Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015129.1 Kokia drynarioides strain JFW-HI SEQ_130173, 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: 947447
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 1279 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:5189 original size:25 final size:25
Alignment explanation
Indices: 5161--5216 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
5151 TTTTATCAGA
*
5161 AAATTTATTACTATATGTGTCTAAC
1 AAATTTATTACAATATGTGTCTAAC
* ** *
5186 AAATTTTTTTGAATTTGTGTCTAAC
1 AAATTTATTACAATATGTGTCTAAC
5211 AAATTT
1 AAATTT
5217 TTGAATTTGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (25 bp):
AAATTTATTACAATATGTGTCTAAC
Found at i:5221 original size:23 final size:24
Alignment explanation
Indices: 5176--5225 Score: 84
Period size: 25 Copynumber: 2.1 Consensus size: 24
5166 TATTACTATA
5176 TGTGTCTAACAAATTTTTTTGAATT
1 TGTGTCTAACAAA-TTTTTTGAATT
5201 TGTGTCTAACAAA-TTTTTGAATT
1 TGTGTCTAACAAATTTTTTGAATT
5224 TG
1 TG
5226 AGAAATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 12 0.48
25 13 0.52
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.50
Consensus pattern (24 bp):
TGTGTCTAACAAATTTTTTGAATT
Found at i:15454 original size:3 final size:3
Alignment explanation
Indices: 15434--15472 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
15424 TCTCGCCATT
* *
15434 AAG AA- AAG AAG AAC AAG AAG AAG AAG AAG AAG CAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
15473 TATTTTGGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.67, C:0.05, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:21236 original size:13 final size:13
Alignment explanation
Indices: 21218--21250 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
21208 ACAATAATAG
21218 AAGAAAACAAAAA
1 AAGAAAACAAAAA
*
21231 AAGAAAA-AGAAA
1 AAGAAAACAAAAA
21243 AAGAAAAC
1 AAGAAAAC
21251 GTTTAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (13 bp):
AAGAAAACAAAAA
Found at i:30561 original size:28 final size:27
Alignment explanation
Indices: 30502--30557 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
30492 TCGAATGAAG
* *
30502 TAAATTGTTAATTTTTTATTTAATCAAT
1 TAAATTATTAATTTATTATTTAA-CAAT
30530 TAAATTATTAATTTAATTATTTAA-AAT
1 TAAATTATTAATTT-ATTATTTAACAAT
30557 T
1 T
30558 TAAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 13 0.52
29 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (27 bp):
TAAATTATTAATTTATTATTTAACAAT
Found at i:38543 original size:6 final size:6
Alignment explanation
Indices: 38528--38570 Score: 77
Period size: 6 Copynumber: 7.2 Consensus size: 6
38518 GAGGAGACAG
*
38528 AGCCAT AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC A
1 AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC AGCCAC A
38571 TCCGGCTCTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.35, C:0.47, G:0.16, T:0.02
Consensus pattern (6 bp):
AGCCAC
Found at i:66572 original size:18 final size:18
Alignment explanation
Indices: 66549--66583 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
66539 CTAAAGCTTT
66549 TTTTAATATTT-TTATACA
1 TTTTAAT-TTTATTATACA
66567 TTTTAATTTTATTATAC
1 TTTTAATTTTATTATAC
66584 GCACTTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTTAATTTTATTATACA
Found at i:67018 original size:206 final size:206
Alignment explanation
Indices: 66650--67274 Score: 903
Period size: 206 Copynumber: 3.0 Consensus size: 206
66640 AAGTGAACTC
* ** *
66650 TATCAACAAATAGCAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATTAGAA
1 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
* *
66715 TATCAATAGCACACTATTTATACAACTCAAGAACTGCTATAGCAGACGATAACAGCTTACTAACT
66 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAGACGATAACAGCTTACTAACT
*
66780 TCAACAACTGACTTCAGCTAACTGACACTAATTGATACTCAGCTAACTGTCAACGACTAACTGCT
131 TCAACAATTGACTTCAGCTAACTGACACTAATTGATACTCAGCTAACTGTCAACGACTAACTGCT
66845 AACTGATACCA
196 AACTGATACCA
66856 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
1 TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
*
66921 TATCAGTAGCACACTATCTATACAACTCAAGAACTGCTATACCAGACGATAACAGCTTACTAACT
66 TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAGACGATAACAGCTTACTAACT
* * * *
66986 TCAACAATTGGCTTCAGCTAACTGACACTAATTGATACTCAACTAACTGTCAACAACTAATTGCT
131 TCAACAATTGACTTCAGCTAACTGACACTAATTGATACTCAGCTAACTGTCAACGACTAACTGCT
67051 AACTGATACCA
196 AACTGATACCA
* *
67062 TATCAGCAAATAACT-GAGACCTAAACAAAGTAATTCATACTTGTATTATCATTCATTCATCAGA
1 TATCAGCAAATAA-TAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGA
* * * * * * *
67126 ATATCAGTAGCACATTATTTATATAACTCAAGAACTGTTATACCAAACGATAATAGTTTA-TAAT
65 ATATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAGACGATAACAGCTTACTAAC
* *
67190 TTCAACAACTGATGACTTCAGTTAACTAACCCCAACTAACACTAACTGATACTCAGCTAACTGTC
130 TTCAACAA-T--TGACTTCAG----CT------AACTGACACTAATTGATACTCAGCTAACTGTC
67255 AACGACTAACTGCTAACTGA
182 AACGACTAACTGCTAACTGA
67275 CATCTAATAA
Statistics
Matches: 377, Mismatches: 28, Indels: 16
0.90 0.07 0.04
Matches are distributed among these distances:
205 11 0.03
206 308 0.82
207 1 0.00
208 8 0.02
212 2 0.01
218 47 0.12
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (206 bp):
TATCAGCAAATAATAGAGAGCTAAACAAAGTAATTCATACTTGTATTTTCATTCATTCATCAGAA
TATCAGTAGCACACTATTTATACAACTCAAGAACTGCTATACCAGACGATAACAGCTTACTAACT
TCAACAATTGACTTCAGCTAACTGACACTAATTGATACTCAGCTAACTGTCAACGACTAACTGCT
AACTGATACCA
Found at i:70513 original size:23 final size:23
Alignment explanation
Indices: 70487--70548 Score: 72
Period size: 25 Copynumber: 2.6 Consensus size: 23
70477 TTTTAACAGC
70487 ATTAAATTTTGAAAAAT-AAAAT
1 ATTAAATTTTGAAAAATAAAAAT
*
70509 GATTAAATTCTTAAAAAATAAAAAT
1 -ATTAAATT-TTGAAAAATAAAAAT
70534 ATATAAATTTATGAA
1 AT-TAAATTT-TGAA
70549 TAATGTAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
23 8 0.24
24 11 0.33
25 14 0.42
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (23 bp):
ATTAAATTTTGAAAAATAAAAAT
Found at i:70530 original size:24 final size:23
Alignment explanation
Indices: 70487--70531 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
70477 TTTTAACAGC
*
70487 ATTAAATTTTGAAAAATAAAATG
1 ATTAAATTTTAAAAAATAAAATG
70510 ATTAAATTCTTAAAAAATAAAA
1 ATTAAATT-TTAAAAAATAAAA
70532 ATATATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.33
Consensus pattern (23 bp):
ATTAAATTTTAAAAAATAAAATG
Found at i:70532 original size:25 final size:22
Alignment explanation
Indices: 70487--70543 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 22
70477 TTTTAACAGC
*
70487 ATTAAATTTTGAAAAATAAAAT
1 ATTAAATTTTAAAAAATAAAAT
70509 GATTAAATTCTTAAAAAATAAAAAT
1 -ATTAAATT-TTAAAAAAT-AAAAT
70534 ATATAAATTT
1 AT-TAAATTT
70544 ATGAATAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 8 0.27
24 11 0.37
25 11 0.37
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.37
Consensus pattern (22 bp):
ATTAAATTTTAAAAAATAAAAT
Found at i:74613 original size:18 final size:18
Alignment explanation
Indices: 74590--74629 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
74580 TGTGTTAGCA
74590 GTTATCAGCGGTTGGGTT
1 GTTATCAGCGGTTGGGTT
*
74608 GTTATCAGCGGTTGTGTT
1 GTTATCAGCGGTTGGGTT
74626 GTTA
1 GTTA
74630 GCAGTTAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.10, G:0.35, T:0.42
Consensus pattern (18 bp):
GTTATCAGCGGTTGGGTT
Found at i:85878 original size:10 final size:10
Alignment explanation
Indices: 85863--85894 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
85853 AACACTACCT
*
85863 CTCTTCCCTA
1 CTCTTCCTTA
85873 CTCTTCCTTA
1 CTCTTCCTTA
85883 CTCTTCCTTA
1 CTCTTCCTTA
85893 CT
1 CT
85895 TACCTCCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.09, C:0.44, G:0.00, T:0.47
Consensus pattern (10 bp):
CTCTTCCTTA
Found at i:89330 original size:15 final size:16
Alignment explanation
Indices: 89296--89332 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
89286 AACAACCAGT
*
89296 TCAA-ACAATGGGTCA
1 TCAATACAATGGGACA
89311 TCAATACAATGGGACA
1 TCAATACAATGGGACA
89327 -CAATAC
1 TCAATAC
89333 GCTCCGGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (16 bp):
TCAATACAATGGGACA
Found at i:104085 original size:4 final size:4
Alignment explanation
Indices: 104071--104122 Score: 95
Period size: 4 Copynumber: 13.0 Consensus size: 4
104061 GGAATACTAA
*
104071 TATG AATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
104119 TATG
1 TATG
104123 CACCTTGAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:118945 original size:2 final size:2
Alignment explanation
Indices: 118938--118964 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
118928 GAAAGTGATA
118938 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
118965 AGAGAGAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:125419 original size:18 final size:17
Alignment explanation
Indices: 125393--125426 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
125383 CAGTTTTGGT
*
125393 TTTGTTTTTCAGTGCTTG
1 TTTGATTTTCAG-GCTTG
125411 TTTGATTTTCAGGCTT
1 TTTGATTTTCAGGCTT
125427 TGCTCGTTTC
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:0.09, C:0.12, G:0.21, T:0.59
Consensus pattern (17 bp):
TTTGATTTTCAGGCTTG
Found at i:126115 original size:33 final size:33
Alignment explanation
Indices: 126050--126114 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 33
126040 TATTTTGATG
* *
126050 ATTTAAAAATTCTCACTATAATGAGATTTTTTT
