Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 2 of 310
Found at i:286262 original size:30 final size:31
Alignment explanation
Indices: 286228--286294 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
286218 TAAATACCAT
286228 CTATATTG-TGT-T-TATTTTTTTATACATATA
1 CTATATTGTTGTATGTA-TTTTTTATACATA-A
*
286258 CTATA-TGTTGTATGTATTTTTTATATATAA
1 CTATATTGTTGTATGTATTTTTTATACATAA
286288 CTATATT
1 CTATATT
286295 ATACGTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 2 0.06
30 14 0.44
31 14 0.44
32 2 0.06
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.58
Consensus pattern (31 bp):
CTATATTGTTGTATGTATTTTTTATACATAA
Found at i:286564 original size:26 final size:26
Alignment explanation
Indices: 286535--286598 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
286525 CCATATTATG
286535 TTTTTATATTTAT-TATGTATATACTT
1 TTTTTATATTTATATATGTATATA-TT
286561 TTTTTA-ATATTATATATGTATATATT
1 TTTTTATAT-TTATATATGTATATATT
*
286587 TTTAATATATTT
1 TTT-TTATATTT
286599 GCGTATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 2 0.06
26 15 0.45
27 14 0.42
28 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTTTATATTTATATATGTATATATT
Found at i:286565 original size:27 final size:27
Alignment explanation
Indices: 286535--286598 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
286525 CCATATTATG
*
286535 TTTTTATATTTAT-TATGTATATACTT
1 TTTTTATATTTATATATGTATATATTT
286561 TTTTTA-ATATTATATATGTATATATTT
1 TTTTTATAT-TTATATATGTATATATTT
**
286588 TTAATATATTT
1 TTTTTATATTT
286599 GCGTATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 2 0.06
26 10 0.31
27 18 0.56
28 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTATATTTATATATGTATATATTT
Found at i:291448 original size:77 final size:77
Alignment explanation
Indices: 291321--291475 Score: 274
Period size: 77 Copynumber: 2.0 Consensus size: 77
291311 TAGTCCTGCT
* *
291321 GATCCACTCGTTCCAAATTTGGACGATCCAGTAGAAATAGCCAATTTGAAAATCGGTGATCACGA
1 GATCCACTCGTTCCAAATTTGGACGATCCAGCAGAAATAGCCAAGTTGAAAATCGGTGATCACGA
291386 GGTTCAAGAGAA
66 GGTTCAAGAGAA
* *
291398 GATCCACTCGTTCCAAATTTGGACGATCCAGCAGAAATAGCTAAGTTGAAAATCGTTGATCACGA
1 GATCCACTCGTTCCAAATTTGGACGATCCAGCAGAAATAGCCAAGTTGAAAATCGGTGATCACGA
291463 GGTTCAAGAGAA
66 GGTTCAAGAGAA
291475 G
1 G
291476 TATAGGAGCT
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (77 bp):
GATCCACTCGTTCCAAATTTGGACGATCCAGCAGAAATAGCCAAGTTGAAAATCGGTGATCACGA
GGTTCAAGAGAA
Found at i:299270 original size:15 final size:15
Alignment explanation
Indices: 299254--299288 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
299244 GCTGAGGTAT
299254 TTTC-AATTTCTGTA
1 TTTCAAATTTCTGTA
299268 TTTCAAATTTCTGT-
1 TTTCAAATTTCTGTA
299282 TTTCAAA
1 TTTCAAA
299289 AATCGACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.26, C:0.14, G:0.06, T:0.54
Consensus pattern (15 bp):
TTTCAAATTTCTGTA
Found at i:299273 original size:14 final size:13
Alignment explanation
Indices: 299253--299287 Score: 52
Period size: 15 Copynumber: 2.5 Consensus size: 13
299243 CGCTGAGGTA
299253 TTTTCAATTTCTG
1 TTTTCAATTTCTG
299266 TATTTCAAATTTCTG
1 T-TTTC-AATTTCTG
299281 TTTTCAA
1 TTTTCAA
299288 AAATCGACTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 3 0.15
14 8 0.40
15 9 0.45
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.57
Consensus pattern (13 bp):
TTTTCAATTTCTG
Found at i:299333 original size:87 final size:87
Alignment explanation
Indices: 299187--299410 Score: 297
Period size: 87 Copynumber: 2.6 Consensus size: 87
299177 TTGATGTTTT
* * * * * **
299187 ATTTCTGTTCTCAGAAATCGACTCATATTGCAAGAAGTGAGTTAAGCCTCAGGGTACGCTGAGGT
1 ATTTCTGTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
299252 ATTTTCAATTTCTGTATTTCAA
66 AATTTCAATTTCTGTATTTCAA
*
299274 ATTTCTGTTTTCAAAAATCGACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
1 ATTTCTGTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
*
299339 AATTTCAATTTCTGTTTTTCAA
66 AATTTCAATTTCTGTATTTCAA
* * * *
299361 A-TTCTGTTTTCGTCAAAAGCAACTCATGTTGCGAGAGGTGAGTTGAGCCT
1 ATTTCTGTTTTC--AAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCT
299411 TTTTAATTTC
Statistics
Matches: 120, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
86 10 0.08
87 78 0.65
88 32 0.27
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (87 bp):
ATTTCTGTTTTCAAAAATCGACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGT
AATTTCAATTTCTGTATTTCAA
Found at i:299360 original size:14 final size:14
Alignment explanation
Indices: 299341--299370 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
299331 GCTGAGGTAA
*
299341 TTTCAATTTCTGTT
1 TTTCAAATTCTGTT
299355 TTTCAAATTCTGTT
1 TTTCAAATTCTGTT
299369 TT
1 TT
299371 CGTCAAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.17, C:0.13, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTCAAATTCTGTT
Found at i:299448 original size:55 final size:54
Alignment explanation
Indices: 299353--299520 Score: 237
Period size: 55 Copynumber: 3.0 Consensus size: 54
299343 TCAATTTCTG
* * *
299353 TTTTTCAAATTCTGTTTTCGTCAAAAGCAACTCATGTTGCGAGAGGTGAGTTGAGCC
1 TTTTT-AATTTCTGTTTT--TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
299410 TTTTTAATTTCTGTTTTTCAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTTAATTTCTGTTTTTCA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
* **
299465 TTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCC
1 TTTTTAATTTCTGTTTTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
299520 T
1 T
299521 CGGGGCACGC
Statistics
Matches: 103, Mismatches: 6, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
54 3 0.03
55 83 0.81
56 12 0.12
57 5 0.05
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.39
Consensus pattern (54 bp):
TTTTTAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
Found at i:299560 original size:73 final size:73
Alignment explanation
Indices: 299465--299840 Score: 266
Period size: 73 Copynumber: 5.2 Consensus size: 73
299455 GAGTTGAGCC
* * *
299465 TTTTTAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGGCACG
*
299530 CCGAGGTA
66 CTGAGGTA
* ** * **
299538 TTTTAAATTTCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGGCACG
299603 CTGAGGTA
66 CTGAGGTA
* * * * ** ** * * ** * ***
299611 ATTTCAATTTCTATTTTTC-AAATTC-TGTTTTCTT-C-A-AAATCAACTCATATTGCGAGAGGT
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCT-CG-G-GG-
* * *
299671 GA-GTTGAGCCT-
62 CACGCTGAG-GTA
* * *
299682 TTTT-AATTTCTGTTTTTCAGAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCATG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGGCACG
299746 AC-GAGGTA
66 -CTGAGGTA
* * ** * **
299754 TTTTAAATTCCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACG
1 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGGCACG
299819 CTGAGGTA
66 CTGAGGTA
* *
299827 ATTTCAATTTCTGT
1 TTTTAAATTTCTGT
299841 CTTTAATTTC
Statistics
Matches: 222, Mismatches: 66, Indels: 30
0.70 0.21 0.09
Matches are distributed among these distances:
68 6 0.03
69 2 0.01
70 15 0.07
71 19 0.09
72 22 0.10
73 147 0.66
74 3 0.01
75 8 0.04
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.35
Consensus pattern (73 bp):
TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGCCTCGGGGCACG
CTGAGGTA
Found at i:299687 original size:216 final size:214
Alignment explanation
Indices: 299410--299951 Score: 910
Period size: 216 Copynumber: 2.5 Consensus size: 214
299400 GAGTTGAGCC
299410 TTTTTAATTTCTGTTTT-TCAGAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAATT
1 TTTTTAATTTCTGTTTTCTCA-AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAATT
* *
299474 TCTATTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGCCGAGGTAT
65 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGACGAGGTAT
*
299539 TTTAAATTTCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACGC
130 TTTAAATTCCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACGC
299604 TGAGGTAATTTCAATTTCTA
195 TGAGGTAATTTCAATTTCTA
*
299624 TTTTTCAAATTCTGTTTTCTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAAT
1 TTTTT-AATTTCTGTTTTC-TCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAAT
* *
299689 TTCTGTTTTTCAGAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCATGACGAGGTA
64 TTCTGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGACGAGGTA
299754 TTTTAAATTCCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACG
129 TTTTAAATTCCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACG
*
299819 CTGAGGTAATTTCAATTTCTG
194 CTGAGGTAATTTCAATTTCTA
* *
299840 TCTTTAATTTCTGCTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTTAATT
1 TTTTTAATTTCTG-TTTTCTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAATT
* * **
299903 TCTGGTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
65 TCTGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCG
299952 AGACATATTG
Statistics
Matches: 309, Mismatches: 15, Indels: 9
0.93 0.05 0.03
Matches are distributed among these distances:
213 52 0.17
214 40 0.13
215 18 0.06
216 196 0.63
217 3 0.01
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (214 bp):
TTTTTAATTTCTGTTTTCTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTTAATTT
CTGTTTTTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCGGGGCACGACGAGGTATT
TTAAATTCCTGTTTGTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGATACGCT
GAGGTAATTTCAATTTCTA
Found at i:299711 original size:55 final size:57
Alignment explanation
Indices: 299624--299736 Score: 169
Period size: 55 Copynumber: 2.0 Consensus size: 57
299614 TCAATTTCTA
**
299624 TTTTTCAAATTCTGTTTTCTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
1 TTTTTCAAATTCTGTTTTCTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCC
*
299681 TTTTT-AATTTCTG-TTT-TTCAGAAATCAACTCATATTGCGAGAAATGAGTTGAGCC
1 TTTTTCAAATTCTGTTTTCTTCA-AAATCAACTCATATTGCGAGAAATGAGTTGAGCC
299736 T
1 T
299737 CGGGGCATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
54 4 0.08
55 36 0.69
56 7 0.13
57 5 0.10
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (57 bp):
TTTTTCAAATTCTGTTTTCTTCAAAATCAACTCATATTGCGAGAAATGAGTTGAGCC
Found at i:299912 original size:54 final size:54
