Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008592.1 Hibiscus syriacus cultivar Beakdansim tig00111541_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 876692
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 2 of 4
Found at i:270896 original size:38 final size:38
Alignment explanation
Indices: 270769--270938 Score: 144
Period size: 33 Copynumber: 4.7 Consensus size: 38
270759 GCGATTCTCT
* *
270769 CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TGT--
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCG
* *
270802 CGTTGCGATTTTCATTTCGCATTGCGA-T-TC-TGT--
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCG
* **
270835 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCG
** **
270873 CGTTGCGATTTTGGTTTTTCGTTGCGATTCTCATTTCG
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCG
* *
270911 CGTTGCGATTTTAAGTTTCGTGTTGCGA
1 CGTTGCGATTTTCA-TTTCGCGTTGCGA
270939 AAGTAAACTA
Statistics
Matches: 116, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
33 59 0.51
34 1 0.01
35 1 0.01
36 2 0.02
38 43 0.37
39 10 0.09
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (38 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCATTTCG
Found at i:272881 original size:14 final size:14
Alignment explanation
Indices: 272862--272897 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
272852 ATTGTTTAAT
272862 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
272876 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
272890 TGATTTGT
1 TGATTTGT
272898 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:273061 original size:20 final size:19
Alignment explanation
Indices: 273004--273083 Score: 98
Period size: 20 Copynumber: 4.4 Consensus size: 19
272994 AAAAATGACT
273004 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
273023 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
273037 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
273057 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
273077 ATCGCAA
1 ATCGCAA
273084 CGAGAGAATC
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 1 0.02
17 3 0.06
19 8 0.15
20 30 0.57
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:273260 original size:105 final size:109
Alignment explanation
Indices: 273098--273367 Score: 425
Period size: 105 Copynumber: 2.6 Consensus size: 109
273088 AGAATCGCAA
273098 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
273163 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TCT-CG-T
66 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
*
273203 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCATTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
*
273268 TTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
66 TTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATCTCCG-AT
*
273314 TGCGATTTTCA--T-G--TTGGGATTTTCATTT-CGCATTGCGATTCTCTCGTTGCGATT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATT
273368 GTAATTTCCG
Statistics
Matches: 155, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
105 120 0.77
106 14 0.09
107 3 0.02
108 3 0.02
109 3 0.02
111 12 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (109 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCAT
TTCGCATTGCGATTTTCATTTCGCATTGCGATTTCATCTCCGAT
Found at i:273335 original size:72 final size:71
Alignment explanation
Indices: 273120--273353 Score: 295
Period size: 72 Copynumber: 3.3 Consensus size: 71
273110 TTCGCATTGC
*
273120 GATTTTCATTTCCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTT-CGCATTGCGATTTT
1 GATTTTCATTT-CGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTT
*
273179 CATTTCG
65 CATTTGG
* * * *
273186 CA-TTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTC
1 GATTTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATT-
*
273250 TCTCA-TTGC
63 T-TCATTTGG
273259 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
1 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
273324 ATGTTGG
66 AT-TTGG
273331 GATTTTCATTTCGCATTGCGATT
1 GATTTTCATTTCGCATTGCGATT
273354 CTCTCGTTGC
Statistics
Matches: 143, Mismatches: 12, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
65 3 0.02
66 12 0.08
67 1 0.01
68 3 0.02
69 4 0.03
70 3 0.02
71 16 0.11
72 88 0.62
73 7 0.05
74 6 0.04
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (71 bp):
GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTC
ATTTGG
Found at i:273382 original size:53 final size:52
Alignment explanation
Indices: 273098--273367 Score: 406
Period size: 53 Copynumber: 5.1 Consensus size: 52
273088 AGAATCGCAA
273098 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
273151 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
273203 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
273256 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
