Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 2 of 133
Found at i:182821 original size:25 final size:25
Alignment explanation
Indices: 182771--182827 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 25
182761 TTATATATTC
* **
182771 ATTTATCTGTTATTATTATTTTTTT
1 ATTTATCTGTTAATATTATTGATTT
182796 ATTTATCT-TGTAATATTATTGATTT
1 ATTTATCTGT-TAATATTATTGATTT
182821 ATCTTAT
1 AT-TTAT
182828 TATTTTTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 22 0.81
26 4 0.15
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (25 bp):
ATTTATCTGTTAATATTATTGATTT
Found at i:182858 original size:14 final size:15
Alignment explanation
Indices: 182841--182871 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
182831 TTTTTTCTAA
182841 TTATCT-ATTTTTTT
1 TTATCTGATTTTTTT
182855 TTATCTGATTTTTTT
1 TTATCTGATTTTTTT
182870 TT
1 TT
182872 TAGGCTGAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTATCTGATTTTTTT
Found at i:183271 original size:38 final size:38
Alignment explanation
Indices: 183229--183304 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 38
183219 AATTTTTCGA
* * * *
183229 CAAAGATTCCGACCAAGTTTGAAGTTTTTGGCCAACTT
1 CAAAGATTCCGACCAACTTCGAAGTTTTCGACCAACTT
* * *
183267 CAAAGCTTTCGGCCAACTTCGAAGTTTTCGACCAACTT
1 CAAAGATTCCGACCAACTTCGAAGTTTTCGACCAACTT
183305 TTCAGTTTTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.30
Consensus pattern (38 bp):
CAAAGATTCCGACCAACTTCGAAGTTTTCGACCAACTT
Found at i:183280 original size:19 final size:19
Alignment explanation
Indices: 183258--183304 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
183248 TGAAGTTTTT
183258 GGCCAACTTCAAAGCTTTC
1 GGCCAACTTCAAAGCTTTC
* *
183277 GGCCAACTTCGAAGTTTTC
1 GGCCAACTTCAAAGCTTTC
*
183296 GACCAACTT
1 GGCCAACTT
183305 TTCAGTTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.28
Consensus pattern (19 bp):
GGCCAACTTCAAAGCTTTC
Found at i:183821 original size:11 final size:11
Alignment explanation
Indices: 183807--183886 Score: 60
Period size: 11 Copynumber: 7.4 Consensus size: 11
183797 TTTAATATTC
183807 TTTTATCTTTA
1 TTTTATCTTTA
*
183818 TTTTATTTTTA
1 TTTTATCTTTA
*
183829 TTTT-TGTTTTA
1 TTTTAT-CTTTA
183840 TTTT-TCTTTA
1 TTTTATCTTTA
* *
183850 TTTTTTTTTTA
1 TTTTATCTTTA
183861 TTTTCA-CTTTTA
1 TTTT-ATC-TTTA
*
183873 TTTTGT-TTTA
1 TTTTATCTTTA
183883 TTTT
1 TTTT
183887 CTTTAAATAA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
10 17 0.29
11 33 0.57
12 8 0.14
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (11 bp):
TTTTATCTTTA
Found at i:183827 original size:17 final size:17
Alignment explanation
Indices: 183807--183876 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
183797 TTTAATATTC
183807 TTTTATCTTTATTTTAT
1 TTTTATCTTTATTTTAT
* *
183824 TTTTATTTTTGTTTTA-
1 TTTTATCTTTATTTTAT
*
183840 TTTT-TCTTTATTTTTT
1 TTTTATCTTTATTTTAT
183856 TTTTAT-TTTCACTTTTAT
1 TTTTATCTTT-A-TTTTAT
183874 TTT
1 TTT
183877 GTTTTATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
15 8 0.19
16 11 0.26
17 16 0.37
18 8 0.19
ACGTcount: A:0.13, C:0.06, G:0.01, T:0.80
Consensus pattern (17 bp):
TTTTATCTTTATTTTAT
Found at i:183831 original size:32 final size:32
Alignment explanation
Indices: 183793--183863 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
183783 TTAGATTAAG
183793 TTTATTTAATATTCT-TTTATCTTTATTTTATT
1 TTTATTT-ATATTCTATTTATCTTTATTTTATT
* * * * *
183825 TTTATTTTTGTTTTATTTTTCTTTATTTTTTT
1 TTTATTTATATTCTATTTATCTTTATTTTATT
183857 TTTATTT
1 TTTATTT
183864 TCACTTTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
31 4 0.12
32 29 0.88
ACGTcount: A:0.15, C:0.04, G:0.01, T:0.79
Consensus pattern (32 bp):
TTTATTTATATTCTATTTATCTTTATTTTATT
Found at i:183864 original size:32 final size:34
Alignment explanation
Indices: 183807--183886 Score: 103
Period size: 33 Copynumber: 2.4 Consensus size: 34
183797 TTTAATATTC
**
183807 TTTTATCTTTATTTTATTTTTATTTT-TGTTTTA
1 TTTTATCTTTATTTTATTTTTATTTTCACTTTTA
*
183840 TTTT-TCTTTATTTTTTTTTTATTTTCACTTTTA
1 TTTTATCTTTATTTTATTTTTATTTTCACTTTTA
*
183873 TTTTGT-TTTATTTT
1 TTTTATCTTTATTTT
183887 CTTTAAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 20 0.48
33 21 0.50
34 1 0.02
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (34 bp):
TTTTATCTTTATTTTATTTTTATTTTCACTTTTA
Found at i:183887 original size:22 final size:22
Alignment explanation
Indices: 183814--183890 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 22
183804 TTCTTTTATC
*
183814 TTTATTTTATTTTTATTTTTGT
1 TTTATTTTACTTTTATTTTTGT
* *
183836 TTTATTTTTC-TTTATTTTTTT
1 TTTATTTTACTTTTATTTTTGT
183857 TTTATTTTCACTTTTA-TTTTGT
1 TTTATTTT-ACTTTTATTTTTGT
183879 TTTATTTT-CTTT
1 TTTATTTTACTTT
183891 AAATAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
20 4 0.08
21 18 0.38
22 22 0.46
23 4 0.08
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.81
Consensus pattern (22 bp):
TTTATTTTACTTTTATTTTTGT
Found at i:183999 original size:27 final size:27
Alignment explanation
Indices: 183911--184001 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 27
183901 CAAAAAAAAT
*
183911 ATTTTTGAAGAAAAGTTGAAAGTATCA
1 ATTTTTGGAGAAAAGTTGAAAGTATCA
* * * *
183938 ATTTTCTTCGAAATTAAAGTTTCAAAAGAAT--
1 A-TTT-TTGGAGA--AAAG-TT-GAAAGTATCA
183969 ATTTTTGGAGAAAAGTTGAAAGTATCA
1 ATTTTTGGAGAAAAGTTGAAAGTATCA
183996 ATTTTT
1 ATTTTT
184002 TCTGCACAAA
Statistics
Matches: 47, Mismatches: 9, Indels: 16
0.65 0.12 0.22
Matches are distributed among these distances:
25 6 0.13
26 2 0.04
27 11 0.23
28 3 0.06
29 9 0.19
30 3 0.06
31 5 0.11
32 2 0.04
33 6 0.13
ACGTcount: A:0.41, C:0.05, G:0.15, T:0.38
Consensus pattern (27 bp):
ATTTTTGGAGAAAAGTTGAAAGTATCA
Found at i:196748 original size:15 final size:16
Alignment explanation
Indices: 196728--196760 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
196718 CCTCCTATGC
196728 TTTTTTC-TTTTCTTT
1 TTTTTTCTTTTTCTTT
196743 TTTTTTCTTTTTCTTT
1 TTTTTTCTTTTTCTTT
196759 TT
1 TT
196761 CACTCTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (16 bp):
TTTTTTCTTTTTCTTT
Found at i:199003 original size:21 final size:20
Alignment explanation
Indices: 198971--199009 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
198961 TCATATGTAA
*
198971 TATTTATAAAATATAAAAAT
1 TATTTATAAAATAGAAAAAT
*
198991 TATTGTATCAAATAGAAAA
1 TATT-TATAAAATAGAAAA
199010 TATATTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.56, C:0.03, G:0.05, T:0.36
Consensus pattern (20 bp):
TATTTATAAAATAGAAAAAT
Found at i:199144 original size:14 final size:15
Alignment explanation
Indices: 199121--199150 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
199111 AAATTGTTTG
199121 TTTTATAAAATTAAT
1 TTTTATAAAATTAAT
199136 TTTTA-AAAATTAAT
1 TTTTATAAAATTAAT
199150 T
1 T
199151 GTGTGAGGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTATAAAATTAAT
Found at i:200607 original size:36 final size:36
Alignment explanation
Indices: 200567--200635 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
200557 TTTCATTATA
* *
200567 AATTTTTCTTCTTTACTTATCTCATTTAA-AAAACAG
1 AATTTTTCTTCATAAC-TATCTCATTTAACAAAACAG
*
200603 AATTTTTCTTGATAACTATCTCATTTAACAAAA
1 AATTTTTCTTCATAACTATCTCATTTAACAAAA
200636 AAAAAATGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
35 12 0.41
36 17 0.59
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (36 bp):
AATTTTTCTTCATAACTATCTCATTTAACAAAACAG
Found at i:201602 original size:2 final size:2
Alignment explanation
Indices: 201595--201624 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
201585 GAAGCATAAA
201595 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
201625 TAATGGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:204863 original size:2 final size:2
Alignment explanation
Indices: 204848--204893 Score: 69
Period size: 2 Copynumber: 24.0 Consensus size: 2
