Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009515.1 Kokia drynarioides strain JFW-HI SEQ_124226, whole genome shotgun sequence
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: 311129
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:616 original size:16 final size:15
Alignment explanation
Indices: 577--622 Score: 58
Period size: 16 Copynumber: 3.0 Consensus size: 15
567 ATATAGAATC
*
577 TAAAAAA-AAATAGA
1 TAAAAAAGAAATAAA
591 TAAAAGAAGAAATAAA
1 TAAAA-AAGAAATAAA
607 GTAAAAAAGAAATAAA
1 -TAAAAAAGAAATAAA
623 CATAAATGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 5 0.18
15 2 0.07
16 16 0.57
17 5 0.18
ACGTcount: A:0.76, C:0.00, G:0.11, T:0.13
Consensus pattern (15 bp):
TAAAAAAGAAATAAA
Found at i:628 original size:17 final size:17
Alignment explanation
Indices: 590--628 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
580 AAAAAAATAG
590 ATAAAAGAAGAAATAAA
1 ATAAAAGAAGAAATAAA
*
607 GTAAAA-AAGAAATAAA
1 ATAAAAGAAGAAATAAA
623 CATAAA
1 -ATAAA
629 TGTAAGAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (17 bp):
ATAAAAGAAGAAATAAA
Found at i:13020 original size:18 final size:18
Alignment explanation
Indices: 12987--13021 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
12977 ACCTACCTTA
*
12987 ATGGTAGGTCTACCCCTG
1 ATGGTAGGCCTACCCCTG
*
13005 ATGGTAGGCCTGCCCCT
1 ATGGTAGGCCTACCCCT
13022 ACACCTACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.31, G:0.29, T:0.26
Consensus pattern (18 bp):
ATGGTAGGCCTACCCCTG
Found at i:25956 original size:18 final size:18
Alignment explanation
Indices: 25908--25956 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
25898 GTCCTTGCAT
* *
25908 TTGTGGTTGCAAACTTGA
1 TTGTGGTTGCAATCTCGA
25926 TTGTGGTTGCAATCTCGA
1 TTGTGGTTGCAATCTCGA
25944 TTGTGGTTGCAAT
1 TTGTGGTTGCAAT
25957 TGACTATGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.29, T:0.41
Consensus pattern (18 bp):
TTGTGGTTGCAATCTCGA
Found at i:37847 original size:7 final size:6
Alignment explanation
Indices: 37829--37875 Score: 55
Period size: 6 Copynumber: 8.2 Consensus size: 6
37819 AATGATGCTC
*
37829 AGAAAA ACAAAA ATGAAAA AGAAAA AG-AAA A-AAAA AGAAAA A-AAAA
1 AGAAAA AGAAAA A-GAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA
37875 A
1 A
37876 AATATGTACT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
5 13 0.36
6 18 0.50
7 5 0.14
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (6 bp):
AGAAAA
Found at i:37848 original size:13 final size:11
Alignment explanation
Indices: 37829--37875 Score: 60
Period size: 11 Copynumber: 4.1 Consensus size: 11
37819 AATGATGCTC
37829 AGAAAAACAAAA
1 AGAAAAA-AAAA
37841 ATGAAAAAGAAAA
1 A-GAAAAA-AAAA
37854 AG-AAAAAAAA
1 AGAAAAAAAAA
37864 AGAAAAAAAAA
1 AGAAAAAAAAA
37875 A
1 A
37876 AATATGTACT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
10 6 0.19
11 13 0.41
12 2 0.06
13 11 0.34
ACGTcount: A:0.85, C:0.02, G:0.11, T:0.02
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:37865 original size:10 final size:10
Alignment explanation
Indices: 37845--37874 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
37835 ACAAAAATGA
37845 AAAAGAAAAAG
1 AAAA-AAAAAG
37856 AAAAAAAAAG
1 AAAAAAAAAG
37866 AAAAAAAAA
1 AAAAAAAAA
37875 AAATATGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:37865 original size:16 final size:15
Alignment explanation
Indices: 37844--37877 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
37834 AACAAAAATG
37844 AAAAAGAAAAAGAAAA
1 AAAAAGAAAAA-AAAA
37860 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
37875 AAA
1 AAA
37878 TATGTACTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:40088 original size:13 final size:13
Alignment explanation
Indices: 40070--40094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40060 ATTAATTTAG
40070 TTTAGATTAATAC
1 TTTAGATTAATAC
40083 TTTAGATTAATA
1 TTTAGATTAATA
40095 TCTCTCACAA
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:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (13 bp):
TTTAGATTAATAC
Found at i:48356 original size:24 final size:24
Alignment explanation
Indices: 48329--48391 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
48319 ATTTCGCCTC
* *
48329 AAGGGTATTACAGAATAAGCCAAA
1 AAGGGCATCACAGAATAAGCCAAA
* *
48353 AA-GGCATCACAGAATACGCCACA
1 AAGGGCATCACAGAATAAGCCAAA
*
48376 AA-GGCATCACATAATA
1 AAGGGCATCACAGAATA
48392 TGTCACAAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 32 0.94
24 2 0.06
ACGTcount: A:0.48, C:0.21, G:0.17, T:0.14
Consensus pattern (24 bp):
AAGGGCATCACAGAATAAGCCAAA
Found at i:48364 original size:23 final size:23
Alignment explanation
Indices: 48338--48448 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
48328 CAAGGGTATT
* *
48338 ACAGAATAAGCCAAAAAGGCATC
1 ACAGAATATGCCACAAAGGCATC
*
48361 ACAGAATACGCCACAAAGGCATC
1 ACAGAATATGCCACAAAGGCATC
* * * *
48384 ACATAATATGTCACAAAGACATT
1 ACAGAATATGCCACAAAGGCATC
* *
48407 ACATAATATGCCACGAAGGCATC
1 ACAGAATATGCCACAAAGGCATC
*
48430 ACA-AATATGCGACAAAGGC
1 ACAGAATATGCCACAAAGGC
48449 TTTACAAAAT
Statistics
Matches: 75, Mismatches: 13, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
22 14 0.19
23 61 0.81
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.14
Consensus pattern (23 bp):
ACAGAATATGCCACAAAGGCATC
Found at i:53874 original size:15 final size:15
Alignment explanation
Indices: 53854--53885 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
53844 CATTTCATTC
*
53854 CTTTTTTTTTTTTAT
1 CTTTTTCTTTTTTAT
53869 CTTTTTCTTTTTTAT
1 CTTTTTCTTTTTTAT
53884 CT
1 CT
53886 ACAACTTTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (15 bp):
CTTTTTCTTTTTTAT
Found at i:59781 original size:26 final size:26
Alignment explanation
Indices: 59707--59784 Score: 84
Period size: 27 Copynumber: 2.9 Consensus size: 26
59697 CAAGAATGTT
* * *
59707 ATATATATGGCAAACTTTGAAGGAATA
1 ATATGTAT-GCAAACTCTAAAGGAATA
* * *
59734 GTACGTATGATAAACTCTAAAGGAATA
1 ATATGTATG-CAAACTCTAAAGGAATA
59761 ATATGTATGCAAACTCTAAAGGAA
1 ATATGTATGCAAACTCTAAAGGAA
59785 CGACTCCCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
26 15 0.37
27 26 0.63
ACGTcount: A:0.45, C:0.10, G:0.18, T:0.27
Consensus pattern (26 bp):
ATATGTATGCAAACTCTAAAGGAATA
Found at i:65942 original size:28 final size:28
Alignment explanation
Indices: 65909--65965 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
65899 TGAGAAATTC
*
65909 TCTGAACTCTGGCTCGAAAGAGCATTAT
1 TCTGAACTCTGGCTCGAAACAGCATTAT
* * *
65937 TCTGAATTTTGGCTCGAAACAGCGTTAT
1 TCTGAACTCTGGCTCGAAACAGCATTAT
65965 T
1 T
65966 TTGGCTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (28 bp):
TCTGAACTCTGGCTCGAAACAGCATTAT
Found at i:65968 original size:21 final size:21
Alignment explanation
Indices: 65942--65986 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
65932 ATTATTCTGA
* *
65942 ATTTTGGCTCGAAACAGCGTT
1 ATTTTGGCTCAAAACAGCATT
*
65963 ATTTTGGCTCAAAAGAGCATT
1 ATTTTGGCTCAAAACAGCATT
65984 ATT
1 ATT
65987 CTAAATTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.36
Consensus pattern (21 bp):
ATTTTGGCTCAAAACAGCATT
Found at i:66017 original size:28 final size:28
Alignment explanation
Indices: 65963--66037 Score: 78
Period size: 28 Copynumber: 2.7 Consensus size: 28
65953 AAACAGCGTT
*
65963 ATTTTGGCTCAAAAGAGCATTATTCTAA
1 ATTTTGGCTCAAAAGAGCATTACTCTAA
* ** *
65991 ATTTTGGCTCGAAAGAGTGTTACTCTAC
