Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007386.1 Hibiscus syriacus cultivar Beakdansim tig00019862_pilon, 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: 903698
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
File 1 of 3
Found at i:5531 original size:32 final size:32
Alignment explanation
Indices: 5486--5596 Score: 159
Period size: 32 Copynumber: 3.5 Consensus size: 32
5476 GGCTTTAAGA
*
5486 CCCTAAGGTAGGCTCTAAGGCTCCAAGGTACT
1 CCCTTAGGTAGGCTCTAAGGCTCCAAGGTACT
5518 CCCTTAGGTAGGCTCTAAGGCTCCAAGGTACT
1 CCCTTAGGTAGGCTCTAAGGCTCCAAGGTACT
* * * *
5550 ACATTAGGTAAGCTCTAAGGCCCCAAGGTACT
1 CCCTTAGGTAGGCTCTAAGGCTCCAAGGTACT
* *
5582 CCCTTATGTTGGCTC
1 CCCTTAGGTAGGCTC
5597 ATATGCTAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.25
Consensus pattern (32 bp):
CCCTTAGGTAGGCTCTAAGGCTCCAAGGTACT
Found at i:10248 original size:32 final size:32
Alignment explanation
Indices: 10212--10274 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 32
10202 TGAGACCCTG
* * *
10212 ACAATATTGTGCATTATATGAGTGCAACACTA
1 ACAATACTGTGCATTATATGAATACAACACTA
*
10244 ACAATACTGTGCATTATCTGAATACAACACT
1 ACAATACTGTGCATTATATGAATACAACACT
10275 GACATTGTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (32 bp):
ACAATACTGTGCATTATATGAATACAACACTA
Found at i:14819 original size:15 final size:15
Alignment explanation
Indices: 14799--14855 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
14789 TAAACAGTAC
14799 GCAAAACAGTAATAA
1 GCAAAACAGTAATAA
*
14814 GCAAAACAGTCATAA
1 GCAAAACAGTAATAA
*
14829 GCAAAACAGTCATAA
1 GCAAAACAGTAATAA
14844 GCAAAACA-TAAT
1 GCAAAACAGTAAT
14856 TCATCATTCA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
14 3 0.08
15 37 0.93
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (15 bp):
GCAAAACAGTAATAA
Found at i:28467 original size:9 final size:9
Alignment explanation
Indices: 28453--28483 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
28443 AGAACCCATG
*
28453 GCCTCCGTC
1 GCCTCCGCC
28462 GCCTCCGCC
1 GCCTCCGCC
28471 GCCTCCGCC
1 GCCTCCGCC
28480 GCCT
1 GCCT
28484 AATGGCTCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.00, C:0.61, G:0.23, T:0.16
Consensus pattern (9 bp):
GCCTCCGCC
Found at i:29973 original size:92 final size:93
Alignment explanation
Indices: 29797--30006 Score: 341
Period size: 92 Copynumber: 2.3 Consensus size: 93
29787 GAAAAAATAT
* * *
29797 TTTATTTTAAAATTATTAATCGAACCAAATTAACCGATTTTTTTTCTTTAACATTAATCGAACCG
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGA-TTTTTTTCTTTAACATTAATCCAACCG
*
29862 AAATTATTTGACCGTTAATCGAACCGAAA
65 AAATTATTTGACCGTTAATCGAACCAAAA
29891 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGA-TTTTTTCTTTAACATTAATCCAACCGA
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTAACATTAATCCAACCGA
* *
29955 AATTATTTGGCCGTTAATCGAATCAAAA
66 AATTATTTGACCGTTAATCGAACCAAAA
*
29983 TTTATTTGAAAAATATTAACCGAA
1 TTTATTTGAAAATTATTAACCGAA
30007 TTTTTTTCTT
Statistics
Matches: 109, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
92 74 0.68
94 35 0.32
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (93 bp):
TTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTTCTTTAACATTAATCCAACCGA
AATTATTTGACCGTTAATCGAACCAAAA
Found at i:30029 original size:55 final size:57
Alignment explanation
Indices: 29968--30126 Score: 178
Period size: 65 Copynumber: 2.7 Consensus size: 57
29958 TATTTGGCCG
*
29968 TTAATCGAATCAAAATTTATTTGAAAAATATTAACCGAA-T-TTTTTTCTTTAACCA
1 TTAATCGAATCAAAATTTATTTGAAAATTATTAACCGAATTATTTTTTCTTTAACCA
* * *
30023 TTAATCGAACCAAAATTTATTTGAAAATTATTAACCAATAAAATAAATTATTTTTTCTTTAACCG
1 TTAATCGAATCAAAATTTATTTGAAAATTATTAACC--------GAATTATTTTTTCTTTAACCA
* *
30088 TTAATCGAATCGAATTTTATTTGAAAATTATTAACCGAA
1 TTAATCGAATCAAAATTTATTTGAAAATTATTAACCGAA
30127 CCAAATCAAC
Statistics
Matches: 86, Mismatches: 8, Indels: 18
0.77 0.07 0.16
Matches are distributed among these distances:
55 34 0.40
57 2 0.02
63 2 0.02
64 1 0.01
65 47 0.55
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.40
Consensus pattern (57 bp):
TTAATCGAATCAAAATTTATTTGAAAATTATTAACCGAATTATTTTTTCTTTAACCA
Found at i:30085 original size:65 final size:66
Alignment explanation
Indices: 30007--30179 Score: 210
Period size: 65 Copynumber: 2.6 Consensus size: 66
29997 ATTAACCGAA
*
30007 TTTTTTTCTTTAACCATTAATCGAACCAAAATTTATTTGAAAATTATTAACC-AATAAAAT-AA-
1 TTTTTTTCTTTAACCATTAATCGAA-CAAAATTTATTTGAAAATTATTAACCGAACAAAATCAAC
30069 AT
65 AT
* * * *
30071 TATTTTTTCTTTAACCGTTAATCGAATCGAATTTTATTTGAAAATTATTAACCGAACCAAATCAA
1 T-TTTTTTCTTTAACCATTAATCGAA-CAAAATTTATTTGAAAATTATTAACCGAACAAAATCAA
*
30136 CCGCT
64 -C-AT
30141 TTTTTTTCTTTAACCATTAATCGAACAGAAA-TTATTTGA
1 TTTTTTTCTTTAACCATTAATCGAACA-AAATTTATTTGA
30180 CCGTTAATCG
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
64 1 0.01
65 47 0.51
66 6 0.07
67 2 0.02
68 9 0.10
69 25 0.27
70 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.41
Consensus pattern (66 bp):
TTTTTTTCTTTAACCATTAATCGAACAAAATTTATTTGAAAATTATTAACCGAACAAAATCAACA
T
Found at i:30240 original size:161 final size:161
Alignment explanation
Indices: 30023--30324 Score: 457
Period size: 161 Copynumber: 1.9 Consensus size: 161
30013 TCTTTAACCA
*
30023 TTAATCGAACCAAAATTTATTTGAAAATTATTAACCAATAAAATAAATTATTTTTTCTTTAACCG
1 TTAATCGAACCAAAATATATTTGAAAATTATTAACCAATAAAATAAATTATTTTTTCTTTAACCG
* * * *
30088 TTAATCGAAT-CGAATTTTATTTGAAAATTATTAACCGAA-CCAAATCAACCG-CTTTTTTTTCT
66 TTAATCG-ATCCGAAATTTATTTGAAAATTATTAAACGAATCCAAAT-AACCGAATTTTTTTCCT
*
30150 TTAACCATTAATCGAACAGAAATTATTTGACCG
129 GTAACCATTAATCGAACAGAAATTATTTGACCG
* * *
30183 TTAATCGAATCGAAATATATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCTTTAACT
1 TTAATCGAACCAAAATATATTTGAAAATTATTAACC-AATAAAATAAATTATTTTTTCTTTAACC
*
30248 GTTAATCGATCCGAAATTTATTTGAAAATTATTAAACGAATCGAAATAACCGAAATTTTTTTCCT
65 GTTAATCGATCCGAAATTTATTTGAAAATTATTAAACGAATCCAAATAACCG-AATTTTTTTCCT
30313 GTAACCATTAAT
129 GTAACCATTAAT
30325 AGAGTTGAAA
Statistics
Matches: 127, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
160 35 0.28
161 67 0.53
162 5 0.04
163 20 0.16
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (161 bp):
TTAATCGAACCAAAATATATTTGAAAATTATTAACCAATAAAATAAATTATTTTTTCTTTAACCG
TTAATCGATCCGAAATTTATTTGAAAATTATTAAACGAATCCAAATAACCGAATTTTTTTCCTGT
AACCATTAATCGAACAGAAATTATTTGACCG
Found at i:31654 original size:55 final size:53
Alignment explanation
Indices: 31608--31854 Score: 300
Period size: 55 Copynumber: 4.5 Consensus size: 53
31598 CCCTCTTTCT
* * *
31608 TTTAGGAAGTATATA-ACTCGAATATCTTCAATAATCGTGTCTGCTCCCTAGTCC
1 TTTA-GAAGTATA-AGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCC
* * * * *
31662 TTCAGAGAGTATAAGACTCAAACATCTTCAACAATCATGTTTGCTCCCTATTTC
1 TTTAGA-AGTATAAGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCC
31716 TTCATAG-AGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTCC
1 TT--TAGAAGTATAAGACTCGAAC-ATCTTCAACAATCGTGTCTGCTCCCTATTCC
* *
31771 TTTAGAGAGTATAAGACTCGAATAATCTTCAACAATCGTGTCCGCTCCCTATTCC
1 TTTAGA-AGTATAAGACTCGAA-CATCTTCAACAATCGTGTCTGCTCCCTATTCC
*
31826 TTCAGAGAGTATAAGACTCGAACATCTTC
1 TTTAGA-AGTATAAGACTCGAACATCTTC
31855 TTCAAACGGG
Statistics
Matches: 168, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
53 6 0.04
54 64 0.38
55 96 0.57
56 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.14, T:0.32
Consensus pattern (53 bp):
TTTAGAAGTATAAGACTCGAACATCTTCAACAATCGTGTCTGCTCCCTATTCC
Found at i:31890 original size:54 final size:54
Alignment explanation
Indices: 31591--32329 Score: 618
Period size: 54 Copynumber: 13.6 Consensus size: 54
31581 CTGGGGACAA
* * * * * *
31591 GTTCGCTCCCTCTTTCTTTTAGGAAGTATATAACTCGAATATCTTCAAT-AATCGT
1 GTTCGCTCCCTCTTTC-TTTAGGGAGTATAGAACTCGAACATCTTC-TTCAAACGG
** * * * * ** * **
31646 G-TCTGCTCCCTAGTCCTTCAGAGAGTATA-AGACTCAAACATCTTCAACAATCAT
1 GTTC-GCTCCCTCTTTCTTTAGGGAGTATAGA-ACTCGAACATCTTCTTCAAACGG
* * * ** ** * *
31700 GTTTGCTCCCTATTTCTTCATAGAGTATA-AGACTCGAACAATCTTCAACAATCGT
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGA-ACTCGAAC-ATCTTCTTCAAACGG
* * * * ** * *
31755 G-TCTGCTCCCTATTCCTTTAGAGAGTATA-AGACTCGAATAATCTTCAACAATCGT
1 GTTC-GCTCCCTCTTTCTTTAGGGAGTATAGA-ACTCGAA-CATCTTCTTCAAACGG
* * * * *
31810 GTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACTCGAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGA-ACTCGAACATCTTCTTCAAACGG
* * * *
31864 GTTTGCTCCCTCCTTCTTTAGGGAGTATGGAACTCGAACATCTTTTTCAAACGG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* *
31918 GTTCGCTCCCTCTTTCTTTAGGGAGTATATAACTCAAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * * * ** **
31972 GTTCACTCCATCCTTCTTTAGGGAGTATAGAACTTGAACGATC-TCCGCAAATAG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGG
* *
32026 GTTCGCTCCCTCTTTCTTTAGGGAGTATGGAACTCAAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * ** *
32080 GTTCGCTCACTCCTTCTTTAGGGAGTATAGAACTCGAACGATC-TCCGCAAACAG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAAC-ATCTTCTTCAAACGG
* * * * *
32134 GTCCACTCCCTCTTTTTTTAGGGAGTATGGAACTCGAACATCTTTTTCAAACGG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
* * ** *
32188 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCAAATGATC-TCCGCAAACAG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAA-CATCTTCTTCAAACGG
32242 GTTCGCTCCCTCTTTCTTTAGGGAGTAT-GAAACTCGAACATCTTCTTCAAACGG
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAG-AACTCGAACATCTTCTTCAAACGG
** *
32296 GTTCGCTCCCTCCGTCTTTAGGGAGTATGGAACT
1 GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACT
32330 TTAACAATCT
Statistics
Matches: 570, Mismatches: 97, Indels: 35
0.81 0.14 0.05
Matches are distributed among these distances:
53 12 0.02
54 440 0.77
55 117 0.21
56 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (54 bp):
GTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACTCGAACATCTTCTTCAAACGG
Found at i:31963 original size:108 final size:107
Alignment explanation
Indices: 31813--32329 Score: 721
Period size: 108 Copynumber: 4.8 Consensus size: 107
31803 CAATCGTGTC
* * * * *
31813 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACATCTTCTTCAAACGGGTTTGCTCCCTCCT
1 CGCTCCCTCTTTCTTTAGGGAGTATAA-ACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCT
* *** *
31878 TCTTTAGGGAGTATGGAACTCGAAC-ATCTTTTTCAAACGGGTT
65 TCTTTAGGGAGTATAGAACTCGAACGATC-TCCGCAAACAGGTT
* * *
31921 CGCTCCCTCTTTCTTTAGGGAGTATATAACTCAAACATCTTCTTCAAACGGGTTCACTCCATCCT
1 CGCTCCCTCTTTCTTTAGGGAGTATA-AACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCT
* *
31986 TCTTTAGGGAGTATAGAACTTGAACGATCTCCGCAAATAGGTT
65 TCTTTAGGGAGTATAGAACTCGAACGATCTCCGCAAACAGGTT
* * *
32029 CGCTCCCTCTTTCTTTAGGGAGTATGGAACTCAAACATCTTCTTCAAACGGGTTCGCTCACTCCT
1 CGCTCCCTCTTTCTTTAGGGAGTAT-AAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCT
*
32094 TCTTTAGGGAGTATAGAACTCGAACGATCTCCGCAAACAGGTC
65 TCTTTAGGGAGTATAGAACTCGAACGATCTCCGCAAACAGGTT
* * * * *
32137 CACTCCCTCTTTTTTTAGGGAGTATGGAACTCGAACATCTTTTTCAAACGGGTTCGCTCCCTCTT
1 CGCTCCCTCTTTCTTTAGGGAGTAT-AAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCT
* *
32202 TCTTTAGGGAGTATAGAACTCAAATGATCTCCGCAAACAGGTT
65 TCTTTAGGGAGTATAGAACTCGAACGATCTCCGCAAACAGGTT
*
32245 CGCTCCCTCTTTCTTTAGGGAGTATGAAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCG
1 CGCTCCCTCTTTCTTTAGGGAGTAT-AAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCT
*
32310 TCTTTAGGGAGTATGGAACT
65 TCTTTAGGGAGTATAGAACT
32330 TTAACAATCT
Statistics
Matches: 368, Mismatches: 38, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
108 364 0.99
109 4 0.01
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.32
Consensus pattern (107 bp):
CGCTCCCTCTTTCTTTAGGGAGTATAAACTCGAACATCTTCTTCAAACGGGTTCGCTCCCTCCTT
CTTTAGGGAGTATAGAACTCGAACGATCTCCGCAAACAGGTT
Found at i:32850 original size:37 final size:37
Alignment explanation
Indices: 32679--32858 Score: 202
Period size: 37 Copynumber: 4.9 Consensus size: 37
32669 TTACTCCAAC
* * * * *
32679 ACTCTTCTGAGAAGGCTTAAAATGGA-TTGCTTCACA
1 ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
*
32715 ACTCTTCGGTGAAGGCTT-AGAATAGATTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAG-ATTGATTTGCTTCACT
* * *
32752 ACTCTTTGGTGAAGGCTTAAGATTAACTTGCTTCACT
1 ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
** * * *
32789 ACTCTTTAGTGAAGGATTAGGATTGATTTGATTCACT
1 ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
32826 ACTCTTCGGTGAAGGCTTAAGATTGACTTTGCT
1 ACTCTTCGGTGAAGGCTTAAGATTGA-TTTGCT
32859 CTAATATCTT
Statistics
Matches: 120, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
35 1 0.01
36 20 0.17
37 92 0.77
38 7 0.06
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (37 bp):
ACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACT
Found at i:39989 original size:22 final size:25
Alignment explanation
Indices: 39946--39996 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 25
39936 TTAATTTATT
*
39946 TAATTACTTATTATATATATATTAA
1 TAATTACTTAGTATATATATATTAA
39971 TAATTACTT-GTA-ATA-ATATTAA
1 TAATTACTTAGTATATATATATTAA
39993 TAAT
1 TAAT
39997 AATAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 11 0.44
23 3 0.12
24 2 0.08
25 9 0.36
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (25 bp):
TAATTACTTAGTATATATATATTAA
Found at i:39997 original size:25 final size:25
Alignment explanation
Indices: 39946--39999 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
39936 TTAATTTATT
* *
39946 TAATTACTTATTATATATATATTAA
1 TAATTACTTATAATATATATAATAA
*
39971 TAATTACTTGTAATA-ATATTAATAA
1 TAATTACTTATAATATATA-TAATAA
39996 TAAT
1 TAAT
40000 AATAAACTTG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (25 bp):
TAATTACTTATAATATATATAATAA
Found at i:43808 original size:20 final size:20
Alignment explanation
Indices: 43780--43820 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
43770 CAACGATCCA
* *
43780 GGTCCGGTTAAACCGGTTTG
1 GGTCAGGTTAAACCGATTTG
*
43800 GGTCAGGTTAACCCGATTTG
1 GGTCAGGTTAAACCGATTTG
43820 G
1 G
43821 TTCTGCATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.20, G:0.34, T:0.29
Consensus pattern (20 bp):
GGTCAGGTTAAACCGATTTG
Found at i:45722 original size:546 final size:545
Alignment explanation
Indices: 44691--45783 Score: 1972
Period size: 546 Copynumber: 2.0 Consensus size: 545
44681 AACCTGATTA
*
44691 TTAACTTTATCTTTGATCGTTGGTAACGTTAAACGTTAACTTTCACCTAAAAGTTAAATTCTTTT
1 TTAACTTTATATTTGATCGTTGGTAACGTTAAACGTTAACTTTCACCTAAAAGTTAAATTCTTTT
*
44756 GAAAACTCTTATTTTATGTTTTTGACGTCCTGAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCA
66 AAAAACTCTTATTTTATGTTTTTGACGTCCTGAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCA
*
44821 AGCTTGATAAGTTGTTTTTCAATATTTCATCTGCCAATTCAATCAAATTTCCATGTTTAAGACAT
131 AACTTGATAAGTTGTTTTTCAATATTTCATCTGCCAATTCAATCAAATTTCCATGTTTAAGACAT
*
44886 ATTTCTGATATAATTCATTTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGAA
196 ATTTCTGATACAATTCATTTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGAA
* * * *
44951 GGTATTTGATTGGAGTTTAACAAATTGAACGATGTAGCTCGAGAATTGAGGTAATATGTTACTCC
261 GGAATTTGATTGCAGTTTAACAAATTAAACGATGTAGCTCGAGAATTGAGGTAATACGTTACTCC
*
45016 CCTTGCATGCAATATGGTATGAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTG
326 CCTTGAATGCAATATGGTATGAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTG
*
45081 TAATAAATATGGATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGAC
391 TAATAAATATGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGAC
*
45146 CCGAATGAATGATATTAAAATTTAAGAAATTTGTATGTAATTCTAATCTCAGTTATTGTTTGAAT
456 CCGAATGAATGATATTAAAATTTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAAT
45211 AAACAATTAATCTTGAAACATTCAT
521 AAACAATTAATCTTGAAACATTCAT
*
45236 TTAACTTTATATTTGATCGTTGGTAACGTTAAACGTTAACTTTCATCTAAAAGTTAAATTCTTTT
1 TTAACTTTATATTTGATCGTTGGTAACGTTAAACGTTAACTTTCACCTAAAAGTTAAATTCTTTT
*
45301 AAAAACTCTTATTTTATGTTTTTTGACGTCCTGAGTCTGAATCTGAAGTCTGTTTCTCCAAATTC
66 AAAAACTCTTATTTTATG-TTTTTGACGTCCTGAGTCTGAATCGGAAGTCTGTTTCTCCAAATTC
*
45366 AAACTTGGTAAGTTGTTTTTCAATATTTCATCTGCCAATTCAATCAAATTTCCATGTTTAAGACA
130 AAACTTGATAAGTTGTTTTTCAATATTTCATCTGCCAATTCAATCAAATTTCCATGTTTAAGACA
*
45431 TATTTCTGATGCAATTCA-TTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGA
195 TATTTCTGATACAATTCATTTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGA
* * *
45495 GGGAATTTGATTGCAGTTTAACAAATTAAATGATGTAGCTCGAGAATTGAGGTAATACGTTATTC
260 AGGAATTTGATTGCAGTTTAACAAATTAAACGATGTAGCTCGAGAATTGAGGTAATACGTTACTC
*
45560 CCCATTGAATGCAATATGGTATGAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGTT
325 CCC-TTGAATGCAATATGGTATGAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGAT
45625 TGTAATAAATATGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAG
389 TGTAATAAATATGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAG
*
45690 ACCCGAATGAATGCTATTAAAATTTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGA
454 ACCCGAATGAATGATATTAAAATTTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGA
*
45755 ATAAACAATTAATCTTGAAACGTTCAT
519 ATAAACAATTAATCTTGAAACATTCAT
45782 TT
1 TT
45784 TGAGTTGTCC
Statistics
Matches: 525, Mismatches: 21, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
545 187 0.36
546 338 0.64
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (545 bp):
TTAACTTTATATTTGATCGTTGGTAACGTTAAACGTTAACTTTCACCTAAAAGTTAAATTCTTTT
AAAAACTCTTATTTTATGTTTTTGACGTCCTGAGTCTGAATCGGAAGTCTGTTTCTCCAAATTCA
AACTTGATAAGTTGTTTTTCAATATTTCATCTGCCAATTCAATCAAATTTCCATGTTTAAGACAT
ATTTCTGATACAATTCATTTTTTCATGTATATGAAATATTATGGGAAGTCGAATTCATGTTTGAA
GGAATTTGATTGCAGTTTAACAAATTAAACGATGTAGCTCGAGAATTGAGGTAATACGTTACTCC
CCTTGAATGCAATATGGTATGAGTTAGGCAATTAGTTGATGCATAAATAAATATGTTTGAGATTG
TAATAAATATGAATTATTCTAAACTCATACTAACATTGGTAAAATGACGATAAATCGATTGAGAC
CCGAATGAATGATATTAAAATTTAAGAAATTTGTATGAAATTCTAATCTCAGTTATTGTTTGAAT
AAACAATTAATCTTGAAACATTCAT
Found at i:59655 original size:21 final size:22
Alignment explanation
Indices: 59621--59676 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
59611 AATCTTTTTT
*
59621 ATTGTGTA-AA-TTATCTTTGA
1 ATTGTGTACAATTTATCTTTAA
*
59641 ATT-TGTACAATTTATTTTTAA
1 ATTGTGTACAATTTATCTTTAA
*
59662 ATTGTTTACAATTTA
1 ATTGTGTACAATTTA
59677 AATGGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 11 0.37
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (22 bp):
ATTGTGTACAATTTATCTTTAA
Found at i:62373 original size:2 final size:2
Alignment explanation
Indices: 62366--62418 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
62356 GCGTAACAAC
62366 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
62408 AT AT AT GAT AT
1 AT AT AT -AT AT
62419 GTTTATTTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68433 original size:90 final size:89
Alignment explanation
Indices: 68313--68485 Score: 285
Period size: 90 Copynumber: 1.9 Consensus size: 89
68303 TAATCTTGAA
* *
68313 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCAC-AATATGA
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CC-CTAATATGA
68377 TTAGGGTAACTTGGATATAAGAGTAT
64 TTAGGGTAACTTGGATATAAGAGTAT
*
68403 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
*
68468 AGGGTAACTTGGCTATAA
66 AGGGTAACTTGGATATAA
68486 AAGGTTGTGT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
88 1 0.01
89 28 0.36
90 49 0.63
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTGGATATAAGAGTAT
Found at i:71064 original size:26 final size:26
Alignment explanation
Indices: 71031--71082 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
71021 CATGAACAGT
71031 GGGGGAATCGGTTCCTTGTTGGGGGG
1 GGGGGAATCGGTTCCTTGTTGGGGGG
71057 GGGGGAATCGGTTCCTTGTTGGGGGG
1 GGGGGAATCGGTTCCTTGTTGGGGGG
71083 AATCGGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.08, C:0.12, G:0.54, T:0.27
Consensus pattern (26 bp):
GGGGGAATCGGTTCCTTGTTGGGGGG
Found at i:71082 original size:21 final size:22
Alignment explanation
Indices: 71031--71091 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 22
71021 CATGAACAGT
71031 GGGGGAATCGGTTCCTTGTTGGGGGG
1 GGGGGAATCGGTTCCTTGTT----GG
71057 GGGGGAATCGGTTCCTTGTT-G
1 GGGGGAATCGGTTCCTTGTTGG
71078 GGGGGAATCGGTTC
1 GGGGGAATCGGTTC
71092 TCCTTTTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 15 0.43
26 20 0.57
ACGTcount: A:0.10, C:0.13, G:0.49, T:0.28
Consensus pattern (22 bp):
GGGGGAATCGGTTCCTTGTTGG
Found at i:71864 original size:24 final size:24
Alignment explanation
Indices: 71832--71877 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
71822 TCTTCCATAT
*
71832 GATGTATAAAACATTTATGTACAC
1 GATGTATAAAACATCTATGTACAC
71856 GATGTATAAAACATCTATGTAC
1 GATGTATAAAACATCTATGTAC
71878 CATGTCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (24 bp):
GATGTATAAAACATCTATGTACAC
Found at i:84469 original size:21 final size:21
Alignment explanation
Indices: 84444--84530 Score: 124
Period size: 21 Copynumber: 4.2 Consensus size: 21
84434 TCGATACCCA
* *
84444 CATCAGTGTTGATACTAATTG
1 CATCAGTATCGATACTAATTG
*
84465 CATCAATATCGATACTAATTG
1 CATCAGTATCGATACTAATTG
84486 CATCAGTATCGATACTAATTG
1 CATCAGTATCGATACTAATTG
*
84507 CGTCAGTATCGATACT-ATT-
1 CATCAGTATCGATACTAATTG
84526 CATCA
1 CATCA
84531 TAATTCTTCA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
19 4 0.07
20 3 0.05
21 53 0.88
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (21 bp):
CATCAGTATCGATACTAATTG
Found at i:89811 original size:116 final size:116
Alignment explanation
Indices: 89543--89818 Score: 275
Period size: 116 Copynumber: 2.4 Consensus size: 116
89533 TTGAACAAGC
* * * * *
89543 TCTCATATATGAACTTTTTCTCCCTAATTTGATGAGTTCTTCTCGTTATGAACCATTCCTCATAA
