Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015353.1 Kokia drynarioides strain JFW-HI SEQ_130400, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 481496
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 571 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:779 original size:2 final size:2
Alignment explanation
Indices: 772--796 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
762 GTCATTAAAA
772 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 A
797 ATAAAACGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8379 original size:54 final size:54
Alignment explanation
Indices: 8315--8422 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
8305 GTGGTGAATC
8315 AGAAGTTTTCCCCTCTGCTGAAGACGAAGTCGAGCTCATACCAGAGGTGTTAGT
1 AGAAGTTTTCCCCTCTGCTGAAGACGAAGTCGAGCTCATACCAGAGGTGTTAGT
*
8369 AGAAGTTTTCCCTTCTGCTGAAGACGAAGTCGAGCTCATACCAGAGGTGTTAGT
1 AGAAGTTTTCCCCTCTGCTGAAGACGAAGTCGAGCTCATACCAGAGGTGTTAGT
8423 TCTCATGTTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (54 bp):
AGAAGTTTTCCCCTCTGCTGAAGACGAAGTCGAGCTCATACCAGAGGTGTTAGT
Found at i:11797 original size:22 final size:22
Alignment explanation
Indices: 11772--11816 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
11762 AATTTTTTAG
11772 ATTTTAAAATTTAAATTAAATT
1 ATTTTAAAATTTAAATTAAATT
* * **
11794 ATTTTTAATTTTTTATTAAATT
1 ATTTTAAAATTTAAATTAAATT
11816 A
1 A
11817 ACTGTTATGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATTTTAAAATTTAAATTAAATT
Found at i:12903 original size:52 final size:52
Alignment explanation
Indices: 12786--12924 Score: 156
Period size: 53 Copynumber: 2.6 Consensus size: 52
12776 TAAAAAAAAA
* * * *
12786 CTTTTTTTTTCCTTTTTTTTCTCCCCCTAATCCTGTCTTTCCTTTTTCCTATT
1 CTTTCTTTTTCTTTTTTTTTCTCCCCCAAAT-CTGTCATTCCTTTTTCCTATT
* *
12839 CTTTCTTTTTCTTTTTTTTTCTTCCCCCAAATCTGTCATTCCTTTTT-TTTTT
1 CTTTCTTTTTCTTTTTTTTTC-TCCCCCAAATCTGTCATTCCTTTTTCCTATT
* *
12891 C-TTCTTTATTCTTCTTCTTTCTCCCCCTAAATCT
1 CTTTCTTT-TTCTTTTTTTTTCTCCCCC-AAATCT
12925 CTTTCACTAC
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
51 12 0.16
52 21 0.28
53 33 0.44
54 9 0.12
ACGTcount: A:0.08, C:0.29, G:0.01, T:0.61
Consensus pattern (52 bp):
CTTTCTTTTTCTTTTTTTTTCTCCCCCAAATCTGTCATTCCTTTTTCCTATT
Found at i:32572 original size:33 final size:31
Alignment explanation
Indices: 32513--32573 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
32503 ATTTATATTA
*
32513 TATTATATTAATATTTAATGATTTTTAAAAT
1 TATTATATTAATATTTAATAATTTTTAAAAT
32544 TATTATA-TAATAATCTTAATAATATTTTAA
1 TATTATATTAAT-AT-TTAATAAT-TTTTAA
32574 TGTTTACATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 9 0.35
32 7 0.27
33 6 0.23
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (31 bp):
TATTATATTAATATTTAATAATTTTTAAAAT
Found at i:32593 original size:24 final size:23
Alignment explanation
Indices: 32560--32623 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 23
32550 ATAATAATCT
*
32560 TAATAATATTTTAATGTTTACATA
1 TAATATTATTTTAATGTTTA-ATA
* *
32584 TAATATTATTAT-ATATTTAATA
1 TAATATTATTTTAATGTTTAATA
32606 TAAGT-TTATTTTTAATGT
1 TAA-TATTA-TTTTAATGT
32624 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 9 0.28
23 10 0.31
24 13 0.41
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (23 bp):
TAATATTATTTTAATGTTTAATA
Found at i:34630 original size:27 final size:27
Alignment explanation
Indices: 34600--34667 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
34590 CGTTCCAGGT
* * *
34600 TCGGGTCCCTTGGAAAGAGGGTTTATG
1 TCGGGTCCCATCGAAAGAGGGTTCATG
* * *
34627 TCGGGTCCGATCGAGAGGGGGTTCATG
1 TCGGGTCCCATCGAAAGAGGGTTCATG
*
34654 TCGGGTCCCCTCGA
1 TCGGGTCCCATCGA
34668 TAATGTTAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.15, C:0.22, G:0.38, T:0.25
Consensus pattern (27 bp):
TCGGGTCCCATCGAAAGAGGGTTCATG
Found at i:39894 original size:7 final size:7
Alignment explanation
Indices: 39878--39926 Score: 62
Period size: 7 Copynumber: 6.7 Consensus size: 7
39868 GCATTATTTG
*
39878 AAAATGA
1 AAAATAA
39885 AAAATAA
1 AAAATAA
*
39892 AAAATGA
1 AAAATAA
39899 AAAATAA
1 AAAATAA
39906 AAATATAA
1 AAA-ATAA
39914 AAAATATA
1 AAAATA-A
39922 AAAAT
1 AAAAT
39927 CTATAAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
7 24 0.65
8 13 0.35
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (7 bp):
AAAATAA
Found at i:39897 original size:14 final size:14
Alignment explanation
Indices: 39878--39926 Score: 71
Period size: 14 Copynumber: 3.4 Consensus size: 14
39868 GCATTATTTG
39878 AAAATGAAAAATAA
1 AAAATGAAAAATAA
39892 AAAATGAAAAATAA
1 AAAATGAAAAATAA
*
39906 AAATATAAAAAATATA
1 AAA-ATGAAAAATA-A
39922 AAAAT
1 AAAAT
39927 CTATAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
14 17 0.53
15 11 0.34
16 4 0.12
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (14 bp):
AAAATGAAAAATAA
Found at i:39924 original size:17 final size:18
Alignment explanation
Indices: 39898--39936 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
39888 ATAAAAAATG
39898 AAAA-ATAAAAATATA-A
1 AAAATATAAAAATATATA
*
39914 AAAATATAAAAATCTATA
1 AAAATATAAAAATATATA
39932 AAAAT
1 AAAAT
39937 TCAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 10 0.50
18 6 0.30
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATATAAAAATATATA
Found at i:42453 original size:21 final size:21
Alignment explanation
Indices: 42404--42460 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
42394 TAACTAAAAA
* * *
42404 ATTTCACTCAATTCG-ATTTG
1 ATTTCACTCGACTCGAATTTC
42424 A-TTCGACTCGACTCGAATTTC
1 ATTTC-ACTCGACTCGAATTTC
*
42445 ATTTCACTCGGCTCGA
1 ATTTCACTCGACTCGA
42461 TTCGAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
19 3 0.10
20 9 0.30
21 15 0.50
22 3 0.10
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (21 bp):
ATTTCACTCGACTCGAATTTC
Found at i:46410 original size:12 final size:12
Alignment explanation
Indices: 46390--46428 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 12
46380 AAGAAAATAC
46390 AAAAGAAAAAAGAGG
1 AAAA-AAAAAA-A-G
46405 AAAAAAAAAAAG
1 AAAAAAAAAAAG
46417 AAAAAAAAAAAG
1 AAAAAAAAAAAG
46429 GCGTTGAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 13 0.54
13 1 0.04
14 6 0.25
15 4 0.17
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:52410 original size:29 final size:28
Alignment explanation
Indices: 52100--52406 Score: 312
Period size: 29 Copynumber: 10.5 Consensus size: 28
52090 CAAAATCGTA
* *
52100 ATTTTTGAAAGTTTCGAGGTTAAAAATGGG
1 ATTTTTGGAAGTTT-G-GGGTAAAAATGGG
* *
52130 ATTTTTAGAAGTTTCGGGTCAAAAATGGG
1 ATTTTTGGAAGTTTGGGGT-AAAAATGGG
*
52159 A-TTTTGGAAGTTTTGGGGTCAAAATGGG
1 ATTTTTGGAAG-TTTGGGGTAAAAATGGG
*
52187 ATTTTTGGAAGTTTGGGGGTAAAAAT-GA
1 ATTTTTGGAAGTTT-GGGGTAAAAATGGG
*
52215 ATTTTTTGGAAGTTTCGGGGTAAAAATTGG
1 A-TTTTTGGAAGTTT-GGGGTAAAAATGGG
*
52245 ATTTTTGGAAATTTGGGGGTAAAAATGGG
1 ATTTTTGGAAGTTT-GGGGTAAAAATGGG
* *
52274 ATTTTTGGAAGTTTGGAGGTAAAAACGAG
1 ATTTTTGGAAGTTTGG-GGTAAAAATGGG
* * *
52303 AATTTTGGAAGTTTTGAGATAAAAAATGGG
1 ATTTTTGGAAG-TTTGGGGT-AAAAATGGG
* *
52333 ATTTTTGGAAGTTTCGGAGTCAAAATTGGG
1 ATTTTTGGAAGTTT-GGGGT-AAAAATGGG
* *
52363 ATTTTTGAAAGTTCGAGGGTAAAAATGGG
1 ATTTTTGGAAGTTTG-GGGTAAAAATGGG
52392 ATTTTTGGACAGTTT
1 ATTTTTGGA-AGTTT
52407 AGGGACCTCC
Statistics
Matches: 231, Mismatches: 34, Indels: 24
0.80 0.12 0.08
Matches are distributed among these distances:
28 27 0.12
29 140 0.61
30 64 0.28
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (28 bp):
ATTTTTGGAAGTTTGGGGTAAAAATGGG
Found at i:53505 original size:27 final size:27
Alignment explanation
Indices: 53470--53526 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
53460 AAAAACTTAT
*
53470 TTATTATTAATGATA-TCATTAATATTA
1 TTATTATTAA-AATAGTCATTAATATTA
*
53497 TTATTATTAAAATAGTTATTAATATTA
1 TTATTATTAAAATAGTCATTAATATTA
53524 TTA
1 TTA
53527 AGAATTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (27 bp):
TTATTATTAAAATAGTCATTAATATTA
Found at i:53515 original size:18 final size:17
Alignment explanation
Indices: 53490--53523 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
53480 TGATATCATT
*
53490 AATATTATTATTATTAA
1 AATATTATTAATATTAA
53507 AATAGTTATTAATATTA
1 AATA-TTATTAATATTA
53524 TTAAGAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
AATATTATTAATATTAA
Found at i:54214 original size:6 final size:6
Alignment explanation
Indices: 54205--54285 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
54195 CTTTTTAATT
* * * *
54205 TTAAAA TTAAAA TTAAAA TT-AAA TTAAAT TTAAAT TTAAGA -TAAAT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
* *
54251 TTAAAT TTAAAA -T-AAA TCTAAAT TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA T-TAAAA TTAAAA TTAAAA
54286 AGGGGCCCGA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
4 3 0.05
5 9 0.15
6 47 0.76
7 3 0.05
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAA
Found at i:54230 original size:17 final size:18
Alignment explanation
Indices: 54198--54284 Score: 108
Period size: 17 Copynumber: 5.0 Consensus size: 18
54188 GTTTGAACTT
*
54198 TTTAATTTTAAAATTAAA
1 TTTAAATTTAAAATTAAA
* *
54216 ATTAAAATT-AAATTAAA
1 TTTAAATTTAAAATTAAA
*
54233 TTTAAATTTAAGA-TAAA
1 TTTAAATTTAAAATTAAA
54250 TTTAAATTTAAAA-TAAA
1 TTTAAATTTAAAATTAAA
*
54267 TCTAAATTTAAAATTAAA
1 TTTAAATTTAAAATTAAA
54285 AAGGGGCCCG
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
17 47 0.80
18 12 0.20
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (18 bp):
TTTAAATTTAAAATTAAA
Found at i:54231 original size:23 final size:24
Alignment explanation
Indices: 54199--54285 Score: 92
Period size: 23 Copynumber: 3.8 Consensus size: 24
54189 TTTGAACTTT
*
54199 TTAATTTTAAAATTAAAATTAAAA
1 TTAAATTTAAAATTAAAATTAAAA
* * *
54223 TTAAA-TTAAATTTAAATTTAAGA
1 TTAAATTTAAAATTAAAATTAAAA
*
54246 -TAAATTTAAATTTAAAA-T-AAA
1 TTAAATTTAAAATTAAAATTAAAA
54267 TCTAAATTTAAAATTAAAA
1 T-TAAATTTAAAATTAAAA
54286 AGGGGCCCGA
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
21 2 0.04
22 5 0.09
23 42 0.79
24 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (24 bp):
TTAAATTTAAAATTAAAATTAAAA
Found at i:55019 original size:202 final size:205
Alignment explanation
Indices: 54704--55246 Score: 718
Period size: 202 Copynumber: 2.6 Consensus size: 205
54694 CGTATTGCAC
* * *
54704 CAAGAAGCTAACCATTTTATTACTTCGA-CTTGCTTCTCAGTGTCTCATCAGGAAGTTGGGGTTC
1 CAAGAAGCTAACC-TTTTATTGCTTC-ACCCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTC
* *
54768 GAAGATTTGCTCACATCAGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATAAGGAAGAT
64 GAAGA-TTGCTCACATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGAT
* * * ** * *
54833 GACTGCGTCGTTTGTTTCAATTTGCTTCTCTATATCTCATCAGGAAGACGAATTTGGTCTACTTC
128 GACTGCGTCATTTATTTCAATTCGCTTCTCTATATCTCATCAAAAAGACAAATTTGGTCCACTTC
54898 TCA-ATATCTCAT
193 TCAGATATCTCAT
* *
54910 CAAGAAGCTAACCCTTTATTGCTTCACCCTGCTTCTCTGTATCTCATCAGGAAGTTGGGGTTCG-
1 CAAGAAGCTAACCTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGA
54974 AG-TTGCTCACATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGAC
66 AGATTGCTCACATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGAC
* *
55038 TGCGTCATTTATTTCAATTCGCTTCTCTGTATCTTATCAAAAAGACAAATTTGGTCCACTTCTCA
131 TGCGTCATTTATTTCAATTCGCTTCTCTATATCTCATCAAAAAGACAAATTTGGTCCACTTCTCA
*
55103 GCTATCTCAT
196 GATATCTCAT
* * * *
55113 -TAGAAAGCTAACCTTTTATTGCTTCACACTGCTTCTCCGTATCTCATCAGAAAGTTGGGGTTCG
1 CAAG-AAGCTAACCTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCG
* * ** * * * *
55177 AAGATTTGCTCACTTTGACCCTCATTTCATTGATTTGGTTTTCTTCTCAGTATCTCATCAGGAAG
65 AAGA-TTGCTCACATCGGGCGTGA-GT--TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAG
