Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012289.1 Kokia drynarioides strain JFW-HI SEQ_127290, 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: 49256
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 10 characters in sequence are not A, C, G, or T
Found at i:3801 original size:39 final size:40
Alignment explanation
Indices: 3748--3827 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
3738 AAGAGGTATG
* *
3748 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTAACTCTTCAAAAGGTGTCCA
* *
3788 TCCAATTTG-AAAGGGTTGTAACTCTTCAAAAGGTGTCCA
1 TCCAATATGAAAAGGATTGTAACTCTTCAAAAGGTGTCCA
3827 T
1 T
3828 TGAGTGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTAACTCTTCAAAAGGTGTCCA
Found at i:8668 original size:39 final size:40
Alignment explanation
Indices: 8624--8717 Score: 99
Period size: 39 Copynumber: 2.4 Consensus size: 40
8614 TGGGACAAGT
8624 CTCTTCCAAGA-G-GT-ATGTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTGTCAT-TCCAATATGAAAAGG-TTGTGA
* * *
8663 CTCTT-CAATAGGTGTCATTCCAATTTGAAACGGTTGTGA
1 CTCTTCCAAGAGGTGTCATTCCAATATGAAAAGGTTGTGA
*
8702 CTCTT-CAAAAGGTGTC
1 CTCTTCCAAGAGGTGTC
8718 CATTAAGTGC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
38 4 0.08
39 27 0.56
40 15 0.31
41 2 0.04
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (40 bp):
CTCTTCCAAGAGGTGTCATTCCAATATGAAAAGGTTGTGA
Found at i:8686 original size:40 final size:39
Alignment explanation
Indices: 8641--8717 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
8631 AAGAGGTATG
*
8641 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCAT
1 TCCAATATGAAAAGG-TTGTGACTCTTCAAAAGGTGTCAT
* *
8681 TCCAATTTGAAACGGTTGTGACTCTTCAAAAGGTGTC
1 TCCAATATGAAAAGGTTGTGACTCTTCAAAAGGTGTC
8718 CATTAAGTGC
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 21 0.62
40 13 0.38
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (39 bp):
TCCAATATGAAAAGGTTGTGACTCTTCAAAAGGTGTCAT
Found at i:10209 original size:15 final size:15
Alignment explanation
Indices: 10189--10244 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
10179 TTGAACTACT
10189 GGAGACTCAACAATG
1 GGAGACTCAACAATG
*
10204 GGAGACTCAATAATG
1 GGAGACTCAACAATG
* **
10219 GGAGATTCAATTATG
1 GGAGACTCAACAATG
10234 GGAGACTCAAC
1 GGAGACTCAAC
10245 TAGGGGACTA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.38, C:0.16, G:0.27, T:0.20
Consensus pattern (15 bp):
GGAGACTCAACAATG
Found at i:10251 original size:15 final size:15
Alignment explanation
Indices: 10189--10251 Score: 74
Period size: 15 Copynumber: 4.2 Consensus size: 15
10179 TTGAACTACT
*
10189 GGAGACTCAACAATG
1 GGAGACTCAACTATG
10204 GGAGACTCAA-TAATG
1 GGAGACTCAACT-ATG
* *
10219 GGAGATTCAATTATG
1 GGAGACTCAACTATG
*
10234 GGAGACTCAACTAGG
1 GGAGACTCAACTATG
10249 GGA
1 GGA
10252 CTACTTGCTG
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 40 0.98
16 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.30, T:0.19
Consensus pattern (15 bp):
GGAGACTCAACTATG
Found at i:10833 original size:23 final size:22
Alignment explanation
Indices: 10807--10923 Score: 94
Period size: 23 Copynumber: 5.1 Consensus size: 22
10797 GTAAGCAAAT
10807 ACAGTGCAATCCAGTAGGCACAC
1 ACAGTGCAAT-CAGTAGGCACAC
*
10830 ACAGTGCAATCAGTAGGCGCAC
1 ACAGTGCAATCAGTAGGCACAC
* *
10852 ATAGCGCAAATCAGTAGGCACAC
1 ACAGTGC-AATCAGTAGGCACAC
* * *
10875 GA-GGTGCGAAACAGTAAGCACAC
1 -ACAGTGC-AATCAGTAGGCACAC
* *
10898 GA-AGTGCGAAACAGTAAGCACAC
1 -ACAGTGC-AATCAGTAGGCACAC
10921 ACA
1 ACA
10924 ATGCTGAACA
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
22 17 0.21
23 63 0.78
24 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.25, T:0.11
Consensus pattern (22 bp):
ACAGTGCAATCAGTAGGCACAC