1 ATTTTGGCTCAAAAGAGCATTACTCTAA
* * *
66019 ATTCTAGCTCAAAGGAGCA
1 ATTTTGGCTCAAAAGAGCA
66038 CCATTTTGTA
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (28 bp):
ATTTTGGCTCAAAAGAGCATTACTCTAA
Found at i:69575 original size:27 final size:29
Alignment explanation
Indices: 69539--69594 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
69529 CGAGAGTGTC
* *
69539 TTTTAATGCTAGATCATT-TTTATTCTTA
1 TTTTAATGCTACATAATTGTTTATTCTTA
*
69567 TTTT-ATGCTACTTAATTGTTTATTCTTA
1 TTTTAATGCTACATAATTGTTTATTCTTA
69595 GATCTAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.59
Consensus pattern (29 bp):
TTTTAATGCTACATAATTGTTTATTCTTA
Found at i:75961 original size:20 final size:21
Alignment explanation
Indices: 75925--75963 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
75915 ATTTTTGTTA
*
75925 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
75946 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
75964 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:78910 original size:25 final size:27
Alignment explanation
Indices: 78869--78926 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 27
78859 TCAATCACTT
*
78869 AGAAAATGAAAATGAGAAAAAGAAAGGA
1 AGAAAATGAAAATGAG-AAAAGAAAAGA
78897 A-AAAAT-AAAA-GAGAAAAGAAAAGA
1 AGAAAATGAAAATGAGAAAAGAAAAGA
78921 AGAAAA
1 AGAAAA
78927 AAATGTTTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 11 0.39
25 7 0.25
26 4 0.14
27 5 0.18
28 1 0.04
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (27 bp):
AGAAAATGAAAATGAGAAAAGAAAAGA
Found at i:78924 original size:13 final size:13
Alignment explanation
Indices: 78886--78926 Score: 50
Period size: 12 Copynumber: 3.3 Consensus size: 13
78876 GAAAATGAGA
*
78886 AAAAGAAAGGAA-
1 AAAAGAAAAGAAG
*
78898 AAAATAAAAG-AG
1 AAAAGAAAAGAAG
78910 AAAAGAAAAGAAG
1 AAAAGAAAAGAAG
78923 AAAA
1 AAAA
78927 AAATGTTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
11 1 0.04
12 17 0.71
13 6 0.25
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAAAGAAAAGAAG
Found at i:85107 original size:52 final size:52
Alignment explanation
Indices: 85043--85275 Score: 331
Period size: 52 Copynumber: 4.5 Consensus size: 52
85033 TTCTCATTAA
* * * *
85043 ATACTCATGATGACACATAGTCATTAGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCATAAAGGATTCAT
*** * * *
85095 ATACTCACGATGACACATAGTCATTGGACCTCATAATCCGTAAATGATCCAT
1 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCATAAAGGATTCAT
*
85147 ATACTCACGATGACACATAGTCATCAAACCTAATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCATAAAGGATTCAT
85199 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAAACCTCATAATCCATAAAGGATTCAT
* * * *
85251 GTACTTACAATGACACATAATCATC
1 ATACTCACGATGACACATAGTCATC
85276 CTTTTACATT
Statistics
Matches: 165, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 165 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAAACCTCATAATCCATAAAGGATTCAT
Found at i:89622 original size:52 final size:52
Alignment explanation
Indices: 89565--89803 Score: 336
Period size: 52 Copynumber: 4.6 Consensus size: 52
89555 TTCTCATTAA
* * *
89565 ATACTCATGATGACACATAGTCATCAGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAAAGGATTCAT
* * * *
89617 ATACTCACGATGACACATAGTTATCAGACCTCATAATCCGTAAATGATCCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAAAGGATTCAT
* * *
89669 ATACTCACGATGACACATAGTTATCGGACCTAATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAAAGGATTCAT
*
89721 ATACTCACGATGACACATAGTCAT-TGAACCTCATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCAG-ACCTCATAATCCATAAAGGATTCAT
* * *
89773 TTACTCACGATGACACATAATCATCGGACCT
1 ATACTCACGATGACACATAGTCATCAGACCT
89804 TTTACATTTT
Statistics
Matches: 169, Mismatches: 16, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
51 1 0.01
52 167 0.99
53 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCAGACCTCATAATCCATAAAGGATTCAT
Found at i:100926 original size:21 final size:21
Alignment explanation
Indices: 100902--100956 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
100892 TAGAGGTAAG
*
100902 ACTTGTATCGGTAG-AGGAGTC
1 ACTTGTATCGGTAGAACGA-TC
* *
100923 ACTTGTATTGGTAGAACTATC
1 ACTTGTATCGGTAGAACGATC
100944 ACTTGTATCGGTA
1 ACTTGTATCGGTA
100957 CAAATCTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACGATC
Found at i:101553 original size:57 final size:55
Alignment explanation
Indices: 101482--101618 Score: 174
Period size: 57 Copynumber: 2.5 Consensus size: 55
101472 CATTAAATAC
* **
101482 TCACGATAACACATAGTCATCGGACCTTATAATCTTTAAA-GAGTTCATATACTCA
1 TCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGA-TTCATATACTCA
* *
101537 CGTCACGATGACACATAGTCATCGAACCTCATAATCCGTAAAGGATTCATATACTCA
1 --TCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCATATACTCA
101594 T---GATGACACATAGTCATCGGACCTT
1 TCACGATGACACATAGTCATCGGACCTT
101619 TTACATTTTG
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
52 22 0.31
55 1 0.01
57 47 0.65
58 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (55 bp):
TCACGATGACACATAGTCATCGGACCTTATAATCCGTAAAGGATTCATATACTCA
Found at i:103034 original size:70 final size:70
Alignment explanation
Indices: 102921--103061 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
102911 GTGGTATCTA
102921 ACCAAGAGATCGTACCCAAGGGATCATTTGCATCGACAAGTGCTACATTGGAGCTGCTAGTTTGT
1 ACCAAGAGATCGTACCCAAGGGATCATTTGCATCGACAAGTGCTACATTGGAGCTGCTAGTTTGT
102986 TCGAT
66 TCGAT
102991 ACCAAGAGATCGTACCCAAGGGATCATTTGCATCGACAAGTGCTACATTGGAGCTGCTAGTTTGT
1 ACCAAGAGATCGTACCCAAGGGATCATTTGCATCGACAAGTGCTACATTGGAGCTGCTAGTTTGT
103056 TCGAT
66 TCGAT
103061 A
1 A
103062 GTTTGTTTTC
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.27
Consensus pattern (70 bp):
ACCAAGAGATCGTACCCAAGGGATCATTTGCATCGACAAGTGCTACATTGGAGCTGCTAGTTTGT
TCGAT
Found at i:113612 original size:29 final size:32
Alignment explanation
Indices: 113549--113612 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
113539 TGTTTGTATG
* *
113549 AAATTGAAGAAAGAGGGAGGAAGGAGAAGGACT
1 AAATTGAAGAAAGAAGGA-GAAGGAGAAAGACT
113582 AAATTGAAGAAA-AAGGA-AAGGAGAAAG-CT
1 AAATTGAAGAAAGAAGGAGAAGGAGAAAGACT
113611 AA
1 AA
113613 GGTGTGAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 4 0.14
30 9 0.31
32 4 0.14
33 12 0.41
ACGTcount: A:0.55, C:0.03, G:0.33, T:0.09
Consensus pattern (32 bp):
AAATTGAAGAAAGAAGGAGAAGGAGAAAGACT
Found at i:113766 original size:23 final size:23
Alignment explanation
Indices: 113739--113784 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
113729 AATTATAAGC
113739 ATGGTAATTATGTGTGATTGGAT
1 ATGGTAATTATGTGTGATTGGAT
113762 ATGGTAATTATGTGTGATTGGAT
1 ATGGTAATTATGTGTGATTGGAT
113785 GAAATATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.43
Consensus pattern (23 bp):
ATGGTAATTATGTGTGATTGGAT
Found at i:114560 original size:23 final size:23
Alignment explanation
Indices: 114514--114616 Score: 93
Period size: 23 Copynumber: 4.4 Consensus size: 23
114504 CACTAGCGCA
* *
114514 CCCTCTATTTAGTAC-GTTTCGTG
1 CCCTCTATTTAGCACTGTGT-GTG
114537 CCCTCTATTTAGCACTGTGTGTG
1 CCCTCTATTTAGCACTGTGTGTG
* * * *
114560 CCCTTTGTTATTAGCACTTTGTTTG
1 CCCTCT-AT-TTAGCACTGTGTGTG
*
114585 CCCTCTGA-TTAGCACTTTGTGTG
1 CCCTCT-ATTTAGCACTGTGTGTG
114608 CCCTCTATT
1 CCCTCTATT
114617 ACCTAGAACT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
22 1 0.01
23 43 0.64
24 4 0.06
25 19 0.28
