Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold142
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: 1427168
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 17476 characters in sequence are not A, C, G, or T
File 3 of 8
Found at i:504116 original size:4 final size:4
Alignment explanation
Indices: 504107--504194 Score: 85
Period size: 4 Copynumber: 23.0 Consensus size: 4
504097 TGTATTTATG
* * *
504107 CATA CATA CATA CATA CATA CATA TATA TATA CATA CAT- -ATA TATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
* * * *
504153 CATA CATA TATA TATA C--A CATA CATA CATA TATA TATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
504195 TACACAAACA
Statistics
Matches: 73, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
2 4 0.05
4 69 0.95
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (4 bp):
CATA
Found at i:504128 original size:16 final size:16
Alignment explanation
Indices: 504107--504194 Score: 108
Period size: 16 Copynumber: 5.5 Consensus size: 16
504097 TGTATTTATG
*
504107 CATACATACATACATA
1 CATACATACATATATA
*
504123 CATACATATATATATA
1 CATACATACATATATA
504139 CATACAT--ATATATA
1 CATACATACATATATA
*
504153 CATACATATATATATACA
1 CATACATACATATAT--A
504171 CATACATACATATATA
1 CATACATACATATATA
*
504187 TATACATA
1 CATACATA
504195 TACACAAACA
Statistics
Matches: 64, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
14 14 0.22
16 35 0.55
18 15 0.23
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (16 bp):
CATACATACATATATA
Found at i:504176 original size:22 final size:22
Alignment explanation
Indices: 504150--504198 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
504140 ATACATATAT
504150 ATACATACATATATATATACAC
1 ATACATACATATATATATACAC
*
504172 ATACATACATATATATATACAT
1 ATACATACATATATATATACAC
504194 ATACA
1 ATACA
504199 CAAACACACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
ATACATACATATATATATACAC
Found at i:507322 original size:105 final size:107
Alignment explanation
Indices: 507130--507338 Score: 264
Period size: 105 Copynumber: 2.0 Consensus size: 107
507120 CTAATGCAGC
* * *
507130 ATCCTCATCTTGGCCTGGGGTCCCGCCTCTTCTTCTCCTCGTGCTCGTATCTGTGCTTACTAGCC
1 ATCCTCATCTTGGCCTGGGGT-CCGCCTCTTCTACTCCTCGTGCTCATATCTGTGCTTACCAGCC
* ** *
507195 GTGAAAGATCCTCTGTCCGCAGCCTT-TCAGCCGATGCTGCTAA
65 GCGAAAGATCCTCCCTCCGCAGCCTTGT-AGCCAATGCTGCTAA
* *
507238 ATCCTCATCTTGGCTTGGGGT-C-CCTCTTCTACTCCTCGTTCTCATAT-TCGTGCTTACCAGCC
1 ATCCTCATCTTGGCCTGGGGTCCGCCTCTTCTACTCCTCGTGCTCATATCT-GTGCTTACCAGCC
* *
507300 GCGAACGATCCTCCCTCTGCAGCCTTGTAGCCAATGCTG
65 GCGAAAGATCCTCCCTCCGCAGCCTTGTAGCCAATGCTG
507339 GATCCTGATC
Statistics
Matches: 88, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
104 1 0.01
105 65 0.74
106 2 0.02
108 20 0.23
ACGTcount: A:0.13, C:0.35, G:0.20, T:0.32
Consensus pattern (107 bp):
ATCCTCATCTTGGCCTGGGGTCCGCCTCTTCTACTCCTCGTGCTCATATCTGTGCTTACCAGCCG
CGAAAGATCCTCCCTCCGCAGCCTTGTAGCCAATGCTGCTAA
Found at i:513367 original size:27 final size:26
Alignment explanation
Indices: 513331--513389 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
513321 TCATTAAAAA
*
513331 TTTTAAATTAATAAATAA-ATTAATATT
1 TTTTATATT-ATAAA-AATATTAATATT
*
513358 TTTTATATTATAAAAATTTTAATATT
1 TTTTATATTATAAAAATATTAATATT
513384 TTTTAT
1 TTTTAT
513390 TTTACTTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 2 0.07
26 19 0.66
27 8 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTTATATTATAAAAATATTAATATT
Found at i:515040 original size:17 final size:17
Alignment explanation
Indices: 514992--515045 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
514982 TTTCTTTTGC
*
514992 AAATTTTAATTTT-TTT
1 AAATTTTTATTTTATTT
** *
515008 TGATTATTTATGTTATTT
1 AAATT-TTTATTTTATTT
515026 AAATTTTTATTTTATTT
1 AAATTTTTATTTTATTT
515043 AAA
1 AAA
515046 GTTTGTGTCT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
16 3 0.10
17 20 0.69
18 6 0.21
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
AAATTTTTATTTTATTT
Found at i:516160 original size:95 final size:95
Alignment explanation
Indices: 516052--516241 Score: 371
Period size: 95 Copynumber: 2.0 Consensus size: 95
516042 TTTAGATAAA
516052 ATTTTTATAAATTTAAATTAATTTAAATTATTTTTTTATATTTTAATATTTTTTAAAATGACGAA
1 ATTTTTATAAATTTAAATTAATTTAAATTATTTTTTTATATTTTAATATTTTTTAAAATGACGAA
516117 ATGAATCGTTAATCCGACTAAAGCTCAATC
66 ATGAATCGTTAATCCGACTAAAGCTCAATC
516147 ATTTTTATAAATTTAAATTAATTTAAATTATTTTTTTATATTTTAATATTTTTTAAAATGACGAA
1 ATTTTTATAAATTTAAATTAATTTAAATTATTTTTTTATATTTTAATATTTTTTAAAATGACGAA
*
516212 ATGAGTCGTTAATCCGACTAAAGCTCAATC
66 ATGAATCGTTAATCCGACTAAAGCTCAATC
516242 CGATAAAATT
Statistics
Matches: 94, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 94 1.00
ACGTcount: A:0.38, C:0.08, G:0.07, T:0.46
Consensus pattern (95 bp):
ATTTTTATAAATTTAAATTAATTTAAATTATTTTTTTATATTTTAATATTTTTTAAAATGACGAA
ATGAATCGTTAATCCGACTAAAGCTCAATC
Found at i:517719 original size:2 final size:2
Alignment explanation
Indices: 517714--517758 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
517704 TTTTTTACTT
*
517714 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
517756 TA T
1 TA T
517759 TTTTTAGGCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:525266 original size:2 final size:2
Alignment explanation
Indices: 525254--525293 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
525244 GCAAATACTG
525254 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
525294 CATTGGGAGT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:525936 original size:22 final size:21
Alignment explanation
Indices: 525898--525957 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
525888 TATTTTTATT
525898 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
525919 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
* *
525939 -ATATTTCAATAATAAAATA
1 TAAATTT-AATTATAAAATA
525958 AATTTTTAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
18 2 0.06
19 5 0.15
20 9 0.27
21 13 0.39
22 4 0.12
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:526877 original size:2 final size:2
Alignment explanation
Indices: 526870--526917 Score: 69
Period size: 2 Copynumber: 23.5 Consensus size: 2
526860 AAGATAAGAC
* *
526870 TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
526912 TCA TA T
1 T-A TA T
526918 TTTATACTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.95
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:527714 original size:2 final size:2
Alignment explanation
Indices: 527701--527741 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
527691 ATCAAACATT
*
527701 TA TA TC TA TA 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 TA TA TA TA TA T
527742 CACAGATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:532525 original size:22 final size:22
Alignment explanation
Indices: 532500--532541 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
532490 ATGTGATAAA
*
532500 GTTAATAAAAGTAATTTAATCT
1 GTTAATAAAAGAAATTTAATCT
*
532522 GTTAATAATAGAAATTTAAT
1 GTTAATAAAAGAAATTTAAT
532542 AATATAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (22 bp):
GTTAATAAAAGAAATTTAATCT
Found at i:532764 original size:2 final size:2
Alignment explanation
Indices: 532757--532782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
532747 TTCCCGTGAC
532757 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
