Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 1 of 373
Found at i:9885 original size:17 final size:19
Alignment explanation
Indices: 9847--9888 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
9837 AAATATGCAT
9847 AAATATATGTAAGTGTATA
1 AAATATATGTAAGTGTATA
9866 AAAT-TATG-AAGTGTGA-A
1 AAATATATGTAAGTGT-ATA
9883 AAATAT
1 AAATAT
9889 GTTTAAGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 11 0.52
18 6 0.29
19 4 0.19
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (19 bp):
AAATATATGTAAGTGTATA
Found at i:12202 original size:44 final size:44
Alignment explanation
Indices: 12131--12585 Score: 481
Period size: 44 Copynumber: 10.3 Consensus size: 44
12121 TGTCAACTAC
* * * * *
12131 AGGAAGGCAAGATCTACAATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * * *
12175 ATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* *
12220 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * * *
12263 AGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * *
12307 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* *
12352 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * * *
12395 AGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
* * *
12439 ATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTC-ACACCAATAT
* *
12484 GGGAAGACAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATAT
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCAC-ACCAATAT
* * * * *
12527 AGGAAGATAGGATCTGATATCTTCGATCTACTTCACGCCAATAC
1 AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
*
12571 ATGAAGACAAGATCT
1 AGGAAGACAAGATCT
12586 ACTTTAATGA
Statistics
Matches: 337, Mismatches: 62, Indels: 24
0.80 0.15 0.06
Matches are distributed among these distances:
42 3 0.01
43 63 0.19
44 202 0.60
45 69 0.20
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.27
Consensus pattern (44 bp):
AGGAAGACAAGATCTGCTATCTTCGATCTACTTCACACCAATAT
Found at i:12368 original size:132 final size:132
Alignment explanation
Indices: 12149--12590 Score: 866
Period size: 132 Copynumber: 3.3 Consensus size: 132
12139 AAGATCTACA
*
12149 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTGCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
12214 CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
66 CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
12279 AT
131 AT
12281 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
12346 CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
66 CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
12411 AT
131 AT
12413 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
12478 CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
66 CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
12543 AT
131 AT
*
12545 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTT
1 ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTT
12591 AATGACTTCA
Statistics
Matches: 308, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 308 1.00
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.28
Consensus pattern (132 bp):
ATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACTTCGCCAC
CAATATGGGAAGACAAGATCTGCATCTTCGATCCACTTCCTACCAATATAGGAAGATAGGATCTG
AT
Found at i:22253 original size:23 final size:21
Alignment explanation
Indices: 22215--22263 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
22205 TATTTTAACA
*
22215 ATTTAAGATTTATTAATT-AT
1 ATTTAAGATTTATTTATTAAT
* *
22235 -TTCAAGATTTATTTTTTAAT
1 ATTTAAGATTTATTTATTAAT
22255 ATTTAAGAT
1 ATTTAAGAT
22264 GAATGTAGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.61
20 2 0.09
21 7 0.30
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (21 bp):
ATTTAAGATTTATTTATTAAT
Found at i:26772 original size:229 final size:225
Alignment explanation
Indices: 26421--26871 Score: 573
Period size: 229 Copynumber: 2.0 Consensus size: 225
26411 TTTTTTTAAA
** * * * *
26421 TTTTATGAAATAGCTTTGAAGTCATTAATCTATGAATCAAAATCGAAATAACTTTTTTTTCGATT
1 TTTTATGAAATAGCTTTGAAGTCACCAATCTATAAATCAAAATCGAAACAACTTTTTCTTCGATA
* * * *
26486 TTCGACTTAACTATTAGATCGCCTGAAACTCACTAATTGGTCTTCTTTTTAAAAAAAAACTTAAC
66 TTCGACTTAACCATTAAATCGCCTGAAACTCACTAATAGGTCTTCTTTTTAAAAAAAAAATTAAC
* * * * * *
26551 AACCCAATTATTTAAATAAAAACGTTCT-AATAGTTTAGT-AGCTAAAATGAAAATTTTTAAATA
131 AACCCAATTATTTAAATAAAAAC-TTCTGAACAGCTCAGTGA-CTAAAATAAAAATTGTCAAATA
* *
26614 TTTCAGGTCTAAAATAAATTTTTTTGAATATTT
194 TTTCAGATCTAAAAT-AATTTTTTTAAATATTT
* * *
26647 TTTTATGAAATAGCTTTTGAAGTCACCAATTTGTAAATTAAAATCGAAACAACTTTCTTCTTCGA
1 TTTTATGAAATAGC-TTTGAAGTCACCAATCTATAAATCAAAATCGAAACAACTTT-TTCTTCGA
** *
26712 TATTCGACATTAACCATTAAATCGTTTGAAACTCACTAATAGGTCTTCTTTTTGAAAAAAAAATT
64 TATTCGAC-TTAACCATTAAATCGCCTGAAACTCACTAATAGGTCTTCTTTTTAAAAAAAAAATT
* * *
26777 AACAATCGAATTATTTAAATAAAAACTTTTGAACAGCTCAGTGACTAAAATAAAAATTGTCAAAT
128 AACAACCCAATTATTTAAATAAAAACTTCTGAACAGCTCAGTGACTAAAATAAAAATTGTCAAAT
* *
26842 ATTTTATATCTAAAATAATTTTTTTAAATA
193 ATTTCAGATCTAAAATAATTTTTTTAAATA
26872 ATTTAGTGTT
Statistics
Matches: 191, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
226 14 0.07
227 34 0.18
228 30 0.16
229 112 0.59
230 1 0.01
ACGTcount: A:0.40, C:0.13, G:0.09, T:0.39
Consensus pattern (225 bp):
TTTTATGAAATAGCTTTGAAGTCACCAATCTATAAATCAAAATCGAAACAACTTTTTCTTCGATA
TTCGACTTAACCATTAAATCGCCTGAAACTCACTAATAGGTCTTCTTTTTAAAAAAAAAATTAAC
AACCCAATTATTTAAATAAAAACTTCTGAACAGCTCAGTGACTAAAATAAAAATTGTCAAATATT
TCAGATCTAAAATAATTTTTTTAAATATTT
Found at i:35809 original size:18 final size:18
Alignment explanation
Indices: 35786--35878 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
35776 CCCAACTACT
*
35786 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
35804 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
35822 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
*
35840 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
35858 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
35876 GTA
1 GTA
35879 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:35838 original size:36 final size:36
Alignment explanation
Indices: 35786--35878 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
35776 CCCAACTACT
*
35786 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
35822 GTATACATGAATAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
35858 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
35879 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:43260 original size:29 final size:29
Alignment explanation
Indices: 43227--43286 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
43217 AGAGAAAGTC
*
43227 ACGAACTCTAAATATAAACTGTAAAATTG
1 ACGAACTCTAAATATAAACTATAAAATTG
43256 ACGAACTCTAAATATAAACTATAAAATTG
1 ACGAACTCTAAATATAAACTATAAAATTG
43285 AC
1 AC
43287 AAAGTAAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.50, C:0.15, G:0.08, T:0.27
Consensus pattern (29 bp):
ACGAACTCTAAATATAAACTATAAAATTG
Found at i:51918 original size:16 final size:16
Alignment explanation
Indices: 51897--51964 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
51887 TTTGGTTCGC
51897 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
51913 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
51929 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
51945 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
51961 TGTA
1 TGTA
51965 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:52220 original size:16 final size:16
Alignment explanation
Indices: 52180--52234 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 16
52170 TTAATCATAT
*
52180 TTAAACATA-ATTTTTA
1 TTAAA-ATATATTTTAA
52196 TT-AAATATATTTTAA
1 TTAAAATATATTTTAA
52211 TTAAAATATATAATTTAA
1 TTAAAATATAT--TTTAA
52229 -TAAAAT
1 TTAAAAT
52235 TCTTAATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 10 0.29
17 6 0.18
18 5 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTTAA
Found at i:52227 original size:18 final size:17
Alignment explanation
Indices: 52200--52234 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52190 TTTTTATTAA
*
52200 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52218 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52235 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52347 original size:18 final size:17
Alignment explanation
Indices: 52320--52354 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
52310 TTACTATTAA
*
52320 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
52338 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
52355 TCTTAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:52400 original size:61 final size:60
Alignment explanation
Indices: 52215--52405 Score: 155
Period size: 61 Copynumber: 3.2 Consensus size: 60
52205 TTTTAATTAA
* *
52215 AATATATAATTTAATAAAATTCTTAATAATT-AATATTCTTATATTAATTTACTGAAATCAT
1 AATATATAATTTAATAAAATTCTTAAT-ATTAAATATTCTTATATAAATTTTCT-AAATCAT
* * * * * *
52276 AATATATGATACT-GTAAAA-T-ATAA-ATTAACATAATTAC-TAT-TAAATATATT-TTAATTA