Alignment explanation
Indices: 299842--299949 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
299832 AATTTCTGTC
*
299842 TTTAATTTCTGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTAATTTCTGCTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
299896 TTTAATTTCTGGTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 TTTAATTTCTGCTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT
299950 CGAGACATAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (54 bp):
TTTAATTTCTGCTTTTCAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGCCT
Found at i:301913 original size:3 final size:3
Alignment explanation
Indices: 301902--301940 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
301892 TTTTTTCTAA
* *
301902 TAT TGT TAT TAT TAT TAC TAT TAT TAT TAT TAT ATAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
301941 GAGTATACTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:302264 original size:20 final size:20
Alignment explanation
Indices: 302209--302285 Score: 68
Period size: 20 Copynumber: 3.8 Consensus size: 20
302199 ATTTTCTTAT
302209 TATATTATTATGTATATTATTC
1 TATA-TATTATGTATATT-TTC
* *
302231 T-TTTAAATAT-TATATTTTC
1 TATAT-ATTATGTATATTTTC
* *
302250 TATATATTATGTATATATTA
1 TATATATTATGTATATTTTC
*
302270 TATATATTACGTATAT
1 TATATATTATGTATAT
302286 ATCTAGTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 8 0.18
20 31 0.69
21 5 0.11
22 1 0.02
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.57
Consensus pattern (20 bp):
TATATATTATGTATATTTTC
Found at i:302445 original size:30 final size:31
Alignment explanation
Indices: 302411--302477 Score: 79
Period size: 30 Copynumber: 2.2 Consensus size: 31
302401 TAAATACCAT
302411 CTATATTG-TGT-T-TATTTTTTTATACATATA
1 CTATATTGTTGTATGTA-TTTTTTATACATA-A
*
302441 CTATA-TGTTGTATGTATTTTTTATATATAA
1 CTATATTGTTGTATGTATTTTTTATACATAA
302471 CTATATT
1 CTATATT
302478 ATACGTATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
29 2 0.06
30 14 0.44
31 14 0.44
32 2 0.06
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.58
Consensus pattern (31 bp):
CTATATTGTTGTATGTATTTTTTATACATAA
Found at i:302747 original size:26 final size:26
Alignment explanation
Indices: 302718--302781 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 26
302708 CCATATTATG
302718 TTTTTATATTTAT-TATGTATATACTT
1 TTTTTATATTTATATATGTATATA-TT
302744 TTTTTA-ATATTATATATGTATATATT
1 TTTTTATAT-TTATATATGTATATATT
*
302770 TTTAATATATTT
1 TTT-TTATATTT
302782 GCGTATATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
25 2 0.06
26 15 0.45
27 14 0.42
28 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (26 bp):
TTTTTATATTTATATATGTATATATT
Found at i:302748 original size:27 final size:27
Alignment explanation
Indices: 302718--302781 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
302708 CCATATTATG
*
302718 TTTTTATATTTAT-TATGTATATACTT
1 TTTTTATATTTATATATGTATATATTT
302744 TTTTTA-ATATTATATATGTATATATTT
1 TTTTTATAT-TTATATATGTATATATTT
**
302771 TTAATATATTT
1 TTTTTATATTT
302782 GCGTATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
25 2 0.06
26 10 0.31
27 18 0.56
28 2 0.06
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (27 bp):
TTTTTATATTTATATATGTATATATTT
Found at i:310940 original size:19 final size:19
Alignment explanation
Indices: 310916--310955 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
310906 AAACATGAAT
*
310916 GAATAAATAATATTTCATA
1 GAATAAAAAATATTTCATA
*
310935 GAATAAAAAATATTTTATA
1 GAATAAAAAATATTTCATA
310954 GA
1 GA
310956 CATCATCAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (19 bp):
GAATAAAAAATATTTCATA
Found at i:312396 original size:25 final size:25
Alignment explanation
Indices: 312362--312412 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
312352 GGGTTAAATT
*
312362 AATTTGTATGTGAATTAGATTTTCA
1 AATTTGTATGTGAATAAGATTTTCA
*
312387 AATTTGTATGTGAATAAGTTTTTCA
1 AATTTGTATGTGAATAAGATTTTCA
312412 A
1 A
312413 GCGATATCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (25 bp):
AATTTGTATGTGAATAAGATTTTCA
Found at i:318887 original size:21 final size:22
Alignment explanation
Indices: 318849--318890 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
318839 AACTTTTTAA
*
318849 TATTAATTATATTTAATATTTT
1 TATTAATTATATTGAATATTTT
*
318871 TATT-ATTGTATTGAATATTT
1 TATTAATTATATTGAATATTT
318891 AAAATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (22 bp):
TATTAATTATATTGAATATTTT
Found at i:324632 original size:25 final size:24
Alignment explanation
Indices: 324594--324802 Score: 83
Period size: 25 Copynumber: 8.5 Consensus size: 24
324584 TTTAGCTCTT
*
324594 ATGAGCATCCCGATATATGGCTTGC
1 ATGAGCTTCCCGATATATGGCTT-C
*
324619 ATGAGCTTCTCGAT-TAATGGCTCTC
1 ATGAGCTTCCCGATAT-ATGGCT-TC
*
324644 -TGGAGCTTTTCC-ATAT-TGGCTTAC
1 AT-GAGC-TTCCCGATATATGGCTT-C
*
324668 ATGAGTTTCCCGAT-TAATGGCTCTC
1 ATGAGCTTCCCGATAT-ATGGCT-TC
* * ** *
324693 -TAGTGCTTCCTGATAT-TAACTAGC
1 AT-GAGCTTCCCGATATATGGCT-TC
* * *
324717 ATGAGCTTCTCGAT-TACGGCTCTT
1 ATGAGCTTCCCGATATATGGCT-TC
* * *
324741 ATGAGCTTCCCGTTACATGGCTCAC
1 ATGAGCTTCCCGATATATGGCT-TC
* *
324766 ATGAGCTTCCCGTTATATGGCTTGG
1 ATGAGCTTCCCGATATATGGCTT-C
*
324791 AAGAGCTTCCCG
1 ATGAGCTTCCCG
324803 GTTACATGTT
Statistics
Matches: 135, Mismatches: 32, Indels: 34
0.67 0.16 0.17
Matches are distributed among these distances:
23 7 0.05
24 41 0.30
25 80 0.59
26 7 0.05
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (24 bp):
ATGAGCTTCCCGATATATGGCTTC
Found at i:324709 original size:49 final size:49
Alignment explanation
Indices: 324603--324787 Score: 148
Period size: 49 Copynumber: 3.8 Consensus size: 49
324593 TATGAGCATC
* * *
324603 CCGATATATGGCTTGCATGAGCTTCTCGATTAATGGCTCTCTGGAGCTTTT
1 CCGATAT-TGGCTTACATGAGCTTCCCGATTAATGGCTCTCTAGAGC-TTT
* *
324654 CC-ATATTGGCTTACATGAGTTTCCCGATTAATGGCTCTCTAGTGC-TT
1 CCGATATTGGCTTACATGAGCTTCCCGATTAATGGCTCTCTAGAGCTTT
** * * *
324701 CCTGATATTAAC-TAGCATGAGCTTCTCGATT-ACGGCTCT-TATGAGCTTC
1 CC-GATATTGGCTTA-CATGAGCTTCCCGATTAATGGCTCTCTA-GAGCTTT
* * *
324750 CCGTTACATGGCTCACATGAGCTTCCCG-TTATATGGCT
1 CCGATA-TTGGCTTACATGAGCTTCCCGATTA-ATGGCT
324788 TGGAAGAGCT
Statistics
Matches: 106, Mismatches: 19, Indels: 19
0.74 0.13 0.13
Matches are distributed among these distances:
47 6 0.06
48 17 0.16
49 71 0.67
50 10 0.09
51 2 0.02
ACGTcount: A:0.19, C:0.24, G:0.21, T:0.36
Consensus pattern (49 bp):
CCGATATTGGCTTACATGAGCTTCCCGATTAATGGCTCTCTAGAGCTTT
Found at i:328613 original size:30 final size:31
Alignment explanation
Indices: 328579--328641 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
328569 TATTTTATTA
*
328579 TTAA-TTTTCTTATTATTTTA-AAGGCATTTG
1 TTAATTTTTATTATTATTTTAGAA-GCATTTG
*
328609 TTAATTTTTATTATTTTTTTAGAAGCATTTG
1 TTAATTTTTATTATTATTTTAGAAGCATTTG
328640 TT
1 TT
328642 TGTTAAGTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 4 0.14
31 23 0.79
32 2 0.07
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (31 bp):
TTAATTTTTATTATTATTTTAGAAGCATTTG
Found at i:328757 original size:18 final size:18
Alignment explanation
Indices: 328722--328761 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
328712 GAAATATTTA
*
328722 TTTTGATGTTTTTAATAT
1 TTTTGATGTTTATAATAT
328740 TTTTGATGTATTATATATAT
1 TTTTGATGT-TTATA-ATAT
328760 TT
1 TT
328762 AAAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 4 0.21
20 6 0.32
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (18 bp):
TTTTGATGTTTATAATAT
Found at i:328796 original size:13 final size:11
Alignment explanation
Indices: 328761--328792 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
328751 TATATATATT
328761 TAAAAATAATA
1 TAAAAATAATA
328772 TAAAAATAATA
1 TAAAAATAATA
328783 TAAAAA-AATA
1 TAAAAATAATA
328793 ATATGGGCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.19
11 17 0.81
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (11 bp):
TAAAAATAATA
Found at i:340984 original size:14 final size:14
Alignment explanation
Indices: 340965--340992 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
340955 GGCAAATTCA
340965 AGTTTGGCAAGATT
1 AGTTTGGCAAGATT
340979 AGTTTGGCAAGATT
1 AGTTTGGCAAGATT
340993 TGACATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
AGTTTGGCAAGATT
Found at i:344162 original size:6 final size:6
Alignment explanation
Indices: 344119--344159 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
344109 GAATTTCAAA
* *
344119 CATGTT CATGTT CATGTT CATGTT CATGTC CATGTC CATGT
1 CATGTT CATGTT CATGTT CATGTT CATGTT CATGTT CATGT
344160 CCAGCTGGGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (6 bp):
CATGTT
Found at i:359835 original size:21 final size:22
Alignment explanation
Indices: 359809--359862 Score: 69
Period size: 21 Copynumber: 2.5 Consensus size: 22
359799 TTCCTTGTTT
359809 CACACGGGCGTGTG-C-CTCTGC
1 CACACGGGCGTGTGTCTCTCT-C
359830 CACAC-GGCTGTGTGTCTCTCTC
1 CACACGGGC-GTGTGTCTCTCTC
359852 CACACGGGCGT
1 CACACGGGCGT
359863 TTTGACTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 3 0.10
21 10 0.34
22 9 0.31
23 7 0.24
ACGTcount: A:0.11, C:0.37, G:0.30, T:0.22
Consensus pattern (22 bp):
CACACGGGCGTGTGTCTCTCTC
Found at i:365406 original size:33 final size:33
Alignment explanation
Indices: 365364--365444 Score: 101
Period size: 33 Copynumber: 2.5 Consensus size: 33
365354 TGGCCCAGCC
* *
365364 ATGGCCTTATATTTATAGTGCCATAACCCAATT
1 ATGGCCTTATATTTAGAATGCCATAACCCAATT
* *
365397 ATGGCCTTATCA-TCAGAATGCCATAGCCCAATT
1 ATGGCCTTAT-ATTTAGAATGCCATAACCCAATT
*
365430 ATGGTCTTATATTTA
1 ATGGCCTTATATTTA
365445 ATCATTGTCA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 1 0.03
33 38 0.95
34 1 0.03
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (33 bp):
ATGGCCTTATATTTAGAATGCCATAACCCAATT
Found at i:375798 original size:44 final size:40
Alignment explanation
Indices: 375740--375815 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
375730 TCTTCTTATA
375740 TATATATATTTATATATATATTTAGAATATACATTCTTCT
1 TATATATATTTATATATATATTTAGAATATACATTCTTCT
375780 TATATATATTTATATATATATTTAGAATATACATTC
1 TATATATATTTATATATATATTTAGAATATACATTC
