Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold471
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1282308
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.29
Warning! 143812 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:644 original size:172 final size:172
Alignment explanation
Indices: 347--1143 Score: 1382
Period size: 172 Copynumber: 4.6 Consensus size: 172
337 GTATCGAGTC
* *
347 TATCGACCAAGGCTGATTTTCGAACTTGACCAACGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
* *
412 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGGT-AAACT
66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC-
*
476 GGGGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
130 GGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
*
519 TATTGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
*
584 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGGT-AAACT
66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAAC-
*
648 GGGGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
130 GGAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
*
691 TATTGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
756 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
*
821 GAGTCATTATTGTGGTCATAGTCCCATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
* *
863 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
**
928 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTTCATAAAACG
66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
* * *
993 GAGTCATTATAGTGGTCAAAGTTCGATAACTCCAACAAAAAG
131 GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
* *
1035 TATCGACCAATGCTGATTTTCGAACTTGACCAAGATAATAGTGGTATAAACATTTGGTATAAATT
1 TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
*
1100 TAATGAAAATCCGTCAAAATTTGTAGGCATGAGAGCGCTTACAA
66 TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAA
1144 AAAAGTGTGA
Statistics
Matches: 607, Mismatches: 17, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
172 603 0.99
173 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (172 bp):
TATCGACCAATGCTGATTTTCGAACTTGACCAAGGTATTAGTGGTATAAACATTTGGTATAAATT
TAATGAAAATCCGTCAAACTTTGTAGGCATGAGAGCGCTTACAAGGTCAATTTTTGGATAAAACG
GAGTCATTATTGTGGTCAAAGTCCCATAACTCCAACAAAAAG
Found at i:1170 original size:8 final size:8
Alignment explanation
Indices: 1152--1251 Score: 83
Period size: 8 Copynumber: 12.5 Consensus size: 8
1142 AAAAAAGTGT
*
1152 GACGGACG
1 GACGCACG
*
1160 GACGCAAG
1 GACGCACG
*
1168 GACACACG
1 GACGCACG
1176 GACGCACG
1 GACGCACG
* *
1184 GACCCACA
1 GACGCACG
* *
1192 GACACACA
1 GACGCACG
*
1200 GACCCACG
1 GACGCACG
*
1208 GACACACG
1 GACGCACG
*
1216 GACCCACG
1 GACGCACG
*
1224 GACCCACG
1 GACGCACG
*
1232 GACCCACG
1 GACGCACG
*
1240 GACACACG
1 GACGCACG
1248 GACG
1 GACG
1252 GACGCCCGGC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 78 1.00
ACGTcount: A:0.32, C:0.40, G:0.28, T:0.00
Consensus pattern (8 bp):
GACGCACG
Found at i:1178 original size:16 final size:16
Alignment explanation
Indices: 1157--1250 Score: 125
Period size: 16 Copynumber: 5.9 Consensus size: 16
1147 AGTGTGACGG
* * *
1157 ACGGACGCAAGGACAC
1 ACGGACACACGGACCC
*
1173 ACGGACGCACGGACCC
1 ACGGACACACGGACCC
* *
1189 ACAGACACACAGACCC
1 ACGGACACACGGACCC
1205 ACGGACACACGGACCC
1 ACGGACACACGGACCC
*
1221 ACGGACCCACGGACCC
1 ACGGACACACGGACCC
1237 ACGGACACACGGAC
1 ACGGACACACGGAC
1251 GGACGCCCGG
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 69 1.00
ACGTcount: A:0.33, C:0.41, G:0.26, T:0.00
Consensus pattern (16 bp):
ACGGACACACGGACCC
Found at i:1184 original size:24 final size:24
Alignment explanation
Indices: 1152--1251 Score: 103
Period size: 24 Copynumber: 4.2 Consensus size: 24
1142 AAAAAAGTGT
* *
1152 GACGGACGGACGCAAGGACACACG
1 GACGCACGGACCCAAGGACACACG
*
1176 GACGCACGGACCCACA-GACACACA
1 GACGCACGGACCCA-AGGACACACG
* * * *
1200 GACCCACGGACACACGGACCCACG
1 GACGCACGGACCCAAGGACACACG
* *
1224 GACCCACGGACCCACGGACACACG
1 GACGCACGGACCCAAGGACACACG
1248 GACG
1 GACG
1252 GACGCCCGGC
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
24 62 0.98
25 1 0.02
ACGTcount: A:0.32, C:0.40, G:0.28, T:0.00
Consensus pattern (24 bp):
GACGCACGGACCCAAGGACACACG
Found at i:7496 original size:1 final size:1
Alignment explanation
Indices: 7490--7514 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
7480 CTCCCTTAAG
7490 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
7515 CAATCTTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:24316 original size:16 final size:16
Alignment explanation
Indices: 24292--24324 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
24282 AACTGAAGTG
24292 GGACAGACAGACGGAC
1 GGACAGACAGACGGAC
*
24308 GGACGGACAGACGGAC
1 GGACAGACAGACGGAC
24324 G
1 G
24325 CAGAGGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.24, G:0.42, T:0.00
Consensus pattern (16 bp):
GGACAGACAGACGGAC
Found at i:27406 original size:14 final size:14
Alignment explanation
Indices: 27387--27413 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
27377 CAAACATAAT
27387 TATAGATACAAACA
1 TATAGATACAAACA
27401 TATAGATACAAAC
1 TATAGATACAAAC
27414 TTCTATACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.15, G:0.07, T:0.22
Consensus pattern (14 bp):
TATAGATACAAACA
Found at i:35917 original size:41 final size:40
Alignment explanation
Indices: 35855--36681 Score: 801
Period size: 41 Copynumber: 20.0 Consensus size: 40
35845 TGATACATGG
* * *
35855 ACAGGAGTCAAACAGCTGTTATACAAGTCAAGGGATCAAT
1 ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* ** * * * *
35895 ACTGTGAGTCATACAGAAGTTATACAAATCAAAGGATCACT
1 ACAG-GAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
35936 ACCAGGAGTCATACAGTTGTTATATACCAGTCAAGGGATCAAT
1 A-CAGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT
*
35979 ACTAGGAGTCATACAGTTGTTATATACCAGTCAAGAGATCAAT
1 AC-AGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT
* *
36022 ACTAGGAGTTATACAGTTGTTATATACCAATCAAGGGATCAAT
1 AC-AGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT
* * *
36065 ---GGTTGTAATAC--TAG---T--CAGTCAAGGGATCAAT
1 ACAGG-AGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* * *
36096 ACCAGGAGTCATACAGTTATTATACTACTCAAGGGATCAAT
1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* * * * *
36137 GCCAGGAGTCATGCCGTTGTTATGCCAGTCAAAGGATCAAT
1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* * *
36178 ACCGGGAGTGATACAGTTGTTATACCAGTCAAAGGATCAAT
1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
*** *
36219 ACCCCAGTCATACAGTTGTTATACTAGTCAAGGGATCAAT
1 ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* * *
36259 GCCAGGAGTCATACAGTTGTTACACTAGTCAAGGGATCAAT
1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
*
36300 ACCAGGAGTCATACAGTTGTTATATACCAATCAAGGGATCAAT
1 A-CAGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT
*
36343 ACCAGGAGTCATACAGTTGTAATACTAGTCAGTCAAGGGATCAAT
1 A-CAGGAGTCATACAGTTGT--TA-TA-CCAGTCAAGGGATCAAT
* *
36388 ACCAGGAGTCATACAGATGTTATACTAGTCAAGGGATCAAT
1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* *
36429 GCCAGGAGTCATACAGTTGTTATGCCAGTCAAGGGATCAAT
1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* * *
36470 ACCGGGAGTGATACAGTTGTTATACCAGTCAAAGGATCAAT
1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
*
36511 ACCAGGAGTCATACAGTTGTTATACCAGTCAAAGGATCAAT
1 A-CAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* *
36552 ACCAGGAGTCATACAGTTGGAATACTAGTCAGTCAAGGGATCAAT
1 A-CAGGAGTCATACAGTT-G-TTA-TA-CCAGTCAAGGGATCAAT
* *
36597 GCCAGGAGTCATACAGTTGTTATACCAGTCAATGGATCAAT
1 -ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
* * *
36638 ACCGGGAGTCATACAGCTGTTATATACCAGTCAAGAGATCAAT
1 A-CAGGAGTCATACAGTTG-T-TATACCAGTCAAGGGATCAAT
36681 A
1 A
36682 TATAAATAGT
Statistics
Matches: 666, Mismatches: 85, Indels: 69
0.81 0.10 0.08
Matches are distributed among these distances:
31 15 0.02
33 1 0.00
34 6 0.01
35 2 0.00
36 1 0.00
38 2 0.00
39 3 0.00
40 42 0.06
41 349 0.52
42 12 0.02
43 163 0.24
44 5 0.01
45 65 0.10
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (40 bp):
ACAGGAGTCATACAGTTGTTATACCAGTCAAGGGATCAAT
Found at i:46950 original size:23 final size:23
Alignment explanation
Indices: 46922--47121 Score: 171
Period size: 23 Copynumber: 8.7 Consensus size: 23
46912 TATTTCTTAA
*
46922 TGACAATTGCTGTCTAGTCCTAC
1 TGACAATTGCTGTCTATTCCTAC
*
46945 TTACAATTGCTGTCTAATTCCTAC
1 TGACAATTGCTGTCT-ATTCCTAC
* *
46969 TGAC-TTTGCTGTCTTTTTCCTAC
1 TGACAATTGCTGTC-TATTCCTAC
* * *
46992 TGACAATTGTTAG-ATATT-CTGC
1 TGACAATTGCT-GTCTATTCCTAC
*
47014 TGACAATTGCTATC---TCCTAC
1 TGACAATTGCTGTCTATTCCTAC
** * *
47034 TGGTAATTGCTGTCTTTTTCCTCC
1 TGACAATTGCTGTC-TATTCCTAC
*
47058 TGACAATTGCTGTCTATTCCTGC
1 TGACAATTGCTGTCTATTCCTAC
47081 TGACAATTGCTGTCTATTTCCTAC
1 TGACAATTGCTGTCTA-TTCCTAC
*
47105 AT-ACAATTACTGTCTAT
1 -TGACAATTGCTGTCTAT
47122 CTCTTCACCT
Statistics
Matches: 141, Mismatches: 24, Indels: 24
0.75 0.13 0.13
Matches are distributed among these distances:
19 1 0.01
20 14 0.10
22 13 0.09
23 60 0.43
24 51 0.36
25 2 0.01
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (23 bp):
TGACAATTGCTGTCTATTCCTAC
Found at i:47101 original size:47 final size:47
Alignment explanation
Indices: 46922--47121 Score: 173
Period size: 47 Copynumber: 4.4 Consensus size: 47
46912 TATTTCTTAA
* * * *
46922 TGACAATTGCTGTCTAGTCCTACTTACAATTGCTGTCTAATTCCTAC
1 TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCTCC
* * ** *
46969 TGAC-TTTGCTGTCTTTTTCCTACTGACAATTG-T-TAGATATT-CTGC
1 TGACAATTGCTGTC-TATTCCTACTGACAATTGCTGTCTAT-TTCCTCC
* ** *
47014 TGACAATTGCTATC---TCCTACTGGTAATTGCTGTCTTTTTCCTCC
1 TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCTCC
* *
47058 TGACAATTGCTGTCTATTCCTGCTGACAATTGCTGTCTATTTCCTACA
1 TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCT-CC
*
47106 T-ACAATTACTGTCTAT
1 TGACAATTGCTGTCTAT
47122 CTCTTCACCT
Statistics
Matches: 120, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
42 13 0.11
43 3 0.03
44 18 0.15
45 9 0.08
46 18 0.15
47 57 0.47
48 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.14, T:0.42
Consensus pattern (47 bp):
TGACAATTGCTGTCTATTCCTACTGACAATTGCTGTCTATTTCCTCC
Found at i:52784 original size:19 final size:19
Alignment explanation
Indices: 52760--52816 Score: 98
Period size: 19 Copynumber: 3.0 Consensus size: 19
52750 ACAGAGATGA
52760 CTAGATGTACAGGTATTAC
1 CTAGATGTACAGGTATTAC
52779 CTAGATGTACAGGTATTAC
1 CTAGATGTACAGGTATTAC
52798 CTA-ATTGTACAGGTATTAC
1 CTAGA-TGTACAGGTATTAC
52817 TAACCATTCC
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
18 1 0.03
19 36 0.97
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (19 bp):
CTAGATGTACAGGTATTAC
Found at i:53961 original size:180 final size:182
Alignment explanation
Indices: 53651--54007 Score: 666
Period size: 180 Copynumber: 2.0 Consensus size: 182
53641 AAATTACACG
53651 GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAATGAT
1 GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAA-GAT
53716 CAGAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAA
65 -AGAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAA
53781 ATCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCCCCCCCCC
129 ATCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCCCCCCCCC
53835 NGGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTC-A-AT
1 -GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAAGAT
53898 -GAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAAA
65 AGAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAAA
53962 TCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCC
130 TCTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCC
54008 NTACATCATG
Statistics
Matches: 172, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
180 110 0.64
182 2 0.01
184 1 0.01
185 59 0.34
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (182 bp):
GGGCGAAAATGACCCTGTATACAGTTTTTATTTGCTATTTATTCAATCAAACAATGTTCAAGATA
GAAGCACATGCAAAAGTATATGCAATACCATTAAATTGATAAAGTTAGTGGGTCATAATTGAAAT
CTTTCTATGACAGAGGTAAAGAGCGATATAAAAGTGGTTGAGCCCCCCCCCC
Found at i:54389 original size:2 final size:2
Alignment explanation
Indices: 54382--54436 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
54372 TATACAAAAA
54382 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
54424 CT CT CT CT CT CT C
1 CT CT CT CT CT CT C
54437 ATTAATTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:58432 original size:2 final size:2
