Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005189.1 Hibiscus syriacus cultivar Beakdansim tig00011718_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1183632
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:443872 original size:70 final size:70
Alignment explanation
Indices: 443727--443872 Score: 170
Period size: 70 Copynumber: 2.1 Consensus size: 70
443717 AACAAGTGTG
* * * ** *
443727 GAAAAAATAAATTTTAAGGGTAACTCCATAATAACAAGTATTGAAAAAATGGGTCTCTAACAACA
1 GAAAAAATAAATTTTAAGAGTAAATCCATAATAACAAATATTGAAAAAATGAATATCTAACAACA
443792 AATAT
66 AATAT
* * * *
443797 AAAAAAATAAATTTTAAGAGTATAAT-CATAATAACAAATTTTGAAAAAATGAATATTTAATAA-
1 GAAAAAATAAATTTTAAGAGTA-AATCCATAATAACAAATATTGAAAAAATGAATATCTAACAAC
443860 AAATACT
65 AAATA-T
443867 GAAAAA
1 GAAAAA
443873 TTGGACTCAT
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
69 5 0.08
70 56 0.89
71 2 0.03
ACGTcount: A:0.55, C:0.08, G:0.10, T:0.27
Consensus pattern (70 bp):
GAAAAAATAAATTTTAAGAGTAAATCCATAATAACAAATATTGAAAAAATGAATATCTAACAACA
AATAT
Found at i:445159 original size:38 final size:39
Alignment explanation
Indices: 445117--445195 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 39
445107 GTAGAAGATG
* *
445117 TTTTAAAATTATGA-TTCTATTTTAAATCAATCTTT-AAA
1 TTTTAAAATTATGACTCCAATTTTAAATCAAT-TTTCAAA
*
445155 TTTTAAAATTATGACTCCAATTTTAAATTAATTTTCAAA
1 TTTTAAAATTATGACTCCAATTTTAAATCAATTTTCAAA
445194 TT
1 TT
445196 AATAATATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
38 17 0.47
39 19 0.53
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (39 bp):
TTTTAAAATTATGACTCCAATTTTAAATCAATTTTCAAA
Found at i:449675 original size:135 final size:136
Alignment explanation
Indices: 449431--449677 Score: 354
Period size: 135 Copynumber: 1.8 Consensus size: 136
449421 AAAATGATGG
* * * * * * * *
449431 TATTCTTACCTGAATGTTAGTCTGTTGACTTTGATATGATAAAATCCGATCCTAGAATTTCAAGT
1 TATTCTGACCTGAATGTTAATCTGTTGACTATGATATAATAAAATCCGATCCCAAAATCTCAAGC
* * *
449496 GACTATCATATCTTAGTCATCATGTTAACTTCCAGCTTAAACAATCGCCCTTTTCTGCTAAAAAT
66 GACTATCATATCCTAGTCATCATGTTAACGTCCAACTTAAACAATCGCCCTTTTCTGCTAAAAAT
449561 AAACGA
131 AAACGA
* *
449567 TATTCTGAGCTGAATGTTAATTTGTTGACTATGATATAAT-AAATCTCGATCCCAAAATCTCAA-
1 TATTCTGACCTGAATGTTAATCTGTTGACTATGATATAATAAAATC-CGATCCCAAAATCTCAAG
449630 CGACTATCATATCCTAGTCATCATGTTAACGTCCAACTTAAACAATCG
65 CGACTATCATATCCTAGTCATCATGTTAACGTCCAACTTAAACAATCG
449678 TCAATTTTTT
Statistics
Matches: 97, Mismatches: 13, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
135 49 0.51
136 48 0.49
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.35
Consensus pattern (136 bp):
TATTCTGACCTGAATGTTAATCTGTTGACTATGATATAATAAAATCCGATCCCAAAATCTCAAGC
GACTATCATATCCTAGTCATCATGTTAACGTCCAACTTAAACAATCGCCCTTTTCTGCTAAAAAT
AAACGA
Found at i:449835 original size:60 final size:60
Alignment explanation
Indices: 449699--449835 Score: 177
Period size: 60 Copynumber: 2.3 Consensus size: 60
449689 ATAGTTGGGT
* * *
449699 GACCATTTTGTAACTTTTAATAGTCGAGGGACTTAACAAAGTAACATTCTATAGTCGAAG
1 GACCATTTTGTAACTTTTAATAGTCGAGGAACTTAACAAAGTAACATACTATAATCGAAG
* * * * * *
449759 AACTATTTTATAACTTTTAATAGTCGAGGAACTTAATAAAGTAATATACTATAATTGAAG
1 GACCATTTTGTAACTTTTAATAGTCGAGGAACTTAACAAAGTAACATACTATAATCGAAG
449819 GACCATTTGTGT-ACTTT
1 GACCATTT-TGTAACTTT
449836 ACCCTAAAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 62 0.97
61 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGAGGAACTTAACAAAGTAACATACTATAATCGAAG
Found at i:451209 original size:2 final size:2
Alignment explanation
Indices: 451202--451235 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
451192 ATCTTAGTAT
451202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
451236 GTTTTATACA
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):
TA
Found at i:453037 original size:17 final size:17
Alignment explanation
Indices: 453006--453038 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
452996 TATAATATAA
453006 ATTTATTAATGTATAGC
1 ATTTATTAATGTATAGC
453023 ATTTAATTAAT-TATAG
1 ATTT-ATTAATGTATAG
453039 ATATAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
ATTTATTAATGTATAGC
Found at i:454629 original size:156 final size:158
Alignment explanation
Indices: 454457--454759 Score: 475
Period size: 159 Copynumber: 1.9 Consensus size: 158
454447 TGTGGTATAT
** ** * *
454457 GAGCATGTGGTTCAAATTTGGT-AAAAATTAACTTAAAATAAATTACAAATTGAAGCAATAAGGA
1 GAGCATGTGGCCCAAATTTGGTAAAAAACGAACTTAAAATAAATAACAAATTGAAGAAATAAGGA
454521 GATTATAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTGAA
66 GATTATAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTGAA
*
454586 AGTA-ACATGTATTTTACTATTGTTTAA
131 AGTACACATCTATTTTACTATTGTTTAA
*
454613 GAGCATGTGGCCCAAATTTGGTAAAAAAAACGAACTTAAAATAAATAACTAATTGAAGAAATAAG
1 GAGCATGTGGCCCAAATTTGGT--AAAAAACGAACTTAAAATAAATAACAAATTGAAGAAATAAG
* * *
454678 GAGATTATAAAAAATTGAAGGATTAAATTGAAGAATAAAAAATTTGTTATCAAAAAGAGGAATTG
64 GAGATTATAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTG
454743 AAAGTACACATCTATTT
129 AAAGTACACATCTATTT
454760 CAAATTTGGT
Statistics
Matches: 132, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
156 20 0.15
159 103 0.78
160 9 0.07
ACGTcount: A:0.50, C:0.06, G:0.16, T:0.28
Consensus pattern (158 bp):
GAGCATGTGGCCCAAATTTGGTAAAAAACGAACTTAAAATAAATAACAAATTGAAGAAATAAGGA
GATTATAAAAAATTGAAGGACTAAATTGAAAAATAAAAAATTTGTTATAAAAAAGAGGAATTGAA
AGTACACATCTATTTTACTATTGTTTAA
Found at i:455686 original size:18 final size:19
Alignment explanation
Indices: 455654--455691 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
455644 TGTTGAAGCT
455654 AACACCAATGGTGATGATG
1 AACACCAATGGTGATGATG
*
455673 AACA-CAATGTTGATGATG
1 AACACCAATGGTGATGATG
455691 A
1 A
455692 TGATGATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (19 bp):
AACACCAATGGTGATGATG
Found at i:460108 original size:20 final size:19
Alignment explanation
Indices: 460060--460111 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
460050 GCCCCATGCA
*
460060 TGCCCATTGCTGCCACTAT
1 TGCCCATTGCTGCCACCAT
*
460079 TGTCCATTGCTGCCACCAT
1 TGCCCATTGCTGCCACCAT
460098 TGCCTCATTGCTGC
1 TGCC-CATTGCTGC
460112 ATGCACCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.13, C:0.37, G:0.17, T:0.33
Consensus pattern (19 bp):
TGCCCATTGCTGCCACCAT
Found at i:462794 original size:17 final size:17
Alignment explanation
Indices: 462763--462795 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
462753 TATAATATAA
462763 ATTTATTAATGTATAGC
1 ATTTATTAATGTATAGC
462780 ATTTAATTAAT-TATAG
1 ATTT-ATTAATGTATAG
462796 ATATAATACA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.39, C:0.03, G:0.09, T:0.48
Consensus pattern (17 bp):
ATTTATTAATGTATAGC
Found at i:463928 original size:2 final size:2
Alignment explanation
Indices: 463921--463954 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
463911 CCATCCATCC
463921 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
463955 TAAAAAAATA
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:464300 original size:17 final size:17
Alignment explanation
Indices: 464251--464300 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
464241 CTGTTCATGT
*
464251 TTTGGTTTCTATGAATG
1 TTTGATTTCTATGAATG
* *
464268 TTTGA---GTATCAATG
1 TTTGATTTCTATGAATG
464282 TTTGATTTCTATGAATG
1 TTTGATTTCTATGAATG
464299 TT
1 TT
464301 AGAAGAATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 6
0.69 0.14 0.17
Matches are distributed among these distances:
14 12 0.48
17 13 0.52
ACGTcount: A:0.22, C:0.06, G:0.20, T:0.52
Consensus pattern (17 bp):
TTTGATTTCTATGAATG
Found at i:465984 original size:2 final size:2
Alignment explanation
Indices: 465977--466004 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
465967 GATGTTACCC
465977 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
466005 TGGATATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:473344 original size:42 final size:42
Alignment explanation
Indices: 473274--473428 Score: 222
Period size: 42 Copynumber: 3.7 Consensus size: 42
473264 TTGTACCAAG
* *
473274 GACGAGAAGAGCATTCATCAAGACGAGAATGTCATTCATCAA
1 GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAA
* *
473316 GACAAGAATG-CCATTCATCAAGACGAGAAGGCCATTCATCAA
1 GACGAGAA-GACCATTCATCAAGACGAGAATGCCATTCATCAA
* *
473358 GACGAGAAGAGCATTCATCAAGAGGAGAATGCCATTCATCAA
1 GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAA
* *
473400 GACGAGAAGACCCTTCATAAAGACGAGAA
1 GACGAGAAGACCATTCATCAAGACGAGAA
473429 GACCACATCG
Statistics
Matches: 99, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
41 1 0.01
42 97 0.98
43 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (42 bp):
GACGAGAAGACCATTCATCAAGACGAGAATGCCATTCATCAA
Found at i:473373 original size:63 final size:63
Alignment explanation
Indices: 473274--473430 Score: 228
Period size: 63 Copynumber: 2.5 Consensus size: 63
473264 TTGTACCAAG
*
473274 GACGAGAAGAG-CATTCATCAAGACGAGAATG-TCATTCATCAAGACAAGAATGCCATTCATCAA
1 GACGAGAAG-GCCATTCATCAAGACGAGAA-GAGCATTCATCAAGACAAGAATGCCATTCATCAA
**
473337 GACGAGAAGGCCATTCATCAAGACGAGAAGAGCATTCATCAAGAGGAGAATGCCATTCATCAA
1 GACGAGAAGGCCATTCATCAAGACGAGAAGAGCATTCATCAAGACAAGAATGCCATTCATCAA
* * *
473400 GACGAGAAGACCCTTCATAAAGACGAGAAGA
1 GACGAGAAGGCCATTCATCAAGACGAGAAGA
473431 CCACATCGCA
Statistics
Matches: 86, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
62 2 0.02
63 84 0.98
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.16
Consensus pattern (63 bp):
GACGAGAAGGCCATTCATCAAGACGAGAAGAGCATTCATCAAGACAAGAATGCCATTCATCAA
Found at i:473430 original size:21 final size:21
Alignment explanation
Indices: 473274--473433 Score: 200
Period size: 21 Copynumber: 7.6 Consensus size: 21
473264 TTGTACCAAG
*
473274 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
473295 GACGAGAATG-TCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
473316 GACAAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
*
473337 GACGAGAAGGCCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
473358 GACGAGAAGAGCATTCATCAA
1 GACGAGAAGACCATTCATCAA
*
473379 GAGGAGAATG-CCATTCATCAA
1 GACGAGAA-GACCATTCATCAA
* *
473400 GACGAGAAGACCCTTCATAAA
1 GACGAGAAGACCATTCATCAA
473421 GACGAGAAGACCA
1 GACGAGAAGACCA
473434 CATCGCATGG
Statistics
Matches: 123, Mismatches: 12, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
20 2 0.02
21 119 0.97
22 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATCAA
Found at i:473695 original size:7 final size:7
Alignment explanation
Indices: 473673--473712 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
473663 TAACACCTCG
473673 TGCA-TT
1 TGCATTT
473679 TGCA-TT
1 TGCATTT
473685 TGCATTT
1 TGCATTT
473692 TGCATTT
1 TGCATTT
473699 TGCATTT
1 TGCATTT
473706 TCGCATT
1 T-GCATT
473713 GCATGTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 10 0.31
7 17 0.53
8 5 0.16
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.53
Consensus pattern (7 bp):
TGCATTT
Found at i:473695 original size:13 final size:13
Alignment explanation
Indices: 473673--473716 Score: 56
Period size: 13 Copynumber: 3.4 Consensus size: 13
473663 TAACACCTCG
473673 TGCA-TTTGCATT
1 TGCATTTTGCATT
473685 TGCATTTTGCATTT
1 TGCATTTTGCA-TT
473699 TGCATTTTCGCA-T
1 TGCATTTT-GCATT
473712 TGCAT
1 TGCAT
473717 GTATTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 10 0.34
15 3 0.10
ACGTcount: A:0.16, C:0.18, G:0.16, T:0.50
Consensus pattern (13 bp):
TGCATTTTGCATT
Found at i:477483 original size:125 final size:124
Alignment explanation