375816 GCTCTCAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.39, C:0.07, G:0.03, T:0.51
Consensus pattern (40 bp):
TATATATATTTATATATATATTTAGAATATACATTCTTCT
Found at i:379341 original size:5 final size:5
Alignment explanation
Indices: 379333--379369 Score: 65
Period size: 5 Copynumber: 7.2 Consensus size: 5
379323 TTTGGAAGAC
379333 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTATAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT-TAT T
379370 AGGATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 27 0.87
6 4 0.13
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:385579 original size:40 final size:40
Alignment explanation
Indices: 385524--385602 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
385514 GCTATTCCCA
*
385524 GGTAAGCTTCGATCTCGATGGCACGGACCTTTTATTGTGG
1 GGTAAGCTTCGATCTCGATGGCAAGGACCTTTTATTGTGG
*
385564 GGTAAGCTTCGATCTCGGTGGCAAGGACCTTTTATTGTG
1 GGTAAGCTTCGATCTCGATGGCAAGGACCTTTTATTGTG
385603 ACTGAAGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.18, C:0.19, G:0.30, T:0.33
Consensus pattern (40 bp):
GGTAAGCTTCGATCTCGATGGCAAGGACCTTTTATTGTGG
Found at i:385849 original size:5 final size:5
Alignment explanation
Indices: 385813--385886 Score: 60
Period size: 5 Copynumber: 14.0 Consensus size: 5
385803 TAATCTTTCT
* * * *
385813 TTTTA TTTTTA TTTATTA TTTTC CTTTC TTTTA TTTTA TTATT- TATTA
1 TTTTA -TTTTA -TT-TTA TTTTA TTTTA TTTTA TTTTA TT-TTA TTTTA
385861 TTTTA TTTTTA TTTTA TTTTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA
385887 GTTAAATATT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
4 2 0.03
5 36 0.62
6 17 0.29
7 3 0.05
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:385857 original size:30 final size:31
Alignment explanation
Indices: 385807--385883 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
385797 GCAACCTAAT
385807 CTTTCTTTT-TATTT-TTATTTATTATTTT-C
1 CTTTCTTTTAT-TTTATTATTTATTATTTTAC
*
385836 CTTTCTTTTATTTTATTATTTATTATTTTAT
1 CTTTCTTTTATTTTATTATTTATTATTTTAC
* *
385867 TTTTATTTTATTTTATT
1 CTTTCTTTTATTTTATT
385884 TTAGTTAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 12 0.29
30 15 0.36
31 15 0.36
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.77
Consensus pattern (31 bp):
CTTTCTTTTATTTTATTATTTATTATTTTAC
Found at i:385872 original size:21 final size:20
Alignment explanation
Indices: 385841--385886 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
385831 TTTTCCTTTC
385841 TTTTATTTTATTATT-TATTA
1 TTTTATTTTATT-TTATATTA
*
385861 TTTTATTTTTATTTTATTTTA
1 TTTTA-TTTTATTTTATATTA
385882 TTTTA
1 TTTTA
385887 GTTAAATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTATTTTATTTTATATTA
Found at i:386039 original size:42 final size:42
Alignment explanation
Indices: 385993--386083 Score: 119
Period size: 42 Copynumber: 2.2 Consensus size: 42
385983 ATCCATGGTA
*
385993 CCAAACAGTTCAATTCCAACCCAAAATGCCATATCCCTGCTG
1 CCAAACAGTTCAATTCCAACCCAAAATGCCATATCCCTGCAG
** * * *
386035 CCAAACAGTTTTATTCCAGCCCAGAATGCCATATCTCTGCAG
1 CCAAACAGTTCAATTCCAACCCAAAATGCCATATCCCTGCAG
*
386077 CCGAACA
1 CCAAACA
386084 ATCCTATTCC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.32, C:0.34, G:0.12, T:0.22
Consensus pattern (42 bp):
CCAAACAGTTCAATTCCAACCCAAAATGCCATATCCCTGCAG
Found at i:386092 original size:42 final size:42
Alignment explanation
Indices: 386005--386104 Score: 119
Period size: 42 Copynumber: 2.4 Consensus size: 42
385995 AAACAGTTCA
* * * * **
386005 ATTCCAACCCAAAATGCCATATCCCTGCTGCCAAACAGTTTT
1 ATTCCAGCCCAGAATGCCATATCCCTGCAGCCAAACAATCCT
* *
386047 ATTCCAGCCCAGAATGCCATATCTCTGCAGCCGAACAATCCT
1 ATTCCAGCCCAGAATGCCATATCCCTGCAGCCAAACAATCCT
386089 ATTCCAGCCCTAGAAT
1 ATTCCAGCCC-AGAAT
386105 CCCCAAAACC
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 44 0.90
43 5 0.10
ACGTcount: A:0.30, C:0.34, G:0.12, T:0.24
Consensus pattern (42 bp):
ATTCCAGCCCAGAATGCCATATCCCTGCAGCCAAACAATCCT
Found at i:387136 original size:11 final size:11
Alignment explanation
Indices: 387122--387171 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
387112 ATAAAATTTA
387122 AAAAAAGAAAG
1 AAAAAAGAAAG
*
387133 AAAAAAAGAAAA
1 -AAAAAAGAAAG
387145 AAAAAAGAAA-
1 AAAAAAGAAAG
387155 AAAAGAAG-AAG
1 AAAA-AAGAAAG
387166 AAAAAA
1 AAAAAA
387172 ATAAGTACTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 8 0.23
11 17 0.49
12 10 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:387140 original size:8 final size:8
Alignment explanation
Indices: 387121--387161 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
387111 AATAAAATTT
387121 AAAAAAAG
1 AAAAAAAG
387129 AAAGAAAA-
1 AAA-AAAAG
*
387137 AAAGAAA-
1 AAAAAAAG
387144 AAAAAAAG
1 AAAAAAAG
387152 AAAAAAAG
1 AAAAAAAG
387160 AA
1 AA
387162 GAAGAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
7 9 0.31
8 16 0.55
9 4 0.14
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:387144 original size:19 final size:19
Alignment explanation
Indices: 387121--387171 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 19
387111 AATAAAATTT
387121 AAAAAAAGAAAGAAAAAAAG
1 AAAAAAA-AAAGAAAAAAAG
387141 AAAAAAAAAAGAAAAAAAG
1 AAAAAAAAAAGAAAAAAAG
387160 AAGAAGAAAAAA
1 AA-AA-AAAAAA
387172 ATAAGTACTA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 14 0.48
20 9 0.31
21 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAAAAAAAG
Found at i:387146 original size:22 final size:23
Alignment explanation
Indices: 387121--387172 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
387111 AATAAAATTT
387121 AAAAAAAGAAAGAAAAAAAGAAA-
1 AAAAAAAGAAA-AAAAAAAGAAAG
*
387144 AAAAAAAGAAAAAAAGAAG-AAG
1 AAAAAAAGAAAAAAAAAAGAAAG
387166 AAAAAAA
1 AAAAAAA
387173 TAAGTACTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 2 0.07
22 14 0.52
23 11 0.41
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (23 bp):
AAAAAAAGAAAAAAAAAAGAAAG
Found at i:391874 original size:10 final size:10
Alignment explanation
Indices: 391855--391883 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
391845 TTTTAGGATT
391855 TTAT-TTTAA
1 TTATCTTTAA
391864 TTATCTTTAA
1 TTATCTTTAA
391874 TTATCTTTAA
1 TTATCTTTAA
391884 CTAAATGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.21
10 15 0.79
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (10 bp):
TTATCTTTAA
Found at i:392273 original size:30 final size:30
Alignment explanation
Indices: 392239--392301 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
392229 ACTTAAGAAG
392239 CAAATG-CTTCTAAAATAATAAAAAAATTAA
1 CAAATGCCTT-TAAAATAATAAAAAAATTAA
*
392269 CAAATGCCTTTAAAATAATAAGAAAATTAA
1 CAAATGCCTTTAAAATAATAAAAAAATTAA
392299 CAA
1 CAA
392302 TAAAATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAAAAAAATTAA
Found at i:394472 original size:15 final size:15
Alignment explanation
Indices: 394452--394484 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
394442 AATCAAAAAA
394452 TAAAA-TAAAATAATT
1 TAAAATTAAAA-AATT
394467 TAAAATTAAAAAATT
1 TAAAATTAAAAAATT
394482 TAA
1 TAA
394485 CATGAAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
TAAAATTAAAAAATT
Found at i:406757 original size:21 final size:23
Alignment explanation
Indices: 406710--406763 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
406700 CATTCAAGAT
**
406710 AAAATAATATATAAAACTCTTTA
1 AAAATAATATATAAAACTAATTA
*
406733 AAAATAATATAT-AAAC-AATTC
1 AAAATAATATATAAAACTAATTA
406754 AAAAT-ATATA
1 AAAATAATATA
406764 ATGTGTAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 7 0.25
22 4 0.14
23 12 0.43
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (23 bp):
AAAATAATATATAAAACTAATTA
Found at i:406808 original size:25 final size:25
Alignment explanation
Indices: 406711--406867 Score: 72
Period size: 25 Copynumber: 6.3 Consensus size: 25
406701 ATTCAAGATA
* * *
406711 AAATAATATATAAAACTCTT-TAA-
1 AAATAATATATAAAAATATTAAAAT
*
406734 AAATAATATATAAACAAT-TCAAAAT
1 AAATAATATATAAA-AATATTAAAAT
* * * *
406759 ATATAATGTGTAAAAAAAAGTTTAAAAT
1 AAATAATATAT-AAAAATA--TTAAAAT
* * *
406787 ACATAATATATGAAAATATTAAAGT
1 AAATAATATATAAAAATATTAAAAT
* *
406812 AAATAATGTATAAAAAT-TTGAAAT
1 AAATAATATATAAAAATATTAAAAT
* *** *
406836 GAACGTTATATAAAAA-GTTAAAAT
1 AAATAATATATAAAAATATTAAAAT
*
406860 AGATAATA
1 AAATAATA
406868 ACCAAAAATG
Statistics
Matches: 96, Mismatches: 30, Indels: 15
0.68 0.21 0.11
Matches are distributed among these distances:
23 15 0.16
24 29 0.30
25 30 0.31
26 3 0.03
27 5 0.05
28 14 0.15
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.31
Consensus pattern (25 bp):
AAATAATATATAAAAATATTAAAAT
Found at i:407002 original size:44 final size:42
Alignment explanation
Indices: 406927--407034 Score: 119
Period size: 44 Copynumber: 2.5 Consensus size: 42
406917 CAAGAGTAAA
* * *
406927 AAATATATATAAGAAAAATAATAATGAAA-ATAATATTAGTATAT
1 AAATATAAAT-AGAAAAATAATAATGAAATATAATAATAGT-T-G
*
406971 AAATATAAATAGAAATATAATAAATAGAAATATAATAATAGTTG
1 AAATATAAATAGAAAAATAAT-AAT-GAAATATAATAATAGTTG
*
407015 AAATATAAATAGATAAATAA
1 AAATATAAATAGAAAAATAA
407035 AAATTAGATA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
43 10 0.18
44 30 0.55
45 5 0.09
46 10 0.18
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (42 bp):
AAATATAAATAGAAAAATAATAATGAAATATAATAATAGTTG
Found at i:407019 original size:17 final size:15
Alignment explanation
Indices: 406975--407022 Score: 69
Period size: 15 Copynumber: 3.1 Consensus size: 15
406965 GTATATAAAT
406975 ATAAATAGAAATATA
1 ATAAATAGAAATATA
406990 ATAAATAGAAATATA
1 ATAAATAGAAATATA
*
407005 ATAATAGTTGAAATATA
1 ATAA-A-TAGAAATATA
407022 A
1 A
407023 ATAGATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 19 0.63
16 1 0.03
17 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.29
Consensus pattern (15 bp):
ATAAATAGAAATATA
Found at i:407042 original size:15 final size:14
Alignment explanation
Indices: 406969--407055 Score: 63
Period size: 15 Copynumber: 6.0 Consensus size: 14
406959 ATATTAGTAT
*
406969 ATAAATATAAATAG
1 ATAAATAAAAATAG
406983 A-AATATAATAAATAG
1 ATAA-ATAA-AAATAG
*
406998 A-AATATAATAATAG
1 ATAA-ATAAAAATAG
* *
407012 TTGAAATATAAATAG
1 AT-AAATAAAAATAG
407027 ATAAATAAAAATTAG
