1.9 Consensus size: 262
66514 AATTGTTCAT
* * *
66524 AATCGGGGATACTCCAATCCCGATTTTATTTTCAAAACACCAATTTTTCTTTAATCAGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTGTAATCAGGGATACT
* * *
66589 CGAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCGAGGATACTCCAACCTTGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCGTTAT
* * * *
66654 TTCATCGGGGATACTCCAACCCTATTACCTCCGAGGGGATACTCCAACCTCGGCTTTATTCCCAA
131 TTCATCGAGGATACTCCAACCCCATTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAA
66719 AATATTGATTTCTCATAATCGGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTTTCC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTTTCC
66784 AC
261 AC
* *
66786 AATCGGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTGTAATCGGGGATACT
1 AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTGTAATCAGGGATACT
66851 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCGTTAT
66 CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCGTTAT
*
66916 TTCATCGAGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAA
131 TTCATCGAGGATACTCCAACCCCATTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAA
*
66981 AATATTGATTTCTCATAATTGGGGATACTCCAACC
196 AATATTGATTTCTCATAATCGGGGATACTCCAACC
67016 TCGTTATTTC
Statistics
Matches: 216, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
262 216 1.00
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (262 bp):
AATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTGTAATCAGGGATACT
CCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCGTTAT
TTCATCGAGGATACTCCAACCCCATTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAA
AATATTGATTTCTCATAATCGGGGATACTCCAACCCTAGTTTTATTTCTAAAACACTAATTTTCC
AC
Found at i:67101 original size:79 final size:79
Alignment explanation
Indices: 66922--67122 Score: 242
Period size: 79 Copynumber: 2.5 Consensus size: 79
66912 TTATTTCATC
** * * *
66922 GAGGATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAAAATATT
1 GAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATC
* *
66987 GATTTCTCATAATT
66 GATTTCTCACAACT
* * * * * *
67001 GGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTTCC-TAATCAT
1 GAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-AT
*
67065 CGATTTTTCACAACT
65 CGATTTCTCACAACT
* *
67080 GAGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACC
1 GAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACC
67123 TCGTTATTAT
Statistics
Matches: 102, Mismatches: 19, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
78 3 0.03
79 99 0.97
ACGTcount: A:0.26, C:0.29, G:0.15, T:0.29
Consensus pattern (79 bp):
GAGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATC
GATTTCTCACAACT
Found at i:71182 original size:52 final size:52
Alignment explanation
Indices: 71097--71221 Score: 214
Period size: 52 Copynumber: 2.4 Consensus size: 52
71087 ATATAAAAAG
*
71097 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
* * *
71149 TTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
71201 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
71222 AAGATCAGTG
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAAT
Found at i:71234 original size:52 final size:51
Alignment explanation
Indices: 71097--71241 Score: 202
Period size: 52 Copynumber: 2.8 Consensus size: 51
71087 ATATAAAAAG
71097 TTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTAGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAAT
* * * *
71149 TTGCTTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTAGGCAAAT
*
71201 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
71242 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 2 0.02
52 81 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTAGGCAAAT
Found at i:71248 original size:13 final size:13
Alignment explanation
Indices: 71230--71254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71220 CAAAGATCAG
71230 TGTATCGATACAA
1 TGTATCGATACAA
71243 TGTATCGATACA
1 TGTATCGATACA
71255 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:71327 original size:25 final size:26
Alignment explanation
Indices: 71299--71351 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
71289 GCTTAAATTG
71299 TATCGATACAAAAC-TTATGTATCGA
1 TATCGATACAAAACTTTATGTATCGA
*
71324 TATCGATACAACACTTTATGTATCGA
1 TATCGATACAAAACTTTATGTATCGA
71350 TA
1 TA
71352 CAAATCATTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (26 bp):
TATCGATACAAAACTTTATGTATCGA
Found at i:77040 original size:55 final size:55
Alignment explanation
Indices: 76955--77324 Score: 384
Period size: 55 Copynumber: 6.4 Consensus size: 55
76945 TTCACCCTTT
* *
76955 AGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
* * * * *
77010 AGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACA-AGAGTCGGTGGCATTTTCT
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACA-AGTTGGTGGCACTTCCC
* * * *
77065 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAAAAAAAGCCCCCACAAGTTGGTGGCATTTT
1 AGTCCTCAAAGAGCAGGACGCC-TTTC-----------AAAGCCCACACAAGTTGGTGGCACTTC
77130 CC
54 CC
* * *
77132 AGTCCTCAAAGAGCAGGACGCCTCTT-AAAGCCCACACATGTTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACAAGTTGGTGGCACTTCCC
*
77187 AGTCCTCAAAGAGCAGGACGCCTTTAAAAGCCCACACAAGTTGGTGGCACTTCCC
1 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
* *
77242 AGTCCTCAAAGAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCT
1 AGTCCTCAAAGAGCAGGACGCCTT-T-C----AAAGCCCACACAAGTTGGTGGCACTTCCC
*
77303 AGTCCTTAAAGAGCAGGACGCC
1 AGTCCTCAAAGAGCAGGACGCC
77325 CTCTCCTTCC
Statistics
Matches: 270, Mismatches: 23, Indels: 38
0.82 0.07 0.11
Matches are distributed among these distances:
54 3 0.01
55 165 0.61
56 5 0.02
61 48 0.18
66 1 0.00
67 47 0.17
68 1 0.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.22
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACTTCCC
Found at i:77198 original size:122 final size:110
Alignment explanation
Indices: 76955--77326 Score: 417
Period size: 122 Copynumber: 3.2 Consensus size: 110
76945 TTCACCCTTT
*
76955 AGTCCTCAAAGAGCAGGACCCCTTTTAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACCCCTTTAAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAA
* * *
77020 GAGCAGGATGCCT-TTCAAAGCCCACA-AGAGTCGGTGGCATTTTCT
66 GAGCAGGACGCCTCTT-AAAGCCCACACA-AGTTGGTGGCATTTTCC
* * *
77065 AGTCCTCAAAGAGCAGGACACCTTTTCTTTTTAAAAAAAAAGCCCCCACAAGTTGGTGGCATTTT
1 AGTCCTCAAAGAGCAGGAC-CC----C--TTT-----AAAAGCCCACACAAGTTGGTGGCACTTC
*
77130 CCAGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACATGTTGGTGGCATTTTCC
54 CCAGTCCTCAAAGAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
77187 AGTCCTCAAAGAGCAGGACGCCTTTAAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAA
1 AGTCCTCAAAGAGCAGGACCCCTTTAAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAA
* *
77252 GAGCAAGACGCCTTCTCCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCC
66 GAGCAGGACG-C--CT-C--TTAAAGCCCACACAAGTTGGTGGCATTTTCC
*
77302 TAGTCCTTAAAGAGCAGGACGCCCT
1 -AGTCCTCAAAGAGCAGGAC-CCCT
77327 CTCCTTCCAC
Statistics
Matches: 223, Mismatches: 17, Indels: 37
0.81 0.06 0.13
Matches are distributed among these distances:
110 65 0.29
111 3 0.01
113 2 0.01
114 1 0.00
115 8 0.04
116 42 0.19
117 7 0.03
121 1 0.00
122 91 0.41
123 3 0.01
ACGTcount: A:0.28, C:0.29, G:0.20, T:0.23
Consensus pattern (110 bp):
AGTCCTCAAAGAGCAGGACCCCTTTAAAAGCCCACACAAGTTGGTGGCACTTCCCAGTCCTCAAA
GAGCAGGACGCCTCTTAAAGCCCACACAAGTTGGTGGCATTTTCC
Found at i:77420 original size:55 final size:55
Alignment explanation