1 ATTTAAAAAGTCGCACTATAATGAGATTTTTTT
126083 ATTTAAAAAGGTCGCACTATAAT-A-ATTTTTTT
1 ATTTAAAAA-GTCGCACTATAATGAGATTTTTTT
126115 TCCTTTTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 8 0.28
33 10 0.34
34 11 0.38
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (33 bp):
ATTTAAAAAGTCGCACTATAATGAGATTTTTTT
Found at i:126115 original size:34 final size:33
Alignment explanation
Indices: 126050--126115 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
126040 TATTTTGATG
* * *
126050 ATTTAAAAATTCTCACTATAATGAGATTTTTTT
1 ATTTAAAAAGTCGCACTATAATAAGATTTTTTT
*
126083 ATTTAAAAAGGTCGCACTATAATAA-TTTTTTTT
1 ATTTAAAAA-GTCGCACTATAATAAGATTTTTTT
126116 CCTTTTAAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (33 bp):
ATTTAAAAAGTCGCACTATAATAAGATTTTTTT
Found at i:127051 original size:22 final size:22
Alignment explanation
Indices: 127001--127051 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
126991 GCTATTCTTT
* **
127001 TTGTTATTTTGCTGTTATTTCA
1 TTGTTATATTGCTAATATTTCA
* *
127023 TTATTATATTGCTAATATTTCG
1 TTGTTATATTGCTAATATTTCA
127045 TTGTTAT
1 TTGTTAT
127052 TATTTGCATA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.08, G:0.12, T:0.61
Consensus pattern (22 bp):
TTGTTATATTGCTAATATTTCA
Found at i:141947 original size:30 final size:30
Alignment explanation
Indices: 141913--142003 Score: 164
Period size: 30 Copynumber: 3.0 Consensus size: 30
141903 ATCATAAAAT
141913 ATGCATCTTAAGAAGCAAGAACCATAAACC
1 ATGCATCTTAAGAAGCAAGAACCATAAACC
*
141943 ATGCATCTTAAGAAGCAAGAACTATAAACC
1 ATGCATCTTAAGAAGCAAGAACCATAAACC
*
141973 ATGCATCTTAAGACGCAAGAACCATAAACC
1 ATGCATCTTAAGAAGCAAGAACCATAAACC
142003 A
1 A
142004 ACTCTCAGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.46, C:0.23, G:0.13, T:0.18
Consensus pattern (30 bp):
ATGCATCTTAAGAAGCAAGAACCATAAACC
Found at i:151700 original size:14 final size:14
Alignment explanation
Indices: 151671--151709 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
151661 CAAACTCTAG
151671 AAACAAGCAGAGAAAA
1 AAACAAG-A-AGAAAA
*
151687 AAAGAAGAAGAAAA
1 AAACAAGAAGAAAA
151701 AAACAAGAA
1 AAACAAGAA
151710 ACAACTACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 14 0.67
15 1 0.05
16 6 0.29
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (14 bp):
AAACAAGAAGAAAA
Found at i:153225 original size:18 final size:17
Alignment explanation
Indices: 153184--153226 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
153174 TTTAACTTTA
153184 TTATATAAATTAATTTT
1 TTATATAAATTAATTTT
* *
153201 CTA-ATAAATATAGTTTT
1 TTATATAAAT-TAATTTT
153218 TTATATAAA
1 TTATATAAA
153227 ATTTTTCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 6 0.29
17 10 0.48
18 5 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (17 bp):
TTATATAAATTAATTTT
Found at i:154487 original size:27 final size:29
Alignment explanation
Indices: 154457--154514 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
154447 TTATAGTTTT
154457 TTTTAAGTT-ATG-AATTTAGTCATTATA
1 TTTTAAGTTAATGAAATTTAGTCATTATA
* **
154484 TTTTAATTTAATGAAATTTAGTTTTTATA
1 TTTTAAGTTAATGAAATTTAGTCATTATA
154513 TT
1 TT
154515 GTTCGAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 3 0.12
29 15 0.58
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.57
Consensus pattern (29 bp):
TTTTAAGTTAATGAAATTTAGTCATTATA
Found at i:156872 original size:21 final size:21
Alignment explanation
Indices: 156846--156885 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
156836 ACACGTGTTT
* *
156846 TTTTAATATTTTTTAAAATTA
1 TTTTAATATATTTAAAAATTA
156867 TTTTAATATATTTAAAAAT
1 TTTTAATATATTTAAAAAT
156886 AAAAAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAATATATTTAAAAATTA
Found at i:157221 original size:4 final size:4
Alignment explanation
Indices: 157212--157277 Score: 64
Period size: 4 Copynumber: 16.2 Consensus size: 4
157202 AACTAAACGG
* * *
157212 GAAA GAAA GAAA GGAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
157262 G-AA G-AA GCAAA GAAA G
1 GAAA GAAA G-AAA GAAA G
157278 GTAATGTGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
3 6 0.11
4 37 0.69
5 11 0.20
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:157234 original size:17 final size:17
Alignment explanation
Indices: 157212--157244 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
157202 AACTAAACGG
157212 GAAAGAAAGAAAGGAAA
1 GAAAGAAAGAAAGGAAA
157229 GAAAGAAAGAAAGGAA
1 GAAAGAAAGAAAGGAA
157245 GAAGGAGAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (17 bp):
GAAAGAAAGAAAGGAAA
Found at i:157278 original size:29 final size:30
Alignment explanation
Indices: 157212--157278 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
157202 AACTAAACGG
157212 GAAAGAAA-GAAAGGAAAGAAAGAAAGAAA
1 GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
* *
157241 GGAAG-AAGGAGAGGAAAGAAAG-AAG-AA
1 GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
157268 GCAAAGAAAGG
1 G-AAAGAAAGG
157279 TAATGTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 3 0.09
28 8 0.25
29 21 0.66
ACGTcount: A:0.64, C:0.01, G:0.34, T:0.00
Consensus pattern (30 bp):
GAAAGAAAGGAAAGGAAAGAAAGAAAGAAA
Found at i:161131 original size:15 final size:15
Alignment explanation
Indices: 161111--161141 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
161101 TAAATTATAA
*
161111 AAAATTTATAAAAAT
1 AAAATTTACAAAAAT
161126 AAAATTTACAAAAAT
1 AAAATTTACAAAAAT
161141 A
1 A
161142 TTAGTTGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAATTTACAAAAAT
Found at i:163458 original size:12 final size:12
Alignment explanation
Indices: 163430--163463 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
163420 CTTTAAAATT
163430 TAAAAAATAAAA
1 TAAAAAATAAAA
*
163442 -CAAAAATAAAA
1 TAAAAAATAAAA
163453 TAAAAAATAAA
1 TAAAAAATAAA
163464 CTCACTCGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (12 bp):
TAAAAAATAAAA
Found at i:168860 original size:55 final size:55
Alignment explanation
Indices: 168790--168902 Score: 181
Period size: 55 Copynumber: 2.1 Consensus size: 55
168780 CAATACTTTC
* *
168790 ATAATTGAATTAGTGTCGAGTTAATTCGTGACACAAATTTAATTAGACATTTTAT
1 ATAATTGAATCAGTGTCGAGTTAATTCGTGACACAAATTTAATTAGACACTTTAT
* * *
168845 ATAATTGAGTCAGTGTCGAGTTAATTCGTGATACAAATTTAATTAGCCACTTTAT
1 ATAATTGAATCAGTGTCGAGTTAATTCGTGACACAAATTTAATTAGACACTTTAT
168900 ATA
1 ATA
168903 TAGTATAGAT
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (55 bp):
ATAATTGAATCAGTGTCGAGTTAATTCGTGACACAAATTTAATTAGACACTTTAT
Found at i:176600 original size:30 final size:31
Alignment explanation
Indices: 176525--176600 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
176515 CGATGCGCAA
* * *
176525 ATCAGCTACTTTTTTTAGCTTAAATAATTTT
1 ATCAACTACCTTTTTTAGCTGAAATAATTTT
*
176556 ATCAACTACC-TTTTTAGCTGAAATACTTTT
1 ATCAACTACCTTTTTTAGCTGAAATAATTTT
176586 ATCAACT-CCTTTTTT
1 ATCAACTACCTTTTTT
176601 TTTTAGCTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 2 0.05
30 30 0.75
31 8 0.20
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.49
Consensus pattern (31 bp):
ATCAACTACCTTTTTTAGCTGAAATAATTTT
Found at i:176609 original size:34 final size:32
Alignment explanation
Indices: 176525--176615 Score: 100
Period size: 30 Copynumber: 2.9 Consensus size: 32
176515 CGATGCGCAA
* * *
176525 ATCAGCTA-CTTTTTTTAGCTTAAATAATTTT
1 ATCAACTACCTTTTTTTAGCTGAAATACTTTT
176556 ATCAACTACC--TTTTTAGCTGAAATACTTTT
1 ATCAACTACCTTTTTTTAGCTGAAATACTTTT
176586 ATCAACT-CCTTTTTTTTTTAGCTGAAATAC
1 ATCAACTACC---TTTTTTTAGCTGAAATAC
176616 CAATATAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
29 2 0.04
30 25 0.49
31 7 0.14
32 1 0.02
34 16 0.31
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (32 bp):
ATCAACTACCTTTTTTTAGCTGAAATACTTTT
Found at i:179686 original size:3 final size:3
Alignment explanation
Indices: 179678--179717 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
179668 TCAATCAATC
179678 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
179718 CAAGTTTATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:183496 original size:17 final size:18
Alignment explanation
Indices: 183448--183498 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
183438 GAAGCAATTA
183448 TTTTAATATTTTTAT-TGT
1 TTTTAAT-TTTTTATATGT
* * *
183466 TTTTGATGTATTATAT-T
1 TTTTAATTTTTTATATGT
183483 TTTTAATTTTTTATAT
1 TTTTAATTTTTTATAT
183499 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 19 0.73
18 7 0.27
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.71
Consensus pattern (18 bp):
TTTTAATTTTTTATATGT
Found at i:183891 original size:21 final size:22
Alignment explanation
Indices: 183862--183902 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
183852 CATACTTTTT
183862 AAATAA-TTTTAAATTTTTTAA
1 AAATAATTTTTAAATTTTTTAA
* *
183883 AAATGATTTTTATATTTTTT
1 AAATAATTTTTAAATTTTTT
183903 GAATTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (22 bp):
AAATAATTTTTAAATTTTTTAA
Found at i:185733 original size:26 final size:26
Alignment explanation
Indices: 185694--185746 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
185684 TGTTATTAAA
* *
185694 TGAAAAATATATAATTTTAGCTTTTT
1 TGAAAAATATATAATTTAAGCATTTT
185720 TGAAAAAT-TAATAATTTAAGCATTTT
1 TGAAAAATAT-ATAATTTAAGCATTTT
185746 T
1 T
185747 AATCCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.47
Consensus pattern (26 bp):
TGAAAAATATATAATTTAAGCATTTT
Found at i:187182 original size:25 final size:25
Alignment explanation