1 AATATATAAT-TTAATAAAATTCTTAATATTAA-AT-ATT-CTTATATAAAT-T-TTCTAAATCA
*
52334 A
60 T
*
52335 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCT-AAATCAT
52396 AATATATAAT
1 AATATATAAT
52406 ACTATGAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 30
0.68 0.12 0.21
Matches are distributed among these distances:
57 3 0.03
58 2 0.02
59 30 0.31
60 18 0.18
61 39 0.40
62 6 0.06
ACGTcount: A:0.48, C:0.06, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATAAATTTTCTAAATCAT
Found at i:52483 original size:120 final size:120
Alignment explanation
Indices: 52178--52461 Score: 446
Period size: 120 Copynumber: 2.4 Consensus size: 120
52168 ATTTAATCAT
*
52178 ATTTAAACATAATTTTTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTT-AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAAT-
* * * *
52243 ATT-AATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATA
64 ATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
* *
52299 AATTAACATAATTACTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
* *
52364 TAAATATTCTTATATGAATTTTCTAAAATCATAATATATAATACTATGAAATATA
66 TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
*
52419 ATTTAACATAATTATTATTAAATATAATTTAA-TAAAATATATA
1 ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATA
52462 TTTTCAATTA
Statistics
Matches: 150, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
119 14 0.09
120 133 0.89
121 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATA
Found at i:54395 original size:19 final size:19
Alignment explanation
Indices: 54371--54407 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
54361 ATAAAATATT
54371 ATCGTTCAGGTACATATAC
1 ATCGTTCAGGTACATATAC
*
54390 ATCGTTCAGGTGCATATA
1 ATCGTTCAGGTACATATA
54408 GAGGTCATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (19 bp):
ATCGTTCAGGTACATATAC
Found at i:71400 original size:28 final size:28
Alignment explanation
Indices: 71360--71417 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
71350 ATCATCATAC
71360 GAGCCGCAGCTAGCATAACCAGCAATCA
1 GAGCCGCAGCTAGCATAACCAGCAATCA
71388 GAGCCGCAGCTAGCATAACCAGCAATCA
1 GAGCCGCAGCTAGCATAACCAGCAATCA
71416 GA
1 GA
71418 CGACAAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.31, G:0.22, T:0.10
Consensus pattern (28 bp):
GAGCCGCAGCTAGCATAACCAGCAATCA
Found at i:80471 original size:16 final size:17
Alignment explanation
Indices: 80450--80490 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
80440 TTCAATCACT
80450 AATATTTTTAA-AATTA
1 AATATTTTTAATAATTA
*
80466 AATA-TTTTAATCATTA
1 AATATTTTTAATAATTA
80482 AAT-TTTTTA
1 AATATTTTTA
80491 TACATACCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATATTTTTAATAATTA
Found at i:81200 original size:23 final size:23
Alignment explanation
Indices: 81174--81222 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
81164 TTTTGAGCAA
*
81174 TTTAA-TTTTCTTTCTTTTATTCT
1 TTTAACTTTCCTTT-TTTTATTCT
*
81197 TTTAACTTTCCTTTTTTTTTTCT
1 TTTAACTTTCCTTTTTTTATTCT
81220 TTT
1 TTT
81223 TTTTTCATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (23 bp):
TTTAACTTTCCTTTTTTTATTCT
Found at i:83343 original size:17 final size:17
Alignment explanation
Indices: 83321--83354 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
83311 AAAAGCTACT
83321 GTACAAGAGCCAAATCA
1 GTACAAGAGCCAAATCA
*
83338 GTACAAGTGCCAAATCA
1 GTACAAGAGCCAAATCA
83355 TAAATACTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.24, G:0.18, T:0.15
Consensus pattern (17 bp):
GTACAAGAGCCAAATCA
Found at i:86271 original size:31 final size:31
Alignment explanation
Indices: 86235--86326 Score: 105
Period size: 31 Copynumber: 3.0 Consensus size: 31
86225 CATTGTGAAG
* *
86235 TATTTAAAATTTTTTATTT-AGATCATTAAAT
1 TATTTAAAAATTTTTATTTAAG-TCACTAAAT
* *
86266 TATTTAAAAATTTTCATTCAAGTCACTAAAT
1 TATTTAAAAATTTTTATTTAAGTCACTAAAT
* * *
86297 TATTTAAAAAATTTTATTTAAATAACTAAA
1 TATTTAAAAATTTTTATTTAAGTCACTAAA
86327 CTGTTAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 49 0.96
32 2 0.04
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.47
Consensus pattern (31 bp):
TATTTAAAAATTTTTATTTAAGTCACTAAAT
Found at i:91580 original size:5 final size:5
Alignment explanation
Indices: 91570--91594 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
91560 TATATTTAAA
91570 ATAAT ATAAT ATAAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT
91595 TTTCAAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:94455 original size:17 final size:20
Alignment explanation
Indices: 94435--94474 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 20
94425 AAAAAAATTC
94435 AAACAAAAC-AA-AAAA-AA
1 AAACAAAACGAAGAAAAGAA
94452 AAACAAAACGAAGAAAAGAA
1 AAACAAAACGAAGAAAAGAA
94472 AAA
1 AAA
94475 GAGAGAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 4 0.20
20 5 0.25
ACGTcount: A:0.82, C:0.10, G:0.07, T:0.00
Consensus pattern (20 bp):
AAACAAAACGAAGAAAAGAA
Found at i:97233 original size:26 final size:27
Alignment explanation
Indices: 97199--97250 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 27
97189 GTTCGGAGTG
*
97199 TAATCAAG-TGGAGCTGAATTCAAATAA
1 TAATCAAGTTCGAG-TGAATTCAAATAA
*
97226 TAAT-AAGTTCGAGTTAATTCAAATA
1 TAATCAAGTTCGAGTGAATTCAAATA
97251 TCAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (27 bp):
TAATCAAGTTCGAGTGAATTCAAATAA
Found at i:99977 original size:22 final size:22
Alignment explanation
Indices: 99951--99995 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
99941 TCTCATGAGA
99951 AACCTTAATAGGCAACAACATG
1 AACCTTAATAGGCAACAACATG
*
99973 AACCTTAATAGGCAGCAACATG
1 AACCTTAATAGGCAACAACATG
99995 A
1 A
99996 TCTTCATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (22 bp):
AACCTTAATAGGCAACAACATG
Found at i:102282 original size:19 final size:20
Alignment explanation
Indices: 102258--102302 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
102248 CGATGAACAT
102258 ATGAAAAAGATAGAAA-ATG
1 ATGAAAAAGATAGAAATATG
***
102277 ATGAAAATTTTAGAAATATG
1 ATGAAAAAGATAGAAATATG
102297 ATGAAA
1 ATGAAA
102303 GAAAAACAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.58, C:0.00, G:0.18, T:0.24
Consensus pattern (20 bp):
ATGAAAAAGATAGAAATATG
Found at i:104642 original size:19 final size:20
Alignment explanation
Indices: 104592--104644 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 20
104582 TATTTAAAAT
*
104592 AAAACATTAAATATAAATTA
1 AAAAAATTAAATATAAATTA
* *
104612 AAAAAATAAAATA-AAATTT
1 AAAAAATTAAATATAAATTA
* *
104631 ATAATATTAAATAT
1 AAAAAATTAAATAT
104645 TTAAATATTA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 15 0.58
20 11 0.42
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATTAAATATAAATTA
Found at i:104651 original size:15 final size:15
Alignment explanation
Indices: 104623--104655 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
104613 AAAAATAAAA
104623 TAAAATTTATAATAT
1 TAAAATTTATAATAT
104638 TAAATATTTA-AATAT
1 TAAA-ATTTATAATAT
104653 TAA
1 TAA
104656 GAAATACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATTTATAATAT
Found at i:104783 original size:22 final size:21
Alignment explanation
Indices: 104746--104795 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 21
104736 TATAATATAT
104746 AAAA-ATTTTTTTAAATT-TA
1 AAAATATTTTTTTAAATTCTA
104765 AAAATATTTTTTATAAAATTCTA
1 AAAATATTTTTT-T-AAATTCTA
104788 AAATATAT
1 AAA-ATAT
104796 ATTTATTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.15
20 7 0.27
21 1 0.04
22 5 0.19
23 5 0.19
24 4 0.15
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (21 bp):
AAAATATTTTTTTAAATTCTA
Found at i:105761 original size:27 final size:27
Alignment explanation
Indices: 105713--105844 Score: 155
Period size: 27 Copynumber: 4.9 Consensus size: 27
105703 GCGAGACTGC
* *
105713 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
105740 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
* *
105766 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
105793 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
105820 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
105845 GACGCTTCCT
Statistics
Matches: 93, Mismatches: 6, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
26 8 0.09
27 82 0.88
28 3 0.03
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:105805 original size:54 final size:53
Alignment explanation
Indices: 105739--105847 Score: 200
Period size: 54 Copynumber: 2.0 Consensus size: 53
105729 GTCACCAGAT
105739 ACAGATATTGTGGCAGAGCCACCAGAACAGATAATTGTGGCATAGCCACCAGG
1 ACAGATATTGTGGCAGAGCCACCAGAACAGATAATTGTGGCATAGCCACCAGG
*
105792 ACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCACCAGG
1 ACAGATAT-TGTGGCAGAGCCACCAGAACAGATAATTGTGGCATAGCCACCAGG
105846 AC
1 AC
105848 GCTTCCTCCA
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
53 8 0.15
54 46 0.85
ACGTcount: A:0.34, C:0.23, G:0.26, T:0.17
Consensus pattern (53 bp):
ACAGATATTGTGGCAGAGCCACCAGAACAGATAATTGTGGCATAGCCACCAGG
Found at i:107963 original size:20 final size:19
Alignment explanation