Alignment explanation
Indices: 58425--58465 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
58415 TTACAAGAAA
58425 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
58466 ATTTTCAGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:63462 original size:133 final size:134
Alignment explanation
Indices: 63223--63490 Score: 520
Period size: 133 Copynumber: 2.0 Consensus size: 134
63213 AAGTAGAAAA
63223 AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT
1 AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT
*
63288 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTTAATGA
66 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA
63353 TATG
131 TATG
63357 AGCACAGGGACATTATCCGACATACCTTGGAGAC-TAACCTGATCGGCGCATTTATTCATCAGGT
1 AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT
63421 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA
66 GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA
63486 TATG
131 TATG
63490 A
1 A
63491 ATACATATAA
Statistics
Matches: 133, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
133 99 0.74
134 34 0.26
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (134 bp):
AGCACAGGGACATTATCCGACATACCTTGGAGACTTAACCTGATCGGCGCATTTATTCATCAGGT
GTGTGTTGTACGTGAATAATTGAAAAATTATAACAATTCCTGTACGAATCGCCACGTTTCAATGA
TATG
Found at i:63812 original size:32 final size:32
Alignment explanation
Indices: 63776--63842 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
63766 TACATGGATG
*
63776 TAGGCTATGCCTGTCCACTTCTCAAAAGAGAA
1 TAGGCTATACCTGTCCACTTCTCAAAAGAGAA
63808 TAGGCTATACCTGTCCACTTCTCAAAAGAGAA
1 TAGGCTATACCTGTCCACTTCTCAAAAGAGAA
63840 TAG
1 TAG
63843 AATTATAGTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.25
Consensus pattern (32 bp):
TAGGCTATACCTGTCCACTTCTCAAAAGAGAA
Found at i:71320 original size:12 final size:12
Alignment explanation
Indices: 71303--71327 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71293 ATAAGATTGG
71303 TTTGTTTAATGT
1 TTTGTTTAATGT
71315 TTTGTTTAATGT
1 TTTGTTTAATGT
71327 T
1 T
71328 ACCAAATCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.68
Consensus pattern (12 bp):
TTTGTTTAATGT
Found at i:73056 original size:8 final size:8
Alignment explanation
Indices: 73043--73087 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
73033 TGGTTTCACC
73043 CTGTCCGT
1 CTGTCCGT
*
73051 CTGTCCTT
1 CTGTCCGT
*
73059 CTGTCTGT
1 CTGTCCGT
73067 CTGTCCGT
1 CTGTCCGT
73075 CTGTCCGT
1 CTGTCCGT
73083 CTGTC
1 CTGTC
73088 TGTAGACGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.00, C:0.36, G:0.22, T:0.42
Consensus pattern (8 bp):
CTGTCCGT
Found at i:73067 original size:4 final size:4
Alignment explanation
Indices: 73043--73090 Score: 53
Period size: 4 Copynumber: 12.0 Consensus size: 4
73033 TGGTTTCACC
* * *
73043 CTGT CCGT CTGT CCT-T CTGT CTGT CTGT CCGT CTGT CCGT CTGT CTGT
1 CTGT CTGT CTGT -CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT CTGT
73091 AGACGCAACT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
3 2 0.06
4 32 0.89
5 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.23, T:0.44
Consensus pattern (4 bp):
CTGT
Found at i:74407 original size:24 final size:24
Alignment explanation
Indices: 74363--74409 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
74353 TTGATATTTA
*
74363 TTTTTAATAAATAATATAATAACT
1 TTTTTAATAAAGAATATAATAACT
74387 TTTTTAATAAAAGAATA-AATAAC
1 TTTTTAAT-AAAGAATATAATAAC
74410 CAATAACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TTTTTAATAAAGAATATAATAACT
Found at i:75509 original size:51 final size:51
Alignment explanation
Indices: 75433--75562 Score: 224
Period size: 51 Copynumber: 2.5 Consensus size: 51
75423 TACCTTCAGG
* * *
75433 ATCTAAGTGATAAAGTTAATGCAGTACAAATGCAGTACCTTTGATGCCTGT
1 ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT
75484 ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT
1 ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT
*
75535 ATCTAAATGATAAAGATAGTGCAGTACA
1 ATCTAAATGATAAAGATAATGCAGTACA
75563 CCTATGACAG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 75 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (51 bp):
ATCTAAATGATAAAGATAATGCAGTACAAATGCAGCACCTTTGATGCCTGT
Found at i:76449 original size:24 final size:23
Alignment explanation
Indices: 76383--76452 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
76373 AAGGCCTCTG
76383 GCAAACAGTTGCCGCAAATTT--
1 GCAAACAGTTGCCGCAAATTTGC
* * *
76404 GCAGAGAGTTTGTCGCAAATTTGC
1 GCAAACAG-TTGCCGCAAATTTGC
76428 GACAAACAGTTGCCGCAAATTTGC
1 G-CAAACAGTTGCCGCAAATTTGC
76452 G
1 G
76453 GCAGGTTCAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
21 6 0.15
22 12 0.31
24 16 0.41
25 5 0.13
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.24
Consensus pattern (23 bp):
GCAAACAGTTGCCGCAAATTTGC
Found at i:76511 original size:59 final size:59
Alignment explanation
Indices: 76437--76693 Score: 442
Period size: 59 Copynumber: 4.4 Consensus size: 59
76427 CGACAAACAG
* *
76437 TTGCCGCAAATTTGCGGCAGGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
* * *
76496 TTGCAGCAAAGTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGGAAACTGT
1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
*
76555 TTGCGGCAAATTTGCCGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
*
76614 TTGCGGCAAATTTGCAGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
1 TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
*
76673 TTGCGGCAAATTTGCCGCAAG
1 TTGCGGCAAATTTGCGGCAAG
76694 CTTACAGATA
Statistics
Matches: 188, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 188 1.00
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (59 bp):
TTGCGGCAAATTTGCGGCAAGTTCAGAATTCGTATGCAAATTAGCTTCTGGCAAACTGT
Found at i:79268 original size:16 final size:15
Alignment explanation
Indices: 79232--79268 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
79222 CTGGTGGATG
79232 CTGGAGAAGTCGTAT
1 CTGGAGAAGTCGTAT
79247 CATGGAGAAGTCGTACT
1 C-TGGAGAAGTCGTA-T
79264 CTGGA
1 CTGGA
79269 AAAATCATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 1 0.05
16 17 0.85
17 2 0.10
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.24
Consensus pattern (15 bp):
CTGGAGAAGTCGTAT
Found at i:80509 original size:17 final size:17
Alignment explanation
Indices: 80487--80521 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
80477 AACTTTGTGG
*
80487 GTGCGTATTATACACGA
1 GTGCGTACTATACACGA
80504 GTGCGTACTATACACGA
1 GTGCGTACTATACACGA
80521 G
1 G
80522 ACATTACGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (17 bp):
GTGCGTACTATACACGA
Found at i:84573 original size:70 final size:70
Alignment explanation
Indices: 84460--84599 Score: 208
Period size: 70 Copynumber: 2.0 Consensus size: 70
84450 TTTATGTGTC
* * * **
84460 AGCTTGCGTGATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGTAACTTATTGTTTGAATCA
1 AGCTTGCGTAATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGCAACTAAACGTTTGAATCA
84525 CAATG
66 CAATG
* * *
84530 AGCTTGCGTAATGTTCCAAAGATTTAAATTCTCAATTGCTTGGTGGCAGCTAAACGTTTGAATCA
1 AGCTTGCGTAATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGCAACTAAACGTTTGAATCA
84595 CAATG
66 CAATG
84600 CAAGATGAGC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (70 bp):
AGCTTGCGTAATGTTCCAAAGATTTAAATTCCCAACTGCTTGGTGGCAACTAAACGTTTGAATCA
CAATG
Found at i:85187 original size:117 final size:118
Alignment explanation
Indices: 84974--85216 Score: 407
Period size: 117 Copynumber: 2.1 Consensus size: 118
84964 GGGAATCTGG
* * * *
84974 CAGGTAATCATAATAAACATTTTTTTAGATGATATATTAAATACACAAAATGGCCCAAAAGATAA
1 CAGGCAATCATAATAAACA-TTTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAA
85039 ATTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA
65 ATTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA
*
85093 TAGGCAATCATAATAAACA-TTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAAA
1 CAGGCAATCATAATAAACATTTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAAA
* *
85157 TTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATGACAAGATTGAAAGA
66 TTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA
85210 CAGGCAA
1 CAGGCAA
85217 AAGATGCTTA
Statistics
Matches: 116, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
117 99 0.85
119 17 0.15
ACGTcount: A:0.51, C:0.13, G:0.12, T:0.24
Consensus pattern (118 bp):
CAGGCAATCATAATAAACATTTTTTAGATAAAATATAAAATACACAAAATGGCCCAAAAGATAAA
TTAATAACAAATATTGCCTAAAATGCCTGAAATGAAATAACAAGACTGAAAGA
Found at i:88322 original size:16 final size:18
Alignment explanation
Indices: 88289--88327 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
88279 TTTGTACATC
88289 AAAAAAGAAAGAAAAAGA
1 AAAAAAGAAAGAAAAAGA
*
88307 AAAAAAG-AAG-ATAAGA
1 AAAAAAGAAAGAAAAAGA
88323 AAAAA
1 AAAAA
88328 TCAGCTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 10 0.50
17 3 0.15
18 7 0.35
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (18 bp):
AAAAAAGAAAGAAAAAGA
Found at i:89240 original size:12 final size:12
Alignment explanation
Indices: 89223--89247 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
89213 GAAAAAGTTC
89223 ATGCTTTAAGTG
1 ATGCTTTAAGTG
89235 ATGCTTTAAGTG
1 ATGCTTTAAGTG
89247 A
1 A
89248 AACTGAATGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
ATGCTTTAAGTG
Found at i:91232 original size:35 final size:35
Alignment explanation
Indices: 91185--91681 Score: 852
Period size: 35 Copynumber: 14.1 Consensus size: 35
91175 ATTGTGTTGT
* * *
91185 AAAAGTGTGGGTGTAAGAAAATGGGGAAAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
*
91220 AAAAGTGGGGGTGTAAGAAAAAGGGGAAAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91255 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91290 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91325 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91360 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
*
91395 AAAAGTGGGGGTGTAAGAAAAAGGGGAAAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91430 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
**
91465 AAAAAAGGGGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
**
91500 AAAAGTGTTGGTGTAAGAAAAAGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91535 AAAAGTGGGGGTGTAAGAAAAAGGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAA-GGGGATAAGACAA
91571 AAAAGTGGGGGTGTAAGAAAAAGGGGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAA-GGGGATAAGACAA
**
91607 AAAAGTGGGGGTGTAAGAAAAAGGGGATATTACAAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGAC-AA
*
91643 AAAAGTGTGGGTGTAAGAAAAA-GGGATAAGACAA
1 AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
91677 AAAAG
1 AAAAG
91682 ATCGAGCGAA
Statistics
Matches: 442, Mismatches: 18, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
34 7 0.02
35 341 0.77
36 94 0.21
ACGTcount: A:0.49, C:0.03, G:0.36, T:0.12
Consensus pattern (35 bp):
AAAAGTGGGGGTGTAAGAAAAAGGGGATAAGACAA
Found at i:91566 original size:15 final size:15
Alignment explanation
Indices: 91548--91608 Score: 50
Period size: 18 Copynumber: 3.6 Consensus size: 15
91538 AGTGGGGGTG
91548 TAAGAAAAAGGGGGA
1 TAAGAAAAAGGGGGA
*
91563 TAAGACAAAAAAGTGGGGGTG
1 TAAG---AAAAA--GGGGG-A
91584 TAAGAAAAAGGGGGA
1 TAAGAAAAAGGGGGA
91599 TAAGACAAAA
1 TAAGA-AAAA
91609 AAGTGGGGGT
Statistics
Matches: 37, Mismatches: 2, Indels: 13
0.71 0.04 0.25
Matches are distributed among these distances:
15 9 0.24
16 9 0.24
18 10 0.27
20 5 0.14
21 4 0.11
ACGTcount: A:0.52, C:0.03, G:0.34, T:0.10
Consensus pattern (15 bp):
TAAGAAAAAGGGGGA
Found at i:104183 original size:192 final size:191
Alignment explanation
Indices: 103856--104239 Score: 759
Period size: 192 Copynumber: 2.0 Consensus size: 191
103846 GGATATCTAT
103856 GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTCA
1 GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTCA
103921 TCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGTT
66 TCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGTT
103986 TGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG
131 TGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG
104047 NGCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTC
1 -GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTC
104112 ATCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGT
65 ATCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGT
104177 TTGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG
130 TTGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG
104239 G
1 G
104240 GGGGGGGGGG
Statistics
Matches: 192, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
191 1 0.01
192 191 0.99
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.36
Consensus pattern (191 bp):
GCTTCTTCAGCAAGTTGCCAACCATTTTCACCCAAATCAATTCTGCAGGTTAAACACGTACTTCA
TCATTTACATACTAGTAACTAAGTTTACTCCAACAATTTAAATTCTAGTGTAGTCACTGTGTGTT
TGATTTTAATTTAGATATAATTTTGTGTACTTTCATCTAAGGATCTACATGTAGGGGGGGG
Found at i:105718 original size:191 final size:190
Alignment explanation
Indices: 105393--105774 Score: 755
Period size: 191 Copynumber: 2.0 Consensus size: 190
105383 AAGTTGACTT
105393 TATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATGC
1 TATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATGC
105458 ATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATATT
66 ATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATATT
105523 TTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG
131 TTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG
105583 TNATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATG
1 T-ATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATG
105648 CATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATAT
65 CATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATAT
105713 TTTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG
130 TTTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG
105774 T
1 T
105775 TTTTTTTTTA
Statistics
Matches: 191, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
190 1 0.01
191 190 0.99
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (190 bp):
TATATTCATTAATTAACACAAACTAAGTAAACGCTGGGTAAGTAGACAACTCCTACGCAGAATGC
ATTCGCCCGCCGAGAAAAGAGCACTCCTGCCGCTTACCTGATTGGTTATTTTAATGTTTTATATT
TTCTAACTTAAAAATGATCATATTAATAAAAAAATGGATATGATTTTTTCATTACCTTAG
Found at i:107233 original size:11 final size:11
Alignment explanation
Indices: 107217--107248 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
107207 CTGCATTTGC
107217 CGTGGGACTTA
1 CGTGGGACTTA
107228 CGTGGGACTTA
1 CGTGGGACTTA
107239 CGTGGGACTT
1 CGTGGGACTT
107249 GTTTTCCCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.28
Consensus pattern (11 bp):
CGTGGGACTTA
Found at i:118161 original size:2 final size:2
Alignment explanation
Indices: 118156--118191 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
118146 ACTAACACAC
118156 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
118192 GCCGGTAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:119166 original size:32 final size:32
Alignment explanation
Indices: 119125--119219 Score: 154
Period size: 32 Copynumber: 3.0 Consensus size: 32
119115 ATCAGAGTCA
*
119125 TAAATAACATCTATATACGATGTTGTAACTCC
1 TAAATAACATCTATATACGGTGTTGTAACTCC
119157 TAAATAACATCTATATACGGTGTTGTAACTCC
1 TAAATAACATCTATATACGGTGTTGTAACTCC
* * *
119189 TAAGTAACATCTATATGCGGTTTTGTAACTC
1 TAAATAACATCTATATACGGTGTTGTAACTC
119220 GATCCTAAGC
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.36
Consensus pattern (32 bp):
TAAATAACATCTATATACGGTGTTGTAACTCC
Found at i:134392 original size:2 final size:2
Alignment explanation
Indices: 134385--134436 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
134375 TTTAGTGGTG
134385 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
134427 GA GA GA GA GA
1 GA GA GA GA GA
134437 AATCATAAAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:134686 original size:4 final size:4
Alignment explanation
Indices: 134677--134719 Score: 86
Period size: 4 Copynumber: 10.8 Consensus size: 4
134667 TAAAAACAAT
134677 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
134720 AGATCATCCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 39 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:135349 original size:251 final size:251
Alignment explanation
Indices: 134906--135405 Score: 1000
Period size: 251 Copynumber: 2.0 Consensus size: 251
134896 ATGCCCGACA
134906 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA
1 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA
134971 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC
66 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC
135036 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT
131 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT
135101 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGCTC
196 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGCTC
135157 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA
1 GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA
135222 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC
66 CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC
135287 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT
131 TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT
135352 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGC
196 CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGC
135406 ATGGATTAAA
Statistics
Matches: 249, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
251 249 1.00
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (251 bp):
GATTAGAATGCACGGTAAAATATTCTATCTCTGCAAATAATTTCGGATATTTAAGCGTGGGTAAA
CTCGCTGAATCCCCCCTATTTTAAGTAAATAATTCATGTCCGATCTGATTGGCTCCTTCACACTC
TTATAAAGGAAATCTAACCAATCACGTCATTGCCTACGAATGCAAATACATGAATAGTGTGTTTT
CAAAACATGATCTTAGTTTTCATACTGAAAAAAAAACCGCTTTTAAATCGGTGCTC
Found at i:153885 original size:38 final size:35
Alignment explanation
Indices: 153842--154014 Score: 103
Period size: 38 Copynumber: 4.6 Consensus size: 35
153832 GATTTCTTGC
*
153842 AAGATTTCTAGGATATCCATCCTCAGATATATTATGAA
1 AAGATTTCT-GGATATCTATCCTCAGATAT-TTAT-AA
* * * * * *
153880 AAGATTACTGGAATATCTATTCTTAGATGTCTTCCTAC
1 AAGATTTCTGG-ATATCTATCCTCAGATAT-TT-ATAA
* ** * *
153918 AAGATTTCTGAGATATCTTTCCTTTGATGTCTACTAA
1 AAGATTTCTG-GATATCTATCCTCAGATATTTA-TAA
* * *
153955 AAAATTTCTAGGATATCCATCCTCAGATATTTTATTAC
1 AAGATTTCT-GGATATCTATCCTCAGATA-TTTA-TAA
153993 AAGATTTCTGGGATATCTATCC
1 AAGATTTCT-GGATATCTATCC
154015 AAATAATTTA
Statistics
Matches: 102, Mismatches: 27, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
37 26 0.25
38 74 0.73
39 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (35 bp):
AAGATTTCTGGATATCTATCCTCAGATATTTATAA
Found at i:155099 original size:32 final size:32
Alignment explanation
Indices: 155058--155156 Score: 189
Period size: 32 Copynumber: 3.1 Consensus size: 32
155048 AAGGATGATT
155058 ATTTAGTGAGGGACCTTAAACTGTACTATTTC
1 ATTTAGTGAGGGACCTTAAACTGTACTATTTC
*
155090 ATTTAGTGAGGCACCTTAAACTGTACTATTTC
1 ATTTAGTGAGGGACCTTAAACTGTACTATTTC
155122 ATTTAGTGAGGGACCTTAAACTGTACTATTTC
1 ATTTAGTGAGGGACCTTAAACTGTACTATTTC
155154 ATT
1 ATT
155157 AAGAAACAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.28, C:0.16, G:0.17, T:0.38
Consensus pattern (32 bp):
ATTTAGTGAGGGACCTTAAACTGTACTATTTC
Found at i:155255 original size:21 final size:21
Alignment explanation
Indices: 155229--155273 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
155219 TAAGCTGCAG
155229 TAACAATCCCAGTCAGGGCAA
1 TAACAATCCCAGTCAGGGCAA
155250 TAACAATCCCAGTCAGGGCAA
1 TAACAATCCCAGTCAGGGCAA
155271 TAA
1 TAA
155274 AACCCTCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.40, C:0.27, G:0.18, T:0.16
Consensus pattern (21 bp):
TAACAATCCCAGTCAGGGCAA
Found at i:157303 original size:23 final size:23
Alignment explanation
Indices: 157277--157320 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
157267 AGTTATATTT
*
157277 TTGGAGTAAAAATAGTTTCTGCC
1 TTGGAGTAAAAACAGTTTCTGCC
*
157300 TTGGAGTAAAGACAGTTTCTG
1 TTGGAGTAAAAACAGTTTCTG
157321 TATTGTAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (23 bp):
TTGGAGTAAAAACAGTTTCTGCC
Found at i:158168 original size:2 final size:2
Alignment explanation
Indices: 158163--158208 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
158153 TCTTATAATT
158163 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
158205 GA GA
1 GA GA
158209 CACTACACCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:158335 original size:2 final size:2
Alignment explanation
Indices: 158328--158354 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
158318 NNNNNNNNNN
158328 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
158355 AACCTAACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:158427 original size:2 final size:2
Alignment explanation
Indices: 158422--158460 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
158412 TTTTTTGATT
158422 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
158461 GAATTAGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:160243 original size:2 final size:2
Alignment explanation
Indices: 160238--160264 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
160228 TATATAATAA
160238 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
160265 AAAACATCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:161561 original size:16 final size:15
Alignment explanation
Indices: 161537--161574 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
161527 CTTATATTTG
161537 TGTCCATCCATCCATC
1 TGTCCATCCATCC-TC
*
161553 TGTCTATCCATCCTC
1 TGTCCATCCATCCTC
161568 TGTCCAT
1 TGTCCAT
161575 TTATTCTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.16, C:0.39, G:0.08, T:0.37
Consensus pattern (15 bp):
TGTCCATCCATCCTC
Found at i:161586 original size:2 final size:2
Alignment explanation
Indices: 161579--161672 Score: 147
Period size: 2 Copynumber: 47.5 Consensus size: 2
161569 GTCCATTTAT
*
161579 TC TC TC TC TT TC TC TC -C ATC TC TC TC TC -C TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC -TC TC TC TC TC TC TC TC TC TC TC TC
*
161620 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TG TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
161662 TC TC TC TC TC T
1 TC TC TC TC TC T
161673 AACAATAAAC
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
1 2 0.02
2 82 0.96
3 1 0.01
ACGTcount: A:0.01, C:0.48, G:0.01, T:0.50
Consensus pattern (2 bp):
TC
Found at i:161784 original size:16 final size:16
Alignment explanation
Indices: 161763--161793 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
161753 AATCCACACC
161763 GCACATTCAAAACCCA
1 GCACATTCAAAACCCA
161779 GCACATTCAAAACCC
1 GCACATTCAAAACCC
161794 CATTCTTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.42, C:0.39, G:0.06, T:0.13
Consensus pattern (16 bp):
GCACATTCAAAACCCA
Found at i:166208 original size:28 final size:25
Alignment explanation
Indices: 166150--166208 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
166140 TCTTATGTCA
166150 CTATCATTTATTAATCATTTATCAT
1 CTATCATTTATTAATCATTTATCAT
* *
166175 C-ATCATTATTTTAATCATCGTTTTCAT
1 CTATCATT-TATTAATCAT--TTATCAT
166202 CTATCAT
1 CTATCAT
166209 CATCTGAATG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.21
25 10 0.36
27 7 0.25
28 5 0.18
ACGTcount: A:0.29, C:0.19, G:0.02, T:0.51
Consensus pattern (25 bp):
CTATCATTTATTAATCATTTATCAT
Found at i:177778 original size:2 final size:2
Alignment explanation
Indices: 177771--177818 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
177761 TACATGCCCC
177771 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
177813 CT CT CT
1 CT CT CT
177819 ACTACCCCTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:178029 original size:2 final size:2
Alignment explanation
Indices: 178022--178149 Score: 89
Period size: 2 Copynumber: 63.0 Consensus size: 2
178012 NNNNNNNNNN
*
178022 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CA CAT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C-T
* ** * * * * * * * *
178065 CA CT CT CT GAG GT CA CAT CAG GT CA CA CA CT -T CT -T CT AT CT
1 CT CT CT CT -CT CT CT C-T C-T CT CT CT CT CT CT CT CT CT CT CT
*
178106 GT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
178148 CT
1 CT
178150 TTACATGCCT
Statistics
Matches: 100, Mismatches: 21, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
1 2 0.02
2 95 0.95
3 3 0.03
ACGTcount: A:0.09, C:0.44, G:0.05, T:0.43
Consensus pattern (2 bp):
CT
Found at i:179063 original size:184 final size:187
Alignment explanation
Indices: 178739--179111 Score: 576
Period size: 184 Copynumber: 2.0 Consensus size: 187
178729 TAAACAGGTA
178739 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTGTAATATGTACAGTATGTATTGA
1 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTG--ATATGTACAGTATGTATTGA