204838 CATCTGAACC
*
204848 AT AT -T AT A- AT AT AT AT AT AT AT AT AT AA 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 AT
204888 AT AT AT
1 AT AT AT
204894 GTAACGGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:205103 original size:2 final size:2
Alignment explanation
Indices: 205096--205126 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
205086 GTTATATGTG
205096 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
205127 AATTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:207541 original size:2 final size:2
Alignment explanation
Indices: 207534--207583 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
207524 CATTAAAGTG
* * *
207534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT TT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
207576 AT AT AT AT
1 AT AT AT AT
207584 CAAGTTTGGG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:219445 original size:23 final size:23
Alignment explanation
Indices: 219419--219464 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
219409 AAATATAGTT
219419 TTGGGGGTAACAAATCATTCTAC
1 TTGGGGGTAACAAATCATTCTAC
*
219442 TTGGGGGTAACTAATCATTCTAC
1 TTGGGGGTAACAAATCATTCTAC
219465 CAGGGTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (23 bp):
TTGGGGGTAACAAATCATTCTAC
Found at i:219990 original size:4 final size:4
Alignment explanation
Indices: 219981--220009 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
219971 ATCTTGATAT
219981 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
220010 CATAAAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:220502 original size:3 final size:3
Alignment explanation
Indices: 220488--220522 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
220478 ATATAAGGCT
*
220488 TTG TTT TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
220523 AATGTTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:225506 original size:6 final size:6
Alignment explanation
Indices: 225469--225504 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
225459 TTTGAATGGA
*
225469 AAGGAGG AAGGAG AAGGAG AAGGAG AAGGAA AAGGA
1 AAGGA-G AAGGAG AAGGAG AAGGAG AAGGAG AAGGA
225505 AATGGGGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
6 23 0.82
7 5 0.18
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (6 bp):
AAGGAG
Found at i:226415 original size:2 final size:2
Alignment explanation
Indices: 226403--226437 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
226393 TCCTTTTACA
*
226403 CT CT CT TT 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
226438 AATAAATATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:235248 original size:31 final size:30
Alignment explanation
Indices: 235213--235271 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
235203 TTTTATTGTG
235213 TTCAAATAAGTCCTTTAATATTTACTTTACA
1 TTCAAATAAGT-CTTTAATATTTACTTTACA
* * * *
235244 TTCAAGTAAGTTTTTAATTTTTATTTTA
1 TTCAAATAAGTCTTTAATATTTACTTTA
235272 TACCCAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.32, C:0.10, G:0.05, T:0.53
Consensus pattern (30 bp):
TTCAAATAAGTCTTTAATATTTACTTTACA
Found at i:235359 original size:17 final size:18
Alignment explanation
Indices: 235324--235365 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
235314 CTCTTAATAT
235324 AAATAAAATTTTCATTTG
1 AAATAAAATTTTCATTTG
235342 AAATAAAGA-TTT-ATTTG
1 AAATAAA-ATTTTCATTTG
235359 -AATAAAA
1 AAATAAAA
235366 ATCAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.04
16 6 0.26
17 5 0.22
18 10 0.43
19 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.38
Consensus pattern (18 bp):
AAATAAAATTTTCATTTG
Found at i:236681 original size:23 final size:22
Alignment explanation
Indices: 236630--236683 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 22
236620 TTTTAATGAG
*
236630 ATTAAAAATAATAATAATTTTA
1 ATTAAAAATAATAATAATTATA
236652 ATTTTAAAAA-AATAATGTAATTATA
1 A--TTAAAAATAATAA--TAATTATA
236677 ATTAAAA
1 ATTAAAA
236684 GAATTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
22 1 0.04
23 11 0.41
24 7 0.26
25 8 0.30
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
ATTAAAAATAATAATAATTATA
Found at i:236724 original size:11 final size:12
Alignment explanation
Indices: 236708--236736 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
236698 TTATATTCAA
236708 TAAATT-ATATT
1 TAAATTAATATT
236719 TAAATTAATATT
1 TAAATTAATATT
236731 TAAATT
1 TAAATT
236737 TAACTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATTAATATT
Found at i:243212 original size:30 final size:30
Alignment explanation
Indices: 243158--243246 Score: 83
Period size: 32 Copynumber: 2.9 Consensus size: 30
243148 AAATAAGTCC
*
243158 TTAATTTTTAATTTCA-CTCAAATAAAT-TA
1 TTAATTTTTAATTTTATC-CAAATAAATATA
*
243187 TTAATTTTTAATTTGTATCCAAATAAATATT
1 TTAATTTTTAATTT-TATCCAAATAAATATA
* * *
243218 TTAAACTTTTAATTTATATCTAAAAAAAT
1 TT-AATTTTTAATTT-TATCCAAATAAAT
243247 CCTTAATATA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.28
30 10 0.20
31 4 0.08
32 22 0.44
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.48
Consensus pattern (30 bp):
TTAATTTTTAATTTTATCCAAATAAATATA
Found at i:243684 original size:16 final size:17
Alignment explanation
Indices: 243663--243694 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
243653 TAATTAATTA
243663 TTTATATTTAT-TTAAT
1 TTTATATTTATATTAAT
243679 TTTATATTTATATTAA
1 TTTATATTTATATTAA
243695 AAAATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATATTTATATTAAT
Found at i:251349 original size:2 final size:2
Alignment explanation
Indices: 251342--251374 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
251332 AAGAATGGAA
251342 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 A
251375 GTTTCTCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:259650 original size:23 final size:21
Alignment explanation
Indices: 259619--259661 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
259609 TTGTCAAATT
259619 TAAAATTTTAAAATTCTTAAAA
1 TAAAATTTTAAAATT-TTAAAA
*
259641 TAAATATTTTTAAATTTTAAA
1 TAAA-ATTTTAAAATTTTAAA
259662 TGTTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TAAAATTTTAAAATTTTAAAA
Found at i:262570 original size:2 final size:2
Alignment explanation
Indices: 262563--262587 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
262553 AATTATGATT
262563 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
262588 AATGGCCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:264188 original size:1 final size:1
Alignment explanation
Indices: 264182--264208 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
264172 AATTTCTTTT
264182 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
264209 CAAGTATACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:267193 original size:54 final size:54
Alignment explanation
Indices: 267110--267233 Score: 151
Period size: 54 Copynumber: 2.3 Consensus size: 54
267100 AGGCACCTGT
* * * * *
267110 ATCACTCCACTTTGAACCAGTCCATGATTTGTCCACC-TCATTTGAAGCATCAGC
1 ATCACTCCATTTTGGACCAGACCAGGATTTCT-CACCTTCATTTGAAGCATCAGC
* *
267164 ATCACCCCATTTTGGACCAGACCAGGATTTCTCACCTTCATTTGAAGCATTAGC
1 ATCACTCCATTTTGGACCAGACCAGGATTTCTCACCTTCATTTGAAGCATCAGC
**
267218 ATTGCTCCATTTTGGA
1 ATCACTCCATTTTGGA
267234 GCATTCCAAG
Statistics
Matches: 59, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
53 4 0.07
54 55 0.93
ACGTcount: A:0.25, C:0.29, G:0.15, T:0.31
Consensus pattern (54 bp):
ATCACTCCATTTTGGACCAGACCAGGATTTCTCACCTTCATTTGAAGCATCAGC
Found at i:267247 original size:54 final size:53
Alignment explanation
Indices: 267110--267250 Score: 138
Period size: 54 Copynumber: 2.6 Consensus size: 53
267100 AGGCACCTGT
* * * * * *
267110 ATCACTCCACTTTGAACCAGTCCATGATTTGTCCACCTCATTTGAAGCATCAGC
1 ATCACCCCATTTTGGACCAGACCAAGATTTCT-CACCTCATTTGAAGCATCAGC