Indices: 107926--107977 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
107916 TTTTATAAAA
*
107926 AATATTTTTA-AACCTTTTT
1 AATATTTTTACAA-ATTTTT
107945 AATATTTTTACAAATTTTT
1 AATATTTTTACAAATTTTT
*
107964 AATAAATTTTACAA
1 AAT-ATTTTTACAA
107978 TTTATTGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (19 bp):
AATATTTTTACAAATTTTT
Found at i:107979 original size:19 final size:19
Alignment explanation
Indices: 107940--107991 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
107930 TTTTTAAACC
*
107940 TTTTTAATATTTTTACAAA
1 TTTTTAATAATTTTACAAA
*
107959 TTTTTAATAAATTTTACAAT
1 TTTTTAAT-AATTTTACAAA
107979 TTATTGTAATAAT
1 TT-TT-TAATAAT
107992 ATTATTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 8 0.29
20 11 0.39
21 5 0.18
22 4 0.14
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTTAATAATTTTACAAA
Found at i:109749 original size:17 final size:17
Alignment explanation
Indices: 109708--109749 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
109698 CCTTTTAAAG
* *
109708 AATTAAATTGTAATTTT
1 AATTTAATTATAATTTT
109725 -ATTATAATTATAATTTT
1 AATT-TAATTATAATTTT
109742 AATTTAAT
1 AATTTAAT
109750 CACTTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 3 0.14
17 15 0.71
18 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
AATTTAATTATAATTTT
Found at i:123430 original size:21 final size:21
Alignment explanation
Indices: 123391--123432 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
123381 CTCACTTCAC
123391 TTTCCTTCTTCTCTTCTTCCCT
1 TTTCCTTCTTCTC-TCTTCCCT
123413 TTTCCTCTCTTCTC-CTTCCC
1 TTTCCT-TCTTCTCTCTTCCC
123433 CTAAACTCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTCCTTCTTCTCTCTTCCCT
Found at i:126408 original size:22 final size:22
Alignment explanation
Indices: 126375--126425 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
126365 AACATTTAGA
126375 AAATGTTAAAATAAT-TAAATATT
1 AAAT-TTAAAATAATATAAATA-T
*
126398 AAATTTAAAATAGTATAAATAT
1 AAATTTAAAATAATATAAATAT
126420 AAATTT
1 AAATTT
126426 TTTTATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 16 0.62
23 10 0.38
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (22 bp):
AAATTTAAAATAATATAAATAT
Found at i:130097 original size:24 final size:25
Alignment explanation
Indices: 130059--130108 Score: 84
Period size: 24 Copynumber: 2.0 Consensus size: 25
130049 AAAAAAACTT
130059 ATTAATATATGTATTTTTTAAATATG
1 ATTAATATA-GTATTTTTTAAATATG
130085 ATTAATATA-TATTTTTTAAATATG
1 ATTAATATAGTATTTTTTAAATATG
130109 CTTCATATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 15 0.62
26 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (25 bp):
ATTAATATAGTATTTTTTAAATATG
Found at i:137985 original size:3 final size:3
Alignment explanation
Indices: 137972--138009 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
137962 AAATGTTTGA
137972 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
138010 CCTGTTGGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:141431 original size:40 final size:40
Alignment explanation
Indices: 141386--141462 Score: 154
Period size: 40 Copynumber: 1.9 Consensus size: 40
141376 GTTACATACG
141386 CAGTTTCACATGTAATTAGCCTCAGCTGACTCAATTTACC
1 CAGTTTCACATGTAATTAGCCTCAGCTGACTCAATTTACC
141426 CAGTTTCACATGTAATTAGCCTCAGCTGACTCAATTT
1 CAGTTTCACATGTAATTAGCCTCAGCTGACTCAATTT
141463 CCTCAGGACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.13, T:0.34
Consensus pattern (40 bp):
CAGTTTCACATGTAATTAGCCTCAGCTGACTCAATTTACC
Found at i:158754 original size:27 final size:27
Alignment explanation
Indices: 158724--158778 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
158714 CTTTTAAGTC
*
158724 TTCATATTTTCATCCTATTAATAGGGA
1 TTCATATTTTCATACTATTAATAGGGA
158751 TTCATATTTTCATACTATTAATAGGGA
1 TTCATATTTTCATACTATTAATAGGGA
158778 T
1 T
158779 GTAGCTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (27 bp):
TTCATATTTTCATACTATTAATAGGGA
Found at i:159492 original size:18 final size:18
Alignment explanation
Indices: 159469--159506 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
159459 TGACCGATTC
159469 AACCACATTCTAATTTAA
1 AACCACATTCTAATTTAA
159487 AACCACATTCTAATTTAA
1 AACCACATTCTAATTTAA
159505 AA
1 AA
159507 AATATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (18 bp):
AACCACATTCTAATTTAA
Found at i:163014 original size:6 final size:7
Alignment explanation
Indices: 162995--163019 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
162985 ATATTTTTAA
162995 AATTTTT
1 AATTTTT
163002 AATTTTT
1 AATTTTT
163009 AATTTTT
1 AATTTTT
163016 AATT
1 AATT
163020 CTAATCTAAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
AATTTTT
Found at i:193602 original size:17 final size:17
Alignment explanation
Indices: 193580--193616 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
193570 GTTTCATTGT
193580 AAACTTAACTAAAATCA
1 AAACTTAACTAAAATCA
* *
193597 AAACTTAATTAAAATTA
1 AAACTTAACTAAAATCA
193614 AAA
1 AAA
193617 GTTTATGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (17 bp):
AAACTTAACTAAAATCA
Found at i:199809 original size:20 final size:20
Alignment explanation
Indices: 199784--199821 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
199774 GCCTCACGGG
199784 CAGGCCACGCGGGCATGTCC
1 CAGGCCACGCGGGCATGTCC
199804 CAGGCCACGCGGGCATGT
1 CAGGCCACGCGGGCATGT
199822 GCCCCTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.16, C:0.37, G:0.37, T:0.11
Consensus pattern (20 bp):
CAGGCCACGCGGGCATGTCC
Found at i:202063 original size:3 final size:3
Alignment explanation
Indices: 202055--202113 Score: 55
Period size: 3 Copynumber: 19.7 Consensus size: 3
202045 CGAGCGAGAC
* * ** * * *
202055 GAA GAA GAA GAA GAT GAC GTT GAA GAT GAA GAA GAG GAA GAG GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
202103 GAA GAA GAA GA
1 GAA GAA GAA GA
202114 GCCGAGGCTT
Statistics
Matches: 44, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.54, C:0.02, G:0.37, T:0.07
Consensus pattern (3 bp):
GAA
Found at i:202079 original size:21 final size:21
Alignment explanation
Indices: 202055--202110 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
202045 CGAGCGAGAC
* * **
202055 GAAGAAGAAGAAGATGACGTT
1 GAAGAAGAAGAAGAGGAAGAG
*
202076 GAAGATGAAGAAGAGGAAGAG
1 GAAGAAGAAGAAGAGGAAGAG
202097 GAAGAAGAAGAAGA
1 GAAGAAGAAGAAGA
202111 AGAGCCGAGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.38, T:0.07
Consensus pattern (21 bp):
GAAGAAGAAGAAGAGGAAGAG
Found at i:205829 original size:28 final size:28
Alignment explanation
Indices: 205789--205844 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
205779 AGGTTTGTTA
205789 GGACAACAACTCTGTGCAAATATTCATG
1 GGACAACAACTCTGTGCAAATATTCATG
205817 GGACAACAACTCTGTGCAAATATTCATG
1 GGACAACAACTCTGTGCAAATATTCATG
205845 TAGTCCACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.25
Consensus pattern (28 bp):
GGACAACAACTCTGTGCAAATATTCATG
Found at i:210789 original size:19 final size:20
Alignment explanation
Indices: 210754--210796 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
210744 GTATATAATT
*
210754 TTTTATAATATTTTTTTAAC
1 TTTTATAATATTATTTTAAC
*
210774 TTTTAT-ATATTATTTTGAC
1 TTTTATAATATTATTTTAAC
210793 TTTT
1 TTTT
210797 TAAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTTATAATATTATTTTAAC
Found at i:210797 original size:20 final size:21
Alignment explanation
Indices: 210753--210806 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
210743 AGTATATAAT
*
210753 TTTTTATAATATTTTTTTAAC
1 TTTTTATAATATTATTTTAAC
*
210774 -TTTTAT-ATATTATTTTGAC
1 TTTTTATAATATTATTTTAAC
*
210793 TTTTTAAAAT-TTAT
1 TTTTTATAATATTAT
210807 AATTATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 11 0.39
20 15 0.54
21 2 0.07
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTATAATATTATTTTAAC
Found at i:211019 original size:20 final size:22
Alignment explanation
Indices: 210976--211022 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
210966 AAGTCAAAAG
210976 TATTTTTAAATATTATAATTTT
1 TATTTTTAAATATTATAATTTT
*
210998 TATTTTTAAAT-TTA-ATTTTT
1 TATTTTTAAATATTATAATTTT
211018 TATTT
1 TATTT
211023 AAATAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 10 0.42
21 3 0.12
22 11 0.46
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TATTTTTAAATATTATAATTTT
Found at i:225762 original size:16 final size:16
Alignment explanation
Indices: 225741--225772 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
225731 TTGTAATGCA
225741 GTATGTATTGTTCCGT
1 GTATGTATTGTTCCGT
225757 GTATGTATTGTTCCGT
1 GTATGTATTGTTCCGT
225773 TTGAGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
GTATGTATTGTTCCGT
Found at i:225981 original size:15 final size:15
Alignment explanation
Indices: 225961--226011 Score: 102
Period size: 15 Copynumber: 3.4 Consensus size: 15
225951 AACAAAAGAG
225961 CCCAATACCCACAAA
1 CCCAATACCCACAAA
225976 CCCAATACCCACAAA
1 CCCAATACCCACAAA
225991 CCCAATACCCACAAA
1 CCCAATACCCACAAA
226006 CCCAAT
1 CCCAAT
226012 TACCATGCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.45, C:0.47, G:0.00, T:0.08
Consensus pattern (15 bp):