55242 ATGAC
126 ATGAC
55247 CGCATCGCTG
Statistics
Matches: 298, Mismatches: 30, Indels: 15
0.87 0.09 0.04
Matches are distributed among these distances:
202 118 0.40
203 64 0.21
204 5 0.02
205 44 0.15
206 26 0.09
207 1 0.00
209 40 0.13
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (205 bp):
CAAGAAGCTAACCTTTTATTGCTTCACCCTGCTTCTCAGTATCTCATCAGGAAGTTGGGGTTCGA
AGATTGCTCACATCGGGCGTGAGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGAC
TGCGTCATTTATTTCAATTCGCTTCTCTATATCTCATCAAAAAGACAAATTTGGTCCACTTCTCA
GATATCTCAT
Found at i:67035 original size:30 final size:29
Alignment explanation
Indices: 67003--67353 Score: 406
Period size: 30 Copynumber: 11.8 Consensus size: 29
66993 TCGGATACTC
* *
67003 GAGGGT-AAAATGGTAAGTTTTGGAAGTTT
1 GAGGGTAAAAATGG-GATTTTTGGAAGTTT
* *
67032 CGAGGTTAAAAAATGGGATTTTTAGAAGTTT
1 -GAGGGT-AAAAATGGGATTTTTGGAAGTTT
* *
67063 TAGGGTTAAAAATGAGATTTTTGGAAGTTTT
1 GAGGG-TAAAAATGGGATTTTTGGAAG-TTT
* *
67094 AAGGTTAAAAATGGGATTTTTGGAAGTTT
1 GAGGGTAAAAATGGGATTTTTGGAAGTTT
* *
67123 GGGGGTCAAAAATGAGATTTTTGGAAGTTT
1 GAGGGT-AAAAATGGGATTTTTGGAAGTTT
*
67153 CGAGGTTAAAAATGGGATTTTTGGAAGTTT
1 -GAGGGTAAAAATGGGATTTTTGGAAGTTT
* *
67183 AAGGGT-AAAATGGGATTTTTAGAAGTTTT
1 GAGGGTAAAAATGGGATTTTTGGAAG-TTT
67212 G-GGGTCAAAAATGGGATTTTTGGAAGTTTT
1 GAGGGT-AAAAATGGGATTTTTGGAAG-TTT
67242 GA-GGTCAAAAATGGGATTTTTGGAAGTTT
1 GAGGGT-AAAAATGGGATTTTTGGAAGTTT
*
67271 -AGGGGTCAAAAATGGGATTTTTGGAAGTTC
1 GA-GGGT-AAAAATGGGATTTTTGGAAGTTT
*
67301 GGGGGTAAAAATGGGATTTTTGGAAGTTT
1 GAGGGTAAAAATGGGATTTTTGGAAGTTT
67330 GAGGGTCAAAAATGGGATTTTTGG
1 GAGGGT-AAAAATGGGATTTTTGG
67354 GGTTAAAAAT
Statistics
Matches: 280, Mismatches: 27, Indels: 28
0.84 0.08 0.08
Matches are distributed among these distances:
28 23 0.08
29 43 0.15
30 184 0.66
31 23 0.08
32 7 0.03
ACGTcount: A:0.31, C:0.02, G:0.31, T:0.35
Consensus pattern (29 bp):
GAGGGTAAAAATGGGATTTTTGGAAGTTT
Found at i:67252 original size:148 final size:148
Alignment explanation
Indices: 66981--67351 Score: 523
Period size: 148 Copynumber: 2.5 Consensus size: 148
66971 TCGGAGTTGG
* * * * *
66981 AAATGAGATTTTTCGGATA-CTCGAGGGT-AAAATGGTAAGTTTTGGAAGTTTCGAGGTTAAAAA
1 AAATGAGATTTTT-GGA-AGTTCGAGGGTAAAAATGG-GATTTTTGGAAGTTT-AAGGGT-AAAA
* *
67044 ATGGGATTTTTAGAAGTTTTAGGGTTAAAAATGAGATTTTTGGAAGTTTTAAGGTTAAAAATGGG
61 ATGGGATTTTTAGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTTAAGGTCAAAAATGGG
*
67109 ATTTTTGGAAGTTTGGGGGTCAA
126 ATTTTTGGAAGTTTAGGGGTCAA
*
67132 AAATGAGATTTTTGGAAGTTTCGAGGTTAAAAATGGGATTTTTGGAAGTTTAAGGGT-AAAATGG
1 AAATGAGATTTTTGGAAG-TTCGAGGGTAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAAATGG
* * *
67196 GATTTTTAGAAGTTTTGGGGTCAAAAATGGGATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTT
65 GATTTTTAGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTTAAGGTCAAAAATGGGATTT
67261 TTGGAAGTTTAGGGGTCAA
130 TTGGAAGTTTAGGGGTCAA
* * *
67280 AAATGGGATTTTTGGAAGTTCGGGGGTAAAAATGGGATTTTTGGAAGTTTGAGGGTCAAAAATGG
1 AAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTAAGGGT-AAAAATGG
67345 GATTTTT
65 GATTTTT
67352 GGGGTTAAAA
Statistics
Matches: 199, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
147 35 0.18
148 102 0.51
149 15 0.08
150 7 0.04
151 33 0.17
152 7 0.04
ACGTcount: A:0.31, C:0.03, G:0.30, T:0.36
Consensus pattern (148 bp):
AAATGAGATTTTTGGAAGTTCGAGGGTAAAAATGGGATTTTTGGAAGTTTAAGGGTAAAAATGGG
ATTTTTAGAAGTTTTAGGGTCAAAAATGAGATTTTTGGAAGTTTTAAGGTCAAAAATGGGATTTT
TGGAAGTTTAGGGGTCAA
Found at i:67371 original size:20 final size:22
Alignment explanation
Indices: 67327--67373 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
67317 TTTTTGGAAG
67327 TTTGAGGGTCAAAAATGGGATT
1 TTTGAGGGTCAAAAATGGGATT
*
67349 TTTG-GGGTTAAAAATGGGATT
1 TTTGAGGGTCAAAAATGGGATT
67370 TTTG
1 TTTG
67374 GAATTTTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.28, C:0.02, G:0.32, T:0.38
Consensus pattern (22 bp):
TTTGAGGGTCAAAAATGGGATT
Found at i:67380 original size:30 final size:29
Alignment explanation
Indices: 67346--67402 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
67336 CAAAAATGGG
* *
67346 ATTTTTGGGGTTAAAAATGGGATTTTTGGA
1 ATTTTAGGGG-TAAAAATGAGATTTTTGGA
67376 ATTTTAGGGGTAAAAATGAGATTTTTG
1 ATTTTAGGGGTAAAAATGAGATTTTTG
67403 AACAGTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
ATTTTAGGGGTAAAAATGAGATTTTTGGA
Found at i:68416 original size:18 final size:19
Alignment explanation
Indices: 68393--68444 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
68383 TTATTTATTT
**
68393 ATTTATTATTATTAATATT
1 ATTTATTATTATTAATAAC
*
68412 A-TTATTATTATCAA-AAC
1 ATTTATTATTATTAATAAC
68429 ATTTATTATTATTAAT
1 ATTTATTATTATTAAT
68445 GAATATTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.89
19 1 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTATTATTATTAATAAC
Found at i:68500 original size:15 final size:15
Alignment explanation
Indices: 68396--68512 Score: 53
Period size: 15 Copynumber: 7.5 Consensus size: 15
68386 TTTATTTATT
*
68396 TATTATTATTAATAT
1 TATTATTATTAATAA
*
68411 TATTATTATTATCAAAA
1 TATTATTATTA--ATAA
* *
68428 CATTTATTATTATTAA
1 TA-TTATTATTAATAA
* **
68444 TGAATATTAAGAA-AA
1 T-ATTATTATTAATAA
*
68459 -ACTTATTTATTATTAA
1 TA-TTA-TTATTAATAA
*
68475 TGA-TATCATTAATAA
1 T-ATTATTATTAATAA
68490 TATTATTATTAA-AA
1 TATTATTATTAATAA
68504 TAGTTATTA
1 TA-TTATTA
68513 ATATTATTAA
Statistics
Matches: 74, Mismatches: 17, Indels: 22
0.65 0.15 0.19
Matches are distributed among these distances:
13 1 0.01
14 7 0.09
15 40 0.54
16 12 0.16
17 4 0.05
18 10 0.14
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.49
Consensus pattern (15 bp):
TATTATTATTAATAA
Found at i:69211 original size:6 final size:6
Alignment explanation
Indices: 69202--69282 Score: 62
Period size: 6 Copynumber: 14.0 Consensus size: 6
69192 TTTTTTAATT
* * * * *
69202 TTAAAA TTAAAA TT-AAA TTTAAA TTAAAT TTAAAT TTAAGA TT-AAT
1 TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA TTAAAA
* *
69248 TTAAAT TTAAAA -T-AAA TCTAAAT TTAAAA TTAAAA
1 TTAAAA TTAAAA TTAAAA T-TAAAA TTAAAA TTAAAA
69283 AGGGGCCCGA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
4 3 0.05
5 9 0.15
6 46 0.75
7 3 0.05
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (6 bp):
TTAAAA
Found at i:69225 original size:11 final size:11
Alignment explanation
Indices: 69205--69281 Score: 75
Period size: 11 Copynumber: 6.8 Consensus size: 11
69195 TTTAATTTTA
*
69205 AAATTAAAATT
1 AAATTTAAATT
69216 AAATTTAAATT
1 AAATTTAAATT
69227 AAATTTAAATTT
1 AAATTTAAA-TT
*
69239 AAGA-TTAATTT
1 AA-ATTTAAATT
*
69250 AAATTTAAAAT
1 AAATTTAAATT
*
69261 AAATCTAAATTT
1 AAATTTAAA-TT
*
69273 AAAATTAAA
1 AAATTTAAA
69282 AAGGGGCCCG
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
10 1 0.02
11 36 0.67
12 16 0.30
13 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:69227 original size:17 final size:17
Alignment explanation
Indices: 69205--69282 Score: 88
Period size: 17 Copynumber: 4.5 Consensus size: 17
69195 TTTAATTTTA
69205 AAATTAAAATTAAATTT
1 AAATTAAAATTAAATTT
*
69222 AAATTAAATTTAAATTT
1 AAATTAAAATTAAATTT
*
69239 AAGATT-AATTTAAATTT
1 AA-ATTAAAATTAAATTT
*
69256 AAAAT-AAATCTAAATTT
1 AAATTAAAAT-TAAATTT
69273 AAAATTAAAA
1 -AAATTAAAA
69283 AGGGGCCCGA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
16 5 0.09
17 38 0.72
18 7 0.13
19 3 0.06
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (17 bp):
AAATTAAAATTAAATTT
Found at i:69229 original size:23 final size:23
Alignment explanation
Indices: 69202--69282 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
69192 TTTTTTAATT
69202 TTAAAATTAAAATTAAATTTAAA
1 TTAAAATTAAAATTAAATTTAAA
* * *
69225 TTAAATTTAAATTTAAGA-TTAAT
1 TTAAAATTAAAATTAA-ATTTAAA
* *
69248 TTAAATTTAAAA-TAAATCTAAA
1 TTAAAATTAAAATTAAATTTAAA
69270 TTTAAAATTAAAA
1 -TTAAAATTAAAA
69283 AGGGGCCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 1 0.02
22 6 0.12
23 40 0.83
24 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (23 bp):
TTAAAATTAAAATTAAATTTAAA
Found at i:74268 original size:25 final size:24
Alignment explanation
Indices: 74219--74268 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
74209 TTAGTCATTG
* *
74219 ATTTTTATCTTTTTAATTTATTTT
1 ATTTTTATCTTTTTAATTAAATTT
74243 ATTTTGTAT-TTTTTAAATTAAATTT
1 ATTTT-TATCTTTTT-AATTAAATTT
74268 A
1 A
74269 GTTCTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (24 bp):
ATTTTTATCTTTTTAATTAAATTT
Found at i:74494 original size:17 final size:17
Alignment explanation
Indices: 74474--74508 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
74464 AAAATTAGTT
* *
74474 TTAAAAAGTAAAGAAAA
1 TTAAAAAGAAAAAAAAA
74491 TTAAAAAGAAAAAAAAA
1 TTAAAAAGAAAAAAAAA
74508 T
1 T
74509 GTCCGATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (17 bp):
TTAAAAAGAAAAAAAAA
Found at i:78652 original size:17 final size:18
Alignment explanation
Indices: 78612--78653 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
78602 CTTCCAGGAG
*
78612 TCTATATATATTTTATATA
1 TCTAT-TATATTGTATATA
78631 T-TATTATATTGTATAT-
1 TCTATTATATTGTATATA
78647 TCTATTA
1 TCTATTA
78654 ATGGAATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 1 0.05
17 16 0.76
18 3 0.14
19 1 0.05
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TCTATTATATTGTATATA
Found at i:81063 original size:6 final size:7
Alignment explanation
Indices: 81044--81068 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
81034 AATTTATATA
81044 TATTTTT
1 TATTTTT
81051 TATTTTT
1 TATTTTT
81058 TATTTTT
1 TATTTTT
81065 TATT
1 TATT
81069 AAAACAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TATTTTT
Found at i:94265 original size:24 final size:25
Alignment explanation
Indices: 94233--94284 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
94223 AAATGATTTT
94233 AAATATTAT-ATCAAAAATATAATTA
1 AAATATTATAAT-AAAAATATAATTA
* *
94258 AAAT-TTATAATAAAATTATTATTA
1 AAATATTATAATAAAAATATAATTA
94282 AAA
1 AAA
94285 AAAAACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
AAATATTATAATAAAAATATAATTA
Found at i:96515 original size:21 final size:21
Alignment explanation
Indices: 96458--96517 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 21
96448 ACTGCCCATC
96458 TTCTGCTGCAATCCATTCATT
1 TTCTGCTGCAATCCATTCATT
* *
96479 TTCAAGGCTTATCAATCCATTCATT
1 TTC--TGC-T-GCAATCCATTCATT
96504 TTCTGCTGCAATCC
1 TTCTGCTGCAATCC
96518 TCCCCATCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
21 9 0.29
22 1 0.03
23 4 0.13
24 1 0.03
25 16 0.52
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (21 bp):
TTCTGCTGCAATCCATTCATT
Found at i:105352 original size:25 final size:26
Alignment explanation
Indices: 105314--105367 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
105304 ATTATATACC
*
105314 TTTTATGATATA-TTTTTATTAATTT
1 TTTTATGATATATTTTTTATTAAATT
105339 TTTTAATGAT-TATTTTTTATTAAATT
1 TTTT-ATGATATATTTTTTATTAAATT
105365 TTT
1 TTT
105368 AAACATAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 6 0.23
26 20 0.77
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTATGATATATTTTTTATTAAATT
Found at i:105378 original size:25 final size:26
Alignment explanation
Indices: 105326--105379 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
105316 TTATGATATA
* ** *
105326 TTTTTATTAATTTTTTTAATGATTAT
1 TTTTTATTAATATTTTTAAACATAAT
105352 TTTTTATTAA-ATTTTTAAACATAAT
1 TTTTTATTAATATTTTTAAACATAAT
105377 TTT
1 TTT
105380 CAATAATTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (26 bp):
TTTTTATTAATATTTTTAAACATAAT
Found at i:126320 original size:27 final size:27
Alignment explanation
