Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold121
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: 1176681
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.32
Warning! 78447 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:314242 original size:30 final size:30
Alignment explanation
Indices: 314199--314257 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
314189 AAACAGTTAA
* *
314199 ACTTTAATCAGTATTCAAGCAAGCCCTTAT
1 ACTTTAATCAGTATCCAAACAAGCCCTTAT
* * *
314229 ACTTTATTTAGTATCCAAATAAGCCCTTA
1 ACTTTAATCAGTATCCAAACAAGCCCTTA
314258 ATTTTTAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (30 bp):
ACTTTAATCAGTATCCAAACAAGCCCTTAT
Found at i:328652 original size:2 final size:2
Alignment explanation
Indices: 328645--328669 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
328635 ACAAGAACTG
328645 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
328670 ATCGATCCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:329802 original size:55 final size:55
Alignment explanation
Indices: 329736--329844 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
329726 GTCCCATGGA
* * *
329736 ATGATAAATCATCACTTTTAATTTTAATAGTGCTTATGAATAATTAATTTGCAAG
1 ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAAG
329791 ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAA
1 ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAA
329845 TCTATAATTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (55 bp):
ATGATAAATCATCACTTTTAATTTGAATAGAGCTAATGAATAATTAATTTGCAAG
Found at i:332397 original size:43 final size:42
Alignment explanation
Indices: 332336--332500 Score: 180
Period size: 43 Copynumber: 3.9 Consensus size: 42
332326 ATTTCTGATA
332336 TGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCATCGACT
1 TGTGTTTA-CGTGTAAGACCACGTCTGGGACGTTGGCATCGA-T
* * *
332379 TGTGTTTACGTGTAAGACCATGTCTGGGACATTGACATCGTAT
1 TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCG-AT
332422 T-TGATTT--GTGTAAGACC-CTGTCTGGGACAG-TGGCATCGAT
1 TGTG-TTTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGAT
* *
332462 ATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 -TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCAT
332501 TGTTTGAGTT
Statistics
Matches: 103, Mismatches: 8, Indels: 22
0.77 0.06 0.17
Matches are distributed among these distances:
40 2 0.02
41 29 0.28
42 5 0.05
43 62 0.60
44 5 0.05
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (42 bp):
TGTGTTTACGTGTAAGACCACGTCTGGGACGTTGGCATCGAT
Found at i:332690 original size:16 final size:17
Alignment explanation
Indices: 332661--332692 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
332651 TGAATTGATG
332661 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
332678 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
332693 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:335978 original size:20 final size:20
Alignment explanation
Indices: 335953--335993 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
335943 TTTCTTAAGA
335953 TAGCCAAAAATCCTACAAAT
1 TAGCCAAAAATCCTACAAAT
335973 TAGCCAAAAATCCTACAAAT
1 TAGCCAAAAATCCTACAAAT
335993 T
1 T
335994 CCTTTCCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.49, C:0.24, G:0.05, T:0.22
Consensus pattern (20 bp):
TAGCCAAAAATCCTACAAAT
Found at i:340100 original size:14 final size:14
Alignment explanation
Indices: 340078--340107 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
340068 ATTTAATTTC
*
340078 TTGTGAAGGATTAT
1 TTGTAAAGGATTAT
340092 TTGTAAAGGATTAT
1 TTGTAAAGGATTAT
340106 TT
1 TT
340108 TAGTGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (14 bp):
TTGTAAAGGATTAT
Found at i:343273 original size:80 final size:80
Alignment explanation
Indices: 343140--343300 Score: 252
Period size: 80 Copynumber: 2.0 Consensus size: 80
343130 AAGTTTGGAA
* *
343140 AACTAGTCAACTTGTGACAACTTTTTGGATGGAATCCATGCATTTCTGGGTTAATATGTCTTCAT
1 AACTAGCCAACTTGTGACAACTTTTTGGATAGAATCCATGCATTTCTGGGTTAATATGTCTTCAT
343205 GGTGTTCTAAGATCT
66 GGTGTTCTAAGATCT
** *
343220 AACTAGCCAACTTGTGATGACTTTTTGGATAGAATTCA-GACATTTCTGGGTTAATATGTCTTCA
1 AACTAGCCAACTTGTGACAACTTTTTGGATAGAATCCATG-CATTTCTGGGTTAATATGTCTTCA
*
343284 TGTTGTTCTAAGATCT
65 TGGTGTTCTAAGATCT
343300 A
1 A
343301 CATCTTATCT
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (80 bp):
AACTAGCCAACTTGTGACAACTTTTTGGATAGAATCCATGCATTTCTGGGTTAATATGTCTTCAT
GGTGTTCTAAGATCT
Found at i:344465 original size:13 final size:13
Alignment explanation
Indices: 344447--344481 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
344437 TATTTATTGT
344447 TTTTGAGAAGTGC
1 TTTTGAGAAGTGC
344460 TTTTGAGAAGTGC
1 TTTTGAGAAGTGC
344473 TTTTGAGAA
1 TTTTGAGAA
344482 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.06, G:0.29, T:0.40
Consensus pattern (13 bp):
TTTTGAGAAGTGC
Found at i:349382 original size:21 final size:21
Alignment explanation
Indices: 349358--349399 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
349348 TCACCTATGC
*
349358 ACCATATAATCCAATAACAAT
1 ACCATATAATACAATAACAAT
349379 ACCATATAATACAATAACAAT
1 ACCATATAATACAATAACAAT
349400 TTATTTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (21 bp):
ACCATATAATACAATAACAAT
Found at i:349569 original size:20 final size:20
Alignment explanation
Indices: 349544--349582 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
349534 GATATTTTTA
349544 AATTTT-AAATAACAAAAATT
1 AATTTTCAAATAA-AAAAATT
*
349564 AATTTTCAATTAAAAAAAT
1 AATTTTCAAATAAAAAAAT
349583 GTGGACGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTTCAAATAAAAAAATT
Found at i:349828 original size:26 final size:26
Alignment explanation
Indices: 349800--349850 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 26
349790 AAATAAGGTT
349800 AAAATATTATTAAATGATAT-TAAATTA
1 AAAATA-TA-TAAATGATATATAAATTA
*
349827 AAAATATATAAATTATATATAAAT
1 AAAATATATAAATGATATATAAAT
349851 GTTGTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 7 0.32
27 6 0.27
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (26 bp):
AAAATATATAAATGATATATAAATTA
Found at i:350454 original size:18 final size:17
Alignment explanation
Indices: 350413--350454 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
350403 CCTCTCTCAA
350413 TTTTCTCCTTTTTTTTT
1 TTTTCTCCTTTTTTTTT
*
350430 TCATTCTCCTTTTGTTTTT
1 T-TTTCTCCTTTT-TTTTT
350449 TTTTCT
1 TTTTCT
350455 TGGCTTCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 14 0.67
19 6 0.29
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTCTCCTTTTTTTTT
Found at i:361526 original size:29 final size:30
Alignment explanation
Indices: 361485--361550 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
361475 ATTATAAATA
361485 TAAATATATATAATTATTATT-TAACATAAG
1 TAAATATATATAA-TATTATTATAACATAAG
*
361515 TAAATA-ATATAATATTTTTATAACATAA-
1 TAAATATATATAATATTATTATAACATAAG
*
361543 TATATATA
1 TAAATATA
361551 CGGGTCAGGC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 11 0.34
29 15 0.47
30 6 0.19
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (30 bp):
TAAATATATATAATATTATTATAACATAAG
Found at i:362635 original size:31 final size:31
Alignment explanation
Indices: 362548--362636 Score: 106
Period size: 31 Copynumber: 2.9 Consensus size: 31
362538 AGTTTAAACT
* * *
362548 CCAATGTGTGAATAACTACCAAGTTCAAGTC
1 CCAATGTGAGAATAATTACCAAGTTTAAGTC
* * *
362579 CCAATATGAAAAGAATTACCAAGTTTAAGTC
1 CCAATGTGAGAATAATTACCAAGTTTAAGTC
* *
362610 TCAATGTGAGAATAATTATCAAGTTTA
1 CCAATGTGAGAATAATTACCAAGTTTA
362637 GGCCCGATAT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (31 bp):
CCAATGTGAGAATAATTACCAAGTTTAAGTC
Found at i:362854 original size:50 final size:50
Alignment explanation
Indices: 362779--362874 Score: 165
Period size: 50 Copynumber: 1.9 Consensus size: 50
362769 GATATGAGAG
* *
362779 TTATTGCCAAATTTAGGCAACTAATAGTGATTTAACCTTCCAACTTAGAA
1 TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTTAGAA
*
362829 TTATTGCCAAATTTAGGCACCTAATAGTAATTTAACCTTCAAACTT
1 TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTT
362875 TAAAGTGAGC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.35
Consensus pattern (50 bp):
TTATTGCCAAATTTAGGCAACTAATAGTAATTTAACCTTCAAACTTAGAA
Found at i:364418 original size:132 final size:131
Alignment explanation
Indices: 363746--364435 Score: 623
Period size: 136 Copynumber: 5.2 Consensus size: 131
363736 GATGTTTTCT
* * *
363746 TTAAAAGATCAATGCTT-ATTCATATTTGCTAATACT--GCGTTTTTGCAATGTAAAAACCAGAT
1 TTAAAAGATCAATG-TTCATTCATATTTGCTAATA-TAAGCGTCTTTGCAGTGTAAAAACCA-AA
* * *
363808 CACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTTAATGTTTCGTCACTTATGTCCAAGA
63 CACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTTGATGTTTTGTCACTTATGTCTAAGA
363873 TTCA
128 TTCA
* * * * * *
363877 TTAAAAGATCAATGTCCATTCATGTATTGCTAATATAAGTGTCTGTGCAGTATAAAAACCAATCT
1 TTAAAAGATCAATGTTCATTCATAT-TTGCTAATATAAGCGTCTTTGCAGTGTAAAAACCAAAC-
* * * * **
363942 ACCA--TCTCAA---C-ATATTTGTTTGGATTTTATGTTGGTTTTTTTGTCACTTATGTCTGTGA
64 ACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTT-GATGTTTTGTCACTTATGTCTAAGA
364001 TTCA
128 TTCA
* * * *
364005 TTACAAGATCAATGTTTATTCATACATTGCTAATATAAGCGTCCTTGCAGTGTAAAAACCAAACC
1 TTAAAAGATCAATGTTCATTCATA-TTTGCTAATATAAGCGTCTTTGCAGTGTAAAAACCAAA-C
* * * * * *
364070 ACCGTGCATTAATCTCAATATATTTGTTTTGATTTTTATGTTGATGTTTTATTAATTATGTCTAA
64 ACCATGTATTAATCTC-A-ATATTTGTTTGGA-TTTTATGTTGATGTTTTGTCACTTATGTCTAA
364135 GATTCA
126 GATTCA
* * * * * * * *
364141 CTAAAAGATCAATTTTTATTCATATATTTCTAGTATAAGTGTCTGTGCAGTGTAAAAAACCAAGC
1 TTAAAAGATCAATGTTCATTCATAT-TTGCTAATATAAGCGTCTTTGCAGTGT-AAAAACCAA-A
* * *
364206 CATCATGTATTTATCTCAATATGTTTGTTTGGATTTTTATGTTGATAGTTTTGTCAGTTATGTCT
63 CACCATGTATTAATCTCAATA--TTTGTTTGGA-TTTTATGTTGAT-GTTTTGTCACTTATGTCT
*
364271 AACATTCA
124 AAGATTCA
* * *
364279 TTAAAAGAGATCAATGCTCATTCATATTTGCTAATAT-TGCGT-TTTCGCAATGTAAAAACCAGA
1 TT-AAA-AGATCAATGTTCATTCATATTTGCTAATATAAGCGTCTTT-GCAGTGTAAAAACCA-A
* * * * * *
364342 ACACCATGTAATAATCTC-A-GTGTGTTAGGATTTTATGTTGATGTTTTTATCATTTATGTCTAA
62 ACACCATGTATTAATCTCAATATTTGTTTGGATTTTATGTTGATG-TTTTGTCACTTATGTCTAA
*
364405 CATTCA
126 GATTCA
*
364411 TTCAAAGATCAATGTTCATTCATAT
1 TTAAAAGATCAATGTTCATTCATAT
364436 GTGTTTTGTC
Statistics
Matches: 453, Mismatches: 78, Indels: 57
0.77 0.13 0.10
Matches are distributed among these distances:
127 22 0.05
128 78 0.17
129 1 0.00
130 23 0.05
131 29 0.06
132 49 0.11
133 31 0.07
135 3 0.01
136 79 0.17
137 77 0.17
138 33 0.07
139 11 0.02
140 17 0.04
ACGTcount: A:0.31, C:0.14, G:0.14, T:0.41