**
178804 ATATCACATACACTATCAATATCTTAAAAGATATACAGAGCCAAATTGTGACTCTACATTGACAG
64 ATATCACATACACTATCAATATCTTAAAAGATATACAGAGCCAAA-TAAGACTCTACATTGACAG
*
178869 ATACTGAGGTGTCAAGTTATCCAGGTCACACTGTTAT-CAGAGTAAGACTGATTATAGTG
128 ATACTGAGGTGTCAAGTTATCCAGGTCACACTGTTATAAAGAGTAAGACTGATTATAGTG
* *
178928 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGAGGGATTATTG-TAT-TACA-TATGTATTGAAT
1 TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTGATATGTACAGTATGTATTGAAT
* *
178990 ATCACATGTACACTATCAATATCTTAATAGATATATAGAGCCAAA-AAGACTCTACATTGACAGA
66 ATCACA--TACACTATCAATATCTTAAAAGATATACAGAGCCAAATAAGACTCTACATTGACAGA
* * *
179054 TATTGAGGTGTCAATTTATCCAGGTCACACTGTTATAAAGAGTTAGACTGATTATAGT
129 TACTGAGGTGTCAAGTTATCCAGGTCACACTGTTATAAAGAGTAAGACTGATTATAGT
179112 ATTTCATTGG
Statistics
Matches: 171, Mismatches: 10, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
184 69 0.40
185 23 0.13
186 38 0.22
189 41 0.24
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (187 bp):
TCAAGTTTGACAGATTTCAATGAAAAGCTGAGACGAATTATTGATATGTACAGTATGTATTGAAT
ATCACATACACTATCAATATCTTAAAAGATATACAGAGCCAAATAAGACTCTACATTGACAGATA
CTGAGGTGTCAAGTTATCCAGGTCACACTGTTATAAAGAGTAAGACTGATTATAGTG
Found at i:184162 original size:2 final size:2
Alignment explanation
Indices: 184155--184195 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
184145 TCTCCACAGC
184155 CT CT CT CT CT CT CT CT CT CT CT CT CT CGT -T CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT C
184196 GCGTTGTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.00, C:0.49, G:0.02, T:0.49
Consensus pattern (2 bp):
CT
Found at i:184200 original size:16 final size:16
Alignment explanation
Indices: 184155--184205 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
184145 TCTCCACAGC
184155 CTCTCTCTCTCTC--T
1 CTCTCTCTCTCTCGTT
184169 CTCTCTCTCTCTCGTT
1 CTCTCTCTCTCTCGTT
*
184185 CTCTCTCTCTCGCGTT
1 CTCTCTCTCTCTCGTT
*
184201 GTCTC
1 CTCTC
184206 AAGCGCGTGC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.39
16 20 0.61
ACGTcount: A:0.00, C:0.45, G:0.08, T:0.47
Consensus pattern (16 bp):
CTCTCTCTCTCTCGTT
Found at i:184743 original size:2 final size:2
Alignment explanation
Indices: 184736--184783 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
184726 TAGCATTCAC
184736 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
184778 GA GA GA
1 GA GA GA
184784 TTAACTAAAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:185495 original size:35 final size:35
Alignment explanation
Indices: 185416--185495 Score: 88
Period size: 35 Copynumber: 2.3 Consensus size: 35
185406 AACTTCACGT
* * * *
185416 AACTCGCTATAGCGCTAATTAGCAAAACTTAACGC
1 AACTCGCCATAGCGCTAATTAACAAAACCTAACAC
* * * *
185451 GACTAGCCATAGCGCTAATTAACACAACCTCACAC
1 AACTCGCCATAGCGCTAATTAACAAAACCTAACAC
185486 AACTCGCCAT
1 AACTCGCCAT
185496 TGTGCTAACA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.36, C:0.31, G:0.12, T:0.20
Consensus pattern (35 bp):
AACTCGCCATAGCGCTAATTAACAAAACCTAACAC
Found at i:185713 original size:31 final size:31
Alignment explanation
Indices: 185675--185754 Score: 97
Period size: 31 Copynumber: 2.6 Consensus size: 31
185665 TTAACATCAT
*
185675 ATAACTCGCTATTGCGCTAACACAACTGCAC
1 ATAACTCGCAATTGCGCTAACACAACTGCAC
* **
185706 ATAACTCGCAAATGTTCTAACACAACTGCAC
1 ATAACTCGCAATTGCGCTAACACAACTGCAC
* * *
185737 AAAACTCGCCATCGCGCT
1 ATAACTCGCAATTGCGCT
185755 TTTTGACACG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.34, C:0.33, G:0.12, T:0.21
Consensus pattern (31 bp):
ATAACTCGCAATTGCGCTAACACAACTGCAC
Found at i:186441 original size:26 final size:26
Alignment explanation
Indices: 186407--186465 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
186397 GCATCACAAG
*
186407 TTATGTTAAGTAGAATGAAAATTTTA
1 TTATTTTAAGTAGAATGAAAATTTTA
186433 TTATTTTAAGTAGAATGAAAATTTTA
1 TTATTTTAAGTAGAATGAAAATTTTA
186459 TTATTTT
1 TTATTTT
186466 CTCTTATTCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (26 bp):
TTATTTTAAGTAGAATGAAAATTTTA
Found at i:187759 original size:2 final size:2
Alignment explanation
Indices: 187754--187800 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
187744 ATCATATATA
187754 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
187796 TC TC T
1 TC TC T
187801 GCATTCACCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:190829 original size:2 final size:2
Alignment explanation
Indices: 190824--190849 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
190814 ATTAATTCAA
190824 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
190850 NNNNNNNNNN
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:193731 original size:2 final size:2
Alignment explanation
Indices: 193689--193719 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
193679 ATATCTTCAT
193689 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
193720 ATGAAGGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:194786 original size:2 final size:2
Alignment explanation
Indices: 194779--194848 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
194769 TGAATTATTT
194779 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
194821 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
194849 NNNNNNNNNN
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:197165 original size:21 final size:21
Alignment explanation
Indices: 197136--197242 Score: 108
Period size: 21 Copynumber: 5.0 Consensus size: 21
197126 GCTACACGCT
* *
197136 CGCTAAACGGTTCACACGAAA
1 CGCTGAACGGTTTACACGAAA
197157 CGCTGAACGGTTTACACGAAA
1 CGCTGAACGGTTTACACGAAA
** * *
197178 CGCTGCGCGCTTTGTC-CGAAA
1 CGCTGAACGGTTT-ACACGAAA
*
197199 CGCTTTGAAGCGATTTACACGAAA
1 CGC--TGAA-CGGTTTACACGAAA
197223 CGCTGAACGGTTTACACGAA
1 CGCTGAACGGTTTACACGAA
197243 TGATTAGTAG
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 49 0.70
22 5 0.07
23 3 0.04
24 13 0.19
ACGTcount: A:0.30, C:0.26, G:0.23, T:0.21
Consensus pattern (21 bp):
CGCTGAACGGTTTACACGAAA
Found at i:199943 original size:75 final size:75
Alignment explanation
Indices: 199820--199972 Score: 261
Period size: 75 Copynumber: 2.0 Consensus size: 75
199810 CTTGTTGAAA
* * * *
199820 GTAAAAGGTTCTGAGTTCACCTGTTGTTTTACTATAACTACTGTATTACATTTAATACCATATTT
1 GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTACTGTATTACATTAAATACCATAGTC
199885 GTATGTACCT
66 GTATGTACCT
*
199895 GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTTCTGTATTACATTAAATACCATAGTC
1 GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTACTGTATTACATTAAATACCATAGTC
199960 GTATGTACCT
66 GTATGTACCT
199970 GTA
1 GTA
199973 TGTACAGCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
75 73 1.00
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (75 bp):
GTAAAAGGTTCTGAGTTCACCTATTGTTTTACTATAACTACTGTATTACATTAAATACCATAGTC
GTATGTACCT
Found at i:200688 original size:2 final size:2
Alignment explanation
Indices: 200677--200722 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
200667 ATCAAAGGTC
200677 AG AG -G AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
200718 AG AG A
1 AG AG A
200723 AAATTGGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:200690 original size:198 final size:198
Alignment explanation
Indices: 200339--200708 Score: 686
Period size: 198 Copynumber: 1.9 Consensus size: 198
200329 CAATTTTAGA
*
200339 ATTACCGGTATTTCTGTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA
1 ATTACCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA
200404 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC
66 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC
* * *
200469 ATCAAAGGTCAGAGGTCAGAGAGAGGGCGAGAGAGAGAGAGAAAAATTGAGAGAGAGAGAGAGAG
131 ATCAAAGGTCAGAGGACAGAGAGAGAGAGAGAGAGAGAGAGAAAAATTGAGAGAGAGAGAGAGAG
200534 AAT
196 AAT
*
200537 ATTANCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA
1 ATTACCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA
200602 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC
66 AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC
*
200667 ATCAAAGGTCAGAGGAGAGAGAGAGAGAGAGAGAGAGAGAGA
131 ATCAAAGGTCAGAGGACAGAGAGAGAGAGAGAGAGAGAGAGA
200709 GAGAGAGAGA
Statistics
Matches: 166, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
198 166 1.00
ACGTcount: A:0.30, C:0.17, G:0.30, T:0.23
Consensus pattern (198 bp):
ATTACCGGTATTTCTCTTTATAGATAGTGTGTCTCGCTGTGCTGTGACGATCTGTAACCGTGGGA
AAGAGGACCTGTCTCCATTACATTGCCAGTCAGGGTCAATCCTGATTACCGAGGTCAAGGACACC
ATCAAAGGTCAGAGGACAGAGAGAGAGAGAGAGAGAGAGAGAAAAATTGAGAGAGAGAGAGAGAG
AAT
Found at i:205732 original size:8 final size:8
Alignment explanation
Indices: 205685--205825 Score: 160
Period size: 8 Copynumber: 17.6 Consensus size: 8
205675 GCGTCAGGTT
*
205685 ATCAATAA
1 ATCAATCA
*
205693 ATCCATCA
1 ATCAATCA
205701 ATCAGA-CA
1 ATCA-ATCA
*
205709 ATAAATCA
1 ATCAATCA
*
205717 GA-CAATAA
1 -ATCAATCA
*
205725 ATCAATAA
1 ATCAATCA
205733 ATCAATCA
1 ATCAATCA
*
205741 ATCCATCA
1 ATCAATCA
205749 ATCAATCA
1 ATCAATCA
205757 ATCAATCA
1 ATCAATCA
*
205765 ATCAACCA
1 ATCAATCA
205773 ATCAATCA
1 ATCAATCA
*
205781 ACCAATCA
1 ATCAATCA
*
205789 ATCAACCA
1 ATCAATCA
205797 ATCAATCA
1 ATCAATCA
205805 ATCAATCA
1 ATCAATCA
*
205813 ACCAATCA
1 ATCAATCA
205821 ATCAA
1 ATCAA
205826 CTGCCGAAGC
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
7 2 0.02
8 108 0.96
9 2 0.02
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (8 bp):
ATCAATCA
Found at i:205739 original size:12 final size:12
Alignment explanation
Indices: 205685--205825 Score: 160
Period size: 12 Copynumber: 11.8 Consensus size: 12
205675 GCGTCAGGTT
* *
205685 ATCAATAAATCC
1 ATCAATCAATCA
205697 ATCAATCAGA-CA
1 ATCAATCA-ATCA
*
205709 ATAAATCAGA-CA
1 ATCAATCA-ATCA
* *
205721 ATAAATCAATAA
1 ATCAATCAATCA
*
205733 ATCAATCAATCC
1 ATCAATCAATCA
205745 ATCAATCAATCA
1 ATCAATCAATCA
205757 ATCAATCAATCA
1 ATCAATCAATCA
*
205769 ACCAATCAATCA
1 ATCAATCAATCA
*
205781 ACCAATCAATCA
1 ATCAATCAATCA
*
205793 ACCAATCAATCA
1 ATCAATCAATCA
*
205805 ATCAATCAACCA
1 ATCAATCAATCA
205817 ATCAATCAA
1 ATCAATCAA
205826 CTGCCGAAGC
Statistics
Matches: 116, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
11 1 0.01
12 114 0.98
13 1 0.01
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (12 bp):
ATCAATCAATCA
Found at i:205742 original size:20 final size:20
Alignment explanation
Indices: 205685--205825 Score: 160
Period size: 20 Copynumber: 7.0 Consensus size: 20
205675 GCGTCAGGTT
* *
205685 ATCAATAAATCCATCAATCA
1 ATCAATCAATCAATCAATCA
* *
205705 GA-CAATAAATCAGA-CAATAA
1 -ATCAATCAATCA-ATCAATCA
* *
205725 ATCAATAAATCAATCAATCC
1 ATCAATCAATCAATCAATCA
205745 ATCAATCAATCAATCAATCA
1 ATCAATCAATCAATCAATCA
* *
205765 ATCAACCAATCAATCAACCA
1 ATCAATCAATCAATCAATCA
*
205785 ATCAATCAACCAATCAATCA
1 ATCAATCAATCAATCAATCA
*
205805 ATCAATCAACCAATCAATCA
1 ATCAATCAATCAATCAATCA
205825 A
1 A
205826 CTGCCGAAGC
Statistics
Matches: 106, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
19 2 0.02
20 102 0.96
21 2 0.02
ACGTcount: A:0.52, C:0.26, G:0.01, T:0.21
Consensus pattern (20 bp):
ATCAATCAATCAATCAATCA
Found at i:208353 original size:2 final size:2
Alignment explanation
Indices: 208346--208398 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
208336 TGAAACTTTG
208346 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
208388 GA GA GA GA GA G
1 GA GA GA GA GA G
208399 GTTTCTCCAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:210068 original size:50 final size:50
Alignment explanation
Indices: 210016--210645 Score: 946
Period size: 50 Copynumber: 12.6 Consensus size: 50
210006 CAGGATGTAT
* * *
210016 GTAGAGAATAACAGCTGTTTTGGTCAAATGTATGAAGG-TTCAGGATAAAT
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTT-AGGATAAAA
*
210066 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
*
210116 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
*
210166 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
*
210216 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
* * *
210266 GTGGAAAATAACAGTTGTATTGGTCAAATGTATGAAGGCTGAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
210316 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
* *
210366 GTAGAAATTAACAGTTGTTTTGGTAAAATGTATGAAGG-TTCAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTT-AGGATAAAA
* * *
210416 GTAGAAATTAACAGTTGTTTTGGTCAAATGTATGAAAGCTTAGGATAAAT
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
* *