Indices: 126264--126318 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
126254 AAAAGTATTC
*
126264 TTATTTAAATTAATTTAAATTTTTATT
1 TTATTTAAATTAATTTAAATTTTAATT
*
126291 TTATTTATATATAA-TT-AATTTTAATT
1 TTATTTAAAT-TAATTTAAATTTTAATT
126317 TT
1 TT
126319 TACAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.44
27 11 0.44
28 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTATTTAAATTAATTTAAATTTTAATT
Found at i:128618 original size:51 final size:50
Alignment explanation
Indices: 128536--128647 Score: 120
Period size: 51 Copynumber: 2.2 Consensus size: 50
128526 TGTACAAATT
* * * * *
128536 TTGACAAAATGTATAAATGTAGCAGCTTAAATTTGTTAAATCAGGACCAGA
1 TTGACAGAATGTATAAATGTAGCAGCTTAAATTTATCAAATCAAGA-CAAA
* *
128587 TTGACAGAATGTATAAATGTTA-TAGGC-TAAATTTATCAAATCAAGATAAA
1 TTGACAGAATGTATAAATG-TAGCA-GCTTAAATTTATCAAATCAAGACAAA
128637 TTGACAGAATG
1 TTGACAGAATG
128648 CGTAAACTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
50 13 0.25
51 35 0.67
52 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (50 bp):
TTGACAGAATGTATAAATGTAGCAGCTTAAATTTATCAAATCAAGACAAA
Found at i:135661 original size:42 final size:42
Alignment explanation
Indices: 135571--135731 Score: 182
Period size: 42 Copynumber: 3.8 Consensus size: 42
135561 TTATGCTCTA
* * * * *
135571 CCGAGTCATAAGTCTTCCTTTTTAAACATAATCC-CATGCTCATT
1 CCGAGACATGAGTCTTCC--TTTAATCAT-ATCCTCATTCTCATC
* *
135615 CCGAGTCATGAGTCTTCCTTTAATCATATTCTCATTCTCATC
1 CCGAGACATGAGTCTTCCTTTAATCATATCCTCATTCTCATC
*
135657 CCGAGACATGAGTCTGCCTTTAATCATATCCTCATTCTCATC
1 CCGAGACATGAGTCTTCCTTTAATCATATCCTCATTCTCATC
* * *
135699 CTGAGACATGACTCTTCCTTAAAT-ATATCCTCA
1 CCGAGACATGAGTCTTCCTTTAATCATATCCTCA
135732 CACTCGTTTT
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
41 12 0.12
42 75 0.72
44 17 0.16
ACGTcount: A:0.25, C:0.29, G:0.10, T:0.36
Consensus pattern (42 bp):
CCGAGACATGAGTCTTCCTTTAATCATATCCTCATTCTCATC
Found at i:136806 original size:2 final size:2
Alignment explanation
Indices: 136799--136823 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
136789 GATCAAAATG
136799 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
136824 TCACTAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:143164 original size:100 final size:98
Alignment explanation
Indices: 142965--143214 Score: 295
Period size: 100 Copynumber: 2.5 Consensus size: 98
142955 GCACCATGAA
* **
142965 ACATGACGGGAAAGATCTAAGACCGTAACGGTGGATCCAATACCGCAAAGACAAAAGGGAAGGGT
1 ACATGACGGGAAAGATCTAAGACCGCAACGGCAGATCCAATACCGCAAAGACAAAAGGGAAGGGT
* *
143030 TTAAGTCGTAACGGCAAACCTTATACCTCAGAG
66 TTAAGTCGCAAAGGCAAACCTTATACCTCAGAG
* * * * *
143063 ACATGACGGGAAAGATTTAAGACCGCAATGGCAGATCTAGTACCGCAAAGATACGAAAGGGAAGG
1 ACATGACGGGAAAGATCTAAGACCGCAACGGCAGATCCAATACCGCAAAG--ACAAAAGGGAAGG
* ** * *
143128 GTTTAAGTTGCAAAGGTGAACCTTGTACCTTAGAG
64 GTTTAAGTCGCAAAGGCAAACCTTATACCTCAGAG
* * * * *
143163 ACATGACGGGAAAGATCTAAG-CCGCAACGACGGATCCAGTGCCGCGAAGACA
1 ACATGACGGGAAAGATCTAAGACCGCAACGGCAGATCCAATACCGCAAAGACA
143215 TGAAGGAAAA
Statistics
Matches: 127, Mismatches: 23, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
97 2 0.02
98 43 0.34
99 22 0.17
100 60 0.47
ACGTcount: A:0.36, C:0.20, G:0.27, T:0.16
Consensus pattern (98 bp):
ACATGACGGGAAAGATCTAAGACCGCAACGGCAGATCCAATACCGCAAAGACAAAAGGGAAGGGT
TTAAGTCGCAAAGGCAAACCTTATACCTCAGAG
Found at i:143260 original size:49 final size:49
Alignment explanation
Indices: 143161--143471 Score: 220
Period size: 49 Copynumber: 6.3 Consensus size: 49
143151 TGTACCTTAG
* * * *
143161 AGACATGACGGGAAAGATCTAAGCCGCAACGACGGATCCAGTGCCGCGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCACGA
* * *
143210 AGACATGAAGGAAAAGATCTAAGTCGCAACGACGGATCTTGTACCACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCACGA
* * * * * * * *
143259 AGACA-CAAGGGAAAGGTTTAAGTCGCAATGGCGGACCTAGTACCTC-A
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCACGA
* * * *
143306 GAGACATAAAGGGAAAGATCT-AGACCGCAACGGCAGATCTAGTACCACAA
1 -AGACATGAAGGGAAAGATCTAAG-CCGCAACGACGGATCTAGTACCACGA
* * * * * *
143356 AGATACA-AAAGGGAAAGATTTAAGTCGCAACGACGGACCGT-GAACCTCAGA
1 AG--ACATGAAGGGAAAGATCTAAGCCGCAACGACGGATC-TAGTACCAC-GA
* * * * * *
143407 AGACAAGAAGGGAAAGATTTAAGCCGCAAAGGCGAATCCAGT-CCACGA
1 AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCACGA
**
143455 AGATTTGAAAGGGAAAG
1 AGACATG-AAGGGAAAG
143472 GTTTAAGTCG
Statistics
Matches: 206, Mismatches: 44, Indels: 24
0.75 0.16 0.09
Matches are distributed among these distances:
47 1 0.00
48 45 0.22
49 94 0.46
50 57 0.28
51 9 0.04
ACGTcount: A:0.39, C:0.21, G:0.27, T:0.14
Consensus pattern (49 bp):
AGACATGAAGGGAAAGATCTAAGCCGCAACGACGGATCTAGTACCACGA
Found at i:143309 original size:146 final size:148
Alignment explanation
Indices: 143119--143442 Score: 368
Period size: 146 Copynumber: 2.2 Consensus size: 148
143109 AAAGATACGA
* * * * * * *
143119 AAGGGAAGGGTTTAAGTTGCAAAGGTGAACCTTGTACCTTAGAGACATGACGGGAAAGATCTA-A
1 AAGGGAAAGGTTTAAGTCGCAAAGGCGAACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAGA
* * * * * *
143183 GCCGCAACGACGGATCCAGTGCCGCGAAG-ACATGAAGGAAAAGATCTAAGTCGCAACGACGGAT
66 -CCGCAACGACAGATCCAGTACCACAAAGAACA-AAAGGAAAAGATCTAAGTCGCAACGACGGAC
* *
143247 CTTGTACCAC-GAAGAC-AC
129 CGTGAACCACAGAAGACAAC
* *
143265 AAGGGAAAGGTTTAAGTCGCAATGGCGGACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAGA
1 AAGGGAAAGGTTTAAGTCGCAAAGGCGAACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAGA
* * * *
143330 CCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGGAAAGATTTAAGTCGCAACGACGGACC
66 CCGCAACGACAGATCCAGTACCACAAAGA-ACAAAAGGAAAAGATCTAAGTCGCAACGACGGACC
* *
143395 GTGAACCTCAGAAGACAAG
130 GTGAACCACAGAAGACAAC
* *
143414 AAGGGAAAGATTTAAGCCGCAAAGGCGAA
1 AAGGGAAAGGTTTAAGTCGCAAAGGCGAA
143443 TCCAGTCCAC
Statistics
Matches: 146, Mismatches: 27, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
146 76 0.52
147 35 0.24
148 9 0.06
149 26 0.18
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.15
Consensus pattern (148 bp):
AAGGGAAAGGTTTAAGTCGCAAAGGCGAACCTAGTACCTCAGAGACATAAAGGGAAAGATCTAGA
CCGCAACGACAGATCCAGTACCACAAAGAACAAAAGGAAAAGATCTAAGTCGCAACGACGGACCG
TGAACCACAGAAGACAAC
Found at i:143385 original size:50 final size:49
Alignment explanation
Indices: 143070--143484 Score: 198
Period size: 49 Copynumber: 8.4 Consensus size: 49
143060 GAGACATGAC
* * * * *
143070 GGGAAAGATTTAAGACCGCAATGGCAGATCTAGTACCGCAAAGATACGAAA
1 GGGAAAGATTTAAG-TCGCAACGGCGGATCTAGTACCACAAAGA-ACAAAA
* * * * * * * * ** * * *
143121 GGGAAGGGTTTAAGTTGCAAAGGTGAACCTTGTACCTTAGAG-ACATGAC
1 GGGAAAGATTTAAGTCGCAACGGCGGATCTAGTACCACAAAGAACA-AAA
* * * * * * * *
143170 GGGAAAGATCTAAGCCGCAACGACGGATCCAGTGCCGCGAAG-ACATGAA
1 GGGAAAGATTTAAGTCGCAACGGCGGATCTAGTACCACAAAGAACA-AAA
* * * * * *
143219 GGAAAAGATCTAAGTCGCAACGACGGATCTTGTACCACGAAG-ACACAA
1 GGGAAAGATTTAAGTCGCAACGGCGGATCTAGTACCACAAAGAACAAAA
* * * * *
143267 GGGAAAGGTTTAAGTCGCAATGGCGGACCTAGTACCTCAGAG-ACATAAA
1 GGGAAAGATTTAAGTCGCAACGGCGGATCTAGTACCACAAAGAACA-AAA
* * *
143316 GGGAAAGATCT-AGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAA
1 GGGAAAGATTTAAG-TCGCAACGGCGGATCTAGTACCACAAAGA-ACAAAA
* * * *
143366 GGGAAAGATTTAAGTCGCAACGACGGACCGT-GAACCTCAGAAG-ACAAGAA
1 GGGAAAGATTTAAGTCGCAACGGCGGATC-TAGTACCACA-AAGAACAA-AA
* * * * * ***
143416 GGGAAAGATTTAAGCCGCAAAGGCGAATCCAGT-CCACGAAGATTTGAAA
1 GGGAAAGATTTAAGTCGCAACGGCGGATCTAGTACCACAAAGA-ACAAAA
*
143465 GGGAAAGGTTTAAGTCGCAA
1 GGGAAAGATTTAAGTCGCAA
143485 TGGCAAACCC
Statistics
Matches: 271, Mismatches: 81, Indels: 26
0.72 0.21 0.07
Matches are distributed among these distances:
48 44 0.16
49 131 0.48
50 75 0.28
51 21 0.08
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (49 bp):
GGGAAAGATTTAAGTCGCAACGGCGGATCTAGTACCACAAAGAACAAAA
Found at i:143405 original size:99 final size:98
Alignment explanation
Indices: 143170--143484 Score: 297
Period size: 99 Copynumber: 3.2 Consensus size: 98
143160 GAGACATGAC
* * * * *
143170 GGGAAAGATCTAAGCCGCAACGACGGATCCAGTG-CCGC-GAAGACATGAAGGAAAAGATCTAAG
1 GGGAAAGATTTAAGTCGCAACGACGGA-CC-GTGACCTCAGAAGACATAAAGGGAAAGATCTAAG
* * * *
143233 TCGCAACGACGGATCTTGTACCACGAAG--ACACAA
64 CCGCAACGGC-GATCTAGTACCACGAAGATACAAAA
* * *
143267 GGGAAAGGTTTAAGTCGCAATGGCGGACC-TAGTACCTCAG-AGACATAAAGGGAAAGATCT-AG
1 GGGAAAGATTTAAGTCGCAACGACGGACCGT-G-ACCTCAGAAGACATAAAGGGAAAGATCTAAG
*
143329 ACCGCAACGGCAGATCTAGTACCACAAAGATACAAAA
64 -CCGCAACGGC-GATCTAGTACCACGAAGATACAAAA
*
143366 GGGAAAGATTTAAGTCGCAACGACGGACCGTGAACCTCAGAAGACA-AGAAGGGAAAGATTTAAG
1 GGGAAAGATTTAAGTCGCAACGACGGACCGTG-ACCTCAGAAGACATA-AAGGGAAAGATCTAAG
* * ***
143430 CCGCAAAGGCGAATCCAGT-CCACGAAGATTTGAAA
64 CCGCAACGGCG-ATCTAGTACCACGAAGATACAAAA
*
143465 GGGAAAGGTTTAAGTCGCAA
1 GGGAAAGATTTAAGTCGCAA
143485 TGGCAAACCC
Statistics
Matches: 180, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
94 1 0.01
95 1 0.01
96 4 0.02
97 66 0.37
98 1 0.01
99 72 0.40
100 33 0.18
101 2 0.01
ACGTcount: A:0.38, C:0.20, G:0.27, T:0.14
Consensus pattern (98 bp):
GGGAAAGATTTAAGTCGCAACGACGGACCGTGACCTCAGAAGACATAAAGGGAAAGATCTAAGCC
GCAACGGCGATCTAGTACCACGAAGATACAAAA
Found at i:143481 original size:246 final size:246
Alignment explanation
Indices: 143012--143484 Score: 592
Period size: 246 Copynumber: 1.9 Consensus size: 246
143002 CAATACCGCA
* * * *
143012 AAGACAAAAGGGAAGGGTTTAAGTCGTAACGGCAAACCTTATACCTCAGAGACATGACGGGAAAG
1 AAGACAAAAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTATACCTCAGAGACATAAAGGGAAAG
* * * * * * *
143077 ATTTAAGACCGCAATGGCAGATCTAGTACCGCAAAGATACGAAAGGGAAGGGTTTAAGTTGCAAA
66 ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGGAAAGATTTAAGTCGCAAA
** * * * * * * * *
143142 GGTGAACCTTGTACCTTAGAGACATGACGGGAAAGATCTAAGCCGCAACGACGGATCCAGTGCCG
131 GACGAACCGTGAACCTCAGAGACAAGAAGGGAAAGATCTAAGCCGCAAAGACGAATCCAGTGCCA
143207 CGAAGACATGAAGGAAAAGATCTAAGTCGCAACGACGGATCTTGTACCACG
196 CGAAGACATGAAGGAAAAGATCTAAGTCGCAACGACGGATCTTGTACCACG
* * **
143258 AAGACACAAGGGAAAGGTTTAAGTCGCAATGGCGGACC-TAGTACCTCAGAGACATAAAGGGAAA
1 AAGACAAAAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTA-TACCTCAGAGACATAAAGGGAAA
143322 GATCT-AGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGGAAAGATTTAAGTCGCAA
65 GATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGGAAAGATTTAAGTCGCAA
* * * *
143386 CGACGGACCGTGAACCTCAGAAGACAAGAAGGGAAAGATTTAAGCCGCAAAGGCGAATCCAGT-C
130 AGACGAACCGTGAACCTCAG-AGACAAGAAGGGAAAGATCTAAGCCGCAAAGACGAATCCAGTGC
** * * *
143450 CACGAAGATTTGAAAGGGAAAGGTTTAAGTCGCAA
194 CACGAAGACATG-AAGGAAAAGATCTAAGTCGCAA
143485 TGGCAAACCC
Statistics
Matches: 190, Mismatches: 34, Indels: 6
0.83 0.15 0.03
Matches are distributed among these distances:
245 78 0.41
246 112 0.59
ACGTcount: A:0.38, C:0.19, G:0.27, T:0.16
Consensus pattern (246 bp):
AAGACAAAAGGGAAAGGTTTAAGTCGCAACGGCAAACCTTATACCTCAGAGACATAAAGGGAAAG
ATCTAAGACCGCAACGGCAGATCTAGTACCACAAAGATACAAAAGGGAAAGATTTAAGTCGCAAA
GACGAACCGTGAACCTCAGAGACAAGAAGGGAAAGATCTAAGCCGCAAAGACGAATCCAGTGCCA
CGAAGACATGAAGGAAAAGATCTAAGTCGCAACGACGGATCTTGTACCACG
Found at i:143792 original size:39 final size:39
Alignment explanation
Indices: 143744--143967 Score: 163
Period size: 39 Copynumber: 5.7 Consensus size: 39
143734 CATCGTTAAT
143744 CAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAAC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAAC
* * *
143783 CAATCTCTTACCCCGAGCTTGGGGCAGAT--TGA--AGC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAAC
* *
143818 CATTTGATCT-TTCACCCCGACCCTGGGGCAGATAATCATCAAC
1 CA----ATCTCTT-ACCCCGAGCCTGGGGCAGATCATCATCAAC
* * * * * **