Indices: 77337--78496 Score: 1330
Period size: 55 Copynumber: 20.4 Consensus size: 55
77327 CTCCTTCCAC
*
77337 CCTTT-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
77391 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTAGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
77446 CCTTTTAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
77501 CCTTTCAGTCCTCAAAAAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
77556 -CTTCCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTT-TCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
77611 -TTTTCCAGTCCTCAAAAAGCAGGACGCATTTCAAAGCCCACACCAGTTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
77666 -TTTTCCAGTCCTCAAAGAGCAGGATGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * * *
77721 -TTTTCCAGTCCTCAAAAAGCAGGATGTTTTCTCTTTGCAAAGCCCACATAAGTTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGACG----C-CTTT-CAAAGCCCACACAAGTTGGTGGCA
* *
77782 CCTTCCATGTCCTCAAAGAGCAGGACGCATTTCCTTTGTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCA-GTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCCACACAAGTTGGTGGCA
* * * *
77844 CCTTCCAGTCCTCAAAAAGTAGGACGTCTTTCCTTTGCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCCACACAAGTTGGTGGCA
* * * *
77905 -TTTTCCAGTCCTTAAAAAGCAGGGCGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
** *
77960 TTTTTCAGTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCCACACAAGTTGGTGGCA
* * ** *
78021 CCTTCCAGTCCTTAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTACTGGAA
1 CCTTTCAGTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCCACACAAGTTGGTGGCA
* * * *
78082 CCTTTCAGTCCTCAAAGAGCAAGATGACTTTCAAAGCCCATACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
78137 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGTCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
78192 -TTTTCCAGTCCTCAAAGAGCAAGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
*
78247 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACCAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* *
78302 -TTTTCTAGTCCTTAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
78357 -TTTTCCAGTCCTCAAAGAGCAGGATGCTTTCCCTGTGCAAAGCCCACACAAGTTGGTGGCA
1 CCTTT-CAGTCCTCAAAGAGCAGGA--C---GCCT-TTCAAAGCCCACACAAGTTGGTGGCA
* * * * *
78418 CTTTTCAGTCTTCAAAGAGTAGGACGTCTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
* * *
78473 CTTTTTAGTCCTCAAAGAGTAGGA
1 CCTTTCAGTCCTCAAAGAGCAGGA
78497 TGCACTTTAT
Statistics
Matches: 985, Mismatches: 85, Indels: 71
0.86 0.07 0.06
Matches are distributed among these distances:
54 15 0.02
55 645 0.65
56 19 0.02
57 2 0.00
59 4 0.00
60 13 0.01
61 225 0.23
62 58 0.06
63 4 0.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (55 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCA
Found at i:79418 original size:21 final size:21
Alignment explanation
Indices: 79392--79433 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
79382 AGCTACTGCC
*
79392 AAGGAAATGTATCGATACATT
1 AAGGAAATATATCGATACATT
79413 AAGGAAATATATCGATACATT
1 AAGGAAATATATCGATACATT
79434 GTATCAATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.17, T:0.29
Consensus pattern (21 bp):
AAGGAAATATATCGATACATT
Found at i:79457 original size:20 final size:21
Alignment explanation
Indices: 79418--79466 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
79408 ACATTAAGGA
*
79418 AATATATCGATACATTGTATC
1 AATACATCGATACATTGTATC
*
79439 AATACATCGAT-CTTTGTATC
1 AATACATCGATACATTGTATC
*
79459 GATACATC
1 AATACATC
79467 TAGGAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.37
Consensus pattern (21 bp):
AATACATCGATACATTGTATC
Found at i:81864 original size:52 final size:52
Alignment explanation
Indices: 81806--82192 Score: 266
Period size: 52 Copynumber: 7.4 Consensus size: 52
81796 TCAATTGTTC
*
81806 ATAATCGGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* * * *
81858 TTAATCGGGGATACTCGAACTCCGATTTTATTTCCAAAAGCACCAATTTTTC-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAA-CACCAATTTTCCT
* * * * * ***** * * * *
81910 ACAATCGAGGATACTCAAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACCT
1 ATAATCGGGGATACTCCAACCCCG--ATTTTATTTCCAAAACACCAA----TTTTCCT
* * ** * ***
81968 CTAA--GGGGATACTCCAACCCGGGCTTTATTTCCAAAATATTGA-TTT-CT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
** * *
82016 CATAATCGGGGATACTTAAACCCCGATTTTATTTCTAAAACACTAATTTTCC-
1 -ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* * * * *
82068 ACAATTGGGGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCT
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
* * *
82120 GTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTC-
1 ATAATCGGGGATACTCCAACCCCGATTTTATTTCC-AAAACACCAATTTTCCT
* **
82172 ACAATCAAGGATACTCCAACC
1 ATAATCGGGGATACTCCAACC
82193 TCGTTATTTC
Statistics
Matches: 247, Mismatches: 73, Indels: 30
0.71 0.21 0.09
Matches are distributed among these distances:
48 2 0.01
49 5 0.02
51 74 0.30
52 100 0.40
53 32 0.13
54 15 0.06
56 14 0.06
57 3 0.01
58 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (52 bp):
ATAATCGGGGATACTCCAACCCCGATTTTATTTCCAAAACACCAATTTTCCT
Found at i:82038 original size:51 final size:51
Alignment explanation
Indices: 81972--82192 Score: 201
Period size: 51 Copynumber: 4.3 Consensus size: 51
81962 TTACCTCTAA
* * * * * * *
81972 GGGGATACTCCAACCCGGGCTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTTCAACCCCGGTTTTATTTCCAAAACACTAATTTTC-CACAATC
* * * *
82023 GGGGATACTTAAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATT
1 GGGGATACTTCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCACAATC
* * **
82074 GGGGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTGTAATC
1 GGGGATACTTCAACCCCGGTTTTATTTCCAAAACACTAATTTTCC-ACAATC
* * * * *
82126 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATC
1 GGGGATACTTCAACCCCGGTTTTATTTCC-AAAACACTAATTTTCCACAATC
** *
82178 AAGGATACTCCAACC
1 GGGGATACTTCAACC
82193 TCGTTATTTC
Statistics
Matches: 138, Mismatches: 29, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
51 75 0.54
52 48 0.35
53 15 0.11
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (51 bp):
GGGGATACTTCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCACAATC
Found at i:82277 original size:262 final size:262
Alignment explanation
Indices: 81812--82302 Score: 829
Period size: 262 Copynumber: 1.9 Consensus size: 262
81802 GTTCATAATC
* *
81812 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTTTAATCGGGGATACTCGAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTGTAATCGGGGATACTCCAA
* *
81877 CTCCGATTTTATTTCCAAAAGCACCAATTTTTCACAATCGAGGATACTCAAACCTCGTTATTTCA
66 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCAAACCTCGTTATTTCA
* * * * *
81942 TCGGGGATACTCCAACCCCGTTACCTCTAAGGGGATACTCCAACCCGGGCTTTATTTCCAAAATA
131 TCGGGAATACTCCAACCCCGTTACCTCCAAGAGGATACTCCAACCCCGGCTTTATTCCCAAAATA
* *
82007 TTGATTTCTCATAATCGGGGATACTTAAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAA
196 TTGATTTCTCATAATCAGGGATACTCAAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAA
82072 TT
261 TT
* *
82074 GGGGATACTTCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTGTAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTGTAATCGGGGATACTCCAA
*
82139 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCCAACCTCGTTATTTCA
66 CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCAAACCTCGTTATTTCA
*
82204 TCGGGAATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAAAATA
131 TCGGGAATACTCCAACCCCGTTACCTCCAAGAGGATACTCCAACCCCGGCTTTATTCCCAAAATA
* *
82269 TTGATTTCTCATAATTAGGGATACTCCAACCCCG
196 TTGATTTCTCATAATCAGGGATACTCAAACCCCG
82303 TTATTTTCGA
Statistics
Matches: 212, Mismatches: 17, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
262 212 1.00
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.31
Consensus pattern (262 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCCTGTAATCGGGGATACTCCAA
CTCCGATTTTATTTCCAAAAACACCAATTTTTCACAATCAAGGATACTCAAACCTCGTTATTTCA
TCGGGAATACTCCAACCCCGTTACCTCCAAGAGGATACTCCAACCCCGGCTTTATTCCCAAAATA
TTGATTTCTCATAATCAGGGATACTCAAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAA
TT
Found at i:82354 original size:79 final size:79
Alignment explanation
Indices: 82210--82408 Score: 220
Period size: 79 Copynumber: 2.5 Consensus size: 79
82200 TTCATCGGGA
** * * ** *
82210 ATACTCCAACCCCGTTACCTCCGAGAGGATACTCCAACCCCGGCTTTATTCCCAAAATATTGATT
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTCCCAAAATATCGATT
**
82275 TCTCATAATTAGGG
66 TCTCATAACCAGGG
* * * *
82289 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCCCAATTTTATTTCC-TAATCATCGAT
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTCCCAAAAT-ATCGAT
* *
82353 TTTTCATAACCGGGG
65 TTCTCATAACCAGGG
* **
82368 ATACTCCAACCCCATTATTTTTAAGGGGATACTCCAACCCC
1 ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCC
82409 CTTATTATCT
Statistics
Matches: 100, Mismatches: 19, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
78 3 0.03
79 97 0.97
ACGTcount: A:0.27, C:0.30, G:0.13, T:0.30
Consensus pattern (79 bp):
ATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCAACTTTATTCCCAAAATATCGATT
TCTCATAACCAGGG
Found at i:84717 original size:20 final size:20
Alignment explanation
Indices: 84692--84746 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
84682 AAAACCCTTA
84692 AAAGTATCGATACATAATT-C
1 AAAGTATCGATACAT-ATTGC
*
84712 AAAGTATCGATACATGTTGC
1 AAAGTATCGATACATATTGC
*
84732 AATGTATCGATACAT
1 AAAGTATCGATACAT
84747 CAAAAATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
AAAGTATCGATACATATTGC
Found at i:84845 original size:21 final size:21
Alignment explanation
Indices: 84798--84851 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
84788 GTAGCCAAAC
* **
84798 TTGTATCGATACACCAAAGTA
1 TTGTATCGATACACAAAAAAA
84819 -TGTATCGATACACAAAAAAA
1 TTGTATCGATACACAAAAAAA
84839 TTGTATCGATACA
1 TTGTATCGATACA
84852 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.17, G:0.13, T:0.28
Consensus pattern (21 bp):
TTGTATCGATACACAAAAAAA
Found at i:88107 original size:34 final size:30
Alignment explanation
Indices: 88066--88157 Score: 134
Period size: 28 Copynumber: 3.0 Consensus size: 30
88056 TCATCCGCAG
88066 AGATAATTCCAAAATTTGTCAATAAATTAGAT
1 AGATAATTCCAAAATTTGTCAATAAATT--AT
88098 AATGATAATTCCAAAATTTGTCAATAAA-T-T
1 -A-GATAATTCCAAAATTTGTCAATAAATTAT
88128 AGATAATTCCAAAATTTGTCAATAAATTAT
1 AGATAATTCCAAAATTTGTCAATAAATTAT
88158 TTAAATATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 9
0.86 0.00 0.14
Matches are distributed among these distances:
28 25 0.45
29 2 0.04
30 2 0.04
33 2 0.04
34 25 0.45
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.36
Consensus pattern (30 bp):
AGATAATTCCAAAATTTGTCAATAAATTAT
Found at i:88789 original size:2 final size:2
Alignment explanation
Indices: 88742--88774 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
88732 TGTAGCAGCA
88742 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
88775 GTCAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:88804 original size:23 final size:23
Alignment explanation
Indices: 88761--88804 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
88751 TATATATATA
*
88761 TATATATATAATATGTCAAATTT
1 TATATATATAATATCTCAAATTT
* *
88784 TATATATTTAATATCTTAAAT
1 TATATATATAATATCTCAAAT
88805 ATAATTATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (23 bp):
TATATATATAATATCTCAAATTT
Found at i:89477 original size:20 final size:21
Alignment explanation
Indices: 89439--89478 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
89429 ATATTTATTT
*
89439 TTAACAAATATTAATTTAATA
1 TTAACAAATACTAATTTAATA
89460 TTAACAAATACT-ATTTAAT
1 TTAACAAATACTAATTTAAT
89479 CTGTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAACAAATACTAATTTAATA
Found at i:90034 original size:5 final size:5
Alignment explanation
Indices: 90024--90051 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
90014 CATAACTGGT
90024 TCTCC TCTCC TCTCC TCTCC TCTCC TCT
1 TCTCC TCTCC TCTCC TCTCC TCTCC TCT
90052 TGTAAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (5 bp):
TCTCC
Found at i:94703 original size:28 final size:28
Alignment explanation
Indices: 94623--94697 Score: 132
Period size: 28 Copynumber: 2.7 Consensus size: 28
94613 GAAAATTAAT
94623 ACTGCTTCCATTTGAATAGCATCATAAA
1 ACTGCTTCCATTTGAATAGCATCATAAA
* *
94651 TCTGTTTCCATTTGAATAGCATCATAAA
1 ACTGCTTCCATTTGAATAGCATCATAAA
94679 ACTGCTTCCATTTGAATAG
1 ACTGCTTCCATTTGAATAG
94698 TGTCATCTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (28 bp):
ACTGCTTCCATTTGAATAGCATCATAAA
Found at i:97052 original size:21 final size:21
Alignment explanation
Indices: 97028--97068 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
97018 TTTTAAAAAA
97028 ATATTTTAT-ATTAATATTTAT
1 ATATTTTATAATTAA-ATTTAT
97049 ATATTTTATAATTAAATTTA
1 ATATTTTATAATTAAATTTA
97069 AATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATATTTTATAATTAAATTTAT
Found at i:99224 original size:13 final size:13
Alignment explanation
Indices: 99206--99232 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
99196 ACAATTCTTC
99206 ATGTATCGATACA
1 ATGTATCGATACA
99219 ATGTATCGATACA
1 ATGTATCGATACA
99232 A
1 A
99233 ATAGTGATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:99323 original size:33 final size:32
Alignment explanation
Indices: 99265--99326 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 32
99255 CAGTTTCATG
*
99265 TATCGATACAATGAACATGTATCGATACAATA
1 TATCGATACAAAGAACATGTATCGATACAATA
99297 TATCGATACAAAGCATA-ATGTATCGATACA
1 TATCGATACAAAG-A-ACATGTATCGATACA
99327 TCTGGATATG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
32 12 0.44
33 14 0.52
34 1 0.04
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (32 bp):
TATCGATACAAAGAACATGTATCGATACAATA
Found at i:101794 original size:13 final size:13
Alignment explanation
Indices: 101773--101812 Score: 62
Period size: 13 Copynumber: 3.1 Consensus size: 13
101763 ATAATAACCC
101773 ATATATCGATACA
1 ATATATCGATACA
* *
101786 TTGTATCGATACA
1 ATATATCGATACA
101799 ATATATCGATACA
1 ATATATCGATACA
101812 A
1 A
101813 AGAACATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (13 bp):
ATATATCGATACA
Found at i:109740 original size:32 final size:32
Alignment explanation
Indices: 109695--109792 Score: 151
Period size: 32 Copynumber: 3.0 Consensus size: 32
109685 AGTAGCTTAT
* * *
109695 ATTATATTGATACAAAACTTATGTATTGATAC
1 ATTATATCGATACAACACTTATGTATCGATAC
*
109727 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTATATCGATACAACACTTATGTATCGATAC
109759 ATTATATCGATACAACACTTTATGTATCGATAC
1 ATTATATCGATACAACAC-TTATGTATCGATAC
109792 A
1 A
109793 AATCGTTGAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
32 45 0.75
33 15 0.25
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (32 bp):
ATTATATCGATACAACACTTATGTATCGATAC
Found at i:111073 original size:199 final size:185
Alignment explanation
Indices: 110697--111267 Score: 725
Period size: 199 Copynumber: 3.0 Consensus size: 185