210466 GTAGAAAATAACAGTTGTTTTGGTCAAATGTACGAAGGCTCAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
*
210516 GTAGAAAATAACAGATGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
1 GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
* * * * *
210566 GTAAAAAATAACAGTTGTTTTGGTAAAAAAAAGTATGAATG-TTATTG-TAAAA
1 GTAGAAAATAACAGTTGTTTTGGT---CAAATGTATGAAGGCTTA-GGATAAAA
* *
210618 ATAGAAAATAACAGTT-TTCTGGTCAAAT
1 GTAGAAAATAACAGTTGTTTTGGTCAAAT
210646 TCTTTATGCA
Statistics
Matches: 539, Mismatches: 34, Indels: 16
0.92 0.06 0.03
Matches are distributed among these distances:
48 3 0.01
49 2 0.00
50 490 0.91
51 10 0.02
52 22 0.04
53 12 0.02
ACGTcount: A:0.41, C:0.06, G:0.23, T:0.29
Consensus pattern (50 bp):
GTAGAAAATAACAGTTGTTTTGGTCAAATGTATGAAGGCTTAGGATAAAA
Found at i:214283 original size:2 final size:2
Alignment explanation
Indices: 214278--214334 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
214268 GTGTGATGTC
214278 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
214320 AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG A
214335 TGAATGATTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:226589 original size:2 final size:2
Alignment explanation
Indices: 226582--226626 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
226572 TAGCAAAATT
226582 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
226624 GA G
1 GA G
226627 TCATCATTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:226809 original size:4 final size:4
Alignment explanation
Indices: 226800--226870 Score: 142
Period size: 4 Copynumber: 17.8 Consensus size: 4
226790 AAATTAATGA
226800 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
1 ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT ATCT
226848 ATCT ATCT ATCT ATCT ATCT ATC
1 ATCT ATCT ATCT ATCT ATCT ATC
226871 CTTTTTCTAC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 67 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.49
Consensus pattern (4 bp):
ATCT
Found at i:227864 original size:267 final size:267
Alignment explanation
Indices: 227523--228320 Score: 1560
Period size: 267 Copynumber: 3.0 Consensus size: 267
227513 TTCAGAATAT
*
227523 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCTCAAGTAAGCAATGAATTGCGCAATG
1 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG
* *
227588 GTATTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTATGTTTATTTTATTGTGTTTTATGT
66 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT
227653 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
131 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
227718 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT
196 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT
227783 AGAATTA
261 AGAATTA
227790 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG
1 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG
227855 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT
66 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT
227920 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
131 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
227985 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT
196 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT
228050 AGAATTA
261 AGAATTA
228057 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG
1 AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG
228122 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT
66 GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT
228187 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
131 TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
*
228252 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTTAAGTTCTGATACTT
196 ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT
228317 AGAA
261 AGAA
228321 CAGGGAAACA
Statistics
Matches: 527, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 527 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (267 bp):
AAATATAAACCTTGATTCTTAGAAGATGAAATATATTGCCCAAGTAAGCAATGAATTGCGCAATG
GTTTTTTGTTTGGAAGTTTAATAATGATGACGTGCTGTGTGTGTTTATTTTATTGTGTTTTATGT
TTGTCAAGAAAGTTATAAAAACTGATTTGATAGACTCACCTTTGCCAGACTTAGAGATGAAAAAA
ACAAATTAGACACTTGGCTAGCGAAGATGTGCTAGACTATGTTTTGACTTCAAGTTCTGATACTT
AGAATTA
Found at i:228827 original size:4 final size:4
Alignment explanation
Indices: 228818--228863 Score: 65
Period size: 4 Copynumber: 11.0 Consensus size: 4
228808 TCTGCACTCC
*
228818 AATA AATA AATA AATA ATGTAA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA A-AT-A AATA AATA AATA AATA AATA AATA
228864 TACAGCTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
4 34 0.89
5 2 0.05
6 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:230963 original size:2 final size:2
Alignment explanation
Indices: 230956--230989 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
230946 GAAAAATAAT
230956 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
230990 TTGGATAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:234350 original size:62 final size:62
Alignment explanation
Indices: 234039--234347 Score: 545
Period size: 62 Copynumber: 5.0 Consensus size: 62
234029 ATAAAGCTAT
234039 AGAGTTTCCCTGAAATATA-TTT-AAAAAAA-ACACCAGTGGTTTCTGTAAATATACATAAA
1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
*
234098 AGAGTTTCCCTGAAATATA-TTTAAAAAAAATACACCAGTGCTTTCTGTAAATACATACATAAA
1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAAT--ATACATAAA
234161 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
234223 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
* *
234285 ACACTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
1 AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
234347 A
1 A
234348 CACCAACGGC
Statistics
Matches: 241, Mismatches: 4, Indels: 7
0.96 0.02 0.03
Matches are distributed among these distances:
59 22 0.09
60 7 0.03
61 20 0.08
62 132 0.55
63 28 0.12
64 32 0.13
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.31
Consensus pattern (62 bp):
AGAGTTTCCCTGAAATATATTTTAAAAAAAATACACCAGTGGTTTCTGTAAATATACATAAA
Found at i:239798 original size:10 final size:10
Alignment explanation
Indices: 239783--239809 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
239773 CAAATACCAA
239783 AAAAAAAAAT
1 AAAAAAAAAT
239793 AAAAAAAAAT
1 AAAAAAAAAT
239803 AAAAAAA
1 AAAAAAA
239810 TTCATCGACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (10 bp):
AAAAAAAAAT
Found at i:251068 original size:53 final size:55
Alignment explanation
Indices: 250999--251110 Score: 194
Period size: 53 Copynumber: 2.1 Consensus size: 55
250989 GTGTTAATTT
250999 TATAGAATGATGATAATATATTATCATACATGTTTCCAATTCCTTACA-A-GGTA
1 TATAGAATGATGATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA
251052 TATAGAATGAAT-ATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA
1 TATAGAATG-ATGATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA
251107 TATA
1 TATA
251111 ACTGGATCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
53 45 0.80
54 3 0.05
55 8 0.14
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (55 bp):
TATAGAATGATGATAATATATTATCATACATGTTTCCAATTCCTTACACACGGTA
Found at i:251404 original size:3 final size:3
Alignment explanation
Indices: 251396--251430 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
251386 AAAAAGGACT
251396 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG
251431 TGTGGTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:261878 original size:15 final size:15
Alignment explanation
Indices: 261854--261892 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
261844 CTTTAAATTT
*
261854 AAAATAAAAAGTAAGA
1 AAAATAAAATGTAA-A
*
261870 AAAATAAAATTTAAA
1 AAAATAAAATGTAAA
261885 AAAATAAA
1 AAAATAAA
261893 TAAAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (15 bp):
AAAATAAAATGTAAA
Found at i:266198 original size:175 final size:174
Alignment explanation
Indices: 265902--266248 Score: 658
Period size: 175 Copynumber: 2.0 Consensus size: 174
265892 GTCTGTTGTT
265902 TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGTT
1 TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGTT
*
265967 GAGATATCTCTTGGTGTTATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACCC
66 GAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACCC
266032 GGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTTCG
131 GGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTTCG
266076 NTGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGT
1 -TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGT
*
266141 TGAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCTAAATGTTCAAGACC
65 TGAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACC
*
266206 CGGAAGTTGACGACGATCGTTCGAATGATCTTGAGGAATACTT
130 CGGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTT
266249 TGATGCTGAC
Statistics
Matches: 169, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
175 169 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (174 bp):
TGGTGGGGGATTTTGATAATTTTCAAAGTTGTTGTTGTTTTCTTTTCAAGTATCTTCTTGTGGTT
GAGATATCTCTTGGTGTAATAATGGCCTCCCCCGATCCTGAAGTTATTCGAAATGTTCAAGACCC
GGAAGTTGACGACGATCGTCCGAATGATCTTGAGGAATACTTCG
Found at i:268000 original size:166 final size:167
Alignment explanation
Indices: 267263--268388 Score: 1755
Period size: 166 Copynumber: 6.8 Consensus size: 167
267253 GTGAATATGC
* * * * * * *
267263 AAAATAAGCAAAGTCGACATTTAACAGAAAGCTGGCATCCGATTGGTACAGAAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * * * *
267328 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAACATCTGCGATAAATAGCTGCTGAAA
66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
267393 AATCTTTGAGGAAAATTTGTTTGAAAATTTTGGCT--
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
* *
267428 AAAATAAACAAAGTAC-TCATTTAACAGGAAGATGACGTCCGATTGGTACAAAAATATATCCCAC
1 AAAATAAGCAAAGT-CGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCAC
* * * *
267492 GATATGGCATGCCTTAAAAAATACTGTGTTAAAATTTAAAGCATCTCCGATAAATAGCTGCTGAG
65 GATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
*
267557 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGG-CAA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
* * * * * *
267594 AAAATAAACAAAGTCATTATTTAACAGGAAGTTG-CGTCTGATTGATACAAAAATATATCCCACA
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
267658 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
267723 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
**
267760 AAAATAAGCAAAGTCGTCATTTAACAATAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* * *
267825 ATATGGCATGCCTTAACAAACACTGTCTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
267890 AATCTTTGACGAAAATTTGTTTGAAAA-TTTGGTTAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
* *
267926 AAAATAAGCAAAGTTGTCATTTAACAGGAAGTTGACGTCCGATTGATACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
267991 ATATGGCATGCCTAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
* *
268056 ATTCTTTGACGAAAATTTGTTTGAAAATTTTGG-CAA
131 AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
* *
268092 AAAATAAACAAAGTCGTCATTTAACAGGAAGTTGACGTCTGATTGGTACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
268157 ATATGGCATGCC-TATACAAATACTGTGTAAAAATTTCAAGCATCTGCGATAAACAGTTGCTGAG
66 ATATGGCATGCCTTA-ACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAG
268221 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
130 AAATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
*
268259 AAAATAAGCAAAGTCGTCATTTAACAAGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
1 AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
* *
268324 ATATGGCATGCCTTAACAAACACTGTGTTAAAATTTCAAGCATCTGCAATAAATAGTTGCTGAGA
66 ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
268389 TAAATGCGAC
Statistics
Matches: 881, Mismatches: 70, Indels: 18
0.91 0.07 0.02
Matches are distributed among these distances:
165 266 0.30
166 372 0.42
167 241 0.27
168 2 0.00
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (167 bp):
AAAATAAGCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAAAATATATCCCACG
ATATGGCATGCCTTAACAAATACTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGA
AATCTTTGACGAAAATTTGTTTGAAAATTTTGGTTAA
Found at i:268421 original size:4 final size:4
Alignment explanation
Indices: 268412--268469 Score: 71
Period size: 4 Copynumber: 14.5 Consensus size: 4
268402 AATTTTTGTT
* * * * *
268412 ACGG ACGG ACAG ACAG ACGG ACGG ACAG ACAG ACAG ACGG ACGG ACGG