143861 CAATCTCTTACCACGAGCCAGAGGCAAATTA-CAGTCATT
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCATCA-TCAAC
* * * *
143900 CGATCTCTTACCCCAAGCTTGGGGCAGATCATCGTCAAC
1 CAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAAC
* * * * *
143939 CAAACTCCTACCTCGATCATGGGGCAGAT
1 CAATCTCTTACCCCGAGCCTGGGGCAGAT
143968 TACGATTATC
Statistics
Matches: 140, Mismatches: 33, Indels: 24
0.71 0.17 0.12
Matches are distributed among these distances:
35 4 0.03
37 2 0.01
38 4 0.03
39 121 0.86
40 3 0.02
41 2 0.01
43 4 0.03
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (39 bp):
CAATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAAC
Found at i:143970 original size:78 final size:78
Alignment explanation
Indices: 143746--143970 Score: 258
Period size: 78 Copynumber: 2.9 Consensus size: 78
143736 TCGTTAATCA
* * *
143746 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCCCGAGCTTGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCACGACCATGGGGCAGA
*
143811 TTGA-AGCCATTTG
66 TT-ACAGCCATTCG
* * *
143824 ATCT-TTCACCCCGACCCTGGGGCAGATAATCATCAACCAATCTCTTACCACGAGCCA-GAGGCA
1 ATCTCTT-ACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCACGA-CCATGGGGCA
* *
143887 AATTACAGTCATTCG
64 GATTACAGCCATTCG
* * * * * * *
143902 ATCTCTTACCCCAAGCTTGGGGCAGATCATCGTCAACCAAACTCCTACCTCGATCATGGGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCACGACCATGGGGCAGA
143967 TTAC
66 TTAC
143971 GATTATCCAC
Statistics
Matches: 122, Mismatches: 20, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
77 5 0.04
78 114 0.93
79 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (78 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCATCATCAACCAATCTCTTACCACGACCATGGGGCAGA
TTACAGCCATTCG
Found at i:144340 original size:201 final size:199
Alignment explanation
Indices: 143991--144546 Score: 665
Period size: 201 Copynumber: 2.8 Consensus size: 199
143981 AAATAATGTG
* * *
143991 GCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCA-----ATGCGAACAAATCTTTG
1 GCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGCTCGATGTGAGCAAATCTTCG
* * * * *
144051 AACCTCAGCTTCCTGATTAGATACTGAGAAGCAGGTTGAAGCAATAAAAAGGTTAGCTTTCTGAT
66 AACCTCAACTTCCTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAT
* * * * * *
144116 GAGACACTGAGAAGTGAACCAAATTTGTCTTTCTGATGAGGTACAGAGAAGCGGATTGAAACAAA
131 GAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACAAA
* **
144181 TGGG
196 CGAC
* *
144185 GCGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGCAAATCTT
1 GCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCA--GCTCGATGTGAGCAAATCTT
* * *
144250 CGAACCTCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGTAATAAAATGGTTAGCTTCCTG
64 CGAACCTCAACTTCCTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTG
144315 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACA
129 ATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACA
144380 AACGAC
194 AACGAC
* * * * * *
144386 GTAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGGTGAGCAA
1 GCAGTCATCTTCCTGATGAGATAC--AG-AGAAG--TATA-CCAACTCA-GCTCGATGTGAGCAA
* * * *
144451 ATCTTCGAATCC-CAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATGGTCATC
59 ATCTTCGAA-CCTCAACTTCCTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGC
* **
144515 TTCTTGATGAGATACTGAGAAGAAGACCAAAT
123 TTCCTGATGAGATACTGAGAAGTGGACCAAAT
144547 CAAACCCACG
Statistics
Matches: 307, Mismatches: 41, Indels: 16
0.84 0.11 0.04
Matches are distributed among these distances:
194 41 0.13
201 152 0.50
203 2 0.01
204 5 0.02
206 99 0.32
207 8 0.03
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (199 bp):
GCAGTCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGCTCGATGTGAGCAAATCTTCG
AACCTCAACTTCCTGATAAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGAT
GAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCGGATTGAAACAAA
CGAC
Found at i:144559 original size:120 final size:120
Alignment explanation
Indices: 144389--144666 Score: 430
Period size: 120 Copynumber: 2.3 Consensus size: 120
144379 AAACGACGTA
* *
144389 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGGTGAGCAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGGTCAGAAAATC
* * *
144454 TTCGAATCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATAAAATG
66 TTCGAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
* *
144509 GTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTCAGAAAATC
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGGTCAGAAAATC
* *
144574 TTCGAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAATATG
66 TTCGAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
* * * **
144629 GTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAAT
1 GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAAT
144667 TCGTCTTCCT
Statistics
Matches: 143, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
120 143 1.00
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.22
Consensus pattern (120 bp):
GTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGAGGTCAGAAAATC
TTCGAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATG
Found at i:144734 original size:86 final size:85
Alignment explanation
Indices: 144586--144752 Score: 228
Period size: 86 Copynumber: 2.0 Consensus size: 85
144576 CGAAACCCAG
* * * *
144586 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAATATGGTTAGCTTCCTGATGAGATACT
1 CTTCCTGATGAGACACAGAGAAGCAGATCGAAACAATAACATGGTTAGCTTCCTGATGAGATACT
**
144651 AAGAAGTGGACCAAATTCGT
66 AAGAAGAAGACCAAATTCGT
* * *
144671 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAA-ACGACATGGTTATCTTCCTGATGAGATA
1 CTTCCTGATGAGACACAGAGAAGCAGATCGAAACAATA--ACATGGTTAGCTTCCTGATGAGATA
144735 CTAAGAAGAAGACCAAAT
64 CTAAGAAGAAGACCAAAT
144753 CAAACCCTCG
Statistics
Matches: 71, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
84 1 0.01
85 31 0.44
86 39 0.55
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (85 bp):
CTTCCTGATGAGACACAGAGAAGCAGATCGAAACAATAACATGGTTAGCTTCCTGATGAGATACT
AAGAAGAAGACCAAATTCGT
Found at i:144823 original size:326 final size:326
Alignment explanation
Indices: 144230--144872 Score: 1020
Period size: 326 Copynumber: 2.0 Consensus size: 326
144220 CCAACTCAGG
* * *
144230 GCTCGATGTGAGCAAATCTTCGAACCTCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGTA
1 GCTCGATGTCAGAAAATCTTCGAACCTCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGCA
*
144295 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
66 ATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
* * *
144360 CAGAGAAGCGGATTGAAACAAACGACGTAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAA
131 CAGAGAAGCAGATTGAAACAAACGACATAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAA
* * *
144425 ATCAAACCCACGCTCGAGGTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGT
196 ATCAAACCCACGCTCGAGGTGAGCAAATCTTCGAACCCCAACTTCCTAATGAGATACTGAGAAGC
*
144490 AGGTCGAAGCAATAAAATGGTCATC-TTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCC
261 AGGTCGAAGCAATAAAATGGTCAGCTTTC-TGATGAGATACTGAGAAGAAGACCAAATCAAACCC
144554 AC
325 AC
* * *
144556 GCTCGATGTCAGAAAATCTTCGAAACC-CAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGC
1 GCTCGATGTCAGAAAATCTTCG-AACCTCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGC
* *
144620 AATAATATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGAT
65 AATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTAATGAGAT
* *
144685 ACAGAGAAGCAGATTGAAACAAACGACATGGTTATCTTCCTGATGAGATACTAAGAAGAAGACCA
130 ACAGAGAAGCAGATTGAAACAAACGACATAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCA
* * * * *
144750 AATCAAACCCTCGCTCGATGTGAGCAAATCTTTGAACCCCAGCTTCCTAATGAGATATTGAGAAG
195 AATCAAACCCACGCTCGAGGTGAGCAAATCTTCGAACCCCAACTTCCTAATGAGATACTGAGAAG
* **
144815 CAGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGGACCAAAT
260 CAGGTCGAAGCAATAAAATGGTCAGCTTTCTGATGAGATACTGAGAAGAAGACCAAAT
144873 TCGTCTTCCT
Statistics
Matches: 289, Mismatches: 26, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
326 282 0.98
327 7 0.02
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.23
Consensus pattern (326 bp):
GCTCGATGTCAGAAAATCTTCGAACCTCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGCA
ATAAAATGGTTAGCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
CAGAGAAGCAGATTGAAACAAACGACATAGTCATCTTCCTGATGAGATACTAAGAAGAAGACCAA
ATCAAACCCACGCTCGAGGTGAGCAAATCTTCGAACCCCAACTTCCTAATGAGATACTGAGAAGC
AGGTCGAAGCAATAAAATGGTCAGCTTTCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCA
C
Found at i:144873 original size:206 final size:206
Alignment explanation
Indices: 144466--145164 Score: 936
Period size: 206 Copynumber: 3.4 Consensus size: 206
144456 CGAATCCCAA
* * * * * * *
144466 CTTCCTGATGAGATACTGAGAAGTAGGTCGAAGCAATA--AAATGGTCATCTTCTTGATGAGATA
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAA-ACGACACGGTCATCTTCCTGATGAGATA
* * * *
144529 CTGAGAAGAAGACCAAATCAAACCCACGCTCGATGTCAGAAAATCTTCGAAACCCAGCTTCCTGA
65 CTAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGA
* * * *
144594 TGAGACACTGAGAAGCAGGTCGAAGCAATAATATGGTTAGCTTCCTGATGAGATACTAAGAAGTG
130 TGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTG
144659 GACCAAATTCGT
195 GACCAAATTCGT
* * *
144671 CTTCCTGATGAGATACAGAGAAGCAGATTGAAACAAACGACATGGTTATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAACGACACGGTCATCTTCCTGATGAGATAC
* * *
144736 TAAGAAGAAGACCAAATCAAACCCTCGCTCGATGTGAGCAAATCTTTGAACCCCAGCTTCCTAAT
66 TAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGAT
*
144801 GAGATATTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGG
131 GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGG
144866 ACCAAATTCGT
196 ACCAAATTCGT
* * * * * * *
144877 CTTCCTGATGAGATACAAAGAAGCGGATTGAAACAAACGACGCGGTCATTTTCTTGATGAGACAC
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAACGACACGGTCATCTTCCTGATGAGATAC
**
144942 -AGAGAAGATTACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGA
66 TA-AGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGA
* * *
145006 TGAGATACTGAGAAGCGGGTCGAAGTAATAAAATGGTTAGCTTTCTGATGAGATACGGAGAAGTG
130 TGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTG
* *
145071 AACCAAATCCGT
195 GACCAAATTCGT
* * ** * ** **
145083 CTTCCTGATGAAACACAGAGAAGTGGATCAAAACAAGTGATGCGGTCATCTTCCTGATGAGATAC
1 CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAACGACACGGTCATCTTCCTGATGAGATAC
* *
145148 TGAGAAGAAGGCCAAAT
66 TAAGAAGAAGACCAAAT
145165 GAATGAAACC
Statistics
Matches: 435, Mismatches: 55, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
204 1 0.00
205 32 0.07
206 402 0.92
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (206 bp):
CTTCCTGATGAGATACAGAGAAGCAGATCGAAACAAACGACACGGTCATCTTCCTGATGAGATAC
TAAGAAGAAGACCAAATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGAT
GAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGG
ACCAAATTCGT
Found at i:145079 original size:532 final size:527
Alignment explanation
Indices: 144042--145068 Score: 1502
Period size: 532 Copynumber: 1.9 Consensus size: 527
144032 CAATGCGAAC
* * * *
144042 AAATCTTTGAACCTCAGCTTCCTGATTAGATACTGAGAAGCAGGTTGAAGCAATAAAAAGGTTAG
1 AAATCTTCGAACCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAG
* * * * * *
144107 CTTTCTGATGAGACACTGAGAAGTGAACCAAATTTGTCTTTCTGATGAGGTACAGAGAAGCGGAT
66 CTTCCTGATGAGACACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGAT
* *** * * * *
144172 TGAAACAAATGGGGCGGTTATCTTCCTGATGAGATACAGAGAAGTATACCAACTCAGGGCTCGAT
131 TGAAACAAACGACACGGTTATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAGCGCTCGAT
* *