532783 TCCCCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:533201 original size:2 final size:2
Alignment explanation
Indices: 533196--533229 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
533186 GATGTGTGTG
533196 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
533230 GAGAGAGAGA
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:533652 original size:22 final size:22
Alignment explanation
Indices: 533627--533668 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
533617 TATATTTATT
533627 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
533649 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
533669 ATATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:539056 original size:18 final size:18
Alignment explanation
Indices: 539032--539075 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
539022 CCTTTAATTC
539032 ATTTTTATATTATTTTAA
1 ATTTTTATATTATTTTAA
* *
539050 TTTTTTAT-TTTTTTTAA
1 ATTTTTATATTATTTTAA
539067 ATTTTTATA
1 ATTTTTATA
539076 GTTAATATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (18 bp):
ATTTTTATATTATTTTAA
Found at i:539177 original size:29 final size:27
Alignment explanation
Indices: 539127--539180 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 27
539117 TTAAAAAATA
539127 TAAAAAATATTATATATATATTTATGT
1 TAAAAAATATTATATATATATTTATGT
*
539154 TAAAAAATTATTATATTTAATATTTAT
1 TAAAAAA-TATTATATAT-ATATTTAT
539181 CTCGAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 7 0.29
28 9 0.38
29 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TAAAAAATATTATATATATATTTATGT
Found at i:539816 original size:50 final size:50
Alignment explanation
Indices: 539740--539947 Score: 299
Period size: 50 Copynumber: 4.2 Consensus size: 50
539730 GTTGTTGTCG
*
539740 TTGTTGACTATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCATAA
1 TTGTTGACGATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCATAA
* * *
539790 TTGTTGACGATTTTTCACCAATCTTTGACAATAAAAGGAGGTGACCATAA
1 TTGTTGACGATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCATAA
* * * * * *
539840 TTGTTGACGATTCTTCATCAACGTTTGACAATAGAAGGAGGTGATCATAG
1 TTGTTGACGATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCATAA
* * *
539890 TTGTTGACGATTCTTCACCAACCTTTGACAATAGAGAGAGGTGGCCATAA
1 TTGTTGACGATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCATAA
539940 TTGTTGAC
1 TTGTTGAC
539948 TCTAAGTATA
Statistics
Matches: 140, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 140 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (50 bp):
TTGTTGACGATTCTTCACCAACCTTTGACAATAAAAAGAGGTGACCATAA
Found at i:543003 original size:98 final size:98
Alignment explanation
Indices: 542824--543005 Score: 319
Period size: 98 Copynumber: 1.9 Consensus size: 98
542814 AAGCAGGAAG
*
542824 GAAATTCCTGCTTAAGTGCTTATTTATTTCCATGTAATGCATTTTTTTCTTACAACCGAAGAAAA
1 GAAATTCCTGCTTAAGTGCTTATTTATTTCCATGTAATGCATTTTTCTCTTACAACCGAAGAAAA
542889 ATGAGGAATGGAATTAGTTGATTAATGCACTAA
66 ATGAGGAATGGAATTAGTTGATTAATGCACTAA
* *
542922 GAAATTCCTGCTTAAGTGCTTATTTATTTCCATGTAATGCATTTTTCTCTTACAACTGAATAAAA
1 GAAATTCCTGCTTAAGTGCTTATTTATTTCCATGTAATGCATTTTTCTCTTACAACCGAAGAAAA
* *
542987 ATGAGGCATGGGATTAGTT
66 ATGAGGAATGGAATTAGTT
543006 TCATTCATGA
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (98 bp):
GAAATTCCTGCTTAAGTGCTTATTTATTTCCATGTAATGCATTTTTCTCTTACAACCGAAGAAAA
ATGAGGAATGGAATTAGTTGATTAATGCACTAA
Found at i:558452 original size:17 final size:17
Alignment explanation
Indices: 558432--558468 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
558422 AAATAACATT
*
558432 ATTAATTTAATATTTAA
1 ATTAATTAAATATTTAA
558449 ATTAATTAAATATTTAA
1 ATTAATTAAATATTTAA
558466 ATT
1 ATT
558469 TTTTATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTAATTAAATATTTAA
Found at i:564991 original size:20 final size:20
Alignment explanation
Indices: 564951--564993 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 20
564941 GTATTGAAAT
564951 ATAAATTTTAAATAAATTAA
1 ATAAATTTTAAATAAATTAA
564971 ATAATATTTTATAA-AAA-TAA
1 ATAA-ATTTTA-AATAAATTAA
564991 ATA
1 ATA
564994 CGTAAATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 10 0.48
21 9 0.43
22 2 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAATTTTAAATAAATTAA
Found at i:565106 original size:2 final size:2
Alignment explanation
Indices: 565099--565123 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
565089 TTACACTATG
565099 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
565124 TAAAATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:565728 original size:31 final size:28
Alignment explanation
Indices: 565692--565750 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
565682 TTTCGTTTAC
565692 TTTAATTTAAATATATATAAAAATAAAAATA
1 TTTAATTT-AATA-ATA-AAAAATAAAAATA
*
565723 TTTAATTTAATAATAAAAAATTAAAATA
1 TTTAATTTAATAATAAAAAATAAAAATA
565751 CATATTTTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.44
29 3 0.11
30 4 0.15
31 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
TTTAATTTAATAATAAAAAATAAAAATA
Found at i:565759 original size:28 final size:30
Alignment explanation
Indices: 565696--565772 Score: 70
Period size: 28 Copynumber: 2.7 Consensus size: 30
565686 GTTTACTTTA
* **
565696 ATTTAAATATATATAAAAATAAAAATATTT
1 ATTTTAATATATATAAAAATAAAAATACAT
* *
565726 AATTTAATA-ATA-AAAAATTAAAATACAT
1 ATTTTAATATATATAAAAATAAAAATACAT
* *
565754 ATTTTACTATA-ATACAAAT
1 ATTTTAATATATATAAAAAT
565773 TTTATTATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 5
0.74 0.16 0.10
Matches are distributed among these distances:
28 21 0.57
29 9 0.24
30 7 0.19
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (30 bp):
ATTTTAATATATATAAAAATAAAAATACAT
Found at i:567010 original size:21 final size:21
Alignment explanation
Indices: 566966--567017 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
566956 ATTTTAAAAA
* *
566966 AATTTATTATAAATAATTTAT
1 AATTTTTTAAAAATAATTTAT
566987 AATTTTTTAAAAATAA-TTATT
1 AATTTTTTAAAAATAATTTA-T
567008 AATATTTTTA
1 AAT-TTTTTA
567018 CTTTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 18 0.67
22 6 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
AATTTTTTAAAAATAATTTAT
Found at i:568441 original size:2 final size:2
Alignment explanation
Indices: 568434--568465 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
568424 TAGAGGGTTT
568434 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
568466 AATCTGAGAC
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:571046 original size:2 final size:2
Alignment explanation
Indices: 571034--571073 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
571024 TTCAATGTAA
* *
571034 AT AT AT GT AT AT AT TT 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 AT AT
571074 TCTTTTCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:571361 original size:2 final size:2
Alignment explanation
Indices: 571354--571393 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
571344 CTGAAGGAAG
571354 AT AT 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 AT AT
571394 TATTGAGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:573692 original size:9 final size:8
Alignment explanation
Indices: 573645--573702 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 8
573635 AAAAAATAAA
*
573645 AAAAAATT
1 AAAATATT
* *
573653 ATAATGTT
1 AAAATATT
573661 AAAATA-T