110687 TGACAAAGAC
* * * * * * *
110697 GCCAATATGCTGATTCAAAGCCAGCGATATTGGACCTAAAGATGACAAAGGTGCCAATATGCTGA
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA--A-GAAGGTGCCAATATGCTGA
* * * * *
110762 TTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGGC
63 TTCAAGGCAAGCGATATTGGATTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
* * *
110827 TTAAAAGATG-AGGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGT
128 TT-AAAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGT
*
110885 GCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTC
* *
110950 AAGGCCAGCGATATTGGACTTAAAGGTAAAAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCT
66 AAGGCAAGCGATATTGGA-TT-----T-----AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCT
* *
111015 ACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGACTTAA
119 ACATTGGACTTAAAGAT-G-AAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAA
111080 AGGT
182 AGGT
*
111084 GCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCGAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTC
* *
111149 AAGGCAAGCTATATTGGATTTAAAGGTGCCAATGTGCTGATTGAAGGCCAGCTACATTGGACTTA
66 AAGGCAAGCGATATTGGATTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
*
111214 AAGAT-AAAGGTGCCAATATGCTGATTCAAGG-CAAGCGATATTGGGCTTAGAAGG
131 AAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAA-CGATATTGGACTTA-AAGG
111268 GTTGCTACCG
Statistics
Matches: 341, Mismatches: 25, Indels: 37
0.85 0.06 0.09
Matches are distributed among these distances:
183 3 0.01
184 38 0.11
185 43 0.13
186 2 0.01
187 41 0.12
188 42 0.12
191 1 0.00
193 1 0.00
196 11 0.03
197 34 0.10
198 2 0.01
199 123 0.36
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.25
Consensus pattern (185 bp):
GCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAAGAAGGTGCCAATATGCTGATTC
AAGGCAAGCGATATTGGATTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
AAGATGAAAGGTGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGGT
Found at i:111196 original size:92 final size:92
Alignment explanation
Indices: 110982--111267 Score: 423
Period size: 92 Copynumber: 3.1 Consensus size: 92
110972 AAGGTAAAAA
*
110982 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA--G-AAAGGTGCCAAT
111047 ATGCTGATTCAAGGCCAA-CTATATTGGACTT
62 ATGCTGATTCAAGG-CAAGCTATATTGGACTT
*
111078 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGA-AGAAGGTGCGAATATG
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAGA-AAGGTGCCAATATG
*
111142 CTGATTCAAGGCAAGCTATATTGGATTT
65 CTGATTCAAGGCAAGCTATATTGGACTT
* * *
111170 AAAGGTGCCAATGTGCTGATTGAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAGAAAGGTGCCAATATGC
* *
111235 TGATTCAAGGCAAGCGATATTGGGCTT
66 TGATTCAAGGCAAGCTATATTGGACTT
111262 AGAAGG
1 A-AAGG
111268 GTTGCTACCG
Statistics
Matches: 177, Mismatches: 9, Indels: 11
0.90 0.05 0.06
Matches are distributed among these distances:
91 4 0.02
92 121 0.68
93 5 0.03
95 42 0.24
96 5 0.03
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.25
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAGAAAGGTGCCAATATGC
TGATTCAAGGCAAGCTATATTGGACTT
Found at i:111257 original size:49 final size:49
Alignment explanation
Indices: 110631--111262 Score: 569
Period size: 43 Copynumber: 13.1 Consensus size: 49
110621 CTTAGGAATG
* * * *
110631 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGAC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
** *
110680 TTAAAGATGACAAAGACGCCAATATGCTGATTCAAAGCCAGCGATATTGGAC
1 TTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
*
110732 CTAAAGATGACAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
110784 -T-----TAAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
110827 TTAAAAGATGAGGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGAC
1 TT-AAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
110877 -T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
110920 TTAAAGA-AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * * * *
110969 TTAAAGGTAAAAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAA-G----ATAAAGG-TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
111024 TTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAACTATATTGGAC
1 TTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
111076 -T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGAAC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * *
111119 TTAAAGA-AGAAGGTGCGAATATGCTGATTCAAGGCAAGCTATATTGGA-
1 TTAAAGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* * * *
111167 TT-----TAAAGGTGCCAATGTGCTGATTGAAGGCCAGCTACATTGGAC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
* *
111211 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCAAGCGATATTGGGC
1 TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
111260 TTA
1 TTA
111263 GAAGGGTTGC
Statistics
Matches: 480, Mismatches: 62, Indels: 82
0.77 0.10 0.13
Matches are distributed among these distances:
43 144 0.30
44 6 0.01
46 2 0.00
48 4 0.01
49 124 0.26
50 37 0.08
51 2 0.00
52 113 0.24
53 5 0.01
54 6 0.01
55 37 0.08
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (49 bp):
TTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
Found at i:111315 original size:33 final size:33
Alignment explanation
Indices: 111262--111488 Score: 329
Period size: 33 Copynumber: 7.0 Consensus size: 33
111252 TATTGGGCTT
*
111262 AGAAGGGTTGCTACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
111295 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
111328 AGAATGGTTGCCACCGACTTGTGCGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
111361 AG--GGGATTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
*
111393 AAGAA-GGTTGCCACCGACTTATGTGGGCTTT-G
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
111425 CGAAGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
111457 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
111489 AAAATGGTGA
Statistics
Matches: 176, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.03
32 81 0.46
33 88 0.50
34 2 0.01
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:111402 original size:65 final size:64
Alignment explanation
Indices: 111262--111488 Score: 314
Period size: 65 Copynumber: 3.5 Consensus size: 64
111252 TATTGGGCTT
* * *
111262 AGAAGGGTTGCTACCGACTTGTGTGGGCTTTAGAGAATGGTTGCCACCAACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG--GGGTTGCCACCGACTTGTGTGGGCTTTA
111327 G
64 G
* *
111328 AGAATGGTTGCCACCGACTTGTGCGGGCTTTAGAGGGGATTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGG-TTGCCACCGACTTGTGTGGGCTTTAG
* * *
111393 AAGAA-GGTTGCCACCGACTTATGTGGGCTTTGCGAAGGGTTGCCACCGACTTGTGTGGGCTTT-
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTT-AGAGGGGTTGCCACCGACTTGTGTGGGCTTTA
111456 G
64 G
*
111457 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTA
111489 AAAATGGTGA
Statistics
Matches: 145, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
63 4 0.03
64 27 0.19
65 73 0.50
66 41 0.28
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (64 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:111608 original size:100 final size:100
Alignment explanation
Indices: 111503--111833 Score: 391
Period size: 100 Copynumber: 3.3 Consensus size: 100
111493 TGGTGAAAGA
*
111503 TGCCACGAAGTTGTGGAC-TTAAAAGGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAATGGAAA
1 TGCCACGAAGTTGTGGACTTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAA-GGAAA
*
111567 AAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGG
65 AAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
* * * *
111603 TGCCACGGAGTCGTGGAC-TTAAAAGGAACAAGGTGCCACGGGGTTGTGGACTTTAAAAGGGGAA
1 TGCCACGAAGTTGTGGACTTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAA-GGAAA
* * *
111667 AAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
65 AAGAGTGCCACGGAGTTGTGGGCTTTGAA--AAGAAG-G
* * * * * *
111706 TGTCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAA
1 TGCCACGAAGTTGTGGACTTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAA
* * *
111770 AGAGTGCCACGGAGTCGTGGGCTTTGGAAAG-AGA
66 AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
* * *
111804 TGGCACTAAATTGTGGACTTTAAGAAGGAA
1 TGCCACGAAGTTGTGGACTTTAA-AAGGAA
111834 AAATGCCACT
Statistics
Matches: 196, Mismatches: 30, Indels: 11
0.83 0.13 0.05
Matches are distributed among these distances:
98 18 0.09
99 7 0.04
100 86 0.44
102 34 0.17
103 21 0.11
104 30 0.15
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (100 bp):
TGCCACGAAGTTGTGGACTTTAAAAGGAACAAGGTGCCACGGAGTTGTGGACTTTAAAAGGAAAA
AGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
Found at i:111713 original size:34 final size:34
Alignment explanation
Indices: 111498--111789 Score: 328
Period size: 34 Copynumber: 8.6 Consensus size: 34
111488 AAAAATGGTG
*
111498 AAAGA-TGCCACGAAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
111531 CAAG-GTGCCACGGAGTTGTGGGCTTTAAAATGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
* * **
111566 AAAGAGTGCCACAGAGTTGTGGGCTTTGAA--AA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* *
111598 GAAG-GTGCCACGGAGTCGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
111631 CAAG-GTGCCACGGGGTTGTGGACTTTAAAAGGGGA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAA-GGAA
*
111666 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
* * *
111700 AAAGAGTGTCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAAAAGGAA
*
111735 AAAG-GTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
*
111768 AAAGAGTGCCACGGAGTCGTGG
1 AAAGAGTGCCACGGAGTTGTGG
111790 GCTTTGGAAA
Statistics
Matches: 218, Mismatches: 30, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
31 20 0.09
32 5 0.02
33 53 0.24
34 70 0.32
35 34 0.16
36 36 0.17
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:111801 original size:68 final size:69
Alignment explanation
Indices: 111532--111927 Score: 314
Period size: 63 Copynumber: 6.0 Consensus size: 69
111522 TAAAAGGAAC
* * * *
111532 AAGGTGCCACGGAGTTGTGGGCTTTAAAATGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT-G-A
1 AAGGTGCCACGGAGTTGTGGACTTTAGAA-GGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAA
*
111595 A-AAG
65 AGAAA
* * * * * * *
111599 AAGGTGCCACGGAGTCGTGGAC-TTAAAAGGAACAAG-GTGCCACGGGGTTGTGGACTTT-AAAA
1 AAGGTGCCACGGAGTTGTGGACTTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAAA
*
111661 GGGGAA
66 --GAAA
* * **
111667 AAGAGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGTCACGGAGTTGTGGGCTTTAAAA
1 AAG-GTGCCACGGAGTTGTGGACTTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAA
111731 AGAAA
65 AGAAA
111736 AAGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAAA
1 AAGGTGCCACGGAGTTGTGGACTTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAAA
111800 G---
66 GAAA
* * ** * * *
111801 -AGATGGCACTAAATTGTGGACTTTAAGAAGG-AAAA-A-TGCCACTGAGCCGTGGGCTTTGGAA
1 AAGGTGCCACGGAGTTGTGGACTTT-AGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAA
111862 AG--A
65 AGAAA
** * ** *
111865 AA--TGCCACTAAATTGTGGACTTTAAGAAGG--AAAGA-TGCCATTGAGCCGTGGGCTTTGGAA
1 AAGGTGCCACGGAGTTGTGGACTTT-AGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAA
111925 AGA
65 AGA
111928 GATTTGAAGA
Statistics
Matches: 287, Mismatches: 29, Indels: 29
0.83 0.08 0.08
Matches are distributed among these distances:
62 3 0.01
63 79 0.28
64 36 0.13
65 16 0.06
66 12 0.04
67 20 0.07
68 62 0.22
69 36 0.13
70 19 0.07
71 4 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (69 bp):
AAGGTGCCACGGAGTTGTGGACTTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTGGAAA
GAAA
Found at i:111868 original size:30 final size:30
Alignment explanation
Indices: 111834--111927 Score: 89
Period size: 30 Copynumber: 3.0 Consensus size: 30
111824 TAAGAAGGAA
111834 AAATGCCACTGAGCCGTGGGCTTTGGAAAG
1 AAATGCCACTGAGCCGTGGGCTTTGGAAAG
* *** * * *
111864 AAATGCCACTAAATTGTGGACTTTAAGAAGG
1 AAATGCCACTGAGCCGTGGGCTTT-GGAAAG
*
111895 AAAGATGCCATTGAGCCGTGGGCTTTGGAAAG
1 -AA-ATGCCACTGAGCCGTGGGCTTTGGAAAG
111927 A
1 A
111928 GATTTGAAGA
Statistics
Matches: 46, Mismatches: 15, Indels: 5
0.70 0.23 0.08
Matches are distributed among these distances:
30 19 0.41
31 5 0.11
32 6 0.13
33 16 0.35
ACGTcount: A:0.32, C:0.16, G:0.30, T:0.22
Consensus pattern (30 bp):
AAATGCCACTGAGCCGTGGGCTTTGGAAAG
Found at i:112890 original size:12 final size:11
Alignment explanation
Indices: 112873--112939 Score: 71
Period size: 11 Copynumber: 5.9 Consensus size: 11
112863 TTTTCCTCTC
112873 TTTTTTTTTGT
1 TTTTTTTTTGT
112884 TTGTTTTTTTGT
1 TT-TTTTTTTGT
* * *
112896 TTGTTTCTTCT
1 TTTTTTTTTGT
*
112907 TTTTTTTTTCT
1 TTTTTTTTTGT
112918 TTTTTGTTTTGT
1 TTTTT-TTTTGT
*
112930 TTCTTTTTTG
1 TTTTTTTTTG
112940 GAAAAGAACA
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
11 27 0.57
12 20 0.43
ACGTcount: A:0.00, C:0.06, G:0.10, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:112928 original size:34 final size:35
Alignment explanation
Indices: 112864--112931 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
112854 AAAAAGGGTT
*
112864 TTTCCTCTCTTTTTTTTTGTTTGTTTTTTTGTTTG
1 TTTCCTCTCTTTTTTTTTCTTTGTTTTTTTGTTTG
*
112899 TTTCTTCT-TTTTTTTTTCTTT-TTTGTTTTGTTT
1 TTTCCTCTCTTTTTTTTTCTTTGTTT-TTTTGTTT
112932 CTTTTTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
33 3 0.10
34 20 0.67
35 7 0.23
ACGTcount: A:0.00, C:0.10, G:0.09, T:0.81
Consensus pattern (35 bp):
TTTCCTCTCTTTTTTTTTCTTTGTTTTTTTGTTTG
Found at i:112939 original size:16 final size:15
Alignment explanation
Indices: 112873--112938 Score: 89
Period size: 16 Copynumber: 4.3 Consensus size: 15
112863 TTTTCCTCTC
*
112873 TTTTTTTTTGTTTGT
1 TTTTTTTTTGTTTCT
112888 TTTTTTGTTTGTTTCT
1 TTTTTT-TTTGTTTCT
*
112904 TCTTTTTTT-TTTCT
1 TTTTTTTTTGTTTCT
112918 TTTTTGTTTTGTTTCT
1 TTTTT-TTTTGTTTCT
112934 TTTTT
1 TTTTT
112939 GGAAAAGAAC
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
14 9 0.20
15 13 0.29
16 23 0.51
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.85
Consensus pattern (15 bp):
TTTTTTTTTGTTTCT
Found at i:116280 original size:19 final size:19
Alignment explanation
Indices: 116256--116310 Score: 101
Period size: 19 Copynumber: 2.9 Consensus size: 19
116246 AATTCAACGA
116256 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
116275 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
116294 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
116311 TTAGCTACTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:116368 original size:13 final size:13
Alignment explanation
Indices: 116350--116375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
116340 CATTTTTCTG
116350 TGTATCGATACAT
1 TGTATCGATACAT
116363 TGTATCGATACAT
1 TGTATCGATACAT
116376 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:116372 original size:33 final size:33
Alignment explanation
Indices: 116330--116396 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
116320 GCCAAGGAAA
***
116330 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
116363 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