CCCAATACCCACAAA
Found at i:225993 original size:8 final size:8
Alignment explanation
Indices: 225967--226009 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
225957 AGAGCCCAAT
225967 ACCCACAA
1 ACCCACAA
*
225975 ACCCA-AT
1 ACCCACAA
225982 ACCCACAA
1 ACCCACAA
*
225990 ACCCA-AT
1 ACCCACAA
225997 ACCCACAA
1 ACCCACAA
226005 ACCCA
1 ACCCA
226010 ATTACCATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.05
Consensus pattern (8 bp):
ACCCACAA
Found at i:227031 original size:3 final size:3
Alignment explanation
Indices: 227023--227075 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
227013 TTAGTCCTAC
* * * * *
227023 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAC TAC TAC TAT TGT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
227071 TAT TA
1 TAT TA
227076 CCTATTTATT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:239947 original size:43 final size:44
Alignment explanation
Indices: 239847--239951 Score: 117
Period size: 45 Copynumber: 2.4 Consensus size: 44
239837 ATACAGGTCT
* * *
239847 TATCTCCTGAGATTACAGTGGAACAGACCAAAGAATTCAGATCT
1 TATCTCCTGAGATTACAGCGGAACAGACCAAAGAAGTCAGATCC
* *
239891 TATCTCCCTGAGATTACAGCGGAGCAGATC-AAGATAGT-A-ATCC
1 TATCT-CCTGAGATTACAGCGGAACAGACCAAAGA-AGTCAGATCC
239934 TATCTCCTTGAGATTACA
1 TATCTCC-TGAGATTACA
239952 ATGGAGCGGA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
42 2 0.04
43 18 0.34
44 10 0.19
45 23 0.43
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (44 bp):
TATCTCCTGAGATTACAGCGGAACAGACCAAAGAAGTCAGATCC
Found at i:240107 original size:84 final size:84
Alignment explanation
Indices: 239844--240112 Score: 263
Period size: 81 Copynumber: 3.2 Consensus size: 84
239834 ATTATACAGG
*
239844 TCTTATCTCCTGAGATTACAGTGGAACAGACCAAAGAA-TTCAGATCTTATCTCCCTGAGATTAC
1 TCTTATCTCCTGAGATTACAGTGG-A-AGACC--AGAATTTCAGATCTTATCTCCCTGAGGTTAC
* *
239908 AGCGGAGCAGATCAAGATAGTA-A
62 AGTGGAGCAGATCAAGACAG-AGA
* * * ** * *
239931 TCCTATCTCCTTGAGATTACAATGG-AG--C-GGATTAAAGATCTTATCTCTCTGAAGTTACAGT
1 TCTTATCTCC-TGAGATTACAGTGGAAGACCAGAATTTCAGATCTTATCTCCCTGAGGTTACAGT
* * *
239992 AGAG-AGATCCA-TCAG-G-
65 GGAGCAGATCAAGACAGAGA
240008 TCTTATCTCCTGAGATTACAGTGGAAGACCAGAATTTCAGAT-TTATCTCCCTGAGGTTACAGTG
1 TCTTATCTCCTGAGATTACAGTGGAAGACCAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTG
* *
240072 GAGCAGATTGAAGCCAGAGA
66 GAGCAGA-TCAAGACAGAGA
240092 TCTTATCTCCTGAGATTACAG
1 TCTTATCTCCTGAGATTACAG
240113 CGGAGCAGAT
Statistics
Matches: 146, Mismatches: 24, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
76 13 0.09
77 11 0.08
79 25 0.17
80 19 0.13
81 28 0.19
82 3 0.02
83 2 0.01
84 21 0.14
85 2 0.01
87 9 0.06
88 13 0.09
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (84 bp):
TCTTATCTCCTGAGATTACAGTGGAAGACCAGAATTTCAGATCTTATCTCCCTGAGGTTACAGTG
GAGCAGATCAAGACAGAGA
Found at i:240111 original size:43 final size:42
Alignment explanation
Indices: 239844--240253 Score: 173
Period size: 43 Copynumber: 9.9 Consensus size: 42
239834 ATTATACAGG
* ** *
239844 TCTTATCTCCTGAGATTACAGTGGAACAGACCAAAGAATTC-AGA
1 TCTTATCTCCTGAGATTACAGTGGAGCAG---ATTGAAGTCAAGA
* *
239888 TCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCAAG--ATAGTAA
1 TCTTATCT-CCTGAGATTACAGTGGAGCAGATTGAAGTCA-AG--A
* * *
239931 TCCTATCTCCTTGAGATTACAATGGAGCGGATT--A---AAGA
1 TCTTATCTCC-TGAGATTACAGTGGAGCAGATTGAAGTCAAGA
* ** *
239969 TCTTATCTCTCTGA-AGTTACAGTAGAG-AGA-TCCA-TC-AGG
1 TCTTATCTC-CTGAGA-TTACAGTGGAGCAGATTGAAGTCAAGA
** *
240008 TCTTATCTCCTGAGATTACAGTGGA--AGACCAGAATTTC-AGA
1 TCTTATCTCCTGAGATTACAGTGGAGCAGA-TTGAA-GTCAAGA
* *
240049 T-TTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCT-CCTGAGATTACAGTGGAGCAGATTGAAGTCA-AGA
* * * **
240092 TCTTATCTCCTGAGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCTGAGATTACAGTGGAGCAGATTGAAGTCAAGA
* * * *
240134 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAAT-AAGGA
1 TCTTATCT-CCTGAGA-TTACAGTGGAGCAGATTGAAGTCAA-GA
* ** * * *
240177 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCA-TCAAG-
1 TCTTATCTC-CTGAGATTACAGTGGAGCAGATTGAAGTCAAGA
* *
240218 TCTTATCTCCTGA-AGTTGCAGTGGAGCAGATAGAAG
1 TCTTATCTCCTGAGA-TTACAGTGGAGCAGATTGAAG
240254 AAACCAATCC
Statistics
Matches: 279, Mismatches: 55, Indels: 67
0.70 0.14 0.17
Matches are distributed among these distances:
36 1 0.00
37 6 0.02
38 35 0.13
39 14 0.05
40 26 0.09
41 36 0.13
42 20 0.07
43 107 0.38
44 15 0.05
45 19 0.07
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCTGAGATTACAGTGGAGCAGATTGAAGTCAAGA
Found at i:240158 original size:86 final size:84
Alignment explanation
Indices: 240051--240253 Score: 223
Period size: 86 Copynumber: 2.4 Consensus size: 84
240041 ATTTCAGATT
* * *
240051 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTC-CTGAGATTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCAAG-GATCTTATCTCTCTGAGATTACAGCA
240115 GAGCAGATCGAAGACACTA-TCC
65 GAGCAGATCGAA-ACA--AGTCC
* * ** *
240137 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAGGATCTTATCTCTCTGAGGTTACAGCAG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCAAGGATCTTATCTCTCTGAGATTACAGCAG
* * * *
240202 AGTAGATCGCATCAAGTCT
66 AGCAGATCGAAACAAGTCC
* *
240221 TATCT-CCTGAAGTTGCAGTGGAGCAGATAGAAG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAG
240254 AAACCAATCC
Statistics
Matches: 98, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
83 24 0.24
84 7 0.07
85 13 0.13
86 54 0.55
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (84 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCAAGGATCTTATCTCTCTGAGATTACAGCAG
AGCAGATCGAAACAAGTCC
Found at i:240276 original size:44 final size:44
Alignment explanation
Indices: 240221--240336 Score: 148
Period size: 44 Copynumber: 2.7 Consensus size: 44
240211 CATCAAGTCT
*
240221 TATCTC-CTGAAGTTGCAGTGGAGCAGATAGAAGAAAC-CA-ATCC
1 TATCTCTCTGAAGTTGCAGTAGAGCAGAT-GAA-AAACACAGATCC
* * * *
240264 TATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGATCT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATGAAAAACACAGATCC
240308 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
1 TATCTCTCTGAAGTTGCAGTAGAGCAGAT
240337 CGCATCAAGT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
42 3 0.05
43 10 0.16
44 51 0.80
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (44 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATGAAAAACACAGATCC
Found at i:240348 original size:128 final size:126
Alignment explanation
Indices: 240092--240361 Score: 366
Period size: 128 Copynumber: 2.1 Consensus size: 126
240082 AAGCCAGAGA
* * *
240092 TCTTATCTCCTG-AGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCTGAAG-TTACAGCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAG
* * *
240156 TGGAGCGGATTAAAATAAGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAG
65 TAGAGCGGATTAAAATAAGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAAG
* * * *
240218 TCTTATCTCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAG
1 TCTTATCTCCTGAAGTTACAGCGGAGCAGATAGAAGAAA-CAATCCTATCTCCCTGAAGTTACAG
* *
240283 TAGAGCGGATTAAAATCACA-GATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAG
65 TAGAGCGGATTAAAAT-A-AGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAAG
240346 TCTTAT-TCCCTGAAGT
1 TCTTATCT-CCTGAAGT
240362 ACAATGGATT
Statistics
Matches: 127, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
126 32 0.25
127 40 0.31
128 54 0.43
129 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (126 bp):
TCTTATCTCCTGAAGTTACAGCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGT
AGAGCGGATTAAAATAAGGATCTTATCTCTCTGAAGTTACAGCAGAGCAGATCGCATCAAG
Found at i:240550 original size:12 final size:12
Alignment explanation
Indices: 240533--240558 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
240523 CCGGCCATAC
240533 AAAAAACCAAAA
1 AAAAAACCAAAA
240545 AAAAAACCAAAA
1 AAAAAACCAAAA
240557 AA
1 AA
240559 CCAATACCAC
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:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAACCAAAA
Found at i:253983 original size:15 final size:15
Alignment explanation
Indices: 253963--254030 Score: 127
Period size: 15 Copynumber: 4.5 Consensus size: 15
253953 CTAACAAAAG
253963 AACCCAATACCCACA
1 AACCCAATACCCACA
253978 AACCCAATACCCACA
1 AACCCAATACCCACA
253993 AACCCAATACCCACA
1 AACCCAATACCCACA
*
254008 AACCCCATACCCACA
1 AACCCAATACCCACA
254023 AACCCAAT
1 AACCCAAT
254031 TACCATGCCC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 51 1.00
ACGTcount: A:0.46, C:0.47, G:0.00, T:0.07
Consensus pattern (15 bp):
AACCCAATACCCACA
Found at i:253997 original size:8 final size:8
Alignment explanation
Indices: 253971--254028 Score: 68
Period size: 8 Copynumber: 7.6 Consensus size: 8
253961 AGAACCCAAT
253971 ACCCACAA
1 ACCCACAA
*
253979 ACCCA-AT
1 ACCCACAA
253986 ACCCACAA
1 ACCCACAA
*
253994 ACCCA-AT
1 ACCCACAA
254001 ACCCACAA
1 ACCCACAA
*
254009 ACCC-CAT
1 ACCCACAA
254016 ACCCACAA
1 ACCCACAA
254024 ACCCA
1 ACCCA
254029 ATTACCATGC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