Found at i:10933 original size:23 final size:23
Alignment explanation
Indices: 10863--10939 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
10853 TAGCGCAAAT
* **
10863 CAGTAGGCACACGAGGTGCGAAA
1 CAGTAAGCACACGAAATGCGAAA
*
10886 CAGTAAGCACACGAAGTGCGAAA
1 CAGTAAGCACACGAAATGCGAAA
10909 CAGTAAGCACAC-ACAATGCTG-AA
1 CAGTAAGCACACGA-AATGC-GAAA
10932 CAGTAAGC
1 CAGTAAGC
10940 GCGCTAGCGT
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
22 1 0.02
23 47 0.96
24 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.10
Consensus pattern (23 bp):
CAGTAAGCACACGAAATGCGAAA
Found at i:15679 original size:24 final size:23
Alignment explanation
Indices: 15652--15711 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
15642 ACAAACATCT
*
15652 TTTTTTTTTTACA-AATTTTAATCA
1 TTTTTTTTTTACATAA-GTTAAT-A
*
15676 TTTTATTTTTTCCATAAGTTAATA
1 TTTT-TTTTTTACATAAGTTAATA
15700 TTTTTATTTTTA
1 TTTTT-TTTTTA
15712 TTTTTGTGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
23 1 0.03
24 14 0.47
25 13 0.43
26 2 0.07
ACGTcount: A:0.27, C:0.07, G:0.02, T:0.65
Consensus pattern (23 bp):
TTTTTTTTTTACATAAGTTAATA
Found at i:15679 original size:25 final size:24
Alignment explanation
Indices: 15651--15711 Score: 61
Period size: 25 Copynumber: 2.5 Consensus size: 24
15641 AACAAACATC
*
15651 TTTTTTTTTTTACA-AATTTTAATCA
1 TTTTTTTTTTTACATAA-GTTAAT-A
* *
15676 TTTTATTTTTTCCATAAGTTAATA
1 TTTTTTTTTTTACATAAGTTAATA
*
15700 TTTTTATTTTTA
1 TTTTTTTTTTTA
15712 TTTTTGTGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 10 0.34
25 17 0.59
26 2 0.07
ACGTcount: A:0.26, C:0.07, G:0.02, T:0.66
Consensus pattern (24 bp):
TTTTTTTTTTTACATAAGTTAATA
Found at i:15863 original size:13 final size:14
Alignment explanation
Indices: 15839--15871 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
15829 GAGTTTTAGT
15839 TTCAAGATTTAAGG
1 TTCAAGATTTAAGG
15853 TTCAAG-TTTAAGG
1 TTCAAGATTTAAGG
*
15866 CTCAAG
1 TTCAAG
15872 GGTTTGAGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (14 bp):
TTCAAGATTTAAGG
Found at i:15939 original size:22 final size:22
Alignment explanation
Indices: 15914--15955 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
15904 AAGTTATGAC
15914 TTTGGGGTTT-AGAGTTTAAGGG
1 TTTGGGGTTTGAGA-TTTAAGGG
15936 TTTGGGGTTTGAGATTTAAG
1 TTTGGGGTTTGAGATTTAAG
15956 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.19, C:0.00, G:0.38, T:0.43
Consensus pattern (22 bp):
TTTGGGGTTTGAGATTTAAGGG
Found at i:16427 original size:17 final size:17
Alignment explanation
Indices: 16405--16457 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
16395 AATATCAAAG
16405 TAAAAGAAAAAAGATAA
1 TAAAAGAAAAAAGATAA
*
16422 TAAAAG--ACAA-AT--
1 TAAAAGAAAAAAGATAA
*
16434 TTAAAGAAAAAAGATAA
1 TAAAAGAAAAAAGATAA
16451 TAAAAGA
1 TAAAAGA
16458 CAAATTTAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 10
0.66 0.10 0.24
Matches are distributed among these distances:
12 5 0.19
14 5 0.19
15 5 0.19
17 12 0.44
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (17 bp):
TAAAAGAAAAAAGATAA
Found at i:16473 original size:29 final size:29
Alignment explanation
Indices: 16407--16466 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
16397 TATCAAAGTA
16407 AAAGAAAAAAGATAATAAAAGACAAATTT
1 AAAGAAAAAAGATAATAAAAGACAAATTT
16436 AAAGAAAAAAGATAATAAAAGACAAATTT
1 AAAGAAAAAAGATAATAAAAGACAAATTT
16465 AA
1 AA
16467 CTCAAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.70, C:0.03, G:0.10, T:0.17
Consensus pattern (29 bp):
AAAGAAAAAAGATAATAAAAGACAAATTT
Found at i:16781 original size:22 final size:23
Alignment explanation
Indices: 16756--16798 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