144237 GTGAGCAAATCTTCGAACCTCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGTAATAAAAT
196 GTGAGCAAATCTTCGAACCCCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
*
144302 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAA
261 GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAA
* * *
144367 GCGGATTGAAACAAACGACGTAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAAC
326 GCGGATTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCAAAC
* *
144432 CCACGCTCGAGGTGAGCAAATCTTCGAATCCCAACTTCCTGATGAGATACTGAGAAGTAGGTCGA
391 CCACGCTCGAGGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
* *
144497 AGCAATAAAATGGTCATCTTCTTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
456 AGCAATAAAATGGTCAGCTTCTTGATGAGATACGGAGAAGAAGACCAAATCAAACCCACGCTCGA
144562 TGTCAGA
521 TGTCAGA
* *
144569 AAATCTTCGAAACC-CAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAATATGGTTA
1 AAATCTTCG-AACCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTA
* *
144633 GCTTCCTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGA
65 GCTTCCTGATGAGACACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGA
* *
144698 TTGAAACAAACGACATGGTTATCTTCCTGATGAGATACTA-AGAAGAAGACCAAATCAAACCCTC
130 TTGAAACAAACGACACGGTTATCTTCCTGATGAGATAC-AGAGAAGAAGACCAAATC--A---GC
* * * * *
144762 GCTCGATGTGAGCAAATCTTTGAACCCCAGCTTCCTAATGAGATATTGAGAAGCAGGTCGAAGCA
189 GCTCGATGTGAGCAAATCTTCGAACCCCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGCA
* *
144827 ATAAAATGGTTAGCTTTCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGATA
254 ATAAAATGGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATA
* * * **
144892 CAAAGAAGCGGATTGAAACAAACGACGCGGTCATTTTCTTGATGAGACACAGAGAAGATTACCAA
319 CAAAGAAGCGGATTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAA
* *
144957 ATCAAACCCACGCTCGATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGC
384 ATCAAACCCACGCTCGAGGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGC
* * *
145022 GGGTCGAAGTAATAAAATGGTTAGCTT-TCTGATGAGATACGGAGAAG
449 AGGTCGAAGCAATAAAATGGTCAGCTTCT-TGATGAGATACGGAGAAG
145069 TGAACCAAAT
Statistics
Matches: 441, Mismatches: 51, Indels: 11
0.88 0.10 0.02
Matches are distributed among these distances:
527 156 0.35
528 5 0.01
529 1 0.00
531 1 0.00
532 278 0.63
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (527 bp):
AAATCTTCGAACCTCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAAAGGTTAG
CTTCCTGATGAGACACTAAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCAGAT
TGAAACAAACGACACGGTTATCTTCCTGATGAGATACAGAGAAGAAGACCAAATCAGCGCTCGAT
GTGAGCAAATCTTCGAACCCCAACTTCCTAATAAGACACTGAGAAGCAGGTCGAAGCAATAAAAT
GGTTAGCTTCCTGATGAGATACTGAGAAGTGGACCAAATTCGTCTTCCTAATGAGATACAAAGAA
GCGGATTGAAACAAACGACGCAGTCATCTTCCTGATGAGACACAGAGAAGAAGACCAAATCAAAC
CCACGCTCGAGGTGAGCAAATCTTCGAACCCCAACTTCCTGATGAGATACTGAGAAGCAGGTCGA
AGCAATAAAATGGTCAGCTTCTTGATGAGATACGGAGAAGAAGACCAAATCAAACCCACGCTCGA
TGTCAGA
Found at i:145476 original size:6 final size:6
Alignment explanation
Indices: 145456--145536 Score: 71
Period size: 6 Copynumber: 14.0 Consensus size: 6
145446 CCGGGCCCCT
* * * *
145456 TTTAAA -TTAAT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
145502 -TTAAT TTTAAA TTTAAA TTT-AT TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
145537 AAAATTATTA
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
5 15 0.26
6 39 0.67
7 4 0.07
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:145488 original size:23 final size:23
Alignment explanation
Indices: 145462--145522 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
145452 CCCTTTTAAA
* * *
145462 TTAATTTTAAATTTAGATTTATT
1 TTAAATTTAAATTTAAATTAATT
*
145485 TTAAATTTGAATTTAAATTAATT
1 TTAAATTTAAATTTAAATTAATT
145508 TTAAATTTAAATTTA
1 TTAAATTTAAATTTA
145523 TTTTCAAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (23 bp):
TTAAATTTAAATTTAAATTAATT
Found at i:145500 original size:40 final size:41
Alignment explanation
Indices: 145456--145533 Score: 140
Period size: 40 Copynumber: 1.9 Consensus size: 41
145446 CCGGGCCCCT
*
145456 TTTAAATTAATTTTAAATTTAGATTTATTTT-AAATTTGAA
1 TTTAAATTAATTTTAAATTTAAATTTATTTTCAAATTTGAA
145496 TTTAAATTAATTTTAAATTTAAATTTATTTTCAAATTT
1 TTTAAATTAATTTTAAATTTAAATTTATTTTCAAATTT
145534 AAAAAAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 30 0.83
41 6 0.17
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (41 bp):
TTTAAATTAATTTTAAATTTAAATTTATTTTCAAATTTGAA
Found at i:145533 original size:18 final size:17
Alignment explanation
Indices: 145456--145536 Score: 72
Period size: 17 Copynumber: 4.4 Consensus size: 17
145446 CCGGGCCCCT
145456 TTTAAATTAATTTTAAA
1 TTTAAATTAATTTTAAA
* *
145473 TTTAGATTTATTTTAAATTTGAA
1 TTTA-A---A--TTAATTTTAAA
145496 TTTAAATTAATTTTAAA
1 TTTAAATTAATTTTAAA
*
145513 TTTAAATTTATTTTCAAA
1 TTTAAATTAATTTT-AAA
145531 TTTAAA
1 TTTAAA
145537 AAAATTATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
17 26 0.50
18 10 0.19
19 1 0.02
21 1 0.02
22 1 0.02
23 13 0.25
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:145565 original size:14 final size:15
Alignment explanation
Indices: 145548--145576 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
145538 AAATTATTAT
145548 AAAGTCC-AATTACA
1 AAAGTCCAAATTACA
145562 AAAGTCCAAATTACA
1 AAAGTCCAAATTACA
145577 TGTCCAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (15 bp):
AAAGTCCAAATTACA
Found at i:147122 original size:29 final size:30
Alignment explanation
Indices: 147078--147182 Score: 112
Period size: 30 Copynumber: 3.6 Consensus size: 30
147068 CCCTAAATTA
147078 TCTAAAAATTCCATTTTTTA-CC-AAAACT
1 TCTAAAAATTCCATTTTTTACCCTAAAACT
**
147106 TCTAAAAATTACCA--TTTTACCCTCGAACT
1 TCTAAAAATT-CCATTTTTTACCCTAAAACT
* *
147135 TCCAAAAATTCCATTTTTAACCCTAAAACT
1 TCTAAAAATTCCATTTTTTACCCTAAAACT
147165 T-TCAAAAATTACCATTTT
1 TCT-AAAAATT-CCATTTT
147183 CCCCTCAGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
27 5 0.08
28 15 0.24
29 16 0.25
30 20 0.32
31 7 0.11
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (30 bp):
TCTAAAAATTCCATTTTTTACCCTAAAACT
Found at i:147165 original size:30 final size:30
Alignment explanation
Indices: 147081--147182 Score: 115
Period size: 29 Copynumber: 3.5 Consensus size: 30
147071 TAAATTATCT
*
147081 AAAAATT-CCATTTTTTA-CC-AAAACTTCT
1 AAAAATTACCA-TTTTTACCCTAAAACTTCC
**
147109 AAAAATTACCA-TTTTACCCTCGAACTTCC
1 AAAAATTACCATTTTTACCCTAAAACTTCC
*
147138 AAAAATT-CCATTTTTAACCCTAAAACTTTC
1 AAAAATTACCATTTTT-ACCCTAAAACTTCC
147168 AAAAATTACCATTTT
1 AAAAATTACCATTTT
147183 CCCCTCAGAT
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
27 5 0.08
28 12 0.19
29 20 0.32
30 18 0.29
31 7 0.11
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAAATTACCATTTTTACCCTAAAACTTCC
Found at i:147248 original size:90 final size:90
Alignment explanation
Indices: 147138--147331 Score: 381
Period size: 90 Copynumber: 2.2 Consensus size: 90
147128 TCGAACTTCC
147138 AAAAATT-CCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTCCCCTCAGATGTTTGAAAA
1 AAAAATTACCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTCCCCTCAGATGTTTGAAAA
147202 TTCCTTTTTTGATCCCGATTTTTCT
66 TTCCTTTTTTGATCCCGATTTTTCT
147227 AAAAATTACCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTCCCCTCAGATGTTTGAAAA
1 AAAAATTACCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTCCCCTCAGATGTTTGAAAA
147292 TTCCTTTTTTGATCCCGATTTTTCT
66 TTCCTTTTTTGATCCCGATTTTTCT
147317 AAAAATTACCATTTT
1 AAAAATTACCATTTT
147332 ACCCTTGAAT
Statistics
Matches: 104, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
89 7 0.07
90 97 0.93
ACGTcount: A:0.32, C:0.22, G:0.05, T:0.41
Consensus pattern (90 bp):
AAAAATTACCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTCCCCTCAGATGTTTGAAAA
TTCCTTTTTTGATCCCGATTTTTCT
Found at i:147321 original size:59 final size:58
Alignment explanation
Indices: 147254--147453 Score: 169
Period size: 59 Copynumber: 3.4 Consensus size: 58
147244 ACCCTAAAAC
*
147254 TTTC-AAAAATTACCATTTTCCCCTCAGATGTTTGAAAATTCCTTTTTTGATCCCGATT
1 TTTCTAAAAATTACCATTTTCCCCTCAGATGTCT-AAAATTCCTTTTTTGATCCCGATT
* * * * *
147312 TTTCTAAAAATTACCATTTTACCCT-TGAATATCCAAAAATT-CTGTTTTTGATCTCGATTT
1 TTTCTAAAAATTACCATTTTCCCCTCAG-ATGT-CTAAAATTCCT-TTTTTGATCCCGA-TT
* * * **
147372 TTTCT-AAAATTACCATTTTACCCC-CGGATGTCTAAAATTCCCTTTTT-AACCTCGAAC
1 TTTCTAAAAATTACCATTTT-CCCCTCAGATGTCTAAAATTCCTTTTTTGATCC-CGATT
**
147429 TTTCCCAAAATTACCATTTTTCCCC
1 TTTCTAAAAATTACCA-TTTTCCCC
147454 CTGAGAGTCC
Statistics
Matches: 115, Mismatches: 16, Indels: 22
0.75 0.10 0.14
Matches are distributed among these distances:
57 6 0.05
58 36 0.31
59 62 0.54
60 11 0.10
ACGTcount: A:0.28, C:0.24, G:0.07, T:0.41
Consensus pattern (58 bp):
TTTCTAAAAATTACCATTTTCCCCTCAGATGTCTAAAATTCCTTTTTTGATCCCGATT
Found at i:147882 original size:96 final size:97
Alignment explanation
Indices: 147716--147908 Score: 277
Period size: 96 Copynumber: 2.0 Consensus size: 97
147706 AAAAATTTAA
* *
147716 AATCGAGGCAATATTCTTTCATTTCGAGTTTCGAAAATTTTGTGCCTTAACTTACTAGGTGCAAT
1 AATCGAGGCAATATTCTTTCATTTCGAGTTTCGAAAATTTTGCGCCTTAACTTACTAGGTGCAAC
* *
147781 TTTTCTTCAAATCGAAATAATCGAATACCTTT
66 CTTTCTTCAAATCGAAATAATCAAATACCTTT
*
147813 AATCGAGGCAATATT-TTATTATCTTCGA--TTCTGAAAA-TTTGCGCCTTAACTTACTAGGTGC
1 AATCGAGGCAATATTCTT-TCAT-TTCGAGTTTC-GAAAATTTTGCGCCTTAACTTACTAGGTGC
*
147874 AACCTTTCTTCAAATCGAAATAATCAAATATCTTT
63 AACCTTTCTTCAAATCGAAATAATCAAATACCTTT
147909 TTCCAAAATT
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
96 59 0.68
97 23 0.26
98 5 0.06
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (97 bp):
AATCGAGGCAATATTCTTTCATTTCGAGTTTCGAAAATTTTGCGCCTTAACTTACTAGGTGCAAC
CTTTCTTCAAATCGAAATAATCAAATACCTTT
Found at i:151958 original size:140 final size:147
Alignment explanation
Indices: 151674--151963 Score: 355
Period size: 149 Copynumber: 2.0 Consensus size: 147
151664 GTTATATATA
* *
151674 TATATATGAGAAGGGGATCTACTTATATTACTGTAAAACTTAAGTGATTTTAAACATTTCCGTAA
1 TATATATGAGAAGGGGATCTACTTATATCACTATAAAACTTAAGTGATTTTAAACATTTCCGTAA
* *
151739 CCTTTTACATAAATTATATTTTAACACTCCAACAGTCAAGTACTTAAGTTTCATATTTCATTCAT
66 CCTTTTACATAAATTATATTCTAACACTCCAACAG-CAAGTAC-TAAGTTTCATACTTCATTCAT
* *
151804 GTAGATTATGCATGTCAAG
129 GTAAATCATGCATGTCAAG
* * *
151823 TATATATGAG-GGAGGGATCTACTTATATCACTATAAAACTTAAGTGGTTTTACACATTT-CGTA
1 TATATATGAGAAG-GGGATCTACTTATATCACTATAAAACTTAAGTGATTTTAAACATTTCCGTA
* * * * *
151886 ACTTTTTACA-CAATTAATATTCTAACAGT-CTA-A-C-AGT-C-AAGTTTCGTACTTCATTCAT
65 ACCTTTTACATAAATT-ATATTCTAACACTCCAACAGCAAGTACTAAGTTTCATACTTCATTCAT
151944 GTAAATCATGCATGTCAAG
129 GTAAATCATGCATGTCAAG
151963 T
1 T
151964 TTAGTATAAA
Statistics
Matches: 125, Mismatches: 14, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
140 36 0.29
142 1 0.01
143 3 0.02
144 1 0.01
146 1 0.01
147 6 0.05
148 25 0.20
149 52 0.42
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (147 bp):
TATATATGAGAAGGGGATCTACTTATATCACTATAAAACTTAAGTGATTTTAAACATTTCCGTAA
CCTTTTACATAAATTATATTCTAACACTCCAACAGCAAGTACTAAGTTTCATACTTCATTCATGT
AAATCATGCATGTCAAG
Found at i:156232 original size:31 final size:30
Alignment explanation
Indices: 156146--156232 Score: 156
Period size: 30 Copynumber: 2.9 Consensus size: 30
156136 ACTTACAACC
156146 TAGTGACTTAAATCAAAATTTTGAATTGTT
1 TAGTGACTTAAATCAAAATTTTGAATTGTT
156176 TAGTGACTTAAATCAAAATTTTGAATTGTT
1 TAGTGACTTAAATCAAAATTTTGAATTGTT
*
156206 TAGTGACTTAAATAAAAACTTTTGAAT
1 TAGTGACTTAAATCAAAA-TTTTGAAT
156233 AGTTCAATGA
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
30 47 0.85
31 8 0.15
ACGTcount: A:0.39, C:0.07, G:0.13, T:0.41