* *
267164 ATCACCCCATTTTGGACCAGACCAGGATTTCTCACCTTCATTTGAAGCATTAGC
1 ATCACCCCATTTTGGACCAGACCAAGATTTCTCACC-TCATTTGAAGCATCAGC
** * * **
267218 ATTGCTCCATTTTGGAGCATTCCAAGATTTCTC
1 ATCACCCCATTTTGGACCAGACCAAGATTTCTC
267251 CACATTGAAT
Statistics
Matches: 72, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 4 0.06
54 68 0.94
ACGTcount: A:0.25, C:0.29, G:0.14, T:0.32
Consensus pattern (53 bp):
ATCACCCCATTTTGGACCAGACCAAGATTTCTCACCTCATTTGAAGCATCAGC
Found at i:267920 original size:24 final size:24
Alignment explanation
Indices: 267886--267931 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
267876 CCACGAACTG
* *
267886 GACTTCGGCTCCTGCTTCTACTAC
1 GACTTCGGCTCCAGCTCCTACTAC
*
267910 GACTTCTGCTCCAGCTCCTACT
1 GACTTCGGCTCCAGCTCCTACT
267932 CCTGCTTCTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.13, C:0.39, G:0.15, T:0.33
Consensus pattern (24 bp):
GACTTCGGCTCCAGCTCCTACTAC
Found at i:272434 original size:18 final size:18
Alignment explanation
Indices: 272413--272465 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
272403 TAAAGGTCAA
272413 AAAGCAAAGAAACCCAAG
1 AAAGCAAAGAAACCCAAG
272431 AAAGCAAAGAAACCCAAG
1 AAAGCAAAGAAACCCAAG
* *
272449 AAATCAACAGAGACCCA
1 AAAGCAA-AGAAACCCA
272466 TTAATCCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 24 0.75
19 8 0.25
ACGTcount: A:0.58, C:0.25, G:0.15, T:0.02
Consensus pattern (18 bp):
AAAGCAAAGAAACCCAAG
Found at i:273120 original size:12 final size:12
Alignment explanation
Indices: 273100--273131 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
273090 ACACTCTGGC
*
273100 AATTATAATTAT
1 AATTTTAATTAT
273112 AATTTTAATTAT
1 AATTTTAATTAT
273124 AATTTTAA
1 AATTTTAA
273132 CATTATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
AATTTTAATTAT
Found at i:273680 original size:3 final size:3
Alignment explanation
Indices: 273672--273705 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
273662 TTAGCTCTGA
273672 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
273706 AACTTAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:277351 original size:18 final size:19
Alignment explanation
Indices: 277328--277376 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 19
277318 ATTTGAGATG
277328 ATATATTTTAAATAT-AAA
1 ATATATTTTAAATATAAAA
277346 ATATA--TT-AATATAAAA
1 ATATATTTTAAATATAAAA
277362 ATATATTTTCAAATA
1 ATATATTTT-AAATA
277377 GCCTAGTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.19
16 10 0.38
18 7 0.27
20 4 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
ATATATTTTAAATATAAAA
Found at i:279889 original size:10 final size:10
Alignment explanation
Indices: 279866--279906 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
279856 TGTTTTATTT
279866 TATAAAAAT-
1 TATAAAAATA
279875 T-TAAAAATA
1 TATAAAAATA
279884 TATAAAAACTA
1 TATAAAAA-TA
279895 -ATAAAAATA
1 TATAAAAATA
279904 TAT
1 TAT
279907 GATTTGGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 7 0.25
9 4 0.14
10 15 0.54
11 2 0.07
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (10 bp):
TATAAAAATA
Found at i:290714 original size:26 final size:25
Alignment explanation
Indices: 290684--290739 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
290674 ACATAAATTT
*
290684 TTTTTAATAAATTATTTAAATTGAATA
1 TTTTGAAT-AATTATTTAAATTGAA-A
**
290711 TTTTGGGTAATTATTTAAATTGAAA
1 TTTTGAATAATTATTTAAATTGAAA
290736 TTTT
1 TTTT
290740 TGCATAAGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 16 0.62
27 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (25 bp):
TTTTGAATAATTATTTAAATTGAAA
Found at i:290751 original size:25 final size:27
Alignment explanation
Indices: 290697--290763 Score: 68
Period size: 26 Copynumber: 2.6 Consensus size: 27
290687 TTAATAAATT
** *
290697 ATTTAAATTG-AATATTTTGGGTAATT
1 ATTTAAATTGAAATATTTTGCATAATG
290723 ATTTAAATTGAAAT-TTTTGCATAA-G
1 ATTTAAATTGAAATATTTTGCATAATG
* *
290748 ATTTGAATTCAAATAT
1 ATTTAAATTGAAATAT
290764 ATTAAATCAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
25 12 0.35
26 19 0.56
27 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.12, T:0.46
Consensus pattern (27 bp):
ATTTAAATTGAAATATTTTGCATAATG
Found at i:292669 original size:6 final size:6
Alignment explanation
Indices: 292658--292703 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
292648 ACGGATGACC
292658 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATA
1 TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATAAA TATA
292704 TAATTAATGG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TATAAA
Found at i:297143 original size:28 final size:28
Alignment explanation
Indices: 297081--297143 Score: 65
Period size: 28 Copynumber: 2.2 Consensus size: 28
297071 AATTTTGTTA
297081 AAAAATTAACAAAATTGAAAGTACAATG
1 AAAAATTAACAAAATTGAAAGTACAATG
** * * *
297109 ATGAATTGAATAAAATT-AGAGTATAATG
1 AAAAATT-AACAAAATTGAAAGTACAATG
297137 AAAAATT
1 AAAAATT
297144 TTAACAAATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
28 19 0.70
29 8 0.30
ACGTcount: A:0.57, C:0.03, G:0.13, T:0.27
Consensus pattern (28 bp):
AAAAATTAACAAAATTGAAAGTACAATG
Found at i:303719 original size:97 final size:97
Alignment explanation
Indices: 303542--303720 Score: 209
Period size: 97 Copynumber: 1.8 Consensus size: 97
303532 GATAGGAGAG
* * * * * * * *
303542 AGGATGGAAGAAAATAGTTAAAAAGAGCAAGGAGAAATAAGATTGAAAGACTTGGTTATTAACAA
1 AGGATGAAAGAAAAGAGTTAAAAAGACCAAAGAGAAACAAGACTGAAAGACTTGATCATTAACAA
*
303607 ATTTGATCAGCACGAAAGAGAATGGGAAAGAA
66 ATTTGATCAACACGAAAGAGAATGGGAAAGAA
* *
303639 AGGATGAAAGAAAAGAGTTAAAAAGACCAAAGA-AAAGCAAGACTGAAA-AGGTTGATCATTGAC
1 AGGATGAAAGAAAAGAGTTAAAAAGACCAAAGAGAAA-CAAGACTGAAAGA-CTTGATCATTAAC
* *
303702 AAATTTGATTAATACGAAA
64 AAATTTGATCAACACGAAA
303721 TAAGTGAAAG
Statistics
Matches: 67, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
96 4 0.06
97 63 0.94
ACGTcount: A:0.51, C:0.07, G:0.23, T:0.18
Consensus pattern (97 bp):
AGGATGAAAGAAAAGAGTTAAAAAGACCAAAGAGAAACAAGACTGAAAGACTTGATCATTAACAA
ATTTGATCAACACGAAAGAGAATGGGAAAGAA
Found at i:303943 original size:12 final size:13
Alignment explanation
Indices: 303921--303945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
303911 TAATTTAAGT
303921 TTTAAATTTTTTC
1 TTTAAATTTTTTC
303934 TTTAAATTTTTT
1 TTTAAATTTTTT
303946 AAATGTTTAA
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTAAATTTTTTC
Found at i:307759 original size:17 final size:17
Alignment explanation
Indices: 307699--307773 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
307689 ATTTATTTTA
* *
307699 TTAATATTACATAAAATT
1 TTAAT-TTAAATAAAAAT
* * *
307717 TTATTTTAATTAAAAAAA
1 TTAATTTAAAT-AAAAAT
* * *
307735 TTAA-TTAATTAAGATT
1 TTAATTTAAATAAAAAT
307751 TTAATTTAAATAAAAAT
1 TTAATTTAAATAAAAAT
307768 TTAATT
1 TTAATT
307774 GAATACAAAT
Statistics
Matches: 43, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
16 7 0.16
17 25 0.58
18 11 0.26
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (17 bp):
TTAATTTAAATAAAAAT
Found at i:307951 original size:23 final size:23
Alignment explanation
Indices: 307909--307962 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
307899 TAAAGAAATT
*
307909 TTTAATT-TTGTTTTCATTAAAA
1 TTTAATTATTATTTTCATTAAAA
307931 TTTAATTATTATTTT-ATTTAAAA
1 TTTAATTATTATTTTCA-TTAAAA
307954 TATT-ATTAT
1 T-TTAATTAT
307963 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.29
23 18 0.64
24 2 0.07
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTAATTATTATTTTCATTAAAA
Found at i:309816 original size:2 final size:2
Alignment explanation
Indices: 309809--309844 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
309799 TCTCTTTTTA
309809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
309845 AAAAAGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:314207 original size:2 final size:2
