Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014248.1 Corchorus capsularis cultivar CVL-1 contig14269, 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: 125933
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:6426 original size:2 final size:2
Alignment explanation
Indices: 6413--6463 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
6403 TAAGTTCCCT
* *
6413 TC TC TG TC TC TC TC TC TC TC TG TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6455 TC TC TC TC T
1 TC TC TC TC T
6464 TCCCTGTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.45, G:0.04, T:0.51
Consensus pattern (2 bp):
TC
Found at i:8809 original size:34 final size:32
Alignment explanation
Indices: 8710--8809 Score: 85
Period size: 34 Copynumber: 3.0 Consensus size: 32
8700 AAAAAAAAGA
* *
8710 AAAAAAAGTTTATACATTATATATATAATATAG
1 AAAAAAAG-ATATACATTATATATATAATATAC
* * * *
8743 AAAAAGACATAATAACA-GAGTATACATAATATAC
1 AAAAAAAGAT-AT-ACATTA-TATATATAATATAC
8777 AAAAAAAGAGTATACATTATATATATATATATA
1 AAAAAAAGA-TATACATTATATATATA-ATATA
8810 TACATAGGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 11
0.71 0.14 0.15
Matches are distributed among these distances:
32 1 0.02
33 19 0.37
34 30 0.59
35 1 0.02
ACGTcount: A:0.57, C:0.06, G:0.07, T:0.30
Consensus pattern (32 bp):
AAAAAAAGATATACATTATATATATAATATAC
Found at i:9485 original size:11 final size:11
Alignment explanation
Indices: 9469--9493 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
9459 AGCAACATCT
9469 AGTCTAAATTC
1 AGTCTAAATTC
9480 AGTCTAAATTC
1 AGTCTAAATTC
9491 AGT
1 AGT
9494 GAGGATCAAT
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:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (11 bp):
AGTCTAAATTC
Found at i:11034 original size:50 final size:51
Alignment explanation
Indices: 10827--11071 Score: 180
Period size: 51 Copynumber: 4.9 Consensus size: 51
10817 AATCTGGTAC
* * * * * *
10827 AAAATTTAAGCTTTTAAGTAATTTGTATATAGAGATTGAATTTTTAAGT-A
1 AAAATTAAATCTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTGA
* * * * * *
10877 AAAGATTGAATTTTTAAAATGATTTGTAAATAAA-AGTGGGA-TTTTAATT-A
1 AAA-ATTAAATCTTTAAAGTAATTTGTAAATAAAGA-TTGAATTTTTAATTGA
* * * * * *
10927 GAAGA-TGAATCATTCAAGTAATTTGTAAATAGAGA-TGAACTTTTAATTGA
1 -AAAATTAAATCTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTGA
* * * * *
10977 AAGATTAAA-CTTTTATGTAATTTGTAAATAAAGATTGAGTTTTTAGTTGA
1 AAAATTAAATCTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTGA
* * *
11027 AAAATTAAATCTTTAAAGTAATTTGTGAATATAGATTGATTTTTT
1 AAAATTAAATCTTTAAAGTAATTTGTAAATAAAGATTGAATTTTT
11072 TTAAGTAACC
Statistics
Matches: 152, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
48 2 0.01
49 55 0.36
50 38 0.25
51 57 0.38
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.42
Consensus pattern (51 bp):
AAAATTAAATCTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTGA
Found at i:11046 original size:100 final size:100
Alignment explanation
Indices: 10827--11062 Score: 226
Period size: 100 Copynumber: 2.4 Consensus size: 100
10817 AATCTGGTAC
* * * * * * *
10827 AAAATTTAAGCTTTTAAGTAATTTGTATATAGAGATTGAATTTTTAAGTAAAAGATTGAATTTTT
1 AAAATTAAATCTTTAAAGTAATTTGTAAATAGAGA-TGAACTTTTAAGTAAAAGATTAAACTTTT
* *
10892 AAAATGATTTGTAAATAAAAGTGGGATTTTAATTAG
65 AAAATAATTTGTAAATAAAAGTGAGATTTTAATTAG
* * * * * *
10928 AAGA-TGAATCATTCAAGTAATTTGTAAATAGAGATGAACTTTTAATTGAAAGATTAAACTTTT-
1 AAAATTAAATCTTTAAAGTAATTTGTAAATAGAGATGAACTTTTAAGTAAAAGATTAAACTTTTA
** * * *
10991 ATGTAATTTGTAAATAAAGATTGAGTTTTTAGTT-G
66 AAATAATTTGTAAATAAA-AGTGAGATTTTAATTAG
* *
11026 AAAAATTAAATCTTTAAAGTAATTTGTGAATATAGAT
1 -AAAATTAAATCTTTAAAGTAATTTGTAAATAGAGAT
11063 TGATTTTTTT
Statistics
Matches: 108, Mismatches: 24, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
98 16 0.15
99 38 0.35
100 51 0.47
101 3 0.03
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (100 bp):
AAAATTAAATCTTTAAAGTAATTTGTAAATAGAGATGAACTTTTAAGTAAAAGATTAAACTTTTA
AAATAATTTGTAAATAAAAGTGAGATTTTAATTAG
Found at i:11071 original size:51 final size:50
Alignment explanation
Indices: 10827--11071 Score: 167
Period size: 49 Copynumber: 4.9 Consensus size: 50
10817 AATCTGGTAC
* * * * * *
10827 AAAATTTAAGCTTTTAAGTAATTTGTATATAGAGATTGAATTTTTAAGT-
1 AAAAATTAAACTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTG
** * * * *
10876 AAAAGATTGAATTTTTAAAATGATTTGTAAATAAA-AGTGGGA-TTTTAATT-
1 AAAA-ATT-AAACTTTAAAGTAATTTGTAAATAAAGA-TTGAATTTTTAATTG
* * * * * * *
10926 AGAAGATGAATCATTCAAGTAATTTGTAAATAGAGA-TGAACTTTTAATTG
1 A-AAAATTAAACTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTG
* * * * *
10976 AAAGATTAAACTTTTATGTAATTTGTAAATAAAGATTGAGTTTTTAGTTG
1 AAAAATTAAACTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTG
* * *
11026 AAAAATTAAATCTTTAAAGTAATTTGTGAATATAGATTGATTTTTT
1 AAAAATTAAA-CTTTAAAGTAATTTGTAAATAAAGATTGAATTTTT
11072 TTAAGTAACC
Statistics
Matches: 151, Mismatches: 36, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
48 2 0.01
49 60 0.40
50 35 0.23
51 54 0.36
ACGTcount: A:0.41, C:0.02, G:0.15, T:0.42
Consensus pattern (50 bp):
AAAAATTAAACTTTAAAGTAATTTGTAAATAAAGATTGAATTTTTAATTG
Found at i:11728 original size:35 final size:35
Alignment explanation
Indices: 11631--12267 Score: 544
Period size: 35 Copynumber: 18.8 Consensus size: 35
11621 TGGATCATAA
*
11631 TAAGCAACTTAATTCAGGGTAA-T---TAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
11662 TAAGTAACTTAATTCAGGGTAATT-A--AA-TCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
**
11693 TAAGTAACTTAATTCAGGGTAATTAAGGGAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* **
11728 TTAGTGGCTTAATTCAGGGTAATTAAGTAAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * * *
11763 TTAGTAACTTAACTCAGGATAATTAAGTCAGTCAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
11798 TAATTAACTTAAGTT-AGGGTAATTAAGTAATTCAA
1 TAAGTAACTTAA-TTCAGGGTAATTAAGTAAGTCAG
* * * * * *
11833 TTATTAATTTAATTCAGGGTAATTAAGAAATTTAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
11868 TAATTATCTTAATTCAGGGTAATTAAG-CAG---G
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
11899 TAA-TCAACTTAATTCAGGGTAATTAAGAAATTTAG
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAG
* * * *
11934 TAATTATCTTAATTCAGGGTAA-T---TAAGCCTG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
11965 TAA-TCAACTTAATTCAGGGTAATTAAGTAAGTCGG
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAG
* *
12000 TAATTAACTTAATTCAGGGTAATTAAGTAAGTCGG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
*
12035 TAA-TCAACTTAATTCAGGGTAATTAAGTAAGTCGG
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAG
* **
12070 TAA-TCAACTTAATTCAAGGTAATTAAGT--GTTTG
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAG
*
12103 TAA-TCGACTTAATTCAGGGTAATTAAGTAAGTC--
1 TAAGT-AACTTAATTCAGGGTAATTAAGTAAGTCAG
* * *
12136 --AGCAACTTAATTCAGGGTAATTAAGTGAGACAG
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
* * * *
12169 TAA-TCAACTTTAATTCAGGGTAATTAAGTGATTTAA
1 TAAGT-AAC-TTAATTCAGGGTAATTAAGTAAGTCAG
* * *
12205 TGAGTAATTTAATTCAGGGTAATTAAGT-AGTTCAA
1 TAAGTAACTTAATTCAGGGTAATTAAGTAAG-TCAG
12240 TAAAG-AACTTAATTCAGGGTAATTAAGT
1 T-AAGTAACTTAATTCAGGGTAATTAAGT
12268 TTAGTAAGAA
Statistics
Matches: 511, Mismatches: 62, Indels: 62
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.00
31 122 0.24
32 6 0.01
33 29 0.06
34 7 0.01
35 312 0.61
36 32 0.06
37 1 0.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (35 bp):
TAAGTAACTTAATTCAGGGTAATTAAGTAAGTCAG
Found at i:18648 original size:34 final size:35
Alignment explanation
Indices: 18569--18654 Score: 122
Period size: 34 Copynumber: 2.5 Consensus size: 35
18559 CATTCAGTTG
*
18569 ATTGACCCAGGGCGGTCTCCATTCAGTAAATTTCA
1 ATTGACCCAGGGCGGTCTCCATTCAATAAATTTCA
* *
18604 TTTGATCCAGGGCGGTCTCTC-TTCAAT-AATTTCA
1 ATTGACCCAGGGCGGTCTC-CATTCAATAAATTTCA
18638 ATTGACCCAGGGCGGTC
1 ATTGACCCAGGGCGGTC
18655 CTTCTTTAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
34 22 0.49
35 22 0.49
36 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (35 bp):
ATTGACCCAGGGCGGTCTCCATTCAATAAATTTCA
Found at i:18847 original size:36 final size:36
Alignment explanation
Indices: 18783--18876 Score: 118
Period size: 36 Copynumber: 2.6 Consensus size: 36
18773 CAATTGACCC
* * *
18783 AGGGTGGTCTTTCTTCAGTTCGAG-TCGGAATGATCG
1 AGGGCGGTCGTTCTTCAGTT-TAGTTCGGAATGATCG
* *
18819 AGGGCGGTTGTTCTTTAGTTTAGTTCGGAATGATCG
1 AGGGCGGTCGTTCTTCAGTTTAGTTCGGAATGATCG
*
18855 AGGGTGGTCGTTCTTCAGTTTA
1 AGGGCGGTCGTTCTTCAGTTTA
18877 TTTTAGTTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 2 0.04
36 47 0.96
ACGTcount: A:0.16, C:0.14, G:0.33, T:0.37
Consensus pattern (36 bp):
AGGGCGGTCGTTCTTCAGTTTAGTTCGGAATGATCG
Found at i:18939 original size:107 final size:107
Alignment explanation
Indices: 18779--18981 Score: 252
Period size: 107 Copynumber: 1.9 Consensus size: 107
18769 ATTTCAATTG
* * **
18779 ACCCAGGGTGGTCTTTCTTCAGTTCGAGTCGGAATGATCGAGGGCGGTTGTTCTT-TAGTTTAGT
1 ACCCAGGGTGGTATTTCTTCAGTTCGAGTCGGAATGATCGAGGGCGGTCGTTCTTCT-GTCCAGT
* *
18843 TCGGAATGAT-CGAGGGTGGTCGTTCTTCAGTTTATTTTAGTTA
65 TCGAAATGATCCG-GGGTGGCCGTTCTTCAGTTTATTTTAGTTA
* * *
18886 ACCCAGGGTGGTATTTCTTCAATTTTC-A-TCGGAGTGATCGAGGGTGGTCGTTCTTCTGTCCAG
1 ACCCAGGGTGGTATTTCTTC-A-GTTCGAGTCGGAATGATCGAGGGCGGTCGTTCTTCTGTCCAG
*
18949 TTCGAAATGATCCGGGGTGGCCTTTCTTCAGTT
64 TTCGAAATGATCCGGGGTGGCCGTTCTTCAGTT
18982 ACTTACTATA
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
107 74 0.90
108 5 0.06
109 3 0.04
ACGTcount: A:0.16, C:0.18, G:0.29, T:0.37
Consensus pattern (107 bp):
ACCCAGGGTGGTATTTCTTCAGTTCGAGTCGGAATGATCGAGGGCGGTCGTTCTTCTGTCCAGTT
CGAAATGATCCGGGGTGGCCGTTCTTCAGTTTATTTTAGTTA
Found at i:20305 original size:11 final size:11
Alignment explanation
Indices: 20289--20313 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
20279 AGCAACATCT
20289 AGTCTAAATTC
1 AGTCTAAATTC
20300 AGTCTAAATTC
1 AGTCTAAATTC
20311 AGT
1 AGT
20314 AAGGATCAAT
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:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (11 bp):
AGTCTAAATTC
Found at i:21717 original size:19 final size:20
Alignment explanation
Indices: 21685--21731 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
21675 GCTTTTAAGT
*
21685 AATTTGTATAT-AAAGATTG
1 AATTTTTATATAAAAGATTG
*
21704 AATTTTTATGTAAAAGATTG
1 AATTTTTATATAAAAGATTG
21724 AATTTTTA
1 AATTTTTA
21732 AAGTGATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (20 bp):
AATTTTTATATAAAAGATTG
Found at i:21794 original size:49 final size:48
Alignment explanation
Indices: 21676--21901 Score: 172
Period size: 49 Copynumber: 4.5 Consensus size: 48
21666 AAAATTTAAG
* * *
21676 CTTTTAAGTAATTTGTATATAAAGATTGAATTTTTATGTAAAAGATTGAAT
1 CTTTTAAGTAATTTGTAAATAAAGA-TGAATTTTAAT-TAGAAGA-TGAAT
* *
21727 -TTTTAAAGTGATTTGTAAATAAA-AGTGGGATTTTAATTAGAAGATGAAT
1 CTTTT-AAGTAATTTGTAAATAAAGA-T-GAATTTTAATTAGAAGATGAAT
* * * *
21776 CTTTCAAGTAATTTGTAAATAGAGATGAACTTTTAATT-GAAAGATTAAG
1 CTTTTAAGTAATTTGTAAATAAAGATGAA-TTTTAATTAG-AAGATGAAT
* * * * *
21825 CTTTTAAGTAATTTATAAATAAAGATTGAGTTTTTAGTT-GAAAAATTAAAT
1 CTTTTAAGTAATTTGTAAATAAAGA-TGA-ATTTTAATTAG-AAGA-TGAAT
* *
21876 CTTTAAAGTAATTTGTGAATAAAGAT
1 CTTTTAAGTAATTTGTAAATAAAGAT
21902 TGATCTTTTT
Statistics
Matches: 143, Mismatches: 23, Indels: 19
0.77 0.12 0.10
Matches are distributed among these distances:
48 3 0.02
49 59 0.41
50 32 0.22
51 49 0.34
ACGTcount: A:0.41, C:0.03, G:0.15, T:0.41
Consensus pattern (48 bp):
CTTTTAAGTAATTTGTAAATAAAGATGAATTTTAATTAGAAGATGAAT
Found at i:21919 original size:33 final size:35
Alignment explanation
Indices: 21881--21946 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
21871 TAAATCTTTA
* *
21881 AAGTAA-TTTGTGAATAAAGATT-GATCTTTTTTT
1 AAGTAACTTTGTAAATAAAGATTAAATCTTTTTTT
21914 AAGTAACTTTTGTAAATAAAGATTAAATCTTTT
1 AAGTAAC-TTTGTAAATAAAGATTAAATCTTTT
21947 AAGTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 6 0.21
35 15 0.54
36 7 0.25
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (35 bp):
AAGTAACTTTGTAAATAAAGATTAAATCTTTTTTT
Found at i:21947 original size:33 final size:31
Alignment explanation
Indices: 21869--21952 Score: 89
Period size: 33 Copynumber: 2.6 Consensus size: 31
21859 TAGTTGAAAA
* *
21869 ATTAAATCTTTAAAGTAATTTGTGAATAAAG
1 ATTAAATCTTTTAAGTAATTTGTAAATAAAG
*
21900 ATT-GATCTTTTTTTAAGTAACTTTTGTAAATAAAG
1 ATTAAATC---TTTTAAGTAA--TTTGTAAATAAAG
21935 ATTAAATCTTTTAAGTAA
1 ATTAAATCTTTTAAGTAA
21953 AAATGAAATC
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
30 3 0.07
31 3 0.07
33 19 0.44
35 15 0.35
36 3 0.07
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (31 bp):
ATTAAATCTTTTAAGTAATTTGTAAATAAAG
Found at i:22577 original size:35 final size:35
Alignment explanation
Indices: 22474--23185 Score: 650
Period size: 35 Copynumber: 20.7 Consensus size: 35
22464 CATAATAAGC
22474 AACTTAATTCAGGGTAA-T--G-AAGTCAG-TAAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAA-T
* * *
22505 AAATTAATTCAGGGTAATTAAGTCAGTAAG---A-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
* *
22536 AACTTAATTCAGGGTAATTAAGTGAGTCAGTTAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
** * * *
22571 GTCTTAATTCATGGTAATTAAGTAAATCAGTTAGT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
* *
22606 AACTTAACTCAGGGTAATTAAGTCAGTCAG-TAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAA-T
* * *
22641 AACTTAAGTT-AGGGTAATTAAGTAATTCAATTATT
1 AACTTAA-TTCAGGGTAATTAAGTAAGTCAGTTAAT
* * * *
22676 AATTTAATTCAGGGTAATTAAGAAATTTAG-TAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAA-T
* *
22711 ATCTTAATTCAGGGTAATTAAGTAAGTC-GGTAATT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAA-T
* * * *
22746 AACTCAATTCAGGGTAATTATGTGAGTC-GGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
*
22780 CAACTTAATTCAGGGTAATTAAGTAAGTC-GGTAATT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAA-T
* *
22816 AACTTAATTCAGGGTAATTTAGTAAGTC-GGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
*
22850 CAACTTAATTCAGGGTAATTAAGTAAGTC-GGTAATT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAA-T
* * *
22886 AACTTAATTCAGGATAACTAAGTAAGTC-GGTAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
*
22920 CAACTTAATTCAGGGTAATTAATTAAGTCAG-TAAT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
*
22955 CAACTTAATTTAGGGTAATTAAGTAAGTCAG-TAAT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
*
22990 CAACTTAATTCAGGGTAATTAAGTAAGTCTG-TAAT
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
* * *
23025 CGACTTAATTAAGGGTAATTAAGTAAGTCAG----C
1 -AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
* *
23057 AACTTAATTCAGGGTAATTAAGTGAGACAG-TAAT
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
* * * * *
23091 CAACTTTAATTCAGGGTAATTAAGTGAGTTAATGAGT
1 -AAC-TTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
* * *
23128 AACTTAATTCAGGGTAATTAAGT-AGTTCAATAAAG
1 AACTTAATTCAGGGTAATTAAGTAAG-TCAGTTAAT
*
23163 AACTTAGTTCAGGGTAATTAAGT
1 AACTTAATTCAGGGTAATTAAGT
23186 TTAGTAAGAA
Statistics
Matches: 583, Mismatches: 71, Indels: 50
0.83 0.10 0.07
Matches are distributed among these distances:
31 69 0.12
32 1 0.00
33 1 0.00
34 13 0.02
35 464 0.80
36 33 0.06
37 2 0.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTTAAT
Found at i:28690 original size:21 final size:21
Alignment explanation
Indices: 28656--28704 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
28646 GTTCCTGGGT
*
28656 ACCCAGCTTAAATGCCCAGGC
1 ACCCAGCTTAAATGCCCAAGC
* * *
28677 GCCCAGGTTCAATGCCCAAGC
1 ACCCAGCTTAAATGCCCAAGC
28698 ACCCAGC
1 ACCCAGC
28705 CGCTTTCCCA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.27, C:0.41, G:0.20, T:0.12
Consensus pattern (21 bp):
ACCCAGCTTAAATGCCCAAGC
Found at i:36736 original size:58 final size:56
Alignment explanation
Indices: 36602--36738 Score: 148
Period size: 56 Copynumber: 2.4 Consensus size: 56
36592 AAGGCAATCC
* * * * *
36602 AAGATTAATATGGAGGACTTTTTCAGGATAACAATAAAACCTAGGAGAGTAAATCT
1 AAGATTAATATGGAGCACTTTTTAAAGATAACAATAAAACCTAGAAGAGTAAATAT
* * * *
36658 GAGATTAATATGAAGCACTTTTTAAAGATAACAATAAAAGCTAAGAATTAGTAAATAT
1 AAGATTAATATGGAGCACTTTTTAAAGATAACAATAAAACCT-AGAA-GAGTAAATAT
* * *
36716 AAGTTTAATATGGTGTACTTTTT
1 AAGATTAATATGGAGCACTTTTT
36739 CAATATAATT
Statistics
Matches: 65, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
56 36 0.55
57 3 0.05
58 26 0.40
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (56 bp):
AAGATTAATATGGAGCACTTTTTAAAGATAACAATAAAACCTAGAAGAGTAAATAT
Found at i:39059 original size:92 final size:92
Alignment explanation
Indices: 38948--39123 Score: 325
Period size: 92 Copynumber: 1.9 Consensus size: 92
38938 ATTTATACAG
* *
38948 GTAAAGGAGCGACACTGTTACTTGAATTTCGTAATAAATTTATCTTTTTAAGTACTTTAATTGTA
1 GTAAAGGAGCAACACTGTTACTTGAATTTCGTAATAAATTTATCTTTTTAAGTAATTTAATTGTA
39013 GTAACTTTTCTTGTTACAGGAGTCCAA
66 GTAACTTTTCTTGTTACAGGAGTCCAA
*
39040 GTAAAGGAGCAACACTGTTACTTGAATTTCGTAATAAATTTATCTTTTTAAGTAATTTCATTGTA
1 GTAAAGGAGCAACACTGTTACTTGAATTTCGTAATAAATTTATCTTTTTAAGTAATTTAATTGTA