Indices: 187137--187184 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
187127 GTTTTCTTTT
*
187137 TAAATTATTATTTAAGCTTTTTTAA
1 TAAATTATTATTCAAGCTTTTTTAA
* *
187162 TAAATTATTATTCGAGGTTTTTT
1 TAAATTATTATTCAAGCTTTTTT
187185 TCGAAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (25 bp):
TAAATTATTATTCAAGCTTTTTTAA
Found at i:196290 original size:18 final size:16
Alignment explanation
Indices: 196259--196302 Score: 56
Period size: 14 Copynumber: 2.8 Consensus size: 16
196249 AGTTTAGGGT
*
196259 TTAAAAATTTTAATTAA
1 TTAAAAA-TTTATTTAA
196276 TT--AAATTTATTTAA
1 TTAAAAATTTATTTAA
196290 TTAAAAATTTATT
1 TTAAAAATTTATT
196303 CTCATTCCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.42
15 3 0.12
16 9 0.38
17 2 0.08
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTAAAAATTTATTTAA
Found at i:196687 original size:24 final size:23
Alignment explanation
Indices: 196644--196688 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
196634 TTTTTTTTCC
* *
196644 CTAAAAGAAGTAAAAGAAAATGG
1 CTAAAAGAAGAAAAAAAAAATGG
196667 CTAAAAGAAAGAAAAAAAAAAT
1 CTAAAAG-AAGAAAAAAAAAAT
196689 AGTGGTACCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.69, C:0.04, G:0.16, T:0.11
Consensus pattern (23 bp):
CTAAAAGAAGAAAAAAAAAATGG
Found at i:207869 original size:14 final size:14
Alignment explanation
Indices: 207850--207880 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
207840 AGAATAAATC
207850 TTTAATTAATTAAA
1 TTTAATTAATTAAA
207864 TTTAATTAATTAAA
1 TTTAATTAATTAAA
207878 TTT
1 TTT
207881 TTTAAACCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTTAATTAATTAAA
Found at i:208575 original size:27 final size:27
Alignment explanation
Indices: 208546--208597 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 27
208536 ATTTTAAATA
208546 AAAAATAAAATTTT-AAAAAATAAAAG
1 AAAAATAAAATTTTAAAAAAATAAAAG
*
208572 AAAAATAATATTTTAAAAAAATAAAA
1 AAAAATAAAATTTTAAAAAAATAAAA
208598 ATTACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.54
27 11 0.46
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (27 bp):
AAAAATAAAATTTTAAAAAAATAAAAG
Found at i:208593 original size:16 final size:16
Alignment explanation
Indices: 208572--208622 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
208562 AAAATAAAAG
208572 AAAAATAATATTTTAA
1 AAAAATAATATTTTAA
**
208588 AAAAATAA-AAATTACA
1 AAAAATAATATTTTA-A
*
208604 AAAAATAATTTCTTTAA
1 AAAAATAATAT-TTTAA
208621 AA
1 AA
208623 TTTAAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 4 0.15
16 17 0.63
17 3 0.11
18 3 0.11
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAAATAATATTTTAA
Found at i:210320 original size:20 final size:22
Alignment explanation
Indices: 210283--210323 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
210273 GTGACAAAAA
*
210283 AATATAAAAATTATTAAATTTT
1 AATATAAAAATCATTAAATTTT
210305 AATA-AAAAATCA-TAAATTT
1 AATATAAAAATCATTAAATTT
210324 ATTAATAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
AATATAAAAATCATTAAATTTT
Found at i:211206 original size:17 final size:17
Alignment explanation
Indices: 211184--211249 Score: 64
Period size: 17 Copynumber: 4.0 Consensus size: 17
211174 ATAATATTTT
211184 ATTAATTTAATATTAAA
1 ATTAATTTAATATTAAA
* *
211201 ATTAATTTAATATTTAT
1 ATTAATTTAATATTAAA
* * *
211218 CTTAA-TAAATATT-AT
1 ATTAATTTAATATTAAA
*
211233 ATTAAATTAATATTAAA
1 ATTAATTTAATATTAAA
211250 GTAATTAAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
15 6 0.15
16 14 0.35
17 20 0.50
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTAATTTAATATTAAA
Found at i:216209 original size:22 final size:22
Alignment explanation
Indices: 216181--216224 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
216171 TCATGCAGTC
216181 CATGATGATTACCTAAAGAGTT
1 CATGATGATTACCTAAAGAGTT
216203 CATGATGATTACCTAAAGAGTT
1 CATGATGATTACCTAAAGAGTT
216225 AGTAAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (22 bp):
CATGATGATTACCTAAAGAGTT
Found at i:220463 original size:644 final size:645
Alignment explanation
Indices: 219183--220474 Score: 2194
Period size: 644 Copynumber: 2.0 Consensus size: 645
219173 CAATTTTTCA
* * *
219183 ATAGTAAGTTACAAAAATGTATGAATAATACTCCATTTTTCAATTTTTTTTATTGGGCTGTGAAA
1 ATAGTAAGTTACAAAAATGTATGAATAATACTCCATTTGTCAATTTTTTTAATTGAGCTGTGAAA
* * **
219248 AACGGATCATCTTTGCACTTTTTTTATAACAAGAAATACACAGTAATCTTCTACAATGGTCTACA
66 AACAGATAATCTTTGCACTTTCATTATAACAAGAAATACACAGTAATCTTCTACAATGGTCTACA
* *
219313 AAATACAGTCAAGACCATCTTCTCAGGGAACTCAAGAATTCATGCCATAACTGCAAAATAAACAA
131 AAATACAGTCAAGAACATCTTCTCAGGGAACTCAAGAATTCACGCCATAACTGCAAAATAAACAA
*
219378 AAGAAAAATGTAGTGCTGTTATTTAACTCCAATCTCGTAAAAATGCAGGAGAAGAAGCTGATGAC
196 AAGAAAAATGTAGTGCCGTTATTTAACTCCAATCTCGTAAAAATGCAGGAGAAGAAGCTGATGAC
*
219443 AACACATGACTATACGAGTTTTTCAGACCCTACACCAAAATTAATAGATACAGGTTTAGGGTATA
261 AACACATGACTATACGAGTTTTTCAGACCCTAAACCAAAATTAATAGATACAGGTTTAGGGTATA
* * *
219508 GTTAAACTCGATCAAACCCAAACAAAAGACGCACCATTTTAAAAGCATTTAATTAAAACGGCATA
326 GTTAAACTCGATCAAACACAAACAAAAGACGCACCATATTAAAAGCATTTAATTAAAACGACATA
*
219573 GCCTCGGTTAAATCCATTAAAACCATTGAATTGCAGCTTCAATCAAGTAGGTTCGTCCTTGGCTC
391 GCCTCGGTTAAATCCATTAAAACCATTGAATTGCAGCTTCAACCAAGTAGGTTCGTCCTTGGCTC
* * *
219638 CACTGCACCTCATACAAAGCGAATTATGTCATCTTCGGCTCACTGGAACTATATAAATATTGTGA
456 CACTGCACCTCAGACAAAGCGAATTATATCATCTTCGGCTCACTGGAACTATATAAATATTGTAA
*
219703 ATATAACACAATTTACAAAAATTATTATTTTCATGAAACCATCTAAAACAAAGCCCCAGAAAAAT
521 ATATAACACAATTTACAAAAATTATTATTTTCATGAAACCATCTAAAACAAAGCCCCAAAAAAAT
* * *
219768 TCAGTAGTTTCATGAATGACGTAACACCCCAAGTGAAGAAGCTGGTGAAAACACTTGACT
586 TCAGTAGTTTCATGAATGACGTAACACCCCAAGAGAAGAAACTGATGAAAACACTTGACT
* *
219828 ATAGTAAGTTACGAAAATGTATGAATAATATTCCATTTGTCAATTTTTTTAATTGAGCTGTGAAA
1 ATAGTAAGTTACAAAAATGTATGAATAATACTCCATTTGTCAATTTTTTTAATTGAGCTGTGAAA
* *
219893 AACAGATAATCTTTGCAC-TTCATTATAATAAGAAATATACAGTAATCTTCTACAATGGTCTACA
66 AACAGATAATCTTTGCACTTTCATTATAACAAGAAATACACAGTAATCTTCTACAATGGTCTACA
* *
219957 AAATACAGTCAAGAACATCTTCTCAGGGAACTGAAGAATTCACGCCATAACTGCAAAATAAACAG
131 AAATACAGTCAAGAACATCTTCTCAGGGAACTCAAGAATTCACGCCATAACTGCAAAATAAACAA
220022 AAGAAAAATGTAGTGCCGTTATTTAACTCCAATCTCGTAAAAATGC-GAGAGAAGAAGCTGATGA
196 AAGAAAAATGTAGTGCCGTTATTTAACTCCAATCTCGTAAAAATGCAG-GAGAAGAAGCTGATGA
*
220086 CAACACATGACTATATGAGTTTTTCAGACCCTAAACCAAAATTAATAGATACAGGTTTAGGGTAT
260 CAACACATGACTATACGAGTTTTTCAGACCCTAAACCAAAATTAATAGATACAGGTTTAGGGTAT
* *
220151 AGTTAAACTC-AGTCAAACACAATCCAAAGACGCACCATATTAAAAGCATTTAATTAAAACGACA
325 AGTTAAACTCGA-TCAAACACAAACAAAAGACGCACCATATTAAAAGCATTTAATTAAAACGACA
* *
220215 TAGCGTCGGTTAAATCCATTAAAACCATTGAATTGCAGCTTCAACCAAGTAGGTTCGTTCTTGGC
389 TAGCCTCGGTTAAATCCATTAAAACCATTGAATTGCAGCTTCAACCAAGTAGGTTCGTCCTTGGC
* * * *
220280 TCCACTGCACCTCAGCCAAAGTGGATTATATCATCTTTGGCTCACTGGAACTATATAAATATTGT
454 TCCACTGCACCTCAGACAAAGCGAATTATATCATCTTCGGCTCACTGGAACTATATAAATATTGT
*
220345 AAATATAACACAATTTACAAAAGTTATTATTTTCATGAAACCATCTAAAACAAAGCCCCAAAAAA
519 AAATATAACACAATTTACAAAAATTATTATTTTCATGAAACCATCTAAAACAAAGCCCCAAAAAA
*
220410 ATTCAGTAGTTTCATGAATGATGTAACACCCCAAGAGAAGAAACTGATGAAAACACTTGACT
584 ATTCAGTAGTTTCATGAATGACGTAACACCCCAAGAGAAGAAACTGATGAAAACACTTGACT
220472 ATA
1 ATA
220475 AAAGTTTTTC
Statistics
Matches: 606, Mismatches: 39, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
643 2 0.00
644 528 0.87
645 76 0.13
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (645 bp):
ATAGTAAGTTACAAAAATGTATGAATAATACTCCATTTGTCAATTTTTTTAATTGAGCTGTGAAA
AACAGATAATCTTTGCACTTTCATTATAACAAGAAATACACAGTAATCTTCTACAATGGTCTACA
AAATACAGTCAAGAACATCTTCTCAGGGAACTCAAGAATTCACGCCATAACTGCAAAATAAACAA
AAGAAAAATGTAGTGCCGTTATTTAACTCCAATCTCGTAAAAATGCAGGAGAAGAAGCTGATGAC
AACACATGACTATACGAGTTTTTCAGACCCTAAACCAAAATTAATAGATACAGGTTTAGGGTATA
GTTAAACTCGATCAAACACAAACAAAAGACGCACCATATTAAAAGCATTTAATTAAAACGACATA
GCCTCGGTTAAATCCATTAAAACCATTGAATTGCAGCTTCAACCAAGTAGGTTCGTCCTTGGCTC
CACTGCACCTCAGACAAAGCGAATTATATCATCTTCGGCTCACTGGAACTATATAAATATTGTAA
ATATAACACAATTTACAAAAATTATTATTTTCATGAAACCATCTAAAACAAAGCCCCAAAAAAAT
TCAGTAGTTTCATGAATGACGTAACACCCCAAGAGAAGAAACTGATGAAAACACTTGACT
Found at i:221347 original size:372 final size:371
Alignment explanation
Indices: 220069--221355 Score: 1935
Period size: 372 Copynumber: 3.5 Consensus size: 371
220059 TAAAAATGCG
* * * * *
220069 AGAGAAGAAGCTGATGACAACACATGACTATATGAGTTTTTCAGACCCTAAACCAAAATTAATAG
1 AGAGAAGAAACTGATGAAAACACTTGACTATATAAGTTTTTCAAACCCTAAACCAAAATTAATAG
* * * * * * **
220134 -ATACAGGTTTAGGGTATAGTTAAACTCAGTCAAACAC-AATCCAAAGACGCACCATA-TTAAAA
66 CA-AAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAA-CCCAAGAATCACCA-AGTTAAAA
* * * * * *
220196 GCATTTAATTAAAACGACATAGCGTCGGTTAAATCCATTAAAACCATTGAATTGCAGCTTCAACC
128 GAATTTAATTAAAAAGAC--AGCCTCAGTTGAATCCATTAAAACCATTGAATTGCAGCTTCTACC
* *
220261 AAGTAGGTTCGTTCTTGGCTCCACTGCACCTCAGCCAAAGTGGATTATATCATCTTTGGCTCACT
191 AAGTAGGTTCGTTCTTGGCTCCACTGCACCTCATCCAAAGTGGATTATATCATCATTGGCTCACT
* *
220326 GGAACTATATAAATATTGTAAATATAACACAATTTACAAAAGTTATTATTTTCATGAAACCATCT
256 GGAAATATATAAACATTGTAAATATAACACAATTTACAAAAGTT-TTATTTTCATGAAACCATCT
* *
220391 AAAACAAAGCCCCAAAAAAATTCAGTAGTTTCATGAATGATGTAACACCCCA
320 AAAACAAAGACCCAAGAAAATTCAGTAGTTTCATGAATGATGTAACACCCCA
* *
220443 AGAGAAGAAACTGATGAAAACACTTGACTATAAAAGTTTTTCAAACCCTAAACCGAAATTAATAG
1 AGAGAAGAAACTGATGAAAACACTTGACTATATAAGTTTTTCAAACCCTAAACCAAAATTAATAG
* *
220508 TAAAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAACCCAAGAATCACCAAGTTGAAAGAA