Alignment explanation
Indices: 314202--314234 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
314192 TCTCTCTCTT
314202 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 T
314235 CAATCCAAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:320257 original size:15 final size:15
Alignment explanation
Indices: 320239--320283 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
320229 AAAAATTATT
320239 AATATTTATATTAAA
1 AATATTTATATTAAA
*
320254 AATATTTAT-CTAAA
1 AATATTTATATTAAA
* *
320268 AATATATATATCAAA
1 AATATTTATATTAAA
320283 A
1 A
320284 TTTATTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATTTATATTAAA
Found at i:320269 original size:14 final size:15
Alignment explanation
Indices: 320239--320277 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
320229 AAAAATTATT
*
320239 AATATTTATATTAAA
1 AATATTTATACTAAA
320254 AATATTTAT-CTAAA
1 AATATTTATACTAAA
*
320268 AATATATATA
1 AATATTTATA
320278 TCAAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTTATACTAAA
Found at i:320414 original size:27 final size:28
Alignment explanation
Indices: 320370--320422 Score: 67
Period size: 27 Copynumber: 1.9 Consensus size: 28
320360 TTAATCATTT
320370 TTAATAAAATTTATTTTATAA-ATTTCAC
1 TTAATAAAATTTATTTTA-AATATTTCAC
320398 TTAA-AAAATTT-TATTTAAATATTTC
1 TTAATAAAATTTAT-TTTAAATATTTC
320423 CCCTACCTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
26 3 0.13
27 16 0.70
28 4 0.17
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (28 bp):
TTAATAAAATTTATTTTAAATATTTCAC
Found at i:325201 original size:2 final size:2
Alignment explanation
Indices: 325194--325222 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
325184 TACACATAAA
325194 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
325223 TTCCATAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:327706 original size:19 final size:20
Alignment explanation
Indices: 327679--327722 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
327669 AAGCTTTGGG
* *
327679 CTATGCTCTGCTTTTC-TTT
1 CTATTCTCTCCTTTTCGTTT
327698 CTATTCTCTCCTTTTCGTTT
1 CTATTCTCTCCTTTTCGTTT
327718 CTATT
1 CTATT
327723 TTTCTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.07, C:0.27, G:0.07, T:0.59
Consensus pattern (20 bp):
CTATTCTCTCCTTTTCGTTT
Found at i:334657 original size:18 final size:17
Alignment explanation
Indices: 334629--334662 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
334619 GAATAAACCA
*
334629 ATGAAAAGAACTTGAAC
1 ATGAAAAGAACCTGAAC
334646 ATGAATAAGAACCTGAA
1 ATGAA-AAGAACCTGAA
334663 AATTTGGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.18
Consensus pattern (17 bp):
ATGAAAAGAACCTGAAC
Found at i:339194 original size:81 final size:82
Alignment explanation
Indices: 339058--339218 Score: 245
Period size: 81 Copynumber: 2.0 Consensus size: 82
339048 TATTGAGGAC
*
339058 ATATCTCCACAAAATCTTCTATTGATAATTTCTAATTCCTTGAAAACTACAAAGGAAAAA-GT-T
1 ATATCTCCACAAAATCTTCTATTGATAATTTCCAATTCCTTGAAAACTACAAAGGAAAAAGGTGT
*
339121 TGTTTTGTCTCTATTGAA
66 T-TCTTGTCTCTATTGAA
* * * *
339139 ATATCTCCGCAAAATCTTCTTTTGATAATTTCCAATTGCTTGAAAACTACGAAGGAAAAAGGTGT
1 ATATCTCCACAAAATCTTCTATTGATAATTTCCAATTCCTTGAAAACTACAAAGGAAAAAGGTGT
339204 TTCTTGTCTCTATTG
66 TTCTTGTCTCTATTG
339219 CAAGTGAGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 55 0.76
82 15 0.21
83 2 0.03
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (82 bp):
ATATCTCCACAAAATCTTCTATTGATAATTTCCAATTCCTTGAAAACTACAAAGGAAAAAGGTGT
TTCTTGTCTCTATTGAA
Found at i:342373 original size:12 final size:12
Alignment explanation
Indices: 342356--342380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
342346 ATTAAATAGA
342356 TAATTTTTAAAT
1 TAATTTTTAAAT
342368 TAATTTTTAAAT
1 TAATTTTTAAAT
342380 T
1 T
342381 TTAAAATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TAATTTTTAAAT
Found at i:346650 original size:18 final size:18
Alignment explanation
Indices: 346629--346676 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
346619 AATACCTTTG
346629 ATTCATTTGATGTAATGT
1 ATTCATTTGATGTAATGT
* *
346647 ATTCGTTTAATGTAATGT
1 ATTCATTTGATGTAATGT
*
346665 ATATCCTTTGAT
1 AT-TCATTTGAT
346677 TCATTCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 18 0.72
19 7 0.28
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (18 bp):
ATTCATTTGATGTAATGT
Found at i:346810 original size:4 final size:4
Alignment explanation
Indices: 346801--346829 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
346791 ACAAACTTGG
346801 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC T
346830 CTCATCTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:349417 original size:28 final size:29
Alignment explanation
Indices: 349366--349449 Score: 98
Period size: 28 Copynumber: 2.9 Consensus size: 29
349356 AATAACATGA
* *
349366 ATAATTTTTGAATTATAATAAAATATTTAAT
1 ATAATATTTAAATTAT-A-AAAATATTTAAT
*
349397 ATAATATTTAAATT-TAAAAATTTTTAAT
1 ATAATATTTAAATTATAAAAATATTTAAT
* *
349425 GTAATATTTAAATTATAAAATTATT
1 ATAATATTTAAATTATAAAAATATT
349450 AACTACTGTG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 24 0.52
29 9 0.20
30 1 0.02
31 12 0.26
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (29 bp):
ATAATATTTAAATTATAAAAATATTTAAT
Found at i:350621 original size:31 final size:30
Alignment explanation
Indices: 350557--350646 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 30
350547 CGATAATTTG
** *
350557 TATAT-TTATATTATATAAAATATTAAAATT
1 TATATATTATATTATATTTAATA-TAAAAGT
*
350587 TATATATTCATATTATATTTTATATAAAAGT
1 TATATATT-ATATTATATTTAATATAAAAGT
350618 TATATATTATAATTCATA-TTAATATAAAA
1 TATATATTAT-ATT-ATATTTAATATAAAA
350647 TATTTTTAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
30 7 0.14
31 29 0.57
32 15 0.29
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (30 bp):
TATATATTATATTATATTTAATATAAAAGT
Found at i:352193 original size:13 final size:12
Alignment explanation
Indices: 352175--352216 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
352165 CATCATTTAA
352175 AAAGAAGAAGAAG
1 AAAGAAGAA-AAG
352188 AAAGAAGAAAAG
1 AAAGAAGAAAAG
*
352200 AAAAGAAAAAAAG
1 -AAAGAAGAAAAG
352213 AAAG
1 AAAG
352217 CCACTTCTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:352200 original size:21 final size:18
Alignment explanation
Indices: 352174--352215 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 18
352164 TCATCATTTA
352174 AAAAGAAGAAGAAGAAAGAAG
1 AAAAGAA-AAGAA-AAA-AAG
352195 AAAAGAAAAGAAAAAAAG
1 AAAAGAAAAGAAAAAAAG
352213 AAA
1 AAA
352216 GCCACTTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 6 0.29
19 3 0.14
20 5 0.24
21 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAGAAAAAAAG
Found at i:352830 original size:19 final size:18
Alignment explanation
Indices: 352799--352834 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
352789 GCCTAATTAA
352799 ATTTTTAATTTTTAATAT
1 ATTTTTAATTTTTAATAT
*
352817 ATTTTTATTATTTTAATA
1 ATTTTTAAT-TTTTAATA
352835 AAAAGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTTTTAATTTTTAATAT
Found at i:353039 original size:12 final size:12
Alignment explanation
Indices: 353017--353053 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
353007 AATTTGATTG
353017 AATTT-AAATCA
1 AATTTCAAATCA
353028 AATTTCAAATCA
1 AATTTCAAATCA
353040 AA-TTCAAACTCA
1 AATTTCAAA-TCA
353052 AA
1 AA
353054 ATTTTCATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (12 bp):
AATTTCAAATCA
Found at i:359705 original size:3 final size:3
Alignment explanation
Indices: 359697--359729 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
359687 TTATAAAATG
359697 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
359730 TTACCCATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:371932 original size:12 final size:12