39105 GTAACTTTTCTTGTTACAG
66 GTAACTTTTCTTGTTACAG
39124 ATTATATATC
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 81 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.41
Consensus pattern (92 bp):
GTAAAGGAGCAACACTGTTACTTGAATTTCGTAATAAATTTATCTTTTTAAGTAATTTAATTGTA
GTAACTTTTCTTGTTACAGGAGTCCAA
Found at i:39575 original size:6 final size:6
Alignment explanation
Indices: 39561--39603 Score: 54
Period size: 6 Copynumber: 7.3 Consensus size: 6
39551 TTCTTTTCAC
*
39561 TTTCTTT TTTCTT TTTCTT TTTCTT TTTC-T TAT-TT TTTCTT TT
1 TTTC-TT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TT
39604 CTGATGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
5 6 0.19
6 22 0.69
7 4 0.12
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTCTT
Found at i:45705 original size:25 final size:25
Alignment explanation
Indices: 45658--45706 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
45648 GTTTTTCTTG
* *
45658 TGACTTACACAGATTGGATATTTAA
1 TGACTTACACAAATTGGAAATTTAA
**
45683 TGACTTACACAAATTTTAAATTTA
1 TGACTTACACAAATTGGAAATTTA
45707 GAATTTTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (25 bp):
TGACTTACACAAATTGGAAATTTAA
Found at i:47819 original size:30 final size:30
Alignment explanation
Indices: 47764--47820 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
47754 CATCTTTAAG
* *
47764 TCCATGATAAGTCCTTGGCGTATCATTCCC
1 TCCATGATAAGTCATTGGCGCATCATTCCC
47794 TCCATGATAAG-CATTGGGCGCATCATT
1 TCCATGATAAGTCATT-GGCGCATCATT
47821 ATCTTTTACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (30 bp):
TCCATGATAAGTCATTGGCGCATCATTCCC
Found at i:50093 original size:17 final size:16
Alignment explanation
Indices: 50065--50107 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
50055 AATCAACATC
* *
50065 ACAAATAGAAAAGAGAA
1 ACAAATAAAAAAAAG-A
*
50082 ACAAATAAAAAAAAGT
1 ACAAATAAAAAAAAGA
50098 ACAAATAAAA
1 ACAAATAAAA
50108 GGAGGCTTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.09
Consensus pattern (16 bp):
ACAAATAAAAAAAAGA
Found at i:50253 original size:21 final size:23
Alignment explanation
Indices: 50219--50260 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
50209 AAAATCAAGG
50219 AGATCCGACGGTGGG-TTTTGCC
1 AGATCCGACGGTGGGATTTTGCC
*
50241 AGATCGGA-GGTGGGATTTTG
1 AGATCCGACGGTGGGATTTTG
50261 ATTCGGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (23 bp):
AGATCCGACGGTGGGATTTTGCC
Found at i:60879 original size:13 final size:13
Alignment explanation
Indices: 60858--60887 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
60848 GGTGAGTACG
*
60858 GCATGGCATGGGT
1 GCATAGCATGGGT
60871 GCATAGCATGGGT
1 GCATAGCATGGGT
60884 GCAT
1 GCAT
60888 GGGTGTTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.40, T:0.23
Consensus pattern (13 bp):
GCATAGCATGGGT
Found at i:67178 original size:21 final size:21
Alignment explanation
Indices: 67135--67178 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
67125 ACAACAACTC
*
67135 AAAGAGAGATTAGACAAAAAA
1 AAAGAGAGATAAGACAAAAAA
* *
67156 AAAGAGAGCTAAG-CAAAAGA
1 AAAGAGAGATAAGACAAAAAA
67176 AAA
1 AAA
67179 CAAAGGGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.66, C:0.07, G:0.20, T:0.07
Consensus pattern (21 bp):
AAAGAGAGATAAGACAAAAAA
Found at i:69097 original size:8 final size:8
Alignment explanation
Indices: 69084--69112 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
69074 ATACTACGTG
69084 AGAGAGAA
1 AGAGAGAA
69092 AGAGAGAA
1 AGAGAGAA
69100 AGAGAGAA
1 AGAGAGAA
69108 AGAGA
1 AGAGA
69113 AAGCGAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (8 bp):
AGAGAGAA
Found at i:72602 original size:3 final size:3
Alignment explanation
Indices: 72596--72639 Score: 70
Period size: 3 Copynumber: 14.7 Consensus size: 3
72586 AGATGATGAT
* *
72596 GAA GAA GAA GAA GAA GAA GAG GAA GAG GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
72640 CATCAAACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:76967 original size:3 final size:3
Alignment explanation
Indices: 76959--76990 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
76949 AGCAATGAAA
76959 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG GTG GT
76991 TGGCACAGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.66, T:0.34
Consensus pattern (3 bp):
GTG
Found at i:77670 original size:22 final size:22
Alignment explanation
Indices: 77627--77671 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
77617 CCAAATTAAG
*
77627 TTAATTCAGATTTGAATCTATT
1 TTAATTCAGATTTAAATCTATT
77649 TTAATTCAGA-TTAAATCATATT
1 TTAATTCAGATTTAAATC-TATT
77671 T
1 T
77672 ATATTGAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (22 bp):
TTAATTCAGATTTAAATCTATT
Found at i:79237 original size:13 final size:13
Alignment explanation
Indices: 79219--79243 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79209 TTGATGGAGA
79219 AGAACTTTGCTTC
1 AGAACTTTGCTTC
79232 AGAACTTTGCTT
1 AGAACTTTGCTT
79244 TGTTGTTGCT
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:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (13 bp):
AGAACTTTGCTTC
Found at i:79246 original size:48 final size:46
Alignment explanation
Indices: 79189--79339 Score: 203
Period size: 48 Copynumber: 3.2 Consensus size: 46
79179 GAGAAAGAAC
79189 TTTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGAA
1 TTTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGCTTCAG-A
79236 CTTTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGA
1 -TTTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGA
* * *** * *
79283 TTCGCTTTGCTTGATGGAGATGTTGATGGAGAAAAACTTTACTTCAGA
1 TTTGCTTTG-TTG-TTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGA
79331 TTTGCTTTG
1 TTTGCTTTG
79340 CTTGATGGAG
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
46 8 0.09
47 4 0.04
48 81 0.87
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (46 bp):
TTTGCTTTGTTGTTGCTTTGTTGATGGAGAAGAACTTTGCTTCAGA
Found at i:81656 original size:3 final size:3
Alignment explanation
Indices: 81650--81684 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
81640 TGATCATCAT
81650 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
81685 TTGTTTGGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:81993 original size:1 final size:1
Alignment explanation
Indices: 81987--82016 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
81977 ATCCTCAACC
81987 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
82017 CAGACTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:82333 original size:46 final size:45
Alignment explanation
Indices: 82268--82476 Score: 184
Period size: 46 Copynumber: 4.6 Consensus size: 45
82258 TTTGAACACT
* * *
82268 CTCTACCTTTGTCTTCGGCTTCTTGGCGGGGTCGATTATTTATCACC
1 CTCTACCTCTG-CATCGGCTTCTTGGCGGGGTTGATT-TTTATCACC
*
82315 CTCTACTTCTGCATCGGCTTCTTGGCGGGGTT--TTTTT-T-A--
1 CTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTTTATCACC
*
82354 -TC-ACCTCTGCATTGG-TGTCTTGGCGGGGTTGATTTTTTTTTTATCACC
1 CTCTACCTCTGCATCGGCT-TCTTGGCGGGGTTGA-----TTTTTATCACC
* * *
82402 CTCTACCTTTGCATCGGCCTCTTGACGGGGTTGATCTTTTATCACC
1 CTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGAT-TTTTATCACC
* *
82448 CTCTACCTCTACATCGGCCTCTTGGCGGG
1 CTCTACCTCTGCATCGGCTTCTTGGCGGG
82477 CCATGAGTAT
Statistics
Matches: 133, Mismatches: 13, Indels: 33
0.74 0.07 0.18
Matches are distributed among these distances:
36 1 0.01
37 24 0.18
38 2 0.02
41 1 0.01
42 1 0.01
43 3 0.02
44 7 0.05
45 2 0.02
46 56 0.42
47 9 0.07
49 2 0.02
50 25 0.19
ACGTcount: A:0.11, C:0.27, G:0.22, T:0.40
Consensus pattern (45 bp):
CTCTACCTCTGCATCGGCTTCTTGGCGGGGTTGATTTTTATCACC
Found at i:85760 original size:48 final size:48
Alignment explanation
Indices: 85707--85802 Score: 165
Period size: 48 Copynumber: 2.0 Consensus size: 48
85697 GTTGTTGCTT
*
85707 TGTTGATGGAGAAGAACTTTGCTTCAGATTCGCTTTGCTTGATGGAGA
1 TGTTGATGGAGAAGAACTTTACTTCAGATTCGCTTTGCTTGATGGAGA
* *
85755 TGTTGATTGAGAAGAACTTTACTTCAGATTTGCTTTGCTTGATGGAGA
1 TGTTGATGGAGAAGAACTTTACTTCAGATTCGCTTTGCTTGATGGAGA
85803 AGAACTTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.24, C:0.11, G:0.27, T:0.38
Consensus pattern (48 bp):
TGTTGATGGAGAAGAACTTTACTTCAGATTCGCTTTGCTTGATGGAGA
Found at i:88678 original size:39 final size:37
Alignment explanation
Indices: 88618--88725 Score: 121
Period size: 39 Copynumber: 2.8 Consensus size: 37
88608 TAGAGAAAAT
* *
88618 TGCCCTTGTGTTACATGTGTTTAGGGACTTTAGTATAGA-
1 TGCCCTTGTGTTATATGTGTTT-GGGACTTT-G-AAAGAG
88657 TG-CCTCTGTGTTATATGTGTTTGAGGACTTTGAAAGAG
1 TGCCCT-TGTGTTATATGTGTTTG-GGACTTTGAAAGAG
88695 TTGCCCTTGTGTTATATGTGTTTGGGGACTT
1 -TGCCCTTGTGTTATATGTGTTT-GGGACTT
88726 CGGGGAGAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
37 4 0.07
38 5 0.08
39 48 0.79
40 4 0.07
ACGTcount: A:0.18, C:0.12, G:0.28, T:0.43
Consensus pattern (37 bp):
TGCCCTTGTGTTATATGTGTTTGGGACTTTGAAAGAG
Found at i:92305 original size:104 final size:104
Alignment explanation
Indices: 92125--92332 Score: 416
Period size: 104 Copynumber: 2.0 Consensus size: 104
92115 GATTTTTCCT
92125 TGATATGAATCGCATATAGGGTATCAATTACATATCATACTTCACTTATGAGTATATGTCTTTCT
1 TGATATGAATCGCATATAGGGTATCAATTACATATCATACTTCACTTATGAGTATATGTCTTTCT
92190 ACATTGAGGACAATGTGTCTTTTAAGTGTGGGGGAGAGA
66 ACATTGAGGACAATGTGTCTTTTAAGTGTGGGGGAGAGA
92229 TGATATGAATCGCATATAGGGTATCAATTACATATCATACTTCACTTATGAGTATATGTCTTTCT
1 TGATATGAATCGCATATAGGGTATCAATTACATATCATACTTCACTTATGAGTATATGTCTTTCT
92294 ACATTGAGGACAATGTGTCTTTTAAGTGTGGGGGAGAGA
66 ACATTGAGGACAATGTGTCTTTTAAGTGTGGGGGAGAGA
92333 GTCTGCATAC
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (104 bp):
TGATATGAATCGCATATAGGGTATCAATTACATATCATACTTCACTTATGAGTATATGTCTTTCT
ACATTGAGGACAATGTGTCTTTTAAGTGTGGGGGAGAGA
Found at i:96336 original size:37 final size:36
Alignment explanation
Indices: 96172--96323 Score: 243
Period size: 37 Copynumber: 4.2 Consensus size: 36
96162 CTCTTCTTAG
* *
96172 ATTAAG-CTCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGCCT-TTTATTGACGCTACTTAATTACCCTGA
96208 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
96244 ATTAAGCCTTTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGCC-TTTTATTGACGCTACTTAATTACCCTGA
*
96281 ATTAAGTCCATTTATTGACGCTACTTAATTACCCTGA
1 ATTAAG-CCTTTTATTGACGCTACTTAATTACCCTGA
96318 ATTAAG
1 ATTAAG
96324 TCCCTAACTT
Statistics
Matches: 110, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
36 39 0.35
37 69 0.63
38 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.39
Consensus pattern (36 bp):
ATTAAGCCTTTTATTGACGCTACTTAATTACCCTGA
Found at i:96408 original size:69 final size:70
Alignment explanation
Indices: 96335--96476 Score: 268
Period size: 69 Copynumber: 2.0 Consensus size: 70
96325 CCCTAACTTG
96335 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATT-CCCTTCCTTGGAATCAAGT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTGGAATCAAGT
96399 CCTGT
66 CCTGT
96404 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTGGAATCAAGT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTGGAATCAAGT
*
96469 CCTTT
66 CCTGT
96474 ACT
1 ACT
96477 CTACTTAATT
Statistics
Matches: 71, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
69 45 0.63
70 26 0.37
ACGTcount: A:0.25, C:0.27, G:0.08, T:0.41
Consensus pattern (70 bp):
ACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTGGAATCAAGT
CCTGT