1 AAAATATT
573668 AAAA-ATT
1 AAAATATT
573675 AAAATTATT
1 AAAA-TATT
573684 ATAAATATT
1 A-AAATATT
573693 AAAAT-TT
1 AAAATATT
573700 AAA
1 AAA
573703 CTTAAATAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
6 1 0.02
7 15 0.37
8 13 0.32
9 9 0.22
10 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (8 bp):
AAAATATT
Found at i:573711 original size:24 final size:24
Alignment explanation
Indices: 573662--573712 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
573652 TATAATGTTA
*
573662 AAATATAAAAATTAAAATTATTAT
1 AAATATAAAAATTAAAATTATAAT
* *
573686 AAATATTAAAATTTAAACTTA-AAT
1 AAATA-TAAAAATTAAAATTATAAT
573710 AAA
1 AAA
573713 AATTTTATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATATAAAAATTAAAATTATAAT
Found at i:574262 original size:17 final size:17
Alignment explanation
Indices: 574240--574272 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
574230 TTTATTAAAT
*
574240 TTAAAAATAATATTATA
1 TTAAAAATAAAATTATA
574257 TTAAAAATAAAATTAT
1 TTAAAAATAAAATTAT
574273 TTTTATTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATAAAATTATA
Found at i:574267 original size:23 final size:21
Alignment explanation
Indices: 574225--574279 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
574215 ATAAATTTAT
**
574225 ATAATTTTATTAAATTTAAAA
1 ATAATTTTATTAAAAATAAAA
574246 ATAATATTATATTAAAAATAAAA
1 ATAAT-TT-TATTAAAAATAAAA
* *
574269 TTATTTTTATT
1 ATAATTTTATT
574280 TATTTTTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 9 0.32
22 4 0.14
23 15 0.54
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATAATTTTATTAAAAATAAAA
Found at i:574866 original size:19 final size:18
Alignment explanation
Indices: 574835--574872 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
574825 TTAATAAAAA
*
574835 ATTATAATTTTAAAATTT
1 ATTATAATATTAAAATTT
574853 ATTATATATATTAAAATTT
1 ATTATA-ATATTAAAATTT
574872 A
1 A
574873 AATTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATAATATTAAAATTT
Found at i:577164 original size:22 final size:22
Alignment explanation
Indices: 577117--577165 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
577107 ATTCATTGAT
*
577117 TTTTTATTTTTTTAAAAATTAC
1 TTTTTATATTTTTAAAAATTAC
* *
577139 TTTTTATGATTTTTTAAATTTA-
1 TTTTTAT-ATTTTTAAAAATTAC
577161 TTTTT
1 TTTTT
577166 CTAATTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (22 bp):
TTTTTATATTTTTAAAAATTAC
Found at i:577229 original size:16 final size:16
Alignment explanation
Indices: 577184--577234 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
577174 AAAGTAAAAT
577184 ATTTAATTTAAATTTAA
1 ATTTAATTT-AATTTAA
* *
577201 ATTT-ATTAAAATTAAA
1 ATTTAATT-TAATTTAA
577217 ATTTAATTTAATTTAA
1 ATTTAATTTAATTTAA
577233 AT
1 AT
577235 AATTATAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
16 21 0.75
17 7 0.25
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTTAATTTAATTTAA
Found at i:579576 original size:48 final size:46
Alignment explanation
Indices: 579516--579622 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 46
579506 ATATATATGA
*
579516 TAATGATATAAAATAAAAATATAT-TAAAAT-TTATATAATATTAATTAT
1 TAAT-ATATAAAATAAAAATAAATATAAAATATTATA-AATA-TAATT-T
* *
579564 TAATATATTAAAATATAAATAAATATAAAATATTTTAAATATAATTT
1 TAATATA-TAAAATAAAAATAAATATAAAATATTATAAATATAATTT
*
579611 TAATACATAAAA
1 TAATATATAAAA
579623 AATGATGAAC
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
46 5 0.10
47 10 0.19
48 23 0.44
49 10 0.19
50 4 0.08
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (46 bp):
TAATATATAAAATAAAAATAAATATAAAATATTATAAATATAATTT
Found at i:581118 original size:29 final size:30
Alignment explanation
Indices: 581078--581136 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
581068 TTATTTAGAT
*
581078 AAATGATAAAATAAATT-TTAATAA-AATAA
1 AAATAATAAAATAAATTATT-ATAATAATAA
*
581107 AAATAATAAAATTAATTATTATAATAATAA
1 AAATAATAAAATAAATTATTATAATAATAA
581137 TATTGAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 19 0.73
30 7 0.27
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATAATAAAATAAATTATTATAATAATAA
Found at i:581132 original size:21 final size:20
Alignment explanation
Indices: 581108--581167 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
581098 ATAAAATAAA
581108 AATAATAAAATTAATTATTAT
1 AATAATAAAATTAA-TATTAT
*
581129 AATAATAATATTGAATATTAT
1 AATAATAAAATT-AATATTAT
*
581150 AATAATAAGATTAA-ATTA
1 AATAATAAAATTAATATTA
581168 ACAGTAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 28 0.78
22 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
AATAATAAAATTAATATTAT
Found at i:581282 original size:15 final size:15
Alignment explanation
Indices: 581232--581311 Score: 56
Period size: 15 Copynumber: 5.3 Consensus size: 15
581222 AAAATAGTTA
*
581232 TTAAAGATATTATA-
1 TTAAAAATATTATAT
* * *
581246 TTAAAATTTATAATAA
1 TTAAAA-ATATTATAT
581262 TTAAAAATATTATAT
1 TTAAAAATATTATAT
* *
581277 TTAAAAAAATTAAAAT
1 TTAAAAATATT-ATAT
*
581293 TTAATAAA-ATGATAT
1 TTAA-AAATATTATAT
581308 TTAA
1 TTAA
581312 TTTTTATTTT
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
14 5 0.10
15 29 0.56
16 15 0.29
17 3 0.06
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (15 bp):
TTAAAAATATTATAT
Found at i:581780 original size:17 final size:17
Alignment explanation
Indices: 581742--581790 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
581732 TTTATTTTTT
581742 ATTTTT-ATAAAATT-A
1 ATTTTTAATAAAATTAA
* *
581757 A--TTTAATCAATTTAA
1 ATTTTTAATAAAATTAA
581772 ATTTTTAATAAAATTAA
1 ATTTTTAATAAAATTAA
581789 AT
1 AT
581791 ATTTGACAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
13 3 0.12
14 6 0.23
15 3 0.12
17 14 0.54
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTTTTAATAAAATTAA
Found at i:582056 original size:21 final size:21
Alignment explanation
Indices: 582022--582075 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 21
582012 TTATTAAAAT
* * *
582022 TTTAATATTTAATTAATTTAA
1 TTTAAAATTAAATTAATATAA
* *
582043 TTTAAAATTAAATTGATATAT
1 TTTAAAATTAAATTAATATAA
*
582064 TTTAAAAATAAA
1 TTTAAAATTAAA
582076 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TTTAAAATTAAATTAATATAA
Found at i:582106 original size:15 final size:15
Alignment explanation
Indices: 582070--582099 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
582060 ATATTTTAAA
582070 AATAA-AATTTTTTT
1 AATAATAATTTTTTT
582084 AATAATAATTTTTTT
1 AATAATAATTTTTTT
582099 A
1 A
582100 TTTATAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATAATAATTTTTTT
Found at i:582430 original size:16 final size:16
Alignment explanation
Indices: 582409--582471 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
582399 TTTTTTGAAC
582409 TTTAATATTAAATAAA
1 TTTAATATTAAATAAA
582425 TTTAATGA--AATATAAA
1 TTTAAT-ATTAA-ATAAA
*
582441 TTTAAATAATAAATAAA
1 TTT-AATATTAAATAAA
582458 TTTAA-ATTTAAATA
1 TTTAATA-TTAAATA
582472 TTTTAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
15 3 0.08
16 23 0.57
17 12 0.30
18 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
TTTAATATTAAATAAA
Found at i:582458 original size:17 final size:17
Alignment explanation
Indices: 582412--582464 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
582402 TTTGAACTTT
*
582412 AATATTAAATAAATTT-
1 AATAATAAATAAATTTA
*
582428 AATGAA-ATATAAATTTA
1 AAT-AATAAATAAATTTA
582445 AATAATAAATAAATTTA
1 AATAATAAATAAATTTA
582462 AAT
1 AAT