Consensus pattern (131 bp):
TTAAAAGATCAATGTTCATTCATATTTGCTAATATAAGCGTCTTTGCAGTGTAAAAACCAAACAC
CATGTATTAATCTCAATATTTGTTTGGATTTTATGTTGATGTTTTGTCACTTATGTCTAAGATTC
A
Found at i:365746 original size:2 final size:2
Alignment explanation
Indices: 365739--365772 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
365729 TTTTGAAGAA
365739 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
365773 GCCAGAACGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:382570 original size:51 final size:52
Alignment explanation
Indices: 382508--382732 Score: 217
Period size: 51 Copynumber: 4.4 Consensus size: 52
382498 TTCGGTGGTT
* * * * *
382508 TGCACATAGTACCACCCATGTGACCATTGTC-ATCCAATACACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* ** * * * * *
382559 TACACATAGTACTACACACGTGGTCA-AG-CTTTCCGGTTCACGTAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* * * *
382609 TGCACATAGTACTACACACGTGACCA-AGGCCATCCGGTACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* * *
382660 TGCAAATAGTACTACACATGTGACCATTATCTAT-CGATACACATAGTAGCC
1 TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
* *
382711 TTCACTTAGTACTACACACGTG
1 TGCACATAGTACTACACACGTG
382733 TTCATAGGTA
Statistics
Matches: 142, Mismatches: 29, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
49 1 0.01
50 42 0.30
51 96 0.68
52 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (52 bp):
TGCACATAGTACTACACACGTGACCATTGTCTATCCGATACACATAGTAGCC
Found at i:385854 original size:50 final size:50
Alignment explanation
Indices: 385786--385903 Score: 130
Period size: 50 Copynumber: 2.4 Consensus size: 50
385776 AGTATGTAAA
* * ** * * *
385786 CGGGAAGCTCTTGTGAGCCATTTATCGGGAAGCTCA-AGAGAGCCAAATAT
1 CGGGAAGCTCGTGAGAGCCAAATATCAGGAAGCTCATA-AGAGCCAAACAG
* * *
385836 CTGGAAGCTCGTGAGAGCCAAATATCAGGATGCTCATAAGAGCTAAACAG
1 CGGGAAGCTCGTGAGAGCCAAATATCAGGAAGCTCATAAGAGCCAAACAG
385886 CGGGAAGCTCGTGAGAGC
1 CGGGAAGCTCGTGAGAGC
385904 TGTGGTGTAT
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
50 55 0.98
51 1 0.02
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (50 bp):
CGGGAAGCTCGTGAGAGCCAAATATCAGGAAGCTCATAAGAGCCAAACAG
Found at i:385904 original size:25 final size:25
Alignment explanation
Indices: 385786--385903 Score: 110
Period size: 25 Copynumber: 4.7 Consensus size: 25
385776 AGTATGTAAA
* * **
385786 CGGGAAGCTCTTGTGAGCCATTTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
*
385811 CGGGAAGCTCAAGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* *
385836 CTGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * * * *
385861 CAGGATGCTCATAAGAGCTAAACAG
1 CGGGAAGCTCATGAGAGCCAAATAT
*
385886 CGGGAAGCTCGTGAGAGC
1 CGGGAAGCTCATGAGAGC
385904 TGTGGTGTAT
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 74 1.00
ACGTcount: A:0.31, C:0.20, G:0.30, T:0.19
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAT
Found at i:386216 original size:22 final size:22
Alignment explanation
Indices: 386191--386235 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
386181 ATATTAGGTT
386191 TATCCGGATCTATATGAATGAA
1 TATCCGGATCTATATGAATGAA
386213 TATCCGGATCTATATGAATGAA
1 TATCCGGATCTATATGAATGAA
386235 T
1 T
386236 TTAACTCGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (22 bp):
TATCCGGATCTATATGAATGAA
Found at i:398518 original size:44 final size:44
Alignment explanation
Indices: 398455--398545 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
398445 GTAGGTCAAA
* *
398455 TAATATTAAAATAACCTACACTAATCAGAGTTTAAGTGGGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGAGAAAC
*
398499 TAATATTAAAATAACCTACACTAATTAGAGCTTAAGTGAGAAAC
1 TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGAGAAAC
398543 TAA
1 TAA
398546 AAACAGAGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.47, C:0.13, G:0.12, T:0.27
Consensus pattern (44 bp):
TAATATTAAAATAACCTACACTAATCAGAGCTTAAGTGAGAAAC
Found at i:401204 original size:16 final size:18
Alignment explanation
Indices: 401171--401211 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
401161 GGGAAGGGAT
401171 AAAAAATTGTCAGAAGAA
1 AAAAAATTGTCAGAAGAA
401189 AAAAAATTG-CAG-AGAA
1 AAAAAATTGTCAGAAGAA
401205 ACAAAAA
1 A-AAAAA
401212 CGTGGGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.23
17 8 0.36
18 9 0.41
ACGTcount: A:0.66, C:0.07, G:0.15, T:0.12
Consensus pattern (18 bp):
AAAAAATTGTCAGAAGAA
Found at i:403503 original size:25 final size:25
Alignment explanation
Indices: 403475--403523 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
403465 TCAAGCCTAA
403475 TTTGATTTGGATCGTAGAGAGCAAC
1 TTTGATTTGGATCGTAGAGAGCAAC
403500 TTTGATTTGGATCGTAGAGAGCAA
1 TTTGATTTGGATCGTAGAGAGCAA
403524 TCTAACCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.29, T:0.33
Consensus pattern (25 bp):
TTTGATTTGGATCGTAGAGAGCAAC
Found at i:405984 original size:41 final size:40
Alignment explanation
Indices: 405939--406100 Score: 184
Period size: 41 Copynumber: 4.0 Consensus size: 40
405929 TTGTATAAAA
* * * *
405939 CACCGGCATAAAGCCTGCTAGGCACAAAGCCCGATACATT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
* *
405979 CCACCGGCACAAAGCCTGCTAGACATAAGGTCTGATACATTT
1 -CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACA-TT
406021 CACCGGCACT-AAGCCTGCTAGACATAAAGTCTGAAGTA-ATT
1 CACCGGCA-TAAAGCCTGCTAGACATAAAGTCTG-A-TACATT
* * *
406062 CACCGGCATCAAGCCTGCTAGACGTAAAGTCTGAAACAT
1 CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACAT
406101 CTTATTTTCA
Statistics
Matches: 105, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
39 1 0.01
40 4 0.04
41 94 0.90
42 4 0.04
43 2 0.02
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (40 bp):
CACCGGCATAAAGCCTGCTAGACATAAAGTCTGATACATT
Found at i:406769 original size:16 final size:17
Alignment explanation
Indices: 406748--406782 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
406738 ATCTAATAAT
406748 TTATACAT-GTATATAC
1 TTATACATCGTATATAC
*
406764 TTATACATCGTTTATAC
1 TTATACATCGTATATAC
406781 TT
1 TT
406783 CGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.49
Consensus pattern (17 bp):
TTATACATCGTATATAC
Found at i:427450 original size:25 final size:25
Alignment explanation
Indices: 427398--427451 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
427388 AAGCTCTTGC
**
427398 GAGCCAAATATCGAGAAACTCATGA
1 GAGCCAAATATCGAGAAACTCAAAA
* * *
427423 GAGCCAAGTATCGGGAAGCTCAAAA
1 GAGCCAAATATCGAGAAACTCAAAA
427448 GAGC
1 GAGC
427452 TATGGTGTAT
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:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (25 bp):
GAGCCAAATATCGAGAAACTCAAAA
Found at i:429098 original size:35 final size:35
Alignment explanation
Indices: 429030--429097 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
429020 CACAATGTTT
* *
429030 GTTATGACCATTTAAAGAATTCAAACATATTTTTA
1 GTTATGACCATCTAAAGAATTCAAAAATATTTTTA
429065 GTTATGACCATCTAAAGAATTCAAAAA-ATTTTT
1 GTTATGACCATCTAAAGAATTCAAAAATATTTTT
429098 TCTTCACAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 6 0.19
35 25 0.81
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (35 bp):
GTTATGACCATCTAAAGAATTCAAAAATATTTTTA
Found at i:435673 original size:21 final size:21
Alignment explanation
Indices: 435634--435676 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
435624 CCGATCAATG
* *
435634 ACCGGGCCCTAGTCGGAGAAC
1 ACCGGGCCCTAGCCAGAGAAC
*
435655 ACCGGGCCCTGGCCAGAGAAC
1 ACCGGGCCCTAGCCAGAGAAC
435676 A
1 A
435677 GGAGGAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.35, G:0.33, T:0.07
Consensus pattern (21 bp):
ACCGGGCCCTAGCCAGAGAAC
Found at i:436222 original size:14 final size:14
Alignment explanation
Indices: 436205--436253 Score: 80
Period size: 14 Copynumber: 3.4 Consensus size: 14
436195 CTGTAATTAG
436205 TTTTTATTTATATTT
1 TTTTTATTTATA-TT
436220 TTTTTATTTATATT
1 TTTTTATTTATATT
*
436234 TATTTATTTATATT
1 TTTTTATTTATATT
436248 TTTTTA
1 TTTTTA
436254 AAAACAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTATTTATATT
Found at i:436223 original size:15 final size:15
Alignment explanation
Indices: 436205--436252 Score: 80
Period size: 15 Copynumber: 3.3 Consensus size: 15
436195 CTGTAATTAG
436205 TTTTTATTTATATTT
1 TTTTTATTTATATTT
436220 TTTTTATTTATA-TT
1 TTTTTATTTATATTT
*
436234 TATTTATTTATATTT
1 TTTTTATTTATATTT
436249 TTTT
1 TTTT
436253 AAAAACAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 13 0.43
15 17 0.57
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTTATTTATATTT
Found at i:436852 original size:19 final size:20
Alignment explanation
Indices: 436822--436862 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
436812 ATATTTAATG
436822 TAGCATCACATCATTTTTTT
1 TAGCATCACATCATTTTTTT
436842 TAGCA-CACATCATTTTTTT
1 TAGCATCACATCATTTTTTT
436861 TA
1 TA
436863 CTCGATTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.27, C:0.20, G:0.05, T:0.49
Consensus pattern (20 bp):
TAGCATCACATCATTTTTTT
Found at i:438340 original size:6 final size:6
Alignment explanation
Indices: 438329--438364 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
438319 CATATATGAA
* *
438329 AAATAT AAATAT AAATAC AAATAC AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
438365 CACATAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.28
Consensus pattern (6 bp):
AAATAT
Found at i:438356 original size:18 final size:18
Alignment explanation
Indices: 438329--438363 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
438319 CATATATGAA
*
438329 AAATATAAATATAAATAC
1 AAATACAAATATAAATAC
438347 AAATACAAATATAAATA
1 AAATACAAATATAAATA
438364 TCACATAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACAAATATAAATAC
Found at i:438782 original size:5 final size:6
Alignment explanation
Indices: 438767--438791 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
438757 GTTTCAACAA
438767 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
438792 GAAATTATAT
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:455630 original size:1 final size:1
Alignment explanation
Indices: 455624--455664 Score: 82
Period size: 1 Copynumber: 41.0 Consensus size: 1
455614 ACCAAAATAC
455624 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
455665 GAAGAAGAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:456787 original size:40 final size:40
Alignment explanation
Indices: 456708--456787 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
456698 CATTATTCAA
* *
456708 TTATAATATAATTATTAATTTATGTGCTTATTTTATTTAT
1 TTATAATATAATTATTAATTTATATGCTTATTATATTTAT
*
456748 TTATAATATAATTATTAATACTTATATTC-TATTAT-TTTAT