1 ATAAATAAAAA-TAG
407042 ATAAA-AAATAATAG
1 ATAAATAAA-AATAG
407056 TATTAGAATA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
13 2 0.03
14 23 0.38
15 33 0.55
16 2 0.03
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (14 bp):
ATAAATAAAAATAG
Found at i:407052 original size:44 final size:44
Alignment explanation
Indices: 406971--407056 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 44
406961 ATTAGTATAT
*
406971 AAATATAAATAGAAATATAATAAATAGAAATATAATAATAGTTG
1 AAATATAAATAGAAATATAATAAATAGAAATAAAATAATAGTTG
407015 AAATATAAATAGATAA-ATAA-AAATTAGATAA-AAAATAATAGT
1 AAATATAAATAGA-AATATAATAAA-TAGA-AATAAAATAATAGT
407057 ATTAGAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
43 3 0.08
44 31 0.82
45 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (44 bp):
AAATATAAATAGAAATATAATAAATAGAAATAAAATAATAGTTG
Found at i:411458 original size:39 final size:39
Alignment explanation
Indices: 411399--411499 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
411389 ATCGTGATCT
** *
411399 GAAGCCCGAAATCTAGCTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
*
411438 GAAGCCCGGAGGCTAACTGAAGCACATAAGTGCTAAACG
1 GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
411477 GAAGCCCGAAGGCTAACTGAAGC
1 GAAGCCCGAAGGCTAACTGAAGC
411500 TCATCAGAGC
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.37, C:0.24, G:0.27, T:0.13
Consensus pattern (39 bp):
GAAGCCCGAAGGCTAACTGAAGCACATAAGTGCTAAACG
Found at i:411481 original size:21 final size:21
Alignment explanation
Indices: 411417--411481 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
411407 AAATCTAGCT
411417 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
*** *
411438 GAAGC-CCGGAG-GCT-AACT
1 GAAGCACATAAGTGCTAAACG
411456 GAAGCACATAAGTGCTAAACG
1 GAAGCACATAAGTGCTAAACG
411477 GAAGC
1 GAAGC
411482 CCGAAGGCTA
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
18 8 0.24
19 6 0.18
20 6 0.18
21 13 0.39
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (21 bp):
GAAGCACATAAGTGCTAAACG
Found at i:413119 original size:104 final size:104
Alignment explanation
Indices: 413008--413216 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 104
412998 TATTTTTAAT
413008 TATATTTATACTTTAATTTTAATTTTAATATAATCAATTTTTATTATATTTTTCAAATTGTGTAT
1 TATATTTATACTTTAATTTTAATTTTAATATAATCAATTTTTATTATATTTTTCAAATTGTGTAT
413073 TGTTTTAAGAATTGTTTTAATATATTTTTTATTTGTTTC
66 TGTTTTAAGAATTGTTTTAATATATTTTTTATTTGTTTC
* *
413112 TATATTTATATTTTAATTTTAATTTTAATATAATCAATTTTTATTATATTTTTCAATTTGTGTAT
1 TATATTTATACTTTAATTTTAATTTTAATATAATCAATTTTTATTATATTTTTCAAATTGTGTAT
413177 TGTTTTAAGAATTGTTTTAATATATTTTTTATTTGTTTC
66 TGTTTTAAGAATTGTTTTAATATATTTTTTATTTGTTTC
413216 T
1 T
413217 TGTTTTAGTA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.62
Consensus pattern (104 bp):
TATATTTATACTTTAATTTTAATTTTAATATAATCAATTTTTATTATATTTTTCAAATTGTGTAT
TGTTTTAAGAATTGTTTTAATATATTTTTTATTTGTTTC
Found at i:413222 original size:40 final size:41
Alignment explanation
Indices: 413150--413236 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
413140 TATAATCAAT
*
413150 TTTTATTATATTTTTCAATTTGTGTATTGTTTTAAG-AATTG
1 TTTTAATATATTTTTCAATTTGTGTATTGTTTT-AGTAATTG
* * * *
413191 TTTTAATATATTTTT-TATTTGTTTCTTGTTTTAGTATTTG
1 TTTTAATATATTTTTCAATTTGTGTATTGTTTTAGTAATTG
413231 TTTTAA
1 TTTTAA
413237 ATGTATTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 2 0.05
40 24 0.60
41 14 0.35
ACGTcount: A:0.22, C:0.02, G:0.10, T:0.66
Consensus pattern (41 bp):
TTTTAATATATTTTTCAATTTGTGTATTGTTTTAGTAATTG
Found at i:422174 original size:13 final size:13
Alignment explanation
Indices: 422156--422180 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
422146 ATAGTTGGGG
422156 AGCTTTGAAACAT
1 AGCTTTGAAACAT
422169 AGCTTTGAAACA
1 AGCTTTGAAACA
422181 GATGAAATTT
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:0.40, C:0.16, G:0.16, T:0.28
Consensus pattern (13 bp):
AGCTTTGAAACAT
Found at i:438682 original size:18 final size:16
Alignment explanation
Indices: 438649--438695 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 16
438639 TTATGTGTAC
*
438649 AATATAAAAATTTTAAA
1 AATA-AAAAATATTAAA
438666 AATACATAAAATATTAAA
1 AATA-A-AAAATATTAAA
438684 AATAAAAAATAT
1 AATAAAAAATAT
438696 AATTCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.26
17 6 0.22
18 14 0.52
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (16 bp):
AATAAAAAATATTAAA
Found at i:442354 original size:129 final size:129
Alignment explanation
Indices: 442183--442434 Score: 468
Period size: 129 Copynumber: 2.0 Consensus size: 129
442173 ACCCTTTCGG
442183 CCAACTTTACTCATGGCCTCAGCAATCATATTTCCTACTTCATAGTTGTTCCCAGCACTAACAGC
1 CCAACTTTACTCATGGCCTCAGCAATCATATTTCCTACTTCATAGTTGTTCCCAGCACTAACAGC
*
442248 AGCAACATCAGCAAGTTCACTGTCTTCAACCTAAACCCCACAGCACACTAGTTATATTTCTCGA
66 AGCAACATCAGCAAGTTCACTGTCTTCAACCTAAACCCCACAGCACACTAATTATATTTCTCGA
* * *
442312 CCAACTTTACTCATGGCCTCGGCAATCATATTTCCTACTTCATTGTTGTTCCCGGCACTAACAGC
1 CCAACTTTACTCATGGCCTCAGCAATCATATTTCCTACTTCATAGTTGTTCCCAGCACTAACAGC
442377 AGCAACATCAGCAAGTTCACTGTCTTCAACCTAAACCCCACAGCACACTAATTATATT
66 AGCAACATCAGCAAGTTCACTGTCTTCAACCTAAACCCCACAGCACACTAATTATATT
442435 CCCTTCAAAT
Statistics
Matches: 119, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 119 1.00
ACGTcount: A:0.29, C:0.32, G:0.11, T:0.28
Consensus pattern (129 bp):
CCAACTTTACTCATGGCCTCAGCAATCATATTTCCTACTTCATAGTTGTTCCCAGCACTAACAGC
AGCAACATCAGCAAGTTCACTGTCTTCAACCTAAACCCCACAGCACACTAATTATATTTCTCGA
Found at i:446816 original size:41 final size:41
Alignment explanation
Indices: 446771--446949 Score: 270
Period size: 41 Copynumber: 4.4 Consensus size: 41
446761 TGTTTTACAA
* * *
446771 AAAACGCCGCTAAAAA-CAGAGCAATAGCGGCGTTTTTTGTT
1 AAAACGCCGCTAAAAACCGGAGCATTAGCGGCGCTTTTTG-T
*
446812 AAAACGCCGCTAAAAATCGGAGCATTAGCGGCGCTTTTTGT
1 AAAACGCCGCTAAAAACCGGAGCATTAGCGGCGCTTTTTGT
* *
446853 AAAACGCCGCTAAAAACCGGAGCACTAGCGGCGCTTTTGGT
1 AAAACGCCGCTAAAAACCGGAGCATTAGCGGCGCTTTTTGT
* *
446894 AAAACGCCGCTAAAAACCGGAGTATTAGCGGCGCTTTTAGT
1 AAAACGCCGCTAAAAACCGGAGCATTAGCGGCGCTTTTTGT
446935 AAAACGCCGCTAAAA
1 AAAACGCCGCTAAAA
446950 GTCATATAAC
Statistics
Matches: 128, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
41 108 0.84
42 20 0.16
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.21
Consensus pattern (41 bp):
AAAACGCCGCTAAAAACCGGAGCATTAGCGGCGCTTTTTGT
Found at i:447038 original size:23 final size:22
Alignment explanation
Indices: 446991--447038 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
446981 AAAAAATCAT
* *
446991 AAACACTAATCTATAATCCTTA
1 AAACACTAAACTATAAACCTTA
*
447013 AAACACTAAACTCCTAAACCTTA
1 AAACACTAAACT-ATAAACCTTA
447036 AAA
1 AAA
447039 AATCTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACACTAAACTATAAACCTTA
Found at i:447477 original size:15 final size:15
Alignment explanation
Indices: 447452--447505 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
447442 AGGTTAGGTG
* *
447452 TTAGGGGTTAAGGGT
1 TTAGGGTTTAAGAGT
* *
447467 TAAGGGTTTAA-TGT
1 TTAGGGTTTAAGAGT
*
447481 TTAGGGATTAAGAGT
1 TTAGGGTTTAAGAGT
447496 TTAGGGTTTA
1 TTAGGGTTTA
447506 GGTTAGTTAG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 11 0.35
15 20 0.65
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (15 bp):
TTAGGGTTTAAGAGT
Found at i:447491 original size:22 final size:21
Alignment explanation
Indices: 447457--447507 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
447447 AGGTGTTAGG
* *
447457 GGTTAAGGGTTAAGGGTTTAA
1 GGTTTAGGGTTAAGAGTTTAA
* *
447478 TGTTTAGGGATTAAGAGTTTAG
1 GGTTTAGGG-TTAAGAGTTTAA
447500 GGTTTAGG
1 GGTTTAGG
447508 TTAGTTAGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.37
Consensus pattern (21 bp):
GGTTTAGGGTTAAGAGTTTAA
Found at i:447666 original size:22 final size:22
Alignment explanation
Indices: 447641--447683 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
447631 GAGTTATTAT
447641 TTTAAGGTTTATGGA-TTATGGG
1 TTTAAGGTTTAT-GATTTATGGG
*
447663 TTTAGGGTTTATGATTTATGG
1 TTTAAGGTTTATGATTTATGG
447684 TTATGTAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 2 0.11
22 17 0.89
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (22 bp):
TTTAAGGTTTATGATTTATGGG
Found at i:447895 original size:22 final size:25
Alignment explanation
Indices: 447859--447904 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
447849 CATATTTCAG
447859 TTAAAAAAATCAAT-ATT-CAAAAT
1 TTAAAAAAATCAATAATTCCAAAAT
447882 TTAAAAAAAT-AATAATTCCAAAA
1 TTAAAAAAATCAATAATTCCAAAA
447905 AATAATAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.14
23 13 0.62
24 5 0.24
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (25 bp):
TTAAAAAAATCAATAATTCCAAAAT
Found at i:447898 original size:16 final size:16
Alignment explanation
Indices: 447879--447918 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
447869 CAATATTCAA
*
447879 AATTTAAAAAAATAAT
1 AATTCAAAAAAATAAT
*
447895 AATTCCAAAAAATAAT
1 AATTCAAAAAAATAAT
447911 AATCTCAA
1 AAT-TCAA
447919 CACAAAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (16 bp):
AATTCAAAAAAATAAT
Found at i:451534 original size:21 final size:21
Alignment explanation
Indices: 451508--451548 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
451498 ACTTAGAGCG
451508 GAGGCAGCAGCGAGGGAGGCA
1 GAGGCAGCAGCGAGGGAGGCA
451529 GAGGCAGCAGCGAGGGAGGC
1 GAGGCAGCAGCGAGGGAGGC
451549 GGAGTAGAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.20, G:0.54, T:0.00
Consensus pattern (21 bp):
GAGGCAGCAGCGAGGGAGGCA
Found at i:451901 original size:43 final size:42
Alignment explanation
Indices: 451845--451980 Score: 218
Period size: 42 Copynumber: 3.2 Consensus size: 42
451835 ACTGGGCAAC
* *
451845 TTAGAGGCGTTTTTTAAAAAGCGCCGCGAAAAGTCCTCGTCT
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCGAAAAGTCCTGGTCT
* *
451887 TTAGCGGCGTTTTTTAAAAAGCGCCGCTAAAGGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCGAAAAGTCCTGGTCT
*
451929 TTAGCGGCGTTTTTTAAAAAAGCACCGCGAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTT-AAAAAGCGCCGCGAAAAGTCCTGGTCT
451972 TTAGCGGCG
1 TTAGCGGCG
451981 GTGTATATAG