Indices: 477261--477638 Score: 497
Period size: 125 Copynumber: 3.0 Consensus size: 124
477251 AATACCCACA
* * * *
477261 TTGGGGCATGACTGAACCCCCATCATTTTGAAATGACAAGATCCAGACGAAGAAGGCATTGAGAA
1 TTGGGGCACGAATGAA-CCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * * **
477326 TGAGCCTTACAATTTGAGGTGTTGGGGTATTTTGAAGACCCGTACCTTTATAAGATAATG
65 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
* **
477386 TTGGGGCACGATTGAACCCCTATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATCAAGAA
1 TTGGGGCACGAATGAACCCC-ATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
*
477451 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATGAGATAATG
65 TGAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
* ** * *
477511 TTGGGGCGCGAATGAACCCACATCATGATGAAATTACAAGATTCAGACCAAGAAGGCATTGAGAA
1 TTGGGGCACGAATGAACCC-CATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAA
* * * * * *
477576 TGAGCCTTATAATTTGAGAT-ATTGAGGCATTCTGAAGGCCCGTACCAGAATAAAATAATG
65 TGAGCCTTACAATTTGAGGTGA-TGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
477636 TTG
1 TTG
477639 CGACATCAGT
Statistics
Matches: 223, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
124 5 0.02
125 217 0.97
126 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (124 bp):
TTGGGGCACGAATGAACCCCATCATTTTGAAATGACAAGATTCAGACAAAGAAGGCATTGAGAAT
GAGCCTTACAATTTGAGGTGATGGGGCATTTTGAAGGCCCGTACCAGTATAAGATAATG
Found at i:478879 original size:36 final size:36
Alignment explanation
Indices: 478839--479073 Score: 201
Period size: 36 Copynumber: 6.5 Consensus size: 36
478829 AAGTCAATCT
478839 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
1 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
* *
478875 TAAGCCTTCACCGGAGAGTAGTGAAGCAAACCAT-C
1 TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
* * *
478910 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAAT-C
1 T-AAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
* * *
478946 TGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACAATCA
1 T-AAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCC
* * *
478983 TAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCT
1 TAAGCCTTCACCGA-AGAGAAGTGAAGCAAACCATCC
* * * * * **
479019 TAAGTCTTCACCAAAAAGTAGTGAAGCAGATCCATTT
1 TAAGCCTTCACCGAAGAGAAGTGAAGCA-AACCATCC
* *
479056 TAAGCCTTCTCAGAAGAG
1 TAAGCCTTCACCGAAGAG
479074 TGTTGGAACA
Statistics
Matches: 172, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
35 2 0.01
36 149 0.87
37 21 0.12
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (36 bp):
TAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCC
Found at i:478917 original size:72 final size:72
Alignment explanation
Indices: 478835--479073 Score: 259
Period size: 72 Copynumber: 3.3 Consensus size: 72
478825 GAGCAAGTCA
478835 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGAA
1 ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGAA
478900 GCAAACC
66 GCAAACC
* * * * *
478907 ATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAATCAAT-CTGAAGCCTTCACCGGAGAATAGTG
1 ATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACCATCCT-AAGCCTTCACCGGAGAGTAGTG
*
478970 AAGCAAACA
64 AAGCAAACC
* * * * * ** *
478979 ATCATAAGTCTTCACC-AGAGAGTAGTGAAGCAAACCATCTTAAGTCTTCACCAAAAAGTAGTGA
1 ATCTTAAGCCTTCACCGA-AGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGA
*
479043 AGCAGATCC
65 AGCA-AACC
* * *
479052 ATTTTAAGCCTTCTCAGAAGAG
1 ATCTTAAGCCTTCACCGAAGAG
479074 TGTTGGAACA
Statistics
Matches: 134, Mismatches: 26, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
71 3 0.02
72 112 0.84
73 18 0.13
74 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (72 bp):
ATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAGAGTAGTGAA
GCAAACC
Found at i:479041 original size:108 final size:108
Alignment explanation
Indices: 478826--479073 Score: 320
Period size: 108 Copynumber: 2.3 Consensus size: 108
478816 ATGAGATTGG
* * *
478826 AGCAAGTCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACCATCCTAAGCCTTCACCGGAG
1 AGCAA-TCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCATAAGCCTTCACCAGAG
* *
478891 AGTAGTGAAGCAAACCATCTGAAGCCTTCACCGGAGAATAGTGA
65 AGTAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGA
* * *
478935 AGCAATCAATCTGAAGCCTTCACCGGAGA-ATAGTGAAGCAAACAATCATAAGTCTTCACCAGAG
1 AGCAATCAATCTTAAGCCTTCACCGAAGAGA-AGTGAAGCAAACAATCATAAGCCTTCACCAGAG
* *
478999 AGTAGTGAAGCAAACCATCTTAAGTCTTCACC-AAAAAGTAGTGA
65 AGTAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAA-TAGTGA
* * * *
479043 AGCAGATCCATTTTAAGCCTTCTCAGAAGAG
1 AGCA-ATCAATCTTAAGCCTTCACCGAAGAG
479074 TGTTGGAACA
Statistics
Matches: 119, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
107 4 0.03
108 91 0.76
109 24 0.20
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.20
Consensus pattern (108 bp):
AGCAATCAATCTTAAGCCTTCACCGAAGAGAAGTGAAGCAAACAATCATAAGCCTTCACCAGAGA
GTAGTGAAGCAAACCATCTGAAGCCTTCACCGAAAAATAGTGA
Found at i:479528 original size:51 final size:51
Alignment explanation
Indices: 479444--479883 Score: 537
Period size: 51 Copynumber: 8.5 Consensus size: 51
479434 TGAAAATATG
*
479444 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * *
479495 CGAGGTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGA-GATGT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATG-T-T
* * * *
479547 CTAAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCAG-TTGAAGATGTT
1 C-GAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCC-GTTTGAAGATGTT
* * * **
479599 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG-TAAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGA-AGATGTT
*
479650 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
*
479701 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
479752 CGAGTTCTATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAGAGATGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGTT
* * * *
479805 CGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTT
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCC--GT-TTGAAGA-TGTT
* *
479860 CGAG-TCTTATACTCTCTGAAGAAA
1 CGAGTTC-TATACTCCCTAAAGAAA
479884 TAGGGGGCAG
Statistics
Matches: 349, Mismatches: 26, Indels: 24
0.87 0.07 0.06
Matches are distributed among these distances:
50 4 0.01
51 224 0.64
52 7 0.02
53 80 0.23
54 7 0.02
55 24 0.07
56 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.24, T:0.24
Consensus pattern (51 bp):
CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
Found at i:479804 original size:206 final size:206
Alignment explanation
Indices: 479444--479842 Score: 626
Period size: 206 Copynumber: 1.9 Consensus size: 206
479434 TGAAAATATG
*
479444 CGAGTTCTATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGGTCCATACTC
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGGTCCATACTC
*
479509 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAGAGAAAGA
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAAAGAAAGA
*
479574 GGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
131 AGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
479639 AAAGAGATGTT
196 AAAGAGATGTT
* * *
479650 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTATACTC
1 CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGGTCCATACTC
* * *
479715 CTTAAAGAAAGAAGGAGCGAACCCGTTTG-A-AGATGT-TCGAGTTCTATACTCCTTAAAGAAAG
66 CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCT-AAGTTCCATACTCCCTAAAGAAAG
* * *
479777 AATGAGCGAACCC-GTTTGAAGAGATGTTCGAGTTCTATACTCCCTAGAGAAATAGGGAGCGAAC
130 AAGGAGCGAACCCAG-TTG-A-AGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAAC
479841 CC
192 CC
479843 ATTTGTTGAA
Statistics
Matches: 177, Mismatches: 12, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
203 2 0.01
204 40 0.23
205 2 0.01
206 133 0.75
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (206 bp):
CGAGTTCTATACTCCCTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGGTCCATACTC
CTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGAGATGTCTAAGTTCCATACTCCCTAAAGAAAGA
AGGAGCGAACCCAGTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGT
AAAGAGATGTT
Found at i:479883 original size:55 final size:54
Alignment explanation
Indices: 479444--480337 Score: 455
Period size: 51 Copynumber: 16.8 Consensus size: 54
479434 TGAAAATATG
* * * *
479444 CGAGTTCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGA-TGTT
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * * * * * *
479495 CGAGGTCCATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGAGATG-T
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGA-TTGTT
* * * *
479547 CTAAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCA--GTTGAAGA-TGTT
1 C-GAGTTCTATACTCTCTGA-AGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * * * *
479599 CGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCC---G-TAAAGAGATGTT
1 CGAGTTCTATACTCTCTGA-AGAAATAGGGAGCGAACCCATTGTTGAAGA-TTGTT
* * * *
479650 CGAGTTCTATACTCCCTAAAGAAAGAGGGAGCGAACCC-GT-TTGAAGA-TGTT
1 CGAGTTCTATACTCTCTGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * * *
479701 CGAGTTCTATACTC-CTTAAAGAAAGAAGGAGCGAACCC-GT-TTGAAGA-TGTT
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
* * ** * *
479752 CGAGTTCTATACTC-CTTAAAGAAAGAATGAGCGAACCC-GT-TTGAAGAGATGTT
1 CGAGTTCTATACTCTC-TGAAGAAATAGGGAGCGAACCCATTGTTGAAGA-TTGTT
*
479805 CGAGTTCTATACTCCCT-AGAGAAATAGGGAGCGAACCCATTTGTTGAAGATTGTT
1 CGAGTTCTATACTCTCTGA-AGAAATAGGGAGCGAACCCA-TTGTTGAAGATTGTT
* * *
479860 CGAG-TCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-AC-CCATTGTTGAAGATTGTT
* * * * *
479915 CG-GGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG-T
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGAAC-CCATTGTTGAAGATTGTT
* * * * *
479969 -G-GGTCTTTTACTCTCTGAAGAAATAGGGGGC-AGACACAATCGTTGAAGATTGTT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-AC-CCATTGTTGAAGATTGTT
* ** * * *
480023 CGAG-TCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATT-AT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGC-GAACCCATTGTTGAAGATTGTT
* * * *
480077 -G-GGTCTTATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGTTGAAGATTGTT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-AC-CCATTGTTGAAGATTGTT
* **
480131 CGAG-TCTTATACTCTCTGAAGAAATAGGGGGC-AGACAAATTTGTTGAAGA-TGATT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGA-ACCCA-TTGTTGAAGATTG-TT
* *
480186 CAAG-TCTTATACTCTCTGAAGAAATAGGGAGCGAACCCATTTTTCTGAAGATT-TAT
1 CGAGTTC-TATACTCTCTGAAGAAATAGGGAGCGAACCCA-TTGT-TGAAGATTGT-T
* * * * * *
480242 TGAATTCTATACTCCCTGAA-AAGGACTAGAGAGCTG-ACGCGATTTTTGAAGA-TGTT
1 CGAGTTCTATACTCTCTGAAGAA--A-TAGGGAGC-GAAC-CCATTGTTGAAGATTGTT
* * *
480298 CGAGTTCTATTCTC-CTGGAGAAAGAGGGAGCGAACCCATT
1 CGAGTTCTATACTCTCTGAAGAAATAGGGAGCGAACCCATT
480338 TTCAGAAGAT
Statistics
Matches: 727, Mismatches: 61, Indels: 109
0.81 0.07 0.12
Matches are distributed among these distances:
49 5 0.01
50 2 0.00
51 221 0.30
52 14 0.02
53 173 0.24
54 15 0.02
55 220 0.30
56 49 0.07
57 12 0.02
58 13 0.02
59 3 0.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (54 bp):
CGAGTTCTATACTCTCTGAAGAAATAGGGAGCGAACCCATTGTTGAAGATTGTT
Found at i:479996 original size:53 final size:55
Alignment explanation
Indices: 479847--480214 Score: 523
Period size: 55 Copynumber: 6.8 Consensus size: 55
479837 GAACCCATTT
479847 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * * *
479902 GTTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * * *
479957 GATGAAGATTG-T-GGGTCTTTTACTCTCTGAAGAAATAGGGGGCAGACACAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
480010 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* * *
480065 GATGAAGATT-AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
* *
480118 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGAC-AAATTT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAA-TC
*
480173 GTTGAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGG
1 GTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
480215 AGCGAACCCA
Statistics
Matches: 278, Mismatches: 29, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
53 92 0.33
54 8 0.03
55 178 0.64
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (55 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATC
Found at i:480009 original size:108 final size:108
Alignment explanation
Indices: 479792--480163 Score: 552
Period size: 108 Copynumber: 3.4 Consensus size: 108
479782 GCGAACCCGT
* * * * * *
479792 TTGAAGAGATGTTCGAGT-TCTATACTCCCT-AGAGAAATAGGGAGCGAAC-CCATTTGTTGAAG
1 TTGAAGA-TTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGGGCAAACGCGA-TTGATGAAG
*
479854 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
62 ATTG-T-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
*
479903 TTGAAGATTGTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
* *
479968 TGGGTCTTTTACTCTCTGAAGAAATAGGGGGCAGACACAATCG
66 TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
* * *
480011 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATTA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
480076 TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
66 TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
480119 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCA
1 TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCA
480164 GACAAATTTG
Statistics
Matches: 242, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
108 186 0.77
109 1 0.00
110 44 0.18
111 11 0.05
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (108 bp):
TTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG
TGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCG
Found at i:480019 original size:163 final size:163
Alignment explanation
Indices: 479847--480214 Score: 555
Period size: 163 Copynumber: 2.3 Consensus size: 163
479837 GAACCCATTT
*
479847 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGATGAAGATT
* * * *
479912 GTTCGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTG-T-GGGTCT
66 -AT-GGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCAATCGATGAAGATTGTTCGAGTCT
*
479975 TTTACTCTCTGAAGAAATAGGGGGCAGACACAA-TC
129 TATACTCTCTGAAGAAATAGGGGGCAGACA-AATTC
* * *
480010 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATT
1 GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGATGAAGATT
* *
480075 ATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTA
66 ATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCAATCGATGAAGATTGTTCGAGTCTTA
*
480140 TACTCTCTGAAGAAATAGGGGGCAGACAAATTT
131 TACTCTCTGAAGAAATAGGGGGCAGACAAATTC
*
480173 GTTGAAGA-TGATTCAAGTCTTATACTCTCTGAAGAAATAGGG
1 GTTGAAGATTG-TTCGAGTCTTATACTCTCTGAAGAAATAGGG
480215 AGCGAACCCA
Statistics
Matches: 188, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
161 48 0.26
162 6 0.03
163 134 0.71
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (163 bp):
GTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGATGAAGATT
ATGGGTCTTATACTCTCTGAAGAAATAGGGGGCAAACGCAATCGATGAAGATTGTTCGAGTCTTA
TACTCTCTGAAGAAATAGGGGGCAGACAAATTC
Found at i:480164 original size:108 final size:107
Alignment explanation
Indices: 479863--480214 Score: 553
Period size: 108 Copynumber: 3.2 Consensus size: 107
479853 GATTGTTCGA
*
479863 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGGGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
* *
479928 CTCTGAAGAAATAGGGGGCAAACGCGATTGATGAAGATTGTGG
66 CTCTGAAGAAATAGGGGGCAGA-GCGATTGATGAAGATTATGG
* *
479971 GTCTTTTACTCTCTGAAGAAATAGGGGGCAGACACAATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
480036 CTCTGAAGAAATAGGGGGCAGATGCGATTGATGAAGATTATGG
66 CTCTGAAGAAATAGGGGGCAGA-GCGATTGATGAAGATTATGG
480079 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
1 GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
* * * **
480144 CTCTGAAGAAATAGGGGGCAGA-CAAATTTGTTGAAGATGATTCAA
66 CTCTGAAGAAATAGGGGGCAGAGC-GA-TTGATGAAGATTA-T-GG
480189 GTCTTATACTCTCTGAAGAAATAGGG
1 GTCTTATACTCTCTGAAGAAATAGGG
480215 AGCGAACCCA
Statistics
Matches: 227, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
106 1 0.00
107 1 0.00
108 198 0.87
109 1 0.00
110 26 0.11
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.28
Consensus pattern (107 bp):
GTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCAATCGTTGAAGATTGTTCGAGTCTTATACT
CTCTGAAGAAATAGGGGGCAGAGCGATTGATGAAGATTATGG
Found at i:480261 original size:56 final size:54
Alignment explanation
Indices: 479556--480350 Score: 194
Period size: 55 Copynumber: 14.9 Consensus size: 54
479546 TCTAAGTTCC
* * * * *
479556 ATACTCCCT-AGAGAAAGAGGGAGCGAACCCA--GT-TGAAGATGTTCGAGTTCC
1 ATACTCCCTGA-AGAAATAGGGAGCGAACCCATTTTCTGAAGATTTTCGAATTCT
* * *** * *
479607 ATACTCCCT-AGAGAAAGAGGGAGCGAACCC--GTAAAG-AGATGTTCGAGTTCT
1 ATACTCCCTGA-AGAAATAGGGAGCGAACCCATTTTCTGAAGATTTTCGAATTCT
* * * * *
479658 ATACTCCCTAAAGAAAGAGGGAGCGAACCC--GTT-TGAAGATGTTCGAGTTCT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTCTGAAGATTTTCGAATTCT
* * * * * * *
479709 ATACTCCTTAAAGAAAGAAGGAGCGAACCC--GTT-TGAAGATGTTCGAGTTCT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTCTGAAGATTTTCGAATTCT
* * * ** * *** * *
479760 ATACTCCTTAAAGAAAGAATGAGCGAACCCGTTTGAAG-AGATGTTCGAGTTCT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTCTGAAGATTTTCGAATTCT
*
479813 ATACTCCCT-AGAGAAATAGGGAGCGAACCCATTTGT-TGAAGATTGTTCG-AGTCTT
1 ATACTCCCTGA-AGAAATAGGGAGCGAACCCATTT-TCTGAAGATT-TTCGAATTC-T
* * * ** **
479868 ATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGT-TGAAGATTGTTCG-GGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGA-AC-CCATTTTCTGAAGATT-TTCGAATTC-T
* * * * ** * **
479923 ATACTCTCTGAAGAAATAGGGGGCAAACGCGA-TTGATGAAGATTGT-G-GGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGAAC-CCATTTTCTGAAGATTTTCGAATTC-T
* * * * ** *
479976 TTACTCTCTGAAGAAATAGGGGGC-AGACACAATCGT-TGAAGATTGTTCG-AGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGA-AC-CCATTTTCTGAAGATT-TTCGAATTC-T
* * ** * ** * **
480031 ATACTCTCTGAAGAAATAGGGGGCAGATGCGA-TTGATGAAGATTAT-G-GGTCTT
1 ATACTCCCTGAAGAAATAGGGAGC-GAACCCATTTTCTGAAGATTTTCGAATTC-T
* * * ** *
480084 ATACTCTCTGAAGAAATAGGGGGC-AGACGCAATCGT-TGAAGATTGTTCG-AGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGA-AC-CCATTTTCTGAAGATT-TTCGAATTC-T
* * ** * *
480139 ATACTCTCTGAAGAAATAGGGGGC-AGACAAATTTGT-TGAAGATGATTC-AAGTCTT
1 ATACTCCCTGAAGAAATAGGGAGCGA-ACCCATTT-TCTGAAGAT-TTTCGAATTC-T
* *
480194 ATACTCTCTGAAGAAATAGGGAGCGAACCCATTTTTCTGAAGATTTATTGAATTCT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCA-TTTTCTGAAGATTT-TCGAATTCT
* * * *
480250 ATACTCCCTGAA-AAGGACTAGAGAGCTG-ACGCGATTTT-TGAAGATGTTCGAGTTCT
1 ATACTCCCTGAAGAA--A-TAGGGAGC-GAAC-CCATTTTCTGAAGATTTTCGAATTCT
* * * *
480306 ATTCT-CCTGGAGAAAGAGGGAGCGAACCCATTTTCAGAAGATTTT
1 ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTCTGAAGATTTT
480351 TTTTCAAGTC
Statistics
Matches: 618, Mismatches: 81, Indels: 88
0.79 0.10 0.11
Matches are distributed among these distances:
50 1 0.00
51 168 0.27
52 11 0.02
53 142 0.23
54 16 0.03
55 208 0.34
56 42 0.07
57 14 0.02
58 13 0.02
59 3 0.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (54 bp):
ATACTCCCTGAAGAAATAGGGAGCGAACCCATTTTCTGAAGATTTTCGAATTCT
Found at i:486242 original size:30 final size:30
Alignment explanation
Indices: 486202--486274 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
486192 GGGAGTATAG
*
486202 TGATGGGGATTTGGCGTTAAATTCTTTGTC
1 TGATGAGGATTTGGCGTTAAATTCTTTGTC
486232 TGATGAGGATTTGGCGTTAAATTCTTTGTC
1 TGATGAGGATTTGGCGTTAAATTCTTTGTC
486262 TGATGAGGATTTG
1 TGATGAGGATTTG
486275 CCTCTCGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.19, C:0.08, G:0.30, T:0.42
Consensus pattern (30 bp):
TGATGAGGATTTGGCGTTAAATTCTTTGTC
Found at i:490511 original size:106 final size:106
Alignment explanation
Indices: 490287--491694 Score: 2335
Period size: 106 Copynumber: 13.3 Consensus size: 106
490277 TCACAAAATT
* *
490287 CGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCTCA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * *
490351 ACGAAGGATCTT-GACTCTAGACAACGTAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
490391 CGACGAAGGGACCGCTAGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
490456 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
490497 CGACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
490561 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
490602 CGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCTAAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
490667 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
490708 CGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTCATAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
490773 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
490814 CGACGAAGGGACCGCTGGTTGTCAATAAACCATTTCTCAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
490879 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
490920 CGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCTAAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
490985 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
491026 CGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAATTTCATAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
491091 ACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
491132 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGA-CTCAATTTCAACTTCTC
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGC-CAATTTCAACTTCAC
* *
491196 AACGAAGGATCTT-GACTCTAGACAACGCAAGTTCAACTTCA
65 AACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
491237 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACC
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
491302 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
491343 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
*
491408 ACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
491449 CGACGAAGGGACCGCTGGTTGTCAATAAAC-ATTTCTCAATTTCAGAGCCAATTTCAACTTCTCA
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
* * *
491513 ACGAAGGATCTT-GACTCTAGACAACGTAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
491553 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACC
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
491618 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
66 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
491659 CGACGAAGGGACCGCTGGTTGTCAACAAACACCTTC
1 CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC
491695 GAGTTCGACT
Statistics
Matches: 1234, Mismatches: 62, Indels: 14
0.94 0.05 0.01
Matches are distributed among these distances:
104 84 0.07
105 329 0.27
106 821 0.67
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (106 bp):
CGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
Found at i:491855 original size:84 final size:84
Alignment explanation
Indices: 491689--491855 Score: 192
Period size: 84 Copynumber: 2.0 Consensus size: 84