1 TTATAATATAATTATTAAT--TTATATGCTTATTATATTTAT
456788 ATCTAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 24 0.69
41 5 0.14
42 6 0.17
ACGTcount: A:0.35, C:0.04, G:0.03, T:0.59
Consensus pattern (40 bp):
TTATAATATAATTATTAATTTATATGCTTATTATATTTAT
Found at i:459008 original size:12 final size:12
Alignment explanation
Indices: 458991--459016 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
458981 ATTTAAACCT
458991 AAAAAATTAGAA
1 AAAAAATTAGAA
459003 AAAAAATTAGAA
1 AAAAAATTAGAA
459015 AA
1 AA
459017 CTATAAAACT
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:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAAAATTAGAA
Found at i:459293 original size:3 final size:3
Alignment explanation
Indices: 459287--459321 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
459277 TCACATGTTG
459287 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
459322 TAAAGAGTGC
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:464707 original size:44 final size:42
Alignment explanation
Indices: 464633--464747 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
464623 ATGTGATTTT
** * *
464633 GTGTAAGACCACATCTGAGACGTTGACATCG-ACTAGAGATTTAC
1 GTGTAAGACCATGTCTGGGACATTGACATCGTA-TA-AGA-TTAC
* *
464677 GTGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTAC
1 GTGTAAGACCATGTCTGGGACATTGACATCGTATAAGATTAC
* *
464719 GTGTAAGACCTTGTCTGGGACAGTGACAT
1 GTGTAAGACCATGTCTGGGACATTGACAT
464748 TGTTATTTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
42 30 0.49
43 2 0.03
44 28 0.46
45 1 0.02
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (42 bp):
GTGTAAGACCATGTCTGGGACATTGACATCGTATAAGATTAC
Found at i:464734 original size:42 final size:43
Alignment explanation
Indices: 464673--464769 Score: 133
Period size: 42 Copynumber: 2.3 Consensus size: 43
464663 GACTAGAGAT
* *
464673 TTACGTGTAAGACCATGTCTGGGACATTGGCATCG-TATATGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
* * *
464715 TTACGTGTAAGACCTTGTCTGGGACAGTGACATTGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
*
464758 TTACATGTAAGA
1 TTACGTGTAAGA
464770 ACACATCTGA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
42 31 0.65
43 17 0.35
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (43 bp):
TTACGTGTAAGACCATGTCTGGGACAGTGACATCGTTATATGA
Found at i:465092 original size:30 final size:28
Alignment explanation
Indices: 465058--465176 Score: 103
Period size: 30 Copynumber: 4.0 Consensus size: 28
465048 ATTAAATTTT
*
465058 TTTTTAAAAATTTGCATTTTAACCCCTAAA
1 TTTTT-AAAA-TTACATTTTAACCCCTAAA
* *
465088 TTTTTCTAAAATTACATTTTGATCCCTAAA
1 -TTTT-TAAAATTACATTTTAACCCCTAAA
*
465118 CTTTCTTAAAATTACATTTCAACCCCTAAA
1 -TTT-TTAAAATTACATTTTAACCCCTAAA
* ** *
465148 TTTCTCAAAATTATGTTTTGACCCCTAAA
1 TTT-TTAAAATTACATTTTAACCCCTAAA
465177 CTTTCTCTGA
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 24 0.32
30 40 0.54
31 9 0.12
32 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.42
Consensus pattern (28 bp):
TTTTTAAAATTACATTTTAACCCCTAAA
Found at i:465190 original size:30 final size:30
Alignment explanation
Indices: 465074--465210 Score: 127
Period size: 30 Copynumber: 4.6 Consensus size: 30
465064 AAAATTTGCA
* * *
465074 TTTTAACCCCTAAA-TTTTTCTAAAATTACA
1 TTTTGACCCCTAAACTTTCTCT-AAATTACG
* *
465104 TTTTGATCCCTAAACTTTCT-TAAAATTACA
1 TTTTGACCCCTAAACTTTCTCT-AAATTACG
** * *
465134 TTTCAACCCCTAAA-TTTCTCAAAATTATG
1 TTTTGACCCCTAAACTTTCTCTAAATTACG
*
465163 TTTTGACCCCTAAACTTTCTCTGAATTACG
1 TTTTGACCCCTAAACTTTCTCTAAATTACG
* *
465193 TTTTGGCCCCAAAACTTT
1 TTTTGACCCCTAAACTTT
465211 TGCTACATTT
Statistics
Matches: 88, Mismatches: 16, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
29 23 0.26
30 61 0.69
31 4 0.05
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTTGACCCCTAAACTTTCTCTAAATTACG
Found at i:465527 original size:17 final size:17
Alignment explanation
Indices: 465490--465533 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
465480 CTCGCCACCG
* **
465490 TCGCGCCACCACTATTG
1 TCGCGCCACCACCATCA
465507 TCGCGCCACCACCATCA
1 TCGCGCCACCACCATCA
*
465524 TCGCTCCACC
1 TCGCGCCACC
465534 GCCGAAACCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.18, C:0.50, G:0.14, T:0.18
Consensus pattern (17 bp):
TCGCGCCACCACCATCA
Found at i:465606 original size:14 final size:14
Alignment explanation
Indices: 465569--465612 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
465559 AAGCATAAAC
*
465569 AAAAAAAATCAGCA
1 AAAAAAAAACAGCA
* * *
465583 AACAAGAAACAACA
1 AAAAAAAAACAGCA
465597 AAAAAAAAACAGCA
1 AAAAAAAAACAGCA
465611 AA
1 AA
465613 GAAGAAAAGA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.75, C:0.16, G:0.07, T:0.02
Consensus pattern (14 bp):
AAAAAAAAACAGCA
Found at i:465711 original size:3 final size:3
Alignment explanation
Indices: 465705--465754 Score: 73
Period size: 3 Copynumber: 16.0 Consensus size: 3
465695 TAGGGTTCGT
*
465705 GAA GAA GAA GAA GAA GAA GAA GAAA GAA GAA GAAA GAA GAA GAA AAA
1 GAA GAA GAA GAA GAA GAA GAA G-AA GAA GAA G-AA GAA GAA GAA GAA
465752 GAA
1 GAA
465755 AGAAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 37 0.86
4 6 0.14
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:465733 original size:10 final size:10
Alignment explanation
Indices: 465705--465759 Score: 80
Period size: 10 Copynumber: 5.7 Consensus size: 10
465695 TAGGGTTCGT
465705 GAAG-AAGAA
1 GAAGAAAGAA
465714 GAAG-AAGAA
1 GAAGAAAGAA
465723 GAAGAAAGAA
1 GAAGAAAGAA
465733 GAAGAAAGAA
1 GAAGAAAGAA
465743 GAAGAAA-AA
1 GAAGAAAGAA
465752 GAAAGAAA
1 G-AAGAAA
465760 AAAAAAAGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
9 16 0.36
10 28 0.64
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:465755 original size:6 final size:6
Alignment explanation
Indices: 465706--465772 Score: 59
Period size: 6 Copynumber: 11.3 Consensus size: 6
465696 AGGGTTCGTG
* * * *
465706 AAGAAG AAGAAG AAGAAG AAGAAA GAAGAAGA AAGAAG AAGAAA AAG--A
1 AAGAAA AAGAAA AAGAAA AAGAAA -AAGAA-A AAGAAA AAGAAA AAGAAA
465754 AAGAAA AA-AAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AA
465773 AAGGAAAAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
4 4 0.08
5 5 0.09
6 33 0.62
7 10 0.19
8 1 0.02
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:465780 original size:15 final size:15
Alignment explanation
Indices: 465709--465781 Score: 71
Period size: 15 Copynumber: 4.9 Consensus size: 15
465699 GTTCGTGAAG
*
465709 AAGAAGAAGAAGAAG-
1 AAGAA-AAGAAAAAGA
*
465724 AAG-AAAGAAGAAGA
1 AAGAAAAGAAAAAGA
465738 AAGAAGAAGAAAAAGA
1 AAGAA-AAGAAAAAGA
*
465754 AAGAAAAAAAAAAGA
1 AAGAAAAGAAAAAGA
465769 AA-AAAAGGAAAAA
1 AAGAAAA-GAAAAA
465782 AAATATAAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
13 9 0.18
14 8 0.16
15 20 0.39
16 14 0.27
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAAGA
Found at i:465782 original size:11 final size:10
Alignment explanation
Indices: 465724--465784 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
465714 GAAGAAGAAG
* *
465724 AAGAAAGAAG
1 AAGAAAAAAA
* *
465734 AAGAAAGAAG
1 AAGAAAAAAA
*
465744 AAGAAAAAGA
1 AAGAAAAAAA
465754 AAGAAAAAAA
1 AAGAAAAAAA
465764 AA-AGAAAAAA
1 AAGA-AAAAAA
*
465774 AGGAAAAAAA
1 AAGAAAAAAA
465784 A
1 A
465785 TATAAATAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
9 1 0.02
10 42 0.95
11 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:466610 original size:16 final size:17
Alignment explanation
Indices: 466591--466628 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
466581 GTACTTCTTA
466591 AAAAAAATCGTG-TTTC
1 AAAAAAATCGTGTTTTC
**
466607 AAAAATTTCGTGTTTTC
1 AAAAAAATCGTGTTTTC
466624 AAAAA
1 AAAAA
466629 TTCTCATGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (17 bp):
AAAAAAATCGTGTTTTC
Found at i:466623 original size:17 final size:17
Alignment explanation
Indices: 466598--466921 Score: 164
Period size: 17 Copynumber: 17.9 Consensus size: 17
466588 TTAAAAAAAA
466598 TCGTG-TTTCAAAAATT
1 TCGTGTTTTCAAAAATT
466614 TCGTGTTTTCAAAAATT
1 TCGTGTTTTCAAAAATT
*
466631 CTCATG-TTTCAAAAATCT
1 -TCGTGTTTTCAAAAAT-T
466649 TCGTGTTTTC-AAAATT
1 TCGTGTTTTCAAAAATT
* *
466665 CCAGAG-TTTCAAAAATTT
1 TC-GTGTTTTCAAAAA-TT
466683 TCGTGTTTTCAAAAAAAATTT
1 TCGTGTTTTC---AAAAA-TT
*
466704 CATCTTCGTGTTTC-AAAATT
1 --TCGT-GT-TTTCAAAAATT
* *
466724 CCAGAG-TTTCAAAAATTT
1 TC-GTGTTTTCAAAAA-TT
466742 TCGTGTTTTCAAAAAATT
1 TCGTGTTTTC-AAAAATT
466760 TCCCGTGTTTTCAAAAATT
1 T--CGTGTTTTCAAAAATT
* * *
466779 CCCGTATTTT-GAAAATT
1 -TCGTGTTTTCAAAAATT
*
466796 TCCTTGTTTTCAAAAAAAATT
1 T-CGTGTTTTC---AAAAATT
*
466817 TCCGTG-TTTCATAAATT
1 T-CGTGTTTTCAAAAATT
*
466834 TCAGTGTTTTCAAAAAAT
1 TC-GTGTTTTCAAAAATT
**
466852 TCCCGTCTTTCAAAAATTT
1 TCGTGT-TTTCAAAAA-TT
466871 TCGTGTTTTCAAGAAATT
1 TCGTGTTTTCAA-AAATT
* *
466889 GACCGTG-TTTCATAAATTT
1 --TCGTGTTTTCA-AAAATT
466908 TCGTG-TTTCAAAAA
1 TCGTGTTTTCAAAAA
466922 AAAATCCTCA
Statistics
Matches: 240, Mismatches: 32, Indels: 72
0.70 0.09 0.21
Matches are distributed among these distances:
16 19 0.08
17 77 0.32
18 63 0.26
19 29 0.12
20 20 0.08
21 23 0.10
23 3 0.01
24 2 0.01
25 4 0.02
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (17 bp):
TCGTGTTTTCAAAAATT
Found at i:466725 original size:59 final size:60
Alignment explanation
Indices: 466645--466818 Score: 229
Period size: 59 Copynumber: 3.0 Consensus size: 60
466635 TGTTTCAAAA
466645 ATCTTCGTGTTTTCAAAATTCCAGAGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTC
1 ATCTTCGTGTTTTCAAAATTCCAGAGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTC
466705 ATCTTCGTG-TTTCAAAATTCCAGAGTTTCAAAAATTTTCGTGTTTTC--AAAAAATTTC
1 ATCTTCGTGTTTTCAAAATTCCAGAGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTC
* ** * *
466762 --C--CGTGTTTTCAAAAATTCCCGTA-TTTTGAAAATTTCCTTGTTTTCAAAAAAAATTTC
1 ATCTTCGTGTTTTC-AAAATTCCAG-AGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTC
466819 CGTGTTTCAT
Statistics
Matches: 104, Mismatches: 5, Indels: 13
0.85 0.04 0.11
Matches are distributed among these distances:
53 4 0.04
54 4 0.04
55 28 0.27
56 1 0.01
57 20 0.19
59 38 0.37
60 9 0.09
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (60 bp):
ATCTTCGTGTTTTCAAAATTCCAGAGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTC
Found at i:466772 original size:38 final size:36
Alignment explanation
Indices: 466599--466921 Score: 208
Period size: 38 Copynumber: 8.9 Consensus size: 36
466589 TAAAAAAAAT
*
466599 CGTG-TTTCAAAAATTT-CGTGTTTTCAAAAATTCT
1 CGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTCC
*
466633 CATG-TTTCAAAAATCTT-CGTGTTTTC-AAAATTCC