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
42 53 0.62
43 33 0.38
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (42 bp):
TTAGCGGCGTTTTTTAAAAAGCGCCGCGAAAAGTCCTGGTCT
Found at i:453568 original size:41 final size:41
Alignment explanation
Indices: 453473--453601 Score: 170
Period size: 41 Copynumber: 3.2 Consensus size: 41
453463 AATAACCAAC
* * *
453473 CAAAATAATTAACAAATATAATTAATCATC-AACAATCCAT
1 CAAAATAATTAACAAATATAACTAATAATCAAATAATCCAT
*
453513 CAAAATAATTAACAAATATAACTAATTATCAAATAATCCAT
1 CAAAATAATTAACAAATATAACTAATAATCAAATAATCCAT
** * *
453554 CAAAATAACCAACAATTATAACTAATAATCAAATAAACCAT
1 CAAAATAATTAACAAATATAACTAATAATCAAATAATCCAT
*
453595 AAAAATA
1 CAAAATA
453602 TTGGATTAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
40 28 0.35
41 51 0.65
ACGTcount: A:0.58, C:0.16, G:0.00, T:0.26
Consensus pattern (41 bp):
CAAAATAATTAACAAATATAACTAATAATCAAATAATCCAT
Found at i:455474 original size:11 final size:11
Alignment explanation
Indices: 455458--455484 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
455448 TTTCACCAAT
455458 AAAAAAAGAAA
1 AAAAAAAGAAA
455469 AAAAAAAGAAA
1 AAAAAAAGAAA
455480 AAAAA
1 AAAAA
455485 GAAAGGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:456009 original size:32 final size:32
Alignment explanation
Indices: 455970--456037 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 32
455960 ACAACTTAAA
455970 AAAAAACAAT-TCCATAATTCTCATAATCAATT
1 AAAAAACAATAT-CATAATTCTCATAATCAATT
*
456002 AAAAAACAATATCATAATTCTCATCATCAATT
1 AAAAAACAATATCATAATTCTCATAATCAATT
456034 AAAA
1 AAAA
456038 TAACGTTTCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (32 bp):
AAAAAACAATATCATAATTCTCATAATCAATT
Found at i:462295 original size:16 final size:16
Alignment explanation
Indices: 462274--462305 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
462264 TGTCATGTCA
462274 CCTCATCTCATGTTTT
1 CCTCATCTCATGTTTT
462290 CCTCATCTCATGTTTT
1 CCTCATCTCATGTTTT
462306 ATTATATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.06, T:0.50
Consensus pattern (16 bp):
CCTCATCTCATGTTTT
Found at i:473826 original size:27 final size:27
Alignment explanation
Indices: 473785--473912 Score: 157
Period size: 27 Copynumber: 4.7 Consensus size: 27
473775 TACAGAGTTT
* *
473785 GCCACACAGGTTATTCTTTCATATTTC
1 GCCACAAAGGCTATTCTTTCATATTTC
* *
473812 GCTACAAAGGCTATTTTTTCATATTTC
1 GCCACAAAGGCTATTCTTTCATATTTC
* * *
473839 GCCACAAAGGCAATTCTTTCGTATTCC
1 GCCACAAAGGCTATTCTTTCATATTTC
** *
473866 GCCACAAAGATTACTCTTTCATATTTC
1 GCCACAAAGGCTATTCTTTCATATTTC
*
473893 GCCACAAAGGCTACTCTTTC
1 GCCACAAAGGCTATTCTTTC
473913 CTGACGTGTT
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 84 1.00
ACGTcount: A:0.26, C:0.27, G:0.12, T:0.36
Consensus pattern (27 bp):
GCCACAAAGGCTATTCTTTCATATTTC
Found at i:476368 original size:99 final size:100
Alignment explanation
Indices: 476212--476415 Score: 374
Period size: 99 Copynumber: 2.0 Consensus size: 100
476202 GCAAGGCTAT
*
476212 TGATCCATTATTGGGATTTAATTTGGAAGGGAGATCGTTTTTTTCATGTCAAT-GGGGGGAGAAT
1 TGATCCAGTATTGGGATTTAATTTGGAAGGGAGATCGTTTTTTTCATGTCAATGGGGGGGAGAAT
476276 TCATTAGTAGGTTAGGCTTAAACTGCAATGGATCA
66 TCATTAGTAGGTTAGGCTTAAACTGCAATGGATCA
*
476311 TGATCCAGTATTGGGATTTAATTTGGAAGGGAGATTGTTTTTTTCATGTCAATGGGGGGGAGAAT
1 TGATCCAGTATTGGGATTTAATTTGGAAGGGAGATCGTTTTTTTCATGTCAATGGGGGGGAGAAT
*
476376 TCATTAGTAGGTTAGGCTTAAACTGCAATGGATTA
66 TCATTAGTAGGTTAGGCTTAAACTGCAATGGATCA
476411 TGATC
1 TGATC
476416 TAGAAGATGA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
99 51 0.50
100 50 0.50
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (100 bp):
TGATCCAGTATTGGGATTTAATTTGGAAGGGAGATCGTTTTTTTCATGTCAATGGGGGGGAGAAT
TCATTAGTAGGTTAGGCTTAAACTGCAATGGATCA
Found at i:483012 original size:16 final size:17
Alignment explanation
Indices: 482981--483013 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
482971 TTCATAAGTA
482981 TATATCAATCATTTCAT
1 TATATCAATCATTTCAT
482998 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
483014 GCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.36, C:0.15, G:0.00, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:483360 original size:46 final size:46
Alignment explanation
Indices: 483295--483614 Score: 435
Period size: 46 Copynumber: 7.0 Consensus size: 46
483285 TTATCTTTGA
* * * * *
483295 CATGATGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-CGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCA-TTTCATGT
**
483341 CATGTTGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
483387 CACGTTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCATGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * * **
483433 AATGCTGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCGT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
483479 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* * *
483525 CATGTTGCCATGGCATCTTTCAACCATGGTCTTACACATTTCATAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
* *
483571 CATGTTGTCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCAT
483615 TTCAGAAAGC
Statistics
Matches: 249, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
45 4 0.02
46 245 0.98
ACGTcount: A:0.21, C:0.24, G:0.15, T:0.40
Consensus pattern (46 bp):
CATGTTGCCATGGTATCTTTCAACCATGGTCTTACTCATTTCATGT
Found at i:487809 original size:11 final size:11
Alignment explanation
Indices: 487793--487840 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
487783 CTTTATATAC
487793 TAATAAAATAA
1 TAATAAAATAA
*
487804 TAATAAAATATCT
1 TAATAAAATA--A
* *
487817 TATTAAAATAT
1 TAATAAAATAA
487828 TAATAAAATAA
1 TAATAAAATAA
487839 TA
1 TA
487841 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 22 0.71
13 9 0.29
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:489749 original size:3 final size:3
Alignment explanation
Indices: 489743--489797 Score: 67
Period size: 3 Copynumber: 18.7 Consensus size: 3
489733 TATTCTATGG
* * * *
489743 TTA TTA TTA TTA TCA TTG TCA -GA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
489790 TTA TTA TT
1 TTA TTA TT
489798 TTACATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 1 0.02
3 43 0.98
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:491664 original size:28 final size:27
Alignment explanation
Indices: 491612--491695 Score: 98
Period size: 28 Copynumber: 3.0 Consensus size: 27
491602 TTTAAAATGT
*
491612 ATAA-ATATAAATTTTTAAAACTTAAA
1 ATAATATATAAATTTTTAAAAATTAAA
491638 ATAATATATAATATTTTTAAAAATTAAA
1 ATAATATATAA-ATTTTTAAAAATTAAA
* * *
491666 AAAAGTATTTAAATTTTAAAAAATTGAAA
1 ATAA-TATATAAATTTTTAAAAATT-AAA
491695 A
1 A
491696 AAGAAAACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
26 4 0.08
27 6 0.12
28 30 0.60
29 10 0.20
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAATATATAAATTTTTAAAAATTAAA
Found at i:491905 original size:22 final size:20
Alignment explanation
Indices: 491880--491935 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 20
491870 GTTTATATAT
491880 TATTTTGAAATTTTAAAATTCA
1 TATTTT-AAATTTTAAAATT-A
*
491902 TATTTATATATTTTAAAATTA
1 TATTT-TAAATTTTAAAATTA
491923 T-TTTTAAAATTTT
1 TATTTT-AAATTTT
491936 TTTGAATTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 1 0.03
20 9 0.30
21 2 0.07
22 17 0.57
23 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
TATTTTAAATTTTAAAATTA
Found at i:491937 original size:22 final size:22
Alignment explanation
Indices: 491889--491935 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
491879 TTATTTTGAA
*
491889 ATTTTAAAATTCATATTTATAT
1 ATTTTAAAATTCATATTTAAAT
*
491911 ATTTTAAAATT-ATTTTTAAA-
1 ATTTTAAAATTCATATTTAAAT
491931 ATTTT
1 ATTTT
491936 TTTGAATTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 5 0.22
21 7 0.30
22 11 0.48
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTAAAATTCATATTTAAAT
Found at i:492550 original size:27 final size:29
Alignment explanation
Indices: 492520--492592 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
492510 CAAAAAAATG
*
492520 ATAAAAAAT-AAAAATTA-TTAAATTTTA
1 ATAAAAAATAAAAAAATATTTAAATTTTA
492547 AT-AAAAATAAAAAAATATTTAAATTTTA
1 ATAAAAAATAAAAAAATATTTAAATTTTA
* * *
492575 TTAAAAATTCAAAAAATA
1 ATAAAAAATAAAAAAATA
492593 AAAATTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 6 0.15
27 9 0.23
28 11 0.28
29 13 0.33
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAAAAAATAAAAAAATATTTAAATTTTA
Found at i:492562 original size:28 final size:29
Alignment explanation
Indices: 492520--492591 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
492510 CAAAAAAATG
*
492520 ATAAAAA-ATAAAAATTA-TTAAATTTTA
1 ATAAAAATAAAAAAATTATTTAAATTTTA
492547 ATAAAAATAAAAAAA-TATTTAAATTTTA
1 ATAAAAATAAAAAAATTATTTAAATTTTA
* *
492575 TTAAAAATTCAAAAAAT
1 ATAAAAA-TAAAAAAAT
492592 AAAAATTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 9 0.24
28 22 0.58
29 7 0.18
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAAAAATAAAAAAATTATTTAAATTTTA
Found at i:492679 original size:9 final size:9
Alignment explanation
Indices: 492513--492685 Score: 58
Period size: 9 Copynumber: 19.0 Consensus size: 9
492503 CATATGACAA
*
492513 AAAAATGAT
1 AAAAATTAT
492522 AAAAA--AT
1 AAAAATTAT
492529 AAAAATTATT
1 AAAAATTA-T
**
492539 AAATTTTAAT
1 AAAAATT-AT
*
492549 AAAAA-TAA
1 AAAAATTAT
*
492557 AAAAATATTT
1 AAAAAT-TAT
**
492567 AAATTTTATT
1 AAAAATTA-T
*
492577 AAAAATT-C
1 AAAAATTAT
492585 AAAAA--AT
1 AAAAATTAT
*
492592 AAAAATTGT
1 AAAAATTAT
*
492601 AAAAAATTGT
1 -AAAAATTAT
*
492611 AAAATTTGAT
1 AAAAATT-AT
492621 -AAAATCCTA-
1 AAAAAT--TAT
492630 AGAAAATTAT
1 A-AAAATTAT
*
492640 AAAAAATAT
1 AAAAATTAT
*
492649 AAAAA-AAT
1 AAAAATTAT
*
492657 ATAAAATTCGT
1 A-AAAATT-AT
492668 AAAAATTAT
1 AAAAATTAT
492677 AAAAATTAT
1 AAAAATTAT
492686 CATACCAAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
7 12 0.10
8 14 0.12
9 47 0.39
10 39 0.32
11 9 0.07
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:492681 original size:19 final size:18
Alignment explanation
Indices: 492513--492685 Score: 58
Period size: 19 Copynumber: 9.5 Consensus size: 18
492503 CATATGACAA
*
492513 AAAAATGATAAAAA--AT