582465 TTAAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AATAATAAATAAATTTA
Found at i:586781 original size:31 final size:34
Alignment explanation
Indices: 586743--586830 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 34
586733 TAAATATGAT
586743 TATATAATATAATATAAAAATAATTAA-AATA-A
1 TATATAATATAATATAAAAATAATTAATAATATA
* * *
586775 T-TATAATA-ATATACTAATAAT-ATTAATTATATC
1 TATATAATATA-ATA-TAAAAATAATTAATAATATA
*
586808 TATATAATATAATATAAACATAA
1 TATATAATATAATATAAAAATAA
586831 AATGATTAGA
Statistics
Matches: 44, Mismatches: 5, Indels: 12
0.72 0.08 0.20
Matches are distributed among these distances:
30 1 0.02
31 15 0.34
32 10 0.23
33 6 0.14
34 11 0.25
35 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (34 bp):
TATATAATATAATATAAAAATAATTAATAATATA
Found at i:586793 original size:20 final size:18
Alignment explanation
Indices: 586770--586821 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
586760 AAATAATTAA
586770 AATAATTATAATAATATACT
1 AATAA-TATAATAATAT-CT
*
586790 AATAATATTAATTATATCT
1 AATAATA-TAATAATATCT
586809 ATATAATATAATA
1 A-ATAATATAATA
586822 TAAACATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 9 0.32
20 19 0.68
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
AATAATATAATAATATCT
Found at i:587457 original size:6 final size:6
Alignment explanation
Indices: 587446--587473 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
587436 CAATAATAAC
587446 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTT
587474 ATTTAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:588527 original size:27 final size:29
Alignment explanation
Indices: 588497--588558 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 29
588487 TAGTTAGATA
588497 TAATTAATATAAATAAA-ATT-ATTTATT
1 TAATTAATATAAATAAATATTAATTTATT
* *
588524 TAATT--TTTAATTAAATATTAATTTATT
1 TAATTAATATAAATAAATATTAATTTATT
588551 TAATTAAT
1 TAATTAAT
588559 TTGATTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
25 8 0.28
26 3 0.10
27 17 0.59
29 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
TAATTAATATAAATAAATATTAATTTATT
Found at i:590077 original size:14 final size:14
Alignment explanation
Indices: 590058--590084 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
590048 TATAATGATT
590058 ATATTAATTATATC
1 ATATTAATTATATC
590072 ATATTAATTATAT
1 ATATTAATTATAT
590085 TTAAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
ATATTAATTATATC
Found at i:590088 original size:24 final size:23
Alignment explanation
Indices: 590055--590105 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
590045 AAATATAATG
*
590055 ATTATATTAATTATATCATATTA
1 ATTATATTAAATATATCATATTA
* *
590078 ATTATATTTAAATATATTATATTT
1 ATTATA-TTAAATATATCATATTA
590102 ATTA
1 ATTA
590106 AATATGTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTATATTAAATATATCATATTA
Found at i:590088 original size:48 final size:43
Alignment explanation
Indices: 589977--590093 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 43
589967 CATATATATA
* *
589977 TATATATTTTAATTATCTATAAATATAAATATAATATAAATTAT
1 TATATATATTAATTAT-TTTAAATATAAATATAATATAAATTAT
* *
590021 TA-AGTATATTAA-AATTTTAAATATAAATATAATGATTATATTAAT
1 TATA-TATATTAATTATTTTAAATATAAATATAAT-A-TAAATT-AT
590066 TATATCATATTAATTATATTTAAATATA
1 TATAT-ATATTAATTAT-TTTAAATATA
590094 TTATATTTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
42 17 0.28
43 4 0.07
44 14 0.23
45 5 0.08
46 8 0.13
47 2 0.03
48 10 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (43 bp):
TATATATATTAATTATTTTAAATATAAATATAATATAAATTAT
Found at i:594226 original size:2 final size:2
Alignment explanation
Indices: 594219--594253 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
594209 GACAGTCATC
594219 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
594254 CATATACATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:595307 original size:19 final size:19
Alignment explanation
Indices: 595275--595314 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
595265 CATATCTTAA
*
595275 TATATTATACTATATTTAT
1 TATATTATACTATATTCAT
**
595294 TATATTATTTTATATTCAT
1 TATATTATACTATATTCAT
595313 TA
1 TA
595315 ATGTGACCAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATTATACTATATTCAT
Found at i:595556 original size:21 final size:20
Alignment explanation
Indices: 595522--595572 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
595512 AAAATAATAA
595522 AAATTTA-T-TTTTAT-ATT
1 AAATTTATTATTTTATAATT
595539 AATATTTATATATTTTATAATT
1 AA-ATTTAT-TATTTTATAATT
595561 AAATTTATTATT
1 AAATTTATTATT
595573 ATTAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 2 0.07
18 5 0.17
20 5 0.17
21 12 0.41
22 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
AAATTTATTATTTTATAATT
Found at i:603122 original size:3 final size:3
Alignment explanation
Indices: 603114--603143 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
603104 AATTAAAGGG
603114 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
603144 TGAGAGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:605079 original size:3 final size:3
Alignment explanation
Indices: 605073--605101 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
605063 TTTTGCATTG
605073 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
605102 TGAAGAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:607793 original size:18 final size:18
Alignment explanation
Indices: 607767--607803 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
607757 TTTGGCTTAT
* *
607767 AAATTTATTTTATTTTTG
1 AAATATATTTTATATTTG
607785 AAATATATTTTATATTTG
1 AAATATATTTTATATTTG
607803 A
1 A
607804 GTTAGGTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
AAATATATTTTATATTTG
Found at i:609655 original size:2 final size:2
Alignment explanation
Indices: 609648--609678 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
609638 AGTGTTTGCC
609648 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
609679 GTTAAGAGTA
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:610430 original size:29 final size:29
Alignment explanation
Indices: 610397--610454 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
610387 TGAATTCTTT
*
610397 TTTTCTCTTCCCATTAAAGTAATTGTTGA
1 TTTTCTCTTCACATTAAAGTAATTGTTGA
610426 TTTTCTCTTCACATTAAAGTAATTGTTGA
1 TTTTCTCTTCACATTAAAGTAATTGTTGA
610455 ATTTAGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.48
Consensus pattern (29 bp):
TTTTCTCTTCACATTAAAGTAATTGTTGA
Found at i:611973 original size:27 final size:27
Alignment explanation
Indices: 611935--611986 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
611925 CAGAAGTCCG
611935 TTAAACTTGGACAGCCTCTTTTTTCCT
1 TTAAACTTGGACAGCCTCTTTTTTCCT
611962 TTAAACTTGGACAGCCTCTTTTTTC
1 TTAAACTTGGACAGCCTCTTTTTTC
611987 TGCATGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (27 bp):
TTAAACTTGGACAGCCTCTTTTTTCCT
Found at i:613108 original size:31 final size:31
Alignment explanation
Indices: 613071--613133 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
613061 ACAATTTTTT
* *
613071 TATTCTACAATTGAAATTAAAAAAAGTTATC
1 TATTCTACAAATGAAATTAAAAAAAATTATC
613102 TATTCTACAAATGAAATTAAAAAAAATTATC
1 TATTCTACAAATGAAATTAAAAAAAATTATC
613133 T
1 T
613134 CATATGATCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.35
Consensus pattern (31 bp):
TATTCTACAAATGAAATTAAAAAAAATTATC
Found at i:613447 original size:55 final size:55