273314 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
273361 TGCGATT
1 TGCGATT
273368 GTAATTTCCG
Statistics
Matches: 205, Mismatches: 5, Indels: 20
0.89 0.02 0.09
Matches are distributed among these distances:
47 8 0.04
49 2 0.01
50 2 0.01
51 3 0.01
52 62 0.30
53 108 0.53
54 3 0.01
55 3 0.01
56 2 0.01
58 12 0.06
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:275052 original size:20 final size:20
Alignment explanation
Indices: 275024--275272 Score: 223
Period size: 20 Copynumber: 12.4 Consensus size: 20
275014 AAATTTCAGT
* * *
275024 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
275044 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
275064 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
275084 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
275104 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
275124 GTTGCGATATACGGATAT-GC
1 GTTGCGATTTACGGAT-TCGC
* * *
275144 ATTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* * *
275164 GTTGCTATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
275184 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
275204 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* * **
275224 GTTGTGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
* **
275244 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
275264 GTTGCGATT
1 GTTGCGATT
275273 CTTAAAAATC
Statistics
Matches: 195, Mismatches: 30, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
20 194 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:275325 original size:21 final size:21
Alignment explanation
Indices: 275220--275337 Score: 80
Period size: 21 Copynumber: 5.7 Consensus size: 21
275210 ATTTATGTGT
* * *
275220 TCGCGTTGTGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
* *
275240 TCGCGTTGCGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
275260 TCGCGTTGCGATTCTT-AAAAA
1 TCGCGTTGCGATT-TTCAAAAA
** * ** **
275281 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTCAAAAA
* *
275302 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAAAAA
275323 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
275338 GGAAATTGAT
Statistics
Matches: 79, Mismatches: 16, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
20 34 0.43
21 45 0.57
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAA
Found at i:275333 original size:42 final size:43
Alignment explanation
Indices: 275240--275338 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
275230 ATTTTCATAT
*
275240 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTCTTAAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTAAAAA
** *
275281 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATT-TTCAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTCTT-AAAAA
*
275323 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
275339 GAAATTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTCTTAAAAA
Found at i:279077 original size:26 final size:24
Alignment explanation
Indices: 279028--279077 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
279018 ATTTACACGT
* *
279028 AAAAAAAATAAAAATTTATCTTGA
1 AAAAAAAATAAAAAATTATATTGA
279052 AAAACAAAATAAAAAATTATTATTGA
1 AAAA-AAAATAAAAAATTA-TATTGA
279078 TTGAAATCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 4 0.18
25 13 0.59
26 5 0.23
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
AAAAAAAATAAAAAATTATATTGA
Found at i:279756 original size:8 final size:8
Alignment explanation
Indices: 279743--279769 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
279733 AACCGAAATT
279743 TTTTAGAA
1 TTTTAGAA
279751 TTTTAGAA
1 TTTTAGAA
279759 TTTTAGAA
1 TTTTAGAA
279767 TTT
1 TTT
279770 AATATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (8 bp):
TTTTAGAA
Found at i:279830 original size:17 final size:17
Alignment explanation
Indices: 279803--279841 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
279793 AATTTACAAT
279803 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
279819 TAATTATAAATAATATC
1 TAATTATAAATAATATC
279836 TAATTA
1 TAATTA
279842 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:280753 original size:2 final size:2
Alignment explanation
Indices: 280746--280842 Score: 72
Period size: 2 Copynumber: 54.0 Consensus size: 2
280736 GAAAATATTT
* *
280746 TA TA TA TA -A T- TA -A TA TA -A AA TA TA TA AA T- TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
280782 TA TA TA -A T- TA -A TA TA AA AA TA TA -A AA TA T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
280819 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
280843 ATCGGGGCGG
Statistics
Matches: 78, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
1 11 0.14
2 67 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:280812 original size:33 final size:34