491679 GTCAACAAAC
* * * * * *
491689 ACCTTCGAGTTCGACTTCATTCAGCTCAGAGGCACATCGTTTACAGCATAACTCAAGGCTAGAAG
1 ACCTTCGAGTTCGACTACACTAAGCTCAGAGGCACATCATTTACAGAATAACTCAAGGCAAGAAG
* * *
491754 GGTTACCTGTCACTAAAAG
66 GGCTACCTATCAATAAAAG
* * * *
491773 ACCTTCGAGTTCGACTACGCTAAGCTCCA-AGGCACGTCATTTGCAGAATAGCTCAAGGCAAGAA
1 ACCTTCGAGTTCGACTACACTAAGCT-CAGAGGCACATCATTTACAGAATAACTCAAGGCAAGAA
*
491837 GGGCTATCTATCAATAAAA
65 GGGCTACCTATCAATAAAA
491856 TTGTCGAGTT
Statistics
Matches: 68, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
84 66 0.97
85 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (84 bp):
ACCTTCGAGTTCGACTACACTAAGCTCAGAGGCACATCATTTACAGAATAACTCAAGGCAAGAAG
GGCTACCTATCAATAAAAG
Found at i:493458 original size:30 final size:30
Alignment explanation
Indices: 493418--493490 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
493408 GGGAGTATAG
*
493418 TGATGGGGATTTGGCGTTAAATTCTTTGTC
1 TGATGAGGATTTGGCGTTAAATTCTTTGTC
493448 TGATGAGGATTTGGCGTTAAATTCTTTGTC
1 TGATGAGGATTTGGCGTTAAATTCTTTGTC
493478 TGATGAGGATTTG
1 TGATGAGGATTTG
493491 CCTCTCAAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.19, C:0.08, G:0.30, T:0.42
Consensus pattern (30 bp):
TGATGAGGATTTGGCGTTAAATTCTTTGTC
Found at i:494108 original size:2 final size:2
Alignment explanation
Indices: 494101--494131 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
494091 ATGATCCATG
494101 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
494132 CATAGGAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:496154 original size:17 final size:18
Alignment explanation
Indices: 496125--496159 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
496115 TTTTTTGTAT
496125 ATATTTAAACGATGTTAA
1 ATATTTAAACGATGTTAA
*
496143 ATATTT-AACGATTTTAA
1 ATATTTAAACGATGTTAA
496160 TTATAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.43, C:0.06, G:0.09, T:0.43
Consensus pattern (18 bp):
ATATTTAAACGATGTTAA
Found at i:498201 original size:57 final size:59
Alignment explanation
Indices: 498133--498244 Score: 183
Period size: 60 Copynumber: 1.9 Consensus size: 59
498123 AACAGTGAAG
* *
498133 AGACCATTATTAA-CG-AGAAGAATATATCTTGAGACAGAGAGTATATGATAGTAGAAA
1 AGACCATTATTAAGAGAAGAAGAATATATCTTGAGACAGAGAGCATATGATAGTAGAAA
498190 AGACCATTATTAATGAGAAGAAGAATATATCTTGAGACAGAGAGCATATGATAGT
1 AGACCATTATTAA-GAGAAGAAGAATATATCTTGAGACAGAGAGCATATGATAGT
498245 GGACAATAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
57 13 0.26
59 1 0.02
60 36 0.72
ACGTcount: A:0.45, C:0.09, G:0.21, T:0.25
Consensus pattern (59 bp):
AGACCATTATTAAGAGAAGAAGAATATATCTTGAGACAGAGAGCATATGATAGTAGAAA
Found at i:501251 original size:18 final size:17
Alignment explanation
Indices: 501228--501268 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
501218 ATGCTTACGA
501228 TTATCAAACATTTAATAG
1 TTATCAAACATTT-ATAG
* *
501246 TTATCAGATATTTATAG
1 TTATCAAACATTTATAG
501263 TTATCA
1 TTATCA
501269 GATGTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.44
Consensus pattern (17 bp):
TTATCAAACATTTATAG
Found at i:501264 original size:17 final size:18
Alignment explanation
Indices: 501237--501288 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
501227 ATTATCAAAC
501237 ATTTAATAGTTATCAGAT-
1 ATTT-ATAGTTATCAGATG
501255 ATTTATAGTTATCAGATG
1 ATTTATAGTTATCAGATG
* *
501273 TTTTACAGTTATCAGA
1 ATTTATAGTTATCAGA
501289 ATTAGATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (18 bp):
ATTTATAGTTATCAGATG
Found at i:508961 original size:19 final size:19
Alignment explanation
Indices: 508915--508961 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
508905 AAAAACTCTA
508915 AAAAATAATATTCAAAAAC
1 AAAAATAATATTCAAAAAC
* *
508934 AAAAGATAAT-TCTTAAAAAT
1 AAAA-ATAATAT-TCAAAAAC
508954 AAAAATAA
1 AAAAATAA
508962 GATGAATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.68, C:0.06, G:0.02, T:0.23
Consensus pattern (19 bp):
AAAAATAATATTCAAAAAC
Found at i:512923 original size:15 final size:14
Alignment explanation
Indices: 512880--512927 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
512870 TAAATTTTTT
512880 TAATTTAATTACT-
1 TAATTTAATTACTC
512893 TAACTTTCAGATTACTCC
1 TAA-TTT-A-ATTACT-C
512911 TAATTTAATTACTC
1 TAATTTAATTACTC
512925 TAA
1 TAA
512928 CTTTCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 7 0.23
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (14 bp):
TAATTTAATTACTC
Found at i:514931 original size:60 final size:60
Alignment explanation
Indices: 514806--514929 Score: 162
Period size: 60 Copynumber: 2.1 Consensus size: 60
514796 TCGAGTGATT
* *
514806 ATTTTGTAACTTTTAATAGTCAAGGGACTCAACAAAGCATCACCCTACAGCTGGGGCACC
1 ATTTTGTAACTTTTAATAATCAAGGGAATCAACAAAGCATCACCCTACAGCTGGGGCACC
* ** * *
514866 ATTTTGTAACTTTTAATAATTAAGGGAATCCGCAAAGCAAT-ACCCTATAGTTGGGG-ACC
1 ATTTTGTAACTTTTAATAATCAAGGGAATCAACAAAGC-ATCACCCTACAGCTGGGGCACC
514925 ATTTT
1 ATTTT
514930 TGCACTTTAC
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
59 8 0.14
60 46 0.82
61 2 0.04
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (60 bp):
ATTTTGTAACTTTTAATAATCAAGGGAATCAACAAAGCATCACCCTACAGCTGGGGCACC
Found at i:515269 original size:2 final size:2
Alignment explanation
Indices: 515218--515253 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
515208 GGTACAATCC
515218 AT 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 AT
515254 TAATTTAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:528855 original size:39 final size:36
Alignment explanation
Indices: 528812--528885 Score: 103
Period size: 39 Copynumber: 2.0 Consensus size: 36
528802 AAGTTTATTC
*
528812 TTTGTTTCATTTTAGTACATGTCGTTAAAAACTTTAATT
1 TTTGTTTCATTTTAG-A-ATCTCGTTAAAAA-TTTAATT
*
528851 TTTGTTTCATTTTAGAATCTCGTTCAAAATTTAAT
1 TTTGTTTCATTTTAGAATCTCGTTAAAAATTTAAT
528886 GTTACGTTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.18
37 11 0.33
38 1 0.03
39 15 0.45
ACGTcount: A:0.28, C:0.11, G:0.09, T:0.51
Consensus pattern (36 bp):
TTTGTTTCATTTTAGAATCTCGTTAAAAATTTAATT
Found at i:538410 original size:48 final size:47
Alignment explanation
Indices: 538354--538507 Score: 218
Period size: 48 Copynumber: 3.2 Consensus size: 47
538344 TCTTTCATTC
*
538354 CATCCAAACGATTCCCAGCAAGCTCGCTTTTTCCCAGATTCTCAGCAT
1 CATCCAAACAATTCCCAGCAAGCTC-CTTTTTCCCAGATTCTCAGCAT
* * **
538402 CATCCAAACAATCCCCAGCAAGCTCATGTTTTCCCAGATTCAAAGCAT
1 CATCCAAACAATTCCCAGCAAGCTCCT-TTTTCCCAGATTCTCAGCAT
*
538450 CATCCAAACAATTCCTAGCAAGCTCACTTTTTCCCAGATTCTCAGCAT
1 CATCCAAACAATTCCCAGCAAGCTC-CTTTTTCCCAGATTCTCAGCAT
*
538498 CACCCAAACA
1 CATCCAAACA
538508 GATAGGAATT
Statistics
Matches: 93, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 91 0.98
49 1 0.01
ACGTcount: A:0.31, C:0.35, G:0.10, T:0.25
Consensus pattern (47 bp):
CATCCAAACAATTCCCAGCAAGCTCCTTTTTCCCAGATTCTCAGCAT
Found at i:540030 original size:15 final size:16
Alignment explanation
Indices: 540010--540044 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
540000 TTAATTAAAA
540010 ATTTTATATAAAT-TT
1 ATTTTATATAAATATT
*
540025 ATTTTATATATATATT
1 ATTTTATATAAATATT
540041 ATTT
1 ATTT
540045 AAATTAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATATAAATATT
Found at i:540269 original size:187 final size:177
Alignment explanation
Indices: 539901--540283 Score: 556
Period size: 187 Copynumber: 2.1 Consensus size: 177
539891 ATAAAATTTT
539901 AAATATTAA-ATATTATATATATACATATGGGCTCAGCCCAAACCATTAAAACCAATTAATAATT
1 AAATATTAATATATTATATATATACATATGGGCTCAGCCCAAACCATTAAAACCAATTAATAATT
539965 TAAGATCCAATAACTTTAAACCTAAATCAATATAATTAATTAAAAATTTTATATAAATTTATTTT
66 TAAGATCCAATAACTTTAAACCTAAATCAATATAATTAATTAAAAATTTTATATAAATTTATTTT
* **
540030 ATATATATATTATTTAAATTAATTGTAAATTGTTTTTCTGAATTAAA
131 ATATATATATTATTTAAATTAATTATAAACAGTTTTTCTGAATTAAA
* *
540077 AAATATTAAATATATTATATATA-ACATATGGGCTTAGCTCAAACCATTTAAAACACAATTAATA
1 AAATATT-AATATATTATATATATACATATGGGCTCAGCCCAAACCA-TTAAAAC-CAATTAATA
*
540141 ATTTAAGATCCAATAACTTTTAAACTTAAATCAATATTAATTAATTAAAAAATTTTATATAAAAT
63 ATTTAAGATCCAATAAC-TTTAAACCTAAATCAATA-TAATTAATT-AAAAATTTTATAT-AAA-
* *
540206 TTTTATTTTATAATTATATATTATTTAAATTAATTATAAACAGTTTTTTTGAATTATA
123 -TTTATTTTAT-A-TATATATTATTTAAATTAATTATAAACAGTTTTTCTGAATTAAA
*
540264 AAATATTTAAT-TTTTATATA
1 AAATA-TTAATATATTATATA
540284 AATTAAAAAA
Statistics
Matches: 185, Mismatches: 9, Indels: 16
0.88 0.04 0.08
Matches are distributed among these distances:
176 7 0.04
177 23 0.12
178 19 0.10
179 26 0.14
180 17 0.09
181 9 0.05
182 13 0.07
183 3 0.02
185 10 0.05
186 9 0.05
187 47 0.25
188 2 0.01
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.42
Consensus pattern (177 bp):
AAATATTAATATATTATATATATACATATGGGCTCAGCCCAAACCATTAAAACCAATTAATAATT
TAAGATCCAATAACTTTAAACCTAAATCAATATAATTAATTAAAAATTTTATATAAATTTATTTT
ATATATATATTATTTAAATTAATTATAAACAGTTTTTCTGAATTAAA
Found at i:540806 original size:15 final size:15
Alignment explanation
Indices: 540781--540814 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
540771 AAATTTAAAA
540781 TTATCATATATTTTAT
1 TTATCATATATTTT-T
540797 TTAT-ATATATTTTT
1 TTATCATATATTTTT
540811 TTAT
1 TTAT
540815 TAAAAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 9 0.50
16 4 0.22
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATCATATATTTTT
Found at i:541031 original size:18 final size:17
Alignment explanation
Indices: 541010--541064 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 17
541000 CAAGGTAGAG
541010 ATATATATTAATAATATA
1 ATATAT-TTAATAATATA
541028 ATAT-TTTATATAA-ATA
1 ATATATTTA-ATAATATA
*
541044 AAATATTCTAATAGATATA
1 ATATATT-TAATA-ATATA
541063 AT
1 AT
541065 TAATAAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
16 9 0.30
17 10 0.33
18 7 0.23
19 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (17 bp):
ATATATTTAATAATATA
Found at i:542489 original size:37 final size:39
Alignment explanation
Indices: 542411--542490 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 39
542401 AACAAGTTAG
*
542411 AAAATATTTATATATTTTCTTTAAAAAAATTAAATTCAT
1 AAAATATTTATATATTTTCTTTAAAAAAATTAAAATCAT
*
542450 AAAAT-TTATATATATTTT-TTT-ACAAAATTAAAAAT-AT
1 AAAATATT-TATATATTTTCTTTAAAAAAATT-AAAATCAT
542487 AAAA
1 AAAA
542491 AGGTTTAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
37 13 0.35
38 9 0.24
39 15 0.41
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (39 bp):
AAAATATTTATATATTTTCTTTAAAAAAATTAAAATCAT
Found at i:542903 original size:13 final size:13
Alignment explanation
Indices: 542885--542909 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
542875 CAGGGATGAT
542885 TAGAGGGTACGAG
1 TAGAGGGTACGAG
542898 TAGAGGGTACGA
1 TAGAGGGTACGA
542910 TGGTCGTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.44, T:0.16
Consensus pattern (13 bp):
TAGAGGGTACGAG
Found at i:542953 original size:17 final size:19
Alignment explanation
Indices: 542925--542965 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
542915 GTTCTTTCAA
542925 ATTTTAAAATTA-TTATAT
1 ATTTTAAAATTATTTATAT
*
542943 ATTTT-AAATTATTTTTAT
1 ATTTTAAAATTATTTATAT
542961 ATTTT
1 ATTTT
542966 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTAAAATTATTTATAT
Found at i:544656 original size:3 final size:3
Alignment explanation
Indices: 544648--544735 Score: 92
Period size: 3 Copynumber: 28.0 Consensus size: 3
544638 TGTAGACACA
544648 ATT ATT ATT ATTT ATCT ATT A-T ATT ATT ATT ATT ATT ATT ATT ATTT
1 ATT ATT ATT A-TT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
544695 ATCT ATT A-T ATT ATT ATTT ATTT ATTT ATT A-T ATT ATT ATT