Consensus pattern (30 bp):
TAGTGACTTAAATCAAAATTTTGAATTGTT
Found at i:159046 original size:22 final size:23
Alignment explanation
Indices: 159021--159063 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
159011 TTGTATTATG
*
159021 AAATTTATAACA-ATTAAAAATT
1 AAATCTATAACACATTAAAAATT
*
159043 AAATCTATAGCACATTAAAAA
1 AAATCTATAACACATTAAAAA
159064 AAATTAAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATCTATAACACATTAAAAATT
Found at i:163655 original size:2 final size:2
Alignment explanation
Indices: 163648--163678 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
163638 TACCTTTCAT
163648 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 G
163679 TTTCAAACCC
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:165542 original size:5 final size:5
Alignment explanation
Indices: 165532--165569 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
165522 AACCCTCTTC
165532 GTGTT GTGTT GTG-T -TGTT GTGTT GTGTT GTGTT GTGTT
1 GTGTT GTGTT GTGTT GTGTT GTGTT GTGTT GTGTT GTGTT
165570 TTAGTTGTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 27 0.87
ACGTcount: A:0.00, C:0.00, G:0.39, T:0.61
Consensus pattern (5 bp):
GTGTT
Found at i:165551 original size:13 final size:13
Alignment explanation
Indices: 165533--165561 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
165523 ACCCTCTTCG
165533 TGTTGTGTTGTGT
1 TGTTGTGTTGTGT
165546 TGTTGTGTTGTGT
1 TGTTGTGTTGTGT
165559 TGT
1 TGT
165562 GTTGTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (13 bp):
TGTTGTGTTGTGT
Found at i:165555 original size:18 final size:18
Alignment explanation
Indices: 165532--165566 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
165522 AACCCTCTTC
165532 GTGTTGTGTTGTGTTGTT
1 GTGTTGTGTTGTGTTGTT
165550 GTGTTGTGTTGTGTTGT
1 GTGTTGTGTTGTGTTGT
165567 GTTTTAGTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (18 bp):
GTGTTGTGTTGTGTTGTT
Found at i:165675 original size:14 final size:14
Alignment explanation
Indices: 165656--165683 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
165646 GCAGTCATGC
165656 CTTGAAGACTCCAT
1 CTTGAAGACTCCAT
165670 CTTGAAGACTCCAT
1 CTTGAAGACTCCAT
165684 TTTGCTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (14 bp):
CTTGAAGACTCCAT
Found at i:171401 original size:48 final size:48
Alignment explanation
Indices: 171344--171447 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
171334 TCGGATGGGT
*
171344 GAACGAGATCTACGATGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
1 GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
171392 GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
1 GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
171440 GAACGAGA
1 GAACGAGA
171448 CTGAGATCTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.31, C:0.21, G:0.34, T:0.14
Consensus pattern (48 bp):
GAACGAGATCTACGACGCACAGGTGTAGGTGACCTGCGCCGATAAGGA
Found at i:174824 original size:29 final size:29
Alignment explanation
Indices: 174791--174849 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
174781 TTTAATCGAG
174791 TATAATTTTAAACTCTCATCAAAATTCAT
1 TATAATTTTAAACTCTCATCAAAATTCAT
174820 TATAATTTTAAACTCTCATCAAAATTCAT
1 TATAATTTTAAACTCTCATCAAAATTCAT
174849 T
1 T
174850 TTTCGAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (29 bp):
TATAATTTTAAACTCTCATCAAAATTCAT
Found at i:180686 original size:196 final size:196
Alignment explanation
Indices: 180254--181306 Score: 1136
Period size: 196 Copynumber: 5.3 Consensus size: 196
180244 AATGTTTATG
* * * *
180254 GGTAGTTTTTAAGCTATGAGAAGCTAATGTAGAACCACATTGTGCATTTTGATATTTGACTTTAT
1 GGTAATTTCTAAGCTATGAGAA-CTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTAT
* * * *
180319 AGTTTTTGACCTTCATTGCTAGTTAGCTGTG-TACAGGGACTTGGGTGTGTGCGTTGAATAGCAT
65 AG-TTTTGACCTTCATTGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
* *
180383 ATATGTCTGATATGCATTAGATATGGGTACTTAAAGAAAAATGAGGAGT-CAAGCAATATAGCTA
129 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
180447 GTT
194 GTT
* * * *
180450 GGTAATTTCTAATCTATAAGAATCTAATGGAGAACCACATTGTGCATTTTGACATTTGAATTTAT
1 GGTAATTTCTAAGCTATGAGAA-CTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTAT
* * * *
180515 ACTTCTTGGCCTTCATTGCTAGTTAGCGGTGTTACCGGGACTTGGGTGTGAGCTTTGGATAGCCT
65 AGTT-TTGACCTTCATTGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
* *
180580 ATATGTCTGATGTGCATTAGATATGGGTACTTCAAGAAAAAT-AGGAGTCCGAGCAGTATAGCTA
129 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
*
180644 GTA
194 GTT
* * * * *
180647 AGTAATTTATAAGCTATGAGAACTAATGAAAAACCACATTGTGCATTTTGATACTTGACTTTATA
1 GGTAATTTCTAAGCTATGAGAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATA
* * * * *
180712 GTTTTTGACCTTCAATGCTAGTTAGTTGTGTTACTGGGACTTGGGTGTGAGTGTTGGGTAGCCTA
66 G-TTTTGACCTTCATTGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT-
* * * *
180777 CATGTCTAATAGGCACTAGATATGGATGTTAGATAAGGGTACTTCAAGAAAAATGAGGAGTCTGA
129 -A----T-AT--G-TCT-GATATGCA--TTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGA
180842 GCAATATAGCTAGTT
182 GCAATATAGCTAGTT
* * * * * *
180857 GGTAATTTCGAAGCTATGAGAAACTAAT---GAACCACATTGTGCATTTTGATAATGGGATCTGT
1 GGTAATTTCTAAGCTATGAG-AACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTAT
* * * * * * *
180919 AGTTTTCAGTCTTTAGTGCTAGTTAACTGTGTTACCGGGACTTGGTTGTTAGCGTTGGATAGCCT
65 AGTTTTGA-CCTTCATTGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
* * * * **
180984 ATATGTCTAATATGCATCATATATGGGTACTTAAAGAAAAATGAGGAGTTTGAGCAATATAGCTA
129 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
181049 GTT
194 GTT
* * *
181052 GGTAATCTCTAAGCTATGAAAACTAATGAAGAACCACATTGTGCATTTTGGTATTTGAATTTATA
1 GGTAATTTCTAAGCTATGAGAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATA
* *
181117 GGTTTTGACCTTCATTGCTA--TAG-TCATGTTACTGGGACTTGGGTGTGA-CGTTGGATAGCCT
66 -GTTTTGACCTTCATTGCTAGTTAGCT-GTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCT
* * ** * ** * ** **
181178 CTAAGTCCAATATGCATTAGATGTTTGTACTTCAAGAAAAATGAGGAGTCCAAATAATATAGCCG
129 ATATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTA
181243 GTT
194 GTT
* * * * * *
181246 GGTAATTTCTAAGCTATGGGAAATTAATGAATAACCACATTTTGCATTCTGCTATTTGAAT
1 GGTAATTTCTAAGCTATGAG-AACTAATGAAGAACCACATTGTGCATTTTGATATTTGAAT
181307 GACATTCAAT
Statistics
Matches: 714, Mismatches: 117, Indels: 53
0.81 0.13 0.06
Matches are distributed among these distances:
194 90 0.13
195 122 0.17
196 178 0.25
197 147 0.21
198 9 0.01
199 1 0.00
201 2 0.00
202 2 0.00
203 2 0.00
205 1 0.00
206 3 0.00
207 11 0.02
208 75 0.11
209 25 0.04
210 39 0.05
211 7 0.01
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (196 bp):
GGTAATTTCTAAGCTATGAGAACTAATGAAGAACCACATTGTGCATTTTGATATTTGAATTTATA
GTTTTGACCTTCATTGCTAGTTAGCTGTGTTACCGGGACTTGGGTGTGAGCGTTGGATAGCCTAT
ATGTCTGATATGCATTAGATATGGGTACTTCAAGAAAAATGAGGAGTCCGAGCAATATAGCTAGT
T
Found at i:184470 original size:25 final size:25
Alignment explanation
Indices: 184431--184485 Score: 94
Period size: 25 Copynumber: 2.2 Consensus size: 25
184421 TAACTTTTAA
*
184431 TATT-AAGTGATTAAAATGTTAATT
1 TATTAAAGTGACTAAAATGTTAATT
184455 TATTAAAGTGACTAAAATGTTAATT
1 TATTAAAGTGACTAAAATGTTAATT
184480 TATTAA
1 TATTAA
184486 TAGTTTAGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.44, C:0.02, G:0.11, T:0.44
Consensus pattern (25 bp):
TATTAAAGTGACTAAAATGTTAATT
Found at i:184592 original size:14 final size:14
Alignment explanation
Indices: 184568--184602 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
184558 TATAATTGTA
*
184568 AAATTTAAATATTT
1 AAATTTGAATATTT
*
184582 GAATTTGAATATTT
1 AAATTTGAATATTT
184596 AAATTTG
1 AAATTTG
184603 CCTAATTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (14 bp):
AAATTTGAATATTT
Found at i:200581 original size:21 final size:21
Alignment explanation
Indices: 200555--200599 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
200545 TTGAAATATT
200555 TTTTTAATTATCATT-TTTGAA
1 TTTTTAATTAT-ATTATTTGAA
* *
200576 TTTTTATTTATATTATTTTAA
1 TTTTTAATTATATTATTTGAA
200597 TTT
1 TTT
200600 CTTTACTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTTTAATTATATTATTTGAA
Found at i:200762 original size:18 final size:18
Alignment explanation
Indices: 200728--200760 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
200718 AAATTTCACT
200728 ATTTATAAATTTATTTTG
1 ATTTATAAATTTATTTTG
200746 ATTT-TAAA-TTATTTT
1 ATTTATAAATTTATTTT
200761 TTATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 4 0.27
18 4 0.27
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTATAAATTTATTTTG
Found at i:205579 original size:6 final size:6
Alignment explanation
Indices: 205562--205592 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
205552 TGAATAATGA
*
205562 AAAGAG AGAGAG AAAGAG AAAGAG AAAGAG A
1 AAAGAG AAAGAG AAAGAG AAAGAG AAAGAG A
205593 GATAGTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:206189 original size:12 final size:12
Alignment explanation
Indices: 206172--206196 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
206162 CAAATATGGT
206172 CACCTAATGAAC
1 CACCTAATGAAC
206184 CACCTAATGAAC
1 CACCTAATGAAC
206196 C
1 C
206197 CATAAATGGT
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:0.40, C:0.36, G:0.08, T:0.16
Consensus pattern (12 bp):
CACCTAATGAAC
Found at i:206645 original size:25 final size:24
Alignment explanation
Indices: 206600--206646 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
206590 TCTAGCAAAA
*
206600 TTTTAATTTTTTTAACTTTTTTTT
1 TTTTAATTTTTTTAACATTTTTTT
206624 TTTTACATTTTTTTAGA-ATTTTT
1 TTTTA-ATTTTTTTA-ACATTTTT
206647 ATAAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 5 0.25
25 14 0.70
26 1 0.05
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTTAATTTTTTTAACATTTTTTT
Found at i:212902 original size:73 final size:73
Alignment explanation
Indices: 212658--212905 Score: 216
Period size: 73 Copynumber: 3.3 Consensus size: 73
212648 TGCATTGAAC
* *
212658 TTTTCCATT-TCATTTTCCTTCAGTCTTTCGTTGAAGCCAAACAGAGCAAGCACATATATATAGC
1 TTTTCC-TTCTCATTTTCCTTCACTCCTTCGTTGAAGCCAAACAGAGCAAGCACATATATAT--C
*
212722 ATGAATCGACA
63 ATGTATCGACA
* ** * * *
212733 TTTTCCTTCTCTTTTTCCTTTTC-CTTCACTTTCGTCAAAGCCAAACCGAGCAAGAAACACACAC
1 TTTTCCTTCTCATTTTCC--TTCAC-TC-C-TTCGTTGAAGCCAAACAGAGCAAG---CACATAT
* *
212797 ATATCAT-TCATTGACG
58 ATATCATGT-ATCGACA
* * *
212813 TTTTACATT-TCATTTTCCTTCACTCCGTCGTTGAAGCCTAACAGAGCAAGCACATATATATCAT
1 TTTT-CCTTCTCATTTTCCTTCACTCCTTCGTTGAAGCCAAACAGAGCAAGCACATATATATCAT
212877 GTATCGACA
65 GTATCGACA
*
212886 TTTTCCTTCTCCTTTTCCTT
1 TTTTCCTTCTCATTTTCCTT
212906 TTCCTTCACT
Statistics
Matches: 135, Mismatches: 24, Indels: 30
0.71 0.13 0.16
Matches are distributed among these distances:
72 3 0.02
73 31 0.23
74 3 0.02
75 14 0.10
76 19 0.14
77 6 0.04
78 5 0.04
79 22 0.16
80 20 0.15
81 3 0.02
82 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.10, T:0.37
Consensus pattern (73 bp):
TTTTCCTTCTCATTTTCCTTCACTCCTTCGTTGAAGCCAAACAGAGCAAGCACATATATATCATG
TATCGACA
Found at i:212923 original size:79 final size:77
Alignment explanation
Indices: 212665--212950 Score: 237
Period size: 79 Copynumber: 3.7 Consensus size: 77
212655 AACTTTTCCA
* *
212665 TTTCATTTTCCTTCAGTCTTTCGTTGAAGCCAAACAGAGCAAGCACATATATATAGCATGAATCG
1 TTTCATTTTCCTTCA--CTTTCGTTAAAGCCAAACAGAGCAAGCACATATATAT--CATGTATCG
*
212730 ACATTTTCCTTCTCTT
62 ACATTTTCCTTCTCCT
* * * * * *
212746 TTTCCTTTTCCTTCACTTTCGTCAAAGCCAAACCGAGCAAGAAACACACACATATCAT-TCATTG
1 TTTCATTTTCCTTCACTTTCGTTAAAGCCAAACAGAGCAAG---CACATATATATCATGT-ATCG
* * *
212810 AC---GT--TT-TACA
62 ACATTTTCCTTCTCCT
* * *