Found at i:96485 original size:107 final size:106
Alignment explanation
Indices: 96317--96508 Score: 305
Period size: 107 Copynumber: 1.8 Consensus size: 106
96307 AATTACCCTG
* *
96317 AATTAAGTCCCTAACTTGACTTAATTTCCTTCCTTGAAATTAAGTCCTTAACTCTACTTAATTCC
1 AATTAAGTCCCTAACTTGACTTAATTCCCTTCCTTGAAATCAAGTCCTTAACTCTACTTAATTCC
*
96382 CTTCCTTGGAATCAAGTCCTGTACTTAATTTCCTTCCTTGA
66 CTTCCTTGGAACCAAGTCCTGTACTTAATTTCCTTCCTTGA
* * *
96423 AATTAAGTCCTTAACTCT-ACTTAATTCCCCTTCCTTGGAATCAAGTCCTTTACTCTACTTAATT
1 AATTAAGTCCCTAACT-TGACTTAATT-CCCTTCCTTGAAATCAAGTCCTTAACTCTACTTAATT
96487 CCCTTCCTTGGAACCAAGTCCT
64 CCCTTCCTTGGAACCAAGTCCT
96509 TTTCTTTACT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
106 23 0.29
107 55 0.71
ACGTcount: A:0.25, C:0.28, G:0.08, T:0.39
Consensus pattern (106 bp):
AATTAAGTCCCTAACTTGACTTAATTCCCTTCCTTGAAATCAAGTCCTTAACTCTACTTAATTCC
CTTCCTTGGAACCAAGTCCTGTACTTAATTTCCTTCCTTGA
Found at i:96522 original size:37 final size:37
Alignment explanation
Indices: 96316--96509 Score: 229
Period size: 37 Copynumber: 5.4 Consensus size: 37
96306 TAATTACCCT
* * *
96316 GAATTAAGTCCCTAACT-TGACTTAATTTCCTTCCTTG
1 GAATCAAGTCCTTAACTCT-ACTTAATTCCCTTCCTTG
* *
96353 AAATTAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* *
96390 GAATCAAGT-C----CTGTACTTAATTTCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
* *
96422 AAATTAAGTCCTTAACTCTACTTAATTCCCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATT-CCCTTCCTTG
*
96460 GAATCAAGTCCTTTACTCTACTTAATTCCCTTCCTTG
1 GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
*
96497 GAACCAAGTCCTT
1 GAATCAAGTCCTT
96510 TTCTTTACTT
Statistics
Matches: 135, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
32 27 0.20
33 1 0.01
36 1 0.01
37 72 0.53
38 34 0.25
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (37 bp):
GAATCAAGTCCTTAACTCTACTTAATTCCCTTCCTTG
Found at i:96608 original size:36 final size:34
Alignment explanation
Indices: 96532--96644 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 34
96522 TCCCCGGAGG
* *
96532 TTAAGTTTTTGTCTGATCTTACTTAATCATCTTTGGA
1 TTAAGTTTTTG-CTGATTTTACTTAAT--TCTTTGAA
*
96569 TTAAGTTTTTGATGATTTTACTTAATTCTTATGAAA
1 TTAAGTTTTTGCTGATTTTACTTAATTCTT-TG-AA
* * **
96605 TTAAGTCTTTGCT-AATTTACTTAATTACCCTGAA
1 TTAAGTTTTTGCTGATTTTACTTAATT-CTTTGAA
96639 TTAAGT
1 TTAAGT
96645 ATGTGTTTGC
Statistics
Matches: 65, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
34 12 0.18
35 16 0.25
36 26 0.40
37 11 0.17
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.50
Consensus pattern (34 bp):
TTAAGTTTTTGCTGATTTTACTTAATTCTTTGAA
Found at i:96684 original size:41 final size:40
Alignment explanation
Indices: 96633--96884 Score: 213
Period size: 41 Copynumber: 6.5 Consensus size: 40
96623 ACTTAATTAC
* * *
96633 CCTG-AATTAAGTATGTGTTTGCCTTTACCTAATTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
*
96672 CCTTGAAATTAAGTCTAG-GATTGTCTTTACCTAATTTCCTTT
1 CC-TGAAATTAAGTCT-GTGCTTGTCTTTACCTAATTTCC-TT
* * * *
96714 ACTGAAATTAAGTCTGTGCTT-ACTTTACTTAA-TTAC--
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* *
96750 CCTG-AATTAAGTCTATGCTTGTCTTTACCTAACTTCCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
* * * * *
96789 CCTTGAAATTAAGATTTGTACTT-ACTTTACTTAA-TTAC--
1 CC-TGAAATTAAG-TCTGTGCTTGTCTTTACCTAATTTCCTT
* *
96827 CCT-AAATTAAGTCTATGCTTGTCTTTACCTAATTTTCTT
1 CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
96866 CCTTGAAATTAAGTCTGTG
1 CC-TGAAATTAAGTCTGTG
96885 ACTATCCTTA
Statistics
Matches: 169, Mismatches: 26, Indels: 34
0.74 0.11 0.15
Matches are distributed among these distances:
35 21 0.12
36 29 0.17
37 7 0.04
38 2 0.01
39 9 0.05
40 18 0.11
41 73 0.43
42 10 0.06
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.44
Consensus pattern (40 bp):
CCTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTT
Found at i:96840 original size:77 final size:76
Alignment explanation
Indices: 96677--96883 Score: 317
Period size: 77 Copynumber: 2.7 Consensus size: 76
96667 TCCTTCCTTG
* * * *
96677 AAATTAAGTCTAGGATTGTCTTTACCTAATTTCCTTTAC-TGAAATTAAGTCTGTGCTTACTTTA
1 AAATTAAGTCTATGCTTGTCTTTACCTAATTTCC-TTCCTTGAAATTAAGTCTGTACTTACTTTA
96741 CTTAATTACCCT
65 CTTAATTACCCT
* * *
96753 GAATTAAGTCTATGCTTGTCTTTACCTAACTTCCTTCCTTGAAATTAAGATTTGTACTTACTTTA
1 AAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAG-TCTGTACTTACTTTA
96818 CTTAATTACCCT
65 CTTAATTACCCT
*
96830 AAATTAAGTCTATGCTTGTCTTTACCTAATTTTCTTCCTTGAAATTAAGTCTGT
1 AAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGT
96884 GACTATCCTT
Statistics
Matches: 118, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
75 3 0.03
76 44 0.37
77 71 0.60
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (76 bp):
AAATTAAGTCTATGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTTACTTTAC
TTAATTACCCT
Found at i:96955 original size:37 final size:37
Alignment explanation
Indices: 96898--97635 Score: 775
Period size: 37 Copynumber: 19.7 Consensus size: 37
96888 ATCCTTACCT
* * *
96898 TTTAACTGTTTTTACTTAATTACCTTGAATTAAGTCC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * *
96935 TTCAACTGCTTTTACATAATTACACTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
**
96972 -TTAACTGCTTTTACTTAATTGTCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* **
97008 -TTAACTGCTTTTACTTTATTGTCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
**
97044 -TTAACTGCTTTTACTTAATTGTCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
*
97080 -TTAACTGTTCTTTACTTAATTACCCTGAATTAAGTTC
1 TTTAACTGCT-TTTACTTAATTACCCTGAATTAAGTTC
* * *
97117 TTTGA-T-CGTGTTTACTTAATTTCCCTGAATTAAGCTCC
1 TTTAACTGC-T-TTTACTTAATTACCCTGAATTAAG-TTC
* * *