Alignment explanation
Indices: 371915--371990 Score: 54
Period size: 12 Copynumber: 6.4 Consensus size: 12
371905 ACATATATAA
*
371915 AATTATTTTTTT
1 AATTATTTATTT
371927 AATTATTTATTT
1 AATTATTTATTT
*
371939 AATT-TATA-TT
1 AATTATTTATTT
371949 AATATATATT-TTT
1 AAT-TAT-TTATTT
*
371962 TA-TATTTATTT
1 AATTATTTATTT
371973 AATT-TTATATTT
1 AATTATT-TATTT
371985 ATATTA
1 A-ATTA
371991 AAAAATAATA
Statistics
Matches: 50, Mismatches: 5, Indels: 16
0.70 0.07 0.23
Matches are distributed among these distances:
10 7 0.14
11 13 0.26
12 23 0.46
13 7 0.14
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
AATTATTTATTT
Found at i:371954 original size:41 final size:38
Alignment explanation
Indices: 371909--371993 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 38
371899 TCCGGTACAT
371909 ATATAAAATTATTTTTTTAATTATTTATTTAA-TTTATATTA
1 ATATAAAA-TA-TTTTTT-A-TATTTATTTAATTTTATATTA
*
371950 ATAT---ATATTTTTTATATTTATTTAATTTTATATTT
1 ATATAAAATATTTTTTATATTTATTTAATTTTATATTA
371985 ATATTAAAA
1 ATA-TAAAA
371994 AATAATATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
34 11 0.29
35 12 0.32
36 7 0.18
37 2 0.05
38 1 0.03
39 1 0.03
41 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (38 bp):
ATATAAAATATTTTTTATATTTATTTAATTTTATATTA
Found at i:371958 original size:25 final size:25
Alignment explanation
Indices: 371930--371991 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 25
371920 TTTTTTTAAT
371930 TATTTATTTAATTTATATTAA-TATA
1 TATTTATTTAATTTAT-TTAATTATA
*
371955 TATTT-TTTATATTTATTTAATTTTA
1 TATTTATTTA-ATTTATTTAATTATA
371980 TATTTATATTAA
1 TATTTAT-TTAA
371992 AAAATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
24 8 0.25
25 19 0.59
26 2 0.06
27 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTTATTTAATTTATTTAATTATA
Found at i:371973 original size:34 final size:37
Alignment explanation
Indices: 371921--371988 Score: 106
Period size: 35 Copynumber: 1.9 Consensus size: 37
371911 ATAAAATTAT
371921 TTTTTTAATTATTTATTTAA-TTTATATTAATATATA
1 TTTTTTAATTATTTATTTAATTTTATATTAATATATA
*
371957 TTTTTT-A-TATTTATTTAATTTTATATTTATAT
1 TTTTTTAATTATTTATTTAATTTTATATTAATAT
371989 TAAAAAATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 11 0.37
35 13 0.43
36 6 0.20
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (37 bp):
TTTTTTAATTATTTATTTAATTTTATATTAATATATA
Found at i:372015 original size:41 final size:39
Alignment explanation
Indices: 371918--372023 Score: 97
Period size: 41 Copynumber: 2.6 Consensus size: 39
371908 TATATAAAAT
* * * * *
371918 TATTTTTTTAATTATTTATTTAATTTATATTAATATATAT
1 TATTTTATTAATT-TTAATTTAATTTATATTAAAAAATAA
* *
371958 TTTTTATATTTA-TTTAATTTTATATTTATATTAAAAAATAA
1 TATTT-TATTAATTTTAA-TTTA-ATTTATATTAAAAAATAA
371999 TATTTTATTAATTTTAAATTTAATT
1 TATTTTATTAATTTT-AATTTAATT
372024 AAAAATAATT
Statistics
Matches: 52, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
39 3 0.06
40 17 0.33
41 30 0.58
42 2 0.04
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (39 bp):
TATTTTATTAATTTTAATTTAATTTATATTAAAAAATAA
Found at i:372038 original size:33 final size:35
Alignment explanation
Indices: 371966--372039 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 35
371956 ATTTTTTATA
*
371966 TTTATTTAATTTTATATTTATATTAAAAAATAATAT
1 TTTA-TTAATTTTAAATTTATATTAAAAAATAATAT
*
372002 TTTATTAATTTTAAATTTA-ATT-AAAAATAATTT
1 TTTATTAATTTTAAATTTATATTAAAAAATAATAT
372035 TTTAT
1 TTTAT
372040 AATATCAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
33 15 0.42
34 3 0.08
35 14 0.39
36 4 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
TTTATTAATTTTAAATTTATATTAAAAAATAATAT
Found at i:377258 original size:15 final size:16
Alignment explanation
Indices: 377238--377276 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
377228 TTAGTTTGAA
*
377238 AATATAAAAT-TTTAT
1 AATATAAAATAATTAT
377253 AATATAAAATAATTAT
1 AATATAAAATAATTAT
377269 AATTATAA
1 AA-TATAA
377277 GATGCAACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
16 6 0.29
17 5 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AATATAAAATAATTAT
Found at i:391131 original size:2 final size:2
Alignment explanation
Indices: 391126--391154 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
391116 TTTGTGAGCT
391126 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 T
391155 GTAGACCTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:397179 original size:81 final size:82
Alignment explanation
Indices: 397042--397207 Score: 262
Period size: 81 Copynumber: 2.0 Consensus size: 82
397032 TTTACTAGCA
* *
397042 CTAATTTGGCCACTTTTGAACTCTCTTTCTTGTCTATTCTTCCCTTTCATATGATCTACATTCAA
1 CTAATTTGGCCACTTTTGAAC-CTCTTTCTTGTCTATTCTCCCCTTTCATACGATCTACATTCAA
*
397107 GTCGAAACTATTTAATTT
65 GTCAAAACTATTTAATTT
* *
397125 CTAATTTGGCCACTTTTGAA-CTCTTTCTTGTCTATTCTCCCCTTTCCTACGATCTACATTCGAG
1 CTAATTTGGCCACTTTTGAACCTCTTTCTTGTCTATTCTCCCCTTTCATACGATCTACATTCAAG
*
397189 TCAAAACTATTTTATTT
66 TCAAAACTATTTAATTT
397206 CT
1 CT
397208 TTCATCTCTG
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
81 57 0.74
83 20 0.26
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.45
Consensus pattern (82 bp):
CTAATTTGGCCACTTTTGAACCTCTTTCTTGTCTATTCTCCCCTTTCATACGATCTACATTCAAG
TCAAAACTATTTAATTT
Found at i:400855 original size:21 final size:21
Alignment explanation
Indices: 400831--400926 Score: 95
Period size: 21 Copynumber: 4.5 Consensus size: 21
400821 TAGTATGAGT
* *
400831 CATAGTGATGAGTAATCGTAC
1 CATAGTAATGAGTCATCGTAC
*
400852 CATAAGTGATGAGTCA-CTGTAC
1 CAT-AGTAATGAGTCATC-GTAC
* * *
400874 CATAATAATAAGTCATTGTAC
1 CATAGTAATGAGTCATCGTAC
*
400895 CATAGTAATGAGTCATTGTAC
1 CATAGTAATGAGTCATCGTAC
*
400916 CATAGTTATGA
1 CATAGTAATGA
400927 CTCACCGTCC
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
21 46 0.72
22 18 0.28
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (21 bp):
CATAGTAATGAGTCATCGTAC
Found at i:410811 original size:2 final size:2
Alignment explanation
Indices: 410804--410833 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
410794 AAACTCGTTT
410804 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
410834 CACACACACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:419529 original size:2 final size:2
Alignment explanation
Indices: 419522--419546 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
419512 ATTCATGATA
419522 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
419547 GAGAGAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:421382 original size:43 final size:43
Alignment explanation
Indices: 421334--421420 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
421324 AGTGATTCCA
*
421334 AAGTTTCTGTGCCTAGAGTTACTTGTTACAGCAGTGAAGATTC
1 AAGTTTCTGTGCCTACAGTTACTTGTTACAGCAGTGAAGATTC
*
421377 AAGTTTCTGTGCCTACAGTTACTTGTTACAGTAGTGAAGATTC
1 AAGTTTCTGTGCCTACAGTTACTTGTTACAGCAGTGAAGATTC
421420 A
1 A
421421 TATTTCCAGG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.16, G:0.22, T:0.36
Consensus pattern (43 bp):
AAGTTTCTGTGCCTACAGTTACTTGTTACAGCAGTGAAGATTC
Found at i:425095 original size:6 final size:6
Alignment explanation
Indices: 425082--425110 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
425072 CACAAAAACG
425082 AAAA-C AAAAGC AAAAGC AAAAGC AAAAGC
1 AAAAGC AAAAGC AAAAGC AAAAGC AAAAGC
425111 TAGCTATCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.69, C:0.17, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:426072 original size:8 final size:8
Alignment explanation
Indices: 426059--426086 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
426049 GAACAAGATT
426059 AAATATTA
1 AAATATTA
426067 AAATATTA
1 AAATATTA
426075 AAATATTA
1 AAATATTA
426083 AAAT
1 AAAT
426087 CTCTATCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (8 bp):