16746 TCTCATTATA
*
16756 TAAA-ATTATTTGCGTTTTTTTC
1 TAAAGATTATTTGCATTTTTTTC
*
16778 TAAAGTTTATTTGCATTTTTT
1 TAAAGATTATTTGCATTTTTT
16799 AAAATTGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.23, C:0.07, G:0.09, T:0.60
Consensus pattern (23 bp):
TAAAGATTATTTGCATTTTTTTC
Found at i:23912 original size:19 final size:19
Alignment explanation
Indices: 23879--23926 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
23869 AAAAATAAAA
*
23879 ATAAAAATAAATAAAAGTT
1 ATAAAAATTAATAAAAGTT
* **
23898 ATAAAAATTATTAAATTTT
1 ATAAAAATTAATAAAAGTT
*
23917 TTAAAAATTA
1 ATAAAAATTA
23927 GAAAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
ATAAAAATTAATAAAAGTT
Found at i:24190 original size:18 final size:17
Alignment explanation
Indices: 24149--24192 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
24139 TTTTAGTACA
24149 ATAATTTTTATATTTTT
1 ATAATTTTTATATTTTT
*
24166 ACGAATTTTTATATATTTT
1 A-TAATTTTTATAT-TTTT
24185 ATAATTTT
1 ATAATTTT
24193 ATAAATTTCC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 1 0.04
18 17 0.74
19 5 0.22
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (17 bp):
ATAATTTTTATATTTTT
Found at i:25592 original size:16 final size:16
Alignment explanation
Indices: 25571--25602 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
25561 CTTAATCCTT
*
25571 AGTTTAATATTTCTAG
1 AGTTTAATATTACTAG
25587 AGTTTAATATTACTAG
1 AGTTTAATATTACTAG
25603 GCAATTAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.47
Consensus pattern (16 bp):
AGTTTAATATTACTAG
Found at i:26828 original size:19 final size:20
Alignment explanation
Indices: 26789--26828 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
26779 AAATTTTTAC
26789 AACTAAACTTCACCTTAAAT
1 AACTAAACTTCACCTTAAAT
* *
26809 AACTTAACTT-ACCTTTAAT
1 AACTAAACTTCACCTTAAAT
26828 A
1 A
26829 GTTTTTAGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (20 bp):
AACTAAACTTCACCTTAAAT
Found at i:27026 original size:23 final size:22
Alignment explanation
Indices: 26961--27028 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
26951 TGCACTAATG
* *
26961 AACGTAGAGTACAAATGTGCTA
1 AACGGAGAGCACAAATGTGCTA
*
26983 GACGGAGAGCACAAATGTGCTA
1 AACGGAGAGCACAAATGTGCTA
*
27005 AACGGAGAGCACTAAATATGCTA
1 AACGGAGAGCAC-AAATGTGCTA
27028 A
1 A
27029 TAAATGGAGA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.41, C:0.16, G:0.25, T:0.18
Consensus pattern (22 bp):
AACGGAGAGCACAAATGTGCTA
Found at i:29515 original size:25 final size:25
Alignment explanation
Indices: 29487--29538 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
29477 GATGCCAAAG
29487 TATGTAAAATTTTTAAAGGAGCTGT
1 TATGTAAAATTTTTAAAGGAGCTGT
*
29512 TATGTAAAATTTTTAAAGGAGTTGT
1 TATGTAAAATTTTTAAAGGAGCTGT
29537 TA
1 TA
29539 ATAAATGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.37, C:0.02, G:0.19, T:0.42
Consensus pattern (25 bp):
TATGTAAAATTTTTAAAGGAGCTGT
Found at i:29977 original size:93 final size:92
Alignment explanation
Indices: 29872--30277 Score: 353
Period size: 93 Copynumber: 4.4 Consensus size: 92
29862 TATTTGAAGT
* * * *
29872 TTCAGTCCACTCCATTGTATCTTTAGGGACGTTGAGCTCTACTTCGTTGTTTTAATCCAACCCAC
1 TTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTC-ACTTCGTTGTTTTAATCCAACCCAC
*
29937 TGTAACTCAGGGGTATAGAATTTGGTAC
65 TGCAACTCAGGGGTATAGAATTTGGTAC
* * *
29965 TTCACTCCACTCCACTGTAACCTTAGGGACGTTGAG---A-TTCGTTTTATTTCGATCC-ACTTC
1 TTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCACTTCGTTGT-TTT-AATCCAAC-CC
* * * * *
30025 TCTGTACCTCACTAGGAAG-ATGGAATTTGAAGT-C
63 ACTGCAACT--C-AGG-GGTATAGAATTTG--GTAC
* * * *
30059 -TCACTCAACT-CACTGTAACCTCAGGGACGTTGAGCTCAGCTTCATTGTTTTAATCTAACCCAC