Alignment explanation
Indices: 613358--613472 Score: 194
Period size: 55 Copynumber: 2.1 Consensus size: 55
613348 ACGGTTTATA
* * *
613358 TTAATTAACTTAAGTTAATTTAATTCATTAAAATAAGTTTAATATTTAAAAAAAT
1 TTAAATAACTCAAGTTAATTTAATTCATCAAAATAAGTTTAATATTTAAAAAAAT
*
613413 TTAAATAACTCAAGTTAATTTAATTCATCAAAATAAGTTTAATATTTAAAAAATT
1 TTAAATAACTCAAGTTAATTTAATTCATCAAAATAAGTTTAATATTTAAAAAAAT
613468 TTAAA
1 TTAAA
613473 ATATTTAATT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (55 bp):
TTAAATAACTCAAGTTAATTTAATTCATCAAAATAAGTTTAATATTTAAAAAAAT
Found at i:613473 original size:28 final size:28
Alignment explanation
Indices: 613450--613501 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
613440 TCAAAATAAG
613450 TTTAA-TATTT-AAAAAATTTTAAAATA
1 TTTAATTATTTAAAAAAATTTTAAAATA
*
613476 TTTAATTTTTTAAAAAAATTTTAAAA
1 TTTAATTATTTAAAAAAATTTTAAAA
613502 GTCAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 5 0.22
27 4 0.17
28 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAATTATTTAAAAAAATTTTAAAATA
Found at i:621243 original size:28 final size:27
Alignment explanation
Indices: 621188--621258 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
621178 GCCACCCATT
621188 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
621215 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
621243 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
621259 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:624996 original size:3 final size:3
Alignment explanation
Indices: 624988--625017 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
624978 AATTAAAGGG
624988 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
625018 TGAGAGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:626953 original size:3 final size:3
Alignment explanation
Indices: 626947--626975 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
626937 TTTTGCATTG
626947 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
626976 TGAAGAAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:629275 original size:2 final size:2
Alignment explanation
Indices: 629268--629294 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
629258 TTAAATGGAT
629268 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 T
629295 TTTTGCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:631826 original size:29 final size:29
Alignment explanation
Indices: 631793--631850 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
631783 TGAATTCTTT
631793 TTTTCTCTTCACATTAAAGTAATTGTTGA
1 TTTTCTCTTCACATTAAAGTAATTGTTGA
631822 TTTTCTCTTCACATTAAAGTAATTGTTGA
1 TTTTCTCTTCACATTAAAGTAATTGTTGA
631851 ATTTAGGTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.14, G:0.10, T:0.48
Consensus pattern (29 bp):
TTTTCTCTTCACATTAAAGTAATTGTTGA
Found at i:633369 original size:27 final size:27
Alignment explanation
Indices: 633331--633382 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
633321 CAGAAGTCCG
633331 TTAAACTTGGACAGCCTCTTTTTTCCT
1 TTAAACTTGGACAGCCTCTTTTTTCCT
633358 TTAAACTTGGACAGCCTCTTTTTTC
1 TTAAACTTGGACAGCCTCTTTTTTC
633383 TGCATGTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.25, G:0.12, T:0.44
Consensus pattern (27 bp):
TTAAACTTGGACAGCCTCTTTTTTCCT
Found at i:634503 original size:31 final size:31
Alignment explanation
Indices: 634466--634528 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
634456 ACAATTTTTT
* *
634466 TATTCTACAATTGAAATTAAAAAAAGTTATC
1 TATTCTACAAATGAAATTAAAAAAAATTATC
*
634497 TATTCTACAAATGAGATTAAAAAAAATTATC
1 TATTCTACAAATGAAATTAAAAAAAATTATC
634528 T
1 T
634529 CATATGATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.49, C:0.10, G:0.06, T:0.35
Consensus pattern (31 bp):
TATTCTACAAATGAAATTAAAAAAAATTATC
Found at i:634915 original size:55 final size:55
Alignment explanation
Indices: 634783--634893 Score: 195
Period size: 55 Copynumber: 2.0 Consensus size: 55
634773 ACGAGTTACA
* *
634783 TTAATTAACTGAAGTTAATTTAATTCATCAAAACAAGTTTAATATTTAAAAAATT
1 TTAAATAACTCAAGTTAATTTAATTCATCAAAACAAGTTTAATATTTAAAAAATT
*
634838 TTAAATAACTCAAGTTAATTTAATTCATCAAAATAAGTTTAATATTTAAAAAATT
1 TTAAATAACTCAAGTTAATTTAATTCATCAAAACAAGTTTAATATTTAAAAAATT
634893 T
1 T
634894 AATTTTTTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.41
Consensus pattern (55 bp):
TTAAATAACTCAAGTTAATTTAATTCATCAAAACAAGTTTAATATTTAAAAAATT
Found at i:638580 original size:20 final size:19
Alignment explanation
Indices: 638509--638602 Score: 77
Period size: 20 Copynumber: 4.7 Consensus size: 19
638499 CATATTTTTT
638509 ATATTTAAATATAAATA-A
1 ATATTTAAATATAAATATA
638527 A-ATTATAAATTATTAAAAATATTA
1 ATATT-TAAA-TA-T--AAATA-TA
638551 ATATTTTAAATATAAATATA
1 ATA-TTTAAATATAAATATA
* *
638571 ATACTGTAAATAT-AATATT
1 ATA-TTTAAATATAAATATA
638590 ATATTTAAATATA
1 ATATTTAAATATA
638603 TTAAATTATA
Statistics
Matches: 62, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
17 3 0.05
18 13 0.21
19 10 0.16
20 14 0.23
21 5 0.08
22 5 0.08
23 1 0.02
24 4 0.06
25 5 0.08
26 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (19 bp):
ATATTTAAATATAAATATA
Found at i:638603 original size:20 final size:21
Alignment explanation
Indices: 638544--638623 Score: 64
Period size: 20 Copynumber: 4.0 Consensus size: 21
638534 AATTATTAAA
*
638544 AATATTAATATTTTAAATATA-
1 AATATT-ATACTTTAAATATAT
* *
638565 AATATAATACTGT-AA-ATAT
1 AATATTATACTTTAAATATAT
638584 AATATTATA-TTTAAATATATT
1 AATATTATACTTTAAATATA-T
*
638605 AA-ATTATA-TTTATATATAT
1 AATATTATACTTTAAATATAT
638624 TAAAAATATT
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
18 5 0.10
19 13 0.27
20 23 0.47
21 8 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (21 bp):
AATATTATACTTTAAATATAT
Found at i:638608 original size:9 final size:9
Alignment explanation
Indices: 638532--638634 Score: 54
Period size: 9 Copynumber: 11.2 Consensus size: 9
638522 AATAAAATTA
638532 TAAAT-TAT
1 TAAATATAT
*
638540 TAAAAATAT
1 TAAATATAT
*
638549 T-AATATTT
1 TAAATATAT
638557 TAAATATA-
1 TAAATATAT
638565 -AATATAATACT
1 TAA-AT-ATA-T
*
638576 GTAAATATAA
1 -TAAATATAT
*
638586 T-ATTATATT
1 TAAATATA-T
638595 TAAATATAT
1 TAAATATAT
638604 TAAATTATATT
1 TAAA-TATA-T
*
638615 TATATATAT
1 TAAATATAT
*
638624 TAAAAATAT
1 TAAATATAT
638633 TA
1 TA
638635 TATTTTTCTA
Statistics
Matches: 72, Mismatches: 11, Indels: 23
0.68 0.10 0.22
Matches are distributed among these distances:
7 2 0.03
8 17 0.24
9 29 0.40
10 13 0.18
11 7 0.10
12 2 0.03
13 2 0.03
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (9 bp):
TAAATATAT
Found at i:638624 original size:20 final size:20
Alignment explanation
Indices: 638587--638627 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
638577 TAAATATAAT
638587 ATTATATTTAAATATATTAA
1 ATTATATTTAAATATATTAA
*
638607 ATTATATTTATATATATTAA
1 ATTATATTTAAATATATTAA
638627 A
1 A
638628 AATATTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTATATTTAAATATATTAA
Found at i:638635 original size:18 final size:20
Alignment explanation
Indices: 638590--638637 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
638580 ATATAATATT
* *
638590 ATATTTAAATATATTAAATT
1 ATATTTATATATATTAAATA
638610 ATATTTATATATATTAAA-A
1 ATATTTATATATATTAAATA
638629 ATA-TTATAT
1 ATATTTATAT
638638 TTTTCTAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 6 0.23
19 3 0.12
20 17 0.65
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTTATATATATTAAATA
Found at i:638794 original size:3 final size:3
Alignment explanation
Indices: 638788--638817 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
638778 CAACAACAAC
638788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
638818 TTAAACAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:642577 original size:28 final size:30
Alignment explanation
Indices: 642535--642590 Score: 73
Period size: 28 Copynumber: 1.9 Consensus size: 30
642525 TTTAGGATAA
642535 AATATAATATAAAA-TATATATTAATATATG
1 AATATAATATAAAATTATATA-TAATATATG
*
642565 AATAT-AT-TAAAATTTTATATAATATA
1 AATATAATATAAAATTATATATAATATA
642591 AATTATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 12 0.50
29 7 0.29
30 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
AATATAATATAAAATTATATATAATATATG
Found at i:642626 original size:18 final size:17
Alignment explanation
Indices: 642565--642627 Score: 51
Period size: 18 Copynumber: 3.7 Consensus size: 17
642555 TTAATATATG
*
642565 AATATATTAAAATTT-T
1 AATATAATAAAATTTAT
642581 -ATATAATATAAA-TTATT
1 AATATAATA-AAATTTA-T
* *
642598 AATGTATTAAAATTTAT
1 AATATAATAAAATTTAT
642615 AAATATAATAAAA
1 -AATATAATAAAA
642628 ATATATGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
15 9 0.25
16 3 0.08
17 5 0.14
18 19 0.53
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
AATATAATAAAATTTAT
Found at i:644188 original size:3 final size:3
Alignment explanation
Indices: 644180--644217 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
644170 ATAAATCATA
644180 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
644218 AAATCACTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:648054 original size:86 final size:86
Alignment explanation
Indices: 647954--648125 Score: 344
Period size: 86 Copynumber: 2.0 Consensus size: 86
647944 GGAGAAAGCG
647954 TAAAAATATAAAAACTTCTAATAAAAGAAAGCAATGTAGATATTAACCTGATCTAAGGATCTGTA
1 TAAAAATATAAAAACTTCTAATAAAAGAAAGCAATGTAGATATTAACCTGATCTAAGGATCTGTA
648019 ATTGTCTGCAATTCTCGAATA
66 ATTGTCTGCAATTCTCGAATA
648040 TAAAAATATAAAAACTTCTAATAAAAGAAAGCAATGTAGATATTAACCTGATCTAAGGATCTGTA
1 TAAAAATATAAAAACTTCTAATAAAAGAAAGCAATGTAGATATTAACCTGATCTAAGGATCTGTA
648105 ATTGTCTGCAATTCTCGAATA
66 ATTGTCTGCAATTCTCGAATA
648126 CCTCCTGTCT
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.30
Consensus pattern (86 bp):
TAAAAATATAAAAACTTCTAATAAAAGAAAGCAATGTAGATATTAACCTGATCTAAGGATCTGTA
ATTGTCTGCAATTCTCGAATA
Found at i:649942 original size:10 final size:10
Alignment explanation
Indices: 649927--649955 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
649917 TGAATTTTAA
649927 ATTTATAAAT
1 ATTTATAAAT
649937 ATTTATAAAT
1 ATTTATAAAT
649947 ATTT-TAAAT
1 ATTTATAAAT
649956 TTAACATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (10 bp):
ATTTATAAAT
Found at i:651810 original size:21 final size:21
Alignment explanation
Indices: 651786--651860 Score: 59
Period size: 21 Copynumber: 3.6 Consensus size: 21
651776 ATTTAGTATG
*
651786 AATATATTA-AAATTTATATAA
1 AATATATTATAAATATAT-TAA
* *
651807 AATAAATTATTAATATATTAA
1 AATATATTATAAATATATTAA
651828 AATATATATATATAAT-T-TT-A
1 AATATAT-TATA-AATATATTAA
651848 AATATAATTATAA
1 AATAT-ATTATAA
651861 GACATAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.02
20 10 0.22
21 21 0.47
22 10 0.22
23 3 0.07
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (21 bp):
AATATATTATAAATATATTAA
Found at i:651838 original size:16 final size:16
Alignment explanation
Indices: 651787--651840 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
651777 TTTAGTATGA
*
651787 ATATATTAAAATTTAT
1 ATATATTAAAATATAT
* * *
651803 ATAAAATAAATTAT-T
1 ATATATTAAAATATAT
651818 AATATATTAAAATATAT
1 -ATATATTAAAATATAT
651835 ATATAT
1 ATATAT
651841 AATTTTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
15 1 0.03
16 27 0.93
17 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATTAAAATATAT
Found at i:651859 original size:20 final size:22
Alignment explanation
Indices: 651800--651859 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 22
651790 TATTAAAATT
*
651800 TATATAAAATA-AATTAT-TAA
1 TATATTAAATATAATTATATAA
651820 TATATTAAA-ATATATATATATAA
1 TATATTAAATATA-AT-TATATAA
651843 T-T-TTAAATATAATTATA
1 TATATTAAATATAATTATA
651860 AGACATAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
19 1 0.03
20 13 0.38
21 9 0.26
22 7 0.21
23 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TATATTAAATATAATTATATAA
Found at i:652128 original size:25 final size:26
Alignment explanation
Indices: 652100--652169 Score: 90
Period size: 25 Copynumber: 2.7 Consensus size: 26
652090 TTATATTTAA
652100 AATATTATATATTTATA-AAAATTTT
1 AATATTATATATTTATATAAAATTTT
* *
652125 AATATTTTATA-TTATATAAATTTTT
1 AATATTATATATTTATATAAAATTTT
652150 ATATATTATTATATTTATAT
1 A-ATATTA-TATATTTATAT
652170 TATTTTTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
24 5 0.13
25 18 0.47
26 5 0.13
27 4 0.11
28 6 0.16
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
AATATTATATATTTATATAAAATTTT
Found at i:652174 original size:27 final size:27
Alignment explanation
Indices: 652076--652214 Score: 119
Period size: 27 Copynumber: 5.2 Consensus size: 27
652066 TGTTTCAAAT
* *
652076 TTATTATA-TTATAATTATATTTAAAATA
1 TTATTATATTTAT-ATTAT-TTTTATATA
** *
652104 TTA-TATATTTATAAAAATTTTA-ATA
1 TTATTATATTTATATTATTTTTATATA
*
652129 TT-TTATA-TTATATAAATTTTTATATA
1 TTATTATATTTATAT-TATTTTTATATA
*
652155 TTATTATATTTATATTATTTTTATATT
1 TTATTATATTTATATTATTTTTATATA
652182 TTATTATATTT-TAATTATATTTTATATA
1 TTATTATATTTAT-ATTAT-TTTTATATA
*
652210 ATATT
1 TTATT
652215 CGTCACGAAA
Statistics
Matches: 93, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
24 5 0.05
25 16 0.17
26 10 0.11
27 37 0.40
28 25 0.27
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
TTATTATATTTATATTATTTTTATATA
Found at i:652188 original size:21 final size:22
Alignment explanation
Indices: 652164--652214 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
652154 ATTATTATAT
*
652164 TTATATTATT-TTTATATTTTA
1 TTATATTATTAATTATATTTTA
652185 TTATATT-TTAATTATATTTTA
1 TTATATTATTAATTATATTTTA
*
652206 -TATAATATT
1 TTATATTATT
652215 CGTCACGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
TTATATTATTAATTATATTTTA
Found at i:652203 original size:11 final size:11
Alignment explanation
Indices: 652175--652205 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
652165 TATATTATTT
652175 TTATATTTT-A
1 TTATATTTTAA
652185 TTATATTTTAA
1 TTATATTTTAA
652196 TTATATTTTA
1 TTATATTTTA
652206 TATAATATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTATATTTTAA
Found at i:652214 original size:44 final size:44
Alignment explanation
Indices: 652129--652214 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
652119 AATTTTAATA
* *
652129 TTTTATATTATATAAATTTTTATATATTATTATATTTATATTAT
1 TTTTATATTATATAAATTTTAATATATTATTATATTAATATTAT
* *
652173 TTTTATATTTTATTATATTTTAATTATATT-TTATA-TAATATT
1 TTTTATATTATA-TAAATTTTAA-TATATTATTATATTAATATT
652215 CGTCACGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 17 0.47
45 13 0.36
46 6 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (44 bp):
TTTTATATTATATAAATTTTAATATATTATTATATTAATATTAT
Found at i:652631 original size:40 final size:44
Alignment explanation
Indices: 652581--652683 Score: 106
Period size: 47 Copynumber: 2.3 Consensus size: 44