116396 T
1 T
116397 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:118798 original size:51 final size:53
Alignment explanation
Indices: 118737--119071 Score: 187
Period size: 52 Copynumber: 6.3 Consensus size: 53
118727 AATTCTCCAC
* * * *
118737 AATCGAGGATATTCCAACTCCGATTTTATTTTC-AAAACACTAA-TT-TTCTAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTC-AT
*
118788 AATCGGGGATACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCAT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAAACACCAATTTCTTCAT
* * * *** * * **
118843 AATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCTCGTT-AT
1 AATCGGGGATACTCCAACTCCGATTTTAT-TTC-CAAAAACACCAATTTC-TTCAT
* * * * *
118896 -TTCCGAGGGGATACTCCAACTCCGGTTTTA--TCGCTAAAACACTAATTT-TTCCAC
1 AAT-C--GGGGATACTCCAACTCCGATTTTATTTC-CAAAAACACCAATTTCTT-CAT
* * *
118950 AATCGGGGATACTCCAA-TCCTGGTTTTATTTTC-AAAACGCCAATTTTCCTT--T
1 AATCGGGGATACTCCAACTCC-GATTTTATTTCCAAAAACACCAA-TTT-CTTCAT
* * *
119002 AATCGGGGATACTTCAACTCCGATTTTATTTCCAAAAATACCAATTT-TTCAC
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
* *
119054 AATCGAGGATGCTCCAAC
1 AATCGGGGATACTCCAAC
119072 CTCGTTATTT
Statistics
Matches: 216, Mismatches: 42, Indels: 51
0.70 0.14 0.17
Matches are distributed among these distances:
50 2 0.01
51 32 0.15
52 75 0.35
53 31 0.14
54 26 0.12
55 44 0.20
56 3 0.01
57 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.33
Consensus pattern (53 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCAT
Found at i:118914 original size:28 final size:27
Alignment explanation
Indices: 118847--118915 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 27
118837 CTTCATAATC
**
118847 GGGGATACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCAGA
* * *
118874 GGGGATACTCCAACCTCGTTATTTCCGA
1 GGGGATACTCCAACCCCGTTA-ATCAGA
118902 GGGGATACTCCAAC
1 GGGGATACTCCAAC
118916 TCCGGTTTTA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 20 0.56
28 16 0.44
ACGTcount: A:0.25, C:0.30, G:0.22, T:0.23
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCAGA
Found at i:119116 original size:212 final size:212
Alignment explanation
Indices: 118732--119138 Score: 597
Period size: 212 Copynumber: 1.9 Consensus size: 212
118722 TTATCAATTC
* *
118732 TCCACAATCGAGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTATAATCGGGGA
1 TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
* *
118797 TACTCTAACTCCGATTTTATTTCCAAAAAAACACCAATTTCTTCATAATCGGGGATACTCCAACC
66 TACTCTAACTCCGATTTTATTTCC-AAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACC
* * * *
118862 CCGTTAATCATCGGGGATACTCCAACCTCGTTATTTCCGAGGGGATACTCCAACTCCGGTTTTAT
130 CCGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTAT
118927 CGCTAAAACACTAATTTT
195 CGCTAAAACACTAATTTT
* * * *
118945 TCCACAATCGGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATCGGG
1 TCCACAATCGAGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTT-CTATAATCGGG
* *
119009 GATACT-TCAACTCCGATTTTATTTCC-AAAAATACCAATTT-TTCACAATCGAGGATGCTCCAA
64 GATACTCT-AACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAA
* *
119071 CCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
128 CCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTT
119136 TAT
192 TAT
119139 TCCCAAAATA
Statistics
Matches: 174, Mismatches: 16, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
211 26 0.15
212 70 0.40
213 44 0.25
214 34 0.20
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
TCCACAATCGAGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATCGGGGA
TACTCTAACTCCGATTTTATTTCCAAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATC
GCTAAAACACTAATTTT
Found at i:119234 original size:79 final size:79
Alignment explanation
Indices: 119085--119287 Score: 230
Period size: 79 Copynumber: 2.6 Consensus size: 79
119075 GTTATTTCAT
* * * *
119085 CGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
* * *
119150 TGATTTCTCATAAT
66 CGATTTCTCACAAC
* * * * ** *
119164 TGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAATCCCGATTTTTTTTTC-TAATCA
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAAT-A
119228 TCGATTTCTCACAAC
65 TCGATTTCTCACAAC
* *
119243 CGGGGATACTCCAGCCCCGTTATTTTC-AAGGGAACACTCCAACCC
1 CGGGGATACTCCAACCCCGTTATTTTCGAAGGG-ATACTCCAACCC
119288 TGTTATTATC
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
78 8 0.08
79 96 0.92
ACGTcount: A:0.25, C:0.30, G:0.16, T:0.29
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGTTATTTTCGAAGGGATACTCCAACCCCGACTTTATTCCCAAAATAT
CGATTTCTCACAAC
Found at i:123477 original size:20 final size:20
Alignment explanation
Indices: 123452--123499 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
123442 TGCAGGTGCT
**
123452 AAACATGCTGTAAATGCATG
1 AAACATGCTCAAAATGCATG
123472 AAACATAGCTCAAAATGCATG
1 AAACAT-GCTCAAAATGCATG
*
123493 AATCATG
1 AAACATG
123500 GGCTGTTAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AAACATGCTCAAAATGCATG
Found at i:124496 original size:52 final size:52
Alignment explanation
Indices: 124348--124476 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
124338 CGAAATATGA
124348 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* * *
124400 AAATTTGCCTGCATATATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
*
124452 AAATTTGCCTGCGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
124477 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:124578 original size:19 final size:19
Alignment explanation
Indices: 124554--124601 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
124544 TTATATTGTG
124554 TCGATACAAAACTTATGTA
1 TCGATACAAAACTTATGTA
*
124573 TCGATACAACACTTATGTA
1 TCGATACAAAACTTATGTA
*
124592 TCGATTCAAA
1 TCGATACAAA
124602 TCGTTGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (19 bp):
TCGATACAAAACTTATGTA
Found at i:126323 original size:13 final size:13
Alignment explanation
Indices: 126305--126334 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
126295 ATAATTCTTC
126305 ATGTATCGATACA
1 ATGTATCGATACA
126318 ATGTATCGATACA
1 ATGTATCGATACA
126331 ATGT
1 ATGT
126335 GTCATGTATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:126324 original size:33 final size:33
Alignment explanation
Indices: 126282--126351 Score: 97
Period size: 33 Copynumber: 2.1 Consensus size: 33
126272 GCCGTTTGGG
* * *
126282 ACAATGTATCGATATAAT-TCTTCATGTATCGAT
1 ACAATGTATCGATACAATGT-GTCATGTATCAAT
126315 ACAATGTATCGATACAATGTGTCATGTATCAAT
1 ACAATGTATCGATACAATGTGTCATGTATCAAT
126348 ACAA
1 ACAA
126352 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (33 bp):
ACAATGTATCGATACAATGTGTCATGTATCAAT
Found at i:128253 original size:16 final size:17
Alignment explanation
Indices: 128215--128258 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
128205 TTGCATTGTT
*
128215 TCACATGCATTTTGCAT
1 TCACATGCATTTTGCAC
* *
128232 TTACATGTA-TTTGCAC
1 TCACATGCATTTTGCAC
128248 TCACATGCATT
1 TCACATGCATT
128259 CTCATTATTT
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (17 bp):
TCACATGCATTTTGCAC
Found at i:133397 original size:13 final size:13
Alignment explanation
Indices: 133379--133404 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
133369 CATTTTGGGA
133379 TGTATCGATACAT
1 TGTATCGATACAT
133392 TGTATCGATACAT
1 TGTATCGATACAT
133405 CTTGTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:133523 original size:13 final size:13
Alignment explanation
Indices: 133493--133517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
133483 ACATTTGGTC