1 TTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCA-CTTCGTTGTTTTAATCCAACCCAC
* ** * *
30122 TACAACTTTGGGGTAAAGGATTTGGTAC
65 TGCAACTCAGGGGTATAGAATTTGGTAC
* * **
30150 TTCATTCCACTCCACTGTAACCTTAGGGACGTTGAACTCTACTTCGTTGTTTTAATCTGACCCAC
1 TTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTC-ACTTCGTTGTTTTAATCCAACCCAC
** * *
30215 TGCAACTCAATGGTATAGGATTTGATAC
65 TGCAACTCAGGGGTATAGAATTTGGTAC
* *
30243 TTCACTCCACTCCACTGTAACCTCAGGGATGTTGA
1 TTCACTCCACTCCACTGTAACCTTAGGGACGTTGA
30278 AATCTGTTTT
Statistics
Matches: 249, Mismatches: 44, Indels: 40
0.75 0.13 0.12
Matches are distributed among these distances:
88 7 0.03
89 6 0.02
90 14 0.06
91 2 0.01
92 41 0.16
93 153 0.61
94 3 0.01
95 12 0.05
96 5 0.02
97 6 0.02
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (92 bp):
TTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCACTTCGTTGTTTTAATCCAACCCACT
GCAACTCAGGGGTATAGAATTTGGTAC
Found at i:30496 original size:42 final size:41
Alignment explanation
Indices: 30419--30837 Score: 311
Period size: 42 Copynumber: 10.5 Consensus size: 41
30409 TTGATTTAGA
* * * *
30419 GGTAAAAGATTAGATGGTGGCTTCAATATGCCCCATGATCAG
1 GGTAAGAGATTGGATGAT-GCTTCAATCTGCCCCATGATCAG
* * *
30461 GGTAAGAGATTGGACGATGTCTTTAATCTGTCCCATGATC-G
1 GGTAAGAGATTGGATGATG-CTTCAATCTGCCCCATGATCAG
* * *
30502 AGGTAAAAAATTGGATGATGACTTCAATCTGCCTCATGATC-G
1 -GGTAAGAGATTGGATGATG-CTTCAATCTGCCCCATGATCAG
* *
30544 AGGTAAGAGATTGGACGAATG---CAATCTGCCCCATGATCGG
1 -GGTAAGAGATTGGATG-ATGCTTCAATCTGCCCCATGATCAG
*
30584 GGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGATTAG
1 GGTAAGAGATTGGATGATG-CTTCAATCTGCCCCATGATCAG
* * * * *
30626 GGTAAAAGATT-G--GATGCTTTAATTTGCCTCATGATCGG
1 GGTAAGAGATTGGATGATGCTTCAATCTGCCCCATGATCAG
* ** *
30664 GGTAAGAGATTGG-TG-TGTCTTCAATCTTCATTC-TGATTAG
1 GGTAAGAGATTGGATGATG-CTTCAATCTGC-CCCATGATCAG
* * *
30704 GGTAA-AGATT-G--GATGCTTTAATCTACCCCATGATCGG
1 GGTAAGAGATTGGATGATGCTTCAATCTGCCCCATGATCAG
*** *
30741 GGTAAGAGATTGG-TG-TGTCTTCAATCTGCCTTTTGATTAG
1 GGTAAGAGATTGGATGATG-CTTCAATCTGCCCCATGATCAG
* * *
30781 GGTAAAAGACT--A-GATGCTTCAATCTACCCCATGATCAG
1 GGTAAGAGATTGGATGATGCTTCAATCTGCCCCATGATCAG
*
30819 GGTAAGAGATTGAATGATG
1 GGTAAGAGATTGGATGATG
30838 ATGTAGCTTC
Statistics
Matches: 298, Mismatches: 56, Indels: 47
0.74 0.14 0.12
Matches are distributed among these distances:
36 1 0.00
37 20 0.07
38 65 0.22
39 48 0.16
40 46 0.15
41 9 0.03
42 106 0.36
43 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (41 bp):
GGTAAGAGATTGGATGATGCTTCAATCTGCCCCATGATCAG
Found at i:30737 original size:77 final size:77
Alignment explanation
Indices: 30476--30830 Score: 372
Period size: 77 Copynumber: 4.5 Consensus size: 77
30466 GAGATTGGAC
** * * * * *
30476 GATGTCTTTAATCTGTCCCATGATCGAGGTAAAAAATTGGATGATGACTTCAATCTGCCTCATGA
1 GATG-CTTTAATCTACCCCATGATCGGGGTAAGAGATTGG-TG-TGTCTTCAATCTGCTTC-TGA
* *
30541 -TCGAGGTAAGAGATTG
62 TTAG-GGTAAAAGATTG
* * ** * **
30557 GACGAATGCAATCTGCCCCATGATCGGGGTAAGAGATTGGATGATGTCTTCAATCTGCCCCATGA
1 GATG-CTTTAATCTACCCCATGATCGGGGTAAGAGATTGG-TG-TGTCTTCAATCTGCTTC-TGA
30622 TTAGGGTAAAAGATTG
62 TTAGGGTAAAAGATTG
* * * *
30638 GATGCTTTAATTTGCCTCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTTCATTCTGATTA
1 GATGCTTTAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGC-TTCTGATTA
30703 GGGT-AAAGATTG
65 GGGTAAAAGATTG
*
30715 GATGCTTTAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCTTTTGATTA
1 GATGCTTTAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTG-CTTCTGATTA
* *
30780 GGGTAAAAGACTA
65 GGGTAAAAGATTG
* *
30793 GATGCTTCAATCTACCCCATGATCAGGGTAAGAGATTG
1 GATGCTTTAATCTACCCCATGATCGGGGTAAGAGATTG
30831 AATGATGATG
Statistics
Matches: 239, Mismatches: 31, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