1 CGTGTTTTCAAAAAT-TTCCGTGTTTTCAAAAATTCC
* * *
466667 AGAG-TTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCATC
1 CGTGTTTTCAAAAATTTCCGTGTTTTC---AAAAA-TTC--C
* **
466708 TTCGTG-TTTC-AAAA-TTCCAGAG-TTTCAAAAATTTT
1 --CGTGTTTTCAAAAATTTCC-GTGTTTTCAAAAATTCC
466743 CGTGTTTTCAAAAAATTTCCCGTGTTTTCAAAAATTCC
1 CGTGTTTTC-AAAAATTT-CCGTGTTTTCAAAAATTCC
* * * *
466781 CGTATTTT-GAAAATTTCCTTGTTTTCAAAAAAAATTTC
1 CGTGTTTTCAAAAATTTCCGTGTTTTC---AAAAATTCC
* *
466819 CGTG-TTTCATAAATTTCAGTGTTTTCAAAAAATTCC
1 CGTGTTTTCAAAAATTTCCGTGTTTTC-AAAAATTCC
* * *
466855 CGT-CTTTCAAAAATTTTCGTGTTTTCAAGAAATTGAC
1 CGTGTTTTCAAAAATTTCCGTGTTTTCAA-AAATT-CC
* *
466892 CGTG-TTTCATAAATTTTCGTG-TTTCAAAAA
1 CGTGTTTTCAAAAATTTCCGTGTTTTCAAAAA
466922 AAAATCCTCA
Statistics
Matches: 234, Mismatches: 29, Indels: 51
0.75 0.09 0.16
Matches are distributed among these distances:
33 6 0.03
34 44 0.19
35 25 0.11
36 53 0.23
37 29 0.12
38 54 0.23
39 3 0.01
41 8 0.03
42 6 0.03
43 6 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (36 bp):
CGTGTTTTCAAAAATTTCCGTGTTTTCAAAAATTCC
Found at i:466794 original size:36 final size:35
Alignment explanation
Indices: 466607--466922 Score: 139
Period size: 36 Copynumber: 8.7 Consensus size: 35
466597 ATCGTGTTTC
* * *
466607 AAAAATTT-CGTGTTTTC-AAAAATTCTCATGTTTC
1 AAAAATTTCCGTGTTTTCAAAAAATTCCCGT-TTTT
* * *
466641 AAAAATCTT-CGTGTTTTC--AAAATTCCAGAGTTTC
1 AAAAAT-TTCCGTGTTTTCAAAAAATTCCCG-TTTTT
* *
466675 AAAAATTTTCGTGTTTTCAAAAAAAATTTCATCTTCGTGTTT
1 AAAAATTTCCGTGTTTTC--AAAAAA-TTC--C--CGTTTTT
* * **
466717 CAAAA-TTCCAGAG-TTTC-AAAAATTTTCGTGTTTT
1 AAAAATTTCC-GTGTTTTCAAAAAATTCCCGT-TTTT
466751 CAAAAAATTTCCCGTGTTTTC-AAAAATTCCCGTATTTT
1 --AAAAATTT-CCGTGTTTTCAAAAAATTCCCGT-TTTT
* * * *
466789 GAAAATTTCCTTGTTTTCAAAAAAAATTTCCGTGTTTC
1 AAAAATTTCCGTGTTTTC--AAAAAATTCCCGT-TTTT
* * *
466827 ATAAATTTCAGTGTTTTCAAAAAATTCCCGTCTTTC
1 AAAAATTTCCGTGTTTTCAAAAAATTCCCGT-TTTT
* * * *
466863 AAAAATTTTCGTGTTTTCAAGAAATTGACCGTGTTTC
1 AAAAATTTCCGTGTTTTCAAAAAATT-CCCGT-TTTT
* *
466900 ATAAATTTTCGTG-TTTCAAAAAA
1 AAAAATTTCCGTGTTTTCAAAAAA
466923 AAATCCTCAT
Statistics
Matches: 221, Mismatches: 38, Indels: 44
0.73 0.13 0.15
Matches are distributed among these distances:
33 5 0.02
34 35 0.16
35 20 0.09
36 58 0.26
37 26 0.12
38 57 0.26
39 3 0.01
41 8 0.04
42 8 0.04
43 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (35 bp):
AAAAATTTCCGTGTTTTCAAAAAATTCCCGTTTTT
Found at i:466888 original size:93 final size:90
Alignment explanation
Indices: 466613--466921 Score: 246
Period size: 93 Copynumber: 3.3 Consensus size: 90
466603 TTTCAAAAAT
* **
466613 TTCGTGTTTTCAAAAATTCTCA-TGTTTCAAAAATCTTCGTGTTTTC--AAAATTCCAGAGTTTC
1 TTCGTG-TTTC-AAAATTC-CAGTGTTTCAAAAAT-TTCGTGTTTTCAAAAAATTCCCGTCTTTC
466675 AAAAATTTTCGTGTTTTCAAAAAAAATTTCATC
62 AAAAATTTTCGTGTTTTC---AAAAATTTCA-C
* *
466708 TTCGTGTTTCAAAATTCCAGAGTTTCAAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTCA
1 TTCGTGTTTCAAAATTCCAGTGTTTCAAAAA-TTTCGTGTTTTCAAAAAA-TTCCCGT-CTTTCA
** * *
466773 AAAATTCCCGTATTTT-GAAAATTTC-C
63 AAAATTTTCGTGTTTTCAAAAATTTCAC
*
466799 TT-GT-TTTCAAAAAAAATTTCC-GTGTTTCATAAATTTCAGTGTTTTCAAAAAATTCCCGTCTT
1 TTCGTGTTTC----AAAA-TTCCAGTGTTTCAAAAATTTC-GTGTTTTCAAAAAATTCCCGTCTT
*
466861 TCAAAAATTTTCGTGTTTTCAAGAAA-TTGAC
60 TCAAAAATTTTCGTGTTTTCAA-AAATTTCAC
*
466892 --CGTGTTTCATAAATTTTC-GTGTTTCAAAAA
1 TTCGTGTTTCA-AAA-TTCCAGTGTTTCAAAAA
466922 AAAATCCTCA
Statistics
Matches: 178, Mismatches: 18, Indels: 41
0.75 0.08 0.17
Matches are distributed among these distances:
89 5 0.03
90 20 0.11
91 21 0.12
92 18 0.10
93 72 0.40
94 9 0.05
95 10 0.06
96 5 0.03
97 18 0.10
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (90 bp):
TTCGTGTTTCAAAATTCCAGTGTTTCAAAAATTTCGTGTTTTCAAAAAATTCCCGTCTTTCAAAA
ATTTTCGTGTTTTCAAAAATTTCAC
Found at i:466925 original size:111 final size:108
Alignment explanation
Indices: 466598--466926 Score: 330
Period size: 110 Copynumber: 3.0 Consensus size: 108
466588 TTAAAAAAAA
* * *
466598 TCGTGTTTCAAAAATTTC-GTGTTTTCAAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTC-AA
1 TCGTGTTTC-AAAATTTCAGTGTTTTCAAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAAA
* *
466661 AATTCCAGAGTTTCAAAAATTTTCGTGTTTTCAAAAAAAATTTCATC
65 AATTCC-GTGTTTC-AAAATTTTCGTGTTTTCAAAAAAAAATT-ATC
* * * * *
466708 TTCGTGTTTCAAAATTCCAGAG-TTTCAAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTC
1 -TCGTGTTTCAAAATTTCAGTGTTTTCAAAAATTCTCGT-CTTTC-AAAAATTT-TCGTGTTTTC
* * * *
466772 AAAAATTCCCGTATTTTGAAAATTTCCTTGTTTTC-AAAAAAAATT-TC
62 AAAAATT-CCGT-GTTTCAAAATTTTCGTGTTTTCAAAAAAAAATTATC
*
466819 -CGTGTTTCATAAATTTCAGTGTTTTCAAAAAATTCCCGTCTTTCAAAAATTTTCGTGTTTTCAA
1 TCGTGTTTCA-AAATTTCAGTGTTTTC-AAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAA
466883 GAAATTGACCGTGTTTCATAAATTTTCGTG-TTTCAAAAAAAAAT
64 -AAATT--CCGTGTTTCA-AAATTTTCGTGTTTTCAAAAAAAAAT
466927 CCTCATGTTT
Statistics
Matches: 180, Mismatches: 24, Indels: 28
0.78 0.10 0.12
Matches are distributed among these distances:
109 20 0.11
110 51 0.28
111 47 0.26
112 17 0.09
113 18 0.10
114 22 0.12
115 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.42
Consensus pattern (108 bp):
TCGTGTTTCAAAATTTCAGTGTTTTCAAAAATTCTCGTCTTTCAAAAATTTTCGTGTTTTCAAAA
ATTCCGTGTTTCAAAATTTTCGTGTTTTCAAAAAAAAATTATC
Found at i:467053 original size:33 final size:33
Alignment explanation
Indices: 467016--467078 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
467006 AAAAATCTTG
* *
467016 TGTTT-CATAAATTTTCGTTTTTTAAAAAAATTA
1 TGTTTCCA-AAATTCTCGTGTTTTAAAAAAATTA
467049 TGTTTCCAAAATTCTCGTGTTTTAAAAAAA
1 TGTTTCCAAAATTCTCGTGTTTTAAAAAAA
467079 AATCTCATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
33 25 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.46
Consensus pattern (33 bp):
TGTTTCCAAAATTCTCGTGTTTTAAAAAAATTA
Found at i:469643 original size:17 final size:17
Alignment explanation
Indices: 469610--469655 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 17
469600 AACACGAAGA
469610 TTTTTG-AAACA--ATT
1 TTTTTGAAAACACGATT
*
469624 TTTTTGAAAATACGATT
1 TTTTTGAAAACACGATT
*
469641 TTTTTTAAAACACGA
1 TTTTTGAAAACACGA
469656 GAATTTTTGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 6 0.23
15 4 0.15
17 16 0.62
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (17 bp):
TTTTTGAAAACACGATT
Found at i:469706 original size:20 final size:20
Alignment explanation
Indices: 469681--469722 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
469671 AAAATTCTTA
469681 AAAACACGA-ATATTTTTTTG
1 AAAACACGACA-ATTTTTTTG
469701 AAAACACGACAATTTTTTTG
1 AAAACACGACAATTTTTTTG
469721 AA
1 AA
469723 TATTTACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 20 0.95
21 1 0.05
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.36
Consensus pattern (20 bp):
AAAACACGACAATTTTTTTG
Found at i:469855 original size:5 final size:5
Alignment explanation
Indices: 469845--469874 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
469835 TAAAATTATT
469845 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA
469875 AACATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TTAAA
Found at i:470053 original size:8 final size:8
Alignment explanation
Indices: 470035--470102 Score: 66
Period size: 8 Copynumber: 7.8 Consensus size: 8
470025 TTAAAACCCC
470035 TTTTTTC-
1 TTTTTTCT
470042 TTTTTTCT
1 TTTTTTCT
470050 TTTTTTCT
1 TTTTTTCT
470058 TCTTTTATCTT
1 T-TTTT-TC-T
470069 CTTTTTTCCT
1 -TTTTTT-CT
470079 CTCTTTTTCT
1 -T-TTTTTCT
470089 TTTTTTCT
1 TTTTTTCT
470097 TTTTTT
1 TTTTTT
470103 TTCTGGACTG
Statistics
Matches: 54, Mismatches: 0, Indels: 13
0.81 0.00 0.19
Matches are distributed among these distances:
7 7 0.13
8 22 0.41
9 5 0.09
10 8 0.15
11 11 0.20
12 1 0.02
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTTTCT
Found at i:470062 original size:18 final size:18
Alignment explanation
Indices: 470035--470106 Score: 83
Period size: 18 Copynumber: 3.9 Consensus size: 18
470025 TTAAAACCCC
470035 TTTT-TTCTTTTTTCTTT
1 TTTTCTTCTTTTTTCTTT
*
470052 TTTTCTTCTTTTATCTTCTT
1 TTTTCTTCTTTTTTC-T-TT
*
470072 TTTTCCTCTCTTTTTCTTT
1 TTTTCTTCT-TTTTTCTTT
*
470091 TTTTCTTTTTTTTTCT
1 TTTTCTTCTTTTTTCT
470107 GGACTGGGCT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
17 4 0.09
18 16 0.35
19 10 0.22
20 11 0.24
21 5 0.11
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTCTTCTTTTTTCTTT
Found at i:470063 original size:10 final size:10
Alignment explanation
Indices: 470035--470106 Score: 73
Period size: 10 Copynumber: 7.6 Consensus size: 10
470025 TTAAAACCCC
470035 TTTT-TTCTT
1 TTTTCTTCTT
470044 TTTTC-T-TT
1 TTTTCTTCTT
470052 TTTTCTTCTT
1 TTTTCTTCTT
*
470062 TTATCTTCTT
1 TTTTCTTCTT
*
470072 TTTTCCTCTCT
1 TTTTCTTCT-T
470083 TTTTC-T-TT
1 TTTTCTTCTT
*
470091 TTTTCTTTTT
1 TTTTCTTCTT
470101 TTTTCT
1 TTTTCT
470107 GGACTGGGCT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
8 13 0.24
9 8 0.15
10 27 0.50
11 6 0.11
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTCTTCTT
Found at i:470227 original size:23 final size:23
Alignment explanation
Indices: 470200--470269 Score: 79
Period size: 25 Copynumber: 3.0 Consensus size: 23
470190 TGCATTTGGG
470200 CTGCTTCTTTCTTCTTCTCTTTT
1 CTGCTTCTTTCTTCTTCTCTTTT
*
470223 CTGCTTCTTTCTTTCTTTCTTTTTT
1 CTGCTTCTTTC-TTC-TTCTCTTTT
* * *
470248 CTGCTGC-TTCTTTTTCTGTTTT
1 CTGCTTCTTTCTTCTTCTCTTTT
470270 GGTTTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.20
23 13 0.32
24 6 0.15
25 14 0.34
ACGTcount: A:0.00, C:0.26, G:0.07, T:0.67
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTCTTTT
Found at i:470373 original size:13 final size:13
Alignment explanation
Indices: 470355--470410 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 13
470345 TTTCTTTTTT
470355 TCTTTTTTCTTTC
1 TCTTTTTTCTTTC
470368 TC-TTTTTC-TTC
1 TCTTTTTTCTTTC
*
470379 TCTCTTTTTCCTTC
1 TCT-TTTTTCTTTC
* *
470393 TTTCTTTTTCTTTT
1 TCT-TTTTTCTTTC
470407 TCTT
1 TCTT
470411 CTTCTTCTTC
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 5 0.14
12 6 0.17
13 9 0.25
14 16 0.44
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (13 bp):
TCTTTTTTCTTTC
Found at i:470387 original size:14 final size:14
Alignment explanation
Indices: 470355--470401 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 14
470345 TTTCTTTTTT
470355 TCTTTTTTCTT-TC
1 TCTTTTTTCTTCTC
470368 TC-TTTTTCTTCTC
1 TCTTTTTTCTTCTC
* *
470381 TCTTTTTCCTTCTT
1 TCTTTTTTCTTCTC
470395 TCTTTTT
1 TCTTTTT
470402 CTTTTTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 8 0.27
13 6 0.20
14 16 0.53