66 CAAAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAACCCAAGAATCACCAAGTTAAAAGAA
*
220573 TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACAATTGAATTGCAGCTTCTACCAAGTA
131 TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACCATTGAATTGCAGCTTCTACCAAGTA
* * * * *
220638 GGTTCGTTCTTGGCTCCAATGCACCTCATCCGAAGTGGTTTATATCATTATTGGCTCACTTGAAA
196 GGTTCGTTCTTGGCTCCACTGCACCTCATCCAAAGTGGATTATATCATCATTGGCTCACTGGAAA
*
220703 TATATATACATTGTAAATATAACACAATTTACAAAAGTTTATCATTTTCATGAAACCATCTAAAA
261 TATATAAACATTGTAAATATAACACAATTTACAAAAGTTT-T-ATTTTCATGAAACCATCTAAAA
*
220768 CAAA-ACCACAGGAAAATTCAGTAGTTTCATGAATGATGTAACACCCC-
324 CAAAGACC-CAAGAAAATTCAGTAGTTTCATGAATGATGTAACACCCCA
* * *
220815 A-AGAAG---CAGATGAAAACACTTGACTATATAAGTTTTTCAGACCCTAAACCAAAATTAATGG
1 AGAGAAGAAACTGATGAAAACACTTGACTATATAAGTTTTTCAAACCCTAAACCAAAATTAATAG
* * * * * *
220876 CAAAAGGTTCAGAGTATAGTTAAACTCAATTAAACCCAAACCCAAGAATCACCAAATTAAAAGCA
66 CAAAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAACCCAAGAATCACCAAGTTAAAAGAA
220941 TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACCATTGAATTGCAGCTTCTACCAAGTA
131 TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACCATTGAATTGCAGCTTCTACCAAGTA
* *
221006 GGTTCGTTCTTGGTTCCACTGCACCTCATCCAAAGTGGATTATATCATCGTTGGCTCACTGGAAA
196 GGTTCGTTCTTGGCTCCACTGCACCTCATCCAAAGTGGATTATATCATCATTGGCTCACTGGAAA
* *
221071 TATATACACATTGTAAAAATAACACAATTTACAAAAGTTGTTATTTTCATGAAACCATCTAAAAC
261 TATATAAACATTGTAAATATAACACAATTTACAAAAGTT-TTATTTTCATGAAACCATCTAAAAC
221136 AAAGACCCAAGAAAATTCAGTAGTTTCATGAATGATGTAACACCCCA
325 AAAGACCCAAGAAAATTCAGTAGTTTCATGAATGATGTAACACCCCA
* * *
221183 AGAGAAGAAACTGATGAAAACACTTGACTATACAAGTTTTTCAAACCCTACACCGAAATTAATAG
1 AGAGAAGAAACTGATGAAAACACTTGACTATATAAGTTTTTCAAACCCTAAACCAAAATTAATAG
*
221248 CAAAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAACCCAAGAATCACCAAGTTGAAAGAA
66 CAAAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAACCCAAGAATCACCAAGTTAAAAGAA
221313 TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACCATT
131 TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACCATT
221356 ACTTGGCTCC
Statistics
Matches: 827, Mismatches: 73, Indels: 28
0.89 0.08 0.03
Matches are distributed among these distances:
367 64 0.08
368 271 0.33
369 6 0.01
371 6 0.01
372 293 0.35
373 64 0.08
374 120 0.15
375 3 0.00
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (371 bp):
AGAGAAGAAACTGATGAAAACACTTGACTATATAAGTTTTTCAAACCCTAAACCAAAATTAATAG
CAAAAGGTTTAGAGTATAATTAAACTCAATCAAACCCTAACCCAAGAATCACCAAGTTAAAAGAA
TTTAATTAAAAAGACAGCCTCAGTTGAATCCATTAAAACCATTGAATTGCAGCTTCTACCAAGTA
GGTTCGTTCTTGGCTCCACTGCACCTCATCCAAAGTGGATTATATCATCATTGGCTCACTGGAAA
TATATAAACATTGTAAATATAACACAATTTACAAAAGTTTTATTTTCATGAAACCATCTAAAACA
AAGACCCAAGAAAATTCAGTAGTTTCATGAATGATGTAACACCCCA
Found at i:223040 original size:24 final size:24
Alignment explanation
Indices: 222983--223041 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
222973 AATTTGATAA
*
222983 TTTTTTAATTTGGTACCTATTTTT
1 TTTTTTAATTTAGTACCTATTTTT
** * *
223007 TTAATCAATTTAGTACTTATTTTT
1 TTTTTTAATTTAGTACCTATTTTT
223031 TTTTTTAATTT
1 TTTTTTAATTT
223042 GATATCTAAG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.07, G:0.05, T:0.66
Consensus pattern (24 bp):
TTTTTTAATTTAGTACCTATTTTT
Found at i:223324 original size:27 final size:26
Alignment explanation
Indices: 223246--223336 Score: 73
Period size: 27 Copynumber: 3.5 Consensus size: 26
223236 AAAGCTTTAA
**
223246 AAATTAAAAATAAAAAATCATTATTTT
1 AAATTAAAAATAAAAAA-CATTAAATT
*
223273 AAATTAACAAAATGAAATAA-A-TAAATT
1 AAATT-A-AAAAT-AAAAAACATTAAATT
*
223300 AAATTAAAAATAAAAAACATTTAAAAT
1 AAATTAAAAATAAAAAACA-TTAAATT
223327 AAA--AAAAATA
1 AAATTAAAAATA
223337 CCATTTTATT
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
24 5 0.09
25 13 0.25
26 1 0.02
27 22 0.42
28 2 0.04
29 5 0.09
30 5 0.09
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (26 bp):
AAATTAAAAATAAAAAACATTAAATT
Found at i:225268 original size:12 final size:12
Alignment explanation
Indices: 225253--225317 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
225243 AAACGCATAA
225253 AAAAATAGCAAC
1 AAAAATAGCAAC
* *
225265 AAAAATAACAGC
1 AAAAATAGCAAC
*
225277 AAAAACAGCAAC
1 AAAAATAGCAAC
* *
225289 AAAAATAACAGC
1 AAAAATAGCAAC
225301 AAAAATAGCAAC
1 AAAAATAGCAAC
*
225313 CAAAA
1 AAAAA
225318 CAGTAAAAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.68, C:0.18, G:0.08, T:0.06
Consensus pattern (12 bp):
AAAAATAGCAAC
Found at i:225280 original size:24 final size:24
Alignment explanation
Indices: 225253--225317 Score: 112
Period size: 24 Copynumber: 2.7 Consensus size: 24
225243 AAACGCATAA
225253 AAAAATAGCAACAAAAATAACAGC
1 AAAAATAGCAACAAAAATAACAGC
*
225277 AAAAACAGCAACAAAAATAACAGC
1 AAAAATAGCAACAAAAATAACAGC
*
225301 AAAAATAGCAACCAAAA
1 AAAAATAGCAACAAAAA
225318 CAGTAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.68, C:0.18, G:0.08, T:0.06
Consensus pattern (24 bp):
AAAAATAGCAACAAAAATAACAGC
Found at i:225325 original size:21 final size:21
Alignment explanation
Indices: 225295--225339 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
225285 CAACAAAAAT
*
225295 AACAGC-AAAAATAGCAACCAA
1 AACAGCAAAAAATA-AAACCAA
*
225316 AACAGTAAAAAATAAAACCAA
1 AACAGCAAAAAATAAAACCAA
225337 AAC
1 AAC
225340 GACAATCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.67, C:0.20, G:0.07, T:0.07
Consensus pattern (21 bp):
AACAGCAAAAAATAAAACCAA
Found at i:225326 original size:33 final size:33
Alignment explanation
Indices: 225289--225360 Score: 90
Period size: 33 Copynumber: 2.2 Consensus size: 33
225279 AAACAGCAAC
* * *
225289 AAAAATAACAGCAAAAATAGCAACCAAAACAGTA
1 AAAAATAAAACCAAAAAGA-CAACCAAAACAGTA
* *
225323 AAAAATAAAACCAAAACGACAATCAAAACAGTA
1 AAAAATAAAACCAAAAAGACAACCAAAACAGTA
225356 AAAAA
1 AAAAA
225361 AGCACCAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
33 18 0.55
34 15 0.45
ACGTcount: A:0.68, C:0.17, G:0.07, T:0.08
Consensus pattern (33 bp):
AAAAATAAAACCAAAAAGACAACCAAAACAGTA
Found at i:227895 original size:133 final size:133
Alignment explanation
Indices: 227657--227920 Score: 519
Period size: 133 Copynumber: 2.0 Consensus size: 133
227647 AAGAAATTGA
227657 TAGTCTGATTGGGAGAGTTGTTAAAATTGATGTTCAAACTAGCAAGGGAACAAGAGGACAATTTG
1 TAGTCTGATTGGGAGAGTTGTTAAAATTGATGTTCAAACTAGCAAGGGAACAAGAGGACAATTTG
227722 CCCGGTTTGCTGTGCAGGTGAATCTCAATCTTCCATTGGTCTCGAAAATTCGTACTGCGAATACT
66 CCCGGTTTGCTGTGCAGGTGAATCTCAATCTTCCATTGGTCTCGAAAATTCGTACTGCGAATACT
227787 CGG
131 CGG
*
227790 TAGTCTGATTGGGAGGGTTGTTAAAATTGATGTTCAAACTAGCAAGGGAACAAGAGGACAATTTG
1 TAGTCTGATTGGGAGAGTTGTTAAAATTGATGTTCAAACTAGCAAGGGAACAAGAGGACAATTTG
227855 CCCGGTTTGCTGTGCAGGTGAATCTCAATCTTCCATTGGTCTCGAAAATTCGTACTGCGAATACT
66 CCCGGTTTGCTGTGCAGGTGAATCTCAATCTTCCATTGGTCTCGAAAATTCGTACTGCGAATACT
227920 C
131 C
227921 TTCATAGGTC
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
133 130 1.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (133 bp):
TAGTCTGATTGGGAGAGTTGTTAAAATTGATGTTCAAACTAGCAAGGGAACAAGAGGACAATTTG
CCCGGTTTGCTGTGCAGGTGAATCTCAATCTTCCATTGGTCTCGAAAATTCGTACTGCGAATACT
CGG
Found at i:243111 original size:12 final size:13
Alignment explanation
Indices: 243089--243115 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
243079 TCTTCAAATA
243089 AATGTTTTTTTTC
1 AATGTTTTTTTTC
243102 AATGTTTTTTTTC
1 AATGTTTTTTTTC
243115 A
1 A
243116 GCGTATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.19, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
AATGTTTTTTTTC
Found at i:243615 original size:21 final size:21
Alignment explanation
Indices: 243589--243628 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
243579 TACGGGACAA
*
243589 CTGACGTGGCCGATTAACTAG
1 CTGACGTGGCCGATCAACTAG
243610 CTGACGTGGCCGATCAACT
1 CTGACGTGGCCGATCAACT
243629 TGCCACGTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.28, G:0.28, T:0.23
Consensus pattern (21 bp):
CTGACGTGGCCGATCAACTAG
Found at i:245399 original size:20 final size:21
Alignment explanation
Indices: 245374--245418 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
245364 ATTACAAAAA
245374 AAAAAAATCAAAATAA-TTTT
1 AAAAAAATCAAAATAACTTTT
*
245394 AAAAAATTCAAAATAACTTTT
1 AAAAAAATCAAAATAACTTTT
245415 AAAA
1 AAAA
245419 TTCAAAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAAATCAAAATAACTTTT
Found at i:245438 original size:19 final size:19
Alignment explanation
Indices: 245375--245439 Score: 80
Period size: 19 Copynumber: 3.4 Consensus size: 19
245365 TTACAAAAAA
*
245375 AAAAAATCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
245394 AAAAAATTCAAAATAACTTTT
1 -AAAAATTCAAAATAA-TTTT
245415 -AAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
245433 AAAAATT
1 AAAAATT
245440 TTAAAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
17 3 0.07
18 2 0.05
19 18 0.44
20 14 0.34
21 4 0.10
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:246523 original size:2 final size:2
Alignment explanation
Indices: 246516--246552 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
246506 AAAAAGAGTC
*
246516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
246553 ATAAGCATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:269853 original size:33 final size:35
Alignment explanation
Indices: 269791--269855 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
269781 AAACTTAGGT
* * *