77 70 0.29
78 66 0.28
79 3 0.01
80 30 0.13
81 68 0.28
82 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (77 bp):
GATGCTTTAATCTACCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCTTCTGATTAG
GGTAAAAGATTG
Found at i:31187 original size:49 final size:49
Alignment explanation
Indices: 31133--31373 Score: 170
Period size: 50 Copynumber: 4.9 Consensus size: 49
31123 GGTATAAGGT
* *
31133 TTGCCGTTGCGGCCTTAACCTTTCCCTTTATAT-TTCCATGGTACTAGA
1 TTGCCGTTGCGGCCTTAACCTTTCCCTTCATATCTTCCATGGTACAAGA
* * * * * *
31181 TCTGCCGTTGCGGCCTTGATCC-TTCCCGTCACATCTTCTAAGGTACAAGG
1 T-TGCCGTTGCGGCCTT-AACCTTTCCCTTCATATCTTCCATGGTACAAGA
* *
31231 TTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTT-CATGGTACCTA-A
1 TT-GCCGTTGCGGCCTTAACCTTTCCCTTCATATCTTCCATGGTA-CAAGA
* * * * * * * *
31280 TTCGCCGCTACGGCCTCAATCC-TTCCCATCATATCTTCTAAGGTATAAGG
1 TT-GCCGTTGCGGCCTTAA-CCTTTCCCTTCATATCTTCCATGGTACAAGA
** * * *
31330 TTCGCTATTACGGCCTCAACCTTTTCCTTCATATCTT-CATGGTA
1 TT-GCCGTTGCGGCCTTAACCTTTCCCTTCATATCTTCCATGGTA
31374 TCGGATTCAC
Statistics
Matches: 152, Mismatches: 31, Indels: 19
0.75 0.15 0.09
Matches are distributed among these distances:
48 1 0.01
49 72 0.47
50 79 0.52
ACGTcount: A:0.18, C:0.31, G:0.16, T:0.35
Consensus pattern (49 bp):
TTGCCGTTGCGGCCTTAACCTTTCCCTTCATATCTTCCATGGTACAAGA
Found at i:31246 original size:50 final size:50
Alignment explanation
Indices: 31116--32017 Score: 253
Period size: 49 Copynumber: 18.2 Consensus size: 50
31106 TTCCATCATG
* * *
31116 CTTCTAAGGTATAAGGTTTGCCGTTGCGGCCTTAACCTTTCCCTTTATAT
1 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * * * * *
31166 -TTCCATGGTACTA-GATCTGCCGTTGCGGCCTTGATCC-TTCCCGTCACAT
1 CTTCTAAGGTACAAGGTTC-GCCGTTGCGGCCTT-AACCTTTCCCTTCATAT
*
31215 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATAT
1 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * * *
31265 CTTC-ATGGTACCTAA--TTCGCCGCTACGGCCTCAATCC-TTCCCATCATAT
1 CTTCTAAGGTA-C-AAGGTTCGCCGTTGCGGCCTTAA-CCTTTCCCTTCATAT
* ** * * *
31314 CTTCTAAGGTATAAGGTTCGCTATTACGGCCTCAACCTTTTCCTTCATAT
1 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * ** * * * *
31364 CTTC-ATGGTATC--GGATTCACCACTGCAGCCTCAATCC-TTCCCATCACAT
1 CTTCTAAGGTA-CAAGG-TTCGCCGTTGCGGCCTTAA-CCTTTCCCTTCATAT
* ** * * *
31413 CTTCTAAGGTACAAGTTTTACCGTTACGGCCTCAACCTTTTCCTTTC-TAT
1 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTAACC-TTTCCCTTCATAT
* * ** * * * * *
31463 CTTC-ATGGTATTGAA--TTCGCTATTACGACCTCAATCC-TTCCCATCACAT
1 CTTCTAAGGTA--CAAGGTTCGCCGTTGCGGCCTTAA-CCTTTCCCTTCATAT
* * * * * *
31512 TTTCTAAGGTAC-CGAGTTCGTCGTTACGACCTCAACCTTTCCCTTCATAT
1 CTTCTAAGGTACAAG-GTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* ** * * * *
31562 CTTC-ATA-GTATC--GGATTCGTCGCCGCGGCCTCAATCTTTCCCATCACAT
1 CTTCTA-AGGTA-CAAGG-TTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * *
31611 CTTCTAAGGTATC-GGGTTCACGGTTGC-GACTTAACCTTTCCCTTCATAT
1 CTTCTAAGGTA-CAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * * ** * * *
31660 ATGC-ATGGTACCAA-ATTCGTTGTTGCGGCCTAAATCC-TTCCCATCACAT
1 CTTCTAAGGTA-CAAGGTTCGCCGTTGCGGCCTTAA-CCTTTCCCTTCATAT
** * ** **
31709 CTTCTAAGGTATTAGGTTCTCTATTATGGCCTTAACCTTTCCCTTCATAT
1 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * * * * *
31759 CGT-TATGGTACCGAA--TTCACCGTTACGGCCTCAATCC-TTCCCATCACAT
1 CTTCTAAGGTA-C-AAGGTTCGCCGTTGCGGCCTTAA-CCTTTCCCTTCATAT
* * ** * *
31808 ATTCTAAGGTATC-AGATTCATCGTTACGACCTTAACCTTTCCCTTCATAT
1 CTTCTAAGGTA-CAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * * * * * ** *
31858 CTTC-ATGGTA-TAGGATTCGTCGTTACGACCTCAA-TTATTCCCAACACAT
1 CTTCTAAGGTACAAGG-TTCGCCGTTGCGGCCTTAACCT-TTCCCTTCATAT
* * * * * *