1 AT-T ATT ATT ATT ATT A-TT A-TT A-TT ATT ATT ATT ATT ATT
544736 TTGTAGGTCA
Statistics
Matches: 77, Mismatches: 0, Indels: 16
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.08
3 48 0.62
4 23 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:544686 original size:31 final size:33
Alignment explanation
Indices: 544648--544735 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 33
544638 TGTAGACACA
544648 ATTATTATTATTTATCTATTA-TATTATTATTATT
1 ATTATTATTATTTATCTATTATTATTATTA-T-TT
544682 ATTATTATTATTTATCTATTA-TATTATTATTT
1 ATTATTATTATTTATCTATTATTATTATTATTT
544714 ATTTATTTATTATATTAT-TATT
1 A-TTA-TTATTAT-TTATCTATT
544736 TTGTAGGTCA
Statistics
Matches: 51, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
32 3 0.06
33 4 0.08
34 40 0.78
35 4 0.08
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (33 bp):
ATTATTATTATTTATCTATTATTATTATTATTT
Found at i:544691 original size:34 final size:36
Alignment explanation
Indices: 544648--544726 Score: 135
Period size: 34 Copynumber: 2.2 Consensus size: 36
544638 TGTAGACACA
544648 ATTATTATTATTTATCTATTATATTATTA-TTA-TT
1 ATTATTATTATTTATCTATTATATTATTATTTATTT
544682 ATTATTATTATTTATCTATTATATTATTATTTATTT
1 ATTATTATTATTTATCTATTATATTATTATTTATTT
544718 ATTTATTAT
1 A-TTATTAT
544727 ATTATTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
34 29 0.69
35 3 0.07
36 3 0.07
37 7 0.17
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (36 bp):
ATTATTATTATTTATCTATTATATTATTATTTATTT
Found at i:544736 original size:23 final size:22
Alignment explanation
Indices: 544652--544735 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 22
544642 GACACAATTA
544652 TTATTAT-TTATCTATTATATTA-
1 TTATTATATTAT-TATTAT-TTAT
544674 TTATTATTATTATTATTATTTAT
1 TTATTA-TATTATTATTATTTAT
*
544697 CTATTATATTATTATTTATTTAT
1 TTATTATATTATTA-TTATTTAT
544720 TTATTATATTATTATT
1 TTATTATATTATTATT
544736 TTGTAGGTCA
Statistics
Matches: 56, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
22 19 0.34
23 33 0.59
24 4 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATTATATTATTATTATTTAT
Found at i:544748 original size:23 final size:23
Alignment explanation
Indices: 544676--544748 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
544666 TTATATTATT
*
544676 ATTATTATTATTA-TTATTTA-TC
1 ATTA-TATTATTATTTATGTAGTC
* * *
544698 TATTATATTATTATTTATTTATTT
1 -ATTATATTATTATTTATGTAGTC
544722 ATTATATTATTATTT-TGTAGGTC
1 ATTATATTATTATTTATGTA-GTC
544745 ATTA
1 ATTA
544749 CAAAGACTCA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
22 11 0.26
23 31 0.72
24 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (23 bp):
ATTATATTATTATTTATGTAGTC
Found at i:545244 original size:23 final size:22
Alignment explanation
Indices: 545218--545261 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
545208 CATTAAGTTA
545218 TAAAAAAAGAAACAG-AGATAAAT
1 TAAAAAAA-AAA-AGTAGATAAAT
*
545241 TAAAGAAAAAAAGTAGATAAA
1 TAAAAAAAAAAAGTAGATAAA
545262 AAGAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 2 0.11
22 10 0.53
23 7 0.37
ACGTcount: A:0.70, C:0.02, G:0.14, T:0.14
Consensus pattern (22 bp):
TAAAAAAAAAAAGTAGATAAAT
Found at i:546112 original size:2 final size:2
Alignment explanation
Indices: 546105--546132 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
546095 ATTTTCTTCA
546105 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
546133 GTTAAGTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:554075 original size:2 final size:2
Alignment explanation
Indices: 554068--554099 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
554058 AATGTCAAGC
554068 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
554100 ACTTATATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:557839 original size:19 final size:19
Alignment explanation
Indices: 557815--557864 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
557805 ATCCAAAGGA
*
557815 TCGATCTTTT-TTAAGTGG
1 TCGATCTTTTGTTAAGCGG
557833 TTCGATCTTTGTGTTAAGCGG
1 -TCGATCTTT-TGTTAAGCGG
557854 TCGATCTTTTG
1 TCGATCTTTTG
557865 AGCAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.39
20 10 0.36
21 7 0.25
ACGTcount: A:0.14, C:0.14, G:0.24, T:0.48
Consensus pattern (19 bp):
TCGATCTTTTGTTAAGCGG
Found at i:557864 original size:21 final size:21
Alignment explanation
Indices: 557815--557862 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
557805 ATCCAAAGGA
*
557815 TCGATCTTT-T-TTAAGTGGT
1 TCGATCTTTGTGTTAAGCGGT
557834 TCGATCTTTGTGTTAAGCGG-
1 TCGATCTTTGTGTTAAGCGGT
557854 TCGATCTTT
1 TCGATCTTT
557863 TGAGCAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 9 0.35
20 10 0.38
21 7 0.27
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.48
Consensus pattern (21 bp):
TCGATCTTTGTGTTAAGCGGT
Found at i:561470 original size:28 final size:28
Alignment explanation
Indices: 561415--561470 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
561405 TTGATCCATA
561415 ATATTTTGAGTTTGAATTTGTAAACCTT
1 ATATTTTGAGTTTGAATTTGTAAACCTT
561443 ATATTTTGAGTTTGAATTTGTAAACCTT
1 ATATTTTGAGTTTGAATTTGTAAACCTT
561471 CATCTTTGTG
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:0.29, C:0.07, G:0.14, T:0.50
Consensus pattern (28 bp):
ATATTTTGAGTTTGAATTTGTAAACCTT
Found at i:561478 original size:28 final size:28
Alignment explanation
Indices: 561419--561478 Score: 95
Period size: 28 Copynumber: 2.1 Consensus size: 28
561409 TCCATAATAT
*
561419 TTTGAGTTTGAATTTGTAAACCTTATAT
1 TTTGAGTTTGAATTTGTAAACCTTATAC
561447 TTTGAGTTTGAATTTGTAAACCTTCAT-C
1 TTTGAGTTTGAATTTGTAAACCTT-ATAC
561475 TTTG
1 TTTG
561479 TGATCTCATG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.25, C:0.10, G:0.15, T:0.50
Consensus pattern (28 bp):
TTTGAGTTTGAATTTGTAAACCTTATAC
Found at i:565649 original size:20 final size:20
Alignment explanation
Indices: 565624--565673 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
565614 ATCCAAATGA
565624 TCGATCCTTT-T-TTAAGGGG
1 TCGATCCTTTGTGTTAA-GGG
565643 TTCGAT-CTTTGTGTTAAGGG
1 -TCGATCCTTTGTGTTAAGGG
565663 TCGATCCTTTG
1 TCGATCCTTTG
565674 AGCCAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 9 0.33
20 14 0.52
21 4 0.15
ACGTcount: A:0.14, C:0.16, G:0.26, T:0.44
Consensus pattern (20 bp):
TCGATCCTTTGTGTTAAGGG
Found at i:571728 original size:174 final size:172
Alignment explanation
Indices: 571398--571744 Score: 644
Period size: 174 Copynumber: 2.0 Consensus size: 172
571388 TAAAACTAAG
571398 TATATTTATATTAATTAAAAAAATAATAAATTATATTACACTTTGGATAATGTAATGTAATATCA
1 TATATTTATATTAATTAAAAAAATAATAAATTATATTACACTTTGGATAATGTAATGTAATATCA
571463 TCTATATTCATTATGAACAAATATTTTGAAGTAGAAATTATAAAAAAAGGCATAATGTCAATTAA
66 TCTATATTCATTATGAACAAATATTTTGAAGTAGAAATTATAAAAAAAGGCATAATGTCAATTAA
571528 CCTCCAGCATTTACTTAAATATTCATTTTGCCCTTTATTTTA
131 CCTCCAGCATTTACTTAAATATTCATTTTGCCCTTTATTTTA
571570 TATATTTATATTAAATTAATAAAAATAATAAATTATATTACACTTTGGATAATGTAATGTAATAT
1 TATATTTATATT-AATTAA-AAAAATAATAAATTATATTACACTTTGGATAATGTAATGTAATAT
571635 CATCTATATTCATTATGAACAAATATTTTGAAGTAGAAATTATAAAAAAAGGCATAATGTCAAAA
64 CATCTATATTCATTATGAACAAATATTTTGAAGTAGAAATTATAAAAAAAGGCATAATGTC--AA
571700 TTAACCTCCAGCATTTACTT-AA-ATTCATTTTGCCCTTTATTTTA
127 TTAACCTCCAGCATTTACTTAAATATTCATTTTGCCCTTTATTTTA
571744 T
1 T
571745 TTTTAATGTT
Statistics
Matches: 171, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
172 12 0.07
173 6 0.04
174 129 0.75
175 2 0.01
176 22 0.13
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.40
Consensus pattern (172 bp):
TATATTTATATTAATTAAAAAAATAATAAATTATATTACACTTTGGATAATGTAATGTAATATCA
TCTATATTCATTATGAACAAATATTTTGAAGTAGAAATTATAAAAAAAGGCATAATGTCAATTAA
CCTCCAGCATTTACTTAAATATTCATTTTGCCCTTTATTTTA
Found at i:571946 original size:19 final size:17
Alignment explanation
Indices: 571902--571937 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
571892 GTTAACTAAT
571902 AGTTTTCATCTATAAAG
1 AGTTTTCATCTATAAAG
571919 AGTTTTCATCTATAAAG
1 AGTTTTCATCTATAAAG
571936 AG
1 AG
571938 AGTTTTCATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (17 bp):
AGTTTTCATCTATAAAG
Found at i:572695 original size:44 final size:47
Alignment explanation
Indices: 572589--572695 Score: 132
Period size: 47 Copynumber: 2.3 Consensus size: 47
572579 CACGTAGAGG
* * *
572589 TATAGCGCGGGGCAGGGGCCATGCCTTACCTTTAATTCTGAATTATA
1 TATAGCGCGGGGCAGGGGCCACGCCATACCTTTAATTATGAATTATA
*
572636 TATAGCGCGGGGCAGGGGCCGCGCCATACCTTT-A-TAT-AATTATA
1 TATAGCGCGGGGCAGGGGCCACGCCATACCTTTAATTATGAATTATA
*
572680 TA-AGGCGCGGTGCAGG
1 TATA-GCGCGGGGCAGG
572696 TATCGCGCCT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 20 0.37
45 2 0.04
46 1 0.02
47 30 0.56
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.25
Consensus pattern (47 bp):
TATAGCGCGGGGCAGGGGCCACGCCATACCTTTAATTATGAATTATA
Found at i:587435 original size:3 final size:3
Alignment explanation
Indices: 587429--587454 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
587419 GAAGAAGGTC
587429 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
587455 TGCGCGAGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:587971 original size:29 final size:30
Alignment explanation
Indices: 587936--587999 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
587926 TTAAGTAGCT
587936 TTTAATCCTTCA-CTTTATATTT-TTTTTAA
1 TTTAAT-CTTCATCTTTATATTTATTTTTAA
* * *
587965 TTTAATCTTTATTTTTATTTTTATTTTTAA
1 TTTAATCTTCATCTTTATATTTATTTTTAA
587995 TTTAA
1 TTTAA
588000 GTAATTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 14 0.47
30 12 0.40
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTAATCTTCATCTTTATATTTATTTTTAA
Found at i:588305 original size:19 final size:21
Alignment explanation
Indices: 588268--588314 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
588258 TAATTTTCAA
*
588268 AAATAA-TATTCAATATTAT-
1 AAATAATTATTAAATATTATC
588287 AAATAATTATTAAAT-TTATC
1 AAATAATTATTAAATATTATC
588307 AAA-AATTA
1 AAATAATTA
588315 ACAACTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 15 0.60
20 10 0.40
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
AAATAATTATTAAATATTATC
Found at i:591138 original size:23 final size:23
Alignment explanation
Indices: 591106--591151 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
591096 AAGATATTCA
*
591106 CAATGGCAATTGGTAATTATCAT
1 CAATGACAATTGGTAATTATCAT
591129 CAATGACAATTGGTAATTATCAT
1 CAATGACAATTGGTAATTATCAT
591152 GATTCATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (23 bp):
CAATGACAATTGGTAATTATCAT
Found at i:593310 original size:103 final size:103
Alignment explanation
Indices: 593131--593330 Score: 332
Period size: 103 Copynumber: 1.9 Consensus size: 103
593121 AAACAGGCCG
*
593131 GGTCAAGTCGGAATCATCGAGTTCGGGTCTCATGCACATTCCTACTTATTCTCATCTTTCAATTC
1 GGTCAAGTCGGAATCATCGAGTTCAGGTCTCATGCACATTCCTACTTATTCTCATCTTTCAATTC
593196 ATCAATTAATAAAAACCTTTTCCAAATTCCAATCTTTA
66 ATCAATTAATAAAAACCTTTTCCAAATTCCAATCTTTA
* *
593234 GGTCAAGTCGGAATCGTCGAGTTCAGGTCTCATG-TC-TATCCTTACTTATTCTCATCTTTCAAT
1 GGTCAAGTCGGAATCATCGAGTTCAGGTCTCATGCACAT-TCC-TACTTATTCTCATCTTTCAAT
*
593297 TCATCGATTAATAAAAACCTTTTCCAAATTCCAA
64 TCATCAATTAATAAAAACCTTTTCCAAATTCCAA
593331 AATAATTTTT
Statistics
Matches: 91, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
101 1 0.01
102 4 0.04
103 86 0.95
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (103 bp):
GGTCAAGTCGGAATCATCGAGTTCAGGTCTCATGCACATTCCTACTTATTCTCATCTTTCAATTC
ATCAATTAATAAAAACCTTTTCCAAATTCCAATCTTTA
Found at i:595009 original size:22 final size:22
Alignment explanation