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (14 bp):
TCTTTTTTCTTCTC
Found at i:470397 original size:33 final size:32
Alignment explanation
Indices: 470346--470416 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 32
470336 GCGGATATAT
*
470346 TTCTT-TTTTT-CTTTTTTCTTTCTCTTTTTC
1 TTCTTCTTTTTCCTTCTTTCTTTCTCTTTTTC
*
470376 TTCTCTCTTTTTCCTTCTTTCTTTTTCTTTTTC
1 TTCT-TCTTTTTCCTTCTTTCTTTCTCTTTTTC
470409 TTCTTCTT
1 TTCTTCTT
470417 CTTCGGGCCG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
30 4 0.11
31 1 0.03
32 9 0.25
33 22 0.61
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (32 bp):
TTCTTCTTTTTCCTTCTTTCTTTCTCTTTTTC
Found at i:470404 original size:6 final size:6
Alignment explanation
Indices: 470351--470416 Score: 69
Period size: 6 Copynumber: 10.3 Consensus size: 6
470341 TATATTTCTT
* *
470351 TTTTTC TTTTTTC TTTCTC TTTTTC TTCTCTC TTTTTCC TTCTTTC TTTTTC
1 TTTTTC -TTTTTC TTTTTC TTTTTC TT-TTTC TTTTT-C TT-TTTC TTTTTC
*
470403 TTTTTC TTCTTC TT
1 TTTTTC TTTTTC TT
470417 CTTCGGGCCG
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
6 31 0.61
7 17 0.33
8 3 0.06
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:471003 original size:4 final size:4
Alignment explanation
Indices: 470996--471025 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
470986 TTTTTGTATT
470996 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
471026 ATTGTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:471012 original size:27 final size:27
Alignment explanation
Indices: 470980--471045 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
470970 CTAACATGTA
*
470980 ATTTATTTTTTGTATTT-TTATT-TATTT
1 ATTTATTTATT-TATTTATTATTGT-TTT
471007 ATTTATTTATTTATTTATTATTGTTTT
1 ATTTATTTATTTATTTATTATTGTTTT
*
471034 ATTAATATTATT
1 ATTTAT-TTATT
471046 AAAACATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
26 5 0.15
27 23 0.68
28 6 0.18
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (27 bp):
ATTTATTTATTTATTTATTATTGTTTT
Found at i:471546 original size:189 final size:189
Alignment explanation
Indices: 471226--471603 Score: 756
Period size: 189 Copynumber: 2.0 Consensus size: 189
471216 AAATGAAATA
471226 CGAAAAACGGATCGGACAAAATTCAGTGATTACAGCTGCCCCTCTTTGCTTGTTGCTGTGAAACA
1 CGAAAAACGGATCGGACAAAATTCAGTGATTACAGCTGCCCCTCTTTGCTTGTTGCTGTGAAACA
471291 GTAATAGAGCAAAGACTTAAAAGCATTGAATTTTGTTCGTTCGTCCAAAAACTCCCTTCCCTTTT
66 GTAATAGAGCAAAGACTTAAAAGCATTGAATTTTGTTCGTTCGTCCAAAAACTCCCTTCCCTTTT
471356 TTTTTAAATAGAGTTTGAAAATAACTCGACGCGCGACCCAAAGCTCGATTCACCTTTCG
131 TTTTTAAATAGAGTTTGAAAATAACTCGACGCGCGACCCAAAGCTCGATTCACCTTTCG
471415 CGAAAAACGGATCGGACAAAATTCAGTGATTACAGCTGCCCCTCTTTGCTTGTTGCTGTGAAACA
1 CGAAAAACGGATCGGACAAAATTCAGTGATTACAGCTGCCCCTCTTTGCTTGTTGCTGTGAAACA
471480 GTAATAGAGCAAAGACTTAAAAGCATTGAATTTTGTTCGTTCGTCCAAAAACTCCCTTCCCTTTT
66 GTAATAGAGCAAAGACTTAAAAGCATTGAATTTTGTTCGTTCGTCCAAAAACTCCCTTCCCTTTT
471545 TTTTTAAATAGAGTTTGAAAATAACTCGACGCGCGACCCAAAGCTCGATTCACCTTTCG
131 TTTTTAAATAGAGTTTGAAAATAACTCGACGCGCGACCCAAAGCTCGATTCACCTTTCG
471604 AGCCGTGAGT
Statistics
Matches: 189, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
189 189 1.00
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (189 bp):
CGAAAAACGGATCGGACAAAATTCAGTGATTACAGCTGCCCCTCTTTGCTTGTTGCTGTGAAACA
GTAATAGAGCAAAGACTTAAAAGCATTGAATTTTGTTCGTTCGTCCAAAAACTCCCTTCCCTTTT
TTTTTAAATAGAGTTTGAAAATAACTCGACGCGCGACCCAAAGCTCGATTCACCTTTCG
Found at i:472118 original size:77 final size:77
Alignment explanation
Indices: 471721--472902 Score: 1340
Period size: 77 Copynumber: 15.5 Consensus size: 77
471711 AATTTAAAAG
* ** * * *
471721 AAATACCTCAGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTGAAAAAC
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA---TTTGAAAAAA
* ** *
471786 ATAA-ATTTAAA--AG
62 AAAAGACATAAATTAA
* ** * *
471799 AAATACCTCAGCATGGTCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTGAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA----TTTGAAAAA
* * ** *
471864 CATAA-ATTTAAA--AT
61 AAAAAGACATAAATTAA
* * *
471878 AAATACCTCGGCGTGACCCGAGGCTCAACTCACCTCTCGCGA-TATGAGTTGATTTTTGAAAAAC
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCT-G-TATTATGAGTTGA--TTTGAAAAAA
* ** *
471942 AGAA-ATTTAAA--AG
62 AAAAGACATAAATTAA
* * ** * * * *
471955 AAATACCTCGGCATGGTCCAAAGCTCAACTCACCTCTGTA-TATGAGTTGATTT----TAAAAGA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
472015 GACATAAATTAA
66 GACATAAATTAA
*
472027 AAATACCTCTGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472092 GACATAAATTAC
66 GACATAAATTAA
* * *
472104 AAATAGCTCAGCGTGACCCTACGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472169 GACATAAATTAC
66 GACATAAATTAA
* * *
472181 AAATAGCTCAGCGTGACCCTACGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472246 GACATAAATTAC
66 GACATAAATTAA
* * *
472258 AAATAGCTCAGCGTGACCCTACGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472323 GACATAAATTAC
66 GACATAAATTAA
*
472335 AAATACCTCAGCGTGACCCGATGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472400 GACATAAATTAC
66 GACATAAATTAA
*
472412 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT--TAAAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472475 GACAGAAATTAA
66 GACATAAATTAA
* ****
472487 AAATACCTCAGCGTGACCCGAGGTTCAACTCACCTCTGTATTATGAGTTGATTT-TTTGAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
* *
472551 GTAGA-AATTTAA
66 G-ACATAAATTAA
* *
472563 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTA-TATGAGTTGATTT----TAAAAGA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
472623 GACATAAATTAA
66 GACATAAATTAA
* *
472635 AAATACATCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAG
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472700 GACATAAATTAC
66 GACATAAATTAA
**
472712 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT---TTAAAAAA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
*
472774 GACAGAAATTAA
66 GACATAAATTAA
* **** *
472786 AAATACCTCAGCGTGATCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAACA
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
* * *
472851 TAGA-AATTTAA
66 GACATAAATTAA
*
472862 AAATACCTCAGCGTGACCCGAGACTCAACTCACCTCTGTAT
1 AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTAT
472903 NNNNNNNNNN
Statistics
Matches: 1012, Mismatches: 71, Indels: 44
0.90 0.06 0.04
Matches are distributed among these distances:
69 3 0.00
70 5 0.00
71 2 0.00
72 86 0.08
73 29 0.03
74 68 0.07
75 95 0.09
76 99 0.10
77 502 0.50
78 52 0.05
79 70 0.07
80 1 0.00
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.27
Consensus pattern (77 bp):
AAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTGAAAAAAAAAA
GACATAAATTAA
Found at i:473761 original size:6 final size:6
Alignment explanation
Indices: 473747--473794 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
473737 TTCATCTTAA
*
473747 TTTTT- TTTTTG TTTTTG -TTTTG TTTTTG TGTTT- TTTTTG TTTTT-
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG
473791 TTTT
1 TTTT
473795 CAGGCATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 18 0.47
6 20 0.53
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:473767 original size:11 final size:10
Alignment explanation
Indices: 473747--473794 Score: 62
Period size: 11 Copynumber: 4.7 Consensus size: 10
473737 TTCATCTTAA
473747 TTTTTTT-TT
1 TTTTTTTGTT
*
473756 TGTTTTTGTT
1 TTTTTTTGTT
473766 TTGTTTTTGTGT
1 TT-TTTTTGT-T
473778 TTTTTTTGTT
1 TTTTTTTGTT
473788 TTTTTTT
1 TTTTTTT
473795 CAGGCATAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
9 6 0.18
10 11 0.32
11 14 0.41
12 3 0.09
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTTTTTTGTT
Found at i:476337 original size:29 final size:29
Alignment explanation
Indices: 476274--476331 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
476264 ACAAAGTTTC
476274 TGGGGTAAAAGTATAATTTTTGCAAAAATA
1 TGGGGTAAAA-TATAATTTTTGCAAAAATA
476304 TGGGGTTAAAATATAATTTTTG-AAAAAT
1 TGGGG-TAAAATATAATTTTTGCAAAAAT
476332 TCGGGGCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 6 0.22
30 16 0.59
31 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.19, T:0.36
Consensus pattern (29 bp):
TGGGGTAAAATATAATTTTTGCAAAAATA
Found at i:476349 original size:29 final size:30
Alignment explanation
Indices: 476274--476351 Score: 90
Period size: 29 Copynumber: 2.6 Consensus size: 30
476264 ACAAAGTTTC
476274 TGGGG-TAAAAGTATAATTTTTGCAAAAATA
1 TGGGGCTAAAA-TATAATTTTTGCAAAAATA
*
476304 TGGGGTTAAAATATAATTTTTG-AAAAAT-
1 TGGGGCTAAAATATAATTTTTGCAAAAATA
* *
476332 TCGGGGCTAACATGTAATTT
1 T-GGGGCTAAAATATAATTT
476352 ATTTTTTGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 1 0.02
29 21 0.49
30 16 0.37
31 5 0.12
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (30 bp):
TGGGGCTAAAATATAATTTTTGCAAAAATA
Found at i:476372 original size:19 final size:19
Alignment explanation
Indices: 476348--476406 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
476338 CTAACATGTA
*
476348 ATTTATTTTTTGTATTT-TT
1 ATTTATTTATT-TATTTATT
476367 ATTTATTTATTTATTTATT
1 ATTTATTTATTTATTTATT
*
476386 ATTGT-TTTATTAATATTATT
1 ATT-TATTTATTTAT-TTATT
476406 A
1 A
476407 AAACATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 5 0.14
19 23 0.66
20 7 0.20
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.71
Consensus pattern (19 bp):
ATTTATTTATTTATTTATT
Found at i:481916 original size:10 final size:10
Alignment explanation
Indices: 481901--481930 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
481891 GGCATATATC
481901 TCATATCATT
1 TCATATCATT
*
481911 TCATATCATC
1 TCATATCATT
481921 TCATATCATT
1 TCATATCATT
481931 GTGTGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.30, C:0.23, G:0.00, T:0.47
Consensus pattern (10 bp):
TCATATCATT
Found at i:481923 original size:20 final size:19
Alignment explanation
Indices: 481893--481930 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
481883 CCTTTTCCGG
481893 CATATATCTCATATCATTT
1 CATATATCTCATATCATTT
481912 CATATCATCTCATATCATT
1 CATAT-ATCTCATATCATT
481931 GTGTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.32, C:0.24, G:0.00, T:0.45
Consensus pattern (19 bp):
CATATATCTCATATCATTT
Found at i:485464 original size:13 final size:13
Alignment explanation
Indices: 485446--485522 Score: 79
Period size: 13 Copynumber: 6.1 Consensus size: 13
485436 TATTATGCCT
485446 AAAAAAAACAAAC
1 AAAAAAAACAAAC
*
485459 -AAAAAAACAAAAT
1 AAAAAAAAC-AAAC
485472 AAAAAAAAC-AAC
1 AAAAAAAACAAAC
*
485484 AAAAAAAACAAAG
1 AAAAAAAACAAAC
* *
485497 AAACAAAACAAAG
1 AAAAAAAACAAAC
*
485510 AAACAAAA-AAAC