212820 TTTCATTTTCCTTCACTCCGTCGTTGAAGCCTAACAGAGCAAGCACATATATATCATGTATCGAC
1 TTTCATTTTCCTTCACT--TTCGTTAAAGCCAAACAGAGCAAGCACATATATATCATGTATCGAC
212885 ATTTTCCTTCTCCT
64 ATTTTCCTTCTCCT
* * * *
212899 TTTCCTTTTCCTTCACTTTCTCGTTAAAGTCAAACAGAGTAAGC-TATATATA
1 TTTCATTTTCCTTCAC-TT-TCGTTAAAGCCAAACAGAGCAAGCACATATATA
212951 ACACGTTAAA
Statistics
Matches: 159, Mismatches: 31, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
73 17 0.11
74 18 0.11
75 2 0.01
76 20 0.13
77 1 0.01
78 9 0.06
79 60 0.38
80 9 0.06
81 14 0.09
82 9 0.06
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.36
Consensus pattern (77 bp):
TTTCATTTTCCTTCACTTTCGTTAAAGCCAAACAGAGCAAGCACATATATATCATGTATCGACAT
TTTCCTTCTCCT
Found at i:214245 original size:30 final size:29
Alignment explanation
Indices: 214205--214281 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 29
214195 GTCTGATAAT
*
214205 AAATTTCAAAAACTTTAAGG-GCCTAATTA
1 AAATTTCAAAAACTTTAAGGTGAC-AATTA
* *
214234 AAATATTCAAAAAAGTTTAAGGTTACAATTA
1 AAAT-TTC-AAAAACTTTAAGGTGACAATTA
*
214265 AAATTTTTAAAAACTTT
1 AAA-TTTCAAAAACTTT
214282 TGGGAGGCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 4 0.10
30 11 0.28
31 22 0.56
32 2 0.05
ACGTcount: A:0.48, C:0.09, G:0.08, T:0.35
Consensus pattern (29 bp):
AAATTTCAAAAACTTTAAGGTGACAATTA
Found at i:224974 original size:14 final size:15
Alignment explanation
Indices: 224954--224987 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
224944 TCTGTCCAAA
*
224954 AAAAAAACTTTCGAT
1 AAAAAAACTTCCGAT
224969 AAAAAAACTTCCGAT
1 AAAAAAACTTCCGAT
224984 AAAA
1 AAAA
224988 GTAGATGGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.59, C:0.15, G:0.06, T:0.21
Consensus pattern (15 bp):
AAAAAAACTTCCGAT
Found at i:229400 original size:24 final size:25
Alignment explanation
Indices: 229368--229414 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
229358 ATTAAACATC
229368 AAAACTAAATTCAAGTACCAAATTG
1 AAAACTAAATTCAAGTACCAAATTG
*
229393 AAAA-TAAATTCATGTACCAAAT
1 AAAACTAAATTCAAGTACCAAAT
229415 GGTATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (25 bp):
AAAACTAAATTCAAGTACCAAATTG
Found at i:231876 original size:19 final size:19
Alignment explanation
Indices: 231852--231888 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
231842 TTTTTAAAAA
*
231852 ATTAAATTAAAATTTTATC
1 ATTAAAATAAAATTTTATC
*
231871 ATTAAAATATAATTTTAT
1 ATTAAAATAAAATTTTAT
231889 TATTTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTAAAATAAAATTTTATC
Found at i:235317 original size:17 final size:17
Alignment explanation
Indices: 235295--235328 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
235285 GATGATAAAT
235295 TTAATTATTTAATTTTA
1 TTAATTATTTAATTTTA
* *
235312 TTAATTTTTTTATTTTA
1 TTAATTATTTAATTTTA
235329 AAAAAATTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTAATTATTTAATTTTA
Found at i:236531 original size:31 final size:31
Alignment explanation
Indices: 236496--236560 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
236486 TTGGAAAAAC
* * **
236496 TCAGATACCAATTTGAATATTGAAGTCAAAT
1 TCAGATACCAAATTGAACATTGAAACCAAAT
*
236527 TCAGATATCAAATTGAACATTGAAACCAAAT
1 TCAGATACCAAATTGAACATTGAAACCAAAT
236558 TCA
1 TCA
236561 AGCACTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.29
Consensus pattern (31 bp):
TCAGATACCAAATTGAACATTGAAACCAAAT
Found at i:240738 original size:26 final size:26
Alignment explanation
Indices: 240706--240760 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
240696 ACTATTATAA
240706 AAATTAAAATTTAATTTCAACCATCG
1 AAATTAAAATTTAATTTCAACCATCG
* * *
240732 AAATTAAAATTTGATTTCGACCCTCG
1 AAATTAAAATTTAATTTCAACCATCG
240758 AAA
1 AAA
240761 AACTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (26 bp):
AAATTAAAATTTAATTTCAACCATCG
Found at i:247519 original size:30 final size:31
Alignment explanation
Indices: 247476--247536 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
247466 ATTCAAAATT
247476 TAAAATAAAAAAATCATCAAAATTAT-ATTAA
1 TAAAATAAAAAAATCATCAAAA-TATCATTAA
* *
247507 TAAAAT-AAAAAATTATTAAAATATCATTAA
1 TAAAATAAAAAAATCATCAAAATATCATTAA
247537 ATAATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 3 0.11
30 18 0.67
31 6 0.22
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (31 bp):
TAAAATAAAAAAATCATCAAAATATCATTAA
Found at i:250109 original size:6 final size:6
Alignment explanation
Indices: 250098--250134 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
250088 TTGAGCCGAA
250098 TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC T
1 TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC TTGAGC T
250135 CAATCAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.16, G:0.32, T:0.35
Consensus pattern (6 bp):
TTGAGC
Found at i:255641 original size:54 final size:54
Alignment explanation
Indices: 255575--255685 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
255565 TTACAATAAT
* *
255575 AACAAACTTAAACTCATTTGTGATAAAATTTATACAGAAATAAAATACAAATAC
1 AACAAACGTAAACTCATTTGTGATAAAATTTACACAGAAATAAAATACAAATAC
* *
255629 AACAAACGTAAACTCATTTGTGATAAAATTTACACGGAAATAAAATATAAATAC
1 AACAAACGTAAACTCATTTGTGATAAAATTTACACAGAAATAAAATACAAATAC
255683 AAC
1 AAC
255686 CTAAATGATT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.26
Consensus pattern (54 bp):
AACAAACGTAAACTCATTTGTGATAAAATTTACACAGAAATAAAATACAAATAC
Found at i:256365 original size:18 final size:16
Alignment explanation
Indices: 256342--256377 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
256332 AGTTTAAAAT
256342 TTTAATTAATTAAATTTA
1 TTTAATTAA--AAATTTA
256360 TTTAATTAAAAATTTA
1 TTTAATTAAAAATTTA
256376 TT
1 TT
256378 ATCATTCCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTAATTAAAAATTTA
Found at i:260229 original size:177 final size:174
Alignment explanation
Indices: 259707--260570 Score: 886
Period size: 176 Copynumber: 4.9 Consensus size: 174
259697 TAATCATTAA
* * * * *
259707 ATCAATTAAACAGATA-ACAGATACATACAATCCCCTACAAAATTATCACAATGCTTAGCAAAAC
1 ATCAATTAAACTGAGAGACA-ATACATACAAT--TCTACAAAATTATCACAATGCTAAGCAAAAT
* * * * * * * *
259771 CATATCGAAAACCAACAATTTATGACGTTATATAATAAAAATG-GAATATGAAGTTTTCATCTGT
63 CAGATCGAAAATCATCAATTTATGATGTTATATAAT-AAAACGAGAATCTGAAATTTTCATCTAT
* * * * * *
259835 TGTCATATTTGTTTCTTATACATCCTCAGGAACCAAACAGTAGATAAAGG
127 TGTCTTCTTT-TTTC-TATATATTCTCAGGAACCAAACAGTAGCTAAACG
** *
259885 AT-AGATTAAACTGAGAGTGAATACATACAATTCCTACAAGATTATCACAATGCTAAGCAAAATC
1 ATCA-ATTAAACTGAGAGACAATACATACAATT-CTACAAAATTATCACAATGCTAAGCAAAATC
* * * ** * *
259949 AGATCGAAAATCAT-AATTCAT-A--CTAAATAATAAAACGTCAATCTGAAAGTTTAATCTATTG
64 AGATCGAAAATCATCAATTTATGATGTTATATAATAAAACGAGAATCTGAAATTTTCATCTATTG
* * *
260010 TCTTCTTCTTTCATATGTATTCTCAGAAACCAAACAGTAGCTAAACG
129 TCTTCTTTTTTC-TATATATTCTCAGGAACCAAACAGTAGCTAAACG
*
260057 ATCAATTAAACTGAGAGACAATACATACAATTCTGACAAAAGTATCACAATGCTAAGCAAAATCA
1 ATCAATTAAACTGAGAGACAATACATACAATTCT-ACAAAATTATCACAATGCTAAGCAAAATCA
* * * * *
260122 GATACGAAGATCATCAATCTATGATGTTATATAATAAAATGTGAATCTGAAATTTCCATCTATTG
65 GAT-CGAAAATCATCAATTTATGATGTTATATAATAAAACGAGAATCTGAAATTTTCATCTATTG
* **
260187 TCCTTTTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAATT
129 T-CTTCTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAACG
* * * * * *
260234 ATCAATTAAACTGAGAG-CGGATACATACAATTCCAACAAAATTATCACAATTCCAAACAAAAGC
1 ATCAATTAAACTGAGAGAC-AATACATACAATT-CTACAAAATTATCACAATGCTAAGCAAAATC
** * * * * *
260298 AGATCGAAAAGAATCAATGTATGATGTCATATAATAAAACAAGAATCTGAAATTTTCATATATAG
64 AGATCGAAAATCATCAATTTATGATGTTATATAATAAAACGAGAATCTGAAATTTTCATCTATTG
* * *
260363 TCTTCTTTTTTCCAGTATACTCTCAAGAACCAAACAGTAGCTAAACG
129 TCTTCTTTTTTCTA-TATATTCTCAGGAACCAAACAGTAGCTAAACG
* * * * * *
260410 ATCAATTAAACTGAGA-ACGGAGACGTACATTTCCTACAAACTTATCGCAATGCTAAGCAAAATC
1 ATCAATTAAACTGAGAGAC-AATACATACAATT-CTACAAAATTATCACAATGCTAAGCAAAATC
* * *
260474 AGATCGAAAATCATCAATTTATGATGTTATAAAATAAAACAAGAATCTGCAATTTTCATCTA--G
64 AGATCGAAAATCATCAATTTATGATGTTATATAATAAAACGAGAATCTGAAATTTTCATCTATTG
* *
260537 TCTTCTTTTTCCAATATATTCTCAGGAACCAAAC
129 TCTTCTTTTTTCTATATATTCTCAGGAACCAAAC
260571 GATCGATTAA
Statistics
Matches: 574, Mismatches: 96, Indels: 37
0.81 0.14 0.05
Matches are distributed among these distances:
171 2 0.00
172 96 0.17
173 57 0.10
174 18 0.03
175 13 0.02
176 194 0.34
177 160 0.28
178 33 0.06
179 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (174 bp):
ATCAATTAAACTGAGAGACAATACATACAATTCTACAAAATTATCACAATGCTAAGCAAAATCAG
ATCGAAAATCATCAATTTATGATGTTATATAATAAAACGAGAATCTGAAATTTTCATCTATTGTC
TTCTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAACG
Found at i:260565 original size:349 final size:341
Alignment explanation
Indices: 259707--260570 Score: 905
Period size: 349 Copynumber: 2.5 Consensus size: 341
259697 TAATCATTAA
* * * * * *
259707 ATCAATTAAACAGATA-ACAGATACATACAATCCCCTACAAAATTATCACAATGCTTAGCAAAAC
1 ATCAATTAAACTGAGAGACA-AGACATACAAT-TCCTACAAAATTATCACAATGCTAAGCAAAAT
* * * * * * *
259771 CATATCGAAAACCAACAATTTATGACGTTATATAATAAAAATGGAATATGAAGTTTTCATCTGTT
64 CAGATCGAAAATCATCAATTTATGATGTTATATAATAAAAA-AGAATCTGAA-TTTTCATC--TA
* * *
259836 GTCATATTTGTTTCTTATACATCCTCAGGAACCAAACAGTAGATAAAGGATAGATTAAACTGAGA
125 GTC-T-TTT-TTTCCTATATATTCTCAGGAACCAAACAGTAGATAAAGGATAGATTAAACTGAGA
* * * * * * **
259901 GTGAATACATACAATTCCTACAAGATTATCACAATGCTAAGCAAAATCAGATCGAAAATCATAAT
187 GCGAATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATAAT
** * * *
259966 TCATACTAAATAATAAAACGTCAATCTGAAAGTTTAATCTATTGTCTTCTTCTTTCATATGTATT
252 TCATACTAAATAATAAAACAACAATCTGAAAGTTTAATATATAGTCTTCTTCTTTCATA-GTACT
260031 CTCAGAAACCAAACAGTAGCTAAACG
316 CTCAGAAACCAAACAGTAGCTAAACG
* *
260057 ATCAATTAAACTGAGAGACAATACATACAATT-CTGACAAAAGTATCACAATGCTAAGCAAAATC
1 ATCAATTAAACTGAGAGACAAGACATACAATTCCT-ACAAAATTATCACAATGCTAAGCAAAATC
* * ** *
260121 AGATACGAAGATCATCAATCTATGATGTTATATAATAAAATGTGAATCTGAAATTTCCATCTATT
65 AGAT-CGAAAATCATCAATTTATGATGTTATATAATAAAA-AAGAATCTG-AATTTTCATCTA--
* * **
260186 GTCCTTTTTTTTTCTATATATTCTCAGGAACCAAACAGTAGCTAAATTATCA-ATTAAACTGAGA
125 GT-C-TTTTTTTCCTATATATTCTCAGGAACCAAACAGTAGATAAAGGAT-AGATTAAACTGAGA
* *
260250 GCGGATACATACAATTCCAACAAAATTATCACAATTCCAAACAAAAGCAGATCGAAAAGAATCAA
187 GCGAATACATACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAAT-AA
* * * * * *
260315 TGT-ATGATGTCATATAATAAAACAAGAATCTGAAATTTTCATATATAGTCTTCTTTTTTCCAGT
251 T-TCAT-A-CT-AAATAATAAAACAACAATCTGAAAGTTTAATATATAGTCTTCTTCTTT-CA-T
260379 A-TACTCTCA-AGAACCAAACAGTAGCTAAACG
310 AGTACTCTCAGA-AACCAAACAGTAGCTAAACG
* * * * *
260410 ATCAATTAAACTGAGA-ACGGAGACGTACATTTCCTACAAACTTATCGCAATGCTAAGCAAAATC
1 ATCAATTAAACTGAGAGAC-AAGACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATC
*
260474 AGATCGAAAATCATCAATTTATGATGTTATAAAATAAAACAAGAATCTGCAATTTTCATCTAGTC
65 AGATCGAAAATCATCAATTTATGATGTTATATAATAAAA-AAGAATCTG-AATTTTCATCTAGTC
*
260539 TTCTTTTTCCAATATATTCTCAGGAACCAAAC
128 TT-TTTTTCCTATATATTCTCAGGAACCAAAC
260571 GATCGATTAA
Statistics
Matches: 431, Mismatches: 63, Indels: 41
0.81 0.12 0.08
Matches are distributed among these distances:
348 5 0.01
349 155 0.36
350 81 0.19
351 9 0.02
352 54 0.13
353 121 0.28
354 4 0.01
355 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.11, T:0.29
Consensus pattern (341 bp):
ATCAATTAAACTGAGAGACAAGACATACAATTCCTACAAAATTATCACAATGCTAAGCAAAATCA
GATCGAAAATCATCAATTTATGATGTTATATAATAAAAAAGAATCTGAATTTTCATCTAGTCTTT
TTTTCCTATATATTCTCAGGAACCAAACAGTAGATAAAGGATAGATTAAACTGAGAGCGAATACA
TACAATTCCAACAAAATTATCACAATGCCAAACAAAAGCAGATCGAAAAGAATAATTCATACTAA
ATAATAAAACAACAATCTGAAAGTTTAATATATAGTCTTCTTCTTTCATAGTACTCTCAGAAACC
AAACAGTAGCTAAACG
Found at i:269100 original size:10 final size:10