Indices: 594967--595009 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
594957 GTTATTAAGA
* *
594967 TTCAAGGATGTGTGTATTTATT
1 TTCAAGGATGTGTGAACTTATT
594989 TTCAAGGAT-TGCTGAACTTAT
1 TTCAAGGATGTG-TGAACTTAT
595010 GCTTGTCATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (22 bp):
TTCAAGGATGTGTGAACTTATT
Found at i:597992 original size:3 final size:3
Alignment explanation
Indices: 597984--598047 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
597974 AAAAAATATG
* **
597984 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
598028 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
598048 CGATAAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:598022 original size:32 final size:32
Alignment explanation
Indices: 597986--598053 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
597976 AAAATATGTA
*
597986 ATAATAAATAATAATAA-AATAATAAGATAACG
1 ATAAT-AATAATAATAATAATAATAAAATAACG
598018 ATAATAATAATAATAATAATAATAAAATAACG
1 ATAATAATAATAATAATAATAATAAAATAACG
598050 ATAA
1 ATAA
598054 AAAAAACCCG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 11 0.32
32 23 0.68
ACGTcount: A:0.66, C:0.03, G:0.04, T:0.26
Consensus pattern (32 bp):
ATAATAATAATAATAATAATAATAAAATAACG
Found at i:598488 original size:130 final size:130
Alignment explanation
Indices: 598258--598556 Score: 474
Period size: 130 Copynumber: 2.3 Consensus size: 130
598248 GTGACATGGT
* * ** * *
598258 TCCTACGTGATGAGGAAATCTGGTCAAGGGTTGACACTGCTCATACGTGATGAAGAGTTCTTGGC
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGC
*
598323 CATCTTAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAGC
66 CATCTAAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAGC
598388 TCCTACGTGATGAAGAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTC-TGG
1 TCCTACGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTTGG
* * * *
598452 CCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGG
65 CCATCTAAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAG
598517 C
130 C
*
598518 TCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGG
1 TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGG
598557 TTCCTACATA
Statistics
Matches: 156, Mismatches: 12, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
129 9 0.06
130 119 0.76
131 28 0.18
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (130 bp):
TCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTTGGC
CATCTAAAGGTGATAACACGGTTCCTACATAATGAGGACGGCTGGTTATCTACGGTTGACACAGC
Found at i:598504 original size:46 final size:45
Alignment explanation
Indices: 598291--598541 Score: 128
Period size: 43 Copynumber: 5.7 Consensus size: 45
598281 TCAAGGGTTG
* * ** **
598291 ACACTGCTCATACGTGATGAAGAGTTCTTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGAGC-TGGTTATC-TAAGGTGATA
* * * * * *
598338 ACACGGTTCCTACATAATGAGGACG-GCTGGTTATCTACGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
* * * *
598381 ACACAGCTCCTACGTGATGAAGAGATCTGG---TCT--GGGGAATG
1 ACACGGCTCCTACGTGATGAAGAGAGCTGGTTATCTAAGGTG-ATA
* ** **
598422 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGAGAGCTGGTTATCT-AAGGTGATA
* * * *
598468 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGT--TG
1 ACACGGCTCCTACGTGATGAAGA-GAGCTGGTTATCTAAGGTGATA
* *
598511 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCCTACGTGATGAAGAGAGCTGGT
598542 CTGGGGATGA
Statistics
Matches: 156, Mismatches: 35, Indels: 30
0.71 0.16 0.14
Matches are distributed among these distances:
38 2 0.01
40 3 0.02
41 29 0.19
42 2 0.01
43 49 0.31
44 3 0.02
45 9 0.06
46 36 0.23
47 22 0.14
48 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (45 bp):
ACACGGCTCCTACGTGATGAAGAGAGCTGGTTATCTAAGGTGATA
Found at i:598540 original size:89 final size:83
Alignment explanation
Indices: 598420--598580 Score: 223
Period size: 83 Copynumber: 1.9 Consensus size: 83
598410 GTCTGGGGAA
* * * *
598420 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATAACACGGTTCCTACATAA
598485 TGAGGACGGCTGGTTATCTATGGT
60 TGAGGACGGCTGGTTATCTATGGT
*
598509 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATAATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATAATGAGGA
598574 CGGCTGG
66 CGGCTGG
598581 CCATCTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
83 33 0.49
86 3 0.04
89 31 0.46
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCTGGGGATAACACGGTTCCTACATAATGAGGA
CGGCTGGTTATCTATGGT
Found at i:598654 original size:28 final size:28
Alignment explanation
Indices: 598623--598680 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
598613 CAAATTAAAT
598623 ATTTGTTTCAA-AAGAAACAAACCCAAAG
1 ATTTGTTTCAAGAA-AAACAAACCCAAAG
* *
598651 ATTTGTTTCAAGAAAAATAAACTCAAAG
1 ATTTGTTTCAAGAAAAACAAACCCAAAG
598679 AT
1 AT
598681 GATATTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (28 bp):
ATTTGTTTCAAGAAAAACAAACCCAAAG
Found at i:598746 original size:65 final size:64
Alignment explanation
Indices: 598687--598811 Score: 162
Period size: 64 Copynumber: 2.0 Consensus size: 64
598677 AGATGATATT
* * *
598687 TTTAAA-AGCAACTGTCTCAAAAAAGACCAAATTCGTTTTAAGGGAAACGACTCAAAGATGACG
1 TTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGATGACG
* ** **
598750 TTTAAAGGGAAACTGTCTCAAATGAGACAAAATTCGTTTAAAGGGAATTGATCTCAAAGATG
1 TTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTCGTTTAAAGGGAAACGA-CTCAAAGATG
598812 TTTGTTTTGT
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
63 6 0.12
64 36 0.69
65 10 0.19
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (64 bp):
TTTAAAGAGAAACTGTCTCAAAAAAGACAAAATTCGTTTAAAGGGAAACGACTCAAAGATGACG
Found at i:599039 original size:15 final size:15
Alignment explanation
Indices: 599015--599073 Score: 100
Period size: 15 Copynumber: 3.9 Consensus size: 15
599005 AAGATGATCT
*
599015 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
599030 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
599045 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
599060 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
599074 CGACTCAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:599301 original size:62 final size:63
Alignment explanation
Indices: 599230--599353 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
599220 AATGTGGGTA
* *
599230 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTATTT-CAAAGGAAACAAACTCAAAGATT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTATTTCCAAA-GAAACAAACTCAAAGATT
* * * * *
599292 TTTTCAAAAGAAATTGTCTTTAAGAGATAAAATTTTGTTTCCAAAGAAAGAGACTCAAAGAT
1 TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGAT
599354 GGATTACATC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
62 17 0.32
63 32 0.60
64 4 0.08
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.31
Consensus pattern (63 bp):
TTTTCAAAAGAAATTGTCTTCAAGAGACAAAATTTTATTTCCAAAGAAACAAACTCAAAGATT
Found at i:599499 original size:30 final size:28
Alignment explanation
Indices: 599448--599504 Score: 69
Period size: 30 Copynumber: 2.0 Consensus size: 28
599438 GACAACATTC
* * *
599448 ATTTTTTAAAGAAATAGACTCACAGATG
1 ATTTTTTAAAGAAACAAACTCAAAGATG
599476 ATTTTGTTAAGAGAAACAAACTCAAAGAT
1 ATTTT-TTAA-AGAAACAAACTCAAAGAT
599505 TTTCAAAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 4 0.17
30 15 0.62
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.30
Consensus pattern (28 bp):
ATTTTTTAAAGAAACAAACTCAAAGATG
Found at i:599633 original size:37 final size:37
Alignment explanation
Indices: 599587--599713 Score: 112
Period size: 37 Copynumber: 3.6 Consensus size: 37
599577 GAAACAGATT
*
599587 CAAAGATTTTTTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGATTTTGTTTCAAAAGAAA-TATCTTAAGAGAGA
* **
599625 CAAA-ATTTTGTTTCCAAAG-AA-A-C---A-A-ACT
1 CAAAGATTTTGTTTCAAAAGAAATATCTTAAGAGAGA
599653 CAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAGAAA-TATCTTAAGAGAGA
*
599692 CAAA-ATTTTGTTTCCAAAGAAA
1 CAAAGATTTTGTTTCAAAAGAAA
599714 CAAACTCAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
28 5 0.07
29 2 0.03
30 14 0.20
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 30 0.43
38 6 0.09
39 5 0.07
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (37 bp):
CAAAGATTTTGTTTCAAAAGAAATATCTTAAGAGAGA
Found at i:599682 original size:67 final size:66
Alignment explanation
Indices: 599534--599731 Score: 276
Period size: 67 Copynumber: 3.0 Consensus size: 66
599524 AAGGATTTAC
* * * * * * *
599534 TTCAAAAGAGACTGTCTCAAGAGATACAAAATTCAT-TTT--AAGAGAAACAGATTCAAAGATTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATT-TTGTTTCCAA-AGAAACAAACTCAAAGATTT
599596 TTT
64 TTT
*
599599 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
599664 GT
66 -T
599666 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
599731 T
66 T
599732 GAAAAGAAAC
Statistics
Matches: 120, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.01
65 31 0.26
66 21 0.17
67 67 0.56
ACGTcount: A:0.44, C:0.13, G:0.12, T:0.31
Consensus pattern (66 bp):
TTCAAAAGAAACTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
T
Found at i:599737 original size:27 final size:27
Alignment explanation
Indices: 599707--599758 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
599697 TTTTGTTTCC
599707 AAAGAAACAAACTCAAAGATTTTTTGA
1 AAAGAAACAAACTCAAAGATTTTTTGA
*
599734 AAAGAAACAATCTCAAAGATTTTTT
1 AAAGAAACAAACTCAAAGATTTTTT
599759 TTCACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.29
Consensus pattern (27 bp):
AAAGAAACAAACTCAAAGATTTTTTGA
Found at i:599892 original size:25 final size:27
Alignment explanation
Indices: 599846--599939 Score: 111
Period size: 28 Copynumber: 3.4 Consensus size: 27
599836 AAAACTTTGT
* *
599846 TTCAAAATAAATAGACTCAAAGATTT-
1 TTCAAAAGAAACAGACTCAAAGATTTA
599872 TTCAAAAGAAACA-ACTCAAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGA--TTTA
*
599900 TTCAAAAGGAACAGACTCAAAGATTTA
1 TTCAAAAGAAACAGACTCAAAGATTTA
*
599927 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
599940 TGTCTCCAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
25 9 0.16
26 11 0.19
27 8 0.14
28 21 0.36
29 9 0.16
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.26
Consensus pattern (27 bp):
TTCAAAAGAAACAGACTCAAAGATTTA
Found at i:600268 original size:36 final size:36
Alignment explanation
Indices: 600184--600287 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
600174 GAGAAAATGA
* * *
600184 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAAT
* **
600218 AGTCTCAAATGAGACAAAGTTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAAT
600254 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAA
600288 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 19 0.32
35 10 0.17
36 30 0.51
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAGTTTGTTTTTAGAGAAAT
Found at i:600315 original size:36 final size:36
Alignment explanation
Indices: 600185--600303 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
600175 AGAAAATGAT
* * * *
600185 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGA-AAAC
* **
600219 GTCTCAAATGAGACAAAGTTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGAAAAC
*
600255 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGAAAAC
600290 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
600304 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 19 0.27
35 12 0.17
36 39 0.56
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAGTTTGTTTTTAGAGAAAAC
Found at i:600317 original size:70 final size:69
Alignment explanation
Indices: 600184--600315 Score: 151