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.44
Consensus pattern (23 bp):
CCCTCTATTTAGCACTGTGTGTG
Found at i:114576 original size:25 final size:23
Alignment explanation
Indices: 114534--114617 Score: 100
Period size: 23 Copynumber: 3.6 Consensus size: 23
114524 AGTACGTTTC
*
114534 GTGCCCTCT-ATTTAGCACTGTGT
1 GTGCCCTCTGA-TTAGCACTTTGT
*
114557 GTGCCCTTTGTTATTAGCACTTTGT
1 GTGCCCTCTG--ATTAGCACTTTGT
*
114582 TTGCCCTCTGATTAGCACTTTGT
1 GTGCCCTCTGATTAGCACTTTGT
114605 GTGCCCTCT-ATTA
1 GTGCCCTCTGATTA
114618 CCTAGAACTT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
22 4 0.08
23 29 0.55
25 19 0.36
26 1 0.02
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (23 bp):
GTGCCCTCTGATTAGCACTTTGT
Found at i:114635 original size:48 final size:45
Alignment explanation
Indices: 114534--114642 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 45
114524 AGTACGTTTC
* * * *
114534 GTGCCCTCTATTTAGCACTGTGTGTGCCCTTTGTTATTAGCACTTT
1 GTGCCCTCTA-TTAGCACTGTGTGTGCCCTCTATTACTAGAACTTT
*
114580 GTTTGCCCTCTGATTAGCACTTTGTGTGCCCTCTATTACCTAGAACTTAT
1 G--TGCCCTCT-ATTAGCACTGTGTGTGCCCTCTATTA-CTAGAACTT-T
114630 GTGCCCTCTATTA
1 GTGCCCTCTATTA
114643 AGTACTTCGG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
46 1 0.02
47 4 0.08
48 38 0.72
49 8 0.15
50 2 0.04
ACGTcount: A:0.16, C:0.26, G:0.17, T:0.41
Consensus pattern (45 bp):
GTGCCCTCTATTAGCACTGTGTGTGCCCTCTATTACTAGAACTTT
Found at i:127384 original size:158 final size:158
Alignment explanation
Indices: 127096--127417 Score: 436
Period size: 158 Copynumber: 2.0 Consensus size: 158
127086 GATTTCGAGA
* * * * *
127096 ATTACAAGTTATATGGATGTTGGTCTTAGATGTCCTATCGATGGCTAAGATCTGGCATTTATTAT
1 ATTACAAGTTATATGGATGCTGGTCTTAGATGTCCTACCCATGGCTAAGATCCGGCATTTATTAC
*
127161 GGATTCTTCACAGCTTGTGTGAGCAGTATCATGTAGCCCAACATCTCGACCCACAACTAGTGTGA
66 GGATTCTTCACAGCTTGTGTGAGCAGCATCATGTAGCCCAACATCTCGACCCACAACTAGTGTGA
127226 GCAAGCC-ATCTTCACAGCTCGTGTGAGC
131 GCAAGCCTAT-TTCACAGCTCGTGTGAGC
* * * *
127254 ATTACAGGTTATATGGGTGCTGGTCTTAGATGTCCTACCCATGGCTGAGATCCGGCATTTATTGC
1 ATTACAAGTTATATGGATGCTGGTCTTAGATGTCCTACCCATGGCTAAGATCCGGCATTTATTAC
* * *
127319 GGATT-TTCCATAGCTTGTGTGAGCAGCAT-AGTGTAGCCCAATATCTCGACCCACAGCTCA-TG
66 GGATTCTT-CACAGCTTGTGTGAGCAGCATCA-TGTAGCCCAACATCTCGACCCACAACT-AGTG
* *
127381 TGAGTAGGCCTATTTCACAGCTCGTGTGAGC
128 TGAGCAAGCCTATTTCACAGCTCGTGTGAGC
*
127412 AATACA
1 ATTACA
127418 TGATACAAAG
Statistics
Matches: 144, Mismatches: 16, Indels: 8
0.86 0.10 0.05
Matches are distributed among these distances:
157 3 0.02
158 138 0.96
159 3 0.02
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (158 bp):
ATTACAAGTTATATGGATGCTGGTCTTAGATGTCCTACCCATGGCTAAGATCCGGCATTTATTAC
GGATTCTTCACAGCTTGTGTGAGCAGCATCATGTAGCCCAACATCTCGACCCACAACTAGTGTGA
GCAAGCCTATTTCACAGCTCGTGTGAGC
Found at i:129136 original size:21 final size:21
Alignment explanation
Indices: 129088--129136 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
129078 TTCGAAACTC
* *
129088 TAGTCCATTTAAATTGCAAAT
1 TAGTCCGTTTAAATTACAAAT
129109 TAGTCCGTTTAAATTACAAAT
1 TAGTCCGTTTAAATTACAAAT
129130 TAGTCCG
1 TAGTCCG
129137 ATAACTTGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (21 bp):
TAGTCCGTTTAAATTACAAAT
Found at i:132145 original size:15 final size:15
Alignment explanation
Indices: 132125--132154 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
132115 TTCCTCAAAT
*
132125 CAAGGGGGTTATAAA
1 CAAGGGAGTTATAAA
132140 CAAGGGAGTTATAAA
1 CAAGGGAGTTATAAA
132155 ACCAATCCAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (15 bp):
CAAGGGAGTTATAAA
Found at i:138660 original size:24 final size:25
Alignment explanation
Indices: 138623--138675 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
138613 GTCGATTGGT
* * *
138623 ACAACGGATAAAAAGAGGAAGAGGC
1 ACAACGGAAAAAAAGAAGAAGAAGC
138648 ACAA-GGAAAAAAAGAAGAAGAAGC
1 ACAACGGAAAAAAAGAAGAAGAAGC
138672 ACAA
1 ACAA
138676 AGACGAGGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.60, C:0.11, G:0.26, T:0.02
Consensus pattern (25 bp):
ACAACGGAAAAAAAGAAGAAGAAGC
Found at i:148511 original size:21 final size:22
Alignment explanation
Indices: 148470--148511 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
148460 AACTGGGCTT
* *
148470 TTTAAATTGGAACTCTAGTCCA
1 TTTAAATTGCAAATCTAGTCCA
148492 TTTAAATTGCAAAT-TAGTCC
1 TTTAAATTGCAAATCTAGTCC
148512 GAGAACTTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (22 bp):
TTTAAATTGCAAATCTAGTCCA
Found at i:151466 original size:31 final size:28
Alignment explanation
Indices: 151428--151507 Score: 81
Period size: 31 Copynumber: 2.8 Consensus size: 28
151418 AATTAAATCC
*
151428 CTTTTAAATTTAATCCTTTTACTGTTTGTTT
1 CTTTTAAATTTAATCCTTTTA---TCTGTTT
** *
151459 CTTTTAAATTTGCTCCTTTGATCTGTTT
1 CTTTTAAATTTAATCCTTTTATCTGTTT
*
151487 -TTTTACATTTAATCCTTTTAT
1 CTTTTAAATTTAATCCTTTTAT
151508 TATTTTATTT
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
27 17 0.41
28 6 0.15
31 18 0.44
ACGTcount: A:0.19, C:0.15, G:0.06, T:0.60
Consensus pattern (28 bp):
CTTTTAAATTTAATCCTTTTATCTGTTT
Found at i:151557 original size:21 final size:20
Alignment explanation
Indices: 151503--151562 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
151493 ATTTAATCCT
*
151503 TTTAT-TATT-TTATTTATT
1 TTTATATATTCTTATTTATA
*
151521 TTTATATATTC-GATTTATA
1 TTTATATATTCTTATTTATA
151540 TTTATATATTGCTTATTTA-A
1 TTTATATATT-CTTATTTATA
151560 TTT
1 TTT
151563 TTTTAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
18 5 0.14
19 20 0.57
20 5 0.14
21 5 0.14
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TTTATATATTCTTATTTATA
Found at i:151599 original size:19 final size:18
Alignment explanation
Indices: 151554--151601 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
151544 TATATTGCTT
**
151554 ATTTAATTTTTTTAAATA
1 ATTTAATTTTAGTAAATA
*
151572 ATTTAAATTTTAGTATAATC
1 ATTT-AATTTTAGTA-AATA
151592 ATTTAATTTT
1 ATTTAATTTT
151602 CACCATGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 4 0.16
19 14 0.56
20 7 0.28
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
ATTTAATTTTAGTAAATA
Found at i:152404 original size:49 final size:49
Alignment explanation
Indices: 152351--152507 Score: 170
Period size: 49 Copynumber: 3.2 Consensus size: 49
152341 GGGGAGGAAA
** *
152351 AGATTGAAGCCGCAAAGGAAAATCTTATACCATAAAGATGAGGAAAGGC
1 AGATTGAAGCCGCAAAGGCGAATCTTATACCATAAAGATGAAGAAAGGC
* * ** * * *
152400 AGATTGAAGTCACAAAGGCGAATCTTATACTTTAAATATGAATAAGGGC
1 AGATTGAAGCCGCAAAGGCGAATCTTATACCATAAAGATGAAGAAAGGC
* * * ***
152449 AGATTGAAGCCGCAAAGGCGAGTCTTATACCCTAAAGATGGAGTGGGGC
1 AGATTGAAGCCGCAAAGGCGAATCTTATACCATAAAGATGAAGAAAGGC
152498 AGATTGAAGC
1 AGATTGAAGC
152508 TACAAAAAGG
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 88 1.00
ACGTcount: A:0.39, C:0.15, G:0.26, T:0.20
Consensus pattern (49 bp):
AGATTGAAGCCGCAAAGGCGAATCTTATACCATAAAGATGAAGAAAGGC
Found at i:159116 original size:22 final size:22
Alignment explanation
Indices: 159086--159146 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
159076 TCTTATCAGA
* **
159086 GAATCTCACTATTCATGGTAGG
1 GAATATCACTATTCATGCCAGG
*
159108 GAATATCACTGTTCATGCCAGG
1 GAATATCACTATTCATGCCAGG
*
159130 GAATATCGCTATTCATG
1 GAATATCACTATTCATG
159147 TCAGAAAATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (22 bp):
GAATATCACTATTCATGCCAGG
Found at i:159548 original size:14 final size:14
Alignment explanation