269791 AAAAAAAAAAAATTCTAAAGTATGGTAAAATTACA
1 AAAAAAAAAAAATCCGAAAGTATGATAAAATTACA
269826 AAAAAAAAAAAATCCGAAA-T-TGATAAAATT
1 AAAAAAAAAAAATCCGAAAGTATGATAAAATT
269856 TATAGAAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 9 0.33
34 1 0.04
35 17 0.63
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.22
Consensus pattern (35 bp):
AAAAAAAAAAAATCCGAAAGTATGATAAAATTACA
Found at i:277869 original size:21 final size:21
Alignment explanation
Indices: 277843--277929 Score: 156
Period size: 21 Copynumber: 4.1 Consensus size: 21
277833 CGATAGTGTG
277843 TGGATTGTGATGTTTGAGAAC
1 TGGATTGTGATGTTTGAGAAC
277864 TGGATTGTGATGTTTGAGAAC
1 TGGATTGTGATGTTTGAGAAC
277885 TGGATTGTGATGTTTGAGAAC
1 TGGATTGTGATGTTTGAGAAC
* *
277906 TGGGTTGTGATGTTTGAAAAC
1 TGGATTGTGATGTTTGAGAAC
277927 TGG
1 TGG
277930 TGGCAGCAAC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.23, C:0.05, G:0.34, T:0.38
Consensus pattern (21 bp):
TGGATTGTGATGTTTGAGAAC
Found at i:292208 original size:135 final size:135
Alignment explanation
Indices: 291962--292212 Score: 439
Period size: 135 Copynumber: 1.9 Consensus size: 135
291952 ATGGTGACTA
*
291962 AGGTGTGGGTTTGCTAACGGGATCGAGGTTGAAGCTAATGGTTTTAAGGGTGGTTTGTGTTTGGC
1 AGGTGTGGGTTTGCTAACGGGATCGAGGTTGAAGCTAATGGTTCTAAGGGTGGTTTGTGTTTGGC
* *
292027 ATGTAATTTTGAGGTTATGGTGAGTCTTCAAAGTTTCTCAATGAATCATATAATGGCGAGTATTC
66 ATGTAATTTTGAGGTTATGATGAGTCTTCAAAGTTTCTCAACGAATCATATAATGGCGAGTATTC
292092 GGAAG
131 GGAAG
* *
292097 AGGTGTGGGTTTGCTAACGGGATCGAGTTTGAAGCTGATGGTTCTAAGGGTGGTTTGTGTTTGGC
1 AGGTGTGGGTTTGCTAACGGGATCGAGGTTGAAGCTAATGGTTCTAAGGGTGGTTTGTGTTTGGC
* *
292162 ATGTAATTTTGGGGTTATGATGAGTCTTCAAAGTTTCTTAACGAATCATAT
66 ATGTAATTTTGAGGTTATGATGAGTCTTCAAAGTTTCTCAACGAATCATAT
292213 TAATATATTG
Statistics
Matches: 109, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 109 1.00
ACGTcount: A:0.23, C:0.09, G:0.31, T:0.37
Consensus pattern (135 bp):
AGGTGTGGGTTTGCTAACGGGATCGAGGTTGAAGCTAATGGTTCTAAGGGTGGTTTGTGTTTGGC
ATGTAATTTTGAGGTTATGATGAGTCTTCAAAGTTTCTCAACGAATCATATAATGGCGAGTATTC
GGAAG
Found at i:296826 original size:25 final size:24
Alignment explanation
Indices: 296775--296822 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
296765 TCTTTTAACC
296775 GTTCTTTTATAAAAAAGAATTTGT
1 GTTCTTTTATAAAAAAGAATTTGT
296799 GTTCTTTTATAAAAAAGAATTTGT
1 GTTCTTTTATAAAAAAGAATTTGT
296823 TGTTTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (24 bp):
GTTCTTTTATAAAAAAGAATTTGT
Found at i:303691 original size:6 final size:6
Alignment explanation
Indices: 303680--303704 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
303670 GGAGCTAAGG
303680 GAGAAA GAGAAA GAGAAA GAGAAA G
1 GAGAAA GAGAAA GAGAAA GAGAAA G
303705 GTAAGGAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:305756 original size:21 final size:21
Alignment explanation
Indices: 305727--305773 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
305717 AGGAAAATAA
*
305727 TTTTT-AAAAAATAAATTTTT
1 TTTTTGAAAAAATAAATATTT
* *
305747 TTTTTGAAAAAGTTAATATTT
1 TTTTTGAAAAAATAAATATTT
305768 TTTTTG
1 TTTTTG
305774 TGTTTGGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (21 bp):
TTTTTGAAAAAATAAATATTT
Found at i:305974 original size:13 final size:14
Alignment explanation
Indices: 305943--305975 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
305933 TTTTTTTGAT
305943 TGAAAATGATTTTC
1 TGAAAATGATTTTC
*
305957 GGAAAATGA-TTTC
1 TGAAAATGATTTTC
305970 TGAAAA
1 TGAAAA
305976 ATGTCTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (14 bp):
TGAAAATGATTTTC
Found at i:308807 original size:26 final size:26
Alignment explanation
Indices: 308736--308807 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 26
308726 TGTTAGACGA
* *
308736 AAGATGTACTGTATGATATTTGGTTT
1 AAGATGTACAGTATGATATTTAGTTT
* * * *
308762 AATATGGACAATATGGTATTTAGTTT
1 AAGATGTACAGTATGATATTTAGTTT
*
308788 AAGATGTACAGTGTGATATT
1 AAGATGTACAGTATGATATT
308808 AATTTTATTT
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.22, T:0.42
Consensus pattern (26 bp):
AAGATGTACAGTATGATATTTAGTTT
Found at i:319345 original size:2 final size:2
Alignment explanation
Indices: 319338--319362 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
319328 TGAATGCGAC
319338 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 G
319363 TACATTGAAC
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:320371 original size:21 final size:23
Alignment explanation
Indices: 320330--320371 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
320320 CGCAACCCCT
*
320330 ACAAATGAAAAGTTCGCTTTTAG
1 ACAAATGAAAAGTTCGATTTTAG
320353 ACAAAT-AAAA-TTCGATTTT
1 ACAAATGAAAAGTTCGATTTT
320372 GAATGTAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 4 0.22
23 6 0.33
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
ACAAATGAAAAGTTCGATTTTAG
Found at i:323480 original size:6 final size:6
Alignment explanation
Indices: 323467--323505 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
323457 GAAGAAGAGA
* *
323467 AAGA-G AAGATG AAGATG AAGATG AAGATG GAGGTG AAGA
1 AAGATG AAGATG AAGATG AAGATG AAGATG AAGATG AAGA
323506 AAGGCAACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
5 4 0.14
6 25 0.86
ACGTcount: A:0.49, C:0.00, G:0.38, T:0.13
Consensus pattern (6 bp):
AAGATG
Found at i:328881 original size:29 final size:30
Alignment explanation
Indices: 328814--328875 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
328804 TAAAATGGGG
*
328814 TTTTAAGTT-CTTTAAAAGTAAGAAAAAAA
1 TTTTAAATTCCTTTAAAAGTAAGAAAAAAA
*
328843 TTTTAAATTCCTTT-AAAGTTAATAAAAAAA
1 TTTTAAATTCCTTTAAAAG-TAAGAAAAAAA
328873 TTT
1 TTT
328876 GGATTCTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 12 0.41
30 17 0.59
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (30 bp):
TTTTAAATTCCTTTAAAAGTAAGAAAAAAA
Found at i:328959 original size:31 final size:32
Alignment explanation
Indices: 328866--328962 Score: 94
Period size: 30 Copynumber: 3.1 Consensus size: 32
328856 TAAAGTTAAT
** *
328866 AAAAAAATTTGG-ATTCTTAAAAACTAAA-AA
1 AAAAAAATTTGGAACCCTTAAAAATTAAATAA
* *
328896 AAAAAAATTTGGGACCCCTTAAAAATT-GATAA
1 AAAAAAATTT-GGAACCCTTAAAAATTAAATAA
* *
328928 AAAAAAATTT-TAACCTTTAAAAATTAAATAA
1 AAAAAAATTTGGAACCCTTAAAAATTAAATAA
328959 AAAA
1 AAAA
328963 TTAGACCCAT
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
30 22 0.41
31 11 0.20
32 21 0.39
ACGTcount: A:0.59, C:0.08, G:0.06, T:0.27
Consensus pattern (32 bp):
AAAAAAATTTGGAACCCTTAAAAATTAAATAA
Found at i:328975 original size:28 final size:30
Alignment explanation
Indices: 328894--328982 Score: 83
Period size: 28 Copynumber: 3.0 Consensus size: 30
328884 AAAAACTAAA
* *
328894 AAAAAAAAATTTGGGACCCCTTAAAAATTGAT
1 AAAAAAAAA-TT-AGACCCATTAAAAATTGAT
** * *
328926 AAAAAAAAATTTTAACCTTTAAAAATT-A-
1 AAAAAAAAATTAGACCCATTAAAAATTGAT
*
328954 AATAAAAAATTAGACCCATTAAAAATTGA
1 AAAAAAAAATTAGACCCATTAAAAATTGA
328983 AAATTAATAT
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 22 0.47
29 2 0.04
30 12 0.26
31 2 0.04
32 9 0.19
ACGTcount: A:0.56, C:0.10, G:0.07, T:0.27
Consensus pattern (30 bp):
AAAAAAAAATTAGACCCATTAAAAATTGAT
Found at i:332013 original size:21 final size:21
Alignment explanation
Indices: 331984--332027 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
331974 ATCCTTCATC
* *
331984 TGTTATGGAGTTAAAGTCAACT
1 TGTTATGGAG-CAAAGACAACT
332006 TGTT-TGGAGCAAAGACAACT
1 TGTTATGGAGCAAAGACAACT
332026 TG
1 TG
332028 GTCATAGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 11 0.55
21 5 0.25
22 4 0.20
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (21 bp):
TGTTATGGAGCAAAGACAACT
Found at i:333827 original size:198 final size:198
Alignment explanation
Indices: 333405--334114 Score: 896
Period size: 198 Copynumber: 3.5 Consensus size: 198
333395 GTAAAAATAA
* * * * *
333405 GTATCGATACTTATATGGGTATAGATACCAAATTGGCATTTTGTTGATTTAAAAATACTATTCAT
1 GTATTGATACTTATATGGGTATCGATACCAAATTGGCATTTTATTGATTTAAAAATATTGTTCAT
* ** * * * *
333470 TTGGAAAAATATCGATACTTCAATTTATAGTATCGTTACTTTTTGCCAAAAAGTTAAAAATTTCA
66 TTGGAAAAATATTGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCTCA
* * *
333535 TGTTTGGTAGGATTTCTTATGCTCAAACCAAAACCAACTAAAAAAGAATCTTAAGTACACATATA
131 T-TTTGGTATGATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAACCTTAAGTACACATATA
333600 ACTT
195 ACTT
*
333604 GTATTGATACTTATATGGATATCGATACCAAATTGGCATTTTATTGATTTAAAAATATTGTTCAT
1 GTATTGATACTTATATGGGTATCGATACCAAATTGGCATTTTATTGATTTAAAAATATTGTTCAT
* *
333669 TTGGAAAAATATTGATATTTCAACCTATAGTATTGATACTTTTTGACAGAAAGTTAAAAATCTCA
66 TTGGAAAAATATTGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCTCA
*
333734 TTTTGGTATGATTTCTCATGCTCAAATCAAAACCAACTAAAAAAGAACCTTAAGTACACATATAA
131 TTTTGGTATGATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAACCTTAAGTACACATATAA
333799 CTT
196 CTT
* *
333802 GTATTGATACTTATATGGGTATCGATACCAAATTGACATTTTGTTGATTTAAAAATATTGTTCAT
1 GTATTGATACTTATATGGGTATCGATACCAAATTGGCATTTTATTGATTTAAAAATATTGTTCAT
**
333867 TTGGAAAAATATCAATACTTCAACCTATAGTATTCATAATACTTCAATAGTATTCATACTTTTTG
66 TTGGAAAAATATTGATACTTCAACCTATAG---------TA--T---T-G-----ATACTTTTTG
* * *
333932 CCAGAAACTTAAAAATCTC--------ATCATTTCTCATGCTCAAACCAAAACCAACTAAAAACG
111 CCAGAAAGTTAAAAATCTCATTTTGGTATGATTTCTCATGCTCAAACCAAAACCAACTAAAAAAG
333989 AACCTTAAGTACACATATAACTT
176 AACCTTAAGTACACATATAACTT
* * * * *
334012 GTATTGATACTTATATGGGTATCGATATCAAATTGGCATTCTATAGTTTTAAAAATAATGTTCAT