7 18 0.44
8 23 0.56
ACGTcount: A:0.45, C:0.50, G:0.00, T:0.05
Consensus pattern (8 bp):
ACCCACAA
Found at i:255111 original size:3 final size:3
Alignment explanation
Indices: 255098--255179 Score: 89
Period size: 3 Copynumber: 27.3 Consensus size: 3
255088 TTATTTGCTC
255098 ATT ATT A-T ATT ATT A-T ATT -TT ATT ATT AGCTT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A--TT ATT ATT ATT ATT
* * *
255142 ATG GTT ATT ATT ATT ATT ACT ATT ATT AATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT A
255180 GTTTTATTTT
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
2 6 0.09
3 55 0.82
4 3 0.04
5 3 0.04
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:267661 original size:43 final size:45
Alignment explanation
Indices: 267549--267874 Score: 179
Period size: 43 Copynumber: 7.6 Consensus size: 45
267539 ATACAGGTCT
* * *
267549 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGTCAGATCC
* *
267594 TATCTCCCTGAGATTACAGCGGAGCAGATC-AAGATAGT-A-ATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGA-AGTCAGATCC
* * * ** *
267637 TATCTCCTTGAGATTACAATGGAGCGGA--TTA-AAG---GATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGTCAGATCC
* * * * * * *
267676 TATCTCTCTGA-AGTTACAGTAGAGAAGATC--A-CA-TCAGGTCT
1 TATCTCCCTGAGA-TTACAGTGGAGCAGACCAAAGAAGTCAGATCC
* * *
267717 TATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAA-GTCAGATCC
* *** * *
267763 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG--AGATCT
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAG-AAGTCAGATCC
* * * *
267807 TATCTCCCTGAGATTACAGCGGAGCAGATC---GAAGACACTATCC
1 TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGTCA-GATCC
267850 TATCTCCCTGA-AGTTACAGTGGAGC
1 TATCTCCCTGAGA-TTACAGTGGAGC
267875 GGATTAAAAT
Statistics
Matches: 221, Mismatches: 40, Indels: 42
0.73 0.13 0.14
Matches are distributed among these distances:
38 1 0.00
39 25 0.11
40 4 0.02
41 29 0.13
42 4 0.02
43 53 0.24
44 39 0.18
45 29 0.13
46 36 0.16
47 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (45 bp):
TATCTCCCTGAGATTACAGTGGAGCAGACCAAAGAAGTCAGATCC
Found at i:267854 original size:87 final size:87
Alignment explanation
Indices: 267714--267969 Score: 250
Period size: 87 Copynumber: 2.9 Consensus size: 87
267704 TCACATCAGG
* * * * * *
267714 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGATCTTATCTCCCTGAGGTTA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAG-A---CACATCTTATCTCCCTGAAGTTA
* *
267779 CAGTGGAGCAGATTGAAGCCAGA-GA
62 CAGTGGAGCAGATTGAAGACAAAGGA
*
267804 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACAC-ATCTTATCTCCCTGAAGTTACAG
* * *
267869 TGGAGCGGATT-AAAATAAAGGA
65 TGGAGCAGATTGAAGACAAAGGA
* * * * * * *
267891 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCA-TCA-AGTCTTATCTCCCTGAAGTTGCAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACA-TCTTATCTCCCTGAAGTTACAG
*
267954 TGGAGCAGATAGAAGA
65 TGGAGCAGATTGAAGA
267970 AACCAATCCT
Statistics
Matches: 139, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
84 1 0.01
85 29 0.21
86 11 0.08
87 64 0.46
89 1 0.01
90 33 0.24
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACATCTTATCTCCCTGAAGTTACAGT
GGAGCAGATTGAAGACAAAGGA
Found at i:267899 original size:44 final size:42
Alignment explanation
Indices: 267546--268084 Score: 205
Period size: 44 Copynumber: 12.6 Consensus size: 42
267536 ATTATACAGG
* *
267546 TCTTATCTCCCTG-AGATTACAGTGGAACAGACCA-AAGAATTCAGA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGA-TAGAAGAA---AGA
* * *
267591 TCTTATCTCCCTG-AGATTACAGCGGAGCAGAT-CAAGATAGTAA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATAGAAGAAAG--A
* * * *
267634 TCCTATCTCCTTG-AGATTACAATGGAGCGGATTA-AAG---GA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGA-TAGAAGAAAGA
* * * * ** *
267673 TCTTATCTCTCTGAAGTTACAGTAGAGAAGATCA-CA-TCAGG
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGAT-AGAAGAAAGA
* *
267714 TCTTATCTCCCTG-AGATTACAGTGGAACAGACCA-AAGAATTTCAGA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGA-TAGAAGAA----AGA
* * *
267760 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAG--AAAGA
* * **
267804 TCTTATCTCCCTG-AGATTACAGCGGAGCAGATCGAAGACACTA
1 TCTTATCTCCCTGAAG-TTACAGTGGAGCAGATAGAAGA-AAGA
* * * *
267847 TCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAGGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TAGAAGAAA-GA
* * ** * * * **
267891 TCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAAGA
* *
267932 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATAGAAGAAACCAA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAA--GA
* * * * * * * *
267976 TCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCACAGA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGA-TAGAA-GAAAGA
* * * * * **
268020 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAG-
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAAGA
*
268061 TCTTAT-TCCCTGAAG-TACAATGGA
1 TCTTATCTCCCTGAAGTTACAGTGGA
268085 TTGAAGCGAC
Statistics
Matches: 375, Mismatches: 88, Indels: 68
0.71 0.17 0.13
Matches are distributed among these distances:
38 1 0.00
39 30 0.08
40 12 0.03
41 66 0.18
42 4 0.01
43 62 0.17
44 131 0.35
45 33 0.09
46 34 0.09
47 1 0.00
48 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATAGAAGAAAGA
Found at i:268009 original size:129 final size:128
Alignment explanation
Indices: 267757--268076 Score: 403
Period size: 129 Copynumber: 2.5 Consensus size: 128
267747 AAAGAATTTC
* * * * *
267757 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTG-AGAT
1 AGATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCA-TCA-AG-TCTTATCTCCCTGAAG-T
* * * *
267821 TACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAGTGGAGCGGATTAAAAT-
62 TACAGCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATC
267885 AA
127 AA
* * *
267887 AGGATCTTATCTCTCTGAGGTTACAGCAGAGTAGATCGCATCAAGTCTTATCTCCCTGAAGTTGC
1 A-GATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTAC
* * * *
267952 AGTGGAGCAGATAGAAGAAACCAATCCTATCTCTCTGAAGTTGCAGTAGAGCGGATTAAAATCAC
65 AGCGGAGCAGATAGAAGAAA-CAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCAA
* *
268017 AGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCAAGTCTTAT-TCCCTGAAGT
1 AGATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGT
268077 ACAATGGATT
Statistics
Matches: 166, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
128 43 0.26
129 86 0.52
130 5 0.03
131 32 0.19
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (128 bp):
AGATCTTATCTCTCTGAGGTTACAGTAGAGCAGATCGCATCAAGTCTTATCTCCCTGAAGTTACA
GCGGAGCAGATAGAAGAAACAATCCTATCTCCCTGAAGTTACAGTAGAGCGGATTAAAATCAA
Found at i:268288 original size:15 final size:15
Alignment explanation
Indices: 268268--268320 Score: 106
Period size: 15 Copynumber: 3.5 Consensus size: 15
268258 CTAACAAAAG
268268 AACCCAATACCCACA
1 AACCCAATACCCACA
268283 AACCCAATACCCACA
1 AACCCAATACCCACA
268298 AACCCAATACCCACA
1 AACCCAATACCCACA
268313 AACCCAAT
1 AACCCAAT
268321 TACCATGCCC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.47, C:0.45, G:0.00, T:0.08
Consensus pattern (15 bp):
AACCCAATACCCACA
Found at i:268302 original size:8 final size:8
Alignment explanation
Indices: 268276--268318 Score: 54
Period size: 8 Copynumber: 5.6 Consensus size: 8
268266 AGAACCCAAT
268276 ACCCACAA
1 ACCCACAA
*
268284 ACCCA-AT
1 ACCCACAA
268291 ACCCACAA
1 ACCCACAA
*
268299 ACCCA-AT
1 ACCCACAA
268306 ACCCACAA
1 ACCCACAA
268314 ACCCA
1 ACCCA
268319 ATTACCATGC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 12 0.41
8 17 0.59
ACGTcount: A:0.47, C:0.49, G:0.00, T:0.05
Consensus pattern (8 bp):
ACCCACAA
Found at i:269270 original size:3 final size:3
Alignment explanation
Indices: 269262--269310 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
269252 TAGTCCTACT
269262 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
269308 TTA
1 TTA
269311 CCTATTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:269522 original size:25 final size:25
Alignment explanation
Indices: 269471--269524 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
269461 TTATAATCCG
*
269471 TATATACACACATTTACTATTAATT
1 TATATACACACATATACTATTAATT
* * * *
269496 TATATACATACATATCCTTTTATTT
1 TATATACACACATATACTATTAATT
269521 TATA
1 TATA
269525 ATATATATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.15, G:0.00, T:0.48
Consensus pattern (25 bp):
TATATACACACATATACTATTAATT
Found at i:271564 original size:16 final size:16
Alignment explanation
Indices: 271532--271573 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
271522 GTTAATAGAA
271532 TAAATTTAGTGTTAATTGT
1 TAAATTTA-T-TTAATT-T
271551 T-AATTTATTTAATTT
1 TAAATTTATTTAATTT
271566 TAAATTTA
1 TAAATTTA
271574 ATTTGTCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 12 0.55
17 1 0.05
18 6 0.27
19 1 0.05
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (16 bp):
TAAATTTATTTAATTT
Found at i:278135 original size:29 final size:29