1 TCTCAT-TATGAACTTATTCTCCTTCATTTGATGAGTTCTTCTCATTATGAACCATTACTCATAA
* * * * *
89608 ATATTGATCCACCTCCTTATCTAATGGTTGTCTCAAGTTTTAAACAAGTTCT
65 ATATTCATCCACCTCCTTATATAATGGATGTCTCAAGTTCTAAACAACTTCT
* * * *
89660 TCTCATTATGAACTTCTTCT-CTCTCGTTGGATGAGTTCTTCTCATTATGAACCCTTACTCATAA
1 TCTCATTATGAACTTATTCTCCT-TCATTTGATGAGTTCTTCTCATTATGAACCATTACTCATAA
* **** * * * * * *
89724 ATGTTCATCTGTTTGCTTGTATGATGGATGTGTCGAGTTCTAAAGAACTTCT
65 ATATTCATCCACCTCCTTATATAATGGATGTCTCAAGTTCTAAACAACTTCT
* * *
89776 TCTTATTATGAACTTATTCTCCTTCATTTGTTGAGTTTTTCTC
1 TCTCATTATGAACTTATTCTCCTTCATTTGATGAGTTCTTCTC
89819 CTTTGTTAGA
Statistics
Matches: 127, Mismatches: 30, Indels: 5
0.78 0.19 0.03
Matches are distributed among these distances:
115 1 0.01
116 118 0.93
117 8 0.06
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (116 bp):
TCTCATTATGAACTTATTCTCCTTCATTTGATGAGTTCTTCTCATTATGAACCATTACTCATAAA
TATTCATCCACCTCCTTATATAATGGATGTCTCAAGTTCTAAACAACTTCT
Found at i:90240 original size:116 final size:113
Alignment explanation
Indices: 89960--90355 Score: 355
Period size: 116 Copynumber: 3.5 Consensus size: 113
89950 AGCTCTCCTA
* * * * ** *
89960 TATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATTATGAACCATTCATTTGAAATGTTGA
1 TATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACCCTTCATAAGAAATATTGA
* ** * * * *
90025 TATACCTCCCTGTGTGATGGATGTGTCTAGTTTTGAACAAGTTATTCTCAT
66 TATA-GTTACT-T-TGATGGACGTGTCGAGTTCTGAACAATTTATTCTCAT
* * * * * * *
90076 TATGAACTTTTTCTCCCTTGTTCGATAAGTTATTCTTATCATGAACCCTTCATAAAAAATATTGA
1 TATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACCCTTCATAAGAAATATTGA
90141 TATAGTTATCTCTTCGATGGACGTGTCGAGTTCTGAACAATTTATTCTCAT
66 TATAGTTA-CT-TT-GATGGACGTGTCGAGTTCTGAACAATTTATTCTCAT
* * * * * * *
90192 TATGAACTTCTTCTCCCTCGTTGGATTAGTTATTCTCAGTATGTACCCTTAATCAGAATTGATTC
1 TATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACCCTTCATAAGAAAT-ATTG
** * * * * *
90257 ACCTCGTTA-TATGATGGGCGTGCCGAGTTCTGAAAAAGTTT-TTCTCAT
65 ATATAGTTACTTTGATGGACGTGTCGAGTTCTGAACAA-TTTATTCTCAT
* * * *
90305 TATGAGCTTCTTCTTCCTCGGTGGACGAGTTATTCTCATTATGAACCCTTC
1 TATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACCCTTC
90356 CTCAAATTTT
Statistics
Matches: 227, Mismatches: 49, Indels: 11
0.79 0.17 0.04
Matches are distributed among these distances:
113 72 0.32
114 4 0.02
115 3 0.01
116 139 0.61
117 9 0.04
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (113 bp):
TATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTCATTATGAACCCTTCATAAGAAATATTGA
TATAGTTACTTTGATGGACGTGTCGAGTTCTGAACAATTTATTCTCAT
Found at i:95015 original size:13 final size:14
Alignment explanation
Indices: 94992--95021 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
94982 TTCCCATTAC
94992 AGACGTGCATATGA
1 AGACGTGCATATGA
95006 AGAC-TGCATATGA
1 AGACGTGCATATGA
95019 AGA
1 AGA
95022 TTGTTCAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (14 bp):
AGACGTGCATATGA
Found at i:118656 original size:2 final size:2
Alignment explanation
Indices: 118649--118680 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
118639 TTTAATTCCG
118649 AT AT AT 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 AT AT AT
118681 GTGTTATTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:123855 original size:40 final size:39
Alignment explanation
Indices: 123783--123861 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
123773 ACTGTGTATA
* * *
123783 AGGTGAGAACGGCTGACCTCAACACTATGGTGCATTATT
1 AGGTGAGAAAGGCTGACCTCAACACTACGGTGCAATATT
* *
123822 AGGTGAGAAAGGCTCGACCTTAACACTGCGGTGCAATATT
1 AGGTGAGAAAGGCT-GACCTCAACACTACGGTGCAATATT
123862 TGACTACTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
39 13 0.38
40 21 0.62
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (39 bp):
AGGTGAGAAAGGCTGACCTCAACACTACGGTGCAATATT
Found at i:133587 original size:20 final size:20
Alignment explanation
Indices: 133557--133605 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
133547 AGTGGCCCAA
133557 ATTTC-ACATTCAAACATCG
1 ATTTCAACATTCAAACATCG
*
133576 ATTTCAACATTCTAACATCG
1 ATTTCAACATTCAAACATCG
133596 ATTTCAACAT
1 ATTTCAACAT
133606 ATTTTAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTCAACATTCAAACATCG
Found at i:143110 original size:26 final size:26
Alignment explanation
Indices: 143081--143182 Score: 80
Period size: 26 Copynumber: 3.9 Consensus size: 26
143071 GAACACCATC
* *
143081 TTTATTACTCGCACTCAAAAGTGTCA
1 TTTATCACTCACACTCAAAAGTGTCA
* **
143107 TTTATCACGCACACTTGAAAGTGAT-A
1 TTTATCACTCACACTCAAAAGTG-TCA
* ** *
143133 TTTATAACTCACACTTTAAAGTGACA
1 TTTATCACTCACACTCAAAAGTGTCA
* * *
143159 CTTATCATTCGCACTCAAAAGTGT
1 TTTATCACTCACACTCAAAAGTGT
143183 TGTTTATACC
Statistics
Matches: 58, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
26 57 0.98
27 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (26 bp):
TTTATCACTCACACTCAAAAGTGTCA
Found at i:144479 original size:20 final size:20
Alignment explanation
Indices: 144449--144497 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
144439 AGTGGCCCAA
144449 ATTTC-ACATTCAAACATCG
1 ATTTCAACATTCAAACATCG
*
144468 ATTTCAACATTCTAACATCG
1 ATTTCAACATTCAAACATCG
144488 ATTTCAACAT
1 ATTTCAACAT
144498 ATTTTAACTA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 5 0.18
20 23 0.82
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTCAACATTCAAACATCG
Found at i:146738 original size:21 final size:21
Alignment explanation
Indices: 146700--146739 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
146690 CAATCATATA
146700 CAACTAGATCTCACACTTTGT
1 CAACTAGATCTCACACTTTGT
*
146721 CAACATAGATTTCA-ACTTT
1 CAAC-TAGATCTCACACTTT
146740 TCTTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.35
Consensus pattern (21 bp):
CAACTAGATCTCACACTTTGT
Found at i:148515 original size:12 final size:12
Alignment explanation
Indices: 148474--148528 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
148464 ATAGTATTAA
* *
148474 TTCATATTGCGT
1 TTCATGTTGCAT
* *
148486 TTCATATTGCAC
1 TTCATGTTGCAT
148498 TTCATGTTGCAT
1 TTCATGTTGCAT
*
148510 TTCATGTTCCAT
1 TTCATGTTGCAT
*
148522 TGCATGT
1 TTCATGT
148529 GAAATAGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (12 bp):
TTCATGTTGCAT
Found at i:152018 original size:19 final size:20
Alignment explanation
Indices: 151996--152057 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 20
151986 TTAGTTTAAA
151996 TAGGTTTTAGTATTTTA-AT
1 TAGGTTTTAGTATTTTAGAT
* * * *
152015 TAGGATTTAGAATATTATAT
1 TAGGTTTTAGTATTTTAGAT
**
152035 TATTTTTTAGGTATTTTAGAT
1 TAGGTTTTA-GTATTTTAGAT
152056 TA
1 TA
152058 AATAGTTTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 14 0.44
20 8 0.25
21 10 0.31
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.55
Consensus pattern (20 bp):
TAGGTTTTAGTATTTTAGAT
Found at i:166143 original size:23 final size:23
Alignment explanation
Indices: 166100--166143 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
166090 TTTGCTTCTC
*
166100 TTTTCTCTTTTCTCTTCCTTTTG
1 TTTTCTCTTTTCTCTTACTTTTG
* *
166123 TTTTGTCTTTTCTTTTACTTT
1 TTTTCTCTTTTCTCTTACTTT
166144 CTTACTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.02, C:0.20, G:0.05, T:0.73
Consensus pattern (23 bp):
TTTTCTCTTTTCTCTTACTTTTG
Found at i:171961 original size:11 final size:11
Alignment explanation
Indices: 171953--171979 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
171943 AACAAAAACA
171953 AAAATAAAAAT
1 AAAATAAAAAT
171964 AAAATAAAAAT
1 AAAATAAAAAT
171975 AAAAT
1 AAAAT
171980 GGGGGTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:171979 original size:5 final size:6
Alignment explanation
Indices: 171940--171978 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
171930 AAGATAAAGG
* *
171940 AAAAAC AAAAAC AAAAAT AAAAAT -AAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
171979 TGGGGGTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (6 bp):
AAAAAT
Found at i:172673 original size:1 final size:1
Alignment explanation
Indices: 172669--172724 Score: 67
Period size: 1 Copynumber: 56.0 Consensus size: 1
172659 AGAAAAAGGG
* * * * *
172669 AAAAAGAAAAAAAAAAAAAAAAGAAAAAAAAGAAAAAAAAAAAAGAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
172725 TAGATCTAAA
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 45 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (1 bp):
A
Found at i:172685 original size:13 final size:13
Alignment explanation
Indices: 172669--172724 Score: 87
Period size: 13 Copynumber: 4.2 Consensus size: 13
172659 AGAAAAAGGG
172669 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
172682 AAAAA-AAAAGAAA
1 AAAAAGAAAA-AAA
172695 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
172708 AAAAAGAAAAAAGA
1 AAAAAGAAAAAA-A
172722 AAA
1 AAA
172725 TAGATCTAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.10
13 28 0.70
14 8 0.20
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAAA
Found at i:173569 original size:43 final size:44
Alignment explanation
Indices: 173468--173578 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
173458 TGTTACTCGA
* * *
173468 TCCTTCACAGAAGGAGTTGGATTAGTGACAAACCTTTGACTTGG
1 TCCTTCACAGAAGGAGTTGGATCAGTGACAAACATTTCACTTGG
* * * *
173512 TCCTTCATAGAAGGAGTTTGATCAGTGA-AAATATTTCTCTTGG
1 TCCTTCACAGAAGGAGTTGGATCAGTGACAAACATTTCACTTGG
* * *
173555 TTCTTCACAAAAGGAGTTGAATCA
1 TCCTTCACAGAAGGAGTTGGATCA
173579 ACGTTAATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 30 0.55
44 25 0.45
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
TCCTTCACAGAAGGAGTTGGATCAGTGACAAACATTTCACTTGG
Found at i:174273 original size:12 final size:12
Alignment explanation
Indices: 174244--174287 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
174234 CATAGTATTA
* *
174244 TTCATATTGAAT
1 TTCATGTTGCAT
174256 TTCATGTTGCAT
1 TTCATGTTGCAT
*
174268 TTCATGTTCCAT
1 TTCATGTTGCAT
*
174280 TGCATGTT
1 TTCATGTT
174288 AAGTAGTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.20, C:0.16, G:0.14, T:0.50
Consensus pattern (12 bp):
TTCATGTTGCAT
Found at i:177203 original size:26 final size:26
Alignment explanation
Indices: 177174--177266 Score: 116
Period size: 26 Copynumber: 3.6 Consensus size: 26
177164 TTGTACACAG
177174 AGTGCCATTTATCACTTGCACTCGAA
1 AGTGCCATTTATCACTTGCACTCGAA
*
177200 AGTG-CAATTATCACTTGCACTCGAA
1 AGTGCCATTTATCACTTGCACTCGAA
* ** * *
177225 AGTTCCATTTATCACTCACAATCAAA
1 AGTGCCATTTATCACTTGCACTCGAA
*
177251 AGAGCCATTTATCACT
1 AGTGCCATTTATCACT
177267 CGCGCTAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
25 23 0.40
26 34 0.60
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (26 bp):
AGTGCCATTTATCACTTGCACTCGAA
Found at i:178936 original size:32 final size:32
Alignment explanation