31907 CTTCTAAGGTAC-CGAGTTTGCCGTTGCGACCTCAACCTTTCCCATCATTT
1 CTTCTAAGGTACAAG-GTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
* * * * * *
31957 CTTC-ATGGTAC-CGGATTCGCCATTGCGGCCTCAATCC-TTCCCATCACAT
1 CTTCTAAGGTACAAGG-TTCGCCGTTGCGGCCTTAA-CCTTTCCCTTCATAT
32006 CTT-TCAAGGTAC
1 CTTCT-AAGGTAC
32018 TGAGTTAGCC
Statistics
Matches: 635, Mismatches: 158, Indels: 118
0.70 0.17 0.13
Matches are distributed among these distances:
48 32 0.05
49 316 0.50
50 268 0.42
51 19 0.03
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (50 bp):
CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTTAACCTTTCCCTTCATAT
Found at i:31294 original size:99 final size:98
Alignment explanation
Indices: 31116--32042 Score: 833
Period size: 99 Copynumber: 9.4 Consensus size: 98
31106 TTCCATCATG
* * * * * *
31116 CTTCTAAGGTATAAGGTTTGCCGTTGCGGCCTTAACCTTTCCCTTTATAT-TTCCATGGTA-CTA
1 CTTCTAAGGTA-CAGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTT-CATGGTACCGA
** *
31179 GA-TCTGCCGTTGCGGCCTTGATCCTTCCCGTCACAT
64 -ATTC-GCCGTTGCGGCCTCAATCCTTCCCATCACAT
* *
31215 CTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCTAA
1 CTTCTAAGGTAC-AGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAA
* * *
31280 TTCGCCGCTACGGCCTCAATCCTTCCCATCATAT
65 TTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* ** * * *
31314 CTTCTAAGGTATAAGGTTCGCTATTACGGCCTCAACCTTTTCCTTCATATCTTCATGGTATCGGA
1 CTTCTAAGGTA-CAGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAA
* ** *
31379 TTCACCACTGCAGCCTCAATCCTTCCCATCACAT
65 TTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* ** * **
31413 CTTCTAAGGTACAAGTTTTACCGTTACGGCCTCAACCTTTTCCTTTC-TATCTTCATGGTATTGA
1 CTTCTAAGGTAC-AGGTTCGCCGTTACGGCCTCAACC-TTTCCCTTCATATCTTCATGGTACCGA
** * *
31477 ATTCGCTATTACGACCTCAATCCTTCCCATCACAT
64 ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * * * * * *
31512 TTTCTAAGGTACCGAGTTCGTCGTTACGACCTCAACCTTTCCCTTCATATCTTCATAGTATCGGA
1 CTTCTAAGGTACAG-GTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAA
* ** *
31577 TTCGTCGCCGCGGCCTCAATCTTTCCCATCACAT
65 TTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * * * * * * * *
31611 CTTCTAAGGTATCGGGTTCACGGTTGC-GACTTAACCTTTCCCTTCATATATGCATGGTACCAAA
1 CTTCTAAGGTA-CAGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAA
** *
31675 TTCGTTGTTGCGGCCTAAATCCTTCCCATCACAT
65 TTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * ** * *
31709 CTTCTAAGGTATTAGGTTCTCTATTATGGCCTTAACCTTTCCCTTCATATCGTT-ATGGTACCGA
1 CTTCTAAGGTA-CAGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATC-TTCATGGTACCGA
* *
31773 ATTCACCGTTACGGCCTCAATCCTTCCCATCACAT
64 ATTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * ** * * ** *
31808 ATTCTAAGGTATCAGATTCATCGTTACGACCTTAACCTTTCCCTTCATATCTTCATGGTATAGGA
1 CTTCTAAGGTA-CAGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAA
* * * ** *
31873 TTCGTCGTTACGACCTCAATTATTCCCAACACAT
65 TTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * * * * * *
31907 CTTCTAAGGTACCGAGTTTGCCGTTGCGACCTCAACCTTTCCCATCATTTCTTCATGGTACCGGA
1 CTTCTAAGGTACAG-GTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAA
*
31972 TTCGCCATTGCGGCCTCAATCCTTCCCATCACAT
65 TTCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
* * * *
32006 CTT-TCAAGGTACTGAGTTAGCCATTGCGGCCTCAACC
1 CTTCT-AAGGTACAG-GTTCGCCGTTACGGCCTCAACC
32043 CCCTTCAAAC
Statistics
Matches: 678, Mismatches: 135, Indels: 30
0.80 0.16 0.04
Matches are distributed among these distances:
98 91 0.13
99 570 0.84
100 17 0.03
ACGTcount: A:0.21, C:0.30, G:0.15, T:0.34
Consensus pattern (98 bp):
CTTCTAAGGTACAGGTTCGCCGTTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAAT
TCGCCGTTGCGGCCTCAATCCTTCCCATCACAT