97155 TTTGACTGCTTTTACCTT-ATTTCCTTGAATTAAGATT-
1 TTTAACTGCTTTTA-CTTAATTACCCTGAATTAAG-TTC
* * * *
97192 TTGGCTGACTATGTTTACTTTT-CTTAATTGCCCCGAATTAAGAT-
1 TT---TAAC--TG----CTTTTACTTAATTACCCTGAATTAAGTTC
* * * *
97236 TTTGACTGTTTTTACTTAATTGCCCTGAATTAAGTTT
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
97273 TTTACCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
97310 -TTAACTACTCCTTTACTTAACTACCCTGAATTAAGTTC
1 TTTAACTGCT--TTTACTTAATTACCCTGAATTAAGTTC
* *
97348 TTTACCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
97385 -TTAACCTGCTTCTTTACTTAATTACCCTGAATTAAGTTC
1 TTTAA-CTGC-T-TTTACTTAATTACCCTGAATTAAGTTC
** *
97424 TTTGCCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
*
97461 -TTAACCTGCTTTTACTTAATTGCCCTGAATTAAGTTC
1 TTTAA-CTGCTTTTACTTAATTACCCTGAATTAAGTTC
97498 -TTAACTTGCTTTTACTTAATTACCCTGAATTAAGTTC
1 TTTAAC-TGCTTTTACTTAATTACCCTGAATTAAGTTC
*
97535 TTTAACTGCTCTTACTTAATTACCCTGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* * *
97572 TTTGACTGCTTTTACTTAATTTCCATGAATTAAGTTC
1 TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
* *
97609 TTTAACTGCTCTTTTCTTAATCACCCT
1 TTTAACTGCT-TTTACTTAATTACCCT
97636 TGATTAAAAC
Statistics
Matches: 610, Mismatches: 61, Indels: 59
0.84 0.08 0.08
Matches are distributed among these distances:
35 4 0.01
36 142 0.23
37 309 0.51
38 74 0.12
39 44 0.07
40 7 0.01
41 4 0.01
42 2 0.00
44 6 0.01
45 13 0.02
46 5 0.01
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (37 bp):
TTTAACTGCTTTTACTTAATTACCCTGAATTAAGTTC
Found at i:97746 original size:41 final size:40
Alignment explanation
Indices: 97621--97756 Score: 174
Period size: 41 Copynumber: 3.5 Consensus size: 40
97611 TAACTGCTCT
* * *
97621 TTTCTTAATCACCCTTGATTAAAACTTTAACTA-ATTTGAC
1 TTTCTTAATCGCCCTGGATTAAAAC-TTAACTATGTTTGAC
*
97661 TTTCTTAATCGCCCTGGATT-AAA---AACTGTGTTTGAC
1 TTTCTTAATCGCCCTGGATTAAAACTTAACTATGTTTGAC
97697 TTTCTTAATCGCCCTGGATTAAAACCTTAACTATGTTTGAC
1 TTTCTTAATCGCCCTGGATTAAAA-CTTAACTATGTTTGAC
*
97738 CTTCTTAATCGCCCTGGAT
1 TTTCTTAATCGCCCTGGAT
97757 GACTTTACTT
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
35 4 0.05
36 26 0.31
37 3 0.04
39 3 0.04
40 18 0.21
41 30 0.36
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.40
Consensus pattern (40 bp):
TTTCTTAATCGCCCTGGATTAAAACTTAACTATGTTTGAC
Found at i:98132 original size:18 final size:18
Alignment explanation
Indices: 98109--98147 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
98099 ATAAGATTAG
98109 TAAGCTTAATTGCTAAAT
1 TAAGCTTAATTGCTAAAT
98127 TAAGCTTAATTGCTAAAT
1 TAAGCTTAATTGCTAAAT
98145 TAA
1 TAA
98148 TAACAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.38
Consensus pattern (18 bp):
TAAGCTTAATTGCTAAAT
Found at i:101177 original size:26 final size:27
Alignment explanation
Indices: 101105--101178 Score: 66
Period size: 26 Copynumber: 2.7 Consensus size: 27
101095 CAACAAGCTT
*
101105 TGACCAAAATGCCCCT-G-AAGCAAAAA
1 TGACTAAAATGCCCCTGGTAA-CAAAAA
*
101131 TGACTAAAATACCCCTATGGTAA-AAAAA
1 TGACTAAAATGCCCC--TGGTAACAAAAA
101159 TGA-TGAAAATGCCCCTGGTA
1 TGACT-AAAATGCCCCTGGTA
101179 TTATCTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
26 18 0.45
27 1 0.03
28 18 0.45
29 1 0.03
30 2 0.05
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
TGACTAAAATGCCCCTGGTAACAAAAA
Found at i:103174 original size:46 final size:46
Alignment explanation
Indices: 103067--103159 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
103057 TTTTGTGGCC
103067 TCTAAAGAATGAAAATGAAGAGCTAAATTGATCATTGCTGTGGACA
1 TCTAAAGAATGAAAATGAAGAGCTAAATTGATCATTGCTGTGGACA
103113 TCTAAAGAATGAAAATGAAGAGCTAAATTGATCATTGCTGTGGACA
1 TCTAAAGAATGAAAATGAAGAGCTAAATTGATCATTGCTGTGGACA
103159 T
1 T
103160 GTGGAGGAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.27
Consensus pattern (46 bp):
TCTAAAGAATGAAAATGAAGAGCTAAATTGATCATTGCTGTGGACA
Found at i:108930 original size:26 final size:26
Alignment explanation
Indices: 108893--108994 Score: 84
Period size: 26 Copynumber: 3.7 Consensus size: 26
108883 ACAATTAAAG
108893 CCCTCAAACACAATGGCATTTATAAGT
1 CCCTCAAACACAA-GGCATTTATAAGT
108920 CCCT-AAACACAGAGGCAGTTCTATATCAAAGT
1 CCCTCAAACACA-AGGCA--T-T-TAT--AAGT
108952 -CCTCAAACACAAGGCCATTTATAAGT
1 CCCTCAAACACAAGG-CATTTATAAGT
*
108978 -CCTTAAACACAGAGGCA
1 CCCTCAAACACA-AGGCA
108995 CCTCTCTAAA
Statistics
Matches: 64, Mismatches: 1, Indels: 21
0.74 0.01 0.24
Matches are distributed among these distances:
26 27 0.42
27 8 0.12
28 4 0.06
29 2 0.03
30 4 0.06
31 6 0.09
32 13 0.20
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.22
Consensus pattern (26 bp):
CCCTCAAACACAAGGCATTTATAAGT
Found at i:108985 original size:58 final size:55
Alignment explanation
Indices: 108889--109110 Score: 209
Period size: 58 Copynumber: 3.9 Consensus size: 55
108879 CCCAACAATT
*
108889 AAAGCCCTCAAACACAATGGCATTTATAAGTCCCTAAACACAGAGGCAGTTCTATATC
1 AAAGTCCTCAAACACAA-GGCATTTATAAGTCCCTAAACACAGAGGCA-TTCTA-ATC
* **
108947 AAAGTCCTCAAACACAAGGCCATTTATAAGTCCTTAAACACAGAGGCACCTCTCTAAAA
1 AAAGTCCTCAAACACAAGG-CATTTATAAGTCCCTAAACACAGAGGCA--T-TCTAATC
* * * *
109006 AAAATCCTCAAACACAAGG-GTAT-TCA-TCCCTAAACACAGAGGCA-TCTACATC
1 AAAGTCCTCAAACACAAGGCATTTATAAGTCCCTAAACACAGAGGCATTCTA-ATC
* *
109058 AAAGTCCTCAAGCACAAGGGCATCTATATTAAAGTCCCTAAACACAGAAGCAT
1 AAAGTCCTCAAACACAA-GGCAT-T-TA-T-AAGTCCCTAAACACAGAGGCAT
109111 CCATACTAAA
Statistics
Matches: 133, Mismatches: 18, Indels: 23
0.76 0.10 0.13
Matches are distributed among these distances:
51 4 0.03
52 16 0.12
53 2 0.02
54 1 0.01
55 17 0.13
56 3 0.02
57 4 0.03
58 44 0.33
59 21 0.16
60 21 0.16
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (55 bp):
AAAGTCCTCAAACACAAGGCATTTATAAGTCCCTAAACACAGAGGCATTCTAATC