Period size: 70 Copynumber: 1.9 Consensus size: 69
600174 GAGAAAATGA
* *
600184 TGTCTCAAGCGAGACAAAATTTGCTTTAAGATATAGTCTCAAATGAGACAAAGTTTGTTTTTAGA
1 TGTCTCAAGCGAGACAAAATTTGCTTTAAGATAAAGTCTCAAATGAGACAAACTTTG-TTTTAGA
600249 GAAAT
65 GAAAT
* * * *
600254 TGTCTCAAGCGAGACAAAGTTTGTTTTTGAGA-AAACGATCTCAAGTGAGATC-AACTTTGTTT
1 TGTCTCAAGCGAGACAAAATTTG-CTTTAAGATAAA-G-TCTCAAATGAGA-CAAACTTTGTTT
600316 AGTGTGAAAC
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
70 24 0.46
71 10 0.19
72 17 0.33
73 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (69 bp):
TGTCTCAAGCGAGACAAAATTTGCTTTAAGATAAAGTCTCAAATGAGACAAACTTTGTTTTAGAG
AAAT
Found at i:600434 original size:105 final size:104
Alignment explanation
Indices: 600255--600494 Score: 301
Period size: 105 Copynumber: 2.3 Consensus size: 104
600245 TAGAGAAATT
* *
600255 GTCTCAAGCGAGAC-AAAGTTTGTTTT-TGAG-AAAACGATCTCAAGTGAGATCAACTTTGTTTA
1 GTCTCAAGCGAGACGAAA-TTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTA
* * *
600317 GTGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 GAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* * *
600357 GTCTCAAGCGAGACGAAATTTGTTTTAAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
600421 TA-AGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
63 TAGAGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
600462 GTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAA
1 GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAA
600495 TTTGTCTCAA
Statistics
Matches: 119, Mismatches: 13, Indels: 9
0.84 0.09 0.06
Matches are distributed among these distances:
102 22 0.18
103 5 0.04
104 4 0.03
105 84 0.71
106 4 0.03
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (104 bp):
GTCTCAAGCGAGACGAAATTTGTTTTAAGAGAAAAACAATCTCAAGTGAGATCAACTTTGTTTAG
AGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:600501 original size:36 final size:36
Alignment explanation
Indices: 600461--600597 Score: 170
Period size: 36 Copynumber: 3.8 Consensus size: 36
600451 AAAGGAAAAA
* * *
600461 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
* * **
600497 TGTCTCAAACGAGACAAAATTTGTTTTTAGA-AAGC
1 TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
*
600532 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAAT
1 TGTCTCAAGCGAGACAAAATTTG-TTTTAAGAGAAAT
600568 TGTCTCAAGCGAGACAAAAATTTGTTTTAA
1 TGTCTCAAGCGAGAC-AAAATTTGTTTTAA
600598 AATTCTCAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
35 25 0.29
36 53 0.62
37 8 0.09
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTAAGAGAAAT
Found at i:600571 original size:71 final size:72
Alignment explanation
Indices: 600461--600595 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 72
600451 AAAGGAAAAA
* * * *
600461 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATTTGTCTCAAACGAGAC-AAAATTTGTTTTT
1 TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
600525 AGAAAGC
66 AGAAAGC
*
600532 TGTCTCAAGCGAGACAAAATTTGCTTTGAA-AGAAATTGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGCGAGACAAAATTTG-TTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTT
600596 AAAATTCTCA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
71 40 0.70
72 17 0.30
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.32
Consensus pattern (72 bp):
TGTCTCAAGCGAGACAAAATTTGTTTGAAGAGAAATTGTCTCAAACGAGACAAAAATTTGTTTTT
AGAAAGC
Found at i:600979 original size:20 final size:20
Alignment explanation
Indices: 600954--601001 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
600944 TGTAACATGC
600954 ATGTATGTGTTGATGTATGT
1 ATGTATGTGTTGATGTATGT
*
600974 ATGTATGAGTTGATGTATGT
1 ATGTATGTGTTGATGTATGT
*
600994 ATATATGT
1 ATGTATGT
601002 ATGTATGAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (20 bp):
ATGTATGTGTTGATGTATGT
Found at i:602223 original size:12 final size:11
Alignment explanation
Indices: 602195--602236 Score: 57
Period size: 12 Copynumber: 3.6 Consensus size: 11
602185 CCTCTTTTTG
*
602195 TTCTTTGCTTT
1 TTCTTTGATTT
602206 TTCTTTGATTT
1 TTCTTTGATTT
602217 TTGCTTTGATTT
1 TT-CTTTGATTT
602229 TCTCTTTG
1 T-TCTTTG
602237 CTCTTTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 12 0.43
12 15 0.54
13 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.12, T:0.69
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:602253 original size:12 final size:12
Alignment explanation
Indices: 602238--602287 Score: 64
Period size: 12 Copynumber: 4.0 Consensus size: 12
602228 TTCTCTTTGC
602238 TCTTTGTTTTTT
1 TCTTTGTTTTTT
*
602250 TCTTTGCTCTTTTC
1 TCTTTG-T-TTTTT
*
602264 TCTTTGATTTTT
1 TCTTTGTTTTTT
602276 TCTTTGTTTTTT
1 TCTTTGTTTTTT
602288 ATTGGATCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 21 0.66
13 1 0.03
14 10 0.31
ACGTcount: A:0.02, C:0.14, G:0.08, T:0.76
Consensus pattern (12 bp):
TCTTTGTTTTTT
Found at i:602260 original size:26 final size:26
Alignment explanation
Indices: 602230--602281 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
602220 CTTTGATTTT
*
602230 CTCTTTGCTCTTTGTTTTTTTCTTTG
1 CTCTTTGCTCTTTGATTTTTTCTTTG
*
602256 CTCTTTTCTCTTTGATTTTTTCTTTG
1 CTCTTTGCTCTTTGATTTTTTCTTTG
602282 TTTTTTATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.02, C:0.19, G:0.10, T:0.69
Consensus pattern (26 bp):
CTCTTTGCTCTTTGATTTTTTCTTTG
Found at i:602280 original size:19 final size:19
Alignment explanation
Indices: 602220--602261 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
602210 TTGATTTTTG
602220 CTTTGATTTTCTCTTTGCT
1 CTTTGATTTTCTCTTTGCT
* *
602239 CTTTGTTTTTTTCTTTGCT
1 CTTTGATTTTCTCTTTGCT
602258 CTTT
1 CTTT
602262 TCTCTTTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.02, C:0.19, G:0.10, T:0.69
Consensus pattern (19 bp):
CTTTGATTTTCTCTTTGCT
Found at i:604381 original size:30 final size:32
Alignment explanation
Indices: 604327--604387 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
604317 TGACAAAATG
604327 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
604359 ACACAAACAAAAGAG-A-AAATAAGTTAGTA
1 ACACAAACAAAAGAGAAGAAATAAGTTAGTA
604388 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 13 0.45
31 1 0.03
32 15 0.52
ACGTcount: A:0.61, C:0.10, G:0.15, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAAGAAATAAGTTAGTAT
Found at i:608247 original size:3 final size:3
Alignment explanation
Indices: 608241--608296 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
608231 AAAAAATATG
* **
608241 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
608285 TAA TAA TAA TAA
1 TAA TAA TAA TAA
608297 AAAAATAACG
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
2 3 0.07
3 38 0.86
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:608296 original size:32 final size:32
Alignment explanation
Indices: 608243--608310 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
608233 AAAATATGTA
* *
608243 ATAATAAATAATAATAAAATAATAAGATAACG
1 ATAATAAATAATAATAAAATAAAAAAATAACG
608275 ATAAT-AATAATAATAATAATAAAAAAATAACG
1 ATAATAAATAATAATAA-AATAAAAAAATAACG
608307 ATAA
1 ATAA
608311 AAAAAACCCG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 11 0.33
32 22 0.67
ACGTcount: A:0.68, C:0.03, G:0.04, T:0.25
Consensus pattern (32 bp):
ATAATAAATAATAATAAAATAAAAAAATAACG
Found at i:612846 original size:67 final size:67
Alignment explanation
Indices: 612740--612866 Score: 168
Period size: 67 Copynumber: 1.9 Consensus size: 67
612730 GATATTATTG
*
612740 AATATAGAGCGAGTTAAAACCAAATGAAAGTCTTTAATTTTTAAATTGAGACATAGGGGTATTAT
1 AATATAGAGCGAGTTAAAACCAAATGAAAGTCTTTAATTTTCAAATTGAGACATAGGGGTATTAT
612805 CA
66 CA
*** * *
612807 AATATAGAGCGAGTTAAATTTATAA-GAAAGT-TTTCAATTTTCGAATTGGGACATAGGGGT
1 AATATAGAGCGAGTTAAAACCA-AATGAAAGTCTTT-AATTTTCAAATTGAGACATAGGGGT
612867 GCAATAGTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 3 0.06
67 47 0.90
68 2 0.04
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (67 bp):
AATATAGAGCGAGTTAAAACCAAATGAAAGTCTTTAATTTTCAAATTGAGACATAGGGGTATTAT
CA
Found at i:613870 original size:203 final size:205
Alignment explanation
Indices: 613231--614139 Score: 1458
Period size: 204 Copynumber: 4.5 Consensus size: 205
613221 ATATATTTAT
*
613231 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATATGCCCAATACGTG
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
* * * *
613296 TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACTGAATCTGATACGACTTTAACTT
66 TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
* *
613361 AAATTTTTAAAAAAAAAATTAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
131 AAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
*
613426 CCCATTCCAG
196 CCCATCCCAG
*
613436 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATT-CCCATGTGCCCAACACGTG
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
* *
613500 TTGTCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAATCGAACCCGATACGACTTGAACTT
66 TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
* *
613565 AATTTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATG
131 AAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
*
613630 CCCATCCCGG
196 CCCATCCCAG
* * *
613640 GGTGCAAATAGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGCGCTCAATACGTG
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
613705 TTGCCGTTTCAGGACCAATGGTTTCA-TTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
66 TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
* *
613769 -AATTTTTTTAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATG
131 AAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
613833 CCCATCCCAG
196 CCCATCCCAG
* *
613843 GGTGCAAATAGGATTTGTGCATTTTGCCA-CTAAAACCCCCCATTTCCCATGTGCCCAATACGTG
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
* * * *
613907 TTTCCGTTTCAAGATCAATGGTTTCATTTTTTCACCCTAAGCCGAACCCGATACGACTTGAACTT
66 TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
* * * *
613972 AAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAAAACCTATCAAGTTTGAGTCTCATA
131 AAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
614037 CCCATCCC--
196 CCCATCCCAG
* *
614045 ---GCAAATGGGATTTATGCATTTTGCCAGCTAAAACCCCCCATTTCACCATGTGCCCAATACGT
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCA-TTCCCCATGTGCCCAATACGT
614107 GTTGCCGTTTCAGGACCAATGGTTTTCATTTTT
65 GTTGCCGTTTCAGGACCAATGG-TTTCATTTTT
614140 CTTTATTTTT
Statistics
Matches: 655, Mismatches: 43, Indels: 15
0.92 0.06 0.02
Matches are distributed among these distances:
199 24 0.04
200 13 0.02
201 38 0.06
202 65 0.10
203 137 0.21
204 292 0.45
205 86 0.13
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (205 bp):
GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
AAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
CCCATCCCAG
Found at i:613988 original size:407 final size:406
Alignment explanation
Indices: 613231--614140 Score: 1472
Period size: 407 Copynumber: 2.2 Consensus size: 406
613221 ATATATTTAT
*
613231 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATATGCCCAATACGTG
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
* * * *
613296 TTGCCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAACTGAATCTGATACGACTTTAACTT
66 TTGCCGTTTCAGGACCAATGGTTTCA-TTTTTCACCCTAAACCGAACCCGATACGACTTGAACTT
*
613361 AAATTTTTAAAAAAAAAATTAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
130 AAATTTTTAAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATA
* *
613426 CCCATTCCAGGGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCATGTGCC
195 CCCATCCCAGGGTGCAAATAGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCATGTGCC
* *
613491 CAACACGTGTTGTCGTTTCAGGACCAATGGTTTCATTTTTTCACCCTAAATCGAACCCGATACGA
260 CAACACGTGTTGTCGTTTCAAGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGA
* * * *
613556 CTTGAACTTAATTTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCG
325 CTTGAACTTAAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAAAACCTATCAAGTTCG
*
613621 AGTCTCATGCCCATCCC
390 AGTCTCATACCCATCCC
* * *
613638 GGGGTGCAAATAGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGCGCTCAATACG
1 --GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACG
613703 TGTTGCCGTTTCAGGACCAATGGTTTCATTTTTCACCCTAAACCGAACCCGATACGACTTGAACT
64 TGTTGCCGTTTCAGGACCAATGGTTTCATTTTTCACCCTAAACCGAACCCGATACGACTTGAACT
**
613768 T-AATTTTTTTAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCAT
129 TAAATTTTTAAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCAT
*
613832 GCCCATCCCAGGGTGCAAATAGGATTTGTGCATTTTGCCA-CTAAAACCCCCCATTTCCCATGTG
194 ACCCATCCCAGGGTGCAAATAGGATTTGTGCATTTTGCCAGCTAAAACCCCCCA-TTCCCATGTG
* * *
613896 CCCAATACGTGTT-TCCGTTTCAAGATCAATGGTTTCATTTTTTCACCCTAAGCCGAACCCGATA
258 CCCAACACGTGTTGT-CGTTTCAAGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATA
613960 CGACTTGAACTTAAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAAAACCTATCAAGT
322 CGACTTGAACTTAAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAAAACCTATCAAGT
*
614025 TTGAGTCTCATACCCATCCC
387 TCGAGTCTCATACCCATCCC
* *
614045 ---GCAAATGGGATTTATGCATTTTGCCAGCTAAAACCCCCCATTTCACCATGTGCCCAATACGT
1 GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCA-TTCCCCATGTGCCCAATACGT
614107 GTTGCCGTTTCAGGACCAATGGTTTTCATTTTTC
65 GTTGCCGTTTCAGGACCAATGG-TTTCATTTTTC
614141 TTTATTTTTT
Statistics
Matches: 467, Mismatches: 30, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
402 38 0.08
403 40 0.09
404 11 0.02
406 14 0.03
407 243 0.52
408 34 0.07
409 87 0.19
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.30
Consensus pattern (406 bp):
GGTGCAAATGGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCCATGTGCCCAATACGTG
TTGCCGTTTCAGGACCAATGGTTTCATTTTTCACCCTAAACCGAACCCGATACGACTTGAACTTA
AATTTTTAAAAAAAAAATCAACTTGACCAAGTCAGATTAGAACCTGTCAGGTTCGAGTCTCATAC
CCATCCCAGGGTGCAAATAGGATTTGTGCATTTTGCCAGCTAAAACCCCCCATTCCCATGTGCCC
AACACGTGTTGTCGTTTCAAGACCAATGGTTTCATTTTTTCACCCTAAACCGAACCCGATACGAC
TTGAACTTAAATTTTTTAAAAAAAAATCAACTTGACCAAGTCAGATTAAAACCTATCAAGTTCGA
GTCTCATACCCATCCC
Found at i:615747 original size:23 final size:22
Alignment explanation
Indices: 615721--615853 Score: 69
Period size: 23 Copynumber: 5.7 Consensus size: 22
615711 TTTATAATAA
615721 TATAATATATATTTTTAATATTT
1 TATAATATATATTTTT-ATATTT
* **
615744 TATAAAATA-ATCAATTATATTAT
1 TATAATATATAT-TTTTATATT-T
*
615767 AATAATATAAGATATTTTT-TATTT
1 TATAATAT---ATATTTTTATATTT
615791 TAATAATATAATATTTTTTATATTT
1 T-ATAATAT-ATA-TTTTTATATTT
*
615816 AATAATGA-ATATTTATTTATATATT
1 TATAAT-ATATA-TT-TTTATAT-TT
615841 TA-AATA-ATATTTT
1 TATAATATATATTTT
615854 AATAAAGATA
Statistics
Matches: 87, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
21 2 0.02
22 9 0.10
23 30 0.34
24 21 0.24
25 20 0.23
26 3 0.03
27 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (22 bp):
TATAATATATATTTTTATATTT
Found at i:615763 original size:31 final size:31
Alignment explanation
Indices: 615699--615774 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 31
615689 AAATATTATT
615699 TATTTATTAATATTTATAATAATATAATATA
1 TATTTATTAATATTTATAATAATATAATATA
615730 TATTT-TTAATATTTTATAA-AATAATCAAT-TA
1 TATTTATTAATA-TTTATAATAAT-AT-AATATA
*
615761 TATTATAATAATAT
1 TATT-TATTAATAT
615775 AAGATATTTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
30 9 0.23
31 20 0.51
32 5 0.13
33 5 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (31 bp):
TATTTATTAATATTTATAATAATATAATATA
Found at i:615770 original size:30 final size:28
Alignment explanation
Indices: 615698--615770 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 28
615688 AAAATATTAT
615698 TTAT-TTATTAATATTTATAATAATATAA
1 TTATATTA-TAATATTTATAATAATATAA
*
615726 TATATATTTTTAATATTTTATAA-AATAATCAA
1 T-TATA-TTATAATA-TTTATAATAAT-AT-AA
615758 TTATATTATAATA
1 TTATATTATAATA
615771 ATATAAGATA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
28 1 0.03
29 3 0.08
30 15 0.41
31 15 0.41
32 3 0.08
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATATTATAATATTTATAATAATATAA
Found at i:615794 original size:25 final size:23
Alignment explanation
Indices: 615722--615835 Score: 92
Period size: 23 Copynumber: 4.8 Consensus size: 23
615712 TTATAATAAT
615722 ATAATAT-ATATTTTTAATATTTT-
1 ATAATATAATATTTTT--TATTTTA
* * * *
615745 ATAAAATAATCA-ATTATATTATA
1 ATAATATAAT-ATTTTTTATTTTA
615768 ATAATATAAGATATTTTTTATTTTA
1 ATAATAT-A-ATATTTTTTATTTTA
615793 ATAATATAATATTTTTTATATTTA
1 ATAATATAATATTTTTTAT-TTTA
*
615817 ATAAT-GAATATTTATTTAT
1 ATAATATAATATTT-TTTAT
615836 ATATTTAAAT
Statistics
Matches: 74, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
22 5 0.07
23 30 0.41
24 21 0.28
25 18 0.24
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.54
Consensus pattern (23 bp):
ATAATATAATATTTTTTATTTTA
Found at i:615854 original size:24 final size:24
Alignment explanation
Indices: 615779--615854 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
615769 TAATATAAGA
* **
615779 TATTTTTTAT-TTTAATAATATAA
1 TATTTTATATATTTAATAATATTT
*
615802 TATTTTTTATATTTAATAATGAATATT
1 TATTTTATATATTTAATAAT--AT-TT
615829 TA-TTTATATATTTAAATAATATTT
1 TATTTTATATATTT-AATAATATTT
615853 TA
1 TA
615855 ATAAAGATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 10 0.22
24 13 0.29
25 2 0.04
26 12 0.27
27 8 0.18
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (24 bp):
TATTTTATATATTTAATAATATTT
Found at i:615872 original size:23 final size:23
Alignment explanation
Indices: 615853--615900 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
615843 AATAATATTT
615853 TAATAAAGATATTTAAAATATAA
1 TAATAAAGATATTTAAAATATAA
* * *
615876 TAATTAATATTTTTAAAATATAA
1 TAATAAAGATATTTAAAATATAA
615899 TA
1 TA
615901 TAACACTATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAA
Found at i:616021 original size:30 final size:28
Alignment explanation
Indices: 615954--616013 Score: 86
Period size: 27 Copynumber: 2.1 Consensus size: 28
615944 TTTATTTCAC
* *
615954 TAAAATATACAAAAATTATTATTTATTAA
1 TAAAAT-TATAAAAATTATTATTTAATAA
615983 TAAAATTATAAAAATTA-TATTTAATAA
1 TAAAATTATAAAAATTATTATTTAATAA
616010 TAAA
1 TAAA
616014 TAAATTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 13 0.45
28 10 0.34
29 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAAATTATAAAAATTATTATTTAATAA
Found at i:616229 original size:14 final size:14
Alignment explanation
Indices: 616195--616235 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
616185 AAATGTAATT
*
616195 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
616209 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
* *
616223 CGTTTTCCAGAAA
1 CATTTTCCGGAAA
616236 TGTAATTCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.29
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:616258 original size:14 final size:15
Alignment explanation
Indices: 616237--616282 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
616227 TTCCAGAAAT
616237 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
** *
616252 G-AATTCAAATTCTA
1 GTAATTCATTTTCCA
616266 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
616281 GT
1 GT
616283 TCCACTAATT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.30, C:0.17, G:0.09, T:0.43
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:616262 original size:20 final size:20
Alignment explanation
Indices: 616225--616263 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
616215 CCGGAAAACG
**
616225 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATCAAATTCA
*
616245 TTTTCCAGAATTCAAATTC
1 TTTTCCAGAAATCAAATTC
616264 TAGTAATTCA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATCAAATTCA
Found at i:616676 original size:49 final size:49
Alignment explanation
Indices: 616604--616698 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
616594 AGCGCGTGTT
*
616604 CAGGGGCGGACCTCCATGGTGCCCAAGGTATCCTAGGCAACCCCTCATC
1 CAGGGGCGGACCTCCATGGTGCCCAAGGTATCCCAGGCAACCCCTCATC
**
616653 CAGGGGCGGACCT-CAGTGGTGCCCGGGGTATCCCAGGCAACCCCTC
1 CAGGGGCGGACCTCCA-TGGTGCCCAAGGTATCCCAGGCAACCCCTC
616699 CACAAGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
48 2 0.05
49 40 0.95
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.15
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGGTGCCCAAGGTATCCCAGGCAACCCCTCATC
Found at i:619313 original size:20 final size:20
Alignment explanation
Indices: 619288--619340 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
619278 TTTATGCTGG
* *
619288 TATCGATACTGATATTTTAA
1 TATCGATACTGACATTTCAA
619308 TATCGATACTGACATTTCAA
1 TATCGATACTGACATTTCAA
*
619328 TATCGGTACTGAC
1 TATCGATACTGAC
619341 CCTTTAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (20 bp):
TATCGATACTGACATTTCAA
Found at i:628630 original size:15 final size:15
Alignment explanation
Indices: 628610--628638 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
628600 TGGCCGACCG
628610 AACCGAATTAACCAT
1 AACCGAATTAACCAT
628625 AACCGAATTAACCA
1 AACCGAATTAACCA
628639 AACTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.28, G:0.07, T:0.17
Consensus pattern (15 bp):
AACCGAATTAACCAT
Found at i:629010 original size:184 final size:183
Alignment explanation
Indices: 628767--629153 Score: 609
Period size: 184 Copynumber: 2.1 Consensus size: 183
628757 TTTTCTAATT
* * * * * *
628767 TATATAA-AAATTAAATATTTTTTAATTCAAAAAAAGTTTATAATTAATTTAAGTAATATATAAT
1 TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
*
628831 TATAAAAT-AAAAATTTAGATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTATT
66 TATAAAATAAAAAATTTAGAT-AATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
* * *
628895 GGATTTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTT-AACCCATATGTTA
130 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGG-TTGAACCCATATGTTA
628949 TATATAATATATTTAATATTTTTTAATTAAAAAAATAGTTTACAAATAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTTTAATTAAAAAAA-AGTTTACAAATAATTTAAATAATATATAA
*
629014 TTATAAAATAAAAAATTTATATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
65 TTATAAAATAAAAAATTTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATT
*
629079 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGTTGAGCCCATATGTTA
130 GGATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGTTGAACCCATATGTTA
*
629133 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
629154 AAAATTTAAT
Statistics
Matches: 188, Mismatches: 13, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
182 7 0.04
183 26 0.14
184 144 0.77
185 11 0.06
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (183 bp):
TATATAATATATTTAATATTTTTTAATTAAAAAAAAGTTTACAAATAATTTAAATAATATATAAT
TATAAAATAAAAAATTTAGATAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAATTATTG
GATCTTAAATTATTAATTAGGTTTTAAATGATTTGGGTTGAACCCATATGTTA
Found at i:630424 original size:5 final size:5
Alignment explanation
Indices: 630416--630442 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
630406 TTCTCTTCTA
630416 TTTTC TTTTC TTTTC TTTTC TTTTC TT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TT
630443 ATATTTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTC
Done.