1 GTATTGATACTTATATGGGTATCGATACCAAATTGGCATTTTATTGATTTAAAAATATTGTTCAT
334077 TTGGAAAAATATTGATACTTCAACCTATAGTATTGATA
66 TTGGAAAAATATTGATACTTCAACCTATAGTATTGATA
334115 ACTTCATTCC
Statistics
Matches: 452, Mismatches: 39, Indels: 49
0.84 0.07 0.09
Matches are distributed among these distances:
190 3 0.01
195 1 0.00
196 1 0.00
198 152 0.34
199 117 0.26
201 2 0.00
207 2 0.00
209 1 0.00
210 144 0.32
212 1 0.00
213 1 0.00
218 27 0.06
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (198 bp):
GTATTGATACTTATATGGGTATCGATACCAAATTGGCATTTTATTGATTTAAAAATATTGTTCAT
TTGGAAAAATATTGATACTTCAACCTATAGTATTGATACTTTTTGCCAGAAAGTTAAAAATCTCA
TTTTGGTATGATTTCTCATGCTCAAACCAAAACCAACTAAAAAAGAACCTTAAGTACACATATAA
CTT
Found at i:336773 original size:24 final size:24
Alignment explanation
Indices: 336740--336839 Score: 103
Period size: 24 Copynumber: 4.1 Consensus size: 24
336730 ATACTGGTTA
336740 AACTCTATCTGGGCTCGAATGAGCT
1 AACT-TATCTGGGCTCGAATGAGCT
*
336765 AACTTATCTAGGCTCGTAA-GAGCT
1 AACTTATCTGGGCTCG-AATGAGCT
* *
336789 AACCTATCTGGGCTCGTATGAGCT
1 AACTTATCTGGGCTCGAATGAGCT
* * * *
336813 AATTTTGTTTGGGCTCGTATGAGCT
1 AA-CTTATCTGGGCTCGAATGAGCT
336838 AA
1 AA
336840 ATTTCTGAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
23 1 0.02
24 37 0.58
25 26 0.41
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (24 bp):
AACTTATCTGGGCTCGAATGAGCT
Found at i:338551 original size:44 final size:44
Alignment explanation
Indices: 338501--338592 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
338491 AAATAAATTG
*
338501 TGGTGATTCCAATACAACGCACTTAGTCACCAAAAATCTGCAAA
1 TGGTGATTCCAATACAACGCACTTAGTCACCAAAAATCAGCAAA
* * * *
338545 TGGTGATTTCAATACAATGCACTTAGTCACTAAAAGTCAGCAAA
1 TGGTGATTCCAATACAACGCACTTAGTCACCAAAAATCAGCAAA
338589 TGGT
1 TGGT
338593 CATATGCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (44 bp):
TGGTGATTCCAATACAACGCACTTAGTCACCAAAAATCAGCAAA
Found at i:338698 original size:23 final size:22
Alignment explanation
Indices: 338656--338699 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
338646 GTACTTTTTT
*
338656 ATACATAAATATTTTAATTTAA
1 ATACATAAATATTGTAATTTAA
338678 ATACAATAAAT-TTGTACATTTA
1 ATAC-ATAAATATTGTA-ATTTA
338700 TATTTAAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (22 bp):
ATACATAAATATTGTAATTTAA
Found at i:356893 original size:20 final size:20
Alignment explanation
Indices: 356821--356892 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
356811 TAAAATACAA
356821 ATTTTGAATTTTTTATAAA-T
1 ATTTTGAATTTTTTA-AAATT
*
356841 ATTTTGAA-TTTTAAAAATT
1 ATTTTGAATTTTTTAAAATT
*
356860 ATTTTCAATTTTTTAAAATT
1 ATTTTGAATTTTTTAAAATT
356880 ATTTTG-ATTTTTT
1 ATTTTGAATTTTTT
356893 TTTTGTAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
18 3 0.07
19 20 0.43
20 23 0.50
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.61
Consensus pattern (20 bp):
ATTTTGAATTTTTTAAAATT
Found at i:361537 original size:47 final size:47
Alignment explanation
Indices: 361478--361571 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
361468 GGATCGAGAT
361478 GTTAGGCTACACGATGCTACTTACACGAGTTGTGGAGAATTCGCAAC
1 GTTAGGCTACACGATGCTACTTACACGAGTTGTGGAGAATTCGCAAC
*
361525 GTTAGGCTACACGATGCTGCTTACACGAGTTGTGGAGAATTCGCAAC
1 GTTAGGCTACACGATGCTACTTACACGAGTTGTGGAGAATTCGCAAC
361572 AAATGTCGTA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.26
Consensus pattern (47 bp):
GTTAGGCTACACGATGCTACTTACACGAGTTGTGGAGAATTCGCAAC
Found at i:361813 original size:158 final size:158
Alignment explanation
Indices: 361525--361946 Score: 657
Period size: 158 Copynumber: 2.7 Consensus size: 158
361515 AATTCGCAAC
* * *
361525 GTTAGGCTACACGATGCTGCTTACACGAGTTGTGGAGAATTCGCAACAAATGTCGTATCTCAGCC
1 GTTAGGCTACACGATGCTGCTTACACGAGCTGTGGAGAATCCGCAACAAATGTCGGATCTCAGCC
* * *
361590 ATCAGTAGGACATCTAAGACCAACACCCATATAACCTGTAATGCTTACACGAGCTGTGAAGTGGG
66 ATCGGTAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTCACACGAGCTGTGAAGTGGG
*
361655 CCTGCTCACACAAGCTGTGGGTCGAGAT
131 CCTGCTCACACAAGCTGTGGGTCAAGAT
* ** *
361683 GTTAGGCTACACGATGCTGCTCACACGAGCTGTAAAGAATCCGCAACAAAAT-TCGGATCTCAAC
1 GTTAGGCTACACGATGCTGCTTACACGAGCTGTGGAGAATCCGCAAC-AAATGTCGGATCTCAGC
*
361747 CATCGGTAGGACATCTAAGACCAGTACCCATATAACCTGTAATGCTCACACGAGCTGTGAAGTGG
65 CATCGGTAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTCACACGAGCTGTGAAGTGG
*
361812 GCCTTCTCACACAAGCTGTGGGTCAAGAT
130 GCCTGCTCACACAAGCTGTGGGTCAAGAT
* * *
361841 GTTAGGCTACACGATACTGCTTACACAAGCTGTGGAGAATCCGCAACAAATGTTGGATCTCAGCC
1 GTTAGGCTACACGATGCTGCTTACACGAGCTGTGGAGAATCCGCAACAAATGTCGGATCTCAGCC
* * *
361906 ATCGATAGAACATCTAAGACCAGCACCCATTTAACCTGTAA
66 ATCGGTAGGACATCTAAGACCAGCACCCATATAACCTGTAA
361947 ATCCCGAAAT
Statistics
Matches: 238, Mismatches: 24, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
157 4 0.02
158 230 0.97
159 4 0.02
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (158 bp):
GTTAGGCTACACGATGCTGCTTACACGAGCTGTGGAGAATCCGCAACAAATGTCGGATCTCAGCC
ATCGGTAGGACATCTAAGACCAGCACCCATATAACCTGTAATGCTCACACGAGCTGTGAAGTGGG
CCTGCTCACACAAGCTGTGGGTCAAGAT
Found at i:363745 original size:3 final size:3
Alignment explanation
Indices: 363737--363771 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
363727 TATAATCCAA
363737 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
363772 CATAATCTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:364461 original size:18 final size:18
Alignment explanation
Indices: 364435--364476 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
364425 AAGTCAACGA
364435 TCAACGAGTC-AGTCAAAG
1 TCAACGAGTCGA-TCAAAG
*
364453 TCAATGAGTCGATCAAAG
1 TCAACGAGTCGATCAAAG
364471 TCAACG
1 TCAACG
364477 GGTTGGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (18 bp):
TCAACGAGTCGATCAAAG
Found at i:364614 original size:19 final size:19
Alignment explanation
Indices: 364586--364625 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
364576 TAATCGATTG
* *
364586 GGCTTCAAGGTTTGGGTTT
1 GGCTTCAAGGATTGGGCTT
*
364605 GGCTTGAAGGATTGGGCTT
1 GGCTTCAAGGATTGGGCTT
364624 GG
1 GG
364626 TATTGTGTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.10, G:0.42, T:0.35
Consensus pattern (19 bp):
GGCTTCAAGGATTGGGCTT
Found at i:370935 original size:12 final size:12
Alignment explanation
Indices: 370920--370945 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
370910 TTAACTAAAA
370920 AATTAAATGAAT
1 AATTAAATGAAT
370932 AATTAAATGAAT
1 AATTAAATGAAT
370944 AA
1 AA
370946 CAAAAACATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (12 bp):
AATTAAATGAAT
Found at i:383334 original size:29 final size:30
Alignment explanation
Indices: 383299--383356 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
383289 CCACATATAT
383299 AATTACAC-CAAATCAAAATTCGTGTATCA
1 AATTACACACAAATCAAAATTCGTGTATCA
383328 AATTACACATCAAATCAAAATTCGTGTAT
1 AATTACACA-CAAATCAAAATTCGTGTAT
383357 ACTTTTAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.45, C:0.19, G:0.07, T:0.29
Consensus pattern (30 bp):
AATTACACACAAATCAAAATTCGTGTATCA
Found at i:384208 original size:17 final size:17
Alignment explanation
Indices: 384186--384235 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
384176 GTTTTTTTCC
384186 ATTACAACTCTATTCAA
1 ATTACAACTCTATTCAA
* * *
384203 ATTACAATTATATTC-T
1 ATTACAACTCTATTCAA
*
384219 ATTACAACCCTATTCAA
1 ATTACAACTCTATTCAA
384236 TTCCAATAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTACAACTCTATTCAA
Found at i:386131 original size:19 final size:21
Alignment explanation
Indices: 386101--386141 Score: 68
Period size: 19 Copynumber: 2.0 Consensus size: 21
386091 ACACCAAACT
386101 CCAAATATTTTTACTT-TTCC
1 CCAAATATTTTTACTTCTTCC
386121 CCAAA-ATTTTTACTTCTTCC
1 CCAAATATTTTTACTTCTTCC
386141 C
1 C
386142 ACTTTCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.46
Consensus pattern (21 bp):
CCAAATATTTTTACTTCTTCC
Found at i:386352 original size:30 final size:29
Alignment explanation
Indices: 386294--386352 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
386284 ATGTTCTCCC
**
386294 AAAACTTTTACTCTCTCCCACTTTACCCT
1 AAAACTTTTACTCTCTCCCACTCAACCCT
386323 AAAACTTTTACTCCTCTCCCA-TCCAACCCT
1 AAAACTTTTACT-CTCTCCCACT-CAACCCT
386353 CCATCTACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 13 0.50
30 13 0.50
ACGTcount: A:0.25, C:0.41, G:0.00, T:0.34
Consensus pattern (29 bp):
AAAACTTTTACTCTCTCCCACTCAACCCT
Found at i:395167 original size:18 final size:18
Alignment explanation
Indices: 395144--395191 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
395134 ACAATTCATA
*
395144 TCACTTCCAATTCCAATT
1 TCACTTTCAATTCCAATT
* * *
395162 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCAATT
395180 TCACTTTCAATT
1 TCACTTTCAATT
395192 TTGATCACAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:395169 original size:6 final size:6
Alignment explanation
Indices: 395160--395188 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
395150 CCAATTCCAA
395160 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
1 TTTCAC TTTCAC TTTCAC TTTCAC TTTCA
395189 ATTTTGATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
TTTCAC
Found at i:398943 original size:3 final size:3
Alignment explanation
Indices: 398905--399055 Score: 54
Period size: 3 Copynumber: 49.0 Consensus size: 3
398895 TGAACATCAT
* * * * * *
398905 TAA TAT TAA TAT TAA TCA TAA T-A TAAA TTA TTA TAA TAAA TAA TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA T-AA TAA TAA