Alignment explanation
Indices: 278087--278144 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
278077 TTCTTGGGAG
278087 TGGATCAAATTAGCCACTATATTATTAAA
1 TGGATCAAATTAGCCACTATATTATTAAA
*
278116 TGGATCAATTTAGTCC-CTATATTATTAAA
1 TGGATCAAATTAG-CCACTATATTATTAAA
278145 AAGAATCAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 25 0.93
30 2 0.07
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (29 bp):
TGGATCAAATTAGCCACTATATTATTAAA
Found at i:287413 original size:19 final size:19
Alignment explanation
Indices: 287389--287427 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
287379 CTAAGGTTAG
287389 TTTATTTTTAAGTTTGTAA
1 TTTATTTTTAAGTTTGTAA
287408 TTTATTTTTAAGTTTGTAA
1 TTTATTTTTAAGTTTGTAA
287427 T
1 T
287428 GTTTTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (19 bp):
TTTATTTTTAAGTTTGTAA
Found at i:289199 original size:17 final size:17
Alignment explanation
Indices: 289179--289212 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
289169 ACTAAAATTT
*
289179 TAAAATTAAATATTAAA
1 TAAAACTAAATATTAAA
*
289196 TAAAACTAAATTTTAAA
1 TAAAACTAAATATTAAA
289213 AGTTTAAAGA
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:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAACTAAATATTAAA
Found at i:290863 original size:31 final size:31
Alignment explanation
Indices: 290825--290895 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
290815 AATGAAATCC
290825 AAGTTCAAGGGCAAAATTAGACCTAATTGCT
1 AAGTTCAAGGGCAAAATTAGACCTAATTGCT
* *
290856 AATTTCAAGGGCAAAATTGGACCTAATTGCT
1 AAGTTCAAGGGCAAAATTAGACCTAATTGCT
290887 AAGTTCAAG
1 AAGTTCAAG
290896 TACTAAATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (31 bp):
AAGTTCAAGGGCAAAATTAGACCTAATTGCT
Found at i:290904 original size:31 final size:31
Alignment explanation
Indices: 290825--290906 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
290815 AATGAAATCC
* *
290825 AAGTTCAAGGGCAAAATTAGACCTAATTGCT
1 AAGTTCAAGGACAAAATTGGACCTAATTGCT
* *
290856 AATTTCAAGGGCAAAATTGGACCTAATTGCT
1 AAGTTCAAGGACAAAATTGGACCTAATTGCT
* *
290887 AAGTTCAAGTACTAAATTGG
1 AAGTTCAAGGACAAAATTGG
290907 TCCAAAAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (31 bp):
AAGTTCAAGGACAAAATTGGACCTAATTGCT
Found at i:295493 original size:31 final size:31
Alignment explanation
Indices: 295458--295520 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
295448 ATCTTCATGG
* *
295458 TTTTTAAAGAATTAAATTAAAATTTTATCAT
1 TTTTTAAAGAATCAAAATAAAATTTTATCAT
* *
295489 TTTTTAAAGAGTCAAAATATAATTTTATCAT
1 TTTTTAAAGAATCAAAATAAAATTTTATCAT
295520 T
1 T
295521 ACTAATTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTTTAAAGAATCAAAATAAAATTTTATCAT
Found at i:298582 original size:5 final size:5
Alignment explanation
Indices: 298572--298597 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
298562 TGAAAACTGT
298572 TAAAA TAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA TAAAA T
298598 CTTGAATGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (5 bp):
TAAAA
Found at i:302229 original size:17 final size:17
Alignment explanation
Indices: 302207--302253 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
302197 TTGAAAACCT
302207 CAAAATTAATATTTTTA
1 CAAAATTAATATTTTTA
*
302224 CAAAATT--TATTTTAA
1 CAAAATTAATATTTTTA
*
302239 CAATATTAAT-TTTTT
1 CAAAATTAATATTTTT
302254 CTTAAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 13 0.52
16 4 0.16
17 8 0.32
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (17 bp):
CAAAATTAATATTTTTA
Found at i:302325 original size:22 final size:21
Alignment explanation
Indices: 302300--302359 Score: 50
Period size: 22 Copynumber: 2.7 Consensus size: 21
302290 TGATTTTAGC
*
302300 AATAGAAAGATTTGATTGATAT
1 AATAGAAAGATTTGA-GGATAT
*
302322 AATATTAATA-ATTTGAGGATAT
1 AATA-GAA-AGATTTGAGGATAT
*
302344 AATTAGAATGATTTGA
1 AA-TAGAAAGATTTGA
302360 AATTTGAGGA
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
22 19 0.63
23 10 0.33
24 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.17, T:0.38
Consensus pattern (21 bp):
AATAGAAAGATTTGAGGATAT
Found at i:318066 original size:24 final size:24
Alignment explanation
Indices: 318039--318148 Score: 76
Period size: 24 Copynumber: 5.2 Consensus size: 24
318029 AGTTAATATA
318039 TATTATATATATGTAAGTAATGAT
1 TATTATATATATGTAAGTAATGAT
318063 TATTAT-TAATAT-T---T--T-A-
1 TATTATAT-ATATGTAAGTAATGAT
318079 TATTATATATATGTAAGTAATGAT
1 TATTATATATATGTAAGTAATGAT
318103 TATTAT-TAATAT-T---T--T-A-
1 TATTATAT-ATATGTAAGTAATGAT
318119 TATTATATATATGTAAGTAATGAT
1 TATTATATATATGTAAGTAATGAT
318143 TATTAT
1 TATTAT
318149 TAATATTTTA
Statistics
Matches: 66, Mismatches: 0, Indels: 40
0.62 0.00 0.38
Matches are distributed among these distances:
16 20 0.30
17 6 0.09
18 2 0.03
20 4 0.06
22 2 0.03
23 6 0.09
24 26 0.39
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (24 bp):
TATTATATATATGTAAGTAATGAT
Found at i:318083 original size:40 final size:40
Alignment explanation
Indices: 318037--318170 Score: 268
Period size: 40 Copynumber: 3.4 Consensus size: 40
318027 CTAGTTAATA
318037 TATATTATATATATGTAAGTAATGATTATTATTAATATTT
1 TATATTATATATATGTAAGTAATGATTATTATTAATATTT
318077 TATATTATATATATGTAAGTAATGATTATTATTAATATTT
1 TATATTATATATATGTAAGTAATGATTATTATTAATATTT
318117 TATATTATATATATGTAAGTAATGATTATTATTAATATTT
1 TATATTATATATATGTAAGTAATGATTATTATTAATATTT
318157 TATATTATATATAT
1 TATATTATATATAT
318171 ATAACAAAAG
Statistics
Matches: 94, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 94 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (40 bp):
TATATTATATATATGTAAGTAATGATTATTATTAATATTT
Found at i:318464 original size:13 final size:13
Alignment explanation
Indices: 318446--318477 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
318436 TTTCCAGCAA
318446 TTATGAATTTATT
1 TTATGAATTTATT
318459 TTATGAATTTATT
1 TTATGAATTTATT
*
318472 TGATGA
1 TTATGA
318478 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:318685 original size:50 final size:50
Alignment explanation
Indices: 318572--318813 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
318562 ATTTGGGTAA
* * *
318572 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
318628 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
318678 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
318728 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
** *
318778 AGAACATCCCATGTAAGACCAGGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
318814 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 28 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.19
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:318761 original size:100 final size:103
Alignment explanation
Indices: 318572--318821 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
318562 ATTTGGGTAA
318572 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
318637 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
318678 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
318740 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* * *
318778 AGAACATCCCATGTAAGACCAGGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
318822 GTTATTATCA
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 38 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.30, T:0.20
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:320825 original size:12 final size:12
Alignment explanation
Indices: 320808--320832 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
320798 TGTTATGTGT
320808 GTATATATATAA
1 GTATATATATAA
320820 GTATATATATAA
1 GTATATATATAA
320832 G
1 G
320833 AGTCAAATTT
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
GTATATATATAA
Found at i:321277 original size:13 final size:13
Alignment explanation
Indices: 321259--321286 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
321249 TGATCTCTTC
321259 TGGGTATTCTATA
1 TGGGTATTCTATA
321272 TGGGTATTCTATA
1 TGGGTATTCTATA
321285 TG
1 TG
321287 CTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:323526 original size:13 final size:13
Alignment explanation
Indices: 323508--323539 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
323498 TTTCCAGCAA
323508 TTATGAATTTATT
1 TTATGAATTTATT
323521 TTATGAATTTATT
1 TTATGAATTTATT
*
323534 TGATGA
1 TTATGA
323540 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:323747 original size:50 final size:50
Alignment explanation
Indices: 323634--323875 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
323624 ATTTGGGTAA
* * *
323634 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
323690 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
323740 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
323790 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
323840 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
323876 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:323823 original size:100 final size:103
Alignment explanation
Indices: 323634--323883 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