1 AAAAAAAACAAAC
485522 A
1 A
485523 GAAGAAAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
12 23 0.41
13 25 0.45
14 8 0.14
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (13 bp):
AAAAAAAACAAAC
Found at i:485468 original size:8 final size:8
Alignment explanation
Indices: 485446--485522 Score: 65
Period size: 8 Copynumber: 9.9 Consensus size: 8
485436 TATTATGCCT
485446 AAAAA-AA
1 AAAAACAA
*
485453 ACAAACAA
1 AAAAACAA
485461 AAAAACAA
1 AAAAACAA
485469 AATAAA-AA
1 AA-AAACAA
485477 AAACAACAAA
1 AAA-AAC-AA
485487 AAAAACAA
1 AAAAACAA
*
485495 AGAAAC--
1 AAAAACAA
485501 -AAAACAA
1 AAAAACAA
*
485508 AGAAACAA
1 AAAAACAA
485516 AAAAACA
1 AAAAACA
485523 GAAGAAAAAG
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
5 4 0.07
7 5 0.09
8 36 0.64
9 6 0.11
10 5 0.09
ACGTcount: A:0.83, C:0.13, G:0.03, T:0.01
Consensus pattern (8 bp):
AAAAACAA
Found at i:485481 original size:26 final size:26
Alignment explanation
Indices: 485445--485531 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 26
485435 ATATTATGCC
485445 TAAAAAAAACAAACAAAAAAACAAAA
1 TAAAAAAAACAAACAAAAAAACAAAA
485471 TAAAAAAAAC-AACAAAAAAAACAAAGA
1 TAAAAAAAACAAAC-AAAAAAACAAA-A
* * *
485498 AACAAAACAAAGAAACAAAAAAACAGAA
1 TA-AAAA-AAACAAACAAAAAAACAAAA
*
485526 GAAAAA
1 TAAAAA
485532 GAAAAATCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
25 3 0.06
26 21 0.40
27 6 0.12
28 6 0.12
29 13 0.25
30 3 0.06
ACGTcount: A:0.82, C:0.11, G:0.05, T:0.02
Consensus pattern (26 bp):
TAAAAAAAACAAACAAAAAAACAAAA
Found at i:485531 original size:13 final size:12
Alignment explanation
Indices: 485447--485520 Score: 75
Period size: 12 Copynumber: 6.3 Consensus size: 12
485437 ATTATGCCTA
485447 AAAAAAACAAAC
1 AAAAAAACAAAC
485459 AAAAAAACAAA-
1 AAAAAAACAAAC
*
485470 ATAAAAA-AAAC
1 AAAAAAACAAAC
485481 AACAAAAA-AAAC
1 AA-AAAAACAAAC
*
485493 AAAGAAACAAAAC
1 AAAAAAAC-AAAC
*
485506 AAAGAAACAAA-
1 AAAAAAACAAAC
485517 AAAA
1 AAAA
485521 CAGAAGAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
10 3 0.06
11 14 0.26
12 25 0.46
13 12 0.22
ACGTcount: A:0.84, C:0.12, G:0.03, T:0.01
Consensus pattern (12 bp):
AAAAAAACAAAC
Found at i:485537 original size:17 final size:16
Alignment explanation
Indices: 485450--485529 Score: 69
Period size: 17 Copynumber: 4.9 Consensus size: 16
485440 ATGCCTAAAA
*
485450 AAAACAAACAAAAAAAC
1 AAAA-AAACAAAGAAAC
*
485467 AAAATAAA-AAAAACAAC
1 AAAA-AAACAAAGA-AAC
485484 AAAAAAAACAAAGAAAC
1 -AAAAAAACAAAGAAAC
485501 ---AAAACAAAGAAAC
1 AAAAAAACAAAGAAAC
485514 AAAAAAACAGAAGAAA
1 AAAAAAACA-AAGAAA
485530 AAGAAAAATC
Statistics
Matches: 54, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
13 13 0.24
16 11 0.20
17 22 0.41
18 8 0.15
ACGTcount: A:0.81, C:0.12, G:0.05, T:0.01
Consensus pattern (16 bp):
AAAAAAACAAAGAAAC
Found at i:486481 original size:77 final size:74
Alignment explanation
Indices: 486373--486570 Score: 272
Period size: 74 Copynumber: 2.6 Consensus size: 74
486363 TTCTGTTTTT
*
486373 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGATATTTC
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGATA--T-
486438 TTTTAAATTTC-TA
62 TTTTAAA-TTCATA
** *
486451 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGATATTTTT
* *
486516 CAATTCATG
66 AAATTCATA
* *
486525 TTTTTCAAAACTCAACTCATATTGCGAGAGGTGACTTGAGCCTCGG
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGG
486571 GGCACATGTC
Statistics
Matches: 111, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
73 3 0.03
74 51 0.46
75 1 0.01
77 50 0.45
78 6 0.05
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (74 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGATATTTTT
AAATTCATA
Found at i:486632 original size:75 final size:73
Alignment explanation
Indices: 486381--486658 Score: 281
Period size: 77 Copynumber: 3.7 Consensus size: 73
486371 TTTTTTTCAA
** * * *
486381 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGATATTTCTTTTAAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTA--T-TTTTCAA-
*
486446 TTC-TATTTTTC
62 TTCATGTTTTTC
*
486457 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTTTCAATTC
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTCAATTC
486522 ATGTTTTTC
65 ATGTTTTTC
* * *
486531 AAAACTCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGGGCACATGTCGAGGTA-TTTTCGAT
1 AAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCAC--GCCGAGGTATTTTTCAAT
**
486595 TTTTGTTTTTC
63 TCATGTTTTTC
* * * * * *
486606 GAAGATCAACTCATAATCCAAGAGGTGAGTTGAGCTTCGAGTCGCACGCCGAG
1 -AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG-G-GGCACGCCGAG
486659 CTTTTCACTA
Statistics
Matches: 174, Mismatches: 20, Indels: 16
0.83 0.10 0.08
Matches are distributed among these distances:
73 7 0.04
74 51 0.29
75 51 0.29
76 12 0.07
77 53 0.30
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.31
Consensus pattern (73 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCCGAGGTATTTTTCAATTCA
TGTTTTTC
Found at i:486654 original size:151 final size:149
Alignment explanation
Indices: 486373--486658 Score: 351
Period size: 149 Copynumber: 1.9 Consensus size: 149
486363 TTCTGTTTTT
*
486373 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGATATTTC
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGACCATGCCGAGATA--T-
* * * *
486438 TTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACG
63 TTTTAAATTTCTATTTTTCAAAAATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGTCACG
486503 CCGAGGTATTTTTCAATTCATG
128 CCGAGGTATTTTTCAATTCATG
* * * *
486525 TTTTTC-AAAACTCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGGGCACATGTCGAGGTA-T
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGACTTGAGCCTC-GGAC-CATGCCGAGATATT
** * * * * *
486588 TTTCGATTTTTGTTTTTCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGCTTCGAGTCGCAC
64 TTTAAATTTCTATTTTTCAAAAATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGT--CAC
486653 GCCGAG
127 GCCGAG
486659 CTTTTCACTA
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
149 50 0.44
151 45 0.39
152 9 0.08
153 10 0.09
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.32
Consensus pattern (149 bp):
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGACTTGAGCCTCGGACCATGCCGAGATATTTT
TAAATTTCTATTTTTCAAAAATCAACTCATAATCCAAGAGGTGAGTTGAGCCTCGAGTCACGCCG
AGGTATTTTTCAATTCATG
Found at i:486982 original size:30 final size:31
Alignment explanation
Indices: 486859--486974 Score: 141
Period size: 30 Copynumber: 3.9 Consensus size: 31
486849 AAAAAATTTG
* *
486859 CATTTTGACCCCTACA-TTTTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTCTCTAAAATTA
*
486889 CATTTTGATCCCTAAACTTTCTC-AAAATTA
1 CATTTTGACCCCTAAACTTTCTCTAAAATTA
**
486919 CATTTAAACCCCTAAAC-TTCT-TAAAATTA
1 CATTTTGACCCCTAAACTTTCTCTAAAATTA
**
486948 TGTTTTGACCCCTAAACTTTCTCTAAA
1 CATTTTGACCCCTAAACTTTCTCTAAA
486975 TTATGTTTCG
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
29 24 0.33
30 39 0.54
31 9 0.12
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (31 bp):
CATTTTGACCCCTAAACTTTCTCTAAAATTA
Found at i:487476 original size:3 final size:3
Alignment explanation
Indices: 487470--487551 Score: 121
Period size: 3 Copynumber: 27.0 Consensus size: 3
487460 TAGGGTTCAT
487470 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
* *
487518 GAAA GAA GAA GAA -AA AAA GAAA GAA GAA AAA GAA
1 G-AA GAA GAA GAA GAA GAA G-AA GAA GAA GAA GAA
487552 AGAAAAAAAA
Statistics
Matches: 73, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.03
3 65 0.89
4 6 0.08
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:487557 original size:9 final size:10
Alignment explanation
Indices: 487470--487570 Score: 110
Period size: 9 Copynumber: 10.8 Consensus size: 10
487460 TAGGGTTCAT
487470 GAAG-AAGAA
1 GAAGAAAGAA
487479 GAAG-AAGAA
1 GAAGAAAGAA
487488 GAAG-AAGAA
1 GAAGAAAGAA
487497 GAAG-AAGAA
1 GAAGAAAGAA
487506 GAAG-AAGAA
1 GAAGAAAGAA
487515 GAAGAAAGAA
1 GAAGAAAGAA
487525 GAAGAAA-AA
1 GAAGAAAGAA
487534 -AAGAAAGAA
1 GAAGAAAGAA
487543 GAA-AAAGAAA
1 GAAGAAAG-AA
* *
487553 GAAAAAAAAA
1 GAAGAAAGAA
*
487563 GAAAAAAG
1 GAAGAAAG
487571 GAAAAAATAT
Statistics
Matches: 85, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
8 6 0.07
9 48 0.56
10 28 0.33
11 3 0.04
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (10 bp):
GAAGAAAGAA
Found at i:487575 original size:13 final size:13
Alignment explanation
Indices: 487483--487576 Score: 64
Period size: 14 Copynumber: 6.6 Consensus size: 13
487473 GAAGAAGAAG
*
487483 AAGAAGAAGAAGAA
1 AAGAAAAAGAA-AA
*
487497 GAAGAAGAAGAAGAA
1 -AAGAAAAAGAA-AA
487512 GAAGAAGAAAGAAGAA
1 -AAGAA-AAAGAA-AA
*
487528 GAA-AAAAAGAAAG
1 -AAGAAAAAGAAAA
487541 AAGAAAAAGAAAGA
1 AAGAAAAAGAAA-A
*
487555 AAAAAAAAGAAAA
1 AAGAAAAAGAAAA
487568 AAGGAAAAA
1 AA-GAAAAA
487577 ATATAAAAAA
Statistics
Matches: 70, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
12 2 0.03
13 13 0.19
14 22 0.31
15 22 0.31
16 11 0.16
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:487695 original size:20 final size:21
Alignment explanation
Indices: 487670--487719 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
487660 CAGCAACCCC
* *
487670 AAAAAAAAGAAACG-GGCCCA
1 AAAAAAAAGAAAAGTAGCCCA
**
487690 AAAAAAGGGAAAAGTAGCCCA
1 AAAAAAAAGAAAAGTAGCCCA
487711 AAAAAAAAG
1 AAAAAAAAG
487720 GAGACAGCAG
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.64, C:0.14, G:0.20, T:0.02
Consensus pattern (21 bp):
AAAAAAAAGAAAAGTAGCCCA
Found at i:488417 original size:18 final size:18
Alignment explanation
Indices: 488391--488694 Score: 198
Period size: 17 Copynumber: 16.8 Consensus size: 18
488381 TTAAAAAAAA
488391 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
488408 TCGTGTTTTCAAAAACTT
1 TCGTGTTTTCAAAAATTT
* * **
488426 CCGTGTTTTAAAAAAAAAAT
1 TCGTGTTTT--CAAAAATTT
*
488446 TCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
488464 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
488481 TCGTGTTTTC-AAAA-TT
1 TCGTGTTTTCAAAAATTT
488497 TCAGTG-TTTCAAAAATTT
1 TC-GTGTTTTCAAAAATTT
488515 TCGTGTTTTCAAAAAATTT
1 TCGTGTTTTC-AAAAATTT
* *
488534 CCCGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTT
* *
488553 CCGT-ATTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
488570 CCTTGTTTTCAAAAAAAAAAT
1 TCGTGTTTTC---AAAAATTT
* *
488591 CCGTG-TTTCATAAA-TT
1 TCGTGTTTTCAAAAATTT
*
488607 TCAGTGTTTTCAAAAAATTC
1 TC-GTGTTTTC-AAAAATTT
* *
488627 CCGT-CTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
488644 TCGTGTTTTCAAGAAATTGA
1 TCGTGTTTTCAA-AAATT-T
* * *
488664 CCGTG-TTTCATAGATTT