Indices: 178874--178955 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
178864 CAGACAACCT
* *
178874 AAGGGA-CTATCTTGGAGCCTTAGAGCCTACCC
1 AAGGGAGC-ATCTTGGGGCCTAAGAGCCTACCC
* * *
178906 AATGGAGTATGTTGGGGCCTAAGAGCCTACCC
1 AAGGGAGCATCTTGGGGCCTAAGAGCCTACCC
178938 AAGGGAGCATCTTGGGGC
1 AAGGGAGCATCTTGGGGC
178956 ATAAAATCTA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (32 bp):
AAGGGAGCATCTTGGGGCCTAAGAGCCTACCC
Found at i:181661 original size:22 final size:23
Alignment explanation
Indices: 181631--181675 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
181621 ATTTTACTAC
181631 TGTTGGGTTGTA-GAGTCATGGT
1 TGTTGGGTTGTAGGAGTCATGGT
* *
181653 TGTTTGGTTGTAGGTGTCATGGT
1 TGTTGGGTTGTAGGAGTCATGGT
181676 ATAAGATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.11, C:0.04, G:0.40, T:0.44
Consensus pattern (23 bp):
TGTTGGGTTGTAGGAGTCATGGT
Found at i:182464 original size:20 final size:19
Alignment explanation
Indices: 182421--182465 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
182411 AAGTGGCTTA
182421 AATTTCACACTCTAACATC
1 AATTTCACACTCTAACATC
* * *
182440 GATTTCAACATTCTAACATT
1 AATTTC-ACACTCTAACATC
182460 AATTTC
1 AATTTC
182466 CAGCATAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTTCACACTCTAACATC
Found at i:187272 original size:3 final size:3
Alignment explanation
Indices: 187260--187309 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
187250 ATTCTTCTTC
* * * * *
187260 TTA TTC TTA TTA TTA TTA TCA TCA TCA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
187308 TT
1 TT
187310 TTACTCATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.30, C:0.10, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:191270 original size:22 final size:22
Alignment explanation
Indices: 191244--191288 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
191234 GTGTTTATTT
* *
191244 TGGATCAGAGCTTGTTTTTGGG
1 TGGATCAAAGCTTGTTATTGGG
191266 TGGATCAAAGCTTGTTATTGGG
1 TGGATCAAAGCTTGTTATTGGG
191288 T
1 T
191289 TGAATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (22 bp):
TGGATCAAAGCTTGTTATTGGG
Found at i:198317 original size:28 final size:28
Alignment explanation
Indices: 198277--198333 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
198267 GACATGACCA
198277 TGGTCACGGTCGCCACTAGATTCAGGAG
1 TGGTCACGGTCGCCACTAGATTCAGGAG
* *
198305 TGGTCGCGGTCGCCACTAGATTCGGGAG
1 TGGTCACGGTCGCCACTAGATTCAGGAG
198333 T
1 T
198334 ATTCCTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.23
Consensus pattern (28 bp):
TGGTCACGGTCGCCACTAGATTCAGGAG
Found at i:200754 original size:16 final size:15
Alignment explanation
Indices: 200733--200769 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
200723 TCCCCCTTTT
200733 ATATTTATTACTATTA
1 ATATTTATTA-TATTA
200749 ATATTTATTATATTA
1 ATATTTATTATATTA
*
200764 TTATTT
1 ATATTT
200770 TTCATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:215716 original size:21 final size:22
Alignment explanation
Indices: 215682--215737 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
215672 AATCTTTTTT
*
215682 ATTGTGTA-AA-TTATCTTTGA
1 ATTGTGTACAATTTATCTTTAA
*
215702 ATT-TGTACAATTTATTTTTAA
1 ATTGTGTACAATTTATCTTTAA
*
215723 ATTGTTTACAATTTA
1 ATTGTGTACAATTTA
215738 AATGGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 11 0.37
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (22 bp):
ATTGTGTACAATTTATCTTTAA
Found at i:215739 original size:16 final size:17
Alignment explanation
Indices: 215718--215753 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
215708 ACAATTTATT
*
215718 TTTAAATTGTTT-ACAA
1 TTTAAATGGTTTGACAA
215734 TTTAAATGGTTTGACAA
1 TTTAAATGGTTTGACAA
215751 TTT
1 TTT
215754 TTTTCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTAAATGGTTTGACAA
Found at i:231074 original size:90 final size:89
Alignment explanation
Indices: 230960--231134 Score: 287
Period size: 90 Copynumber: 2.0 Consensus size: 89
230950 AATAATCCCG
* * *
230960 ATTATTTAATTTCAATTAATTAAATATATATTTAATTAATTTAAAATAATAAAATCCCTAATATG
1 ATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATG
231025 ATTAGGGTAACTTGGATATAAGAGT
65 ATTAGGGTAACTTGGATATAAGAGT
* *
231050 ATTATTAAATTCCAATTTATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGA
1 ATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGA
*
231115 TTAGGGTAACTTGGCTATAA
66 TTAGGGTAACTTGGATATAA
231135 AAGGTTGTGT
Statistics
Matches: 79, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 30 0.38
90 49 0.62
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (89 bp):
ATTATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGA
TTAGGGTAACTTGGATATAAGAGT
Found at i:259819 original size:16 final size:16
Alignment explanation
Indices: 259798--259829 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
259788 GAAAGTATGC
*
259798 TTCTAATCTTATTTCG
1 TTCTAATATTATTTCG
259814 TTCTAATATTATTTCG
1 TTCTAATATTATTTCG
259830 ATGGAGGCTC
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:0.22, C:0.16, G:0.06, T:0.56
Consensus pattern (16 bp):
TTCTAATATTATTTCG
Found at i:264240 original size:116 final size:115
Alignment explanation
Indices: 263999--264274 Score: 273
Period size: 116 Copynumber: 2.4 Consensus size: 115
263989 TTGAACAAGC
* ** *
263999 TCTCATATATGAACTTTTTCTCCCTAATTTGATGAGTTATTCTCATTATGAACCATTCCTCATAA
1 TCTCAT-TATGAACTTATTCT-CCTCGTTTGATGAGTTATTCTCATTATGAACCATTACTCATAA
* * * * * *
264064 ATGTTGATCCACCTCCTTATCCAATGGTTGTCTCAAGTTTTAAACAAGTTAT
64 ATGTTCATCCACCACCTTATACAATGGATGTCTCAAGTTCTAAACAACTTAT
* * * *
264116 TCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACCCTTACTCATAAA
1 TCTCATTATGAACTTATTCTC-CTCGTTTGATGAGTTATTCTCATTATGAACCATTACTCATAAA
** * * ** * * * *
264181 TGTTCATCCGTCAGCTTGTATGATGGATGTGTCGAGTTCTAAAGAACTTCT
65 TGTTCATCCACCACCTTATACAATGGATGTCTCAAGTTCTAAACAACTTAT
* * *
264232 TCTTATTATGAACTTATTCTCCTTCGTTTGTTGAGTTTTTCTC
1 TCTCATTATGAACTTATTCTCC-TCGTTTGATGAGTTATTCTC
264275 CTTCGTTAGA
Statistics
Matches: 129, Mismatches: 28, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
115 2 0.02
116 121 0.94
117 6 0.05
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (115 bp):
TCTCATTATGAACTTATTCTCCTCGTTTGATGAGTTATTCTCATTATGAACCATTACTCATAAAT
GTTCATCCACCACCTTATACAATGGATGTCTCAAGTTCTAAACAACTTAT
Found at i:264273 original size:22 final size:22
Alignment explanation
Indices: 264248--264290 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
264238 TATGAACTTA
* *
264248 TTCTCCTTCGTTTGTTGAGTTT
1 TTCTCCTTCGTTAGATGAGTTT
264270 TTCTCCTTCGTTAGATGAGTT
1 TTCTCCTTCGTTAGATGAGTT
264291 CTTATCATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (22 bp):
TTCTCCTTCGTTAGATGAGTTT
Found at i:264696 original size:116 final size:115
Alignment explanation
Indices: 264420--264811 Score: 344
Period size: 116 Copynumber: 3.4 Consensus size: 115
264410 CTCCTATATA
* * * * * * * *
264420 AACTTCTTCTCCCTCTTTGGATGAGTTCTTCTCATTATGAACCATTCCTTAGAAATGTTGATATA
1 AACTTCTTCTCCCTCGTTGGATAAGTTATTCTCA-TATGAACCCTTCATAAAAAATGTTGATACA
* * * * *
264485 CCTCCTTGTGTGATGGATGTGTCTATTTTTGAACAAGTTATTCTCATTATG
65 CCTCCTTGTGCGATGGACGTGTCGAGTTCTGAACAAGTTATTCTCATTATG
* * * *
264536 AACTTTTTCTCCCTTGTTGGATAAGTTATTCTTATCATGAACCCTTCATAAAAAATGTTGATCCA
1 AACTTCTTCTCCCTCGTTGGATAAGTTATTCTCAT-ATGAACCCTTCATAAAAAATGTTGATACA
* *
264601 GCTCTCTCT-T-CGATGGACGTGTCGAGTTCTGAACAATTTATTCTCATTATG
65 CCTC-CT-TGTGCGATGGACGTGTCGAGTTCTGAACAAGTTATTCTCATTATG
* * * * * *
264652 AACTTCTTCTCCCTCGTTGGATTAGTTATTCTCAGTATGTACCCTTAAT-CAGAA--TTGATTCA
1 AACTTCTTCTCCCTCGTTGGATAAGTTATTCTCA-TATGAACCCTTCATAAAAAATGTTGATACA
* ** * * * *
264714 CCTCCTTATATGATGGATGTGCCGAGTTCTGAAAAAGTTTTTCTCATTATG
65 CCTCCTTGTGCGATGGACGTGTCGAGTTCTGAACAAGTTATTCTCATTATG
* * * * * * *
264765 AGCTTATTTTTCCTCGGTGAATAAGTTATTCTCATTATAAACCCTTC
1 AACTTCTTCTCCCTCGTTGGATAAGTTATTCTCA-TATGAACCCTTC
264812 CTCAGAAAAG
Statistics
Matches: 224, Mismatches: 46, Indels: 15
0.79 0.16 0.05
Matches are distributed among these distances:
111 1 0.00
112 3 0.01
113 81 0.36
115 4 0.02
116 130 0.58
117 4 0.02
118 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (115 bp):
AACTTCTTCTCCCTCGTTGGATAAGTTATTCTCATATGAACCCTTCATAAAAAATGTTGATACAC
CTCCTTGTGCGATGGACGTGTCGAGTTCTGAACAAGTTATTCTCATTATG
Found at i:268194 original size:21 final size:21
Alignment explanation
Indices: 268168--268209 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
268158 ATCCTAACTA
268168 CTTATATCTGGGTGATTTGTG
1 CTTATATCTGGGTGATTTGTG
268189 CTTATATCTGGGTGATTTGTG
1 CTTATATCTGGGTGATTTGTG
268210 ATATGTAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.14, C:0.10, G:0.29, T:0.48
Consensus pattern (21 bp):
CTTATATCTGGGTGATTTGTG
Found at i:282305 original size:17 final size:18
Alignment explanation
Indices: 282273--282306 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
282263 TAATCATTTC
282273 ATAAACCCTAATATTTTT
1 ATAAACCCTAATATTTTT
282291 ATAAACCCTAA-ATTTT
1 ATAAACCCTAATATTTT
282307 AGGATTTTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (18 bp):
ATAAACCCTAATATTTTT
Found at i:291735 original size:39 final size:39
Alignment explanation
Indices: 291664--291741 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
291654 ACTGTGTATA
* * * *
291664 AGGTGAGAACGGCTGACCTCAGCACCATGGTGCATTATT
1 AGGTGAGAAAGGCTGACCTCAACACCACGGTGCAATATT
*
291703 AGGTGAGAAAGGCTCGACC-CAACACTACGGTGCAATATT
1 AGGTGAGAAAGGCT-GACCTCAACACCACGGTGCAATATT
291742 TGACTCCTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 29 0.88
40 4 0.12
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (39 bp):
AGGTGAGAAAGGCTGACCTCAACACCACGGTGCAATATT
Found at i:300039 original size:26 final size:26
Alignment explanation
Indices: 300010--300111 Score: 71
Period size: 26 Copynumber: 3.9 Consensus size: 26
300000 AACACCATCC
*
300010 TTTATTACTCGCACTCAAAAGTGTCA
1 TTTATCACTCGCACTCAAAAGTGTCA
* * * **
300036 TTTATCACGCACATTTGAAAGTGAT-A
1 TTTATCACTCGCACTCAAAAGTG-TCA
* ** * *
300062 TTTATAACTCGCACTTTAAACTGACA
1 TTTATCACTCGCACTCAAAAGTGTCA
* *
300088 CTTATCATTCGCACTCAAAAGTGT
1 TTTATCACTCGCACTCAAAAGTGT
300112 TGTTTATACC
Statistics
Matches: 54, Mismatches: 20, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
26 53 0.98
27 1 0.02
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (26 bp):
TTTATCACTCGCACTCAAAAGTGTCA
Found at i:301411 original size:20 final size:20
Alignment explanation
Indices: 301381--301437 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
301371 AGTGGCCCAA
*
301381 ATTTC-ACATTCAAACATCG
1 ATTTCAACATTCTAACATCG
301400 ATTTCAACATTCTAACATCG
1 ATTTCAACATTCTAACATCG
*
301420 ATTTAAACATTCTAACAT
1 ATTTCAACATTCTAACAT
301438 TAATTTACAG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 5 0.14
20 30 0.86
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTCAACATTCTAACATCG
Found at i:305594 original size:12 final size:12
Alignment explanation
Indices: 305553--305607 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 12
305543 ATAGTATTAA
* *
305553 TTCATATTGCGT
1 TTCATGTTGCAT
* *
305565 TTCATATTGCAC
1 TTCATGTTGCAT
305577 TTCATGTTGCAT
1 TTCATGTTGCAT
*
305589 TTCATGTTCCAT
1 TTCATGTTGCAT
*
305601 TGCATGT
1 TTCATGT
305608 GAAAAAGTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 37 1.00
ACGTcount: A:0.18, C:0.20, G:0.15, T:0.47
Consensus pattern (12 bp):
TTCATGTTGCAT
Found at i:309055 original size:33 final size:33
Alignment explanation
Indices: 309011--309074 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 33
309001 TTTAAATAGG
309011 TTTTTAGTATTTTAAT-TTAGTTTTAGGATATTAT
1 TTTTTAGTATTTT-ATCTTAGTTTTAGG-TATTAT
*
309045 TTTTTA-TATTTTATCTTTGTTTTAGGTATT
1 TTTTTAGTATTTTATCTTAGTTTTAGGTATT
309075 TTAGTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
32 6 0.21
33 16 0.57
34 6 0.21
ACGTcount: A:0.22, C:0.02, G:0.11, T:0.66
Consensus pattern (33 bp):
TTTTTAGTATTTTATCTTAGTTTTAGGTATTAT
Found at i:325702 original size:19 final size:17
Alignment explanation
Indices: 325667--325715 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
325657 TCAAATGGCA
*
325667 ATCATTTTTTCTTTCAT
1 ATCATTTTTTTTTTCAT
325684 ATCATTATTTTTTTATCAT
1 ATCATT-TTTTTTT-TCAT
*
325703 TTC-TTTTTTTTTT
1 ATCATTTTTTTTTT
325716 GTTTTGCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 8 0.29
19 6 0.21
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.71
Consensus pattern (17 bp):
ATCATTTTTTTTTTCAT
Found at i:329252 original size:1 final size:1
Alignment explanation
Indices: 329242--329282 Score: 55
Period size: 1 Copynumber: 41.0 Consensus size: 1
329232 AAGATAAAGG
* * *
329242 AAAAACAAAAACAAAAATAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
329283 TGGGGGTTCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.93, C:0.05, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:329981 original size:13 final size:13
Alignment explanation
Indices: 329950--330007 Score: 52
Period size: 13 Copynumber: 4.7 Consensus size: 13
329940 CACATTTTTT
*
329950 AAAATAAAAGAGA
1 AAAAGAAAAGAGA
* *
329963 ATAAGAAAAGGGA
1 AAAAGAAAAGAGA
329976 AAAAGAAAA-A-A
1 AAAAGAAAAGAGA
329987 AAGAA-AAAAGA-A
1 AA-AAGAAAAGAGA
329999 AAAAGAAAA
1 AAAAGAAAA
330008 TAGGAGAAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
11 9 0.24
12 10 0.27
13 18 0.49
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAGAGA
Found at i:329985 original size:7 final size:7
Alignment explanation
Indices: 329983--330007 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
329973 GGAAAAAGAA
329983 AAAAAAG
1 AAAAAAG
329990 AAAAAAG
1 AAAAAAG
329997 AAAAAAG
1 AAAAAAG
330004 AAAA
1 AAAA
330008 TAGGAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:330018 original size:14 final size:14
Alignment explanation
Indices: 329955--330007 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
329945 TTTTTAAAAT
*
329955 AAAAGAGAATAAGAA
1 AAAAGA-AAAAAGAA
** *
329970 AAGGGAAAAAGAAAA
1 AAAAGAAAAA-AGAA
329985 AAAAGAAAAAAGAA
1 AAAAGAAAAAAGAA
329999 AAAAGAAAA
1 AAAAGAAAA
330008 TAGGAGAAAG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
14 15 0.50
15 15 0.50
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.02
Consensus pattern (14 bp):
AAAAGAAAAAAGAA
Found at i:331720 original size:19 final size:20
Alignment explanation
Indices: 331696--331733 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
331686 CAAAAAAATA
*
331696 AGTCCATTT-TATTAGTTTT
1 AGTCCATTTGCATTAGTTTT
331715 AGTCCATTTGCATTAGTTT
1 AGTCCATTTGCATTAGTTT
331734 ACATAGACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.21, C:0.13, G:0.13, T:0.53
Consensus pattern (20 bp):
AGTCCATTTGCATTAGTTTT
Found at i:334501 original size:26 final size:26
Alignment explanation
Indices: 334472--334628 Score: 127
Period size: 26 Copynumber: 6.1 Consensus size: 26
334462 TTGTACACAG
*
334472 AGTGCCATTTATCACTTGCACTCGAA
1 AGTGCCATTTATCACTCGCACTCGAA
* * *
334498 AGTG-CAATTATCACTTGCAGTCGAA
1 AGTGCCATTTATCACTCGCACTCGAA
* * * *
334523 AGTTCCATTTATCACTCACAATCAAA
1 AGTGCCATTTATCACTCGCACTCGAA
* *
334549 AGAGCCATTTATCACTCGCACTAGAA
1 AGTGCCATTTATCACTCGCACTCGAA
* * * **
334575 AATTCTATTTATCACTCATACTCGAA
1 AGTGCCATTTATCACTCGCACTCGAA
** * * *
334601 AGTGTTATTTGTGACTCGCACTCAAA
1 AGTGCCATTTATCACTCGCACTCGAA
334627 AG
1 AG
334629 CATTATTTAT
Statistics
Matches: 101, Mismatches: 29, Indels: 2
0.77 0.22 0.02
Matches are distributed among these distances:
25 22 0.22
26 79 0.78
ACGTcount: A:0.32, C:0.24, G:0.13, T:0.31
Consensus pattern (26 bp):
AGTGCCATTTATCACTCGCACTCGAA
Found at i:336222 original size:32 final size:32
Alignment explanation
Indices: 336181--336241 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
336171 TTGGATCCTT
* * *
336181 AGAGCCTACCCAATGGAGTATGTTGGGGCCTA
1 AGAGCCTACCCAAGGGAGAATCTTGGGGCCTA
336213 AGAGCCTACCCAAGGGAGAATCTTGGGGC
1 AGAGCCTACCCAAGGGAGAATCTTGGGGC
336242 ATAAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.33, T:0.18
Consensus pattern (32 bp):
AGAGCCTACCCAAGGGAGAATCTTGGGGCCTA
Found at i:340122 original size:20 final size:19
Alignment explanation
Indices: 340079--340123 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
340069 AAGTGGCTCA
340079 AATTTCACAGTCTAACATC
1 AATTTCACAGTCTAACATC
* * *
340098 GATTTCAACATTCTAACATT
1 AATTTC-ACAGTCTAACATC
340118 AATTTC
1 AATTTC
340124 CAGCATAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.22, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTTCACAGTCTAACATC
Found at i:349941 original size:3 final size:3
Alignment explanation
Indices: 349933--349967 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
349923 TCAAATTCCA
* *
349933 TTC TTC TTC TTA TTC TTC TTC TTA TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
349968 ATTATTATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.26, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:349948 original size:6 final size:6
Alignment explanation
Indices: 349932--350006 Score: 69
Period size: 6 Copynumber: 12.5 Consensus size: 6
349922 TTCAAATTCC
* * * * *
349932 ATTCTT CTTCTT ATTCTT CTTCTT ATTCTT CTTCTT ATTATT ATTATT
1 ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT ATTCTT
* * * *
349980 ATTGTT ATTATT ATTATT ATTATT ATT
1 ATTCTT ATTCTT ATTCTT ATTCTT ATT
350007 ATTACTATTC
Statistics
Matches: 60, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.20, C:0.12, G:0.01, T:0.67
Consensus pattern (6 bp):
ATTCTT
Found at i:349949 original size:12 final size:12
Alignment explanation
Indices: 349932--349970 Score: 78
Period size: 12 Copynumber: 3.2 Consensus size: 12
349922 TTCAAATTCC
349932 ATTCTTCTTCTT
1 ATTCTTCTTCTT
349944 ATTCTTCTTCTT
1 ATTCTTCTTCTT
349956 ATTCTTCTTCTT
1 ATTCTTCTTCTT
349968 ATT
1 ATT
349971 ATTATTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTCTTCTTCTT
Found at i:349972 original size:3 final size:3
Alignment explanation
Indices: 349966--350015 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
349956 ATTCTTCTTC
* *
349966 TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
350014 TT
1 TT
350016 CTATTCATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:361085 original size:28 final size:28
Alignment explanation
Indices: 361045--361101 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
361035 GACATGACCA
*
361045 TGGTCACGGTCGCCACTAGATTTGGGAG
1 TGGTCACGGTCGCCACTAGATTCGGGAG
* *
361073 TGGTCGCGGTCGCCGCTAGATTCGGGAG
1 TGGTCACGGTCGCCACTAGATTCGGGAG
361101 T
1 T
361102 ATTCGTTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.14, C:0.23, G:0.39, T:0.25
Consensus pattern (28 bp):
TGGTCACGGTCGCCACTAGATTCGGGAG
Found at i:363538 original size:7 final size:7
Alignment explanation
Indices: 363506--363565 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
363496 AAATCCCCCT
363506 TTTA-TA
1 TTTATTA
363512 TTTATTA
1 TTTATTA
*
363519 CTATTAATA
1 -T-TTATTA
363528 TTTATTA
1 TTTATTA
363535 TTTATTA
1 TTTATTA
363542 TTT-TTCA
1 TTTATT-A
*
363549 TTTTTTA
1 TTTATTA
*
363556 TTTTTTA
1 TTTATTA
363563 TTT
1 TTT
363566 TAATATATCT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
6 6 0.13
7 32 0.68
8 4 0.09
9 5 0.11
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATTA
Found at i:363556 original size:21 final size:21
Alignment explanation
Indices: 363527--363566 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
363517 TACTATTAAT
363527 ATTTATTATTTATTATTTTTC
1 ATTTATTATTTATTATTTTTC
* *
363548 ATTTTTTATTTTTTATTTT
1 ATTTATTATTTATTATTTT
363567 AATATATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (21 bp):
ATTTATTATTTATTATTTTTC
Found at i:363566 original size:7 final size:7
Alignment explanation
Indices: 363526--363566 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
363516 TTACTATTAA
*
363526 TATTTAT
1 TATTTTT
*
363533 TATTTAT
1 TATTTTT
363540 TATTTTT
1 TATTTTT
*
363547 CATTTTT
1 TATTTTT
363554 TATTTTT
1 TATTTTT
363561 TATTTT
1 TATTTT
363567 AATATATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (7 bp):
TATTTTT
Found at i:374391 original size:17 final size:18
Alignment explanation
Indices: 374369--374415 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
374359 TCAAATGGCA
374369 ATCATTTTTTCTT-TCAT
1 ATCATTTTTTCTTATCAT
*
374386 ATCATTATTTTTTTATCAT
1 ATCATT-TTTTCTTATCAT
* *
374405 TTCTTTTTTTC
1 ATCATTTTTTC
374416 GTTTTGCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.17, C:0.15, G:0.00, T:0.68
Consensus pattern (18 bp):
ATCATTTTTTCTTATCAT
Found at i:377142 original size:19 final size:20
Alignment explanation
Indices: 377107--377144 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
377097 CATATCATTA
377107 TTTGTTTATCATTTCTTTTT
1 TTTGTTTATCATTTCTTTTT
*
377127 TTTGTTT-TCCTTTCTTTT
1 TTTGTTTATCATTTCTTTT
377145 CTCCAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.05, C:0.13, G:0.05, T:0.76
Consensus pattern (20 bp):
TTTGTTTATCATTTCTTTTT
Found at i:383921 original size:232 final size:232
Alignment explanation
Indices: 383506--383924 Score: 540
Period size: 233 Copynumber: 1.8 Consensus size: 232
383496 AGAGAAGAAC
* *
383506 AAAAATAAAATCAGAATATATTTGCTAAGAGTCCAACTCAAAAGACACAATAATATGTTACAAAG
1 AAAAATAAAATCAGAATATAATTGCTAAGAGTCCAACTCAAAAAACACAATAATATGTTACAAAG
* * * * * *
383571 GGTAATTTTCTTTTGTAATAAATTAGGATATATGATGAGAAATTGAGTTATGAAATAATAAGAAA
66 GGT-ATCTTCTTTTATAATAAATTAGGATATATAAGGAGAAATTGAATTATAAAATAATAAGAAA
* * *** * *
383636 TTACTTTGGTTATTTTGTGTGATTTAGGGGTTGCAAGTTTTATAATCTCATAATTAGGAAAATTT
130 TTACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATAATATCATAATTAGGAAAATTT
383701 TAAAGATGAGATTTGAAAAGCGCATATAAAGATTAGGG