* ** *** *
398951 TAA TAA TAA TAA TAA CTACT TGT TAA TAA TAA TAA CGT TAG TAA TAA
1 TAA TAA TAA TAA TAA -TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
** * * * *
398998 TAA TAA TAA TAA -ACA TCG TAA TAA TGA TAG TAT TAA TTAA TAT TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA
*
399044 TAT TAA TAA TAA
1 TAA TAA TAA TAA
399056 AAAAGAAAAG
Statistics
Matches: 106, Mismatches: 34, Indels: 16
0.68 0.22 0.10
Matches are distributed among these distances:
2 3 0.03
3 92 0.87
4 11 0.10
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:398947 original size:22 final size:22
Alignment explanation
Indices: 398922--398965 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
398912 AATATTAATC
* *
398922 ATAATATAAATTATTATAATAA
1 ATAATATAAATAATAATAATAA
*
398944 ATAATATTAATAATAATAATAA
1 ATAATATAAATAATAATAATAA
398966 CTACTTGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
ATAATATAAATAATAATAATAA
Found at i:398951 original size:15 final size:15
Alignment explanation
Indices: 398905--399055 Score: 61
Period size: 15 Copynumber: 9.4 Consensus size: 15
398895 TGAACATCAT
*
398905 TAATATTAATATTAA
1 TAATAATAATATTAA
* *
398920 TCATAATATAAATTATTA
1 TAATAATA-ATATTA--A
398938 TAATAAATAATATTAA
1 TAAT-AATAATATTAA
* *
398954 TAATAATAATAACTACT
1 TAATAATAAT-ATTA-A
** *
398971 TGTTAATAATAATAA
1 TAATAATAATATTAA
* *
398986 CGTTAGTAATAATAATAA
1 ---TAATAATAATATTAA
**
399004 TAATAA-ACATCGTAA
1 TAATAATA-ATATTAA
* *
399019 TAATGATAGTATTAA
1 TAATAATAATATTAA
*
399034 TTAATATTAATATTAA
1 -TAATAATAATATTAA
399050 TAATAA
1 TAATAA
399056 AAAAGAAAAG
Statistics
Matches: 100, Mismatches: 24, Indels: 24
0.68 0.16 0.16
Matches are distributed among these distances:
14 1 0.01
15 36 0.36
16 29 0.29
17 8 0.08
18 22 0.22
19 4 0.04
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (15 bp):
TAATAATAATATTAA
Found at i:399018 original size:24 final size:24
Alignment explanation
Indices: 398974--399022 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
398964 AACTACTTGT
*
398974 TAATAATAATAACGTTAGTAATAA
1 TAATAATAATAACGATAGTAATAA
*
398998 TAATAATAATAAAC-ATCGTAATAA
1 TAATAATAAT-AACGATAGTAATAA
399022 T
1 T
399023 GATAGTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (24 bp):
TAATAATAATAACGATAGTAATAA
Found at i:400319 original size:29 final size:28
Alignment explanation
Indices: 400115--400321 Score: 166
Period size: 29 Copynumber: 7.1 Consensus size: 28
400105 AACTATCAAG
* * * *
400115 AAATTATATTTTGACCCCAAACATCTCTA
1 AAATTACATTTTGACCCCTAACTTC-CAA
* * *
400144 AAATTATATTTTTGACCCCGAACTTCAAA
1 AAATTACA-TTTTGACCCCTAACTTCCAA
* * *
400173 AAATTACATTTTTACTCCCAAATTTCCAA
1 AAATTACATTTTGAC-CCCTAACTTCCAA
*
400202 AAATTCCATTTTGACCCCTAACTTTCCAA
1 AAATTACATTTTGACCCCTAAC-TTCCAA
* *
400231 AAATTACATTTTAACCCTTGAACTTCCAA
1 AAATTACATTTTGACCCCT-AACTTCCAA
* * *
400260 AAATTTCATTTTTGACCCCAAAACTTTCAA
1 AAATTACA-TTTTGACCCC-TAACTTCCAA
400290 AAATTATCATTTT-ACCCTCTAA-TGTCCAA
1 AAATTA-CATTTTGACCC-CTAACT-TCCAA
400319 AAA
1 AAA
400322 ATTCCGTTTT
Statistics
Matches: 145, Mismatches: 24, Indels: 18
0.78 0.13 0.10
Matches are distributed among these distances:
28 12 0.08
29 87 0.60
30 44 0.30
31 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.35
Consensus pattern (28 bp):
AAATTACATTTTGACCCCTAACTTCCAA
Found at i:400437 original size:58 final size:58
Alignment explanation
Indices: 400151--400479 Score: 248
Period size: 58 Copynumber: 5.6 Consensus size: 58
400141 CTAAAATTAT
* *
400151 ATTTTTGACCCCG-AAC-TTCAAAAAATTACATTTTTACTCC-CAAATTTCCAAAAATTCC
1 ATTTTTGACCCCGAAACTTTC-AAAAATTACA-TTTTAC-CCTCGAATGTCCAAAAATTCC
* * *
400209 A-TTTTGACCCC-TAACTTTCCAAAAATTACATTTTAACCCTTGAACT-TCCAAAAATTTC
1 ATTTTTGACCCCGAAACTTT-CAAAAATTACATTTT-ACCCTCGAA-TGTCCAAAAATTCC
* *
400267 ATTTTTGACCCCAAAACTTTCAAAAATTATCATTTTACCCTCTAATGTCCAAAAAATTCC
1 ATTTTTGACCCCGAAACTTTCAAAAATTA-CATTTTACCCTCGAATGTCC-AAAAATTCC
* * ** *** * * * *
400327 GTTTTT-AGTCTTGATTTTTTTCTAAAATTACCGTTTTACCCTCGAATATCCAAAAAATCC
1 ATTTTTGA-CCCCGA-AACTTTCAAAAATTA-CATTTTACCCTCGAATGTCCAAAAATTCC
*
400387 ATTTTTGACCCCGAAACTTT-AAAAATTATCATTTTATCCC-CGGATGTCC-AAAATTCC
1 ATTTTTGACCCCGAAACTTTCAAAAATTA-CATTTTA-CCCTCGAATGTCCAAAAATTCC
* * *
400444 ATTTTTGATCCCGATA-TTTGTAAAAATTACCATTTT
1 ATTTTTGACCCCGAAACTTT-CAAAAATTA-CATTTT
400480 TGCTTCGAGA
Statistics
Matches: 217, Mismatches: 37, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
56 3 0.01
57 40 0.18
58 64 0.29
59 38 0.18
60 43 0.20
61 29 0.13
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (58 bp):
ATTTTTGACCCCGAAACTTTCAAAAATTACATTTTACCCTCGAATGTCCAAAAATTCC
Found at i:408959 original size:33 final size:34
Alignment explanation
Indices: 408917--408984 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
408907 GCTCCAATAG
408917 AGAACCATCAGGTTG-GTGATTGCCACAAATTCT
1 AGAACCATCAGGTTGAGTGATTGCCACAAATTCT
*
408950 AGAACCATCAGGTTGATTGATTGCCACAAATTCT
1 AGAACCATCAGGTTGAGTGATTGCCACAAATTCT
408984 A
1 A
408985 TCTTTCGACT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 15 0.45
34 18 0.55
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (34 bp):
AGAACCATCAGGTTGAGTGATTGCCACAAATTCT
Found at i:415367 original size:325 final size:324
Alignment explanation
Indices: 414778--415429 Score: 1250
Period size: 325 Copynumber: 2.0 Consensus size: 324
414768 ATAGGTTGCG
414778 AAAGTGTTCGAAGAAGTTTGCCATCAAAGGGGACGATAGGGCATACAGCACCTAAGAAGCTTGGT
1 AAAGTGTTCGAAGAAGTTTGCCATCAAAGGGGACGATAGGGCATACAGCACCTAAGAAGCTTGGT
414843 CGAGCAAGGAAAAGTCGAAGCCAAGGGAGCAGGAGAAAAAAGAAGTGAATAAAGTACTTCTTGTG
66 CGAGCAAGGAAAAGTCGAAGCCAAGGGAGCAGGAGAAAAAAGAAGTGAATAAAGTACTTCTTGTG
*
414908 CCGTGGTTTGCATGAGTTGCGAGACTGTATAAAGCAAACTGTGGTGGTCAAGGAAAAGGCAACAT
131 CCGTGGTTCGCATGAGTTGCGAGACTGTATAAAGCAAACTGTGGTGGTCAAGGAAAAGGCAACAT
*
414973 CAGAGTTTGTTGAGTCATTGGAGGGGTTTTGGGCTTCAACCCAAGGAATAGGTGAGTTTGTCATT
196 CAGAGCTTGTTGAGTCATTGGAGGGGTTTTGGGCTTCAACCCAAGGAATAGGTGAGTTTGTCATT
*
415038 GGACTTAATGGAGCAAGCCGCGATGAAAATAGTGAAGCTGGGACTAATGAGGCTTAATTTAAAA
261 GGACTTAATGGAGCAAGCCGCGATGAAAATAGTGAAGCTGGGACTAATAAGGCTTAATTTAAAA
*
415102 AAAGTGTTCGAAGAAGTTTGCCATCAAAGGGGACGATAGGGCATATAGCACCTAAGAAGCTTGGG
1 AAAGTGTTCGAAGAAGTTTGCCATCAAAGGGGACGATAGGGCATACAGCACCTAAGAAGCTT-GG
415167 TCGAGCAAGGAAAAGTCGAAGCCAAGGGAGCAGGAGAAAAAAGAAGTGAATAAAGTACTTCTTGT
65 TCGAGCAAGGAAAAGTCGAAGCCAAGGGAGCAGGAGAAAAAAGAAGTGAATAAAGTACTTCTTGT
415232 GCCGTGGTTCGCATGAGTTGCGAGACTGTATAAAGCAAACTGTGGTGGTCAAGGAAAAGGCAACA
130 GCCGTGGTTCGCATGAGTTGCGAGACTGTATAAAGCAAACTGTGGTGGTCAAGGAAAAGGCAACA
*
415297 TCAGAGCTTGTTGAGTCATTGGAGGGGTTTTGGGCTTTAACCCAAGGAATAGGTGAGTTTGTCAT
195 TCAGAGCTTGTTGAGTCATTGGAGGGGTTTTGGGCTTCAACCCAAGGAATAGGTGAGTTTGTCAT
415362 TGGACTTAATGGAGCAAGCCGCGATGAAAATAGTGAAGCTGGGACTAATAAGGCTTAATTTAAAA
260 TGGACTTAATGGAGCAAGCCGCGATGAAAATAGTGAAGCTGGGACTAATAAGGCTTAATTTAAAA
415427 AAA
1 AAA
415430 ACGATGGAGT
Statistics
Matches: 322, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
324 61 0.19
325 261 0.81
ACGTcount: A:0.34, C:0.14, G:0.30, T:0.22
Consensus pattern (324 bp):
AAAGTGTTCGAAGAAGTTTGCCATCAAAGGGGACGATAGGGCATACAGCACCTAAGAAGCTTGGT
CGAGCAAGGAAAAGTCGAAGCCAAGGGAGCAGGAGAAAAAAGAAGTGAATAAAGTACTTCTTGTG
CCGTGGTTCGCATGAGTTGCGAGACTGTATAAAGCAAACTGTGGTGGTCAAGGAAAAGGCAACAT
CAGAGCTTGTTGAGTCATTGGAGGGGTTTTGGGCTTCAACCCAAGGAATAGGTGAGTTTGTCATT
GGACTTAATGGAGCAAGCCGCGATGAAAATAGTGAAGCTGGGACTAATAAGGCTTAATTTAAAA
Found at i:417125 original size:25 final size:25
Alignment explanation
Indices: 417097--417160 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
417087 ATTGGAAGTA
*
417097 ATCTTAGAAGATTAAGGGAAATCAT
1 ATCTTATAAGATTAAGGGAAATCAT
417122 ATCTTATAAGATTAAGGGAAATCAT
1 ATCTTATAAGATTAAGGGAAATCAT
417147 ATCTTATAAGATTA
1 ATCTTATAAGATTA
417161 GACTAGATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.33
Consensus pattern (25 bp):
ATCTTATAAGATTAAGGGAAATCAT
Found at i:423366 original size:46 final size:46
Alignment explanation
Indices: 423299--423391 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
423289 GGAGAATGAC
423299 TACCAATTTTAAATTTCTTGCTGTCATACAAACGTATAAGATGATA
1 TACCAATTTTAAATTTCTTGCTGTCATACAAACGTATAAGATGATA
423345 TACCAATTTTAAATTTCTTGCTGTCATACAAACGTATAAGATGATA
1 TACCAATTTTAAATTTCTTGCTGTCATACAAACGTATAAGATGATA
423391 T
1 T
423392 TTTTTTGGGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.38
Consensus pattern (46 bp):
TACCAATTTTAAATTTCTTGCTGTCATACAAACGTATAAGATGATA
Found at i:430466 original size:54 final size:54
Alignment explanation
Indices: 430384--430491 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
430374 ATAGAAGAAA
430384 CCTTTTATTTTTGAGTTTTCACAATCACAAGGGAACAGAACAGATTTTTATGTT
1 CCTTTTATTTTTGAGTTTTCACAATCACAAGGGAACAGAACAGATTTTTATGTT
430438 CCTTTTATTTTTGAGTTTTCACAATCACAAGGGAACAGAACAGATTTTTATGTT
1 CCTTTTATTTTTGAGTTTTCACAATCACAAGGGAACAGAACAGATTTTTATGTT
430492 ACTTATTAAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (54 bp):
CCTTTTATTTTTGAGTTTTCACAATCACAAGGGAACAGAACAGATTTTTATGTT
Found at i:439798 original size:136 final size:137
Alignment explanation
Indices: 439545--439820 Score: 527
Period size: 136 Copynumber: 2.0 Consensus size: 137
439535 TACATCTTTC
439545 TTCATGAAGAAAAATCAATAACCATCACATAGTAATTAAATCATTTTTCTTACAACAAATAAGTC
1 TTCATGAAGAAAAATCAATAACCATCACATAGTAATTAAATCATTTTTCTTACAACAAATAAGTC
*
439610 ATGGCCACATTACTTTTTCAACAACCATGTAATGTCAATGAGAGGATATCATTTACTCTTATAGG