323624 ATTTGGGTAA
323634 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
323699 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
323740 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
323802 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
323840 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
323884 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:328653 original size:20 final size:20
Alignment explanation
Indices: 328611--328660 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
328601 AGTTTAGTGC
***
328611 TTAAGGTTTAGAGTTCGGGG
1 TTAAGGTTTAGAGTTCAAAG
*
328631 TTAAGGTTTAGAGTTTAAAG
1 TTAAGGTTTAGAGTTCAAAG
328651 TTAGAGGTTT
1 TTA-AGGTTT
328661 TTGATTTGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 19 0.76
21 6 0.24
ACGTcount: A:0.26, C:0.02, G:0.32, T:0.40
Consensus pattern (20 bp):
TTAAGGTTTAGAGTTCAAAG
Found at i:331097 original size:32 final size:32
Alignment explanation
Indices: 331056--331118 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
331046 GTTTTTCATA
331056 TATTACCTCCAAATAAAAGCCCAATTAATTCT
1 TATTACCTCCAAATAAAAGCCCAATTAATTCT
* *
331088 TATTACCTCCAAATCAAAGCCGAATTAATTC
1 TATTACCTCCAAATAAAAGCCCAATTAATTC
331119 ACAGAAAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.40, C:0.25, G:0.05, T:0.30
Consensus pattern (32 bp):
TATTACCTCCAAATAAAAGCCCAATTAATTCT
Found at i:338010 original size:47 final size:47
Alignment explanation
Indices: 337954--338064 Score: 159
Period size: 47 Copynumber: 2.4 Consensus size: 47
337944 TTTTAGGTTA
* **
337954 AAATCAATTCAAGTTCACATTCTCAAGATTTGCATTGAATCGGATTC
1 AAATCAATTCAAGTTCACATTCTCAAAATTCACATTGAATCGGATTC
* * * *
338001 AGATCAATTCAAGCTCACATTCTTAAAATTCACGTTGAATCGGATTC
1 AAATCAATTCAAGTTCACATTCTCAAAATTCACATTGAATCGGATTC
338048 AAATCAATTCAAGTTCA
1 AAATCAATTCAAGTTCA
338065 GTTGTTGAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 55 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (47 bp):
AAATCAATTCAAGTTCACATTCTCAAAATTCACATTGAATCGGATTC
Found at i:347888 original size:22 final size:23
Alignment explanation
Indices: 347863--347906 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
347853 TTTTTTAGAG
* *
347863 ACGA-AATTAAAATTTAATTTTT
1 ACGATAATAAAAATATAATTTTT
*
347885 ACGATAGTAAAAATATAATTTT
1 ACGATAATAAAAATATAATTTT
347907 ATTATTTTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (23 bp):
ACGATAATAAAAATATAATTTTT
Found at i:352037 original size:3 final size:3
Alignment explanation
Indices: 352029--352061 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
352019 ATTCCAAACC
352029 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
352062 TATGGTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:353759 original size:17 final size:19
Alignment explanation
Indices: 353723--353761 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
353713 TTTAAATTCG
*
353723 AATATTATTATTATTATAA
1 AATATTATTATCATTATAA
353742 AATATTA-TATCA-TATAA
1 AATATTATTATCATTATAA
353759 AAT
1 AAT
353762 TATAATTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 4 0.21
19 7 0.37
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
AATATTATTATCATTATAA
Found at i:358158 original size:29 final size:30
Alignment explanation
Indices: 358123--358180 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
358113 ATGCTTTAGC
* *
358123 GTGCAATTGTATATATG-AACTTTGATTTT
1 GTGCAATTCTATAGATGAAACTTTGATTTT
*
358152 GTGCAATTCTATAGATGAAATTTTGATTT
1 GTGCAATTCTATAGATGAAACTTTGATTT
358181 GATCTAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.29, C:0.07, G:0.17, T:0.47
Consensus pattern (30 bp):
GTGCAATTCTATAGATGAAACTTTGATTTT
Found at i:358407 original size:29 final size:30
Alignment explanation
Indices: 358375--358433 Score: 93
Period size: 31 Copynumber: 2.0 Consensus size: 30
358365 TCACGGGTAT
358375 AATTGCAC-CAAATTAAAGTTCATGTATAC
1 AATTGCACACAAATTAAAGTTCATGTATAC
*
358404 AATTGCACATTAAATTAAAGTTCATGTATA
1 AATTGCACA-CAAATTAAAGTTCATGTATA
358434 ATTTTGAGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.30
31 19 0.70
ACGTcount: A:0.42, C:0.14, G:0.10, T:0.34
Consensus pattern (30 bp):
AATTGCACACAAATTAAAGTTCATGTATAC
Found at i:358436 original size:29 final size:27
Alignment explanation
Indices: 358371--358436 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 27
358361 AGTTTCACGG
358371 GTATAATTGCACCAAATTAAAGTTCAT
1 GTATAATTGCACCAAATTAAAGTTCAT
*
358398 GTATACAATTGCACATTAAATTAAAGTTCAT
1 GTAT--AATTGCAC--CAAATTAAAGTTCAT
358429 GTATAATT
1 GTATAATT
358437 TTGAGATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 4 0.12
29 12 0.35
31 18 0.53
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (27 bp):
GTATAATTGCACCAAATTAAAGTTCAT
Found at i:361945 original size:26 final size:26
Alignment explanation
Indices: 361894--361964 Score: 106
Period size: 26 Copynumber: 2.6 Consensus size: 26
361884 AATAACGAGA
*
361894 CTAAATTTCTAAAAGTAAAAGTGGATGAG
1 CTAAATTT-T-AAA-TATAAGTGGATGAG
361923 CTAAATTTTAAATATAAGTGGATGAG
1 CTAAATTTTAAATATAAGTGGATGAG
361949 CTAAATTTTAAATATA
1 CTAAATTTTAAATATA
361965 CGAAATGTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 29 0.71
27 3 0.07
28 1 0.02
29 8 0.20
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (26 bp):
CTAAATTTTAAATATAAGTGGATGAG
Found at i:363730 original size:23 final size:22
Alignment explanation
Indices: 363672--363731 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
363662 AAATAAATAT
* *
363672 ATAAAAATT-CAAAAAGTATAT
1 ATAAAAATTACAAAAAATATAA
*
363693 AT-AAAATCTAGAAAAAATATAAA
1 ATAAAAAT-TACAAAAAATAT-AA
363716 ATAAAAATTACAAAAA
1 ATAAAAATTACAAAAA
363732 TTATGATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
20 5 0.16
21 3 0.10
22 8 0.26
23 10 0.32
24 5 0.16
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.23
Consensus pattern (22 bp):
ATAAAAATTACAAAAAATATAA
Found at i:363857 original size:15 final size:16
Alignment explanation
Indices: 363833--363864 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
363823 AAATTCTTTT
363833 TATATAAATTCTAAAA
1 TATATAAATTCTAAAA
363849 TATAT-AATTCTAAAA
1 TATATAAATTCTAAAA
363864 T
1 T
363865 TCTCAAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (16 bp):
TATATAAATTCTAAAA
Found at i:366972 original size:11 final size:10
Alignment explanation
Indices: 366930--366974 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
366920 CACGTATATG
366930 TATATAAAAAA
1 TATAT-AAAAA
366941 TATATAAAAA
1 TATATAAAAA
366951 T-TAT-AAAA
1 TATATAAAAA
*
366959 TATA-AAATA
1 TATATAAAAA
366968 TATATAA
1 TATATAA
366975 GTATGTATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
8 5 0.17
9 12 0.40
10 8 0.27
11 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TATATAAAAA
Found at i:366988 original size:27 final size:27
Alignment explanation
Indices: 366930--366991 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 27
366920 CACGTATATG
366930 TATATAAAAAATATATAAAAATTATAA
1 TATATAAAAAATATATAAAAATTATAA
* * **
366957 AATATAAAATATATATAAGTATGTAT-A
1 TATATAAAAAATATATAAAAAT-TATAA
366984 TATATAAA
1 TATATAAA
366992 TGAGGAAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
27 26 0.90
28 3 0.10
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.35
Consensus pattern (27 bp):
TATATAAAAAATATATAAAAATTATAA
Found at i:368027 original size:44 final size:44
Alignment explanation
Indices: 367920--368308 Score: 248
Period size: 44 Copynumber: 8.9 Consensus size: 44
367910 AGATAAGATC
* * * *
367920 CTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGT-GT-
1 CTTTAATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTTA
** *
367963 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTA
1 CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA
* * * * *
368007 TTTTAATCCGCTCCACTGTAA-CTTCAGGGAGATAGGATAGT-GT-
1 CTTTAATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT-CTCTTA
** * **
368050 CTTCGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGG
1 CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA
* * * *
368094 CTTCAATCTGCTCCACTGTAACCTCAGGGATATAAGATCTGAAATT-
1 CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT---CTTA
** * *
368140 CTTTGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-C-CTGA
1 CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA
* * * * *
368182 -TGTGATCTTCTCTACTGTAA-CTTCAGAGAGATAAGATC-CTTTA
1 CTTTAATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCTC-TTA
* ** *
368225 TTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAT-TAC-TA
1 CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT-CTTA
* * *
368268 GCTTCAATCTGCCCCACTGTAATTTCAGGGAGATAAGATCT
1 -CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCT
368309 GAAATTCTTT
Statistics
Matches: 266, Mismatches: 59, Indels: 40
0.73 0.16 0.11
Matches are distributed among these distances:
40 1 0.00
41 29 0.11
42 4 0.02
43 67 0.25
44 128 0.48
45 5 0.02
46 31 0.12
47 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (44 bp):