Alignment explanation
Indices: 269067--269100 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
269057 ATTGAAGTAA
269067 AGGGAAGAGAG
1 AGGG-AGAGAG
*
269078 AGAGAGAGAG
1 AGGGAGAGAG
269088 AGGGAGAGAG
1 AGGGAGAGAG
269098 AGG
1 AGG
269101 ACTCAACAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 18 0.86
11 3 0.14
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (10 bp):
AGGGAGAGAG
Found at i:269457 original size:20 final size:20
Alignment explanation
Indices: 269407--269458 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
269397 AATGAGATAT
269407 TTATAAATAAATACTAATAA
1 TTATAAATAAATACTAATAA
* **
269427 TTTTATTTAAATA-TAATTAA
1 TTATAAATAAATACTAA-TAA
269447 TTATAAATAAAT
1 TTATAAATAAAT
269459 GCTTGATATT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (20 bp):
TTATAAATAAATACTAATAA
Found at i:275476 original size:14 final size:15
Alignment explanation
Indices: 275433--275478 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
275423 ATAAGATGTT
275433 AACATAAGTGATTAA
1 AACATAAGTGATTAA
275448 AACATAA-T-ATTTTAA
1 AACATAAGTGA--TTAA
275463 AA-ATAAGTGATTAA
1 AACATAAGTGATTAA
275477 AA
1 AA
275479 TGTAATCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.04
14 11 0.41
15 14 0.52
16 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.09, T:0.30
Consensus pattern (15 bp):
AACATAAGTGATTAA
Found at i:276010 original size:28 final size:28
Alignment explanation
Indices: 275970--276029 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 28
275960 TACATGGATC
275970 GATTATTTAACTA-ATAAACGAAGTATAA-
1 GATTATTTAACTACATAAAC-AA-TATAAT
275998 GATTATTTAACTACATAAACAATATAAT
1 GATTATTTAACTACATAAACAATATAAT
276026 GATT
1 GATT
276030 TTACCTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
27 5 0.17
28 19 0.63
29 6 0.20
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.35
Consensus pattern (28 bp):
GATTATTTAACTACATAAACAATATAAT
Found at i:283715 original size:2 final size:2
Alignment explanation
Indices: 283710--283739 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
283700 AAAAAAAAAA
283710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
283740 TTTATATTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:284023 original size:11 final size:12
Alignment explanation
Indices: 284007--284043 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
283997 ACTGGCAATA
284007 TCTTTT-ATTTT
1 TCTTTTAATTTT
284018 TCTTTTTAATTTT
1 TC-TTTTAATTTT
284031 T-TTTTAATTTT
1 TCTTTTAATTTT
284042 TC
1 TC
284044 AAAACGACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 13 0.57
12 4 0.17
13 6 0.26
ACGTcount: A:0.14, C:0.08, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTTTTAATTTT
Found at i:289905 original size:16 final size:14
Alignment explanation
Indices: 289873--289900 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
289863 ATAATATATC
289873 ATATTATGTTATTT
1 ATATTATGTTATTT
289887 ATATTATGTTATTT
1 ATATTATGTTATTT
289901 TTATAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
ATATTATGTTATTT
Found at i:289927 original size:19 final size:18
Alignment explanation
Indices: 289889--289927 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
289879 TGTTATTTAT
* *
289889 ATTATGTTATTTTTATAA
1 ATTATGTAATTTTAATAA
289907 ATTATGTAATTTATAATAA
1 ATTATGTAATTT-TAATAA
289926 AT
1 AT
289928 AAAAATTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (18 bp):
ATTATGTAATTTTAATAA
Found at i:302558 original size:44 final size:44
Alignment explanation
Indices: 302508--302599 Score: 184
Period size: 44 Copynumber: 2.1 Consensus size: 44
302498 TTATATGATG
302508 AAAAATAAATTATATGAAAATAGGGACTAAATTGAAAATTGTAC
1 AAAAATAAATTATATGAAAATAGGGACTAAATTGAAAATTGTAC
302552 AAAAATAAATTATATGAAAATAGGGACTAAATTGAAAATTGTAC
1 AAAAATAAATTATATGAAAATAGGGACTAAATTGAAAATTGTAC
302596 AAAA
1 AAAA
302600 GTTTAAGTGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (44 bp):
AAAAATAAATTATATGAAAATAGGGACTAAATTGAAAATTGTAC
Found at i:306118 original size:224 final size:223
Alignment explanation
Indices: 305776--306221 Score: 553
Period size: 225 Copynumber: 2.0 Consensus size: 223
305766 TTTCCTTTGT
* * **
305776 AAAGCTCAAGCTTGATTCGAGAAGAAGATTGAATTGCTCAAGCTTGATTTGAGAAAAAAATTTGG
1 AAAGCTCAAGCTTGATTCGAGAAAAAGATTGAATTGCTCAAGCTTGACTTGAGAAAAAAATTTCA
* * * *
305841 TCACTTGTATTCGTTGTATTTGATAACTTGAGGAACTTCGTCCAACTTGGTCTCTGAACTCTT-T
66 TCACTTGTATTCGTTGCACTTGATAACTTGAGCAACTTCGTCCAACTTGGTCTCTAAACT-TTCT
* * * * * *
305905 TTTTG-TCCATTAGTTTGTAAACTTGACAACTTTTACCAATTTGATCTTTGAACTTGTATTCTAT
130 TTTTGTTCCATTAGTTTCTAAACTTGACAACTTTTACCAAATTGATCCTTGAACTCGGATTCCAT
*
305969 GAAGTTGTGACAAGTACAAGGACCAAAGA
195 CAAGTTGTGACAAGTACAAGGACCAAAGA
* * *
305998 AAAGCTCAAGCTTGATTTGAGTAAAAAGATTGAATTGCTCAAGCTTG-CTTGATTAAATCAAGTA
1 AAAGCTCAAGCTTGATTCGAG-AAAAAGATTGAATTGCTCAAGCTTGACTTGA-GAAA--AA-AA
** **
306062 TTTCATCACTCT-TA-T-GTTGCACTTGATAACTTGAGCAACTTTTTCCTTCTTGGTCTCTAAAC
61 TTTCATCACT-TGTATTCGTTGCACTTGATAACTTGAGCAACTTCGTCCAACTTGGTCTCTAAAC
* *
306124 TTTCTTTTTGTTCCATTAGTTTCTAAATTTGACAACTTTTCCCAAATTGATCCTTGAACTCGGAT
125 TTTCTTTTTGTTCCATTAGTTTCTAAACTTGACAACTTTTACCAAATTGATCCTTGAACTCGGAT
* *
306189 TCCATCTAGTTGTGACAAGTTCAAGGACCAAAG
190 TCCATCAAGTTGTGACAAGTACAAGGACCAAAG
306222 TGGGAAATTT
Statistics
Matches: 190, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
222 24 0.13
223 29 0.15
224 46 0.24
225 79 0.42
226 11 0.06
227 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (223 bp):
AAAGCTCAAGCTTGATTCGAGAAAAAGATTGAATTGCTCAAGCTTGACTTGAGAAAAAAATTTCA
TCACTTGTATTCGTTGCACTTGATAACTTGAGCAACTTCGTCCAACTTGGTCTCTAAACTTTCTT
TTTGTTCCATTAGTTTCTAAACTTGACAACTTTTACCAAATTGATCCTTGAACTCGGATTCCATC
AAGTTGTGACAAGTACAAGGACCAAAGA
Found at i:306800 original size:9 final size:9
Alignment explanation
Indices: 306786--306810 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
306776 AAACTAATAA
306786 TATAGTTAT
1 TATAGTTAT
306795 TATAGTTAT
1 TATAGTTAT
306804 TATAGTT
1 TATAGTT
306811 TAACTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
TATAGTTAT
Found at i:307173 original size:63 final size:63
Alignment explanation
Indices: 307074--307215 Score: 234
Period size: 63 Copynumber: 2.3 Consensus size: 63
307064 TTATGAAGCG
307074 ACTAATATATTGTAATGTTATATCAGATTATAATTTTTATATATTATTCA-TTCAGAAAATTTC
1 ACTAATATATTGTAATGTTATATCAGATTATAATTTTTATATATTATTCACTT-AGAAAATTTC
* *
307137 ACTAATATATTGTAGTGTTATGTCAGATTATAATTTTTATATATTATTCACTTAGAAAATTTC
1 ACTAATATATTGTAATGTTATATCAGATTATAATTTTTATATATTATTCACTTAGAAAATTTC
*
307200 ACTAATAAATTG-AATG
1 ACTAATATATTGTAATG
307216 GTTGTCATTT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
62 3 0.04
63 69 0.93
64 2 0.03
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (63 bp):
ACTAATATATTGTAATGTTATATCAGATTATAATTTTTATATATTATTCACTTAGAAAATTTC
Found at i:307179 original size:34 final size:32
Alignment explanation
Indices: 307078--307181 Score: 85
Period size: 34 Copynumber: 3.2 Consensus size: 32
307068 GAAGCGACTA
307078 ATATATTGTAATGTTATATCAGATTATAATTTTT
1 ATATATTGT-ATGTTAT-TCAGATTATAATTTTT
* *
307112 ATATA-T-TAT-TCATTCAGA--A-AATTTCACTA
1 ATATATTGTATGTTATTCAGATTATAATTT---TT
307141 ATATATTGTAGTGTTATGTCAGATTATAATTTTT
1 ATATATTGTA-TGTTAT-TCAGATTATAATTTTT
307175 ATATATT
1 ATATATT
307182 ATTCACTTAG
Statistics
Matches: 55, Mismatches: 4, Indels: 22
0.68 0.05 0.27
Matches are distributed among these distances:
26 5 0.09
27 1 0.02
29 11 0.20
30 4 0.07
31 4 0.07
32 2 0.04
33 4 0.07
34 18 0.33
36 1 0.02
37 5 0.09
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.50
Consensus pattern (32 bp):
ATATATTGTATGTTATTCAGATTATAATTTTT
Found at i:312377 original size:42 final size:42
Alignment explanation
Indices: 312312--312406 Score: 120
Period size: 42 Copynumber: 2.3 Consensus size: 42
312302 TCTTATGCGG
* * * *
312312 TCATA-ATTGTATGAATTTGTTGATTATGATTGTAATTTCAT
1 TCATACATTGTATGAATGTATTGATTATAATTATAATTTCAT
* *
312353 TCATGCATTGTATGAATGTATTGATTATAATTATAATTTTAT
1 TCATACATTGTATGAATGTATTGATTATAATTATAATTTCAT
*
312395 TTATACATTGTA
1 TCATACATTGTA
312407 CTAATTTAGT
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 4 0.09
42 41 0.91
ACGTcount: A:0.32, C:0.05, G:0.13, T:0.51
Consensus pattern (42 bp):
TCATACATTGTATGAATGTATTGATTATAATTATAATTTCAT
Found at i:313492 original size:30 final size:31
Alignment explanation
Indices: 313461--313518 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
313451 AAAATTATAT
313461 TTTAATC-CTT-AAAATTGA-TAAAAATATTA
1 TTTAATCTCTTAAAAATT-ATTAAAAATATTA
*
313490 TTTAATCTTTTAAAAATTATTAAAAATAT
1 TTTAATCTCTTAAAAATTATTAAAAATAT
313519 AGGCTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 7 0.28
30 3 0.12
31 15 0.60
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (31 bp):
TTTAATCTCTTAAAAATTATTAAAAATATTA
Found at i:315822 original size:4 final size:4
Alignment explanation
Indices: 315813--315845 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
315803 AGTTAAGGCA
*
315813 AAAT AAAT AAAT AAAT AAAT AAAT AAAC AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
315846 GATAGTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:319221 original size:14 final size:14
Alignment explanation
Indices: 319202--319243 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
319192 ACCAAACATG
*
319202 TTTTAATAATTTAA
1 TTTTAATAATTCAA
*
319216 TTTTAATTAAATCAA
1 TTTTAA-TAATTCAA
319231 TTTTAA-AATTCAA
1 TTTTAATAATTCAA
319244 ATTAAACATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 6 0.25
14 6 0.25
15 12 0.50
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTAATAATTCAA
Found at i:322619 original size:26 final size:28
Alignment explanation
Indices: 322581--322633 Score: 74
Period size: 26 Copynumber: 1.9 Consensus size: 28
322571 TGAAGAATAT
*
322581 AAAAAAAATAT-AATTAA-TAAATATTA
1 AAAAAAAACATAAATTAACTAAATATTA
322607 AAAAAAAACATAAATTAACTTAAATAT
1 AAAAAAAACATAAATTAAC-TAAATAT
322634 ATGTCGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 10 0.43
27 6 0.26
29 7 0.30
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (28 bp):
AAAAAAAACATAAATTAACTAAATATTA
Found at i:326522 original size:3 final size:3
Alignment explanation
Indices: 326514--326542 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
326504 GTGGAAGATA
326514 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
326543 AGAAGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.34, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:326547 original size:3 final size:3
Alignment explanation
Indices: 326541--326574 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
326531 TGATGATGAT
326541 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAGA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GA-A GAA
326575 AGGTGTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:328732 original size:21 final size:20
Alignment explanation
Indices: 328703--328741 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
328693 AAAATTATTA
*
328703 TTTTTTAATTTTATTATTGT
1 TTTTTTAATTATATTATTGT
328723 TTTTTCTAATTATATTATT
1 TTTTT-TAATTATATTATT
328742 TCGAGGATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTTAATTATATTATTGT
Found at i:331650 original size:13 final size:13
Alignment explanation
Indices: 331632--331656 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
331622 ATAGTTATTA
331632 AAATTATATTTTT
1 AAATTATATTTTT
331645 AAATTATATTTT
1 AAATTATATTTT
331657 AGTAGAATTA
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:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
AAATTATATTTTT
Done.