AAATATTA
Found at i:437340 original size:3 final size:3
Alignment explanation
Indices: 437332--437368 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
437322 GTTTTTGATA
437332 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
437369 CTATGATTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:438110 original size:29 final size:29
Alignment explanation
Indices: 438078--438148 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 29
438068 AAATTATCTT
438078 TTTAAAAAATTTATATAAGACATTAAAAA
1 TTTAAAAAATTTATATAAGACATTAAAAA
* * ** *
438107 TTTAAGTAATTTTATATAAGATTTTGAAAA
1 TTTAA-AAAATTTATATAAGACATTAAAAA
*
438137 TTCAAAAAATTT
1 TTTAAAAAATTT
438149 TTATCTTAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.41
Consensus pattern (29 bp):
TTTAAAAAATTTATATAAGACATTAAAAA
Found at i:459777 original size:19 final size:20
Alignment explanation
Indices: 459738--459777 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
459728 TTTTCTATAC
*
459738 ATTCACAATAGAATTTTAAA
1 ATTCACAATAGAATGTTAAA
*
459758 ATTCACAA-ATAATGTTAAA
1 ATTCACAATAGAATGTTAAA
459777 A
1 A
459778 ATAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.53, C:0.10, G:0.05, T:0.33
Consensus pattern (20 bp):
ATTCACAATAGAATGTTAAA
Found at i:460204 original size:19 final size:19
Alignment explanation
Indices: 460160--460214 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
460150 TTTATCATAA
460160 AAATAGTTTAATAATTATT-T
1 AAATA-TTTAATAATT-TTAT
* *
460180 ATATATTTATTAATTTTAT
1 AAATATTTAATAATTTTAT
*
460199 AAATATTAAATAATTT
1 AAATATTTAATAATTT
460215 AAAATTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 2 0.07
19 23 0.79
20 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
AAATATTTAATAATTTTAT
Found at i:465201 original size:6 final size:6
Alignment explanation
Indices: 465192--465226 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
465182 CTTTCTAATT
465192 CTATAA CTATAA CTATAA CTATAA CTATAA CTATA
1 CTATAA CTATAA CTATAA CTATAA CTATAA CTATA
465227 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
CTATAA
Found at i:467019 original size:24 final size:24
Alignment explanation
Indices: 466966--467046 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 24
466956 TGCAGCTGAG
466966 AGTGACAAC-ACAA-CATCAGAGCC
1 AGTGA-AACAACAATCATCAGAGCC
466989 A-TCGAAA-AACGAATCA-CTAGAGCC
1 AGT-GAAACAAC-AATCATC-AGAGCC
*
467013 AGTGAAACAACAATCATCGGAGCC
1 AGTGAAACAACAATCATCAGAGCC
*
467037 AGTGAGACAA
1 AGTGAAACAA
467047 GAGCCAGTAG
Statistics
Matches: 48, Mismatches: 2, Indels: 15
0.74 0.03 0.23
Matches are distributed among these distances:
22 5 0.10
23 6 0.12
24 32 0.67
25 5 0.10
ACGTcount: A:0.44, C:0.25, G:0.20, T:0.11
Consensus pattern (24 bp):
AGTGAAACAACAATCATCAGAGCC
Found at i:471029 original size:34 final size:34
Alignment explanation
Indices: 470975--471040 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 34
470965 GACAGAAATA
*
470975 CAACAAATCAGATAGGAAGTTTA-AGAATTTGATT
1 CAACAAATCAGATAGAAAGTTTAGA-AATTTGATT
471009 CAACAAATCAGACTA-AAAGTTTAGAAATTTGA
1 CAACAAATCAGA-TAGAAAGTTTAGAAATTTGA
471041 CCCAAAATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.47, C:0.11, G:0.15, T:0.27
Consensus pattern (34 bp):
CAACAAATCAGATAGAAAGTTTAGAAATTTGATT
Found at i:471414 original size:62 final size:61
Alignment explanation
Indices: 471345--471544 Score: 147
Period size: 62 Copynumber: 3.2 Consensus size: 61
471335 AGAAAACACA
* *
471345 TTGAATAATCTTTTACAAAAACTTGAATCGGGTTATTCAAGGCGTTTCTAGCCAAAAATACC
1 TTGAATAATCTTTTACAAAAA-TTAAATAGGGTTATTCAAGGCGTTTCTAGCCAAAAATACC
* * *** * * * * * *
471407 TTGAATAATTTTGTTTC----ATTTTTTTGGGATTATTCGAGGTGTTTTTGGCCAAAAAATACT
1 TTGAATAATCTT-TTACAAAAATTAAATAGGG-TTATTCAAGGCGTTTCTAGCC-AAAAATACC
** * * *
471467 TTGAATAATCTTTTACAAAATATTAAATAGGGTTATTCAAGGCACTTCAAGCTAAAAACACC
1 TTGAATAATCTTTTACAAAA-ATTAAATAGGGTTATTCAAGGCGTTTCTAGCCAAAAATACC
*
471529 TTAAATAATCTATTTA
1 TTGAATAATCT-TTTA
471545 ATTTTTTGAG
Statistics
Matches: 101, Mismatches: 28, Indels: 17
0.69 0.19 0.12
Matches are distributed among these distances:
58 6 0.06
59 21 0.21
60 19 0.19
62 28 0.28
63 20 0.20
64 7 0.07
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (61 bp):
TTGAATAATCTTTTACAAAAATTAAATAGGGTTATTCAAGGCGTTTCTAGCCAAAAATACC
Found at i:471472 original size:122 final size:122
Alignment explanation
Indices: 471303--471537 Score: 321
Period size: 122 Copynumber: 1.9 Consensus size: 122
471293 TTCCAATTTT
*
471303 TTTTTTTGAGATTATTGAAGGTGTTTTTGACCAGAAAACACATTGAATAATCTTTTACAAAA-AC
1 TTTTTTTGAGATTATTGAAGGTGTTTTTGACCAAAAAACACATTGAATAATCTTTTACAAAATA-
* * ** * * *
471367 TTGAATCGGGTTATTCAAGGCGTTTCTAGCCAAAAATACCTTGAATAATTTTGTTTCA
65 TTAAATAGGGTTATTCAAGGCACTTCAAGCCAAAAACACCTTAAATAATTTTGTTTCA
* * * *
471425 TTTTTTTGGGATTATTCG-AGGTGTTTTTGGCCAAAAAATACTTTGAATAATCTTTTACAAAATA
1 TTTTTTTGAGATTATT-GAAGGTGTTTTTGACCAAAAAACACATTGAATAATCTTTTACAAAATA
*
471489 TTAAATAGGGTTATTCAAGGCACTTCAAGCTAAAAACACCTTAAATAAT
65 TTAAATAGGGTTATTCAAGGCACTTCAAGCCAAAAACACCTTAAATAAT
471538 CTATTTAATT
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
122 96 0.98
123 2 0.02
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (122 bp):
TTTTTTTGAGATTATTGAAGGTGTTTTTGACCAAAAAACACATTGAATAATCTTTTACAAAATAT
TAAATAGGGTTATTCAAGGCACTTCAAGCCAAAAACACCTTAAATAATTTTGTTTCA
Found at i:471573 original size:122 final size:122
Alignment explanation
Indices: 471304--471566 Score: 316
Period size: 122 Copynumber: 2.2 Consensus size: 122
471294 TCCAATTTTT
* *
471304 TTTTTTGAGATTATTGAAGGTGTTTTTGACCAGAAAACACATTGAATAATCTTTTACAAAAACTT
1 TTTTTTGAGATTATTCAAGGTGTTTTTGACCAAAAAACACATTGAATAATCTTTTACAAAAACTT
* * ** * * * * * *
471369 GAATCGGGTTATTCAAGGCGTTTCTAGCCAAAAATACCTTGAATAATTTTGTTTCAT
66 AAATAGGGTTATTCAAGGCACTTCAAGCCAAAAACACCTTAAATAATTCTATTTCAA
* * * * *
471426 TTTTTTGGGATTATTCGAGGTGTTTTTGGCCAAAAAATACTTTGAATAATCTTTTACAAAATA-T
1 TTTTTTGAGATTATTCAAGGTGTTTTTGACCAAAAAACACATTGAATAATCTTTTACAAAA-ACT
*
471490 TAAATAGGGTTATTCAAGGCACTTCAAGCTAAAAACACCTTAAATAA-TCTATTT-AA
65 TAAATAGGGTTATTCAAGGCACTTCAAGCCAAAAACACCTTAAATAATTCTATTTCAA
471546 TTTTTTGAGAAATTATTCAAG
1 TTTTTTGAG--ATTATTCAAG
471567 ACGTTTTCTA
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
120 9 0.08
121 5 0.04
122 103 0.87
123 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (122 bp):
TTTTTTGAGATTATTCAAGGTGTTTTTGACCAAAAAACACATTGAATAATCTTTTACAAAAACTT
AAATAGGGTTATTCAAGGCACTTCAAGCCAAAAACACCTTAAATAATTCTATTTCAA
Found at i:473341 original size:28 final size:28
Alignment explanation
Indices: 473286--473368 Score: 87
Period size: 28 Copynumber: 3.0 Consensus size: 28
473276 ACCCAAACCT
* *
473286 GATTCTGATTCAACTGGGCTCCAGGCCC
1 GATTCTGATTCAACTAGGCTCCAAGCCC
* *
473314 GATTTTGATTCAACTAGGCTTCAAGCCC
1 GATTCTGATTCAACTAGGCTCCAAGCCC
* * * *
473342 AATTC-GATTTAACCAGGCTCGAAGCCC
1 GATTCTGATTCAACTAGGCTCCAAGCCC
473369 AATCTCGTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 18 0.40
28 27 0.60
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (28 bp):
GATTCTGATTCAACTAGGCTCCAAGCCC
Found at i:473359 original size:27 final size:27
Alignment explanation
Indices: 473320--473371 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
473310 GCCCGATTTT
*
473320 GATTCAACTAGGCTTC-AAGCCCAATTC
1 GATTCAACCAGGC-TCGAAGCCCAATTC
*
473347 GATTTAACCAGGCTCGAAGCCCAAT
1 GATTCAACCAGGCTCGAAGCCCAAT
473372 CTCGTTCTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (27 bp):
GATTCAACCAGGCTCGAAGCCCAATTC
Found at i:474842 original size:12 final size:12
Alignment explanation
Indices: 474813--474853 Score: 64
Period size: 12 Copynumber: 3.3 Consensus size: 12
474803 TATTAATAAC
474813 AAATTTTCTTAAA
1 AAATTTT-TTAAA
474826 AAATTTTTTAAA
1 AAATTTTTTAAA
*
474838 TAATTTTTTAAA
1 AAATTTTTTAAA
474850 AAAT
1 AAAT