652571 CACCAGGAGA
*
652581 ATAATTAAAATAAA-TATATAT-AAATATATTAAAAT-TTTAT-
1 ATAATAAAAATAAATTATATATAAAATATATTAAAATATTTATG
*
652621 ATAATAAAAATATATTAATTTATATATAAAATATTTTAAAATATTTATG
1 ATAAT-AAAA-ATA--AA-TTATATATAAAATATATTAAAATATTTATG
652670 ATATATAAAAATAA
1 ATA-ATAAAAATAA
652684 TATGAATATA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
40 5 0.10
41 3 0.06
42 3 0.06
44 2 0.04
46 8 0.16
47 13 0.25
48 8 0.16
49 7 0.14
50 2 0.04
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (44 bp):
ATAATAAAAATAAATTATATATAAAATATATTAAAATATTTATG
Found at i:652644 original size:21 final size:21
Alignment explanation
Indices: 652594--652659 Score: 69
Period size: 21 Copynumber: 2.9 Consensus size: 21
652584 ATTAAAATAA
652594 ATATATATAAATATATTAAAATTTT
1 ATATATA-AAATATATT--AA-TTT
652619 ATATAATAAAAATATATTAATTT
1 ATAT-AT-AAAATATATTAATTT
*
652642 ATATATAAAATATTTTAA
1 ATATATAAAATATATTAA
652660 AATATTTATG
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
21 11 0.29
22 2 0.05
23 7 0.18
24 2 0.05
25 4 0.11
26 11 0.29
27 1 0.03
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATATAAAATATATTAATTT
Found at i:652646 original size:25 final size:25
Alignment explanation
Indices: 652594--652682 Score: 80
Period size: 26 Copynumber: 3.6 Consensus size: 25
652584 ATTAAAATAA
*
652594 ATAT-ATATAAATATATTAAAATTTT
1 ATATAATAAAAATATATT-AAATTTT
652619 ATATAATAAAAATATATT-AA-TTT
1 ATATAATAAAAATATATTAAATTTT
*
652642 ATAT-AT-AAAATATTTTAAAATATTT
1 ATATAATAAAAATATATT-AAAT-TTT
652667 ATGATATATAAAAATA
1 AT-ATA-ATAAAAATA
652683 ATATGAATAT
Statistics
Matches: 53, Mismatches: 2, Indels: 14
0.77 0.03 0.20
Matches are distributed among these distances:
21 9 0.17
22 2 0.04
23 9 0.17
24 2 0.04
25 9 0.17
26 14 0.26
28 2 0.04
29 6 0.11
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
ATATAATAAAAATATATTAAATTTT
Found at i:661308 original size:55 final size:56
Alignment explanation
Indices: 661205--661317 Score: 165
Period size: 55 Copynumber: 2.0 Consensus size: 56
661195 GTAAAAGGCT
* *
661205 GAACGGCCAGTTTTATAGGATACGTTATCACATTATGGCATGCAACCTATTTA-CC
1 GAACAGCCAGTTTTATAGGATACGTTATCACATGATGGCATGCAACCTATTTATCC
* * * *
661260 GAACAGCCAGTTTTATAGGCTACGTTATTACATGATGGTATGCGACCTATTTATCC
1 GAACAGCCAGTTTTATAGGATACGTTATCACATGATGGCATGCAACCTATTTATCC
661316 GA
1 GA
661318 TATGTTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
55 47 0.92
56 4 0.08
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (56 bp):
GAACAGCCAGTTTTATAGGATACGTTATCACATGATGGCATGCAACCTATTTATCC
Found at i:663635 original size:22 final size:21
Alignment explanation
Indices: 663604--663670 Score: 59
Period size: 22 Copynumber: 3.2 Consensus size: 21
663594 TATTTTTATT
663604 TAAATTTAATTATAA-AATATA
1 TAAATTTAA-TATAATAATATA
*
663625 TAAATATTAATATAATAATATT
1 TAAAT-TTAATATAATAATATA
* * *
663647 TTAATTT-TTTTAATAAT-TA
1 TAAATTTAATATAATAATATA
663666 TAAAT
1 TAAAT
663671 AATAAATATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.13
20 8 0.21
21 12 0.32
22 13 0.34
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAAATTTAATATAATAATATA
Found at i:664581 original size:21 final size:21
Alignment explanation
Indices: 664557--664596 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
664547 CTCAGATAAT
*
664557 AAATTTTAATATTATTATTTC
1 AAATTTAAATATTATTATTTC
*
664578 AAATTTAAATGTTATTATT
1 AAATTTAAATATTATTATT
664597 ATTATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (21 bp):
AAATTTAAATATTATTATTTC
Found at i:668752 original size:11 final size:11
Alignment explanation
Indices: 668736--668780 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
668726 TAACAATTCA
668736 TATATTTATAT
1 TATATTTATAT
668747 TATATTTATAT
1 TATATTTATAT
* *
668758 TTTTTATTATAT
1 TATAT-TTATAT
*
668770 TATAATTATAT
1 TATATTTATAT
668781 AAAAATTATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 20 0.71
12 8 0.29
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TATATTTATAT
Found at i:668794 original size:22 final size:22
Alignment explanation
Indices: 668763--668805 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
668753 TATATTTTTT
668763 ATTATATTATAATTATATAAAA
1 ATTATATTATAATTATATAAAA
*
668785 ATTATTTTATAATTATATAAA
1 ATTATATTATAATTATATAAA
668806 TTTTAATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTATATTATAATTATATAAAA
Found at i:668885 original size:12 final size:11
Alignment explanation
Indices: 668854--668892 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
668844 AAAATTGTAA
*
668854 ATTTATGTTAT
1 ATTTATTTTAT
668865 ATTTATTTTAT
1 ATTTATTTTAT
668876 ATTGTATTTTAT
1 ATT-TATTTTAT
*
668888 TTTTA
1 ATTTA
668893 AATTATGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (11 bp):
ATTTATTTTAT
Found at i:669347 original size:18 final size:17
Alignment explanation
Indices: 669304--669350 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
669294 AAAATTTAAA
*
669304 TTATAATATTTTATATAT
1 TTATAA-ATTATATATAT
*
669322 TT-TTAATTATATCATAT
1 TTATAAATTATAT-ATAT
669339 TTATAAATTATA
1 TTATAAATTATA
669351 ATAAATATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 10 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (17 bp):
TTATAAATTATATATAT
Found at i:670821 original size:4 final size:4
Alignment explanation
Indices: 670812--670838 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
670802 ATTCGTGTAA
670812 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
670839 GGAGAAAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:671299 original size:9 final size:9
Alignment explanation
Indices: 671258--671309 Score: 50
Period size: 9 Copynumber: 5.3 Consensus size: 9
671248 AGTTTTTTTA
671258 ATTTTAAAT
1 ATTTTAAAT
*
671267 ATATTTATAT
1 AT-TTTAAAT
*
671277 TTTATTAAATAT
1 ATT-TT-AA-AT
671289 ATTTTAAAT
1 ATTTTAAAT
671298 ATTTTAAAT
1 ATTTTAAAT
671307 ATT
1 ATT
671310 AATTTAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
9 17 0.49
10 11 0.31
11 3 0.09
12 4 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:671304 original size:20 final size:19
Alignment explanation
Indices: 671258--671308 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
671248 AGTTTTTTTA
*
671258 ATTTTAAATATATTTATAT
1 ATTTTAAATATATTTAAAT
*
671277 TTTATTAAATATATTTTAAAT
1 ATT-TTAAATATA-TTTAAAT
671298 ATTTTAAATAT
1 ATTTTAAATAT
671309 TAATTTAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATTTTAAATATATTTAAAT
Found at i:672252 original size:9 final size:9
Alignment explanation
Indices: 672230--672295 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
672220 TACAAATATA
672230 ATATT-AAT
1 ATATTAAAT
672238 -TATTAAAT
1 ATATTAAAT
672246 ATATTAAA-
1 ATATTAAAT
*
672254 ATTTTAAATT
1 ATATTAAA-T
*
672264 AAATATAAAT
1 ATAT-TAAAT
* *
672274 ATAATACAT
1 ATATTAAAT
672283 ATATTAAAT
1 ATATTAAAT
672292 ATAT
1 ATAT
672296 CACATTAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
7 4 0.09
8 10 0.22
9 22 0.49
10 5 0.11
11 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATTAAAT
Found at i:672289 original size:29 final size:30
Alignment explanation
Indices: 672213--672291 Score: 83
Period size: 29 Copynumber: 2.7 Consensus size: 30
672203 TATGTTATTT
*
672213 ATATAAATACAAATA-TAATATTAATTATTAA
1 ATAT-AATACAAATATTAA-ATTAAATATTAA
* *
672244 ATATATTA-AAATTTTAAATTAAATA-TAA
1 ATATAATACAAATATTAAATTAAATATTAA
*
672272 ATATAATACATATATTAAAT
1 ATATAATACAAATATTAAAT