1 ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG ACGG
268460 ACGG ACGG AC
1 ACGG ACGG AC
268470 AGACAGACAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 50 1.00
ACGTcount: A:0.34, C:0.26, G:0.40, T:0.00
Consensus pattern (4 bp):
ACGG
Found at i:268433 original size:16 final size:16
Alignment explanation
Indices: 268412--268477 Score: 105
Period size: 16 Copynumber: 4.1 Consensus size: 16
268402 AATTTTTGTT
268412 ACGGACGGACAGACAG
1 ACGGACGGACAGACAG
268428 ACGGACGGACAGACAG
1 ACGGACGGACAGACAG
* * *
268444 ACAGACGGACGGACGG
1 ACGGACGGACAGACAG
268460 ACGGACGGACAGACAG
1 ACGGACGGACAGACAG
268476 AC
1 AC
268478 ACACAAGGGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (16 bp):
ACGGACGGACAGACAG
Found at i:268437 original size:20 final size:20
Alignment explanation
Indices: 268412--268461 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
268402 AATTTTTGTT
268412 ACGGACGGACAGACAGACGG
1 ACGGACGGACAGACAGACGG
*
268432 ACGGACAGACAGACAGACGG
1 ACGGACGGACAGACAGACGG
268452 ACGGACGGAC
1 ACGGACGGAC
268462 GGACGGACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.36, C:0.26, G:0.38, T:0.00
Consensus pattern (20 bp):
ACGGACGGACAGACAGACGG
Found at i:268448 original size:8 final size:8
Alignment explanation
Indices: 268415--268478 Score: 74
Period size: 8 Copynumber: 8.0 Consensus size: 8
268405 TTTTGTTACG
268415 GACGGACA
1 GACGGACA
* *
268423 GACAGACG
1 GACGGACA
268431 GACGGACA
1 GACGGACA
*
268439 GACAGACA
1 GACGGACA
*
268447 GACGGACG
1 GACGGACA
*
268455 GACGGACG
1 GACGGACA
268463 GACGGACA
1 GACGGACA
*
268471 GACAGACA
1 GACGGACA
268479 CACAAGGGTA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
8 47 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (8 bp):
GACGGACA
Found at i:268474 original size:4 final size:4
Alignment explanation
Indices: 268419--268478 Score: 57
Period size: 4 Copynumber: 15.0 Consensus size: 4
268409 GTTACGGACG
* * * * * * *
268419 GACA GACA GACG GACG GACA GACA GACA GACG GACG GACG GACG GACG
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA GACA
268467 GACA GACA GACA
1 GACA GACA GACA
268479 CACAAGGGTA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.38, C:0.25, G:0.37, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:270073 original size:20 final size:20
Alignment explanation
Indices: 270048--270121 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
270038 AGTGCCATTT
270048 TTTACTGATAATTTCTGATA
1 TTTACTGATAATTTCTGATA
*
270068 TTTACTGAT-ATTGTACTGTTA
1 TTTACTGATAATT-T-CTGATA
* * * *
270089 -GTGCTGAGAATTGCTGATA
1 TTTACTGATAATTTCTGATA
270108 TTTACTGATAATTT
1 TTTACTGATAATTT
270122 TACTGCTGTT
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 8 0.20
20 24 0.60
21 8 0.20
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.47
Consensus pattern (20 bp):
TTTACTGATAATTTCTGATA
Found at i:270078 original size:10 final size:10
Alignment explanation
Indices: 270048--270117 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
270038 AGTGCCATTT
270048 TTTACTGATAA
1 TTTACTGAT-A
270059 TTT-CTGATA
1 TTTACTGATA
270068 TTTACTGATA
1 TTTACTGATA
*
270078 TTGTACTGTTA
1 TT-TACTGATA
* * *
270089 -GTGCTGAGA
1 TTTACTGATA
* *
270098 ATTGCTGATA
1 TTTACTGATA
270108 TTTACTGATA
1 TTTACTGATA
270118 ATTTTACTGC
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
9 9 0.19
10 28 0.60
11 10 0.21
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.46
Consensus pattern (10 bp):
TTTACTGATA
Found at i:270142 original size:41 final size:40
Alignment explanation
Indices: 270050--270145 Score: 113
Period size: 40 Copynumber: 2.4 Consensus size: 40
270040 TGCCATTTTT
* *
270050 TACTGATAATTTCTGATATTTACTGATATTGTACTGTTAG
1 TACTGATAATTGCTGATATTTACTGATATTGTACTGCTAG
* * *
270090 TGCTGAGAATTGCTGATATTTACTGATAATTTTACTGCT-G
1 TACTGATAATTGCTGATATTTACTGAT-ATTGTACTGCTAG
*
270130 TTATTGATAATTGCTG
1 -TACTGATAATTGCTG
270146 TTGGTTCTGA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
40 25 0.54
41 21 0.46
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.46
Consensus pattern (40 bp):
TACTGATAATTGCTGATATTTACTGATATTGTACTGCTAG
Found at i:270870 original size:2 final size:2
Alignment explanation
Indices: 270865--270900 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
270855 GGATAAATAA
270865 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
270901 CTACCATTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:271296 original size:2 final size:2
Alignment explanation
Indices: 271289--271318 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
271279 ATGCTTAAAT
271289 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
271319 AGATAATCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:271439 original size:2 final size:2
Alignment explanation
Indices: 271434--271464 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
271424 CCCCCCCCCC
271434 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
271465 ATTAATACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:271846 original size:134 final size:134
Alignment explanation
Indices: 271606--271857 Score: 398
Period size: 134 Copynumber: 1.9 Consensus size: 134
271596 CAGAAAATTT
* * *
271606 TTTGTATGTCTGGGATTAAGAATAACCTCAGAACTAACAGAGAGCACTCAGACTATACACACGAC
1 TTTGTATGTCTGGGATCAAGAATAACCTCAGAACTAACAGACAGCACTCAGAATATACACACGAC
* *
271671 AGGGTGACCACGGCAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAGA
66 AGAGTGACCACGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAGA
271736 TTCG
131 TTCG
* *
271740 TTTGTATGTCTGGGATCAAGAA-AACCCTCAGAACTAACAGACAGCGCTCAGAATATATACACGA
1 TTTGTATGTCTGGGATCAAGAATAA-CCTCAGAACTAACAGACAGCACTCAGAATATACACACGA
** *
271804 CAGAGTGACCGTGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTTGCAG
65 CAGAGTGACCACGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAG
271858 CCTCAGAATA
Statistics
Matches: 107, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
133 2 0.02
134 105 0.98
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (134 bp):
TTTGTATGTCTGGGATCAAGAATAACCTCAGAACTAACAGACAGCACTCAGAATATACACACGAC
AGAGTGACCACGACAAGGTGTGAAAATTGACCACCTGTGTATATGTCTGGCAGTCGCTGAAAAGA
TTCG
Found at i:272534 original size:10 final size:10
Alignment explanation
Indices: 272519--272696 Score: 80
Period size: 10 Copynumber: 17.7 Consensus size: 10
272509 TCAGTACCAA
*
272519 CAGTAAATCT
1 CAGTAAATAT
272529 CAGTAAATAT
1 CAGTAAATAT
*
272539 CAGTAATTAT
1 CAGTAAATAT
**
272549 CAG-AGCTCA-
1 CAGTAAAT-AT
* *
272558 CAGCAAAAGCAT
1 CAG-TAAA-TAT
272570 CAGTAAATAT
1 CAGTAAATAT
272580 CAGTAAATAT
1 CAGTAAATAT
** *
272590 CAG-AACCAA
1 CAGTAAATAT
* *
272599 CAGCAATTAT
1 CAGTAAATAT
* *
272609 CAGT-AACAG
1 CAGTAAATAT
272618 CAGTAAAATTAT
1 CAGT-AAA-TAT
272630 CAGTAAATAT
1 CAGTAAATAT
* * *
272640 CAGCAATTCT
1 CAGTAAATAT
* * *
272650 CAG-CACTAA
1 CAGTAAATAT
272659 CAGTACAATAT
1 CAGTA-AATAT
272670 CAGTAAATAT
1 CAGTAAATAT
272680 CAG-AAACTAT
1 CAGTAAA-TAT
272690 CAGTAAA
1 CAGTAAA
272697 AAATGGCACT
Statistics
Matches: 124, Mismatches: 31, Indels: 25
0.69 0.17 0.14
Matches are distributed among these distances:
9 25 0.20
10 70 0.56
11 21 0.17
12 8 0.06
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.24
Consensus pattern (10 bp):
CAGTAAATAT
Found at i:282365 original size:13 final size:13
Alignment explanation
Indices: 282347--282371 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
282337 GGCTGAAGCT
282347 AGCAGCCACTAAC
1 AGCAGCCACTAAC
282360 AGCAGCCACTAA
1 AGCAGCCACTAA
282372 GCCCGTAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (13 bp):
AGCAGCCACTAAC
Found at i:283863 original size:303 final size:311
Alignment explanation
Indices: 283072--284692 Score: 2143
Period size: 303 Copynumber: 5.1 Consensus size: 311
283062 AAGAGACGGT
* * * **
283072 TTAGCTCACCCGAACTTTTTCATATTTTAGCATTTCACAATGATAAAGGGGTGAAAAGCGGGGCA
1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
* * * * *
283137 TTATCTCTTTTATCTTTAAAGTGTGCATCAAACGGATGCCAGGGTAATGTAGGGGACCTATTGGG
66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
* * * * * *
283202 CTATTATTTCCCGGTCTCCAATTTGGGCTGTA-AGGGTACCACCAAGTGGCTTCCAAGGTTTCCG
131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGA-GGCACCACCAAGTGGCTCCCAGGGGTTCTG
* *
283266 GCTCATTTCAGGGGTTTATATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAAGATTAA
195 GCTCATTTCAGGGGTTTA-A-CTCAC-T---ACT-A-CAC---AA----GAAACACTAGGATTAA
* *
283331 GTAGAGGACCTCAAGGGGTATTCATAATAAGCGCTAAATGGCACCTATGATCCCTGCAAGGGTTC
245 GTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTC
283396 AA
310 AA
283398 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
*
283463 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACGGATACCAGGGCAATGTAGGGGACCTATGGGG
66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
* * *
283528 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGTACCACCAAGTGGCTCCCA-AGGTTTTCG
131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCT-G
*
283592 GCTCATTTCAGGGGTTT-A-T-A-T-CT-CAC-A-AAACACTAGGATTAAGTATAGGACCTCAAA
195 GCTCATTTCAGGGGTTTAACTCACTACTACACAAGAAACACTAGGATTAAGTAGAGGACCTCAAA
*
283649 GGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGTTTCAA
260 GGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCAA
283701 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
283766 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
* *
283831 CTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTGGCTCCCAGGGGTTCTGG
131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCTGG
*
283896 CTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAGGATTAAG
196 CTCATTTCAGGGGTTTA-A-CTCAC-T---ACT-A-CAC---AA----GAAACACTAGGATTAAG
* * *
283961 TAGAGGACCTC-AAGGGTATTCATAATAAGCGTTGAAGGGCACCTATGACCCCTGCAAGGGTTCA
246 TAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCA
284025 A
311 A
* * **
284026 TTAGTTCACCCGAACTTTGTCATATTTTAGCATTTCACAATTATATAGGGGTGAAAGGCGGGGCA
1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
* * * * * * *
284091 TTATCTCTTTTATTTTTAAAGTGTGCATTAAACGGATACCAGGGCAATGTAGGTGAGCAATGGGG
66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
* * *
284156 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGTACCACCAAGTGGCTCCCA-AGGTTTTCG
131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCT-G
*
284220 GCTCATTTCAGGGGTTT-A-T-A-T-CT-CA-TA-AAACACTAGGATTAAGTAGAGGACCTCAAA
195 GCTCATTTCAGGGGTTTAACTCACTACTACACAAGAAACACTAGGATTAAGTAGAGGACCTCAAA
*
284277 GGGTATTCATAATAAGCGCTAAATGGCACCTATGATCCCTGCAAGGGTTCAA
260 GGGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCAA
284329 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
284394 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
66 TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
* * *
284459 CTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTGGATCCCAGGGGTTCTGG
131 CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCTGG
*
284524 CTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTGGAAACACTAGGATTAAG
196 CTCATTTCAGGGGTTTA-A-CTCAC-T---ACT-A-CAC---AA----GAAACACTAGGATTAAG
* * * *
284589 TAGAGGACCTC-AAGGGTATTCATAACAAGCGTCT-AAGGGCACCTATGACCCCTGCAAGAGTTC
246 TAGAGGACCTCAAAGGGTATTCATAATAAGCGT-TAAATGGCACCTATGATCCCTGCAAGGGTTC
284652 AA
310 AA
284654 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA
1 TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA
284693 TTGAGACCGG
Statistics
Matches: 1163, Mismatches: 79, Indels: 107
0.86 0.06 0.08
Matches are distributed among these distances:
302 27 0.02
303 514 0.44
304 10 0.01
305 2 0.00
307 3 0.00
308 3 0.00
310 2 0.00
311 2 0.00
312 3 0.00
314 3 0.00
315 1 0.00
317 5 0.00
318 1 0.00
319 1 0.00
320 1 0.00
321 4 0.00
322 1 0.00
323 1 0.00
324 6 0.01
325 328 0.28
326 244 0.21
327 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (311 bp):
TTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAGGGGTGAAAGGCGGACCA
TTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAATGTAGGGGACCTATGGGG
CTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGCACCACCAAGTGGCTCCCAGGGGTTCTGG
CTCATTTCAGGGGTTTAACTCACTACTACACAAGAAACACTAGGATTAAGTAGAGGACCTCAAAG
GGTATTCATAATAAGCGTTAAATGGCACCTATGATCCCTGCAAGGGTTCAA
Found at i:284237 original size:325 final size:326
Alignment explanation
Indices: 283619--284692 Score: 1689
Period size: 325 Copynumber: 3.4 Consensus size: 326
283609 ATATCTCACA
* *