474854 CATAAAAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 19 0.73
13 7 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTTTTTAAA
Found at i:475009 original size:14 final size:14
Alignment explanation
Indices: 474984--475035 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
474974 CATAATCCCC
* *
474984 AAACCTTAAAATTA
1 AAACCCTAAAATCA
*
474998 AAACCCTAAAATCC
1 AAACCCTAAAATCA
475012 AAACCCTAAAATCA
1 AAACCCTAAAATCA
*
475026 AAATCCTAAA
1 AAACCCTAAA
475036 CCCCCCAAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (14 bp):
AAACCCTAAAATCA
Found at i:475013 original size:28 final size:28
Alignment explanation
Indices: 474941--475095 Score: 121
Period size: 28 Copynumber: 5.4 Consensus size: 28
474931 TAAAAAATCC
* *
474941 AAACCCTAAATTCCACAACCTTAAAACTA
1 AAACCCTAAACTCCA-AACCTTAAAATTA
* * *
474970 AAACCATAATCCCCAAACCTTAAAATTA
1 AAACCCTAAACTCCAAACCTTAAAATTA
* * *
474998 AAACCCTAAAATCCAAACCCTAAAATCA
1 AAACCCTAAACTCCAAACCTTAAAATTA
* * *
475026 AAATCCTAAACCCCCCAAACCTTGAAATTA
1 AAACCCTAAA--CTCCAAACCTTAAAATTA
* * * * *
475056 AGACCCCAAACCTACAAACCCTAAAATCA
1 AAACCCTAAA-CTCCAAACCTTAAAATTA
*
475085 AAATCCTAAAC
1 AAACCCTAAAC
475096 CCTAAAATCA
Statistics
Matches: 96, Mismatches: 28, Indels: 5
0.74 0.22 0.04
Matches are distributed among these distances:
28 44 0.46
29 32 0.33
30 20 0.21
ACGTcount: A:0.49, C:0.32, G:0.01, T:0.17
Consensus pattern (28 bp):
AAACCCTAAACTCCAAACCTTAAAATTA
Found at i:475082 original size:29 final size:29
Alignment explanation
Indices: 474941--475174 Score: 123
Period size: 29 Copynumber: 8.3 Consensus size: 29
474931 TAAAAAATCC
* * *
474941 AAACCCTAAA-TTCCACAACCTTAAAACTA
1 AAACCCTAAACCTCCA-AACCCTAAAATTA
* * *
474970 AAACCATAATCC-CCAAACCTTAAAATTA
1 AAACCCTAAACCTCCAAACCCTAAAATTA
* *
474998 AAACCCTAAA-ATCCAAACCCTAAAATCA
1 AAACCCTAAACCTCCAAACCCTAAAATTA
* * * *
475026 AAATCCTAAACCCCCCAAACCTTGAAATTA
1 AAACCCTAAA-CCTCCAAACCCTAAAATTA
* * * *
475056 AGACCCCAAACCTACAAACCCTAAAATCA
1 AAACCCTAAACCTCCAAACCCTAAAATTA
*
475085 AAA---T---CCT--AAACCCTAAAATCA
1 AAACCCTAAACCTCCAAACCCTAAAATTA
** * *
475106 AAATTCTAAACCCTCCAAACCTTGAAATTA
1 AAACCCTAAA-CCTCCAAACCCTAAAATTA
* * * *
475136 AGA-CTTCAAACCTACAAGCCCTAAAATTA
1 AAACCCT-AAACCTCCAAACCCTAAAATTA
475165 AAACCCTAAA
1 AAACCCTAAA
475175 ATCAAAATCC
Statistics
Matches: 153, Mismatches: 37, Indels: 30
0.70 0.17 0.14
Matches are distributed among these distances:
21 17 0.11
23 3 0.02
24 1 0.01
28 46 0.30
29 48 0.31
30 38 0.25
ACGTcount: A:0.48, C:0.31, G:0.02, T:0.19
Consensus pattern (29 bp):
AAACCCTAAACCTCCAAACCCTAAAATTA
Found at i:475086 original size:21 final size:20
Alignment explanation
Indices: 475071--475119 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 20
475061 CCAAACCTAC
475071 AAACCCTAAAATCAAAATCCT
1 AAACCCTAAAATC-AAATCCT
*
475092 AAACCCTAAAATCAAAATTCT
1 AAACCCTAAAATC-AAATCCT
475113 AAACCCT
1 AAACCCT
475120 CCAAACCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.20
Consensus pattern (20 bp):
AAACCCTAAAATCAAATCCT
Found at i:475087 original size:59 final size:58
Alignment explanation
Indices: 474980--475097 Score: 182
Period size: 59 Copynumber: 2.0 Consensus size: 58
474970 AAACCATAAT
* *
474980 CCCCAAACCTTAAAATTAAAACCCTAAAATCCAAACCCTAAAATCAAAATCCTAAACC
1 CCCCAAACCTTAAAATTAAAACCCCAAAATACAAACCCTAAAATCAAAATCCTAAACC
* * *
475038 CCCCAAACCTTGAAATTAAGACCCCAAACCTACAAACCCTAAAATCAAAATCCTAAACC
1 CCCCAAACCTTAAAATTAAAACCCCAAA-ATACAAACCCTAAAATCAAAATCCTAAACC
475097 C
1 C
475098 TAAAATCAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
58 25 0.46
59 29 0.54
ACGTcount: A:0.47, C:0.35, G:0.02, T:0.16
Consensus pattern (58 bp):
CCCCAAACCTTAAAATTAAAACCCCAAAATACAAACCCTAAAATCAAAATCCTAAACC
Found at i:475108 original size:80 final size:79
Alignment explanation
Indices: 475004--475250 Score: 301
Period size: 80 Copynumber: 3.2 Consensus size: 79
474994 ATTAAAACCC
475004 TAAAATCC-AAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCCAAACC
1 TAAAATCCTAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCCAAACC
475068 TACAAACCCTAAAA
66 TACAAACCCTAAAA
* * **
475082 TCAAAATCCTAAACCCTAAAATCAAAATTCTAAACCCTCCAAACCTTGAAATTAAGACTTCAAAC
1 T-AAAATCCTAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCCAAAC
*
475147 CTACAAGCCCTAAAA
65 CTACAAACCCTAAAA
* * ** * *
475162 T----T--AAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCCTGAAAGCAAAACCCTAAACC
1 TAAAATCCTAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCCAAA-C
*
475221 CTTCAAACCCTAAAA
65 CTACAAACCCTAAAA
* *
475236 TTAAACCCTAAACCC
1 TAAAATCCTAAACCC
475251 CTTAAAACCT
Statistics
Matches: 141, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
73 45 0.32
74 15 0.11
75 1 0.01
78 1 0.01
79 7 0.05
80 72 0.51
ACGTcount: A:0.47, C:0.33, G:0.03, T:0.17
Consensus pattern (79 bp):
TAAAATCCTAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCCAAACC
TACAAACCCTAAAA
Found at i:475173 original size:14 final size:14
Alignment explanation
Indices: 475154--475188 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
475144 AACCTACAAG
*
475154 CCCTAAAATTAAAA
1 CCCTAAAATCAAAA
475168 CCCTAAAATCAAAA
1 CCCTAAAATCAAAA
*
475182 TCCTAAA
1 CCCTAAA
475189 CCCCCCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.54, C:0.26, G:0.00, T:0.20
Consensus pattern (14 bp):
CCCTAAAATCAAAA
Found at i:475200 original size:30 final size:29
Alignment explanation
Indices: 475165--475399 Score: 170
Period size: 30 Copynumber: 8.0 Consensus size: 29
475155 CCTAAAATTA
*
475165 AAACCCTAAAATCAAAATCCTAAACCCCCC
1 AAACCCTAAAATCAAAA-CCTAAACCCCTC
* * *
475195 AAACCCTGAAAGCAAAACCCTAAACCCTTC
1 AAACCCTAAAATCAAAA-CCTAAACCCCTC
* * *
475225 AAACCCTAAAATTAAACCCTAAACCCCTT
1 AAACCCTAAAATCAAAACCTAAACCCCTC
* * *
475254 AAAACCTAAAATCAAAACTCTAAATCCTTC
1 AAACCCTAAAATCAAAAC-CTAAACCCCTC
* * * *
475284 AAACCGTAAAA-CTAAGACCTTAAACCCTTT
1 AAACCCTAAAATC-AAAACC-TAAACCCCTC
* * *
475314 AAACACTAAAATAAAAAACCT-AATCCC-C
1 AAACCCTAAAAT-CAAAACCTAAACCCCTC
** * *
475342 AAACCCTAAAATCAAGCCCTAAAACTCTC
1 AAACCCTAAAATCAAAACCTAAACCCCTC
* * *
475371 TAAACCCTAAAACCAAATCCTAAAACCCT
1 -AAACCCTAAAATCAAAACCTAAACCCCT
475400 TGAAACTCAA
Statistics
Matches: 158, Mismatches: 39, Indels: 16
0.74 0.18 0.08
Matches are distributed among these distances:
27 5 0.03
28 15 0.09
29 32 0.20
30 101 0.64
31 5 0.03
ACGTcount: A:0.47, C:0.33, G:0.02, T:0.18
Consensus pattern (29 bp):
AAACCCTAAAATCAAAACCTAAACCCCTC
Found at i:475220 original size:73 final size:72
Alignment explanation
Indices: 475091--475247 Score: 199
Period size: 73 Copynumber: 2.2 Consensus size: 72
475081 ATCAAAATCC
* * * *
475091 TAAACCCTAAAATCAAAATTCTAAACCCTCCAAACCTTGAAATTAAGA-CTTCAAACCTACAAGC
1 TAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCT-AAACCTACAAAC
475155 CCTAAAAT
65 CCTAAAAT
* ** * *
475163 TAAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCCTGAAAGCAAAACCCTAAACCCTTCAAA
1 T-AAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCTAAA-CCTACAAA
475228 CCCTAAAAT
64 CCCTAAAAT
475237 TAAACCCTAAA
1 TAAACCCTAAA
475248 CCCCTTAAAA
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
72 1 0.01
73 54 0.74
74 18 0.25
ACGTcount: A:0.47, C:0.31, G:0.03, T:0.18
Consensus pattern (72 bp):
TAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCTTGAAATTAAGACCCTAAACCTACAAACC
CTAAAAT
Found at i:475230 original size:16 final size:15
Alignment explanation
Indices: 475209--475263 Score: 60
Period size: 16 Copynumber: 3.7 Consensus size: 15
475199 CCTGAAAGCA
475209 AAACCCTAAACCCTT
1 AAACCCTAAACCCTT
*
475224 CAAACCCTAAA--ATT
1 -AAACCCTAAACCCTT
475238 AAACCCTAAACCCCTT
1 AAACCCTAAA-CCCTT
*
475254 AAAACCTAAA
1 AAACCCTAAA
475264 ATCAAAACTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
13 10 0.30
14 2 0.06