Indices: 159523--159576 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
159513 AGTCGTAATG
*
159523 AAATTAAAATTTGAA
1 AAATT-AAATTTTAA
159538 AAATTAAATTTTAA
1 AAATTAAATTTTAA
* *
159552 AATTTGAATTTTAA
1 AAATTAAATTTTAA
*
159566 AACTTAAATTT
1 AAATTAAATTT
159577 AATTTTGAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 29 0.85
15 5 0.15
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (14 bp):
AAATTAAATTTTAA
Found at i:159555 original size:28 final size:28
Alignment explanation
Indices: 159523--159576 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
159513 AGTCGTAATG
159523 AAATTAAAATTTGAAAAATTAAATTTTA
1 AAATTAAAATTTGAAAAATTAAATTTTA
** * *
159551 AAATTTGAATTTTAAAACTTAAATTT
1 AAATTAAAATTTGAAAAATTAAATTT
159577 AATTTTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.04, T:0.43
Consensus pattern (28 bp):
AAATTAAAATTTGAAAAATTAAATTTTA
Found at i:159576 original size:20 final size:20
Alignment explanation
Indices: 159551--159590 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
159541 TTAAATTTTA
159551 AAATTTGAATTTT-AAAACTT
1 AAATTT-AATTTTGAAAACTT
159571 AAATTTAATTTTGAAAACTT
1 AAATTTAATTTTGAAAACTT
159591 TGGAGAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (20 bp):
AAATTTAATTTTGAAAACTT
Found at i:159601 original size:11 final size:11
Alignment explanation
Indices: 159585--159609 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
159575 TTAATTTTGA
159585 AAACTTTGGAG
1 AAACTTTGGAG
159596 AAACTTTGGAG
1 AAACTTTGGAG
159607 AAA
1 AAA
159610 AAATTCATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.24, T:0.24
Consensus pattern (11 bp):
AAACTTTGGAG
Found at i:159750 original size:16 final size:17
Alignment explanation
Indices: 159724--159756 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
159714 ATTTCAATCC
159724 CTTACATCATTACATAA
1 CTTACATCATTACATAA
159741 CTTA-ATCATTACATAA
1 CTTACATCATTACATAA
159757 TTTTTTCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (17 bp):
CTTACATCATTACATAA
Found at i:159861 original size:22 final size:22
Alignment explanation
Indices: 159826--159875 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
159816 GAATCTCATA
*
159826 ATTCATGACTGAAAATATCACT
1 ATTCATGACAGAAAATATCACT
* * *
159848 GTTCATGTCAGAAAATCTCACT
1 ATTCATGACAGAAAATATCACT
159870 ATTCAT
1 ATTCAT
159876 TTTTGTTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (22 bp):
ATTCATGACAGAAAATATCACT
Found at i:159943 original size:21 final size:22
Alignment explanation
Indices: 159901--159944 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
159891 AAGATAATAT
*
159901 TGCTAGAGAATCTTACTGTTCA
1 TGCTAGAGAATCTCACTGTTCA
159923 TGCTAGAGAATCTCA-TGTTCA
1 TGCTAGAGAATCTCACTGTTCA
159944 T
1 T
159945 TTTGTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (22 bp):
TGCTAGAGAATCTCACTGTTCA
Found at i:165071 original size:17 final size:17
Alignment explanation
Indices: 165046--165079 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
165036 ATCACTCGTT
* *
165046 ATTTTAATAGCATTTTC
1 ATTTCAATAACATTTTC
165063 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
165080 CATATCAACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:166227 original size:17 final size:17
Alignment explanation
Indices: 166206--166241 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
166196 TCATTCTATT
166206 TATTATTAT-TAT-A-A
1 TATTATTATGTATCATA
166220 TATTATTATGTATCATA
1 TATTATTATGTATCATA
166237 TATTA
1 TATTA
166242 CCACTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 9 0.47
15 3 0.16
16 1 0.05
17 6 0.32
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTATTATGTATCATA
Found at i:176258 original size:12 final size:12
Alignment explanation
Indices: 176225--176265 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
176215 GCAAAAAGGG
176225 AAAAATAA-AACT
1 AAAAATAATAA-T
176237 AAAAATAATAA-
1 AAAAATAATAAT
176248 AAAAATAAATAAT
1 AAAAAT-AATAAT
176261 AAAAA
1 AAAAA
176266 ATGGCTAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.23
12 13 0.50
13 7 0.27
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.17
Consensus pattern (12 bp):
AAAAATAATAAT
Found at i:179278 original size:16 final size:15
Alignment explanation
Indices: 179244--179307 Score: 51
Period size: 16 Copynumber: 4.1 Consensus size: 15
179234 TTAATTAGTA
*
179244 TAAAATATTAACAATT
1 TAAAA-ATTAAAAATT
179260 TAAAAATTTAATAAATT
1 TAAAAA-TTAA-AAATT
*
179277 AAATAAATTAAAAA-T
1 TAA-AAATTAAAAATT
179292 TAGAAAA-TAAAAATT
1 TA-AAAATTAAAAATT
179307 T
1 T
179308 CTTACTACCT
Statistics
Matches: 40, Mismatches: 3, Indels: 11
0.74 0.06 0.20
Matches are distributed among these distances:
14 6 0.15
15 8 0.20
16 13 0.32
17 10 0.25
18 3 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (15 bp):
TAAAAATTAAAAATT
Found at i:193558 original size:50 final size:50
Alignment explanation
Indices: 193472--193602 Score: 156
Period size: 50 Copynumber: 2.6 Consensus size: 50
193462 TGCATGACTT
*
193472 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AG
1 GATTT-ATGATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAG
* * * *
193524 GATTTATGATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCAT
1 GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
* *
193574 TATTTATGATGCAAACTTAACTAATCATG
1 GATTTATGATGCAAATTTAACTAA-CATG
193603 CGAGTTAATG
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 1 0.01
50 50 0.72
51 13 0.19
52 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (50 bp):
GATTTATGATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAG
Found at i:197477 original size:99 final size:98
Alignment explanation
Indices: 197298--197667 Score: 322
Period size: 99 Copynumber: 3.7 Consensus size: 98
197288 TAAAGCTAGA
* * * **
197298 AGCAGATCTCAATGTCTCTGAGGTTACAGTGGAATGGAGTGAAGCTT-TAACAGAAAAT-CT-TA
1 AGCAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAG-TTACAACACCAAATCCTATA
** * *
197360 CCTTTTTGAAGTTGCAGTGAAGCAAATTACAACAAGT
65 CC--CCTGAAGTTACAGTGAAGCAGATTA-AACAAGT
* * * * * *
197397 AGTAGATCTTAATGTCCTTGAGATTACAGTGGAATGGAGTGAAGTTACAACACCAAACCCTATAC
1 AGCAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATAC
* *
197462 CCCTGAAGTTACAGTG-GGTCAGATTAAAGCCAA-A
66 CCCTGAAGTTACAGTGAAG-CAGATTAAA--CAAGT
* * * * *
197496 AGCAAATCTCAATGTCCCTGAGGTTATAGTGGAATGTAGTGAAACTT-CAATACCAAATTCTAT-
1 AGCAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTG-AAGTTACAACACCAAATCCTATA
* * * *
197559 CTTCCTAAAGTTACAGTGAAGCGGATTAAAATAAGT
65 C-CCCTGAAGTTACAGTGAAGCAGATT-AAACAAGT
* * * *
197595 AACGGATCACAATGTCCCTGAGGTTATAGTTGAATGGAGTGAAGTTACAACACCAAATCCTATAC
1 AGCAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATAC
*
197660 CCCAGAAG
66 CCCTGAAG
197668 CCGCATGAGA
Statistics
Matches: 214, Mismatches: 44, Indels: 26
0.75 0.15 0.09
Matches are distributed among these distances:
98 12 0.06
99 184 0.86
100 14 0.07
101 4 0.02
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (98 bp):
AGCAGATCTCAATGTCCCTGAGGTTATAGTGGAATGGAGTGAAGTTACAACACCAAATCCTATAC
CCCTGAAGTTACAGTGAAGCAGATTAAACAAGT
Found at i:197611 original size:198 final size:198
Alignment explanation
Indices: 197252--197667 Score: 485
Period size: 198 Copynumber: 2.1 Consensus size: 198
197242 AATATAGAAG
* ** * * * *
197252 CAAATCCTATACCCCTGAGGTTGTAGTGGGTCGAAGTAAAGCTAGAAGCAGATCTCAATGTCTCT