1 AAAAATTATAAAAATTAT
**
492529 AAAAATTATTAAATTTTAAT
1 AAAAATTA-TAAAAATT-AT
* *
492549 AAAAA-TAAAAAAATATTT
1 AAAAATTATAAAAAT-TAT
** *
492567 AAATTTTATTAAAAATT-C
1 AAAAATTA-TAAAAATTAT
*
492585 AAAAA--ATAAAAATTGT
1 AAAAATTATAAAAATTAT
* *
492601 AAAAAATTGTAAAATTTGAT
1 -AAAAATTATAAAAATT-AT
492621 -AAAATCCTA-AGAAAATTAT
1 AAAAAT--TATA-AAAATTAT
* *
492640 AAAAAATATAAAAA-AAT
1 AAAAATTATAAAAATTAT
*
492657 ATAAAATTCGTAAAAATTAT
1 A-AAAATT-ATAAAAATTAT
492677 AAAAATTAT
1 AAAAATTAT
492686 CATACCAAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 38
0.64 0.14 0.22
Matches are distributed among these distances:
15 8 0.07
16 8 0.07
17 12 0.11
18 28 0.25
19 29 0.26
20 27 0.24
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:493865 original size:27 final size:29
Alignment explanation
Indices: 493835--493907 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
493825 CAAAAAAATG
*
493835 ATAAAAAAT-AAAAATTA-TTAAATTTTA
1 ATAAAAAATAAAAAAATATTTAAATTTTA
493862 AT-AAAAATAAAAAAATATTTAAATTTTA
1 ATAAAAAATAAAAAAATATTTAAATTTTA
* * *
493890 TTAAAAATTCAAAAAATA
1 ATAAAAAATAAAAAAATA
493908 AAAATTGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
26 6 0.15
27 9 0.23
28 11 0.28
29 13 0.33
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (29 bp):
ATAAAAAATAAAAAAATATTTAAATTTTA
Found at i:493877 original size:28 final size:29
Alignment explanation
Indices: 493835--493906 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
493825 CAAAAAAATG
*
493835 ATAAAAA-ATAAAAATTA-TTAAATTTTA
1 ATAAAAATAAAAAAATTATTTAAATTTTA
493862 ATAAAAATAAAAAAA-TATTTAAATTTTA
1 ATAAAAATAAAAAAATTATTTAAATTTTA
* *
493890 TTAAAAATTCAAAAAAT
1 ATAAAAA-TAAAAAAAT
493907 AAAAATTGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
27 9 0.24
28 22 0.58
29 7 0.18
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (29 bp):
ATAAAAATAAAAAAATTATTTAAATTTTA
Found at i:493994 original size:9 final size:9
Alignment explanation
Indices: 493828--494000 Score: 58
Period size: 9 Copynumber: 19.0 Consensus size: 9
493818 CATATGACAA
*
493828 AAAAATGAT
1 AAAAATTAT
493837 AAAAA--AT
1 AAAAATTAT
493844 AAAAATTATT
1 AAAAATTA-T
**
493854 AAATTTTAAT
1 AAAAATT-AT
*
493864 AAAAA-TAA
1 AAAAATTAT
*
493872 AAAAATATTT
1 AAAAAT-TAT
**
493882 AAATTTTATT
1 AAAAATTA-T
*
493892 AAAAATT-C
1 AAAAATTAT
493900 AAAAA--AT
1 AAAAATTAT
*
493907 AAAAATTGT
1 AAAAATTAT
*
493916 AAAAAATTGT
1 -AAAAATTAT
*
493926 AAAATTTGAT
1 AAAAATT-AT
493936 -AAAATCCTA-
1 AAAAAT--TAT
493945 AGAAAATTAT
1 A-AAAATTAT
*
493955 AAAAAATAT
1 AAAAATTAT
*
493964 AAAAA-AAT
1 AAAAATTAT
*
493972 ATAAAATTCGT
1 A-AAAATT-AT
493983 AAAAATTAT
1 AAAAATTAT
493992 AAAAATTAT
1 AAAAATTAT
494001 CATACCAAAA
Statistics
Matches: 121, Mismatches: 23, Indels: 40
0.66 0.12 0.22
Matches are distributed among these distances:
7 12 0.10
8 14 0.12
9 47 0.39
10 39 0.32
11 9 0.07
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:493996 original size:19 final size:18
Alignment explanation
Indices: 493828--494000 Score: 58
Period size: 19 Copynumber: 9.5 Consensus size: 18
493818 CATATGACAA
*
493828 AAAAATGATAAAAA--AT
1 AAAAATTATAAAAATTAT
**
493844 AAAAATTATTAAATTTTAAT
1 AAAAATTA-TAAAAATT-AT
* *
493864 AAAAA-TAAAAAAATATTT
1 AAAAATTATAAAAAT-TAT
** *
493882 AAATTTTATTAAAAATT-C
1 AAAAATTA-TAAAAATTAT
*
493900 AAAAA--ATAAAAATTGT
1 AAAAATTATAAAAATTAT
* *
493916 AAAAAATTGTAAAATTTGAT
1 -AAAAATTATAAAAATT-AT
493936 -AAAATCCTA-AGAAAATTAT
1 AAAAAT--TATA-AAAATTAT
* *
493955 AAAAAATATAAAAA-AAT
1 AAAAATTATAAAAATTAT
*
493972 ATAAAATTCGTAAAAATTAT
1 A-AAAATT-ATAAAAATTAT
493992 AAAAATTAT
1 AAAAATTAT
494001 CATACCAAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 38
0.64 0.14 0.22
Matches are distributed among these distances:
15 8 0.07
16 8 0.07
17 12 0.11
18 28 0.25
19 29 0.26
20 27 0.24
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (18 bp):
AAAAATTATAAAAATTAT
Found at i:494826 original size:338 final size:338
Alignment explanation
Indices: 494210--494887 Score: 1356
Period size: 338 Copynumber: 2.0 Consensus size: 338
494200 TGAAATTCGA
494210 ATCGAATATATTTGTTCGAGTTAAACTTTAAAAAATAATTTTGGGTCATTGTAACCACTGTTATC
1 ATCGAATATATTTGTTCGAGTTAAACTTTAAAAAATAATTTTGGGTCATTGTAACCACTGTTATC
494275 CACCGTAATCAAATTTGTCCATATAATCAAATTTGCTATTAACTTTCATCACATCATAATTTATT
66 CACCGTAATCAAATTTGTCCATATAATCAAATTTGCTATTAACTTTCATCACATCATAATTTATT
494340 TATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTTTGATTA
131 TATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTTTGATTA
494405 TGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTATTTTAA
196 TGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTATTTTAA
494470 AGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTATTAATA
261 AGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTATTAATA
494535 ATTCAATTTTAAT
326 ATTCAATTTTAAT
494548 ATCGAATATATTTGTTCGAGTTAAACTTTAAAAAATAATTTTGGGTCATTGTAACCACTGTTATC
1 ATCGAATATATTTGTTCGAGTTAAACTTTAAAAAATAATTTTGGGTCATTGTAACCACTGTTATC
494613 CACCGTAATCAAATTTGTCCATATAATCAAATTTGCTATTAACTTTCATCACATCATAATTTATT
66 CACCGTAATCAAATTTGTCCATATAATCAAATTTGCTATTAACTTTCATCACATCATAATTTATT
494678 TATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTTTGATTA
131 TATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTTTGATTA
494743 TGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTATTTTAA
196 TGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTATTTTAA
494808 AGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTATTAATA
261 AGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTATTAATA
494873 ATTCAATTTTAAT
326 ATTCAATTTTAAT
494886 AT
1 AT
494888 AATATTCAAT
Statistics
Matches: 340, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
338 340 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (338 bp):
ATCGAATATATTTGTTCGAGTTAAACTTTAAAAAATAATTTTGGGTCATTGTAACCACTGTTATC
CACCGTAATCAAATTTGTCCATATAATCAAATTTGCTATTAACTTTCATCACATCATAATTTATT
TATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTTTGATTA
TGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTATTTTAA
AGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTATTAATA
ATTCAATTTTAAT
Found at i:495486 original size:437 final size:437
Alignment explanation
Indices: 494672--495545 Score: 1748
Period size: 437 Copynumber: 2.0 Consensus size: 437
494662 CACATCATAA
494672 TTTATTTATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTT
1 TTTATTTATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTT
494737 TGATTATGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTA
66 TGATTATGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTA
494802 TTTTAAAGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTA
131 TTTTAAAGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTA
494867 TTAATAATTCAATTTTAATATAATATTCAATATGATTAAACAATTCAATAATTTAAATAGTACAA
196 TTAATAATTCAATTTTAATATAATATTCAATATGATTAAACAATTCAATAATTTAAATAGTACAA
494932 AATGTGAAATTTAATTTAATAATATAAATCATATATATAAATAAAATTATTATTTAGGTTTAGGG
261 AATGTGAAATTTAATTTAATAATATAAATCATATATATAAATAAAATTATTATTTAGGTTTAGGG
494997 ATTTTTTTGGATGATTTTAACTTTTACTTCCCACCCTTTACCTTAGGGGAAATAAAAAGTTTTGG
326 ATTTTTTTGGATGATTTTAACTTTTACTTCCCACCCTTTACCTTAGGGGAAATAAAAAGTTTTGG
495062 GGAGTAAAATATTGGAGAGAAAATATTTTTAAAAAAGGGGGGATGGG
391 GGAGTAAAATATTGGAGAGAAAATATTTTTAAAAAAGGGGGGATGGG
495109 TTTATTTATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTT
1 TTTATTTATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTT
495174 TGATTATGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTA
66 TGATTATGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTA
495239 TTTTAAAGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTA
131 TTTTAAAGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTA
495304 TTAATAATTCAATTTTAATATAATATTCAATATGATTAAACAATTCAATAATTTAAATAGTACAA
196 TTAATAATTCAATTTTAATATAATATTCAATATGATTAAACAATTCAATAATTTAAATAGTACAA
495369 AATGTGAAATTTAATTTAATAATATAAATCATATATATAAATAAAATTATTATTTAGGTTTAGGG
261 AATGTGAAATTTAATTTAATAATATAAATCATATATATAAATAAAATTATTATTTAGGTTTAGGG
495434 ATTTTTTTGGATGATTTTAACTTTTACTTCCCACCCTTTACCTTAGGGGAAATAAAAAGTTTTGG
326 ATTTTTTTGGATGATTTTAACTTTTACTTCCCACCCTTTACCTTAGGGGAAATAAAAAGTTTTGG
495499 GGAGTAAAATATTGGAGAGAAAATATTTTTAAAAAAGGGGGGATGGG
391 GGAGTAAAATATTGGAGAGAAAATATTTTTAAAAAAGGGGGGATGGG
495546 AGGGGAGTAA
Statistics
Matches: 437, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
437 437 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.41
Consensus pattern (437 bp):
TTTATTTATTAATCTTTTATATACGAGTTAGCTTCTTTGCTTACTTAGTTGCTTCAACAATCTTT
TGATTATGTATTTTGAAATTAAAAAATATATTAAATGTAAAAATGTGATTTTTTAATAAAATTTA
TTTTAAAGAAAAAATATGAAATTGATACCAACATAAAATTTTAACACAAATATTTTATGGCATTA
TTAATAATTCAATTTTAATATAATATTCAATATGATTAAACAATTCAATAATTTAAATAGTACAA
AATGTGAAATTTAATTTAATAATATAAATCATATATATAAATAAAATTATTATTTAGGTTTAGGG
ATTTTTTTGGATGATTTTAACTTTTACTTCCCACCCTTTACCTTAGGGGAAATAAAAAGTTTTGG
GGAGTAAAATATTGGAGAGAAAATATTTTTAAAAAAGGGGGGATGGG
Found at i:496132 original size:19 final size:18
Alignment explanation
Indices: 496097--496163 Score: 71
Period size: 19 Copynumber: 3.4 Consensus size: 18
496087 TTTTGATGCA
496097 TTTTATAAATTATTTTATGAT
1 TTTTATAAA--ATTTTAT-AT
*
496118 ATTTATAAAATTTTATAT
1 TTTTATAAAATTTTATAT
*
496136 TTTTATTAAAATTTAATAAT
1 TTTTA-TAAAATTTTAT-AT
496156 TTTTATAA
1 TTTTATAA
496164 TTTTTTTGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 6 0.15
19 20 0.49
20 7 0.17
21 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (18 bp):
TTTTATAAAATTTTATAT
Found at i:497252 original size:3 final size:3
Alignment explanation
Indices: 497244--497303 Score: 68
Period size: 3 Copynumber: 19.0 Consensus size: 3
497234 AATAGGGGTG
*
497244 ATA ATA ATA ATA ATA ATA ATA ATA ATA CA-A ACA ATA ATA CATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA -ATA -ATA
497291 TATA ATA ATA ATA
1 -ATA ATA ATA ATA
497304 GTCAGAAATA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
2 1 0.02
3 40 0.77
4 11 0.21
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:497388 original size:3 final size:3
Alignment explanation