283619 AAACACTAGGATTAAGTATAGGACCTCAAAGGGTATTCATAATAAGCGTTAAATGGCACCTATGA
1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA
* *
283684 TCCCTGCAAGGTTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG
66 CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG
283749 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT
131 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT
283814 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG
196 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG
283879 GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG
261 GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG
283944 G
326 G
*
283945 AAACACTAGGATTAAGTAGAGGACCTC-AAGGGTATTCATAATAAGCGTTGAAGGGCACCTATGA
1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA
* *
284009 CCCCTGCAAGGGTTCAATTAGTTCACCCGAACTTTGTCATATTTTAGCATTTCACAATTATATAG
66 CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG
** * * * *
284074 GGGTGAAAGGCGGGGCATTATCTCTTTTATTTTTAAAGTGTGCATTAAACGGATACCAGGGCAAT
131 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT
* * * * * *
284139 GTAGGTGAGCAATGGGGCTATTATTTCCCGGTCTCAAATTTGGGCTGTAGAGGTACCACCAAGTG
196 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG
* * *
284204 GCTCCCA-AGGTTTTCGGCTCATTTCAGGGGTTTATATCT--C-----A-T----------A---
261 GCTCCCAGGGGTTCT-GGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTT
284247 --
325 GG
* *
284247 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGCTAAATGGCACCTATGA
1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA
*
284312 TCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG
66 CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG
284377 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT
131 GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT
284442 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG
196 GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG
*
284507 GATCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG
261 GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG
284572 G
326 G
*
284573 AAACACTAGGATTAAGTAGAGGACCTC-AAGGGTATTCATAACAAGCGTCT-AAGGGCACCTATG
1 AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGT-TAAAGGGCACCTATG
*
284636 ACCCCTGCAAGAGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA
65 ACCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACA
284693 TTGAGACCGG
Statistics
Matches: 672, Mismatches: 49, Indels: 55
0.87 0.06 0.07
Matches are distributed among these distances:
302 27 0.04
303 243 0.36
304 5 0.01
305 1 0.00
307 1 0.00
310 1 0.00
311 1 0.00
317 1 0.00
318 1 0.00
321 1 0.00
323 1 0.00
324 5 0.01
325 330 0.49
326 54 0.08
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (326 bp):
AAACACTAGGATTAAGTAGAGGACCTCAAAGGGTATTCATAATAAGCGTTAAAGGGCACCTATGA
CCCCTGCAAGGGTTCAATTAGCTCACCCGAACTTTGTCATATTTTAGCATTTCACAATGATATAG
GGGTGAAAGGCGGACCATTATCTCTTTTATCTTTGAAGTGTGCATCAAACAGATACCAGGGCAAT
GTAGGGGACCTATGGGGCTATTATTTCCTGGTCTCAAATTTGGGCTGTAGGGGCACCACCAAGTG
GCTCCCAGGGGTTCTGGCTCATTTCAGGGGTTTACATCTCACTTGAGATTGACCACAAGAACTTG
G
Found at i:286364 original size:4 final size:4
Alignment explanation
Indices: 286357--286435 Score: 68
Period size: 4 Copynumber: 19.8 Consensus size: 4
286347 GCTACCGTGC
* * * * * *
286357 GTGT GTGT GTGT GTGT GCGT GTGT GCGT GCGT GCGT GTGC GTGT GCGT
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTGT
* * * *
286405 GGGG GTGG GTGG GTGT GTGT GTGT GTGT GTG
1 GTGT GTGT GTGT GTGT GTGT GTGT GTGT GTG
286436 CACCCCATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 64 1.00
ACGTcount: A:0.00, C:0.08, G:0.56, T:0.37
Consensus pattern (4 bp):
GTGT
Found at i:286368 original size:6 final size:6
Alignment explanation
Indices: 286357--286435 Score: 68
Period size: 6 Copynumber: 13.2 Consensus size: 6
286347 GCTACCGTGC
* * * * * *
286357 GTGTGT GTGTGT GTGTGC GTGTGT GCGTGC GTGCGT GTGCGT GTGCGT
1 GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT
* * * *
286405 GGGGGT GGGTGG GTGTGT GTGTGT GTGTGT G
1 GTGTGT GTGTGT GTGTGT GTGTGT GTGTGT G
286436 CACCCCATTT
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.00, C:0.08, G:0.56, T:0.37
Consensus pattern (6 bp):
GTGTGT
Found at i:287254 original size:2 final size:2
Alignment explanation
Indices: 287247--287282 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
287237 AAAAGAATTT
*
287247 GA GA GA GA GA GA GA GA GA GA GA CA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
287283 TTGTCAGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:290611 original size:21 final size:21
Alignment explanation
Indices: 290587--290676 Score: 135
Period size: 21 Copynumber: 4.3 Consensus size: 21
290577 CAATAGTGAT
**
290587 ATCATTATATGCAGTGGAAAC
1 ATCATTATATGCAGTGCTAAC
290608 ATCATTATATGCAGTGCTAAC
1 ATCATTATATGCAGTGCTAAC
* * *
290629 ACCATTATATGTAGTGGTAAC
1 ATCATTATATGCAGTGCTAAC
290650 ATCATTATATGCAGTGCTAAC
1 ATCATTATATGCAGTGCTAAC
290671 ATCATT
1 ATCATT
290677 GTATACTGTA
Statistics
Matches: 61, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (21 bp):
ATCATTATATGCAGTGCTAAC
Found at i:290997 original size:21 final size:21
Alignment explanation
Indices: 290948--290998 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
290938 CAATTGCATG
* *
290948 TAAAGCTTTCACCACAATACA
1 TAAAGGTTTAACCACAATACA
*
290969 TAAAGGTTTAACCACCATACA
1 TAAAGGTTTAACCACAATACA
*
290990 TAATGGTTT
1 TAAAGGTTT
290999 TAATACACCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (21 bp):
TAAAGGTTTAACCACAATACA
Found at i:291315 original size:21 final size:21
Alignment explanation
Indices: 291291--291347 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
291281 AAATTCCAGT
*
291291 ATATAATGATGTTAGCACTGC
1 ATATAATGATGTTACCACTGC
291312 ATATAATGATGTTACCACTGC
1 ATATAATGATGTTACCACTGC
*
291333 ATATAATGATATTAC
1 ATATAATGATGTTAC
291348 TATTGCAAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (21 bp):
ATATAATGATGTTACCACTGC
Found at i:304632 original size:433 final size:433
Alignment explanation
Indices: 303826--305144 Score: 2026
Period size: 433 Copynumber: 3.0 Consensus size: 433
303816 AGTACTTTGA
303826 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA
1 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA
303891 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC
66 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC
303956 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC
131 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC
304021 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG
196 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG
304086 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT
261 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT
304151 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC
326 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC
304216 ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT
391 ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT
304259 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA
1 TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA
304324 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC
66 TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC
304389 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC
131 TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC
304454 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG
196 GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG
304519 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT
261 AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT
304584 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC
326 TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC
* * *
304649 ACTATCTTTTACGGTTAATGAGGAGTAGCAATAAGAAGTATTT
391 ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT
* * * * * * * * * *
304692 TATACAAAAGGGGTAATAACTCTGTAACTTTTTA-AAGG-AAGGAGCCAAGGGGCTATATTTTAA
1 TGTACAATAGGGGCAATAACTCTATAA-TTGTTACATGGTAAGG-GTCAATGGGTTATATTTTGA
* * * * * * * * * * *
304755 AATGTCTGAAGATGTCCTATTACATCCATGAAAAAGTTTTTCTTTACCACACTAAACAATAGAGA
64 AATGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGA
** * * * * *
304820 TCTAAAAACTCATTAATT-GGGAGATTT-TCGGATGACCTTGACCATTGTCCTTTATGTCATTTT
129 TCTAAAAACTCATTAATTAACG-GATTTCT-GAATGATCTTGACCCTTGACCTTTATGTCAATTT
* * * * *
304883 GTTCGGCCAAGATAAACGCTTCTATCCCAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAG
192 GTTCGGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAG
* * * * * * *
304948 TTGGAAGTGATTTTATAGATATGTAGATAATTTCAAGGACAATAACTACTAGAAGGCGGG-CTCA
257 TTAGAAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGG-GGGCCTCA
* * * *
305012 GATCCTTTCGGTATGAAAAGATTGAAGAACCCTCTAAGTGTACTGAAGACATTGGTAAAAGTTCC
321 GATCTTTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCA
* * * * * *
305077 AAGTTTA-TATCTCTTATGGTTTCA-GAGGAGAAGCGATAACAAGCTTTT
386 AAG-TCACTATCTTTTACGG-TTAATGAGGAGTAGCGATAACAAGCATTT
305125 TGTACACA-A-GGGCAATAACT
1 TGTACA-ATAGGGGCAATAACT
305145 TTGTAAGTTC
Statistics
Matches: 820, Mismatches: 58, Indels: 17
0.92 0.06 0.02
Matches are distributed among these distances:
432 16 0.02
433 790 0.96
434 14 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (433 bp):
TGTACAATAGGGGCAATAACTCTATAATTGTTACATGGTAAGGGTCAATGGGTTATATTTTGAAA
TGTCTTAAGATGTCCTACTACATCCATGAACAAGCTTTTCTCTAGCACCCCACAGAAAAGAGATC
TAAAAACTCATTAATTAACGGATTTCTGAATGATCTTGACCCTTGACCTTTATGTCAATTTGTTC
GGCCAAGGTAGACGCTTCAATCCCAAGTGGTCCAAAGTCTCTAAGACAAATAATAAAAAAGTTAG
AAGTGATTTCATAGAAATGTAAATACTTTCAGGGGCAATAACTACTAGAAGGGGGCCTCAGATCT
TTTCGGTATGAATAGATTGAAGAACCCTCTAAGTGTACTGAAGGCATTGGTAAAAGTTCAAAGTC
ACTATCTTTTACGGTTAATGAGGAGTAGCGATAACAAGCATTT
Found at i:308122 original size:434 final size:432
Alignment explanation
Indices: 307276--308186 Score: 1253
Period size: 434 Copynumber: 2.1 Consensus size: 432
307266 AACGGTTAAT
* * * *
307276 GAGGAGTAGCGATAACAAGCATTTTGTACAATA-GGGGCAATAACTTTATAATTGTTACATGGTA
1 GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACTCTATAATTATTACAAGGTA
* ** *
307340 ACGGTCAAAGGGTTATATTTTGAAATGTCCTAAGATGTCCTACTACATCCATGAAAAAGTGTTTC
66 AC-G-CAAAGGGCTATATTTAAAAATGTCCTAAGATGGCCTACTACATCCATGAAAAAGTGTTTC
* * * *
307405 TCTACCATCCAAAACCAAAAAAATACAAAAACTCATAAATTAAGAGATTCTCAGATGATCTTGAC
129 TCTACCACCCAAAACCAAAAAAATACAAAAACTCATAAATTAAGAAATTCTCAAATGACCTTGAC
* * *
307470 CTTTGACCTTAATGTCATTTTGTTCGGCCAAAATAGACGCTTCCATCCCAAGTGGTCCGAAGTCT
194 CTTTGACCTTAATATCATTATGTTCGGCCAAAATAGACGCTTCCATCCCAAGTAGTCCGAAGTCT
* * * * * *
307535 CTATGATAAGTAATAAAAAAGTTAGAAGTGATTTTATGGAAATTTAAATTCTTTCAGGGGCAATA
259 CTATGACAAATAATAAAAAAGTTAGAAGGGATTTTATAGAAATGTAAATACTTTCAGGGGCAATA
* * * *
307600 ACTACTAGAAGGGGGCCTCAGATCATTTCATTATGAATAGATTGAAGAACCCTGTAAGTGTACTG
324 ACTAATAGAAGGGGGCCTCAGATCATTTCAGTATGAATAGATTGAAGAACCCTCTAAGTGTACTA
307665 AAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA
389 AAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA
* * *
307709 GAGGAGTAGCGATAACAAGCATTTCGTACAAAAGGGGGTAATAACTCTGTAATTATT-CAAAGGC
1 GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACTCTATAATTATTAC-AAGG-
* * * *
307773 ATGAAC-CAAGGGGCTATATTTAAAAATGTCTTAAGATGGCCTACTATATCCATGAAAAAGTTTT
64 -T-AACGCAAAGGGCTATATTTAAAAATGTCCTAAGATGGCCTACTACATCCATGAAAAAGTGTT
** *
307837 TCTCTACCACCCTTAA-CAAAAGAAAT-CTAAAAACTCATTAATTAAGAAATT-TCCAAATGACC
127 TCTCTACCACCCAAAACCAAAA-AAATAC-AAAAACTCATAAATTAAGAAATTCT-CAAATGACC
* * **
307899 TTGACCTTTGACCTTTATATCATTATGTTTGGCCAAGGTAGACGCTTCCATCCCAAGTAGTCCGA
189 TTGACCTTTGACCTTAATATCATTATGTTCGGCCAAAATAGACGCTTCCATCCCAAGTAGTCCGA
* *
307964 AGTCTCTATGACAAATAATAAAAAAGTTGGAAGGGGTTTTATAGAAATGTAAATACTTTCAGGGG
254 AGTCTCTATGACAAATAATAAAAAAGTTAGAAGGGATTTTATAGAAATGTAAATACTTTCAGGGG
* * * *
308029 CAATAACTAATAGAAGGGGGGCTCAGATCCTTTCGGTATGAATAGATTGGAGAACCCTCTAAGTG
319 CAATAACTAATAGAAGGGGGCCTCAGATCATTTCAGTATGAATAGATTGAAGAACCCTCTAAGTG
308094 TACTAAAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA
384 TACTAAAGACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA
* * *
308143 GAGGAGTAGCGATAACAATCTTTTTGTACACAA--GGGCAATAACT
1 GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACT
308187 TTGTAAGTTC
Statistics
Matches: 420, Mismatches: 50, Indels: 17
0.86 0.10 0.03
Matches are distributed among these distances:
432 10 0.02
433 39 0.09
434 367 0.87
436 1 0.00
437 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.30