672292 ATATCACATT
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
28 10 0.25
29 20 0.50
30 6 0.15
31 4 0.10
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (30 bp):
ATATAATACAAATATTAAATTAAATATTAA
Found at i:675168 original size:26 final size:28
Alignment explanation
Indices: 675118--675174 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
675108 ATGCATGCAA
*
675118 ATTTTTTATATATTAAAAATATTTAATT
1 ATTTTTTATATATTAAAAATATTTAACT
675146 ATTTTTTA-AT-TTAAAAA-ATTTTAACT
1 ATTTTTTATATATTAAAAATA-TTTAACT
675172 ATT
1 ATT
675175 AAATCATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
25 1 0.04
26 16 0.59
27 2 0.07
28 8 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATTTTTTATATATTAAAAATATTTAACT
Found at i:675792 original size:13 final size:13
Alignment explanation
Indices: 675774--675798 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
675764 AGGGAGAAAA
675774 TTTTTTATTTTTC
1 TTTTTTATTTTTC
675787 TTTTTTATTTTT
1 TTTTTTATTTTT
675799 TGGAAGATCA
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:0.08, C:0.04, G:0.00, T:0.88
Consensus pattern (13 bp):
TTTTTTATTTTTC
Found at i:679397 original size:36 final size:34
Alignment explanation
Indices: 679319--679425 Score: 98
Period size: 33 Copynumber: 3.2 Consensus size: 34
679309 AATATTTTTA
* **
679319 TTTAAATTTAATTATA--AAAATATAAAAATAAAT
1 TTTAAATTTAATTATATTTAAAT-TAAATTTAAAT
* *
679352 TTT--TTTTAA-TATATATTAAATTATTATTTAAAT
1 TTTAAATTTAATTATAT-TTAAATTA-AATTTAAAT
679385 TATTAAATTTAATTATATTTAAATTAAATTTAAAT
1 T-TTAAATTTAATTATATTTAAATTAAATTTAAAT
679420 TTTAAA
1 TTTAAA
679426 ATTTTTTTAA
Statistics
Matches: 59, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
30 4 0.07
31 5 0.08
32 2 0.03
33 14 0.24
34 7 0.12
35 9 0.15
36 13 0.22
37 5 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
TTTAAATTTAATTATATTTAAATTAAATTTAAAT
Found at i:679403 original size:35 final size:35
Alignment explanation
Indices: 679356--679455 Score: 108
Period size: 29 Copynumber: 3.0 Consensus size: 35
679346 ATAAATTTTT
*
679356 TTTAATATATATTAAATTATTATTTAAATTATTAAA
1 TTTAAT-TATATTAAATTATAATTTAAATTATTAAA
679392 TTTAATTATATTTAAATTA-AATTTAAATT-TTAAA
1 TTTAATTATA-TTAAATTATAATTTAAATTATTAAA
*
679426 ATT--TT-T-TTAAATTATAATTT-AATTA-TAAA
1 TTTAATTATATTAAATTATAATTTAAATTATTAAA
679455 T
1 T
679456 ATATTTTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
29 16 0.28
30 5 0.09
31 1 0.02
32 2 0.03
34 7 0.12
35 13 0.22
36 14 0.24
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (35 bp):
TTTAATTATATTAAATTATAATTTAAATTATTAAA
Found at i:679407 original size:24 final size:24
Alignment explanation
Indices: 679370--679452 Score: 73
Period size: 24 Copynumber: 3.3 Consensus size: 24
679360 ATATATATTA
679370 AATTATTATTTAAATTATTAAATTT
1 AATTA-TATTTAAATTATTAAATTT
679395 AATTATATTTAAATTAAATTTAAATTTT
1 AATTATATTTAAATT--A-TTAAA-TTT
*
679423 AAAATT-TTTTTAAATTA-T-AATTT
1 --AATTATATTTAAATTATTAAATTT
679446 AATTATA
1 AATTATA
679453 AATATATTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
21 4 0.08
22 1 0.02
23 3 0.06
24 12 0.24
25 6 0.12
26 1 0.02
27 6 0.12
28 3 0.06
29 9 0.18
30 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
AATTATATTTAAATTATTAAATTT
Found at i:679415 original size:11 final size:11
Alignment explanation
Indices: 679386--679420 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
679376 TATTTAAATT
679386 ATTAAATTT-A
1 ATTAAATTTAA
*
679396 ATTATATTTAA
1 ATTAAATTTAA
679407 ATTAAATTTAA
1 ATTAAATTTAA
679418 ATT
1 ATT
679421 TTAAAATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:679462 original size:29 final size:28
Alignment explanation
Indices: 679387--679466 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 28
679377 ATTTAAATTA
*
679387 TTAAATTTAATTATA-TTTAAATTAAAT
1 TTAAATTTAAATATATTTTAAATTAAAT
*
679414 TTAAATTTTAAA-ATTTTTTTAAATTATAAT
1 TTAAA-TTTAAATA-TATTTTAAATTA-AAT
679444 TT-AATTATAAATATATTTTAAAT
1 TTAAATT-TAAATATATTTTAAAT
679467 AGCAACCCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
27 6 0.14
28 8 0.18
29 24 0.55
30 6 0.14
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (28 bp):
TTAAATTTAAATATATTTTAAATTAAAT
Found at i:679874 original size:3 final size:3
Alignment explanation
Indices: 679861--679900 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
679851 ATGATTTGTT
*
679861 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
679901 ATGTAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:680080 original size:15 final size:15
Alignment explanation
Indices: 680060--680092 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
680050 ATATTTAACA
680060 TAATATAAATATATT
1 TAATATAAATATATT
*
680075 TAATATAAATATTTT
1 TAATATAAATATATT
680090 TAA
1 TAA
680093 ATTTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATATAAATATATT
Found at i:685465 original size:17 final size:16
Alignment explanation
Indices: 685443--685497 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
685433 CACCTCCAAT
685443 ATTTTATATTTATATAA
1 ATTTTATA-TTATATAA
685460 A-TTT-TATTATAGTAA
1 ATTTTATATTATA-TAA
*
685475 TAATTTATATTATATAA
1 -ATTTTATATTATATAA
685492 ATTTTA
1 ATTTTA
685498 AAATATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 5 0.15
15 5 0.15
16 9 0.27
17 7 0.21
18 7 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:685514 original size:33 final size:32
Alignment explanation
Indices: 685440--685522 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 32
685430 TCACACCTCC
* **
685440 AATATTTTATATTTATATAAATTTTATTATAGT
1 AATAATTTATA-TTATATAAATTTTAAAATAGT
*
685473 AATAATTTATATTATATAAATTTTAAAATATT
1 AATAATTTATATTATATAAATTTTAAAATAGT
* *
685505 ATTATATTTATTTTATAT
1 AATA-ATTTATATTATAT
685523 TTTAATTATT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
32 21 0.49
33 22 0.51
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (32 bp):
AATAATTTATATTATATAAATTTTAAAATAGT
Found at i:691790 original size:18 final size:18
Alignment explanation
Indices: 691754--691788 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
691744 AATATATATT
*
691754 TTAAAGATAAAATAAAAA
1 TTAAAAATAAAATAAAAA
691772 TTAAAAAT-AAATAAAAA
1 TTAAAAATAAAATAAAAA
691789 ATAAGATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (18 bp):
TTAAAAATAAAATAAAAA
Found at i:692588 original size:21 final size:21
Alignment explanation
Indices: 692564--692629 Score: 59
Period size: 20 Copynumber: 3.2 Consensus size: 21
692554 ATGTGTATAT
692564 AATTTATAATAATTATATTAA
1 AATTTATAATAATTATATTAA
* * *
692585 AA-TTA-ATTAATTTTATTTTA
1 AATTTATAATAATTATA-TTAA
692605 AATTTAT-ATAAATTA-ATTAA
1 AATTTATAAT-AATTATATTAA
692625 AATTT
1 AATTT
692630 TATATAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
19 8 0.23
20 16 0.46
21 7 0.20
22 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTATAATAATTATATTAA
Found at i:692618 original size:30 final size:31
Alignment explanation
Indices: 692584--692642 Score: 84
Period size: 32 Copynumber: 1.9 Consensus size: 31
692574 AATTATATTA
* *
692584 AAATTAATT-AATTTTATTTTAAATTTATAT
1 AAATTAATTAAATTTTATATAAAATTTATAT
692614 AAATTAATTAAAATTTTATATAAAATTTA
1 AAATTAATT-AAATTTTATATAAAATTTA
692643 AAATCATACG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 9 0.36
32 16 0.64
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (31 bp):
AAATTAATTAAATTTTATATAAAATTTATAT
Done.