195 TAAAGATGAGATTTGAAAAGCGCATATAAAGATTAGGG
* * * * * *
383739 AAAAATAAAATCATAATGTAATTGTTAAGGGTCCAACTCAAAAAAGATAATAATATGTTACATAA
1 AAAAATAAAATCAGAATATAATTGCTAAGAGTCCAACTCAAAAAACACAATAATATGTTACA-AA
* *
383804 TGTGGT-TCTT-TTTTATATTAAGTTATGGA-ATATAAGGAGAAATTGAATTA-AAAATAATAAG
65 -G-GGTATCTTCTTTTATAATAAATTA-GGATATATAAGGAGAAATTGAATTATAAAATAATAAG
* *
383865 CAATTACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATGATATCATAATTAG
127 AAATTACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATAATATCATAATTAG
383925 TAATACTTTT
Statistics
Matches: 157, Mismatches: 25, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
232 61 0.39
233 84 0.54
234 8 0.05
235 1 0.01
236 3 0.02
ACGTcount: A:0.41, C:0.07, G:0.17, T:0.35
Consensus pattern (232 bp):
AAAAATAAAATCAGAATATAATTGCTAAGAGTCCAACTCAAAAAACACAATAATATGTTACAAAG
GGTATCTTCTTTTATAATAAATTAGGATATATAAGGAGAAATTGAATTATAAAATAATAAGAAAT
TACTTTGGTTACTCTACATGATTTAGGGGTTACAAGTTTTATAATATCATAATTAGGAAAATTTT
AAAGATGAGATTTGAAAAGCGCATATAAAGATTAGGG
Found at i:390209 original size:3 final size:3
Alignment explanation
Indices: 390173--390258 Score: 127
Period size: 3 Copynumber: 28.7 Consensus size: 3
390163 TCAAATTCCA
* * * *
390173 TTC TTC TTT TTC TTT TTC TTA TTC TTC TTA TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
*
390221 TTC TTC TTC TTC TTC GTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
390259 ATTATTATTA
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.02, C:0.28, G:0.01, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:390263 original size:3 final size:3
Alignment explanation
Indices: 390257--390333 Score: 147
Period size: 3 Copynumber: 26.0 Consensus size: 3
390247 CTTCTTCTTC
390257 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
390305 -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
390334 CTACTATTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 71 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:394822 original size:54 final size:54
Alignment explanation
Indices: 394750--395016 Score: 385
Period size: 54 Copynumber: 4.9 Consensus size: 54
394740 CGTAGTACTT
* * **
394750 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTTA
1 ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
* * *
394804 ATACAGTAGTTCATCAACATATGATAAATTTCGTGGGTTGCACACTTAGTATCG
1 ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
* * * * *
394858 ATACGGTCGTTCATCAACACATGTTGAGTTTCGTGGGTTGCACACTTAGTGTTG
1 ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
394912 ATACAGTCGTTCATCAACATATGATGAATTAT-GTGGGTTGCACACTTAGTGTCG
1 ATACAGTCGTTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTAGTGTCG
*
394966 ATACGGTCGTTCATCAACATATGATGAA-TTCGATGGGTTGCACACTTAGTG
1 ATACAGTCGTTCATCAACATATGATGAATTTCG-TGGGTTGCACACTTAGTG
395017 CTGATAGTAC
Statistics
Matches: 189, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
52 1 0.01
53 2 0.01
54 185 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (54 bp):
ATACAGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTAGTGTCG
Found at i:395022 original size:108 final size:107
Alignment explanation
Indices: 394750--395022 Score: 431
Period size: 108 Copynumber: 2.5 Consensus size: 107
394740 CGTAGTACTT
*
394750 ATACGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCACACTTAGTGTTAATACAGTAGTT
1 ATACGGTCGTTCATCAACATATGATGAATT-CGTGGGTTGCACACTTAGTGTTGATACAGTAGTT
394815 CATCAACATATGATAAATTTCGTGGGTTGCACACTTAGTATCG
65 CATCAACATATGATAAATTTCGTGGGTTGCACACTTAGTATCG
* * * *
394858 ATACGGTCGTTCATCAACACATGTTGAGTTTCGTGGGTTGCACACTTAGTGTTGATACAGTCGTT
1 ATACGGTCGTTCATCAACATATGATGA-ATTCGTGGGTTGCACACTTAGTGTTGATACAGTAGTT
* *
394923 CATCAACATATGATGAATTAT-GTGGGTTGCACACTTAGTGTCG
65 CATCAACATATGATAAATT-TCGTGGGTTGCACACTTAGTATCG
*
394966 ATACGGTCGTTCATCAACATATGATGAATTCGATGGGTTGCACACTTAGTGCTGATA
1 ATACGGTCGTTCATCAACATATGATGAATTCG-TGGGTTGCACACTTAGTGTTGATA
395023 GTACACATAG
Statistics
Matches: 151, Mismatches: 11, Indels: 6
0.90 0.07 0.04
Matches are distributed among these distances:
107 4 0.03
108 144 0.95
109 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (107 bp):
ATACGGTCGTTCATCAACATATGATGAATTCGTGGGTTGCACACTTAGTGTTGATACAGTAGTTC
ATCAACATATGATAAATTTCGTGGGTTGCACACTTAGTATCG
Found at i:401534 original size:54 final size:54
Alignment explanation
Indices: 401468--402217 Score: 913
Period size: 54 Copynumber: 13.9 Consensus size: 54
401458 AATAGTGCCT
* * *
401468 ATACGGTCGTTCATCAATATACGATGAATTCTGTGGGTTGCACACTTAGTGCCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
* *
401522 ATACGGTCGTTCATCAACATATAATGAATTC-GTGGGTTGCACACTTAG-GGCTG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTC-G
* * * * * *
401575 ATACAGTCATTCATTAACATATGATGAATTCCGTGGGTTGCACATTTAGCGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
* ** * *
401629 ATACGGTCGTTCATCAAAATATGATGAATTCCATGGGTTGTACACTTAGTGCCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
* * * *
401683 ATACAGTCATTCATCAACATATGATGCATT-TCGTGGGTTGCACACTTAGTGTCA
1 ATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACTTAGTGTCG
* *
401737 ATACGGTAGTTCATCAACATATGATAAATT-TCGTGGGTTGCACACTTAGTGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACTTAGTGTCG
* * * * * * *
401791 ATATGGTCATTCATCCACATATGATGAATTTTGTGGGTTTCACACTTTGCGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
* * * ** *
401845 ATAGGGTCGTTCATCAAAATATAATGAATTCCT-TATGTTGCACACTTAGTGCCG
1 ATACGGTCGTTCATCAACATATGATGAATT-CTGTGGGTTGCACACTTAGTGTCG
*
401899 ATACAGTCGTTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTAGTGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACTTAGTGTCG
* * * * *
401953 ATACGGTCGTTCATCAACATATGGTGAATTATATGGGTTGCACACTAAGTGCCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
* * *
402007 ATACAGTCTTTCATCAACATATGATGAATT-TCGTGGGTTGCACACTTACTGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCT-GTGGGTTGCACACTTAGTGTCG
* * * * *
402061 ATACGGTCGTTCATCAACATATGGTGAATTATATAGGTTGCACATTTAGTGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
*
402115 ATACGGTCATTCATCAACATATGATGAATTC-GTGGGTTGCACACTTAGTGTCG
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
* * *
402168 ATTCAGTCGTTCATCAACATATGATGAATTCAGTGGGTTGCACACTTAGT
1 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGT
402218 CCCGATAATA
Statistics
Matches: 595, Mismatches: 89, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
52 3 0.01
53 93 0.16
54 493 0.83
55 6 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (54 bp):
ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTGCACACTTAGTGTCG
Found at i:403760 original size:19 final size:19
Alignment explanation
Indices: 403721--403770 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
403711 TACTTCTATT
*
403721 ATTT-TTTTA-TTATTTTG
1 ATTTATTTTATTTAATTTG
403738 ATTTGATTTTATTTAATTT-
1 ATTT-ATTTTATTTAATTTG
*
403757 ATTTAGTTTATTTA
1 ATTTATTTTATTTA
403771 GCTATGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 4 0.14
18 9 0.32
19 9 0.32
20 6 0.21
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (19 bp):
ATTTATTTTATTTAATTTG
Found at i:408781 original size:65 final size:68
Alignment explanation
Indices: 408615--408792 Score: 213
Period size: 65 Copynumber: 2.6 Consensus size: 68
408605 TTTTATCTTT
* * * *
408615 GTATTTTAGTTTAAATAGGTTTTTAGTATTTTAATTA-AATTTTAGGATATTTTTTTTATCTTTG
1 GTATTTTAGTTTAAATA-GTTTTTAGTATTTTAATTAGGA-TTTAGAATATTTATATTA-CTTTG
**
408679 TTTTAG
63 TTAGAG
*
408685 GTATTTTAGTTGAAATAAG-TTTTAGTATTTTAATTAGGATTTAGAATA-TTATATTA-TTT-TT
1 GTATTTTAGTTTAAAT-AGTTTTTAGTATTTTAATTAGGATTTAGAATATTTATATTACTTTGTT
408746 AGAG
65 AGAG
*
408750 GTATTTTAGTTTAAATAGTTTTTAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAGGATTTA
408793 AGATGTTTTA
Statistics
Matches: 96, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
64 2 0.02
65 42 0.44
66 3 0.03
68 6 0.06
69 25 0.26
70 17 0.18
71 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.15, T:0.56
Consensus pattern (68 bp):
GTATTTTAGTTTAAATAGTTTTTAGTATTTTAATTAGGATTTAGAATATTTATATTACTTTGTTA
GAG
Found at i:411425 original size:21 final size:23
Alignment explanation
Indices: 411389--411431 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
411379 CTCTATCCTT
411389 TCTTTATTTCATTTCATTTATTA
1 TCTTTATTTCATTTCATTTATTA
411412 TCTTTA-TT-ATTTCATTTATT
1 TCTTTATTTCATTTCATTTATT
411432 TTCCCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.60
22 2 0.10
23 6 0.30
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (23 bp):
TCTTTATTTCATTTCATTTATTA
Found at i:414064 original size:16 final size:16
Alignment explanation
Indices: 414023--414064 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
414013 ATATCTTTGT
*
414023 TTTTATTTTCATTTCA
1 TTTTATTTTTATTTCA
* *
414039 TTTTATTTTTGTTTTA
1 TTTTATTTTTATTTCA
414055 TTTTATTTTT
1 TTTTATTTTT
414065 CTTAGTGAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (16 bp):
TTTTATTTTTATTTCA
Found at i:415802 original size:65 final size:68
Alignment explanation
Indices: 415650--415817 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 68
415640 TAAGATTCTG
* * * *
415650 GAAATATGTTTTTAGTATTTTAATTAGG-TTTGAGGATATTATTTTTTATCTTTGTTTTAGGTAT
1 GAAATA-GGTTTTAGTGTTTTAATTAGGATTT-AGAATATTA-TTATTA-CTTTGTTTTAGGTAT
415714 TTTAGTT
62 TTTAGTT
415721 GAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTA-TATTA-TTT-TTTTAGGTATTTTA
1 GAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATTATTACTTTGTTTTAGGTATTTTA
415783 GTT
66 GTT
*
415786 TAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 GAAATAGGTTTT-AGTGTTTTAATTAGGATTTA
415818 AGATGTTTTA
Statistics
Matches: 90, Mismatches: 5, Indels: 10
0.86 0.05 0.10
Matches are distributed among these distances:
64 5 0.06
65 42 0.47
66 3 0.03
68 4 0.04
70 27 0.30
71 9 0.10
ACGTcount: A:0.28, C:0.01, G:0.17, T:0.55
Consensus pattern (68 bp):
GAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATTATTACTTTGTTTTAGGTATTTTA
GTT
Found at i:421585 original size:20 final size:21
Alignment explanation
Indices: 421544--421593 Score: 75
Period size: 20 Copynumber: 2.4 Consensus size: 21
421534 GCACATGTTC
421544 ATTATTTTTAGGTTATTTTTCA
1 ATTA-TTTTAGGTTATTTTTCA
*
421566 ATTATTTTAGTTTA-TTTTCA
1 ATTATTTTAGGTTATTTTTCA
421586 ATTATTTT
1 ATTATTTT
421594 TTGTTAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
20 14 0.52
21 9 0.33
22 4 0.15
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.66
Consensus pattern (21 bp):
ATTATTTTAGGTTATTTTTCA
Found at i:427178 original size:21 final size:22
Alignment explanation
Indices: 427152--427203 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
427142 TACATTGGGC
*
427152 TATGAAAAT-AAAGATGAATGT
1 TATGAAAATGAAAGATGAAAGT
*
427173 TATGAAAATGAAATATGAAAGT