Found at i:31861 original size:395 final size:396
Alignment explanation
Indices: 31190--32017 Score: 1067
Period size: 395 Copynumber: 2.1 Consensus size: 396
31180 ATCTGCCGTT
** * * *
31190 GCGGCCTTGATCCTTCCCGTCACATCTTCTAAGGTACAAGGTTCGCCGTTGCGGCCTCAACCTTT
1 GCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTCACCGTTGCGGACTCAACCTTT
* * * * *
31255 CCCTTCATATCTTCATGGTACCTAATTCGCCGCTACGGCCTCAATCCTTCCCATCATATCTTCTA
66 CCCTTCATATATGCATGGTACCAAATTCGCCGCTACGGCCTAAATCCTTCCCATCACATCTTCTA
* * *
31320 AGGTATAAGGTTCGCTATTACGGCCTCAACCTTTTCCTTCATATCTTCATGGTATCGGATTCACC
131 AGGTATAAGGTTCGCTATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCACC
* * * * *
31385 ACTGCAGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGTTTTACCGTTACGGCCTCAACC
196 ACTACAGCCTCAATCCTTCCCATCACATATTCTAAGGTACAAGATTCACCGTTACGACCTCAACC
* * * * *
31450 TTTTCCTTTCTATCTTCATGGTATTGAATTCG-CTATTACGACCTCAATCCTTCCCATCACATTT
261 TTTTCCCTTCTATCTTCATGGTATAGAATTCGTC-ATTACGACCTCAATCATTCCCAACACATCT
* * *
31514 TCTAAGGTACCGAGTTCGTCGTTACGACCTCAACCTTTCCCTTCATATCTTCATAGTATCGGATT
325 TCTAAGGTACCGAGTTCGCCGTTACGACCTCAACCTTTCCCATCATATCTTCATAGTACCGGATT
* *
31579 CGTCGCC
390 CGCCACC
* * * *
31586 GCGGCCTCAATCTTTCCCATCACATCTTCTAAGGTATC-GGGTTCACGGTTGC-GACTTAACCTT
1 GCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTA-CAAGGTTCACCGTTGCGGACTCAACCTT
** * *
31649 TCCCTTCATATATGCATGGTACCAAATTCGTTGTTGCGGCCTAAATCCTTCCCATCACATCTTCT
65 TCCCTTCATATATGCATGGTACCAAATTCGCCGCTACGGCCTAAATCCTTCCCATCACATCTTCT
* * * *
31714 AAGGTATTAGGTTCTCTATTATGGCCTTAACCTTTCCCTTCATATCGTT-ATGGTACCGAATTCA
130 AAGGTATAAGGTTCGCTATTACGGCCTCAACCTTTCCCTTCATATC-TTCATGGTACCGAATTCA
** * * *
31778 CCGTTACGGCCTCAATCCTTCCCATCACATATTCTAAGGTATC-AGATTCATCGTTACGACCTTA
194 CCACTACAGCCTCAATCCTTCCCATCACATATTCTAAGGTA-CAAGATTCACCGTTACGACCTCA
* * *
31842 ACC-TTTCCCTTCATATCTTCATGGTATAGGATTCGTCGTTACGACCTCAATTATTCCCAACACA
258 ACCTTTTCCCTTC-TATCTTCATGGTATAGAATTCGTCATTACGACCTCAATCATTCCCAACACA
* * * *
31906 TCTTCTAAGGTACCGAGTTTGCCGTTGCGACCTCAACCTTTCCCATCATTTCTTCATGGTACCGG
322 TCTTCTAAGGTACCGAGTTCGCCGTTACGACCTCAACCTTTCCCATCATATCTTCATAGTACCGG
**
31971 ATTCGCCATT
387 ATTCGCCACC
31981 GCGGCCTCAATCCTTCCCATCACATCTT-TCAAGGTAC
1 GCGGCCTCAATCCTTCCCATCACATCTTCT-AAGGTAC
32018 TGAGTTAGCC
Statistics
Matches: 371, Mismatches: 55, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
394 10 0.03
395 313 0.84
396 47 0.13
397 1 0.00
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (396 bp):
GCGGCCTCAATCCTTCCCATCACATCTTCTAAGGTACAAGGTTCACCGTTGCGGACTCAACCTTT
CCCTTCATATATGCATGGTACCAAATTCGCCGCTACGGCCTAAATCCTTCCCATCACATCTTCTA
AGGTATAAGGTTCGCTATTACGGCCTCAACCTTTCCCTTCATATCTTCATGGTACCGAATTCACC
ACTACAGCCTCAATCCTTCCCATCACATATTCTAAGGTACAAGATTCACCGTTACGACCTCAACC
TTTTCCCTTCTATCTTCATGGTATAGAATTCGTCATTACGACCTCAATCATTCCCAACACATCTT
CTAAGGTACCGAGTTCGCCGTTACGACCTCAACCTTTCCCATCATATCTTCATAGTACCGGATTC
GCCACC
Found at i:33244 original size:16 final size:16
Alignment explanation
Indices: 33225--33255 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
33215 GTTTTAACCC
*
33225 TTTTTTGTTTGTTTTA
1 TTTTTTGTTTATTTTA
33241 TTTTTTGTTTATTTT
1 TTTTTTGTTTATTTT
33256 TTATATATAC
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:0.06, C:0.00, G:0.10, T:0.84
Consensus pattern (16 bp):
TTTTTTGTTTATTTTA
Found at i:34582 original size:73 final size:74
Alignment explanation
Indices: 34500--34692 Score: 196
Period size: 75 Copynumber: 2.6 Consensus size: 74
34490 ACTCACATGA
* * *
34500 TCTGACACACGCTCGTGTGTCCAGCCCGTGTAACTCACTATTTCTCATTCCAT-AAAACAGCA-T
1 TCTGGCACACGCCCGTGTGTCCAGCCCGTGTAACTCACTATTTCTAATTCCATAAAAACAG-AGT
*
34563 -GTCCACACGG
65 GGT-CACAAGG
* * * * * *