66 ATGGCCACATTACTTTTTCAACAACCATGTAACGTCAATGAGAGGATATCATTTACTCTTATAGG
439675 GCTATGA
131 GCTATGA
439682 TTCATGAA-AAAAATCAATAACCATCACATAGTAATTAAATCATTTTTCTTACAACAAATAAGTC
1 TTCATGAAGAAAAATCAATAACCATCACATAGTAATTAAATCATTTTTCTTACAACAAATAAGTC
*
439746 ATGGCCACATTACTTTTTCAACAACCATGTAACGTCAATGGGAGGATATCATTTACTCTTATAGG
66 ATGGCCACATTACTTTTTCAACAACCATGTAACGTCAATGAGAGGATATCATTTACTCTTATAGG
439811 GCTATGA
131 GCTATGA
439818 TTC
1 TTC
439821 CACTATTGTG
Statistics
Matches: 137, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
136 129 0.94
137 8 0.06
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (137 bp):
TTCATGAAGAAAAATCAATAACCATCACATAGTAATTAAATCATTTTTCTTACAACAAATAAGTC
ATGGCCACATTACTTTTTCAACAACCATGTAACGTCAATGAGAGGATATCATTTACTCTTATAGG
GCTATGA
Found at i:454024 original size:62 final size:59
Alignment explanation
Indices: 453907--454026 Score: 143
Period size: 62 Copynumber: 2.0 Consensus size: 59
453897 TCCGAATTTT
* * **
453907 TTTTTAACTTTTAAAGGTCAAAATTTTTTTACCAACTTTTAAGGGGCCTCCAAAAATTA
1 TTTTTAACTTTTAAAGGTCAAAATTTTTTTACCAACTTTTAAAGGACCTAAAAAAATTA
* *
453966 TTTTTAGCTTTT-AAGGATCCAAAATTTTGTATTACCAACTTTTAAAGGACTTAAAAAAATT
1 TTTTTAACTTTTAAAGG-T-CAAAATTTT-T-TTACCAACTTTTAAAGGACCTAAAAAAATT
454027 CTCTAACTTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
58 4 0.08
59 12 0.24
60 9 0.18
61 1 0.02
62 25 0.49
ACGTcount: A:0.36, C:0.13, G:0.10, T:0.41
Consensus pattern (59 bp):
TTTTTAACTTTTAAAGGTCAAAATTTTTTTACCAACTTTTAAAGGACCTAAAAAAATTA
Found at i:456156 original size:11 final size:11
Alignment explanation
Indices: 456142--456166 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
456132 CATAAAAAAA
456142 TAAATATATAT
1 TAAATATATAT
456153 TAAATATATAT
1 TAAATATATAT
456164 TAA
1 TAA
456167 TACGCTAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAATATATAT
Found at i:464311 original size:14 final size:14
Alignment explanation
Indices: 464279--464310 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
464269 TTTTGGATCA
464279 TTTTTTCTTTTCAT
1 TTTTTTCTTTTCAT
464293 TTTTTTC-TTTC-T
1 TTTTTTCTTTTCAT
464305 TTTTTT
1 TTTTTT
464311 TATGGATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 4 0.22
14 7 0.39
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTCTTTTCAT
Found at i:470443 original size:24 final size:24
Alignment explanation
Indices: 470385--470444 Score: 93
Period size: 24 Copynumber: 2.5 Consensus size: 24
470375 ATTTAGCCCA
*
470385 TACGAGCCTAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
470409 TACGAGTCCAGAATGGTTAGCTCT
1 TACGAGCCCAGAATGGTTAGCTCT
*
470433 TATGAGCCCAGA
1 TACGAGCCCAGA
470445 TAGAGTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.27
Consensus pattern (24 bp):
TACGAGCCCAGAATGGTTAGCTCT
Found at i:470613 original size:82 final size:82
Alignment explanation
Indices: 470472--470680 Score: 346
Period size: 82 Copynumber: 2.5 Consensus size: 82
470462 ATGATTTTGC
470472 TCACACAAGCTGATGAGAATCCGCGACATACACGAAGACTCAGCCGTCGATACGATCTAGAATTT
1 TCACACAAGCTGATGAGAATCCGCGACATACACGAAGACTCAGCCGTCGATACGATCTAGAATTT
470537 CTCACTCTCGATGCTGT
66 CTCACTCTCGATGCTGT
* * * *
470554 TCACACAAGCTGATGAGAATCCGCGACATACACGAAGATTGAGCCGTTGATACGGTCTAGAATTT
1 TCACACAAGCTGATGAGAATCCGCGACATACACGAAGACTCAGCCGTCGATACGATCTAGAATTT
*
470619 CTCACTCTCGATGTTGT
66 CTCACTCTCGATGCTGT
***
470636 TCACACAAGCTGATGAGAATCCGCGACATATGTGAAGACTCAGCC
1 TCACACAAGCTGATGAGAATCCGCGACATACACGAAGACTCAGCC
470681 ATCGGAGGAA
Statistics
Matches: 117, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 117 1.00
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (82 bp):
TCACACAAGCTGATGAGAATCCGCGACATACACGAAGACTCAGCCGTCGATACGATCTAGAATTT
CTCACTCTCGATGCTGT
Found at i:475341 original size:14 final size:15
Alignment explanation
Indices: 475322--475350 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
475312 AGTAAGTAAT
475322 AAATTTTTAA-ACTA
1 AAATTTTTAACACTA
475336 AAATTTTTAACACTA
1 AAATTTTTAACACTA
475351 TTCCAATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
AAATTTTTAACACTA
Found at i:477763 original size:3 final size:3
Alignment explanation
Indices: 477757--477781 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
477747 TTGCTATCAT
477757 TGA TGA TGA TGA TGA TGA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA T
477782 ATAAATGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:477933 original size:18 final size:18
Alignment explanation
Indices: 477910--477950 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
477900 TTGATAGTAG
*
477910 TAGTGCAAGCTATGATAA
1 TAGTGCAAACTATGATAA
*
477928 TAGTGCAAACTATGATGA
1 TAGTGCAAACTATGATAA
477946 TAGTG
1 TAGTG
477951 ATAGTGAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.37, C:0.10, G:0.24, T:0.29
Consensus pattern (18 bp):
TAGTGCAAACTATGATAA
Found at i:480678 original size:12 final size:13
Alignment explanation
Indices: 480661--480693 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
480651 ATAATTATTC
480661 ATATATAA-ATAA
1 ATATATAATATAA
480673 ATATATAATATAA
1 ATATATAATATAA
480686 AT-TATAAT
1 ATATATAAT
480694 TTAACTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 14 0.70
13 6 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATATAATATAA
Found at i:481833 original size:80 final size:80
Alignment explanation
Indices: 481700--481860 Score: 322
Period size: 80 Copynumber: 2.0 Consensus size: 80
481690 AATTCAAAGA
481700 TATAGAGATTGACCCAAACACGAGGGGCCCAAGTGCAAAATGAATCATCTCACAGACCTGATTGA
1 TATAGAGATTGACCCAAACACGAGGGGCCCAAGTGCAAAATGAATCATCTCACAGACCTGATTGA
481765 TTATTGGGCTAATAT
66 TTATTGGGCTAATAT
481780 TATAGAGATTGACCCAAACACGAGGGGCCCAAGTGCAAAATGAATCATCTCACAGACCTGATTGA
1 TATAGAGATTGACCCAAACACGAGGGGCCCAAGTGCAAAATGAATCATCTCACAGACCTGATTGA
481845 TTATTGGGCTAATAT
66 TTATTGGGCTAATAT
481860 T
1 T
481861 TTTAAGGACT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 81 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (80 bp):
TATAGAGATTGACCCAAACACGAGGGGCCCAAGTGCAAAATGAATCATCTCACAGACCTGATTGA
TTATTGGGCTAATAT
Found at i:481891 original size:17 final size:17
Alignment explanation
Indices: 481871--481903 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
481861 TTTAAGGACT
481871 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
481888 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
481904 TAAGTGTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:482176 original size:50 final size:50
Alignment explanation
Indices: 482097--482252 Score: 145
Period size: 50 Copynumber: 3.1 Consensus size: 50
482087 TGACATCCAT
* * *
482097 TAACTCTTATGATTAGTTAAGTTTGCATCATGAATAATGA-CATGCATTAAG
1 TAACTCATATG-TTAGTTAAATTTGCATCATAAATAAT-ATCATGCATTAAG
* * ** *
482148 TAACTTATATGTTAGTTAAATATGCATCATAAATCCTATCATGCATTATG
1 TAACTCATATGTTAGTTAAATTTGCATCATAAATAATATCATGCATTAAG
** * *
482198 TAACTCCCATGTTAGTTAAAGTTTGCATCATTAAATCAA-GTCATGCATTTAG
1 TAACTCATATGTTAGTTAAA-TTTGCATCA-TAAAT-AATATCATGCATTAAG
482250 TAA
1 TAA
482253 TCCATTAGTT
Statistics
Matches: 84, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
49 1 0.01
50 48 0.57
51 17 0.20
52 18 0.21
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (50 bp):
TAACTCATATGTTAGTTAAATTTGCATCATAAATAATATCATGCATTAAG
Found at i:483513 original size:27 final size:28
Alignment explanation
Indices: 483463--483527 Score: 96
Period size: 27 Copynumber: 2.3 Consensus size: 28
483453 AAAATATTGA
*
483463 AAAAAAAAATTCGAAGCTTGAAAAAAAAG
1 AAAAAAAAATTCGAA-CTTAAAAAAAAAG
*
483492 AAGAAAAAATTCGAA-TTAAAAAAAAAG
1 AAAAAAAAATTCGAACTTAAAAAAAAAG
483519 AAAAAAAAA
1 AAAAAAAAA
483528 AGAATTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 19 0.58
29 14 0.42
ACGTcount: A:0.72, C:0.05, G:0.11, T:0.12
Consensus pattern (28 bp):
AAAAAAAAATTCGAACTTAAAAAAAAAG
Found at i:483528 original size:29 final size:29
Alignment explanation
Indices: 483461--483528 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
483451 TAAAAATATT
*
483461 GAAAAAAAAAATTCGAAGCTTGAAAAAAAA
1 GAAAAAAAAAATTCGAA-CTTAAAAAAAAA
*
483491 G-AAGAAAAAATTCGAA-TTAAAAAAAAA
1 GAAAAAAAAAATTCGAACTTAAAAAAAAA
483518 GAAAAAAAAAA
1 GAAAAAAAAAA
483529 GAATTGAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.32
28 8 0.24
29 14 0.41
30 1 0.03
ACGTcount: A:0.72, C:0.04, G:0.12, T:0.12
Consensus pattern (29 bp):
GAAAAAAAAAATTCGAACTTAAAAAAAAA
Found at i:483532 original size:25 final size:25
Alignment explanation
Indices: 483483--483564 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 25
483473 TCGAAGCTTG
**
483483 AAAAAAAAGAAGAAAAAATTCGAATT
1 AAAAAAAAGAA-AAAAAATAAGAATT
483509 AAAAAAAAAGAAAAAAAA-AAGAATT
1 -AAAAAAAAGAAAAAAAATAAGAATT
* * * *
483534 -GAAAGAAGAAAAAAAATTGAGTATT
1 AAAAAAAAGAAAAAAAA-TAAGAATT
483559 AAAAAA
1 AAAAAA
483565 TCATTTTCTG
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
23 14 0.32
25 10 0.23
26 9 0.20
27 11 0.25
ACGTcount: A:0.73, C:0.01, G:0.12, T:0.13
Consensus pattern (25 bp):
AAAAAAAAGAAAAAAAATAAGAATT
Found at i:484340 original size:17 final size:17
Alignment explanation
Indices: 484320--484367 Score: 89
Period size: 16 Copynumber: 2.9 Consensus size: 17
484310 AAGAGTGGAG
484320 AAAAAGAAATTGAGAAA
1 AAAAAGAAATTGAGAAA
484337 AAAAAGAAATTGAG-AA
1 AAAAAGAAATTGAGAAA
484353 AAAAAGAAATTGAGA
1 AAAAAGAAATTGAGA
484368 TAAGAGAGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.69, C:0.00, G:0.19, T:0.12
Consensus pattern (17 bp):
AAAAAGAAATTGAGAAA
Done.