133493 ATGTATCGATACA
1 ATGTATCGATACA
133506 ATGTATCGATAC
1 ATGTATCGATAC
133518 TGTGTAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:135538 original size:52 final size:52
Alignment explanation
Indices: 135390--135518 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
135380 CGAAATATGA
* *
135390 AAATTTGTCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGCC
135442 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGCC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGCC
135494 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
135519 AAGATCAGTA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGCC
Found at i:135618 original size:19 final size:18
Alignment explanation
Indices: 135594--135691 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
135584 TAGCTTAAAT
135594 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
135613 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
135626 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
135645 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
135658 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
135678 TGTATCGATACAAA
1 TGTATCGATACAAA
135692 TCATTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:135631 original size:13 final size:13
Alignment explanation
Indices: 135613--135669 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
135603 ACAAAACTTA
135613 TGTATCGATACAT
1 TGTATCGATACAT
135626 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
135644 ATGTATCGATACAT
1 -TGTATCGATACAT
135658 TGTATCGATACA
1 TGTATCGATACA
135670 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:135633 original size:32 final size:32
Alignment explanation
Indices: 135592--135689 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
135582 AGTAGCTTAA
*
135592 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
135624 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
135656 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
135689 A
1 A
135690 AATCATTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:136478 original size:43 final size:43
Alignment explanation
Indices: 136416--136738 Score: 358
Period size: 43 Copynumber: 7.1 Consensus size: 43
136406 AAAGATGATG
* *
136416 AAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
136459 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-A
* * *
136503 AGATGAAGATGTCAATATGCTAATTCAAGGCCAGCGATATTGGACTTA
1 A-A-G--G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
136551 AAAGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A
*
136598 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* *
136643 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A
*
136690 TGAAGGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTA
1 --AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
136735 AAGG
1 AAGG
136739 AAGATGCCAC
Statistics
Matches: 237, Mismatches: 25, Indels: 36
0.80 0.08 0.12
Matches are distributed among these distances:
43 114 0.48
44 3 0.01
45 3 0.01
46 1 0.00
47 3 0.01
48 3 0.01
49 110 0.46
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (43 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
Found at i:136545 original size:92 final size:92
Alignment explanation
Indices: 136412--136738 Score: 591
Period size: 92 Copynumber: 3.6 Consensus size: 92
136402 GTTTAAAGAT
*
136412 GATGAAGGTGCCAATATGTTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
136477 TTCAAGGCCAGCTACATTGGACTTAAA
66 TTCAAGGCCAGCTACATTGGACTTAAA
* * * *
136504 GATGAAGATGTCAATATGCTAATTCAAGGCCAGCGATATTGGACTTAAAAGTGCCAATGTGCTGA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
136569 TTCAAGGCCAGCTACATTGGACTTAAA
66 TTCAAGGCCAGCTACATTGGACTTAAA
136596 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
136661 TTCAAGGCCAGCTACATTGGACTTAAA
66 TTCAAGGCCAGCTACATTGGACTTAAA
* *
136688 GATGAAGGTGCCAATATGCTGATTTAAGGCCAGCTATATTGGACTTAAAGG
1 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGG
136739 AAGATGCCAC
Statistics
Matches: 224, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 224 1.00
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (92 bp):
GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGA
TTCAAGGCCAGCTACATTGGACTTAAA
Found at i:136820 original size:32 final size:32
Alignment explanation
Indices: 136743--137000 Score: 324
Period size: 32 Copynumber: 8.0 Consensus size: 32
136733 TAAAGGAAGA
*
136743 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAA-AAGGT
* **
136776 TGCCACCGACTTGTGTGGGCTTTAG-AGGGGAT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAGG-T
136808 TGCCACCAACTTGTGTGGGCTTTAGAAGAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAA-AAGGT
* * *
136841 TGCCACCGACTTGTGTGAGCTTT-GAGAATGGT
1 TGCCACCAACTTGTGTGGGCTTTAGA-AAAGGT
* *
136873 TGCCACCAACTTGTGTGGGCTTTGGAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAGGT
*
136905 TGCCACCGACTTGTGTGGGCTTTAGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTTAG-AAAAGGT
136938 TGCCACCAACTTGTGTGGGCTTT-GAAAAGGGT
1 TGCCACCAACTTGTGTGGGCTTTAGAAAA-GGT
* * *
136970 TACCACCGACTTGTGTGGGCTTTTGAAAAGG
1 TGCCACCAACTTGTGTGGGCTTTAGAAAAGG
137001 AGAAAGATGC
Statistics
Matches: 198, Mismatches: 19, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
31 6 0.03
32 108 0.55
33 82 0.41
34 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.32, T:0.29
Consensus pattern (32 bp):
TGCCACCAACTTGTGTGGGCTTTAGAAAAGGT
Found at i:136847 original size:65 final size:62
Alignment explanation
Indices: 136743--136997 Score: 357
Period size: 65 Copynumber: 4.0 Consensus size: 62
136733 TAAAGGAAGA
**
136743 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAGGGGAT
1 TGCCACCAACTTGTGTGGGC-TTTGAA-AAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAGG-T
* *
136808 TGCCACCAACTTGTGTGGGCTTTAGAAGAAGGTTGCCACCGACTTGTGTGAGCTTTGAGAATGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAA-AAGGTTGCCACCGACTTGTGTGGGCTTT-AGAAAGGT
*
136873 TGCCACCAACTTGTGTGGGCTTTGGAAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAAAAAGGT
1 TGCCACCAACTTGTGTGGGCTTT-GAAAAGGTTGCCACCGACTTGTGTGGGCTTTAG--AAAGGT
* *
136938 TGCCACCAACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAAA
136998 AGGAGAAAGA
Statistics
Matches: 175, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
63 5 0.03
64 33 0.19
65 132 0.75
66 5 0.03
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (62 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAGGT
Found at i:136910 original size:97 final size:97
Alignment explanation
Indices: 136743--136997 Score: 370
Period size: 97 Copynumber: 2.6 Consensus size: 97
136733 TAAAGGAAGA
*
136743 TGCCACCAACTTGTGTGGGCTTTTGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAG-AGGGGA
1 TGCCACCAACTTGTGTGGGC-TTTG-AGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAGGGA
*
136807 TTGCCACCAACTTGTGTGGGCTTTAGAAGAAGGT
64 TTGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
* * * *
136841 TGCCACCGACTTGTGTGAGCTTTGAGAATGGTTGCCACCAACTTGTGTGGGCTTTGGAAAGGG-T
1 TGCCACCAACTTGTGTGGGCTTTGAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAAAGGGAT
*
136905 TGCCACCGACTTGTGTGGGCTTTAGAAAAAGGT
65 TGCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
* * *
136938 TGCCACCAACTTGTGTGGGCTTTGAAAAGGGTTACCACCGACTTGTGTGGGCTTTTGAAA
1 TGCCACCAACTTGTGTGGGCTTTGAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAGAAA
136998 AGGAGAAAGA
Statistics
Matches: 141, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