1 CAAATCCTATACCCCTGAAGTTACAGTGGGTCGAAGTAAAGCCAAAAGCAAATCTCAATGTCCCT
* * * ** * *
197317 GAGGTTACAGTGGAATGGAGTGAAGCTTTAACAGAAAATCTTACCTTTTTGAAGTTGCAGTGAAG
66 GAGGTTACAGTGGAATGGAGTGAAACTTCAACACAAAATCTTACCTTCCTAAAGTTACAGTGAAG
* ** ** *
197382 CAAATTACAACAAGTAGTAGATCTTAATGTCCTTGAGATTACAGTGGAATGGAGTGAAGTTACAA
131 CAAATTAAAACAAGTAACAGATCACAATGTCCCTGAGATTACAGTGGAATGGAGTGAAGTTACAA
197447 CAC
196 CAC
* *
197450 CAAACCCTATACCCCTGAAGTTACAGTGGGTC-AGATTAAAGCCAAAAGCAAATCTCAATGTCCC
1 CAAATCCTATACCCCTGAAGTTACAGTGGGTCGA-AGTAAAGCCAAAAGCAAATCTCAATGTCCC
* * * * *
197514 TGAGGTTATAGTGGAATGTAGTGAAACTTCAATACCAAAT-TCTATCTTCCTAAAGTTACAGTGA
65 TGAGGTTACAGTGGAATGGAGTGAAACTTCAACACAAAATCT-TACCTTCCTAAAGTTACAGTGA
** * * * * *
197578 AGCGGATTAAAATAAGTAACGGATCACAATGTCCCTGAGGTTATAGTTGAATGGAGTGAAGTTAC
129 AGCAAATTAAAACAAGTAACAGATCACAATGTCCCTGAGATTACAGTGGAATGGAGTGAAGTTAC
197643 AACAC
194 AACAC
*
197648 CAAATCCTATACCCCAGAAG
1 CAAATCCTATACCCCTGAAG
197668 CCGCATGAGA
Statistics
Matches: 180, Mismatches: 36, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
197 2 0.01
198 178 0.99
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (198 bp):
CAAATCCTATACCCCTGAAGTTACAGTGGGTCGAAGTAAAGCCAAAAGCAAATCTCAATGTCCCT
GAGGTTACAGTGGAATGGAGTGAAACTTCAACACAAAATCTTACCTTCCTAAAGTTACAGTGAAG
CAAATTAAAACAAGTAACAGATCACAATGTCCCTGAGATTACAGTGGAATGGAGTGAAGTTACAA
CAC
Found at i:197739 original size:50 final size:50
Alignment explanation
Indices: 197664--197948 Score: 266
Period size: 50 Copynumber: 5.7 Consensus size: 50
197654 CTATACCCCA
* * * * *
197664 GAAGCCGCATGAGAGAATCTTATACTCCTAAAGCTGTAGAGAAACAAATT
1 GAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGAACAAATT
* * *
197714 GAAGCCGCAAGGGCGAATCTTATACTCCTAAAGCTGTAGAGAAACAGATT
1 GAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGAACAAATT
* * * ** *
197764 GAAGCCGTAAGGGCGAATCTTATACACCTAAAGCTTTGGAGGGGCACATT
1 GAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGAACAAATT
* *** * * *
197814 GAAGCTGCAAGGAAAAATATTATAC-CCTTAAAGCTATAGAGGAGCAAATT
1 GAAGCCGCAAGGGCGAATCTTATACACC-TAAAGCTGTAGAGGAACAAATT
* * * * * *
197864 GAAGCCACAAGGGTGAATCTCATACACCTAAAGCAGTAGAGGGACAAATA
1 GAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGAACAAATT
* * * * *
197914 AAAGCCGTAAAGGCGAACCTTATACCCCTAAAGCT
1 GAAGCCGCAAGGGCGAATCTTATACACCTAAAGCT
197949 ATGAAGGGAA
Statistics
Matches: 190, Mismatches: 43, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
49 2 0.01
50 186 0.98
51 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (50 bp):
GAAGCCGCAAGGGCGAATCTTATACACCTAAAGCTGTAGAGGAACAAATT
Found at i:197987 original size:150 final size:149
Alignment explanation
Indices: 197664--197989 Score: 361
Period size: 150 Copynumber: 2.2 Consensus size: 149
197654 CTATACCCCA
* * * *
197664 GAAGCCGCATGAGAGAATCTTATACTCCTAAAGCTGTAGAGAAACAAATTGAAGCCGCAAGGGCG
1 GAAGCCGCAAGAAAGAATCTTATAC-CCTAAAGCTATAGAGAAACAAATTGAAGCCACAAGGGCG
* * * * ** * *
197729 AATCTTATACTCCTAAAGCTGTAGAGAAACAGATTGAAGCCGTAAGGGCGAATCTTATACACCTA
65 AATCTCATACACCTAAAGCAGTAGAGAAACAAATAAAAGCCGTAAAGGCGAACCTTATACACCTA
* * *
197794 AAGCTTTGGAGGGGCACATT
130 AAGCTATGGAAGGGAACATT
* * * * *
197814 GAAGCTGCAAGGAAA-AATATTATACCCTTAAAGCTATAGAGGAGCAAATTGAAGCCACAAGGGT
1 GAAGCCGCAA-GAAAGAATCTTATACCC-TAAAGCTATAGAGAAACAAATTGAAGCCACAAGGGC
** *
197878 GAATCTCATACACCTAAAGCAGTAGAGGGACAAATAAAAGCCGTAAAGGCGAACCTTATACCCCT
64 GAATCTCATACACCTAAAGCAGTAGAGAAACAAATAAAAGCCGTAAAGGCGAACCTTATACACCT
*
197943 AAAGCTAT-GAAGGGAAGGATT
129 AAAGCTATGGAAGGGAA-CATT
*
197964 GAAGCCGTAA-AAATGAATCTTATACC
1 GAAGCCGCAAGAAA-GAATCTTATACC
197990 TTAGAGATGT
Statistics
Matches: 144, Mismatches: 27, Indels: 10
0.80 0.15 0.06
Matches are distributed among these distances:
148 3 0.02
149 8 0.06
150 130 0.90
151 3 0.02
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.20
Consensus pattern (149 bp):
GAAGCCGCAAGAAAGAATCTTATACCCTAAAGCTATAGAGAAACAAATTGAAGCCACAAGGGCGA
ATCTCATACACCTAAAGCAGTAGAGAAACAAATAAAAGCCGTAAAGGCGAACCTTATACACCTAA
AGCTATGGAAGGGAACATT
Found at i:198040 original size:49 final size:49
Alignment explanation
Indices: 197978--198292 Score: 249
Period size: 49 Copynumber: 6.4 Consensus size: 49
197968 CCGTAAAAAT
197978 GAATCTTATACCTTAGAGATGT-GATGGGAAAGATTGAAG-TCACAAAGGC
1 GAATCTTATACCTTAGAGATGTGGA-GGGAAAGATTGAAGCT-ACAAAGGC
* * * *
198027 GAATTTTACACCTTAGAGATGTGGAGGGAATGATTGAAGCTACAAGGGC
1 GAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCTACAAAGGC
* * * * *
198076 AAATCTTATACCCTAGAGTTGTGGAGGGAAAAATTGAAGCTGCAAAGGC
1 GAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCTACAAAGGC
* * * * * * *** * *
198125 AAATATTATACCATAAAGGTGTGGAGGGAAAGGTTGAAGCCGTAAGGGT
1 GAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCTACAAAGGC
* * * * * **
198174 GAATCTTATACCCTAGAGATGTGTAAGGAAAGATTGAAGTTGCAAAGTT
1 GAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCTACAAAGGC
* * * * * * * *
198223 GAATCTTATAACATAAAGACGTGGAGGGAAATATTAAAG-TCAGAAAGGT
1 GAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCT-ACAAAGGC
* *
198272 AAATCTTATACCTTAAAGATG
1 GAATCTTATACCTTAGAGATG
198293 AAGAAGGGCA
Statistics
Matches: 212, Mismatches: 51, Indels: 6
0.79 0.19 0.02
Matches are distributed among these distances:
48 1 0.00
49 208 0.98
50 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (49 bp):
GAATCTTATACCTTAGAGATGTGGAGGGAAAGATTGAAGCTACAAAGGC
Found at i:198122 original size:98 final size:97
Alignment explanation
Indices: 197979--198292 Score: 279
Period size: 98 Copynumber: 3.2 Consensus size: 97
197969 CGTAAAAATG
* * * * * *
197979 AATCTTATACCTTAGAGATGT-GATGGGAAAGATTGAAGTCACAAAGGCGAATTTTACACCTTAG
1 AATCTTATACCCTAGAGATGTGGA-GGGAAAGATTGAAGT-GCAAAGGCAAATATTACACCATAA
* *
198043 AGATGTGGAGGGAATGATTGAAGCTACAAGGGCA
64 AGATGTGGAGGGAAAGATTGAAGCCACAAGGGCA
* * *
198077 AATCTTATACCCTAGAGTTGTGGAGGGAAAAATTGAAGCTGCAAAGGCAAATATTATACCATAAA
1 AATCTTATACCCTAGAGATGTGGAGGGAAAGATTGAAG-TGCAAAGGCAAATATTACACCATAAA
* * ** **
198142 GGTGTGGAGGGAAAGGTTGAAGCCGTAAGGGTG
65 GATGTGGAGGGAAAGATTGAAGCCACAAGGGCA
* * *** * * *
198175 AATCTTATACCCTAGAGATGTGTAAGGAAAGATTGAAGTTGCAAAGTTGAATCTTATAACATAAA
1 AATCTTATACCCTAGAGATGTGGAGGGAAAGATTGAAG-TGCAAAGGCAAATATTACACCATAAA
* * * * * * *
198240 GACGTGGAGGGAAATATTAAAGTCAGAAAGGTA
65 GATGTGGAGGGAAAGATTGAAGCCACAAGGGCA
* *
198273 AATCTTATACCTTAAAGATG
1 AATCTTATACCCTAGAGATG
198293 AAGAAGGGCA
Statistics
Matches: 175, Mismatches: 39, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
98 172 0.98
99 3 0.02
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (97 bp):
AATCTTATACCCTAGAGATGTGGAGGGAAAGATTGAAGTGCAAAGGCAAATATTACACCATAAAG
ATGTGGAGGGAAAGATTGAAGCCACAAGGGCA
Found at i:202424 original size:17 final size:17
Alignment explanation
Indices: 202402--202434 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
202392 CCTTTTATTC
202402 TTTTAT-ATTTATTTAAG
1 TTTTATAATTT-TTTAAG
202419 TTTTATAATTTTTTAA
1 TTTTATAATTTTTTAA
202435 TTAAATCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (17 bp):
TTTTATAATTTTTTAAG
Found at i:202463 original size:15 final size:16
Alignment explanation
Indices: 202427--202462 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
202417 AGTTTTATAA
*
202427 TTTTTTAATTAAATCC
1 TTTTTAAATTAAATCC
*
202443 TTTTTAAATTTAATCC
1 TTTTTAAATTAAATCC
202459 TTTT
1 TTTT
202463 ACCGTTTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTTAAATTAAATCC
Found at i:203496 original size:2 final size:2
Alignment explanation
Indices: 203489--203514 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
203479 AGAAAGATAC
203489 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
203515 CATTAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204923 original size:60 final size:61
Alignment explanation
Indices: 204809--204930 Score: 219
Period size: 60 Copynumber: 2.0 Consensus size: 61
204799 CTATAATTTA
* *
204809 AACATAAAATATATTATGAAGCATAAAAAAATATATATTTATAATGAGAGTAGCATATAAC
1 AACATAAAATATATTATGAAACATAAAAAAATATAGATTTATAATGAGAGTAGCATATAAC
204870 AACATAAAATATATTATGAAACAT-AAAAAATATAGATTTATAATGAGAGTAGCATATAAC
1 AACATAAAATATATTATGAAACATAAAAAAATATAGATTTATAATGAGAGTAGCATATAAC
204930 A
1 A
204931 TTAAGCAACA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
60 36 0.61
61 23 0.39
ACGTcount: A:0.55, C:0.07, G:0.10, T:0.29
Consensus pattern (61 bp):
AACATAAAATATATTATGAAACATAAAAAAATATAGATTTATAATGAGAGTAGCATATAAC
Found at i:211763 original size:24 final size:23
Alignment explanation
Indices: 211714--211763 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
211704 TAAAGTAAGT
* *
211714 TATATATTATTTTTCTAATATTA
1 TATATATGATTTTTCTAATATCA
211737 TATATTATGATTTTTACTAAT-TCA
1 TATA-TATGATTTTT-CTAATATCA
211761 TAT
1 TAT
211764 TTTAATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 4 0.17
24 14 0.61
25 5 0.22
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATATATGATTTTTCTAATATCA
Found at i:211842 original size:57 final size:58
Alignment explanation
Indices: 211728--211889 Score: 177
Period size: 57 Copynumber: 2.7 Consensus size: 58
211718 TATTATTTTT
* * *
211728 CTAATATTATATATTATGATTT-TTACTAATTCATATTTTAATAATAATTATATTAAAA-ATTTA
1 CTAA-ATTATATATTAT-TTTTATTA--AATT-ATA-TTTAATAATAAATATATTAAAATA-TAA
* *
211791 CTAAATTATATATTA-TTTTATTAAATTGTATTTAATAATAAATATGTTAAAATATAA
1 CTAAATTATATATTATTTTTATTAAATTATATTTAATAATAAATATATTAAAATATAA
* *
211848 TTAAATTATTTATTATTTTTATTAAATTATATTTAATAATAA
1 CTAAATTATATATTATTTTTATTAAATTATATTTAATAATAA
211890 TCTTATTAAA
Statistics
Matches: 88, Mismatches: 8, Indels: 11
0.82 0.07 0.10
Matches are distributed among these distances:
57 35 0.40
58 28 0.32
59 4 0.05
60 3 0.03
61 3 0.03
62 11 0.12
63 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (58 bp):
CTAAATTATATATTATTTTTATTAAATTATATTTAATAATAAATATATTAAAATATAA
Found at i:211888 original size:58 final size:58
Alignment explanation
Indices: 211741--211889 Score: 178
Period size: 58 Copynumber: 2.6 Consensus size: 58
211731 ATATTATATA
* * * *
211741 TTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATTTACTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAAATATATTAAAAATTAACTAAATTAT
* * * *
211800 ATATTA-TTTTATTAAATTGTATTTAATAATAAATATGTT-AAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAATATATTAAAAAT-TAACTAAATTAT
211857 TTATTATTTTTATTAAATTATATTTAATAATAA
1 TTATTATTTTTATTAAATTATATTTAATAATAA
211890 TCTTATTAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
56 5 0.06
57 31 0.40
58 33 0.43
59 8 0.10
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAAATATATTAAAAATTAACTAAATTAT
Found at i:211899 original size:58 final size:57
Alignment explanation
Indices: 211741--211906 Score: 176
Period size: 58 Copynumber: 2.9 Consensus size: 57
211731 ATATTATATA
* * * *
211741 TTATGATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAA-ATTTACTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATT-TATTAAAATA-TAATTAAATTAT
* * * *
211800 ATATTA-TTTTATTAAATTGTATTTAATAATAAATATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAAT-AATTTATTAAAATATAATTAAATTAT
*
211857 TTATTATTTTTATTAAATTATATTTAATAATAATCTTATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TTATTAAAATATAAT
211907 AACAATAATC
Statistics
Matches: 89, Mismatches: 13, Indels: 11
0.79 0.12 0.10
Matches are distributed among these distances:
57 34 0.38
58 47 0.53
59 8 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (57 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTTATTAAAATATAATTAAATTAT
Found at i:212091 original size:16 final size:16
Alignment explanation
Indices: 212071--212117 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
212061 GATTATAGCC
212071 CTATTCCATTACAGCT
1 CTATTCCATTACAGCT
* * *
212087 GTATTCCATTAGAACT
1 CTATTCCATTACAGCT
212103 CTATTCCATTACAGC
1 CTATTCCATTACAGC
212118 GAACCAAACG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.28, C:0.28, G:0.09, T:0.36
Consensus pattern (16 bp):
CTATTCCATTACAGCT
Found at i:217197 original size:38 final size:39
Alignment explanation
Indices: 217141--217270 Score: 131
Period size: 38 Copynumber: 3.4 Consensus size: 39
217131 TCGTTTTAGA
* * * *
217141 AAACGTTCAGTAGAATCAGTGGATTCAG-TCATTTGAAT
1 AAACATTCAGTATAATCAGTGGATTCAGCTCACTTGAAC
** * *
217179 AAGTATTCAGTATAATCAGTGGATTC-GCTCGCTTGAGC
1 AAACATTCAGTATAATCAGTGGATTCAGCTCACTTGAAC
* *
217217 AAACATTCAGTATAATCAGTGGATTCA-CTCGCTTGAGC
1 AAACATTCAGTATAATCAGTGGATTCAGCTCACTTGAAC
* *
217255 AAGCATTTAGTATAAT
1 AAACATTCAGTATAAT
217271 TTGTATTCCA
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
37 1 0.01
38 77 0.99
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (39 bp):
AAACATTCAGTATAATCAGTGGATTCAGCTCACTTGAAC
Found at i:217267 original size:76 final size:76
Alignment explanation
Indices: 217127--217270 Score: 180
Period size: 76 Copynumber: 1.9 Consensus size: 76
217117 CTAGTAGTTA
* * * * * * *
217127 TCGCTCGTTTTAGAAAACGTTCAGTAGAATCAGTGGATTCAGTCATTTGAATAAGTATTCAGTAT
1 TCGCTCGCTTGAGAAAACATTCAGTAGAATCAGTGGATTCACTCACTTGAACAAGCATTCAGTAT
217192 AATCAGTGGAT
66 AATCAGTGGAT
* * * * *
217203 TCGCTCGCTTGAGCAAACATTCAGTATAATCAGTGGATTCACTCGCTTGAGCAAGCATTTAGTAT
1 TCGCTCGCTTGAGAAAACATTCAGTAGAATCAGTGGATTCACTCACTTGAACAAGCATTCAGTAT
217268 AAT
66 AAT
217271 TTGTATTCCA
Statistics
Matches: 56, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
76 56 1.00
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.33
Consensus pattern (76 bp):
TCGCTCGCTTGAGAAAACATTCAGTAGAATCAGTGGATTCACTCACTTGAACAAGCATTCAGTAT
AATCAGTGGAT
Found at i:219405 original size:14 final size:16
Alignment explanation
Indices: 219386--219422 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
219376 ACTAACTTTT
219386 AATTCAAT-AATT-AA
1 AATTCAATCAATTCAA
219400 AATTC-ATCAATTCAA
1 AATTCAATCAATTCAA
219415 AATTCAAT
1 AATTCAAT
219423 TAAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 9 0.45
15 7 0.35
16 2 0.10
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (16 bp):
AATTCAATCAATTCAA
Found at i:221272 original size:22 final size:22
Alignment explanation
Indices: 221247--221315 Score: 138
Period size: 22 Copynumber: 3.1 Consensus size: 22
221237 TGTCGGACCG
221247 CCACCGTCGTGTCGTCGCTCCT
1 CCACCGTCGTGTCGTCGCTCCT
221269 CCACCGTCGTGTCGTCGCTCCT
1 CCACCGTCGTGTCGTCGCTCCT
221291 CCACCGTCGTGTCGTCGCTCCT
1 CCACCGTCGTGTCGTCGCTCCT
221313 CCA
1 CCA
221316 TCGGCTTTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.06, C:0.46, G:0.22, T:0.26
Consensus pattern (22 bp):
CCACCGTCGTGTCGTCGCTCCT
Found at i:222686 original size:38 final size:38
Alignment explanation
Indices: 222633--222719 Score: 106
Period size: 38 Copynumber: 2.3 Consensus size: 38
222623 CTGGGTGTAA
* * * *
222633 TTGAAGAATACTTATGCTACGATAGTTTTGGATGCAAT-
1 TTGAAGAATATTTATGCAACGACAGTCTTGGATGC-ATC