Indices: 497375--497454 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
497365 GATGGTATAT
497375 ATA AT- ATA ATA AT- ATAA ATA ATA ATA TATA CATGA GA-A ATA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA -ATA -AT-A -ATA ATA ATA
* *
497419 ATA ATA AT- ATAA ATA ATA GTA AAA ATA ATA A-A ATA A
1 ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
497455 AAAAAATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 9 0.15
3 42 0.68
4 9 0.15
5 2 0.03
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:497397 original size:12 final size:12
Alignment explanation
Indices: 497373--497455 Score: 71
Period size: 12 Copynumber: 6.6 Consensus size: 12
497363 GAGATGGTAT
497373 ATATAATATAATA
1 ATATAA-ATAATA
497386 ATATAAATAATA
1 ATATAAATAATA
497398 ATATATACATGAGA-A
1 ATATA-A-AT-A-ATA
497413 ATA-ATAATAATA
1 ATATA-AATAATA
497425 ATATAAATAATA
1 ATATAAATAATA
* *
497437 GTAAAAATAATA
1 ATATAAATAATA
*
497449 AAATAAA
1 ATATAAA
497456 AAAAATAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
11 1 0.02
12 37 0.63
13 10 0.17
14 5 0.08
15 5 0.08
16 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (12 bp):
ATATAAATAATA
Found at i:497416 original size:21 final size:18
Alignment explanation
Indices: 497375--497436 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
497365 GATGGTATAT
*
497375 ATAAT-ATAATAATATAA
1 ATAATAATAATAATAGAA
497392 ATAATAATATATACATGAGAA
1 ATAATAATA-ATA-AT-AGAA
*
497413 ATAATAATAATAATATAA
1 ATAATAATAATAATAGAA
497431 ATAATA
1 ATAATA
497437 GTAAAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 5 0.13
18 12 0.31
19 5 0.13
20 5 0.13
21 12 0.31
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (18 bp):
ATAATAATAATAATAGAA
Found at i:497445 original size:27 final size:27
Alignment explanation
Indices: 497373--497462 Score: 73
Period size: 27 Copynumber: 3.4 Consensus size: 27
497363 GAGATGGTAT
* *
497373 ATATAATATAATAATATAAATAATAAT-
1 ATATAA-ATAATAGTAAAAATAATAATA
* *
497400 ATATACAT--GAG-AAATAATAATAATA
1 ATATAAATAATAGTAAA-AATAATAATA
497425 ATATAAATAATAGTAAAAATAATAA-A
1 ATATAAATAATAGTAAAAATAATAATA
* *
497451 ATAAAAAAAATA
1 ATATAAATAATA
497463 AAACAAAGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
23 2 0.04
24 10 0.20
25 7 0.14
26 13 0.26
27 15 0.30
28 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (27 bp):
ATATAAATAATAGTAAAAATAATAATA
Found at i:497997 original size:30 final size:30
Alignment explanation
Indices: 497956--498047 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
497946 CTTCTCCATT
* *
497956 TGATGGTGTAGGTGCAAGTGGGAGATAAGG
1 TGATGGAGTAGGTGCAAGTGGGAGACAAGG
* *
497986 TGGTGGAGTAGGTGCAAGTGGGAGGCAAGG
1 TGATGGAGTAGGTGCAAGTGGGAGACAAGG
498016 TGATGGAGTAGGTGCAAGTGGGA-AGCAAGG
1 TGATGGAGTAGGTGCAAGTGGGAGA-CAAGG
498046 TG
1 TG
498048 GCTAGGGTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.26, C:0.05, G:0.49, T:0.20
Consensus pattern (30 bp):
TGATGGAGTAGGTGCAAGTGGGAGACAAGG
Found at i:500720 original size:38 final size:36
Alignment explanation
Indices: 500623--500734 Score: 170
Period size: 36 Copynumber: 3.0 Consensus size: 36
500613 TCCTCCATAT
*
500623 CAAATAAAGCCAAAGTCTATCTATTCTTCGCCAGGGA
1 CAAA-AAAGCCAAAGTCTATCTATTCTCCGCCAGGGA
500660 CAAAAAAGCCAAAGTCTATCTATTCTCCGCCAGGGA
1 CAAAAAAGCCAAAGTCTATCTATTCTCCGCCAGGGA
* *
500696 CAAAAAAGAGTCAAAGTCTATCTATTCTCTGCCAGGGA
1 C-AAAAA-AGCCAAAGTCTATCTATTCTCCGCCAGGGA
500734 C
1 C
500735 GAAATTTTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
36 32 0.46
37 9 0.13
38 29 0.41
ACGTcount: A:0.36, C:0.25, G:0.17, T:0.22
Consensus pattern (36 bp):
CAAAAAAGCCAAAGTCTATCTATTCTCCGCCAGGGA
Found at i:501881 original size:42 final size:42
Alignment explanation
Indices: 501822--501906 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
501812 AAATCAATTA
501822 CCATTTAATTAAACTTCGATATCTTTCAAAACGTTACCTATT
1 CCATTTAATTAAACTTCGATATCTTTCAAAACGTTACCTATT
501864 CCATTTAATTAAACTTCGATATCTTTCAAAACGTTACCTATT
1 CCATTTAATTAAACTTCGATATCTTTCAAAACGTTACCTATT
501906 C
1 C
501907 ATCTTTTGAG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (42 bp):
CCATTTAATTAAACTTCGATATCTTTCAAAACGTTACCTATT
Found at i:504163 original size:3 final size:3
Alignment explanation
Indices: 504155--504407 Score: 114
Period size: 3 Copynumber: 85.0 Consensus size: 3
504145 TTGAACATTT
* * * *
504155 TTA TTA TTAA TTA TT- TTA ATA ATA TTA CTA TT- GTA TTCA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
* * * * *
504200 TTA TTA TATG TTA CTA TTA -CA TTCA TTA TTT TTA CTT- TTA TTA TTC
1 TTA TTA T-TA TTA TTA TTA TTA TT-A TTA TTA TTA -TTA TTA TTA TTA
* ** * * * * * * *
504246 TTT TTA TTA AAA TTA TTT TTA CTA TTA TTT TTA -TA CTA TAA TCA TTC
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
504293 TTA TTA ATA -TA TTA TTA TT- TT- TCTA TTA TTA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * *
504335 TTA TTA TTA TTA TTAA TGTA TTA TTA TTG TTA TTT TCTA CT- TTA TTA
1 TTA TTA TTA TTA TT-A T-TA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
* * *
504382 TTA TT- GTA TTA TCA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
504408 CCATATCATT
Statistics
Matches: 185, Mismatches: 46, Indels: 38
0.69 0.17 0.14
Matches are distributed among these distances:
2 17 0.09
3 148 0.80
4 19 0.10
5 1 0.01
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:504324 original size:17 final size:17
Alignment explanation
Indices: 504302--504386 Score: 71
Period size: 17 Copynumber: 4.6 Consensus size: 17
504292 CTTATTAATA
504302 TATTATTATTTTTCTAT
1 TATTATTATTTTTCTAT
* *
504319 TATTATTATTATTATAT
1 TATTATTATTTTTCTAT
*
504336 TATTATTATTATTAATGTAT
1 TATTATTATT-TT--TCTAT
*
504356 TATTATTGTTATTTTCTACTT
1 TATTATT-AT-TTTTCTA--T
504377 TATTATTATT
1 TATTATTATT
504387 GTATTATCAC
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
17 25 0.46
18 1 0.02
19 4 0.07
20 12 0.22
21 11 0.20
22 1 0.02
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (17 bp):
TATTATTATTTTTCTAT
Found at i:504327 original size:20 final size:20
Alignment explanation
Indices: 504302--504386 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
504292 CTTATTAATA
504302 TATTATTATTTTTCTATTAT
1 TATTATTATTTTTCTATTAT
*
504322 TATTATTA---TTATATTAT
1 TATTATTATTTTTCTATTAT
** *
504339 TATTATTATTAATGTATTAT
1 TATTATTATTTTTCTATTAT
* *
504359 TATTGTTA-TTTTCTACT-T
1 TATTATTATTTTTCTATTAT
504377 TATTATTATT
1 TATTATTATT
504387 GTATTATCAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 16 0.31
18 8 0.15
19 6 0.12
20 22 0.42
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (20 bp):
TATTATTATTTTTCTATTAT
Found at i:512100 original size:24 final size:24
Alignment explanation
Indices: 512055--512101 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
512045 ATATTAAAAG
*
512055 ATATATATATAAAATGTATACATA
1 ATATATATATAAAATATATACATA
*
512079 ATATA-ATATTAAAATATTTACAT
1 ATATATATA-TAAAATATATACAT
512102 GGTATATACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATATATATAAAATATATACATA
Found at i:512649 original size:39 final size:39
Alignment explanation
Indices: 512623--512763 Score: 176
Period size: 39 Copynumber: 3.6 Consensus size: 39
512613 CCCATGCTAC
* * *
512623 TTTGTTTTATTATTAATCAAAACCAC-TCCCAATGCCAT
1 TTTGTTTTATTATTAATTAAAACCACTTCCCCATACCAT
* ** *
512661 TTTGTTTTATTGTTAATTAAAATTACTTCCCCATACTAT
1 TTTGTTTTATTATTAATTAAAACCACTTCCCCATACCAT
* * * *
512700 TTTGTTTTATTGTTAATTAAAACTACTTCCTCATACCGT
1 TTTGTTTTATTATTAATTAAAACCACTTCCCCATACCAT
512739 TTTGTTTTATTATTAATTAAAACCA
1 TTTGTTTTATTATTAATTAAAACCA
512764 TACTTTATTT
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 22 0.25
39 67 0.75
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.48
Consensus pattern (39 bp):
TTTGTTTTATTATTAATTAAAACCACTTCCCCATACCAT
Found at i:515061 original size:16 final size:16
Alignment explanation
Indices: 515040--515082 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
515030 AAAAAAAGAA
515040 AGAAGGGAGAGAGGGG
1 AGAAGGGAGAGAGGGG
*
515056 AGAAGGAAGAGAGGGG
1 AGAAGGGAGAGAGGGG
515072 A-AAGGG-GAGAG
1 AGAAGGGAGAGAG
515083 CTCCGGCCAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 5 0.20
15 4 0.16
16 16 0.64
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (16 bp):
AGAAGGGAGAGAGGGG
Found at i:516968 original size:45 final size:44
Alignment explanation
Indices: 516895--516979 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
516885 CGATATCTGC
* *
516895 TATCTTTGATCTGCCCCCGTCTACTACAGAAACGCCAAATCTAT
1 TATCTTCGATCTGCCCCCGTCTAATACAGAAACGCCAAATCTAT
*
516939 TATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAAAT
1 TATCTTCGATCTGC-CCCCGTCTAATACAGAAACGCCAAAT
516980 TTGCTTCTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 13 0.35
45 24 0.65
ACGTcount: A:0.27, C:0.32, G:0.13, T:0.28
Consensus pattern (44 bp):
TATCTTCGATCTGCCCCCGTCTAATACAGAAACGCCAAATCTAT
Found at i:516989 original size:44 final size:45
Alignment explanation
Indices: 516889--516998 Score: 143
Period size: 44 Copynumber: 2.5 Consensus size: 45
516879 GGAAGGCGAT
* *
516889 ATCTGCTATCTTTGATCTGC-CCCCGTCTACTACAGAAACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAAACGCCAA
** *
516933 ATCTATTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAAACGCCAA
* *
516978 ATTTGCT-TCTTCAATCTGCTC
1 ATCTGCTATCTTCGATCTGCTC
516999 ATTGCAAACT
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 30 0.54
45 26 0.46
ACGTcount: A:0.24, C:0.32, G:0.13, T:0.32
Consensus pattern (45 bp):
ATCTGCTATCTTCGATCTGCTCCCCGTCTAATACAGAAACGCCAA
Found at i:517079 original size:44 final size:44
Alignment explanation
Indices: 516889--517110 Score: 134
Period size: 44 Copynumber: 5.1 Consensus size: 44
516879 GGAAGGCGAT
* * *
516889 ATCTGCTATCTTTGATCTGC-CCCCGTCTACTACAGAAACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCTGTCAAC-ACAGAAACGCCAA
** * * *
516933 ATCTATTATCTTCGATCTGCTCCCCGTCTAATACAGAGACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCTGTC-AACACAGAAACGCCAA
* * ** * * *
516978 ATTTGCT-TCTTCAATCTGCTCATTG-CAAACTCATG--ACTGCTAT
1 ATCTGCTATCTTCGATCTGCTCCCTGTC-AACACA-GAAAC-GCCAA
* * *