1 TATGAAAATGAAAGATGAAAGT
427195 TATGAAAAT
1 TATGAAAAT
427204 TTTATGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 9 0.32
22 19 0.68
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (22 bp):
TATGAAAATGAAAGATGAAAGT
Found at i:431995 original size:37 final size:37
Alignment explanation
Indices: 431938--432042 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
431928 CATTTTCGTC
* *
431938 CTACTATGATTCAAACTCCTAAAAATATGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
431975 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
432012 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
432043 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:432653 original size:38 final size:39
Alignment explanation
Indices: 432610--432686 Score: 95
Period size: 38 Copynumber: 2.0 Consensus size: 39
432600 ATATAATACG
* *
432610 TATATTACTTTGATTTTC-TTTTTTATTAT-TATTTTACT
1 TATATTA-TATGATTTACTTTTTTTATTATATATTTTACT
* *
432648 TATATTATATGCTTTACTTTTTTTTTTATATATTTTACT
1 TATATTATATGATTTACTTTTTTTATTATATATTTTACT
432687 CATTTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 7 0.21
38 17 0.52
39 9 0.27
ACGTcount: A:0.22, C:0.08, G:0.03, T:0.68
Consensus pattern (39 bp):
TATATTATATGATTTACTTTTTTTATTATATATTTTACT
Found at i:432684 original size:21 final size:21
Alignment explanation
Indices: 432660--432766 Score: 64
Period size: 21 Copynumber: 5.1 Consensus size: 21
432650 TATTATATGC
*
432660 TTTACTTTTTTTTTTATATAT
1 TTTACTTTTTTATTTATATAT
** *
432681 TTTACTCATTTATTTATCTAT
1 TTTACTTTTTTATTTATATAT
*
432702 TTT-CTTTTTATCTTTATCCTATAT
1 TTTACTTTTT-TATTTA---TATAT
*
432726 TTTA-TGTTTTTA--TAT-TCT
1 TTTACT-TTTTTATTTATATAT
432744 TTTACTTGTTTTATTTAT-TAT
1 TTTACTT-TTTTATTTATATAT
432765 TT
1 TT
432767 GCATTATCAT
Statistics
Matches: 65, Mismatches: 11, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
18 7 0.11
19 7 0.11
20 4 0.06
21 32 0.49
22 2 0.03
24 9 0.14
25 4 0.06
ACGTcount: A:0.19, C:0.09, G:0.02, T:0.70
Consensus pattern (21 bp):
TTTACTTTTTTATTTATATAT
Found at i:432691 original size:105 final size:108
Alignment explanation
Indices: 432496--432702 Score: 377
Period size: 105 Copynumber: 1.9 Consensus size: 108
432486 TACATGTATA
432496 AATACGTATATTACTTTTGATTTTCTTTTTTTATTATTATTTTACTTATATATATATGCTTTTAC
1 AATACGTATATTACTTTTGATTTTCTTTTTTTATTATTATTTTACTTATATATATATGCTTTTAC
432561 TTTTTTTTTTATATTTTTACTCATTTATTTATCTATTACATAT
66 TTTTTTTTTTATATTTTTACTCATTTATTTATCTATTACATAT
432604 AATACGTATATTAC-TTTGATTTTC-TTTTTTATTATTATTTTACTTATAT-TATATGC-TTTAC
1 AATACGTATATTACTTTTGATTTTCTTTTTTTATTATTATTTTACTTATATATATATGCTTTTAC
432665 TTTTTTTTTTATATATTTTACTCATTTATTTATCTATT
66 TTTTTTTTTTATAT-TTTTACTCATTTATTTATCTATT
432703 TTCTTTTTAT
Statistics
Matches: 98, Mismatches: 0, Indels: 5
0.95 0.00 0.05
Matches are distributed among these distances:
104 19 0.19
105 30 0.31
106 25 0.26
107 10 0.10
108 14 0.14
ACGTcount: A:0.25, C:0.09, G:0.03, T:0.63
Consensus pattern (108 bp):
AATACGTATATTACTTTTGATTTTCTTTTTTTATTATTATTTTACTTATATATATATGCTTTTAC
TTTTTTTTTTATATTTTTACTCATTTATTTATCTATTACATAT
Found at i:436984 original size:14 final size:14
Alignment explanation
Indices: 436965--436997 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
436955 AAAGAAGAAG
*
436965 AATTCATCTGAAAT
1 AATTCATCCGAAAT
436979 AATTCATCCGAAAT
1 AATTCATCCGAAAT
436993 AATTC
1 AATTC
436998 TATCATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (14 bp):
AATTCATCCGAAAT
Found at i:437343 original size:21 final size:20
Alignment explanation
Indices: 437312--437382 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 20
437302 ATCAAGAAAA
437312 AAAATAAAAAAAGCAAAAGAAG
1 AAAA-AAAAAAAG-AAAAGAAG
*
437334 AAAAAAAAAAGGAAAA-AGAG
1 AAAAAAAAAAAGAAAAGA-AG
*
437354 AAACAAAAGAAA-AAAAGAATG
1 AAA-AAAAAAAAGAAAAGAA-G
437375 AACAAAAA
1 AA-AAAAA
437383 TCAAAAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
19 1 0.02
20 14 0.34
21 21 0.51
22 5 0.12
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.03
Consensus pattern (20 bp):
AAAAAAAAAAAGAAAAGAAG
Found at i:437349 original size:9 final size:8
Alignment explanation
Indices: 437309--437372 Score: 53
Period size: 8 Copynumber: 8.2 Consensus size: 8
437299 CCAATCAAGA
*
437309 AAAAAAAT
1 AAAAAAAG
437317 AAAAAAAG
1 AAAAAAAG
*
437325 --CAAAAG
1 AAAAAAAG
*
437331 AAGAAAA-
1 AAAAAAAG
*
437338 AAAAAAGG
1 AAAAAAAG
*
437346 AAAAAGAG
1 AAAAAAAG
437354 AAACAAAAG
1 AAA-AAAAG
437363 AAAAAAAG
1 AAAAAAAG
437371 AA
1 AA
437373 TGAACAAAAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
6 5 0.11
7 5 0.11
8 27 0.61
9 7 0.16
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.02
Consensus pattern (8 bp):
AAAAAAAG
Found at i:437352 original size:18 final size:18
Alignment explanation
Indices: 437307--437367 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
437297 ATCCAATCAA
437307 GAAAAA-AAATAAAAAAAG
1 GAAAAAGAAA-AAAAAAAG
*
437325 CAAAAGAAGAAAAAAAAAAG
1 -GAAA-AAGAAAAAAAAAAG
* *
437345 GAAAAAGAGAAACAAAA-
1 GAAAAAGAAAAAAAAAAG
437362 GAAAAA
1 GAAAAA
437368 AAGAATGAAC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 6 0.17
18 11 0.31
19 6 0.17
20 10 0.28
21 3 0.08
ACGTcount: A:0.80, C:0.03, G:0.15, T:0.02
Consensus pattern (18 bp):
GAAAAAGAAAAAAAAAAG
Found at i:437355 original size:20 final size:21
Alignment explanation
Indices: 437317--437382 Score: 68
Period size: 20 Copynumber: 3.2 Consensus size: 21
437307 GAAAAAAAAT
*
437317 AAAAAAAGCAAAAGAAGAAA-
1 AAAAAAAGAAAAAGAAGAAAC
437337 AAAAAAAGGAAAAAG-AGAAAC
1 AAAAAAA-GAAAAAGAAGAAAC
*
437358 AAAAGAA-AAAAAGAATG-AAC
1 AAAAAAAGAAAAAGAA-GAAAC
437378 AAAAA
1 AAAAA
437383 TCAAAAAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 6 0.15
20 20 0.51
21 13 0.33
ACGTcount: A:0.79, C:0.05, G:0.15, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAGAAGAAAC
Found at i:438073 original size:22 final size:22
Alignment explanation
Indices: 437999--438075 Score: 136
Period size: 22 Copynumber: 3.5 Consensus size: 22
437989 GCTACCCCAT
*
437999 CAAACCGTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
438021 CAAACCTATGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
438043 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
438065 CAAACCTTTGA
1 CAAACCTTTGA
438076 CCAAACATAA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:439109 original size:106 final size:106
Alignment explanation
Indices: 438899--440061 Score: 1565
Period size: 106 Copynumber: 11.0 Consensus size: 106
438889 ATATCGTGCC
* * * * * *
438899 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTCTCAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
438963 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
439004 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAAAAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* **
439069 AATTTCAGATCCAATTTCAACTTCACATTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
439110 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
*
439174 CAATTTCAGAGCTAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
439216 ACTCTAGACAACGCAAGTTTAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
439281 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
439322 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTTTCAATAATCAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
439387 AATTTCAGAGCCAATTTCAATTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
439428 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
439493 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATTTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
439534 ACTCCAGAAAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
**
439599 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
439640 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
439705 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
439746 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * * **
439811 AATTTCAGAGCCAGTTTTAACTTCTCAGCGAAGGATCTTAA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
439852 AC-CCAAGGCAACACAAGCTCAACTTCATGATGAAGGGGCGGCTGATTGTCAAC-AA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
*
439912 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
439952 ACTCGAGACAACACAAGTTTAACTTCACAATGAAGGGACGGCTGGTTGTCAAAAAATAATTT-CC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
440016 AGGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 A-ATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
440058 ACTC
1 ACTC
440062 AGAACAATGC
Statistics
Matches: 940, Mismatches: 106, Indels: 23
0.88 0.10 0.02
Matches are distributed among these distances:
100 73 0.08
101 4 0.00
102 6 0.01
103 1 0.00
104 4 0.00
105 52 0.06
106 797 0.85
107 3 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:440834 original size:37 final size:37
Alignment explanation
Indices: 440784--440884 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
440774 TTCGTCCTAT
* * *
440784 TAGGATTCAAACTCCTAAAAATATGATAAAATTTTGC
1 TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* *
440821 TAGGATTCAAACTCCTAAAAATAGGATAGAGTTCTAC
1 TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
* * *
440858 TATGATTTAAACTCCTAAAGATAGGAT
1 TAGGATTCAAACTCCTAAAAATAGGAT
440885 CCACAAGAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 56 1.00
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.31
Consensus pattern (37 bp):
TAGGATTCAAACTCCTAAAAATAGGATAAAATTCTAC
Found at i:440966 original size:21 final size:22
Alignment explanation
Indices: 440937--440980 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
440927 ACACGATTTA
*
440937 CACACAAAACACAGAGG-AAAG
1 CACACAAAACACAAAGGCAAAG
* *
440958 CACAGAAAATACAAAGGCAAAG
1 CACACAAAACACAAAGGCAAAG
440980 C
1 C
440981 TATTGTAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.57, C:0.23, G:0.18, T:0.02
Consensus pattern (22 bp):
CACACAAAACACAAAGGCAAAG
Found at i:441442 original size:21 final size:20
Alignment explanation
Indices: 441372--441442 Score: 56
Period size: 21 Copynumber: 3.5 Consensus size: 20
441362 TTTTTTATTA
*
441372 TTAT-TATTTTACT-TATAT
1 TTATATATTTTACTCTTTAT
* * *
441390 ATATATGCTTTTACTCTTTTT
1 TTATAT-ATTTTACTCTTTAT
*
441411 TTTTATATTTTACTCATTTAT
1 TTATATATTTTACTC-TTTAT
*
441432 TTATCTATTTT
1 TTATATATTTT
441443 TTTTATCTTA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 15 0.38
21 20 0.51
ACGTcount: A:0.23, C:0.10, G:0.01, T:0.66
Consensus pattern (20 bp):
TTATATATTTTACTCTTTAT
Found at i:457648 original size:134 final size:132
Alignment explanation
Indices: 457422--457875 Score: 455
Period size: 134 Copynumber: 3.4 Consensus size: 132
457412 TTCAAAAAGA
* * * * *
457422 TTTGATTCACTTCGCTGCTCTTCAGGGAAGGTTGAACCGAACTTGATTTGCTTC-ATTACTATTC