1 TCGTGTTTTCAAAAATTT
488681 TCGTG-TTTCAAAAA
1 TCGTGTTTTCAAAAA
488695 AAAATCCTCA
Statistics
Matches: 224, Mismatches: 42, Indels: 42
0.73 0.14 0.14
Matches are distributed among these distances:
16 9 0.04
17 75 0.33
18 66 0.29
19 31 0.14
20 33 0.15
21 10 0.04
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.41
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:488451 original size:38 final size:36
Alignment explanation
Indices: 488407--488652 Score: 166
Period size: 36 Copynumber: 6.8 Consensus size: 36
488397 TTCAAAAATT
*
488407 TTCGTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAAAA
1 TTCGTGTTTTCAAAAATTTCCGTGTTTT--AAAAAAAA
* * **
488445 TTCGTGTTTTCAAAAA-TTCTCATG-TTTCAAAAATC
1 TTCGTGTTTTCAAAAATTTC-CGTGTTTTAAAAAAAA
* * **
488480 TTCGTGTTTTC-AAAATTTCAGTG-TTTCAAAAATT
1 TTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAAAAA
*
488514 TTCGTGTTTTCAAAAAATTTCCCGTGTTTT--CAAAAA
1 TTCGTGTTTTC-AAAAATTT-CCGTGTTTTAAAAAAAA
** *
488550 TTCCCGTATTTCAAAAATTTCCTTGTTTTCAAAAAAAAAA
1 TTCGTGT-TTTCAAAAATTTCCGTGTTTT---AAAAAAAA
* * * *
488590 TCCGTG-TTTCATAAATTTCAGTGTTTT-CAAAAAA
1 TTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAAAAA
** *
488624 TTCCCGTCTTTCAAAAATTTTCGTGTTTT
1 TTCGTGT-TTTCAAAAATTTCCGTGTTTT
488653 CAAGAAATTG
Statistics
Matches: 166, Mismatches: 28, Indels: 30
0.74 0.12 0.13
Matches are distributed among these distances:
34 36 0.22
35 27 0.16
36 41 0.25
37 14 0.08
38 40 0.24
40 8 0.05
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (36 bp):
TTCGTGTTTTCAAAAATTTCCGTGTTTTAAAAAAAA
Found at i:488459 original size:21 final size:21
Alignment explanation
Indices: 488418--488460 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
488408 TCGTGTTTTC
*
488418 AAAAACTTCCGTGTTTTAAAA
1 AAAAAATTCCGTGTTTTAAAA
*
488439 AAAAAATT-CGTGTTTTCAAA
1 AAAAAATTCCGTGTTTTAAAA
488459 AA
1 AA
488461 TTCTCATGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.33
Consensus pattern (21 bp):
AAAAAATTCCGTGTTTTAAAA
Found at i:488529 original size:89 final size:88
Alignment explanation
Indices: 488391--488583 Score: 223
Period size: 89 Copynumber: 2.2 Consensus size: 88
488381 TTAAAAAAAA
488391 TCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAAAATT-CGTGTTT
1 TCGTGTTTTC-AAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTT--AAAAAAAATTCCGTGTTT
* *
488454 TCAAAAATTCTCATGTTTCAAAAATCT
63 TCAAAAATTCCCATATTTCAAAAAT-T
* * * *
488481 TCGTGTTTTCAAAA-TTTCAGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTT
1 TCGTGTTTTCAAAATTTTC-GTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAATT-CCGTGTTTT
*
488544 CAAAAATTCCCGTATTTCAAAAATT
64 CAAAAATTCCCATATTTCAAAAATT
*
488569 TCCTTGTTTTCAAAA
1 T-CGTGTTTTCAAAA
488584 AAAAAATCCG
Statistics
Matches: 90, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
87 8 0.09
88 2 0.02
89 64 0.71
90 12 0.13
91 4 0.04
ACGTcount: A:0.32, C:0.16, G:0.10, T:0.42
Consensus pattern (88 bp):
TCGTGTTTTCAAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTTAAAAAAAATTCCGTGTTTTCA
AAAATTCCCATATTTCAAAAATT
Found at i:488566 original size:36 final size:35
Alignment explanation
Indices: 488487--488694 Score: 154
Period size: 36 Copynumber: 5.8 Consensus size: 35
488477 ATCTTCGTGT
* ** *
488487 TTTC-AAAATTTCAGTG-TTTCAAAAATTTTCGTGT
1 TTTCAAAAATTTCCGTGTTTTCAAAAATTCCCGT-A
488521 TTTCAAAAAATTTCCCGTGTTTTCAAAAATTCCCGTA
1 TTTC-AAAAATTT-CCGTGTTTTCAAAAATTCCCGTA
* * *
488558 TTTCAAAAATTTCCTTGTTTTCAAAAAAAAAAT-CCGTG
1 TTTCAAAAATTTCCGTGTTTTC----AAAAATTCCCGTA
* * *
488596 TTTCATAAATTTCAGTGTTTTCAAAAAATTCCCGTC
1 TTTCAAAAATTTCCGTGTTTTC-AAAAATTCCCGTA
* * *
488632 TTTCAAAAATTTTCGTGTTTTCAAGAAATTGACCGTG
1 TTTCAAAAATTTCCGTGTTTTCAA-AAATT-CCCGTA
* * *
488669 TTTCATAGATTTTCGTG-TTTCAAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAA
488695 AAAATCCTCA
Statistics
Matches: 144, Mismatches: 19, Indels: 21
0.78 0.10 0.11
Matches are distributed among these distances:
34 4 0.03
35 21 0.15
36 49 0.34
37 27 0.19
38 37 0.26
39 6 0.04
ACGTcount: A:0.32, C:0.16, G:0.11, T:0.41
Consensus pattern (35 bp):
TTTCAAAAATTTCCGTGTTTTCAAAAATTCCCGTA
Found at i:488606 original size:55 final size:55
Alignment explanation
Indices: 488473--488587 Score: 142
Period size: 55 Copynumber: 2.1 Consensus size: 55
488463 CTCATGTTTC
* * * * *
488473 AAAAATCTTCGTGTTTTC-AAAATTTCAGTGTTTCAAAAATTTTCGTGTTTTCAAA
1 AAAAATC-CCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCGTGTTTTCAAA
** *
488528 AAATTTCCCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCTTGTTTTCAAA
1 AAAAATCCCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCGTGTTTTCAAA
488583 AAAAA
1 AAAAA
488588 AATCCGTGTT
Statistics
Matches: 49, Mismatches: 10, Indels: 2
0.80 0.16 0.03
Matches are distributed among these distances:
54 9 0.18
55 40 0.82
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (55 bp):
AAAAATCCCGTGTTTTCAAAAATTCCCGTATTTCAAAAATTTCCGTGTTTTCAAA
Found at i:488622 original size:73 final size:74
Alignment explanation
Indices: 488393--488655 Score: 251
Period size: 74 Copynumber: 3.6 Consensus size: 74
488383 AAAAAAAATC
** * *
488393 GTGTTTCAAAAATTTTCGTGTTTTCAAAAACTTCCGTGTTTT-AAAAAAAAAATTCGTGTTTTCA
1 GTGTTTCAAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTCA
488457 AAAATTCTCA
66 AAAATT-TCA
* * ** *
488467 -TGTTTCAAAAA-TCTTCGTGTTTTC-AAAATTTCAGTG-TTTC---AAAAATTTTCGTGTTTTC
1 GTGTTTCAAAAATTC-CCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTC
*
488525 AAAAAATTTCCC
65 -AAAAATTT-CA
* *
488537 GTGTTTTCAAAAATTCCCGT-ATTTCAAAAATTTCCTTGTTTTCAAAAAAAAAATCCGTG-TTTC
1 GTG-TTTCAAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTC
*
488600 ATAAATTTCA
65 AAAAATTTCA
* *
488610 GTGTTTTCAAAAAATTCCCGT-CTTTCAAAAATTTTCGTGTTTTCAA
1 GTG-TTTC-AAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAA
488656 GAAATTGACC
Statistics
Matches: 158, Mismatches: 18, Indels: 26
0.78 0.09 0.13
Matches are distributed among these distances:
69 17 0.11
70 8 0.05
71 9 0.06
72 33 0.21
73 36 0.23
74 41 0.26
75 4 0.03
76 10 0.06
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (74 bp):
GTGTTTCAAAAATTCCCGTGTTTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTTCA
AAAATTTCA
Found at i:488682 original size:37 final size:35
Alignment explanation
Indices: 488536--488695 Score: 135
Period size: 37 Copynumber: 4.4 Consensus size: 35
488526 AAAAATTTCC
* * * *
488536 CGTGTTTTC-AAAAATTCCCGTATTTCAAAAATTTC
1 CGTGTTTTCAAAAAATTACCGTGTTTC-ATAATTTT
* ** *
488571 CTTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTT
1 CGTGTTTTC-AAAAAATTA-CCGTGTTTCATAATTTT
* * *
488608 CAGTGTTTTCAAAAAATTCCCGTCTTTCAAAAATTTT
1 C-GTGTTTTCAAAAAATTACCGTGTTTC-ATAATTTT
*
488645 CGTGTTTTCAAGAAATTGACCGTGTTTCATAGATTTT
1 CGTGTTTTCAAAAAATT-ACCGTGTTTCATA-ATTTT
488682 CGTG-TTTCAAAAAA
1 CGTGTTTTCAAAAAA
488696 AAATCCTCAT
Statistics
Matches: 98, Mismatches: 20, Indels: 13
0.75 0.15 0.10
Matches are distributed among these distances:
35 8 0.08
36 34 0.35
37 41 0.42
38 15 0.15
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.40
Consensus pattern (35 bp):
CGTGTTTTCAAAAAATTACCGTGTTTCATAATTTT
Found at i:488697 original size:74 final size:74
Alignment explanation
Indices: 488414--488695 Score: 230
Period size: 74 Copynumber: 3.9 Consensus size: 74
488404 ATTTTCGTGT
* * *
488414 TTTCAAAAACTTCCGTGTTTT-AAAAAAAAAATTCGTGTTTTCAAAAATTCTCA-TG-TTTCAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTG-TTTCATAAATT-TCAGTGTTTTCAAA
* **
488476 AATCTTCGTGT-
64 AA-ATTCCCGTA
* ** * * *
488487 TTTC-AAAATTTCAGTG-TTTC---AAAAATTTTCGTGTTTTCAAAAAATTTCCCGTGTTTTC-A
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTG-TTTC-ATAAATTT-CAGTGTTTTCAA
488546 AAAATTCCCGTA
63 AAAATTCCCGTA
*
488558 TTTCAAAAATTTCCTTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTTCAGTGTTTTCAAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTTCAGTGTTTTCAAAAA
*
488623 ATTCCCGTC
66 ATTCCCGTA
* * *** *
488632 TTTCAAAAATTTTCGTGTTTTCAAGAAATTGA-CCGTGTTTCATAGATTTTC-GTG-TTTCAAAA
1 TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTCATA-AATTTCAGTGTTTTCAAAA
488694 AA
65 AA
488696 AAATCCTCAT
Statistics
Matches: 173, Mismatches: 23, Indels: 27
0.78 0.10 0.12
Matches are distributed among these distances:
69 17 0.10
70 13 0.08
71 13 0.08
72 34 0.20
73 32 0.18
74 50 0.29
75 4 0.02
76 10 0.06
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.41
Consensus pattern (74 bp):
TTTCAAAAATTTCCGTGTTTTCAAAAAAAAAATCCGTGTTTCATAAATTTCAGTGTTTTCAAAAA
ATTCCCGTA
Found at i:488802 original size:38 final size:38
Alignment explanation
Indices: 488558--488867 Score: 173
Period size: 38 Copynumber: 8.1 Consensus size: 38
488548 AATTCCCGTA
* * *
488558 TTTCAAAAATTTCCTTGTTTTCAAAAAAAAAATC-CGTG
1 TTTCATAAATTTTCGTGTTTTC-AAAAAAAAATCTCGTG
* * *
488596 TTTCATAAA-TTTCAGTGTTTTC--AAAAAATTCCCGTC
1 TTTCATAAATTTTC-GTGTTTTCAAAAAAAAATCTCGTG
* ***
488632 TTTCAAAAATTTTCGTGTTTTCAAGAAATTGA-C-CGTG
1 TTTCATAAATTTTCGTGTTTTCAA-AAAAAAATCTCGTG
*
488669 TTTCATAGATTTTCGTG-TTTCAAAAAAAAATCCTCATGTTTCG
1 TTTCATAAATTTTCGTGTTTTCAAAAAAAAAT-CTC--G--T-G
* ** *
488712 TACTTTATTAAAATTTTTATGTTTTCAAAAACAAAT-TCGGTG
1 T--TTCA-T-AAATTTTCGTGTTTTCAAAAAAAAATCTC-GTG
*
488754 TCTTGA-AAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
1 T-TTCATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
* ** *
488792 TTTCATAAATTTT--TATTTTTTAAAAAAAAT-T-ATG
1 TTTCATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
* *
488826 TTTACA-AAATTCTCGTGTTTT-AAAAAAAAATCTCATG
1 TTT-CATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
488863 TTTCA
1 TTTCA
488868 ATCGGCTCGC
Statistics
Matches: 212, Mismatches: 34, Indels: 54
0.71 0.11 0.18
Matches are distributed among these distances:
34 11 0.05
35 24 0.11
36 47 0.22
37 35 0.17
38 51 0.24
39 5 0.02
40 1 0.00
41 4 0.02
42 3 0.01
43 3 0.01
45 4 0.02
46 3 0.01
47 8 0.04
48 13 0.06
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (38 bp):
TTTCATAAATTTTCGTGTTTTCAAAAAAAAATCTCGTG
Found at i:494516 original size:43 final size:40
Alignment explanation
Indices: 494437--494517 Score: 99
Period size: 41 Copynumber: 1.9 Consensus size: 40
494427 TATTTTTATC
*
494437 TATTTTATAATTTGTATACGTATAATTATATCTACATACA
1 TATTTTATAATTTGTATAAGTATAATTATATCTACATACA
* * *
494477 TATTTTCTAAATTTTTATAAGTATATATTTATATGTACATA
1 TATTTTAT-AATTTGTATAAGTATA-A-TTATATCTACATA
494518 TGTTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 7 0.21
41 14 0.41
42 1 0.03
43 12 0.35
ACGTcount: A:0.37, C:0.07, G:0.05, T:0.51
Consensus pattern (40 bp):