517021 GT-TGATATCTTCGATCTGCTCTCTGTCGAACACAGAAACGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCTGTC-AACACAGAAACGCCAA
* * * * *
517065 ATCTGCT-TCTTCGATTTGTTCCCTGACAATACAGAAATGCCAA
1 ATCTGCTATCTTCGATCTGCTCCCTGTCAACACAGAAACGCCAA
517108 ATC
1 ATC
517111 ATCTTAGATT
Statistics
Matches: 134, Mismatches: 35, Indels: 19
0.71 0.19 0.10
Matches are distributed among these distances:
42 5 0.04
43 42 0.31
44 58 0.43
45 28 0.21
46 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (44 bp):
ATCTGCTATCTTCGATCTGCTCCCTGTCAACACAGAAACGCCAA
Found at i:517970 original size:205 final size:205
Alignment explanation
Indices: 517073--518073 Score: 1182
Period size: 210 Copynumber: 4.8 Consensus size: 205
517063 AAATCTGCTT
* * * * * * **
517073 CTTCGATTTGTTCCCTGACAATACAGAAATGCCAAATCATCTTAGATTTGCTTTAACGTAAGTAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
** * * *
517138 GTGAAAGCCAAATCAAATATG-ATTCGATTTGCTCCTTGTAAACATAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCTAAACCATCTT
* * * *
517202 GGATCCGCTTCAGCATAAACATCCGAAGG-CGAGATCTGCTGTGTGTCTG-CTCTCCACCAAAGC
131 GGATCTGCTTCAGCATAAACATCTGAAGGTC-AGATCTGCTATGTGTCTGCCT-TCCATCAAAG-
517265 T--AAGATGCCAAA
193 TGGAA-ATGCCAAA
* ** * * *
517277 CTTTGATTCATTCTCTGACAATACAGAGACGACAAATTATCTTAGATTTGCTTCATTGAAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * ** * *
517342 GTGAAAGCCAAATCAGCTATATCTTCGATCTGTTCCTTGCCGAATAC-AGAGA-GATAAGATCTG
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTG-TAAACACAAG-GATGCTAA-A-C--
* * *
517405 TCATCTTGGATCTGCTTCAGCGTAAACATCTGAGGGTAAGATCTGCTATGTGTCTGCCTTCCATC
125 -CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCTTCCATC
*
517470 AAAGTGGAAATGCCAGA
189 AAAGTGGAAATGCCAAA
*
517487 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGGAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* * * ** * *
517552 GTGAAAGCCAAATCAGCTATATCTTCGATCTGCTCCCTGCCGAATAC-AGAGA-GATAAGATCTG
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTG-TAAACACAAG-GATGCTAA-A-C--
* * *
517615 TCATCTTGGATCTGTTTCAGCGTAAACATCTGAAGGTAAGATCTGCTATGTGTCTGCCTTCCATC
125 -CATCTTGGATCTGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCTTCCATC
*
517680 AAAGTGGAAATGCCAGA
189 AAAGTGGAAATGCCAAA
* *
517697 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGTTTCAACGTAAACAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
* *
517762 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGTTCCTTGTAAACACAAGGATGCTAAACCATATT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCTAAACCATCTT
*
517827 GGAT-TCGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATATGTCTG-CTCTCCATCAAAGT
131 GGATCT-GCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCT-TCCATCAAAGT
517890 -GAAGATGCCAAA
194 GGAA-ATGCCAAA
* * * *
517902 CTTTGATTCGTTCTCTGACAATACAAAGACGACAAATCATCTTAGATTTGCTTCATCGTAATCAC
1 CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
*
517967 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCCAAACCATCTT
66 GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCTAAACCATCTT
* * * *
518032 GGATCTGCTTCAGTAT-AACATCTGTAGGCCAGATCTGTTATG
131 GGATCTGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATG
518074 CTGCGGCCTA
Statistics
Matches: 704, Mismatches: 75, Indels: 36
0.86 0.09 0.04
Matches are distributed among these distances:
204 97 0.14
205 219 0.31
206 7 0.01
207 1 0.00
208 1 0.00
209 8 0.01
210 367 0.52
211 4 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (205 bp):
CTTCGATTTGTTCTCTGACAATACAGAGACGACAAATCATCTTAGATTTGCTTCATCGTAAACAC
GTGAAAGCCAAATCAGCTATGTCTTCGATTTGCTCCTTGTAAACACAAGGATGCTAAACCATCTT
GGATCTGCTTCAGCATAAACATCTGAAGGTCAGATCTGCTATGTGTCTGCCTTCCATCAAAGTGG
AAATGCCAAA
Found at i:526024 original size:13 final size:15
Alignment explanation
Indices: 525994--526024 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
525984 TTCCAGATTT
525994 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
526009 TCTTTTCTACCTCTC
1 TCTTTTCTACCTCTC
526024 T
1 T
526025 GGAAAGTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.39, G:0.00, T:0.55
Consensus pattern (15 bp):
TCTTTTCTACCTCTC
Found at i:526110 original size:15 final size:14
Alignment explanation
Indices: 526068--526117 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
526058 ATAACTTTGA
*
526068 ATGCAAATGATGTG
1 ATGCAAATGATGAG
526082 ATG-AAATGTTATGAG
1 ATGCAAATG--ATGAG
526097 ATGCAAATGCATGA-
1 ATGCAAATG-ATGAG
526111 ATGCAAA
1 ATGCAAA
526118 AAGAATATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
13 5 0.16
14 10 0.32
15 11 0.35
16 5 0.16
ACGTcount: A:0.42, C:0.08, G:0.24, T:0.26
Consensus pattern (14 bp):
ATGCAAATGATGAG
Found at i:529997 original size:38 final size:39
Alignment explanation
Indices: 529925--530021 Score: 151
Period size: 38 Copynumber: 2.5 Consensus size: 39
529915 AAACAACAAA
*
529925 AATACAATATTAAAAGATATATATATATAAAATGTATACAT
1 AATATAATATT-AAA-ATATATATATATAAAATGTATACAT
*
529966 AATATAATATTAAAAT-TATATATATATAATGTATACAT
1 AATATAATATTAAAATATATATATATAAAATGTATACAT
530004 AATATAATATTAAAATAT
1 AATATAATATTAAAATAT
530022 TTACATGGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
38 37 0.70
39 3 0.06
40 3 0.06
41 10 0.19
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (39 bp):
AATATAATATTAAAATATATATATATAAAATGTATACAT
Found at i:530587 original size:38 final size:39
Alignment explanation
Indices: 530535--530692 Score: 194
Period size: 39 Copynumber: 4.1 Consensus size: 39
530525 AAAGCTGATT
* * * *
530535 CCACTTCCCTCATGCTACTTTGTTTTATTATTAATCAAAA
1 CCACTTCCC-CATACCATTTTGTTTTATTATTAATTAAAA
*
530575 CCAC-TCCCCATGCCATTTTGTTTTATTATTAATTAAAA
1 CCACTTCCCCATACCATTTTGTTTTATTATTAATTAAAA
* * * *
530613 CTACTTCCCCATACTATTTTCTTTTATTGTTAATTAAAA
1 CCACTTCCCCATACCATTTTGTTTTATTATTAATTAAAA
* *
530652 CTACTTCCTCATACCATTTTG-TTTATTATTAATTAAAA
1 CCACTTCCCCATACCATTTTGTTTTATTATTAATTAAAA
530690 CCA
1 CCA
530693 TACTTTATTT
Statistics
Matches: 104, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
38 48 0.46
39 52 0.50
40 4 0.04
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (39 bp):
CCACTTCCCCATACCATTTTGTTTTATTATTAATTAAAA
Found at i:530638 original size:39 final size:39
Alignment explanation
Indices: 530553--530690 Score: 199
Period size: 39 Copynumber: 3.6 Consensus size: 39
530543 CTCATGCTAC
* * *
530553 TTTGTTTTATTATTAATCAAAACCAC-TCCCCATGCCAT
1 TTTGTTTTATTATTAATTAAAACTACTTCCCCATACCAT
*
530591 TTTGTTTTATTATTAATTAAAACTACTTCCCCATACTAT
1 TTTGTTTTATTATTAATTAAAACTACTTCCCCATACCAT
* * *
530630 TTTCTTTTATTGTTAATTAAAACTACTTCCTCATACCAT
1 TTTGTTTTATTATTAATTAAAACTACTTCCCCATACCAT
530669 TTTG-TTTATTATTAATTAAAAC
1 TTTGTTTTATTATTAATTAAAAC
530691 CATACTTTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
38 41 0.46
39 48 0.54
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (39 bp):
TTTGTTTTATTATTAATTAAAACTACTTCCCCATACCAT
Found at i:530646 original size:77 final size:78
Alignment explanation
Indices: 530537--530690 Score: 213
Period size: 77 Copynumber: 2.0 Consensus size: 78
530527 AGCTGATTCC
* * *
530537 ACTTCCCTCATGCTACTTTGTTTTATTATTAATCAAAACCAC-TCCCCATGCCATTTTGTTTTAT
1 ACTTCCCTCATACTACTTTCTTTTATTATTAATCAAAACCACTTCCCCATACCATTTTG-TTTAT
530601 TATTAATTAAAACT
65 TATTAATTAAAACT
* * * * *
530615 ACTTCCC-CATACTATTTTCTTTTATTGTTAATTAAAACTACTTCCTCATACCATTTTGTTTATT
1 ACTTCCCTCATACTACTTTCTTTTATTATTAATCAAAACCACTTCCCCATACCATTTTGTTTATT
530679 ATTAATTAAAAC
66 ATTAATTAAAAC
530691 CATACTTTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 46 0.69
78 21 0.31
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.45
Consensus pattern (78 bp):
ACTTCCCTCATACTACTTTCTTTTATTATTAATCAAAACCACTTCCCCATACCATTTTGTTTATT
ATTAATTAAAACT
Found at i:554899 original size:20 final size:19
Alignment explanation
Indices: 554858--554904 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
554848 TTAAAATTTT
554858 ATTTTAA-TTTATTTATAC
1 ATTTTAATTTTATTTATAC
554876 ATTTTAATTTTA-TTATGCAC
1 ATTTTAATTTTATTTAT--AC
554896 ATTTTAATT
1 ATTTTAATT
554905 GTATATCTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 11 0.42
19 4 0.15
20 11 0.42
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTAATTTTATTTATAC
Found at i:555206 original size:20 final size:20
Alignment explanation
Indices: 555181--555219 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
555171 CACACGCCCG
555181 TGTGGCCTGGGACATGGCCA
1 TGTGGCCTGGGACATGGCCA
*
555201 TGTGGCTTGGGACATGGCC
1 TGTGGCCTGGGACATGGCC
555220 GTGGGGCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.41, T:0.23
Consensus pattern (20 bp):
TGTGGCCTGGGACATGGCCA
Found at i:559050 original size:3 final size:3
Alignment explanation
Indices: 559042--559161 Score: 64
Period size: 3 Copynumber: 39.7 Consensus size: 3
559032 AGTTTTATAT
* * * *
559042 TTA TTA TTA -TA TTTA TTA TTA TT- TCTG TTA TTA TTG TTA CTA CTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
* * * * * * *
559087 TTA TTA TTA TTA TTT TTCA CTA CTG TCA TTA TTA TTA TTA GTA CTA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
559133 TTA TTA CTA ATA TTT TTA TTA TCA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
559162 TTTTTAAAAC
Statistics
Matches: 89, Mismatches: 23, Indels: 10
0.73 0.19 0.08
Matches are distributed among these distances:
2 3 0.03
3 82 0.92
4 4 0.04
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:559053 original size:12 final size:12
Alignment explanation
Indices: 559036--559063 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
559026 AATTTGAGTT
559036 TTATATTTATTA
1 TTATATTTATTA
559048 TTATATTTATTA
1 TTATATTTATTA
559060 TTAT
1 TTAT
559064 TTCTGTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATTTATTA
Found at i:559117 original size:25 final size:24
Alignment explanation
Indices: 559069--559125 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
559059 ATTATTTCTG
*
559069 TTATTATTGTTACTACTATTATTA
1 TTATTATTGTTACTACTATCATTA
* *
559093 TTATTATTTTTCACTACTGTCATTA
1 TTATTATTGTT-ACTACTATCATTA
559118 TTATTATT
1 TTATTATT
559126 AGTACTATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.26, C:0.11, G:0.04, T:0.60
Consensus pattern (24 bp):
TTATTATTGTTACTACTATCATTA
Done.