*
222671 TTGAAGAATATTTATGCAACGACAGTCTTGGGTGCATC
1 TTGAAGAATATTTATGCAACGACAGTCTTGGATGCATC
222709 TTGAA-AATATT
1 TTGAAGAATATT
222720 CCTGCAACAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
37 8 0.19
38 35 0.81
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (38 bp):
TTGAAGAATATTTATGCAACGACAGTCTTGGATGCATC
Found at i:222726 original size:37 final size:37
Alignment explanation
Indices: 222671--222742 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
222661 TGGATGCAAT
* * *
222671 TTGAAGAATATTTATGCAACGACAGTCTTGGGTGCATC
1 TTGAAGAATATTCATGCAACAACAAT-TTGGGTGCATC
*
222709 TTGAA-AATATTCCTGCAACAACAATTTGGGTGCA
1 TTGAAGAATATTCATGCAACAACAATTTGGGTGCA
222743 ATTTGGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 9 0.30
37 16 0.53
38 5 0.17
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.31
Consensus pattern (37 bp):
TTGAAGAATATTCATGCAACAACAATTTGGGTGCATC
Found at i:222789 original size:37 final size:37
Alignment explanation
Indices: 222733--222804 Score: 117
Period size: 37 Copynumber: 1.9 Consensus size: 37
222723 GCAACAACAA
* * *
222733 TTTGGGTGCAATTTGGAAGTGCTCATGCAGCGACAGT
1 TTTGGGTGCAATCTAGAAGTGCTCAAGCAGCGACAGT
222770 TTTGGGTGCAATCTAGAAGTGCTCAAGCAGCGACA
1 TTTGGGTGCAATCTAGAAGTGCTCAAGCAGCGACA
222805 TTAGTAGTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (37 bp):
TTTGGGTGCAATCTAGAAGTGCTCAAGCAGCGACAGT
Found at i:227196 original size:37 final size:37
Alignment explanation
Indices: 227137--227213 Score: 118
Period size: 37 Copynumber: 2.1 Consensus size: 37
227127 TCCTGTGGTG
* * *
227137 ACAGTTTTGGGTGTAATCTAGAAGTGCTCATGCGGCA
1 ACAGTTTTGAGTGCAATCTAGAAGTGCTCATGCAGCA
*
227174 ACAGTTTTGAGTGCAATGTAGAAGTGCTCATGCAGCA
1 ACAGTTTTGAGTGCAATCTAGAAGTGCTCATGCAGCA
227211 ACA
1 ACA
227214 TTAGTAGTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (37 bp):
ACAGTTTTGAGTGCAATCTAGAAGTGCTCATGCAGCA
Found at i:231120 original size:103 final size:102
Alignment explanation
Indices: 230941--231250 Score: 478
Period size: 103 Copynumber: 3.0 Consensus size: 102
230931 AAATTAAAAC
* *
230941 CCAATCATTGGATTTTTGCTCAGTACGATTAATTGAACGTCAAATAGGA-ATTTTTCTCCAATAT
1 CCAATCATTGGATTTTTGCTCAGAACGATTAATTGAACTTCAAATA--ACATTTTTCTCCAATAT
*
231005 TCGGTTTTTCAAACTCACCATGATATATGTTTATGGAAT
64 TCGATTTTTCAAACTCACCATGATATATGTTTATGGAAT
* *
231044 CCAATCATTGGATTTTTGCTCAGCACGATTAATTGAACTTCAAATAACATTTTTTCTCTAATATT
1 CCAATCATTGGATTTTTGCTCAGAACGATTAATTGAACTTCAAATAACA-TTTTTCTCCAATATT
231109 CGATTTTTCAAACTCACCATGATATATGTTTATGGAAT
65 CGATTTTTCAAACTCACCATGATATATGTTTATGGAAT
* * * * *
231147 CCAATCATTGGACTTTTGCTTAGAATGATTAATTGAACTTCAAATAGCCAATTTTCTCCAATATT
1 CCAATCATTGGATTTTTGCTCAGAACGATTAATTGAACTTCAAATA-ACATTTTTCTCCAATATT
*
231212 CAATTTTTCAAACTCACCATGATATATGTTTATGGAAT
65 CGATTTTTCAAACTCACCATGATATATGTTTATGGAAT
231250 C
1 C
231251 AACATTTTTA
Statistics
Matches: 192, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
101 1 0.01
102 1 0.01
103 188 0.98
104 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.39
Consensus pattern (102 bp):
CCAATCATTGGATTTTTGCTCAGAACGATTAATTGAACTTCAAATAACATTTTTCTCCAATATTC
GATTTTTCAAACTCACCATGATATATGTTTATGGAAT
Found at i:235222 original size:37 final size:37
Alignment explanation
Indices: 235172--235245 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
235162 TTGGCTTTTC
235172 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
1 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
235209 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
1 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
235246 TGCATCCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (37 bp):
GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
Found at i:237741 original size:28 final size:28
Alignment explanation
Indices: 237710--237806 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
237700 AGCCCAGAAT
*
237710 AGAATAATGCTCTTTCCAAGCCAGTACC
1 AGAATAATGCTCTTTCCAAGCCAGAACC
* ** * *
237738 AGAATATTGCTCTTTCTGAGCCAGGATC
1 AGAATAATGCTCTTTCCAAGCCAGAACC
* **
237766 AGAAT-ATCACTCTTTCCAAGCCAGAAGT
1 AGAATAAT-GCTCTTTCCAAGCCAGAACC
237794 AGAATAATGCTCT
1 AGAATAATGCTCT
237807 ACCCAAGTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.02
28 51 0.94
29 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (28 bp):
AGAATAATGCTCTTTCCAAGCCAGAACC
Found at i:237812 original size:28 final size:28
Alignment explanation
Indices: 237788--237986 Score: 91
Period size: 28 Copynumber: 7.1 Consensus size: 28
237778 TTTCCAAGCC
* *
237788 AGAAGTAGAATAATGCTCTACCCAAGTA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
* * ** * * *
237816 AG-ATTCAGAGTAACACTCTTCTCGAGCC
1 AGAAGT-AGAATAATGCTCTACCCGAGCA
* *
237844 AGATGTAGAATAATGCTTTACCCGAGCA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
** * * * *
237872 AGATTTA-AAGTGACGCTCTACTCGAGCT
1 AGAAGTAGAA-TAATGCTCTACCCGAGCA
* *
237900 AGATGTAGAATAATGCTCTAACCGAGCA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
* * * *
237928 AGATACT-GAGTAATGCTCTTCCCAAGCCA
1 AGA-AGTAGAATAATGCTCTACCCGAG-CA
* * **
237957 A-ATGTAGAATAATGCTTTACTTGAGCA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
237984 AGA
1 AGA
237987 TTCAGATTAT
Statistics
Matches: 119, Mismatches: 44, Indels: 16
0.66 0.25 0.09
Matches are distributed among these distances:
27 8 0.07
28 104 0.87
29 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (28 bp):
AGAAGTAGAATAATGCTCTACCCGAGCA
Found at i:237824 original size:56 final size:56
Alignment explanation
Indices: 237764--237992 Score: 176
Period size: 56 Copynumber: 4.1 Consensus size: 56
237754 TGAGCCAGGA
* *
237764 TCAGAATATCACTCTT-TCCAAGCCAGAAGTAGAATAATGCTCTACCCAAGTAAGAT
1 TCAGAATAACACTCTTCT-CAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
* * * * *
237820 TCAGAGTAACACTCTTCTCGAGCCAGATGTAGAATAATGCTTTACCCGAGCAAGAT
1 TCAGAATAACACTCTTCTCAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
* * * * * * * * *
237876 TTA-AAGTGACGCTCTACTCGAGCTAGATGTAGAATAATGCTCTAACCGAGCAAGAT
1 TCAGAA-TAACACTCTTCTCAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
* * * ** * * ***
237932 ACTGAGTAATGCTCTTCCCAAGCCA-AATGTAGAATAATGCTTTACTTGAGCAAGAT
1 TCAGAATAACACTCTTCTCAAGCCAGAA-GTAGAATAATGCTCTACCCAAGCAAGAT
237988 TCAGA
1 TCAGA
237993 TTATCGCTTT
Statistics
Matches: 137, Mismatches: 32, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
55 2 0.01
56 133 0.97
57 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (56 bp):
TCAGAATAACACTCTTCTCAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
Found at i:244927 original size:20 final size:21
Alignment explanation
Indices: 244891--244929 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
244881 ATTTTTGTTA
*
244891 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTACTTGTTTCACT
244912 TTTACTTTT-CTTGTTTCA
1 TTTACTTTTACTTGTTTCA
244930 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTACTTTTACTTGTTTCACT
Found at i:249849 original size:37 final size:37
Alignment explanation
Indices: 249799--249872 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
249789 TTGGCTTTTC
249799 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
1 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
249836 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
1 GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