Consensus pattern (432 bp):
GAGGAGTAGCGATAACAAGCATTTTGTACAAAAGGGGGCAATAACTCTATAATTATTACAAGGTA
ACGCAAAGGGCTATATTTAAAAATGTCCTAAGATGGCCTACTACATCCATGAAAAAGTGTTTCTC
TACCACCCAAAACCAAAAAAATACAAAAACTCATAAATTAAGAAATTCTCAAATGACCTTGACCT
TTGACCTTAATATCATTATGTTCGGCCAAAATAGACGCTTCCATCCCAAGTAGTCCGAAGTCTCT
ATGACAAATAATAAAAAAGTTAGAAGGGATTTTATAGAAATGTAAATACTTTCAGGGGCAATAAC
TAATAGAAGGGGGCCTCAGATCATTTCAGTATGAATAGATTGAAGAACCCTCTAAGTGTACTAAA
GACATTGGTAAAAGTTCCAAGTCTCTATCTCTTATGGTTTCA
Found at i:308319 original size:3 final size:3
Alignment explanation
Indices: 308313--308365 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
308303 AAAAAAAGAG
308313 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
308361 AAT AA
1 AAT AA
308366 AAAACATAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:309330 original size:433 final size:430
Alignment explanation
Indices: 308733--309726 Score: 1230
Period size: 433 Copynumber: 2.3 Consensus size: 430
308723 TACTTTGGAC
* * * * * * *
308733 CCTTTCGGTATGAATAGACTGAAGAAATATCTTAGTGTACTGAATACATTAGTAAAAGTTTTAAG
1 CCTTTTGGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAAG
* * * * *
308798 TCTCTATCTCTAACGG-TTAATGAGGAGTAGCGATAACAAGCTTTTCGTAAATAGGGGCAGTAAC
66 TCTCTATCTCTTATGGTTTCA-GAGGAGTAGCGATAACAAGCTTTTCGTAAATAAGGGCAATAAC
** * ** * * *
308862 TCTATAATTGTAACATGGTAAGGGTCAAAGGGTTATATTTTGAAATTTCATATGATGTCTTACTA
130 TC-ATAATTGTAACATAATAAGGGCCAAAGGGTTATATTTCAAAATGTCATAAGATGTCCTACTA
* * * * * *
308927 CATCCTTGAAAAAGTTTTTTTCTACCACCCTAAGCAAAAGAGATCTTAAAACTCATTTAGTCTAT
194 CATCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCTAAAAACTCA-TTAAT-TA-
* * *
308992 A-GATTTCCCAATGACCATGACCTTTGACCTTTATGTTATTTTGTTCGGCCAAGGGCGACGCTTC
256 ACGATTTCCAAATGACCATGACCTTTGACCTTTATGTTATTTTGGTCGGCCAAGGGAGACGCTTC
* *
309056 CATCCAAAGTGGTCCGAAGTCTCTATGACAAATTATAAAAAAGTTGGAAGTGATTTTATAGATAT
321 CATCCAAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTATAGAAAT
* *
309121 GT-AAATAATTTCAGGGGCAA-AAATTACCAGAAGGGGGCCTCAGAT
386 -TCAAATAATTTCAGGGGCAATAAATGA-CAGAACGGGGCCTCAGAT
* * * **
309166 CCTTTTGGTATGAATAGGTTGAAGAACTCTCAAAGTGTTCTGAAGACATTGGTAAAAGTTCCAAG
1 CCTTTTGGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAAG
*
309231 TTTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTACAATAAGGGCAATAAC
66 TCTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTA-AATAAGGGCAATAAC
* * * * * *
309296 TC-T-GTTGTTATATAAATAAGGAGCCAAGGGGTTATATTTCAAAATGTCTTAAGATGTCCTATT
130 TCATAATTGTAACAT-AATAAGG-GCCAAAGGGTTATATTTCAAAATGTCATAAGATGTCCTACT
*
309359 ACATCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGTTCTAAAAACTCATTAATTAAC
193 ACATCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCTAAAAACTCATTAATTAAC
* * * *
309424 GGATTTCTAAATGACCTTGACCTTTGACCTTTATGTTTTTTTGGTCGGCCAAGGTAGACGCTTCC
258 -GATTTCCAAATGACCATGACCTTTGACCTTTATGTTATTTTGGTCGGCCAAGGGAGACGCTTCC
* * * *
309489 ATCCCAAGTGGTCCGAAGTCTCTATGATAAATAATAAAATAGTTGGAAGTGATTTTATGGAAATT
322 ATCCAAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTATAGAAATT
* * * * *
309554 CAAATACTTTCAGGGGCAATAACTGATAGAACGGGGTCTCGGAT
387 CAAATAATTTCAGGGGCAATAAATGACAGAACGGGGCCTCAGAT
* * * *
309598 -CTTTTCGGTATTAGTAGATT-AAGAACCCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAG
1 CCTTTT-GGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAA
* * *
309661 GTCTCTGTCTCTTATGGTTTCAGAGAAGTAGCGATAACAAGCTTTTCGTAAACAAGGGCAATAAC
65 GTCTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTAAATAAGGGCAATAAC
309726 T
130 T
309727 TTGTAAGTTC
Statistics
Matches: 480, Mismatches: 72, Indels: 21
0.84 0.13 0.04
Matches are distributed among these distances:
430 16 0.03
431 99 0.21
432 167 0.35
433 180 0.38
434 18 0.04
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (430 bp):
CCTTTTGGTATGAATAGATTGAAGAACTCTCTAAGTGTACTGAAGACATTGGTAAAAGTTTTAAG
TCTCTATCTCTTATGGTTTCAGAGGAGTAGCGATAACAAGCTTTTCGTAAATAAGGGCAATAACT
CATAATTGTAACATAATAAGGGCCAAAGGGTTATATTTCAAAATGTCATAAGATGTCCTACTACA
TCCATAAAAAAGTTTTTCTCTACCACCCTAAACAAAAGAGATCTAAAAACTCATTAATTAACGAT
TTCCAAATGACCATGACCTTTGACCTTTATGTTATTTTGGTCGGCCAAGGGAGACGCTTCCATCC
AAAGTGGTCCGAAGTCTCTATGACAAATAATAAAAAAGTTGGAAGTGATTTTATAGAAATTCAAA
TAATTTCAGGGGCAATAAATGACAGAACGGGGCCTCAGAT
Found at i:309930 original size:57 final size:57
Alignment explanation
Indices: 309867--310358 Score: 556
Period size: 50 Copynumber: 9.0 Consensus size: 57
309857 AAATAATAAG
309867 AATAATAAAAAACATAAAGAAA-ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
1 AATAATAAAAAACAT-AAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
* *
309924 AATAATAAAAATCATAAGAAATACAACAGGTCTTTCACCTGAAAGGTGGAAAGACC-
1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
*
309980 -----T-AAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC-
1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
*
310030 -----T-AAAAACATAAGAAATACAAAAGATCTTTCACCTGAAAGGTGGAAAGACCT
1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
*
310081 AATAATAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACC-
1 AATAAT-AAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
*
310138 --T--T--AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACCT
1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
*
310189 AATAAAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
1 AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
* * * * * * *
310246 -A-AA-AATAAACAGAA-CAATATCAATAGGCCTTT-ACACTG--TGGTGTAAAGACCT
1 AATAATAAAAAACATAAGAAATA-CAAAAGGTCTTTCAC-CTGAAAGGTGGAAAGACCT
* * * *
310298 AATAATAATACAAAACAGAAGAAATGCAATATGTCTTTCACCTGAAAGGTGGAAAGACCT
1 AATAAT-A-A-AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
310358 A
1 A
310359 CATACAAAAG
Statistics
Matches: 380, Mismatches: 27, Indels: 53
0.83 0.06 0.12
Matches are distributed among these distances:
50 140 0.37
51 1 0.00
52 12 0.03
53 9 0.02
54 24 0.06
55 3 0.01
56 9 0.02
57 96 0.25
58 68 0.18
59 5 0.01
60 13 0.03
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19
Consensus pattern (57 bp):
AATAATAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCT
Found at i:310004 original size:107 final size:103
Alignment explanation
Indices: 309871--310250 Score: 502
Period size: 107 Copynumber: 3.6 Consensus size: 103
309861 AATAAGAATA
309871 ATAAAAAACATAA-AGAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAAAAA
1 ATAAAAAACATAAGA-AAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC---T--TAAAAA
*
309935 TCATAAGAAATACAACAGGTCTTTCACCTGAAAGGTGGAAAGACC
60 -CATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
309980 -T-AAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC-TAAAAACATAAG
1 ATAAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAACATAAG
*
310042 AAATACAAAAGATCTTTCACCTGAAAGGTGGAAAGACC
66 AAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
* *
310080 TAATAATAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACCTT-AAAA
1 -----AT-AAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAA
*
310144 CATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACC
60 CATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
*
310188 TAATAAAAAAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC-TAAAAA
1 --AT---AAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAA
310251 TAAACAGAAC
Statistics
Matches: 251, Mismatches: 7, Indels: 28
0.88 0.02 0.10
Matches are distributed among these distances:
100 42 0.17
101 6 0.02
105 4 0.02
106 2 0.01
107 101 0.40
108 95 0.38
109 1 0.00
ACGTcount: A:0.51, C:0.15, G:0.16, T:0.18
Consensus pattern (103 bp):
ATAAAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTTAAAAACATAAG
AAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC
Found at i:310104 original size:58 final size:58
Alignment explanation
Indices: 310031--310358 Score: 375
Period size: 58 Copynumber: 5.9 Consensus size: 58
310021 GGAAAGACCT
*
310031 AAAAACATAAGAAATACAAAAGATCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
*
310089 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACC---T--T--
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
*
310140 -AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACCTAATAA-AA
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
310196 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACC---TAA-AA
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
* * * * * * *
310250 ATAAACAGAA-CAATATCAATAGGCCTTT-ACACTG--TGGTGTAAAGACCTAATAATAA
1 AAAAACATAAGAAATA-CAAAAGGTCTTTCAC-CTGAAAGGTGGAAAGACCTAATAATAA
* * * *
310306 TACAAAACAGAAGAAATGCAATATGTCTTTCACCTGAAAGGTGGAAAGACCTA
1 -A-AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTA
310359 CATACAAAAG
Statistics
Matches: 231, Mismatches: 19, Indels: 38
0.80 0.07 0.13
Matches are distributed among these distances:
50 46 0.20
52 11 0.05
53 8 0.03
54 26 0.11
55 4 0.02
56 2 0.01
57 48 0.21
58 68 0.29
59 5 0.02
60 13 0.06
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (58 bp):
AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
Found at i:310129 original size:108 final size:108
Alignment explanation
Indices: 309981--310358 Score: 530
Period size: 108 Copynumber: 3.5 Consensus size: 108
309971 GGAAAGACCT
*
309981 AAAAACATAAGAAAAACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT
*
310046 ACAAAAGATCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
66 ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
* *
310089 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAGAGACCTTAAAACATAAGAAAT
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT
*
310154 ACAAAAGGTCTTTCACCTGAAAGGTGGAAAAACCTAATAA-AA
66 ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
* *
310196 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAATAAACAGAAC
1 AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATA-AG-A-
* * * *
310261 AATATCAATAGGCCTTT-ACACTG--TGGTGTAAAGACCTAATAATAA
63 AATA-CAAAAGGTCTTTCAC-CTGAAAGGTGGAAAGACCTAATAATAA
* * * *
310306 TACAAAACAGAAGAAATGCAATATGTCTTTCACCTGAAAGGTGGAAAGACCTA
1 -A-AAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTA
310359 CATACAAAAG
Statistics
Matches: 244, Mismatches: 18, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
107 57 0.23
108 102 0.42
109 17 0.07
110 8 0.03
111 14 0.06
112 46 0.19
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19
Consensus pattern (108 bp):
AAAAACATAAGAAATACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAAAAACATAAGAAAT
ACAAAAGGTCTTTCACCTGAAAGGTGGAAAGACCTAATAATAA
Found at i:310746 original size:4 final size:4
Alignment explanation
Indices: 310737--310774 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
310727 ACTGAAGTGG
*
310737 GACA GACA GAGA GACA GACA GACA GACA GACA GA-A GAC
1 GACA GACA GACA GACA GACA GACA GACA GACA GACA GAC
310775 GGACGGACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 3 0.10
4 28 0.90
ACGTcount: A:0.50, C:0.21, G:0.29, T:0.00
Consensus pattern (4 bp):
GACA
Found at i:314500 original size:22 final size:22
Alignment explanation
Indices: 314450--314502 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
314440 TATATGTATT
*
314450 GCTTAAAGGTGGCCTAAAGAAA
1 GCTTAAAGATGGCCTAAAGAAA
* * **
314472 GCGTAAAGATGGCTTAAAGGCA
1 GCTTAAAGATGGCCTAAAGAAA
314494 GCTTAAAGA
1 GCTTAAAGA
314503 CTATCTTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.13, G:0.28, T:0.19
Consensus pattern (22 bp):
GCTTAAAGATGGCCTAAAGAAA
Found at i:314584 original size:11 final size:11
Alignment explanation
Indices: 314567--314620 Score: 81
Period size: 11 Copynumber: 4.9 Consensus size: 11
314557 GTCCAAAATT
314567 CTTTAAGCCAC
1 CTTTAAGCCAC
* *
314578 ATTTAAGCTAC
1 CTTTAAGCCAC
*
314589 CTTTAAGCTAC
1 CTTTAAGCCAC
314600 CTTTAAGCCAC
1 CTTTAAGCCAC
314611 CTTTAAGCCA
1 CTTTAAGCCA
314621 TTAATAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.31
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:317253 original size:50 final size:50
Alignment explanation
Indices: 317198--317299 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
317188 AAATAAGAAG
*
317198 AAACAGTACGAAAACTATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
*
317248 AAACAGTACGCAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
1 AAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
317298 AA
1 AA
317300 CCGGTGACGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (50 bp):
AAACAGTACGAAAACAATAAGGTCTTCCGTTGGAAACGGAAGACCTTAAT
Done.