CTTTAATCTGCTCCACTGTAATCTCAGGGAGATAAGATCTCTTA
Found at i:368036 original size:87 final size:84
Alignment explanation
Indices: 367884--368176 Score: 349
Period size: 87 Copynumber: 3.4 Consensus size: 84
367874 AGACTTGATG
* * * *
367884 CGATCTACTCTGCTGTAACCTCAGAGAGATAAGATC-C-TTTAATCCGCTCCACTGTAACTTCAG
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAACTTCAG
367947 GGAGATAGGATAGTGTCTT
66 GGAGATAGGATAGTGTCTT
367966 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTATTTTAATCCGCTCCACTGTAACTT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTC---TTTTAATCCGCTCCACTGTAACTT
368031 CAGGGAGATAGGATAGTGTCTT
63 CAGGGAGATAGGATAGTGTCTT
* * *
368053 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTGGCTTCAATCTGCTCCACTGTAACCT
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCT---TTTAATCCGCTCCACTGTAACTT
* * *
368118 CAGGGATATAAGAT-CTGAAATTCTT
63 CAGGGAGATAGGATAGTG----TCTT
* * * *
368143 TGGTCTGTTCCACTGTAATCTCAGGGAGATAAGA
1 CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGA
368177 CCTGATGTGA
Statistics
Matches: 185, Mismatches: 14, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
82 32 0.17
83 1 0.01
84 1 0.01
86 2 0.01
87 115 0.62
90 34 0.18
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.30
Consensus pattern (84 bp):
CGATCTGCTCCGCTGTAATCTCAGGGAGATAAGATCTCTTTTAATCCGCTCCACTGTAACTTCAG
GGAGATAGGATAGTGTCTT
Found at i:380970 original size:14 final size:12
Alignment explanation
Indices: 380958--381003 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
380948 CACGTATATG
380958 TATATAAAAATA
1 TATATAAAAATA
380970 TATATAAAAATTA
1 TATATAAAAA-TA
*
380983 TAAAATATAAAATA
1 T-ATATA-AAAATA
380997 TATATAA
1 TATATAA
381004 GTATGTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 11 0.38
13 7 0.24
14 7 0.24
15 4 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
TATATAAAAATA
Found at i:381727 original size:3 final size:3
Alignment explanation
Indices: 381719--381774 Score: 66
Period size: 3 Copynumber: 20.0 Consensus size: 3
381709 TAAATTCATA
* *
381719 TAT TAT TAT CAT TAT T-T T-T TA- TGT TA- TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
381763 TAT TAT TAT TAT
1 TAT TAT TAT TAT
381775 CATTGTCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 7 0.15
3 39 0.85
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:381734 original size:29 final size:29
Alignment explanation
Indices: 381702--381763 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
381692 CATATATATA
381702 TATTTTTTAAATTCATA-TATTATTATCAT
1 TATTTTTTAAATT-ATATTATTATTATCAT
** *
381731 TATTTTTTATGTTATATTATTATTATTAT
1 TATTTTTTAAATTATATTATTATTATCAT
381760 TATT
1 TATT
381764 ATTATTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (29 bp):
TATTTTTTAAATTATATTATTATTATCAT
Found at i:384051 original size:84 final size:84
Alignment explanation
Indices: 383874--384052 Score: 304
Period size: 84 Copynumber: 2.1 Consensus size: 84
383864 AATTCAATAG
* *
383874 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAATGAATTTAAACTAACGAAACAGA
1 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
383939 GATCTCCTCGAGTTCTTAT
66 GATCTCCTCGAGTTCTTAT
* *
383958 AATCAATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTATACTAACCAAACAGA
1 AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
*
384023 GATCTCCTCGCGTTCTTAT
66 GATCTCCTCGAGTTCTTAT
*
384042 AATTGATTATT
1 AATCGATTATT
384053 GCATTTTGTC
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
84 88 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.31
Consensus pattern (84 bp):
AATCGATTATTACAAGCATCAAACTAAACAATTATTCAATAACGAATTTAAACTAACCAAACAGA
GATCTCCTCGAGTTCTTAT
Found at i:396159 original size:10 final size:11
Alignment explanation
Indices: 396131--396156 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
396121 TGTTTTTATT
396131 AAAAATTAGAA
1 AAAAATTAGAA
396142 AAAAATTAGAA
1 AAAAATTAGAA
396153 AAAA
1 AAAA
396157 TTAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:396240 original size:10 final size:9
Alignment explanation
Indices: 396187--396291 Score: 56
Period size: 9 Copynumber: 11.2 Consensus size: 9
396177 AATTTTTTTT
*
396187 AAAATTTAA
1 AAAATATAA
*
396196 TAAAATATTA
1 -AAAATATAA
396206 AAAAT-T-A
1 AAAATATAA
396213 AAAAT-TAA
1 AAAATATAA
396221 AAAATATAA
1 AAAATATAA
*
396230 AAAATCGTAAA
1 AAAAT-AT-AA
396241 AATATATATAA
1 AA-A-ATATAA
*
396252 AAAATTTGTAA
1 AAAA--TATAA
*
396263 AAAAT-TAT
1 AAAATATAA
396271 AAAATATATA
1 AAAATATA-A
*
396281 GAAATATAA
1 AAAATATAA
396290 AA
1 AA
396292 TTTTATAAAG
Statistics
Matches: 76, Mismatches: 9, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
7 7 0.09
8 14 0.18
9 19 0.25
10 16 0.21
11 16 0.21
12 2 0.03
13 2 0.03
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAATATAA
Found at i:396240 original size:26 final size:25
Alignment explanation
Indices: 396185--396253 Score: 77
Period size: 24 Copynumber: 2.6 Consensus size: 25
396175 ATAATTTTTT
* *
396185 TTAAAATTTAATAAAATATTAAAAA
1 TTAAAAATTAATAAAATATAAAAAA
396210 TTAAAAATTAA-AAAATATAAAAAA
1 TTAAAAATTAATAAAATATAAAAAA
396234 TCGTAAAAATATATATAAAA
1 T--TAAAAAT-TA-ATAAAA
396254 AATTTGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
24 13 0.35
25 10 0.27
26 7 0.19
27 2 0.05
28 1 0.03
29 4 0.11
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.30
Consensus pattern (25 bp):
TTAAAAATTAATAAAATATAAAAAA
Found at i:396249 original size:22 final size:22
Alignment explanation
Indices: 396219--396274 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
396209 ATTAAAAATT
396219 AAAAA-ATATAAAAAA-TCGTA
1 AAAAATATATAAAAAATTCGTA
*
396239 AAAATATATATAAAAAATTTGTA
1 AAAA-ATATATAAAAAATTCGTA
396262 AAAAAT-TATAAAA
1 AAAAATATATAAAA
396275 TATATAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.12
21 8 0.25
22 12 0.38
23 8 0.25
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (22 bp):
AAAAATATATAAAAAATTCGTA
Found at i:396360 original size:48 final size:46
Alignment explanation
Indices: 396205--396364 Score: 130
Period size: 48 Copynumber: 3.4 Consensus size: 46
396195 ATAAAATATT
* * *
396205 AAAAATT-AAAAATTAAAAAATATAAA-AAATCGTAAAAATATATATAA
1 AAAAATTAAAAAATTATAAAATATAAAGAAAT-AT-AAAAT-TTTATAA
* *
396252 AAAATTTGTAAAAAATTATAAAATATATAGAAATATAAAATTTTATAA
1 AAAA-AT-TAAAAAATTATAAAATATAAAGAAATATAAAATTTTATAA
****
396300 AGTCGTTAAAAAATTATACAAAATATAAAGAAATAT-AAATTTCT-TAA
1 AAAAATTAAAAAATTAT--AAAATATAAAGAAATATAAAATTT-TATAA
396347 AAAAATTATAAAAATTAT
1 AAAAATTA-AAAAATTAT
396365 CGTACCAAAA
Statistics
Matches: 91, Mismatches: 14, Indels: 15
0.76 0.12 0.12
Matches are distributed among these distances:
46 11 0.12
47 18 0.20
48 34 0.37
49 6 0.07
50 18 0.20
51 4 0.04
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (46 bp):
AAAAATTAAAAAATTATAAAATATAAAGAAATATAAAATTTTATAA
Found at i:396422 original size:18 final size:19
Alignment explanation
Indices: 396381--396423 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
396371 AAAAGAAACA
396381 TTTTATATTTTTTCTATAC
1 TTTTATATTTTTTCTATAC
*
396400 TTTTAT-TTATTTT-TATTC
1 TTTTATATT-TTTTCTATAC
396418 TTTTAT
1 TTTTAT
396424 CAATTTCTGC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTATATTTTTTCTATAC
Found at i:396583 original size:38 final size:37
Alignment explanation
Indices: 396514--396591 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 37
396504 TGATTTTTAT
* *
396514 AAAATTTTAATTTTTTTATTTTTTACGATTTTTATAAA
1 AAAATTTTAATTTTTATAATTTTTAC-ATTTTTATAAA
*
396552 AAAATTTCTAATTTTTAATAATTTTTA-ATTTTTATTAA
1 AAAATTT-TAATTTTT-ATAATTTTTACATTTTTATAAA
396590 AA
1 AA
396592 TTTAATAGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
38 19 0.54
39 8 0.23
40 8 0.23
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (37 bp):
AAAATTTTAATTTTTATAATTTTTACATTTTTATAAA
Found at i:397512 original size:34 final size:34
Alignment explanation
Indices: 397474--397539 Score: 123
Period size: 34 Copynumber: 1.9 Consensus size: 34
397464 TTTGGGCGGC
397474 AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
1 AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
*
397508 AAAGATTGGGCATATTTCAGTGTTAGGGTTTG
1 AAAGATTGGGCATACTTCAGTGTTAGGGTTTG
397540 ATATAAGTCT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.36
Consensus pattern (34 bp):
AAAGATTGGGCATACTTCAGTGTTAGGGTTTGGT
Found at i:399949 original size:47 final size:47
Alignment explanation
Indices: 399840--399950 Score: 127
Period size: 47 Copynumber: 2.4 Consensus size: 47
399830 CCGGGATAAG
* * * **
399840 CACATAGTGCTTCATCGGAATAAATCCGGAACTTTAACATTATATTA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATACGA
* *
399887 CACAAAGTACTTCATCGGAACAAATCCGAAACTTTAACAGTAGT-CGA
1 CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTA-TACGA
399934 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
399951 ACTCAATGTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
46 1 0.02
47 51 0.96
48 1 0.02
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGAAACTTTAACAGTATACGA
Done.