249873 TGCATCCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.19, G:0.08, T:0.43
Consensus pattern (37 bp):
GACAGATTAAATTTCTTCTTCAACATTTTTTCAAGCT
Found at i:252368 original size:28 final size:28
Alignment explanation
Indices: 252337--252433 Score: 97
Period size: 28 Copynumber: 3.5 Consensus size: 28
252327 AGCCCAGAAT
*
252337 AGAATAATGCTCTTTCCAAGCCAGTACC
1 AGAATAATGCTCTTTCCAAGCCAGAACC
* ** * *
252365 AGAATATTGCTCTTTCTGAGCCAGGATC
1 AGAATAATGCTCTTTCCAAGCCAGAACC
* **
252393 AGAAT-ATCACTCTTTCCAAGCCAGAAGT
1 AGAATAAT-GCTCTTTCCAAGCCAGAACC
252421 AGAATAATGCTCT
1 AGAATAATGCTCT
252434 ACCCAAGTAA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.02
28 51 0.94
29 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (28 bp):
AGAATAATGCTCTTTCCAAGCCAGAACC
Found at i:252439 original size:28 final size:28
Alignment explanation
Indices: 252415--252613 Score: 91
Period size: 28 Copynumber: 7.1 Consensus size: 28
252405 TTTCCAAGCC
* *
252415 AGAAGTAGAATAATGCTCTACCCAAGTA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
* * ** * * *
252443 AG-ATTCAGAGTAACACTCTTCTCGAGCC
1 AGAAGT-AGAATAATGCTCTACCCGAGCA
* *
252471 AGATGTAGAATAATGCTTTACCCGAGCA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
** * * * *
252499 AGATTTA-AAGTGACGCTCTACTCGAGCT
1 AGAAGTAGAA-TAATGCTCTACCCGAGCA
* *
252527 AGATGTAGAATAATGCTCTAACCGAGCA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
* * * *
252555 AGATACT-GAGTAATGCTCTTCCCAAGCCA
1 AGA-AGTAGAATAATGCTCTACCCGAG-CA
* * **
252584 A-ATGTAGAATAATGCTTTACTTGAGCA
1 AGAAGTAGAATAATGCTCTACCCGAGCA
252611 AGA
1 AGA
252614 TTCAGATTAT
Statistics
Matches: 119, Mismatches: 44, Indels: 16
0.66 0.25 0.09
Matches are distributed among these distances:
27 8 0.07
28 104 0.87
29 7 0.06
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (28 bp):
AGAAGTAGAATAATGCTCTACCCGAGCA
Found at i:252451 original size:56 final size:56
Alignment explanation
Indices: 252391--252619 Score: 176
Period size: 56 Copynumber: 4.1 Consensus size: 56
252381 TGAGCCAGGA
* *
252391 TCAGAATATCACTCTT-TCCAAGCCAGAAGTAGAATAATGCTCTACCCAAGTAAGAT
1 TCAGAATAACACTCTTCT-CAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
* * * * *
252447 TCAGAGTAACACTCTTCTCGAGCCAGATGTAGAATAATGCTTTACCCGAGCAAGAT
1 TCAGAATAACACTCTTCTCAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
* * * * * * * * *
252503 TTA-AAGTGACGCTCTACTCGAGCTAGATGTAGAATAATGCTCTAACCGAGCAAGAT
1 TCAGAA-TAACACTCTTCTCAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
* * * ** * * ***
252559 ACTGAGTAATGCTCTTCCCAAGCCA-AATGTAGAATAATGCTTTACTTGAGCAAGAT
1 TCAGAATAACACTCTTCTCAAGCCAGAA-GTAGAATAATGCTCTACCCAAGCAAGAT
252615 TCAGA
1 TCAGA
252620 TTATCGCTTT
Statistics
Matches: 137, Mismatches: 32, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
55 2 0.01
56 133 0.97
57 2 0.01
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.26
Consensus pattern (56 bp):
TCAGAATAACACTCTTCTCAAGCCAGAAGTAGAATAATGCTCTACCCAAGCAAGAT
Found at i:259554 original size:20 final size:21
Alignment explanation
Indices: 259518--259556 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
259508 ATTTTTGTTA
*
259518 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTACTTGTTTCACT
259539 TTTACTTTT-CTTGTTTCA
1 TTTACTTTTACTTGTTTCA
259557 AATTCCTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.15, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTACTTTTACTTGTTTCACT
Found at i:268816 original size:2 final size:2
Alignment explanation
Indices: 268809--268834 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
268799 AAGTAATTTC
268809 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
268835 CATTTAACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:270617 original size:24 final size:24
Alignment explanation
Indices: 270585--270803 Score: 260
Period size: 24 Copynumber: 9.1 Consensus size: 24
270575 GCAAGTTTAT
* * *
270585 TACGTTTACACTCATTAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* * * *
270609 TACGTTTACGCTTGCCAGTAGGAA
1 TACGTTTACGCTCGTCAGCATGAA
* **
270633 TACGTTTATGCTCACCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
270657 TACGTTTACGCTCGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
*
270681 TACGTTTACACTCGTCAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* * *
270705 TACATTTACTCTCGTTAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
* *
270729 TACATTTACACTCG-CTAGCATGAA
1 TACGTTTACGCTCGTC-AGCATGAA
*
270753 TACGTTTACGCTCGTCAGTATGAA
1 TACGTTTACGCTCGTCAGCATGAA
*
270777 TACGTTTACGCTCGTTAGCATGAA
1 TACGTTTACGCTCGTCAGCATGAA
270801 TAC
1 TAC
270804 AAGAAACATT
Statistics
Matches: 167, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
24 166 0.99
25 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (24 bp):
TACGTTTACGCTCGTCAGCATGAA
Found at i:271829 original size:21 final size:20
Alignment explanation
Indices: 271791--271829 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
271781 TTTCATAGCT
* *
271791 TCAAAATCTAACACTTTCTA
1 TCAAAATCAAACAATTTCTA
271811 TCAAAATTCAAACAATTTC
1 TCAAAA-TCAAACAATTTC
271830 ACTCTAAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.44, C:0.23, G:0.00, T:0.33
Consensus pattern (20 bp):
TCAAAATCAAACAATTTCTA
Found at i:290701 original size:16 final size:16
Alignment explanation
Indices: 290676--290706 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
290666 TTGCATACTT
290676 AGGATAATTTGCATTA
1 AGGATAATTTGCATTA
*
290692 AGGATCATTTGCATT
1 AGGATAATTTGCATT
290707 TAGTTTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (16 bp):
AGGATAATTTGCATTA
Found at i:293610 original size:30 final size:30
Alignment explanation
Indices: 293576--293636 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
293566 TTATTTAGGT
293576 GATTGTCCTACTTTACCTGTGATTATTCTA
1 GATTGTCCTACTTTACCTGTGATTATTCTA
293606 GATTGTCCTACTTTACCTGTGATTATTCTA
1 GATTGTCCTACTTTACCTGTGATTATTCTA
293636 G
1 G
293637 TAGAACTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.20, G:0.15, T:0.46
Consensus pattern (30 bp):
GATTGTCCTACTTTACCTGTGATTATTCTA
Found at i:293837 original size:14 final size:14
Alignment explanation
Indices: 293818--293850 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
293808 ATCCTATTAT
293818 GAAAGAAATTGTGA
1 GAAAGAAATTGTGA
293832 GAAAGAAATTGTGA
1 GAAAGAAATTGTGA
293846 GAAAG
1 GAAAG
293851 GAAGTGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.30, T:0.18
Consensus pattern (14 bp):
GAAAGAAATTGTGA
Found at i:300668 original size:18 final size:16
Alignment explanation
Indices: 300645--300691 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
300635 TTGTAGTTGC
300645 AATTTTTTTTCTTACTT
1 AATTTTTTTTCTTAC-T
300662 AACTTTTTATTT-TTACT
1 AA-TTTTT-TTTCTTACT
*
300679 AATTTGTTTTCTT
1 AATTTTTTTTCTT
300692 TCTTTTGATT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
15 3 0.12
16 6 0.23
17 5 0.19
18 9 0.35
19 3 0.12
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (16 bp):
AATTTTTTTTCTTACT
Found at i:310781 original size:17 final size:18
Alignment explanation
Indices: 310750--310785 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
310740 AATTTAGTTT
310750 TCATTGCATTTTTATTTG
1 TCATTGCATTTTTATTTG
310768 TCATTGCA-TTTTATTTG
1 TCATTGCATTTTTATTTG
310785 T
1 T
310786 TAGCGCATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (18 bp):
TCATTGCATTTTTATTTG
Done.