1 TTTGATCCACTTCGCTGCTCTTCA-GGAAGATTGAATCGAACTTGATTTGCTTCGA-TGCTCTTC
* ** * * *
457486 AGGAAGACCAAATATGAAAGAA-ATAGAATCTAATGCACTACTATTTAGGGGAAATCAGACTCGA
64 AAGAAGACCAAATATGAAAGAAGA-AGAATCTGCTCCACTACTCTTTAGGGAAAATCA-ACTCGA
*
457550 GAAAGT
127 GAAAAT
* * * * *
457556 TTTGATCCACTTCACTGCTCTTCAGGAAAGATTAAATTGAATTTGATTTGGTTCGATGCTCTTCA
1 TTTGATCCACTTCGCTGCTCTTCAGG-AAGATTGAATCGAACTTGATTTGCTTCGATGCTCTTCA
* * * * *
457621 AGAAGGCCAAATCTGAAAGAAGAAGAATCTGCCCCACTACTCTTTA-GAAAAGATCAAGTTCGAG
65 AGAAGACCAAATATGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGAAA-ATCAA-CTCGAG
457685 AAAAT
128 AAAAT
* * * * *
457690 TTTTATCCACTTCGCTACTCTTCAAGGAAGAATGAATCAAACTTGATTTTCTTCGATGCTCTTCA
1 TTTGATCCACTTCGCTGCTCTTC-AGGAAGATTGAATCGAACTTGATTTGCTTCGATGCTCTTCA
* * * * *
457755 AGAATACCAAATATGAAAGGAGAAGAATATGCTCCACTACTCTTTAGGGTATATCAAACTCGAGA
65 AGAAGACCAAATATGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGAAAATC-AACTCGAGA
457820 AAAT
129 AAAT
* * * * * *
457824 TTTGATCCACTTTGGTGGTCTTCAGAGAATACTGAACCGAACTTGATTTGCT
1 TTTGATCCACTTCGCTGCTCTTCAG-GAAGATTGAATCGAACTTGATTTGCT
457876 CCTCTTATCT
Statistics
Matches: 259, Mismatches: 52, Indels: 18
0.79 0.16 0.05
Matches are distributed among these distances:
133 8 0.03
134 242 0.93
135 9 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (132 bp):
TTTGATCCACTTCGCTGCTCTTCAGGAAGATTGAATCGAACTTGATTTGCTTCGATGCTCTTCAA
GAAGACCAAATATGAAAGAAGAAGAATCTGCTCCACTACTCTTTAGGGAAAATCAACTCGAGAAA
AT
Found at i:458515 original size:51 final size:51
Alignment explanation
Indices: 458417--458516 Score: 146
Period size: 51 Copynumber: 2.0 Consensus size: 51
458407 TCTCCATACG
** * *
458417 AGAAAGTCAAGTTGAGGAATGATACTACTAAAAAGTTGACTTATCTCCGTA
1 AGAAAGTCAAGTTGAAAAATGATACTACTAAAAAGTTGAATCATCTCCGTA
* *
458468 AGAAAGTCAAGTTGAAAAATGATACTACTACAAAGTTGAATCCTCTCCG
1 AGAAAGTCAAGTTGAAAAATGATACTACTAAAAAGTTGAATCATCTCCG
458517 CTGTTAGAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 43 1.00
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (51 bp):
AGAAAGTCAAGTTGAAAAATGATACTACTAAAAAGTTGAATCATCTCCGTA
Found at i:459692 original size:90 final size:90
Alignment explanation
Indices: 459534--459713 Score: 281
Period size: 90 Copynumber: 2.0 Consensus size: 90
459524 TAATCCTGAA
*
459534 TATTTAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCGCTAATATGAT
1 TATTAAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCGCTAATATGAT
*
459599 TAGGGTAACTTGAATATAAAAGGAT
66 TAGGGTAACTCGAATATAAAAGGAT
** * *
459624 TATTAAATTCCAGTTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATAC-CTAATGTGA
1 TATTAAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAATAAAAT-CGCTAATATGA
*
459688 TTAGGGTAACTCGGATATAAAAGGAT
65 TTAGGGTAACTCGAATATAAAAGGAT
459714 GTGTTAGGTC
Statistics
Matches: 82, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
90 81 0.99
91 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.36
Consensus pattern (90 bp):
TATTAAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCGCTAATATGAT
TAGGGTAACTCGAATATAAAAGGAT
Found at i:466567 original size:89 final size:89
Alignment explanation
Indices: 466394--466571 Score: 252
Period size: 89 Copynumber: 2.0 Consensus size: 89
466384 TAATCCCGAA
* *
466394 TATTTAATTCCAACTAATTAAATATAGATTTAATTAATTTGAAATAAGAAAATCCTAATATGATT
1 TATTAAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAAGAAAATCCTAATATGATT
*
466459 AGGGTAACTTGGATATAAAAGGAT
66 AGGGTAACTTCGATATAAAAGGAT
* * *
466483 TATTAAATTCTAATTAATTAAATATAAATTTAATTAATTTGAAATAATG-AAATCCCTAATGTGA
1 TATTAAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAA-GAAAAT-CCTAATATGA
* *
466547 TTAGGGTAGC-TCGATTTAAAAGGAT
64 TTAGGGTAACTTCGATATAAAAGGAT
466572 GTGTTAGGTC
Statistics
Matches: 79, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
89 60 0.76
90 19 0.24
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (89 bp):
TATTAAATTCCAACTAATTAAATATAAATTTAATTAATTTGAAATAAGAAAATCCTAATATGATT
AGGGTAACTTCGATATAAAAGGAT
Found at i:466808 original size:45 final size:42
Alignment explanation
Indices: 466695--466922 Score: 149
Period size: 44 Copynumber: 5.1 Consensus size: 42
466685 ATACTGAAAT
* * * * *
466695 ATTGATTTTTCTTCAAGAAAAATTCAAGAATGACATCACTAAAAG
1 ATTGACTTCTCTTCATGAAAAAGTCAAGAA--AAATCACT-AAAG
* *
466740 GTTGACTTCTC-TCAACT-AAAAAGTCAAGAACAACTCCACTAAAAG
1 ATTGACTTCTCTTC-A-TGAAAAAGTCAAGAA-AAAT-CACT-AAAG
* * *
466785 GTTGACTTCTCTTCATGAGAAAGTCAAGAATAAAATAACTAAAG
1 ATTGACTTCTCTTCATGAAAAAGTCAAG-A-AAAATCACTAAAG
** * *
466829 ATTGACACCTCTTCATGAGAAAGTCAAGAATAATAACACTAAAG
1 ATTGACTTCTCTTCATGAAAAAGTCAAGAA-AA-ATCACTAAAG
*
466873 ATTGAC-TCATCTTCAAGAAAAAGTCAAGAATGACAA-CACTAAAG
1 ATTGACTTC-TCTTCATGAAAAAGTCAAGAA--A-AATCACTAAAG
466917 ATTGAC
1 ATTGAC
466923 ACCTCTTTCA
Statistics
Matches: 151, Mismatches: 20, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
42 1 0.01
43 4 0.03
44 81 0.54
45 57 0.38
46 7 0.05
47 1 0.01
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (42 bp):
ATTGACTTCTCTTCATGAAAAAGTCAAGAAAAATCACTAAAG
Found at i:466848 original size:44 final size:43
Alignment explanation
Indices: 466793--466929 Score: 193
Period size: 44 Copynumber: 3.1 Consensus size: 43
466783 AGGTTGACTT
*
466793 CTCTTCATGAGAAAGTCAAGAATAAAATAACTAAAGATTGACAC
1 CTCTTCATGAGAAAGTCAAGAATAAAA-CACTAAAGATTGACAC
*
466837 CTCTTCATGAGAAAGTCAAGAATAATAACACTAAAGATTGACTC
1 CTCTTCATGAGAAAGTCAAGAATAA-AACACTAAAGATTGACAC
* * * *
466881 ATCTTCAAGAAAAAGTCAAGAATGACAACACTAAAGATTGACAC
1 CTCTTCATGAGAAAGTCAAGAAT-AAAACACTAAAGATTGACAC
466925 CTCTT
1 CTCTT
466930 TCAATTTGTT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
44 80 0.96
45 3 0.04
ACGTcount: A:0.45, C:0.18, G:0.13, T:0.23
Consensus pattern (43 bp):
CTCTTCATGAGAAAGTCAAGAATAAAACACTAAAGATTGACAC
Found at i:466902 original size:88 final size:89
Alignment explanation
Indices: 466759--466929 Score: 224
Period size: 88 Copynumber: 1.9 Consensus size: 89
466749 TCTCAACTAA
* * * *
466759 AAAGTCAAGAACAACTCCACTAAAAGGTTGACTTCTCTTCATGAGAAAGTCAAGAAT-AAAATAA
1 AAAGTCAAGAACAACTACACTAAAAGATTGACTTCTCTTCAAGAAAAAGTCAAGAATGAAAA-AA
466823 CTAAAGATTGACACCTCTTCATGAG
65 CTAAAGATTGACACCTCTTCATGAG
* * *
466848 AAAGTCAAGAATAA-TAACACT-AAAGATTGAC-TCATCTTCAAGAAAAAGTCAAGAATGACAAC
1 AAAGTCAAGAACAACT-ACACTAAAAGATTGACTTC-TCTTCAAGAAAAAGTCAAGAATGAAAAA
466910 ACTAAAGATTGACACCTCTT
64 ACTAAAGATTGACACCTCTT
466930 TCAATTTGTT
Statistics
Matches: 72, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
87 2 0.03
88 50 0.69
89 20 0.28
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (89 bp):
AAAGTCAAGAACAACTACACTAAAAGATTGACTTCTCTTCAAGAAAAAGTCAAGAATGAAAAAAC
TAAAGATTGACACCTCTTCATGAG
Found at i:467544 original size:258 final size:256
Alignment explanation
Indices: 467093--467727 Score: 741
Period size: 258 Copynumber: 2.5 Consensus size: 256
467083 TGGTCCAATT
* * * * * *
467093 TTTTTGAAATAATTTACT-AGTAAGGAACTTTGGAAATCGCTTTCTTACTTTTAAAAATTTTATT
1 TTTTGGAAATAATTTACTGGGTAA-GAACTTTGGAAATCACTTTCTTACTTTCAAAAATATCATT
* *
467157 TTCTGAAAACAATAAA-GGGAAACTTTGAAAAT---ATTCTCATCTTTTTTGAAAATAGTGTGAA
65 TTCTGAAAACAATAAATGAGAAACTTTGAAAATCGCTTTCTCA--TTTTTTGAAAATAGTGTGAA
* * * * * * *
467218 AACATCATGCCTGAAGATCTTATAGATGGTCCGAAGGACTTATATTCTTGCTCGAAAGACTAACA
128 AACATAATACCCGAAGATATTACAGATGGACCGAAGGACATATATTCTTGCTCGAAAGACTAACA
* * * * *
467283 GATGACACAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTTCCCAA
193 GATGACACAAAGGATTTAACCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACATACCAA
* *
467347 TTTTGGAAATAGTTTATTGGGTAAGAAGCTTTGGAAATCACTTTCTTACTCTTCAAAAATATCAT
1 TTTTGGAAATAATTTACTGGGTAAGAA-CTTTGGAAATCACTTTCTTACT-TTCAAAAATATCAT
*
467412 TTTCTGAAAATAATAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTGAAAATCA-TGTGAA
64 TTTCTGAAAACAATAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTGAAAAT-AGTGTGAA
* * * * * *
467476 AATATAATACCCGAAGGTATTACGGTTGGACCGAAGGACATATCA-TCTTTCTTGAAAGAC-ATA
128 AACATAATACCCGAAGATATTACAGATGGACCGAAGGACATAT-ATTCTTGCTCGAAAGACTA-A
* * *
467539 CAGATGACCCTAAGTATTTAACCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACATACCA
191 CAGATGACACAAAGGATTTAACCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACATACCA
467604 A
256 A
467605 TTTTGGAAATAATTTACTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTTCAAAAA-ATTC
1 TTTTGGAAATAATTTACTGGGTAAG-AACTTTGGAAATCACTTTCTTAC--TTTCAAAAATA-TC
** * * * *
467669 ATTTTGAGAAAAGATTTAAATAAGAAACTTTGGAAATCGCTTTCTCATTTTTT-AAAATA
62 ATTTTCTGAAAACA-ATAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTGAAAATA
467728 ACTTAATGAT
Statistics
Matches: 326, Mismatches: 40, Indels: 26
0.83 0.10 0.07
Matches are distributed among these distances:
254 18 0.06
255 25 0.08
256 27 0.08
257 16 0.05
258 168 0.52
259 30 0.09
260 42 0.13
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (256 bp):
TTTTGGAAATAATTTACTGGGTAAGAACTTTGGAAATCACTTTCTTACTTTCAAAAATATCATTT
TCTGAAAACAATAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTTTGAAAATAGTGTGAAAAC
ATAATACCCGAAGATATTACAGATGGACCGAAGGACATATATTCTTGCTCGAAAGACTAACAGAT
GACACAAAGGATTTAACCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACATACCAA
Found at i:472256 original size:53 final size:53
Alignment explanation
Indices: 472192--472296 Score: 156
Period size: 53 Copynumber: 2.0 Consensus size: 53
472182 CGAAGTTCCT
* * *
472192 AAATGGAAATTCACATACTTATTATGAATTCCATGGATGCACACATAGTGCCG
1 AAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCG
* * *
472245 AAATGGTAATTCACAAACTCATTATGACTACCATGGGTGCACACATAGTGCC
1 AAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCC
472297 AAAAGTGCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 46 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (53 bp):
AAATGGAAATTCACAAACTCATTATGAATACCATGGATGCACACATAGTGCCG
Found at i:475148 original size:12 final size:13
Alignment explanation
Indices: 475128--475167 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
475118 ATGTTTACCC
*
475128 GACCCGACCTGTT
1 GACCCGACCCGTT
475141 GA-CCGACCCGTT
1 GACCCGACCCGTT
475153 GACCCGACCCGTT
1 GACCCGACCCGTT
475166 GA
1 GA
475168 TCCGTTGACC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 11 0.44
13 14 0.56
ACGTcount: A:0.17, C:0.40, G:0.25, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:475148 original size:17 final size:18
Alignment explanation
Indices: 475106--475150 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
475096 ACCGGTCATA
*
475106 ACCCGACCCGACATGTTT
1 ACCCGACCCGACATGTTG
*
475124 ACCCGACCCGACCTGTTG
1 ACCCGACCCGACATGTTG
475142 A-CCGACCCG
1 ACCCGACCCG
475151 TTGACCCGAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.20, C:0.44, G:0.20, T:0.16
Consensus pattern (18 bp):
ACCCGACCCGACATGTTG
Done.