16 21 0.64
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (15 bp):
AAACCCTAAACCCTT
Found at i:475277 original size:59 final size:58
Alignment explanation
Indices: 475165--475405 Score: 191
Period size: 59 Copynumber: 4.1 Consensus size: 58
475155 CCTAAAATTA
* * ** * * *
475165 AAACCCTAAAATCAAAATCCTAAACCCCCCAAACCCTGAAAGCAAAACCCTAAACCCTTC
1 AAACCCTAAAAT-TAAACCCTAAACCCCTTAAAACCTAAAATCAAAA-CCTAAACCCTTC
*
475225 AAACCCTAAAATTAAACCCTAAACCCCTTAAAACCTAAAATCAAAACTCTAAATCCTTC
1 AAACCCTAAAATTAAACCCTAAACCCCTTAAAACCTAAAATCAAAAC-CTAAACCCTTC
* * * * * *
475284 AAACCGTAAAACTAAGACCTTAAA-CCCTTTAAACACTAAAATAAAAAACCTAATCCC--C
1 AAACCCTAAAATTAA-ACCCTAAACCCCTTAAAAC-CTAAAAT-CAAAACCTAAACCCTTC
* * * * * * * *
475342 AAACCCTAAAATCAAGCCCTAAAACTCTCTAAACCCTAAAACCAAATCCTAAAACCCTTG
1 AAACCCTAAAATTAAACCCTAAACCCCT-TAAAACCTAAAATCAAAACCT-AAACCCTTC
475402 AAAC
1 AAAC
475406 TCAAACCAAA
Statistics
Matches: 144, Mismatches: 28, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
57 12 0.08
58 28 0.19
59 63 0.44
60 36 0.25
61 5 0.03
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.18
Consensus pattern (58 bp):
AAACCCTAAAATTAAACCCTAAACCCCTTAAAACCTAAAATCAAAACCTAAACCCTTC
Found at i:475382 original size:88 final size:88
Alignment explanation
Indices: 475163--475405 Score: 215
Period size: 89 Copynumber: 2.7 Consensus size: 88
475153 GCCCTAAAAT
* * ** * * * *
475163 TAAAACCCTAAAATCAAAATCCTAAACCCCCCAAACCCTGAAAGCAAAACCCTAAACCCTTCAAA
1 TAAAA-CCTAAAATCAAAACCCTAAAACCTTCAAACCCTAAAACCAAATCCTTAAACCCTTCAAA
* * *
475228 CCCTAAAATTAAACCCTAAACCCC
65 CACTAAAATAAAAACCTAAACCCC
* * * * *
475252 TTAAAACCTAAAATCAAAACTCTAAATCCTTCAAACCGTAAAACTAAGA-CCTTAAACCCTTTAA
1 -TAAAACCTAAAATCAAAACCCTAAAACCTTCAAACCCTAAAACCAA-ATCCTTAAACCCTTCAA
*
475316 ACACTAAAATAAAAAACCTAATCCCC
64 ACACTAAAAT-AAAAACCTAAACCCC
* * * *
475342 -AAACCCTAAAATC-AAGCCCTAAAA-CTCTCTAAACCCTAAAACCAAATCCTAAAACCCTTGAA
1 TAAAACCTAAAATCAAAACCCTAAAACCT-TC-AAACCCTAAAACCAAATCCTTAAACCCTTCAA
475404 AC
64 AC
475406 TCAAACCAAA
Statistics
Matches: 125, Mismatches: 23, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
86 2 0.02
87 11 0.09
88 40 0.32
89 54 0.43
90 18 0.14
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.18
Consensus pattern (88 bp):
TAAAACCTAAAATCAAAACCCTAAAACCTTCAAACCCTAAAACCAAATCCTTAAACCCTTCAAAC
ACTAAAATAAAAACCTAAACCCC
Found at i:475397 original size:21 final size:19
Alignment explanation
Indices: 475372--475430 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 19
475362 AAAACTCTCT
475372 AAACCCTAAAACCAAATCCTA
1 AAACCCTAAAACCAAA-CC-A
*
475393 AAACCCTTGAAACTCAAACCA
1 AAACCC-TAAAAC-CAAACCA
*
475414 AAACCCCAAAATCCAAA
1 AAACCCTAAAA-CCAAA
475431 ACTCCAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
20 7 0.22
21 14 0.44
22 7 0.22
23 4 0.12
ACGTcount: A:0.53, C:0.34, G:0.02, T:0.12
Consensus pattern (19 bp):
AAACCCTAAAACCAAACCA
Found at i:475447 original size:15 final size:15
Alignment explanation
Indices: 475411--475441 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
475401 GAAACTCAAA
475411 CCAAAACCCCAAAAT
1 CCAAAACCCCAAAAT
*
475426 CCAAAACTCCAAAAT
1 CCAAAACCCCAAAAT
475441 C
1 C
475442 TGAAACCCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.39, G:0.00, T:0.10
Consensus pattern (15 bp):
CCAAAACCCCAAAAT
Found at i:476934 original size:29 final size:29
Alignment explanation
Indices: 476866--476921 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
476856 TTTTTCACCG
* *
476866 AAATATCAATAAAATTGAATGTATAGTGCA
1 AAAT-TCAATAAAATTGAAAGTATAATGCA
476896 AAATTCAATAAAATT-AAAGTATAATG
1 AAATTCAATAAAATTGAAAGTATAATG
476922 ATAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 9 0.38
29 11 0.46
30 4 0.17
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.30
Consensus pattern (29 bp):
AAATTCAATAAAATTGAAAGTATAATGCA
Found at i:489926 original size:20 final size:19
Alignment explanation
Indices: 489901--489943 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
489891 TTTACAAATC
489901 TTTAAAATAAATACAT-AAAA
1 TTTAAAATAAA-A-ATAAAAA
*
489921 TTTAAATTAAAAATAAAAA
1 TTTAAAATAAAAATAAAAA
489940 TTTA
1 TTTA
489944 TTAATAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 2 0.10
19 9 0.43
20 10 0.48
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAAATAAAAATAAAAA
Found at i:494170 original size:46 final size:46
Alignment explanation
Indices: 494088--494175 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
494078 GGCCCAAATT
*** * *
494088 GTGAAAAATTTAAAAATTTCGAAAAAGAAAATATTTCTAAATTGAC
1 GTGAAAAATTTAAAAATTAAAAAAAAAAAAAAATTTCTAAATTGAC
494134 GTGAAAAATTTAAAAA-TAAAAAAATAAAAAAAATTTCTAAAT
1 GTGAAAAATTTAAAAATTAAAAAAA-AAAAAAAATTTCTAAAT
494176 AGACCAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 5 0.14
46 31 0.86
ACGTcount: A:0.59, C:0.05, G:0.08, T:0.28
Consensus pattern (46 bp):
GTGAAAAATTTAAAAATTAAAAAAAAAAAAAAATTTCTAAATTGAC
Found at i:498412 original size:7 final size:7
Alignment explanation
Indices: 498400--498427 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
498390 ATTCAATGAA
498400 ATATTTT
1 ATATTTT
498407 ATATTTT
1 ATATTTT
498414 ATATTTT
1 ATATTTT
498421 ATATTTT
1 ATATTTT
498428 CAATATTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATATTTT
Found at i:509809 original size:9 final size:10
Alignment explanation
Indices: 509768--509809 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
509758 GATTCAAACG
*
509768 ATACAAACTCA
1 ATACAAA-TAA
509779 ATACAAATAA
1 ATACAAATAA
509789 ATACAAATAA
1 ATACAAATAA
*
509799 AT-CAAACAA
1 ATACAAATAA
509808 AT
1 AT
509810 TCATAATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 8 0.28
10 14 0.48
11 7 0.24
ACGTcount: A:0.64, C:0.17, G:0.00, T:0.19
Consensus pattern (10 bp):
ATACAAATAA
Found at i:510522 original size:2 final size:2
Alignment explanation
Indices: 510517--510545 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
510507 ATATATATCT
510517 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
510546 AGTGTAAAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:513189 original size:42 final size:42
Alignment explanation
Indices: 513142--513221 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
513132 CTTTGTACGA
* * *
513142 ACTTTACACGATTGAAAATATAAGGATTTCTTTTCTTGACAG
1 ACTTTACACAATTGAAAATATAAGAATTCCTTTTCTTGACAG
*
513184 ACTTTACACAATTGAGAATATAAGAATTCCTTTTCTTG
1 ACTTTACACAATTGAAAATATAAGAATTCCTTTTCTTG
513222 TAACATTTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (42 bp):
ACTTTACACAATTGAAAATATAAGAATTCCTTTTCTTGACAG
Found at i:518146 original size:20 final size:22
Alignment explanation
Indices: 518107--518147 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
518097 TTTGAACACT
*
518107 TAAAATTCATTTTTTTATATTA
1 TAAAATTCATTTTTTCATATTA
518129 TAAAATT-A-TTTTTCATATT
1 TAAAATTCATTTTTTCATATT
518148 TTTTAGTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (22 bp):
TAAAATTCATTTTTTCATATTA
Found at i:520900 original size:23 final size:23
Alignment explanation
Indices: 520874--520917 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
520864 TAATACATAA
*
520874 AAATTAAAAAAAATTGATAAATC
1 AAATCAAAAAAAATTGATAAATC
**
520897 AAATCAAATTAAATTGATAAA
1 AAATCAAAAAAAATTGATAAA
520918 ATTTAGTACG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (23 bp):
AAATCAAAAAAAATTGATAAATC
Found at i:524964 original size:15 final size:15
Alignment explanation
Indices: 524940--524981 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
524930 AAAATAATAA
*
524940 TTTAATTAATTTAAT
1 TTTAAATAATTTAAT
524955 TTTAAATAATTTAAT
1 TTTAAATAATTTAAT
*
524970 TTAAAATTAATT
1 TTTAAA-TAATT
524982 AAATCGATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.79
16 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTAAATAATTTAAT
Done.