Found at i:109111 original size:30 final size:30
Alignment explanation
Indices: 109032--109125 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
109022 AGGGTATTCA
* *
109032 TCCCTAAACACAGAGGCATCTACATCAAAG
1 TCCCTAAACACAGAGGCATCTATATTAAAG
*
109062 T-CCTCAAGCACA-AGGGCATCTATATTAAAG
1 TCCCT-AAACACAGA-GGCATCTATATTAAAG
* * *
109092 TCCCTAAACACAGAAGCATCCATACTAAAG
1 TCCCTAAACACAGAGGCATCTATATTAAAG
109122 TCCC
1 TCCC
109126 CAAGCACATA
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
29 4 0.08
30 45 0.85
31 4 0.08
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.19
Consensus pattern (30 bp):
TCCCTAAACACAGAGGCATCTATATTAAAG
Found at i:117581 original size:29 final size:29
Alignment explanation
Indices: 117542--117638 Score: 90
Period size: 29 Copynumber: 3.3 Consensus size: 29
117532 ACAAAATGTT
117542 CAAATAAGGGCCCGATCTTTTAATTTGGC
1 CAAATAAGGGCCCGATCTTTTAATTTGGC
** * * **
117571 CAAATAAGGG-CATAACGTTATCGAAAAT-GC
1 CAAATAAGGGCCCGATC-TT-T-TAATTTGGC
117601 TCAAATAAGGGCCCGATCTTTTAATTTGGC
1 -CAAATAAGGGCCCGATCTTTTAATTTGGC
117631 CAAATAAG
1 CAAATAAG
117639 AGTCTAACAT
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
28 3 0.06
29 23 0.46
30 6 0.12
31 15 0.30
32 3 0.06
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (29 bp):
CAAATAAGGGCCCGATCTTTTAATTTGGC
Found at i:117598 original size:60 final size:60
Alignment explanation
Indices: 117534--117680 Score: 242
Period size: 60 Copynumber: 2.5 Consensus size: 60
117524 AACATTTGAC
* *
117534 AAAATGTTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAG-GGCATAACGTTATCG
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGGC-TAACATTATCG
*
117594 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGTCTAACATTATCG
1 AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGGCTAACATTATCG
*
117654 AAAATGCTCAAATAAGGGGCCGATCTT
1 AAAATGCTCAAATAAGGGCCCGATCTT
117681 GATCGATTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
60 80 0.98
61 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (60 bp):
AAAATGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGAGGCTAACATTATCG
Found at i:118280 original size:16 final size:16
Alignment explanation
Indices: 118253--118286 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
118243 TTTTAAAGTG
118253 AACAATAAAAATAAATA
1 AACAATAAAAAT-AATA
118270 AACAA-AAAAATAATA
1 AACAATAAAAATAATA
118285 AA
1 AA
118287 ATTAAGTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 6 0.35
17 5 0.29
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AACAATAAAAATAATA
Found at i:120224 original size:45 final size:45
Alignment explanation
Indices: 120173--120262 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
120163 TAATAGAGTA
120173 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
* *
120218 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
120263 AAAAGTAATC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCGAATTAATGATAAGCTGG
Found at i:121381 original size:164 final size:164
Alignment explanation
Indices: 121109--121420 Score: 452
Period size: 164 Copynumber: 1.9 Consensus size: 164
121099 ATGCATGGAC
* * *
121109 TTTTTGGTCATTTCTCAATTGACTTTAATAGAGTAGTGGAATTACTAAAAGATCCCTACCAAGGC
1 TTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGGA
* ** * * * *
121174 TTGCTTTTGGAGTTAGAGAACTTTTTTTTTGTCTTTTCCTACTTGGCAGATTACTTAAATGTCCT
66 TTGATGATGGAGCTAGAGAACTTTTTTTTTGTCTTTACCTACTTGGCAGATTACTTAAATATCAT
121239 AAATTTTGATTCTTGAGGAGATTAAATAAGTAAT
131 AAATTTTGATTCTTGAGGAGATTAAATAAGTAAT
*
121273 TTTTTGGTCATTTCTCAA-TGAACTTGAATAGAGTAGTGGAATTAATAAAAGATCCC-ATCAAGG
1 TTTTTGGTCATTTCTCAATTG-ACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGG
121336 ATTGATGAT-GAGCTAGAGAA-TTAATTTTTTTCGTCTTTACCTACTTGGCAGATTACTTAAATA
65 ATTGATGATGGAGCTAGAGAACTT--TTTTTTT-GTCTTTACCTACTTGGCAGATTACTTAAATA
*
121399 TCATAACTTTTGATTCTTGAGG
127 TCATAAATTTTGATTCTTGAGG
121421 GCAGCGGCGG
Statistics
Matches: 132, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
161 2 0.02
162 10 0.08
163 20 0.15
164 100 0.76
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (164 bp):
TTTTTGGTCATTTCTCAATTGACTTGAATAGAGTAGTGGAATTAATAAAAGATCCCTACCAAGGA
TTGATGATGGAGCTAGAGAACTTTTTTTTTGTCTTTACCTACTTGGCAGATTACTTAAATATCAT
AAATTTTGATTCTTGAGGAGATTAAATAAGTAAT
Found at i:124954 original size:16 final size:16
Alignment explanation
Indices: 124935--124995 Score: 79
Period size: 16 Copynumber: 3.8 Consensus size: 16
124925 GGTTCGGACT
*
124935 TTTTCAGGTTCGGGTA
1 TTTTCGGGTTCGGGTA
*
124951 TTTTCGGGCTCGGGT-
1 TTTTCGGGTTCGGGTA
*
124966 TATGTCGGGTTCGGGTA
1 T-TTTCGGGTTCGGGTA
124983 TTTTCGGGTTCGG
1 TTTTCGGGTTCGG
124996 TCTCGGGTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
15 1 0.03
16 36 0.95
17 1 0.03
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.41
Consensus pattern (16 bp):
TTTTCGGGTTCGGGTA
Found at i:125011 original size:17 final size:17
Alignment explanation
Indices: 124988--125037 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
124978 GGGTATTTTC
*
124988 GGGTTCGGTCTCGGGTA
1 GGGTTCGGACTCGGGTA
* * * *
125005 TGGTTCGGGCTCGAGTC
1 GGGTTCGGACTCGGGTA
125022 GGGTTCGGACTCGGGT
1 GGGTTCGGACTCGGGT
125038 TTGATTTCGA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.06, C:0.20, G:0.46, T:0.28
Consensus pattern (17 bp):
GGGTTCGGACTCGGGTA
Found at i:125761 original size:2 final size:2
Alignment explanation
Indices: 125754--125784 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
125744 TGCTTTTAGT
125754 TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
125785 GTAGTTTAGC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Done.