TATTTTATAATTTGTATAAGTATAATTATATCTACATACA
Found at i:496609 original size:15 final size:16
Alignment explanation
Indices: 496583--496612 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
496573 GCATTGAATA
496583 AAATATTTATAATTTT
1 AAATATTTATAATTTT
496599 AAATA-TTATAATTT
1 AAATATTTATAATTT
496613 GACTTTAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTTATAATTTT
Found at i:503444 original size:43 final size:43
Alignment explanation
Indices: 503379--503543 Score: 176
Period size: 43 Copynumber: 3.9 Consensus size: 43
503369 TACCGTAACA
* * * *
503379 ATGCCAA-ATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCATATCG
* * *** *
503421 ATGCCAATAGCCCAGCCACGGTCTTACAAAAAATCACATATCG
1 ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCATATCG
503464 ATGCCAAT-GTCCCAGACATGGTCTTACACG-AAGTCTCATATCG
1 ATGCCAATAG-CCCAGACATGGTCTTACACGTAA-TCTCATATCG
* *
503507 ATGCC-ATATCCCAGATATGGTCTTACACGTAATCTCA
1 ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCA
503544 GTAACCCTAA
Statistics
Matches: 102, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
42 36 0.35
43 66 0.65
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
ATGCCAATAGCCCAGACATGGTCTTACACGTAATCTCATATCG
Found at i:504893 original size:16 final size:18
Alignment explanation
Indices: 504858--504900 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
504848 CTCCTTGCTA
*
504858 CTTCTTTTTTTCCTTATT
1 CTTCTTTTTTTCCATATT
504876 CTTCTTTTTTT-CAT-TT
1 CTTCTTTTTTTCCATATT
504892 CTTCCTTTT
1 CTT-CTTTT
504901 AGTTTTCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 5 0.22
17 7 0.30
18 11 0.48
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (18 bp):
CTTCTTTTTTTCCATATT
Found at i:505638 original size:64 final size:64
Alignment explanation
Indices: 505559--505684 Score: 207
Period size: 64 Copynumber: 2.0 Consensus size: 64
505549 AGTGCAGGGG
* * *
505559 TCACACAGGCCAAGGACACGGGTGTGTGTCTAGGCCGTGTAACTCACTGATTACAAAATAAGAA
1 TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCCGTGTAACCCACTGATTACAAAATAAGAA
* *
505623 TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCTGTGTAACCCACTGATTATAAAATAAG
1 TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCCGTGTAACCCACTGATTACAAAATAAG
505685 GACCATACGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 57 1.00
ACGTcount: A:0.32, C:0.23, G:0.25, T:0.20
Consensus pattern (64 bp):
TCACACAGGCCAAGGACACGGGCGTGTGTCCAGGCCGTGTAACCCACTGATTACAAAATAAGAA
Found at i:508156 original size:11 final size:11
Alignment explanation
Indices: 508140--508166 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
508130 TTGACGAATG
508140 AAAACAAACCC
1 AAAACAAACCC
508151 AAAACAAACCC
1 AAAACAAACCC
508162 AAAAC
1 AAAAC
508167 CGAAAACTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAACAAACCC
Found at i:509055 original size:32 final size:32
Alignment explanation
Indices: 508989--509056 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
508979 CACGCCCCTA
* *
508989 TGGCCCACACGGCCTAAATGACCTAACCCGTG
1 TGGCCCACACGGCCCAAATGACCTAACCCATG
*
509021 TGGCCCACATGGCCCAAAT-AGCCTAGA-CCATG
1 TGGCCCACACGGCCCAAATGA-CCTA-ACCCATG
509053 TGGC
1 TGGC
509057 TTACAAGATC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 1 0.03
32 29 0.94
33 1 0.03
ACGTcount: A:0.25, C:0.35, G:0.24, T:0.16
Consensus pattern (32 bp):
TGGCCCACACGGCCCAAATGACCTAACCCATG
Found at i:519716 original size:9 final size:9
Alignment explanation
Indices: 519674--519717 Score: 61
Period size: 9 Copynumber: 4.9 Consensus size: 9
519664 NNNNNNNNNN
*
519674 GACGATGAC
1 GACGATGAG
*
519683 GACGATGAC
1 GACGATGAG
519692 GACGATGAG
1 GACGATGAG
519701 GACGATGAG
1 GACGATGAG
*
519710 GATGATGA
1 GACGATGA
519718 TGTTTCTTCG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.34, C:0.14, G:0.39, T:0.14
Consensus pattern (9 bp):
GACGATGAG
Found at i:519792 original size:19 final size:19
Alignment explanation
Indices: 519770--519870 Score: 84
Period size: 17 Copynumber: 5.2 Consensus size: 19
519760 GTTGATGGAC
519770 AATTTATATTTTGTTATGA
1 AATTTATATTTTGTTATGA
* *
519789 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
519808 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
* *
519828 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
519847 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
519867 AATT
1 AATT
519871 AAATATGTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
17 12 0.19
18 10 0.16
19 12 0.19
20 8 0.12
21 10 0.16
22 12 0.19
ACGTcount: A:0.36, C:0.02, G:0.14, T:0.49
Consensus pattern (19 bp):
AATTTATATTTTGTTATGA
Found at i:519796 original size:39 final size:39
Alignment explanation
Indices: 519753--520002 Score: 373
Period size: 39 Copynumber: 6.4 Consensus size: 39
519743 GCTTTCCTTC
519753 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
519792 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
519831 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
* *** ***
519870 TAAATATGTTGATGGTAGC--TTTTTAAGATGCTT-T-CCTT
1 TAAATATGTTGATGG-A-CAATTTATATTTTG-TTATGAAAT
519908 CTAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 -TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
519948 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
519987 TAAATATGTTGATGGA
1 TAAATATGTTGATGGA
520003 TTAATGTATG
Statistics
Matches: 189, Mismatches: 14, Indels: 16
0.86 0.06 0.07
Matches are distributed among these distances:
37 1 0.01
38 4 0.02
39 179 0.95
40 4 0.02
41 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (39 bp):
TAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
Found at i:519940 original size:22 final size:22
Alignment explanation
Indices: 519915--519979 Score: 77
Period size: 22 Copynumber: 3.2 Consensus size: 22
519905 CTTCTAAATA
519915 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
* *
519937 TGTT-AT-GA-AA-TTA-AATA
1 TGTTGATGGACAATTTATATTT
519954 TGTTGATGGACAATTTATATTT
1 TGTTGATGGACAATTTATATTT
519976 TGTT
1 TGTT
519980 ATGAAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 4 0.12
20 4 0.12
21 5 0.15
22 10 0.29
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (22 bp):
TGTTGATGGACAATTTATATTT
Found at i:519948 original size:19 final size:19
Alignment explanation
Indices: 519926--519987 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
519916 GTTGATGGAC
519926 AATTTATATTTTGTTATGA
1 AATTTATATTTTGTTATGA
* *
519945 AA-TTA-AATATGTTGATGGA
1 AATTTATATTTTGTT-AT-GA
519964 CAATTTATATTTTGTTATGA
1 -AATTTATATTTTGTTATGA
519984 AATT
1 AATT
519988 AAATATGTTG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
17 6 0.18
18 5 0.15
19 8 0.24
20 4 0.12
21 5 0.15
22 6 0.18
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (19 bp):
AATTTATATTTTGTTATGA
Found at i:520021 original size:156 final size:155
Alignment explanation
Indices: 519727--520021 Score: 520
Period size: 156 Copynumber: 1.9 Consensus size: 155
519717 ATGTTTCTTC
519727 GGTAGCTTTTTAAGATGCTTTCCTTCTAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 GGTAGCTTTTTAAGATGCTTTCCTTCTAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
*
519792 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGACAATTTATAT
66 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGACAATGTATA-
* *
519857 TTTGTTATGAAATTAAATATGTTGAT
130 TATATTATGAAATTAAATATGTTGAT
519883 GGTAGCTTTTTAAGATGCTTTCCTTCTAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
1 GGTAGCTTTTTAAGATGCTTTCCTTCTAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
*
519948 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGATTAATGTATG
66 TAAATATGTTGATGGACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGA-CAATGTAT-
520013 A-ATATTATG
129 ATATATTATG
520022 GTTTGTTGCT
Statistics
Matches: 133, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
156 126 0.95
157 6 0.05
158 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.46
Consensus pattern (155 bp):
GGTAGCTTTTTAAGATGCTTTCCTTCTAAATATGTTGATGGACAATTTATATTTTGTTATGAAAT
TAAATATGTTGATGGACAATTTATATTTTGTTATGAAATTAAATATGTTGATGGACAATGTATAT
ATATTATGAAATTAAATATGTTGAT
Found at i:522714 original size:55 final size:55
Alignment explanation
Indices: 522630--522743 Score: 158
Period size: 55 Copynumber: 2.1 Consensus size: 55
522620 GAAAGTGGCG
* *
522630 AGCACTCATAACGGGTGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
1 AGCACTCACAACGGGAGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
*** *
522685 AGCACTCACAACGGGCAG-GCTCTTAGGGAGCTCGTTAGAGCCTACGTGTCAAGCG
1 AGCACTCACAACGGG-AGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
522740 AGCA
1 AGCA
522744 GGGTTTACGT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
55 51 0.98
56 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.29, T:0.18
Consensus pattern (55 bp):
AGCACTCACAACGGGAGAGCTCTTAGGGAGCTCACCAGAGCCTACGTGTCAAGCA
Found at i:529506 original size:25 final size:25
Alignment explanation
Indices: 529424--529657 Score: 174
Period size: 25 Copynumber: 9.5 Consensus size: 25
529414 AGTTGTATAA
* *
529424 CGGGAAGCT--TGCGAGCCAATTAT
1 CGGGAAGCTCATGAGAGCCAAATAT
529447 CGGGAAGCTCAT-ACGAGCCATAA-A-
1 CGGGAAGCTCATGA-GAGCCA-AATAT
* *
529471 CAGGAAGCTCATGCGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * *
529496 TGGGAAGCTCATGAGAGTCATATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* * * *
529521 CGGGAAGCTCGTGAGAGACATATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
* ** *
529546 CGGGAAGCTCAAGAGAATC-ATTAAT
1 CGGGAAGCTCATGAGAGCCAAAT-AT
* * *
529571 CGAGAAGCTCATGAGAGCTAAATAA
1 CGGGAAGCTCATGAGAGCCAAATAT
*
529596 CGGGAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
** * *
529621 TAGAAAGCTCGTGAGAGCCAAATAT
1 CGGGAAGCTCATGAGAGCCAAATAT
* *
529646 AGGGACGCTCAT
1 CGGGAAGCTCAT
529658 AATAGTTATG
Statistics
Matches: 163, Mismatches: 39, Indels: 16
0.75 0.18 0.07
Matches are distributed among these distances:
23 11 0.07
24 19 0.12
25 130 0.80
26 3 0.02
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.18
Consensus pattern (25 bp):
CGGGAAGCTCATGAGAGCCAAATAT
Found at i:532035 original size:31 final size:31
Alignment explanation
Indices: 532000--532064 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
531990 TATAAAATGA
* *
532000 TCACTAAATTATTCAAAAATTTTCATTTAAG
1 TCACTAAACTACTCAAAAATTTTCATTTAAG
* * *
532031 TCACTGAACTACTCAAAAGTTTTTATTTAAG
1 TCACTAAACTACTCAAAAATTTTCATTTAAG
532062 TCA
1 TCA
532065 TTGGTTGATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.06, T:0.40
Consensus pattern (31 bp):
TCACTAAACTACTCAAAAATTTTCATTTAAG
Done.