96 4 0.03
97 115 0.82
98 22 0.16
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (97 bp):
TGCCACCAACTTGTGTGGGCTTTGAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGAAAGGGATT
GCCACCAACTTGTGTGGGCTTTAGAAAAAGGT
Found at i:137032 original size:33 final size:34
Alignment explanation
Indices: 136995--137332 Score: 219
Period size: 36 Copynumber: 10.1 Consensus size: 34
136985 TGGGCTTTTG
136995 AAAAGGAGAAAGATGCCACGGAGTTGTGGAC-TT
1 AAAAGGAGAAAGATGCCACGGAGTTGTGGACTTT
137028 AAAA-G-G---G-TGCCACGGAGTTGTGGAC-TT
1 AAAAGGAGAAAGATGCCACGGAGTTGTGGACTTT
* *
137055 AAAAGG-GACAAGGTGCCACGGGGTTGTGGACTTT
1 AAAAGGAGA-AAGATGCCACGGAGTTGTGGACTTT
* * *
137089 AAAAAGGAAAAAGAGTGCCACTAGAGTTGTGGGCTTT
1 -AAAAGGAGAAAGA-TGCCAC-GGAGTTGTGGACTTT
* * * * *
137126 GAAA--AG-AAGGTGCTATGGAGTCGTGGACTTT
1 AAAAGGAGAAAGATGCCACGGAGTTGTGGACTTT
* * *
137157 GAAAGGA-ACAAGATGCCACGGGGTCAGTGGAC-TT
1 AAAAGGAGA-AAGATGCCACGGAGT-TGTGGACTTT
* *
137191 AAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGG-AGAAAGA-TGCCACGGAGTTGTGGACTTT
* * *
137227 GAAA--AG-AAGGTGCCACGGAGTCGTGGAC-TT
1 AAAAGGAGAAAGATGCCACGGAGTTGTGGACTTT
* *
137257 AAAAGGA-ACAAGGTGCCACAGAGTTGTGGACTTT
1 AAAAGGAGA-AAGATGCCACGGAGTTGTGGACTTT
* * * *
137291 AAAAGGGAAAAATAGTGCCACAGAGTTGTGGGCTTT
1 AAAA-GGAGAAAGA-TGCCACGGAGTTGTGGACTTT
137327 GAAAAG
1 -AAAAG
137333 AAGGTGCCAT
Statistics
Matches: 242, Mismatches: 34, Indels: 55
0.73 0.10 0.17
Matches are distributed among these distances:
27 24 0.10
28 3 0.01
30 5 0.02
31 33 0.14
32 10 0.04
33 46 0.19
34 27 0.11
35 30 0.12
36 48 0.20
37 16 0.07
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAAGGAGAAAGATGCCACGGAGTTGTGGACTTT
Found at i:137040 original size:27 final size:27
Alignment explanation
Indices: 137008--137061 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
136998 AGGAGAAAGA
137008 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
137035 TGCCACGGAGTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGG
137062 ACAAGGTGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGG
Found at i:137153 original size:101 final size:100
Alignment explanation
Indices: 136995--137356 Score: 486
Period size: 100 Copynumber: 3.6 Consensus size: 100
136985 TGGGCTTTTG
* * * *
136995 AAAAGGAGAAAGA-TGCCACGGAGTTGTGGAC-TT-AAAAG--GGTGCCACGGAGTTGTGGACTT
1 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
*
137055 AAAAGGGACAAGGTGCCACGGGGTTGTGGACTTTA
66 AAAAGGAACAAGGTGCCACGGGGTTGTGGACTTTA
* *
137090 AAAAGGAAAAAGAGTGCCACTAGAGTTGTGGGCTTTGAAAAGAAGGTGCTATGGAGTCGTGGACT
1 AAAAGGAAAAAGAGTGCCAC-AGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGAC-
* * *
137155 TTGAAAGGAACAAGATGCCACGGGGTCAGTGGAC-TT-
64 TTAAAAGGAACAAGGTGCCACGGGGT-TGTGGACTTTA
*
137191 AAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACT
1 AAAAGGAA-AAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACT
* *
137256 TAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTTA
65 TAAAAGGAACAAGGTGCCACGGGGTTGTGGACTTTA
* * **
137292 AAAGGGAAAAATAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCATAGAGTCGTGGACTT
1 AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
137357 TAAGAAGGTA
Statistics
Matches: 233, Mismatches: 23, Indels: 17
0.85 0.08 0.06
Matches are distributed among these distances:
95 12 0.05
96 6 0.03
97 10 0.04
98 2 0.01
99 11 0.05
100 77 0.33
101 72 0.31
102 37 0.16
103 6 0.03
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.20
Consensus pattern (100 bp):
AAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACTT
AAAAGGAACAAGGTGCCACGGGGTTGTGGACTTTA
Found at i:137261 original size:202 final size:195
Alignment explanation
Indices: 136995--137357 Score: 573
Period size: 202 Copynumber: 1.8 Consensus size: 195
136985 TGGGCTTTTG
* *
136995 AAAAGGAGAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG
1 AAAAGGACAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTCGTGGACTTAAAAG
* * *
137060 GGACAAGGTGCCACGGGGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACTAGAGTTGTGGGCTT
66 GAACAAGGTGCCACAGAGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCAC-AGAGTTGTGGGCTT
* *
137125 TGAAAAGAAGGTGCTATGGAGTCGTGGACTTTGAAAGGAACAAGATGCCACGGGGTCAGTGGACT
130 TGAAAAGAAGGTGCCATAGAGTCGTGGACTTTGAAAGGAACAAGATGCCACGGGGTCAGTGGACT
137190 T
195 T
*
137191 AAAAGGAACAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGGTGCCACGGAGTCGTGGACT
1 AAAAGG-ACAAAGA-TGCCACGGAGTTGTGGAC-TT-AAAAG--GGTGCCACGGAGTCGTGGACT
* *
137256 TAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTTAAAAGGGAAAAATAGTGCCACAGAGTTGTG
60 TAAAAGGAACAAGGTGCCACAGAGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTG
137321 GGCTTTGAAAAGAAGGTGCCATAGAGTCGTGGACTTT
125 GGCTTTGAAAAGAAGGTGCCATAGAGTCGTGGACTTT
137358 AAGAAGGTAT
Statistics
Matches: 151, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
196 6 0.04
197 6 0.04
198 17 0.11
199 2 0.01
200 5 0.03
201 44 0.29
202 71 0.47
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (195 bp):
AAAAGGACAAAGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTCGTGGACTTAAAAG
GAACAAGGTGCCACAGAGTTGTGGACTTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTT
GAAAAGAAGGTGCCATAGAGTCGTGGACTTTGAAAGGAACAAGATGCCACGGGGTCAGTGGACTT
Found at i:137347 original size:31 final size:31
Alignment explanation
Indices: 137008--137357 Score: 156
Period size: 31 Copynumber: 10.7 Consensus size: 31
136998 AGGAGAAAGA
*
137008 TGCCACGGAGTTGTGGAC-TT-AAAAG--GG
1 TGCCACAGAGTTGTGGACTTTGAAAAGAAGG
*
137035 TGCCACGGAGTTGTGGAC-TT-AAAAGGGACAAGG
1 TGCCACAGAGTTGTGGACTTTGAAAA--G--AAGG
* * *
137068 TGCCACGGGGTTGTGGACTTTAAAAAGGAAAAAGAG
1 TGCCACAGAGTTGTGGACTTTGAAAA-G---AAG-G
*
137104 TGCCACTAGAGTTGTGGGCTTTGAAAAGAAGG
1 TGCCAC-AGAGTTGTGGACTTTGAAAAGAAGG
* ** * * *
137136 TGCTATGGAGTCGTGGACTTTGAAAGGAACAAGA
1 TGCCACAGAGTTGTGGACTTTG-AA--AAGAAGG
* * * ** *
137170 TGCCACGGGGTCAGTGGACTTAAAAGGAACAAAGAG
1 TGCCACAGAGT-TGTGGACTTTGAA--AA-GAAG-G
* *
137206 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGG
1 TGCCACAGAGTTGTGGACTTTGAAAAGAAGG
* * ** *
137237 TGCCACGGAGTCGTGGACTTAAAAGGAACAAGG
1 TGCCACAGAGTTGTGGACTTTGAA--AAGAAGG
*
137270 TGCCACAGAGTTGTGGACTTT-AAAAGGGAAAAATAG
1 TGCCACAGAGTTGTGGACTTTGAAAA--G---AA-GG
*
137306 TGCCACAGAGTTGTGGGCTTTGAAAAGAAGG
1 TGCCACAGAGTTGTGGACTTTGAAAAGAAGG
* *
137337 TGCCATAGAGTCGTGGACTTT
1 TGCCACAGAGTTGTGGACTTT
137358 AAGAAGGTAT
Statistics
Matches: 255, Mismatches: 42, Indels: 48
0.74 0.12 0.14
Matches are distributed among these distances:
27 24 0.09
29 1 0.00
30 2 0.01
31 53 0.21
32 14 0.05
33 48 0.19
34 23 0.09
35 31 0.12
36 39 0.15
37 20 0.08
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (31 bp):
TGCCACAGAGTTGTGGACTTTGAAAAGAAGG
Found at i:138689 original size:15 final size:14
Alignment explanation
Indices: 138671--138712 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
138661 ACTTTGCACC
*
138671 TTTTTTCTGTGTTT
1 TTTTTTTTGTGTTT
*
138685 TTTTTTGTTTTG-TT
1 TTTTTT-TTGTGTTT
138699 TTTTTTTTGTGTTT
1 TTTTTTTTGTGTTT
138713 ACTTTTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 4 0.17
14 16 0.70
15 3 0.13
ACGTcount: A:0.00, C:0.02, G:0.14, T:0.83
Consensus pattern (14 bp):
TTTTTTTTGTGTTT
Found at i:145696 original size:13 final size:13
Alignment explanation
Indices: 145678--145702 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
145668 CAAAGATCAG
145678 TGTATCGATACAA
1 TGTATCGATACAA
145691 TGTATCGATACA
1 TGTATCGATACA
145703 TTTGAGCAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Done.