34573 TCTGGCACACGCCCATGTGTCCAACTCATGTAACTCATTGTTTCTAATTCCATGAAAAACAGAGT
1 TCTGGCACACGCCCGTGTGTCCAGCCCGTGTAACTCACTATTTCTAATTCCAT-AAAAACAGAGT
34638 GGTCACAAGG
65 GGTCACAAGG
* * * *
34648 TCTAGCACACACCCGTGTG-CCTAGACTGTGTAACTCACTATTTCT
1 TCTGGCACACGCCCGTGTGTCC-AGCCCGTGTAACTCACTATTTCT
34693 GATTATGCCT
Statistics
Matches: 95, Mismatches: 20, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
73 44 0.46
74 3 0.03
75 46 0.48
76 2 0.02
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (74 bp):
TCTGGCACACGCCCGTGTGTCCAGCCCGTGTAACTCACTATTTCTAATTCCATAAAAACAGAGTG
GTCACAAGG
Found at i:42549 original size:12 final size:12
Alignment explanation
Indices: 42532--42569 Score: 62
Period size: 11 Copynumber: 3.3 Consensus size: 12
42522 TTTATTACTT
42532 AAAAAATTGAAA
1 AAAAAATTGAAA
42544 AAAAAATTG-AA
1 AAAAAATTGAAA
42555 AAAAAATT-AAA
1 AAAAAATTGAAA
42566 AAAA
1 AAAA
42570 CTGGTCCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (12 bp):
AAAAAATTGAAA
Found at i:42944 original size:17 final size:17
Alignment explanation
Indices: 42913--42972 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
42903 AACCAAAGTT
*
42913 ATTTCATTTAGTTTTATA
1 ATTT-ATTTATTTTTATA
42931 ATTTATTTATTTTTAT-
1 ATTTATTTATTTTTATA
* *
42947 TTTTGTTTCATTTTTA-A
1 ATTTATTT-ATTTTTATA
42964 ATTTTATTT
1 A-TTTATTT
42973 TATTATGCAC
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
16 6 0.18
17 18 0.53
18 10 0.29
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTATTTATTTTTATA
Found at i:44913 original size:37 final size:37
Alignment explanation
Indices: 44843--44919 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
44833 TTACAACCAA
* *
44843 TTAAGACTTATACCCCAAAGTCTTAATGGACAACACC
1 TTAAGACTTATACCCCAAAGTCCTAATGAACAACACC
*
44880 TTAAGACTTATACCCCAAAGTCCTAA-GAAACAACTCC
1 TTAAGACTTATACCCCAAAGTCCTAATG-AACAACACC
44917 TTA
1 TTA
44920 TGGTTTCTAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 1 0.03
37 35 0.97
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.25
Consensus pattern (37 bp):
TTAAGACTTATACCCCAAAGTCCTAATGAACAACACC
Found at i:46208 original size:55 final size:55
Alignment explanation
Indices: 46149--46265 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 55
46139 GCAATTTGAC
* * * *
46149 CCACACGACCTTAGTGTGTTACACGGTCTGGATACATGATCGTGTGACTCTAGTT
1 CCACACGACCTCAGTGTGTTACACAGTCTAGATACATGATCGTGTGACTCCAGTT
* * *
46204 CCACATGACCTCAGTGTGTTACACAGTCTAGATACATGTTCGTGTGTCTCCAGTT
1 CCACACGACCTCAGTGTGTTACACAGTCTAGATACATGATCGTGTGACTCCAGTT
*
46259 CTACACG
1 CCACACG
46266 GTTACAGCTT
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.22, C:0.26, G:0.21, T:0.31
Consensus pattern (55 bp):
CCACACGACCTCAGTGTGTTACACAGTCTAGATACATGATCGTGTGACTCCAGTT
Found at i:47001 original size:22 final size:22
Alignment explanation
Indices: 46976--47019 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
46966 CATCGACCGG
46976 TTTTCAATTTAATAT-TTTAATA
1 TTTT-AATTTAATATCTTTAATA
*
46998 TTTTAATTTAATGTCTTTAATA
1 TTTTAATTTAATATCTTTAATA
47020 ATTATTTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAATTTAATATCTTTAATA
Found at i:47532 original size:31 final size:30
Alignment explanation
Indices: 47497--47578 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
47487 TTTTCTTGTT
* * *
47497 TAACTTTTAAGAGATCCAAAATATTTTTTAC
1 TAACTTTTAAGGGATCCAAAAAATTTTCT-C
* * *
47528 TAACTTTTGAGGGGTCTAAAAAATTTTCTC
1 TAACTTTTAAGGGATCCAAAAAATTTTCTC
*
47558 GAACTTTTAAGGGATCCAAAA
1 TAACTTTTAAGGGATCCAAAA
47579 CTTTAATTTA
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
30 18 0.44
31 23 0.56
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (30 bp):
TAACTTTTAAGGGATCCAAAAAATTTTCTC
Done.