Alignment explanation
Indices: 280737--280843 Score: 144
Period size: 34 Copynumber: 3.1 Consensus size: 34
280727 CCTAAACCCG
*
280737 AAAATATTTTATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
*
280771 AAATTATTATATATATAATTAATATAAAA-ATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
*
280804 AAAATATTATATATATATATATATATATATATATATAT
1 AAAATATTATATATATA-AT-TA-ATATA-AAATATAT
280842 AA
1 AA
280844 TCGGGGCGGG
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
33 20 0.31
34 29 0.45
35 2 0.03
36 5 0.08
37 2 0.03
38 6 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAATATAT
Found at i:283224 original size:31 final size:31
Alignment explanation
Indices: 283166--283251 Score: 120
Period size: 31 Copynumber: 2.8 Consensus size: 31
283156 AAATCACTTA
*
283166 TTTAGTACATAAACTATC-AGTTTGGTATAT
1 TTTAGTACATAAACTATCAATTTTGGTATAT
*
283196 TTTAGTACATAAACTATCAATTTTGGTATGT
1 TTTAGTACATAAACTATCAATTTTGGTATAT
* *
283227 TTTAGTACCTAAACTTTCAACTTTT
1 TTTAGTACATAAACTATCAA-TTTT
283252 TTCAAAACTT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 18 0.36
31 28 0.56
32 4 0.08
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.45
Consensus pattern (31 bp):
TTTAGTACATAAACTATCAATTTTGGTATAT
Found at i:287743 original size:2 final size:2
Alignment explanation
Indices: 287736--287771 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
287726 ATTGGTGTAA
287736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
287772 TAGGATCCAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:288124 original size:2 final size:2
Alignment explanation
Indices: 288117--288175 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
288107 TTCTAACCCA
288117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
288159 AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT
288176 GGTGGCCGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:290027 original size:2 final size:2
Alignment explanation
Indices: 290020--290068 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
290010 ATTAAAGTAA
290020 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
290062 AT AT AT A
1 AT AT AT A
290069 GTTTTGATAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:290385 original size:26 final size:26
Alignment explanation
Indices: 290356--290436 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
290346 ATATAAACAA
290356 TTAATCAAATCAATTTATCAAATCAG
1 TTAATCAAATCAATTTATCAAATCAG
* *
290382 TTAATCAAATCAGTTAATCAAATCAG
1 TTAATCAAATCAATTTATCAAATCAG
** * *
290408 TTGGTCAAAACAA-TTACTGAAATCAG
1 TTAATCAAATCAATTTA-TCAAATCAG
290434 TTA
1 TTA
290437 TCAGTTGTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 2 0.04
26 43 0.96
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (26 bp):
TTAATCAAATCAATTTATCAAATCAG
Found at i:290416 original size:13 final size:13
Alignment explanation
Indices: 290356--290409 Score: 90
Period size: 13 Copynumber: 4.2 Consensus size: 13
290346 ATATAAACAA
*
290356 TTAATCAAATCAA
1 TTAATCAAATCAG
*
290369 TTTATCAAATCAG
1 TTAATCAAATCAG
290382 TTAATCAAATCAG
1 TTAATCAAATCAG
290395 TTAATCAAATCAG
1 TTAATCAAATCAG
290408 TT
1 TT
290410 GGTCAAAACA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (13 bp):
TTAATCAAATCAG
Found at i:290416 original size:39 final size:39
Alignment explanation
Indices: 290356--290436 Score: 99
Period size: 39 Copynumber: 2.1 Consensus size: 39
290346 ATATAAACAA
* * *
290356 TTAATCAAATCAATTTATCAAATCAGTTAATCAAATCAG
1 TTAATCAAATCAATTGATCAAAACAATTAATCAAATCAG
* * * *
290395 TTAATCAAATCAGTTGGTCAAAACAATTACTGAAATCAG
1 TTAATCAAATCAATTGATCAAAACAATTAATCAAATCAG
290434 TTA
1 TTA
290437 TCAGTTGTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (39 bp):
TTAATCAAATCAATTGATCAAAACAATTAATCAAATCAG
Found at i:299927 original size:16 final size:16
Alignment explanation
Indices: 299884--299915 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
299874 TTAAAAACTC
299884 AAATAAATAATTATTT
1 AAATAAATAATTATTT
299900 AAATAAATAATTATTT
1 AAATAAATAATTATTT
299916 GAAAGAATAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATAAATAATTATTT
Found at i:300636 original size:21 final size:23
Alignment explanation
Indices: 300611--300658 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
300601 TAATACCGTC
300611 AAATTTT-AA-ATAGAAAATAA-T
1 AAATTTTAAACATA-AAAATAATT
300632 AAATTTTAAACATAAAAATAATT
1 AAATTTTAAACATAAAAATAATT
300655 AAAT
1 AAAT
300659 AATTATTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.29
22 9 0.38
23 8 0.33
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATTTTAAACATAAAAATAATT
Found at i:302358 original size:60 final size:60
Alignment explanation
Indices: 302251--302393 Score: 155
Period size: 60 Copynumber: 2.4 Consensus size: 60
302241 GTACATCCTC
** * *
302251 AAACTATGTTCCTTATTCTAAATTAGTTCTTAAACCATTAAGTATTCTAAGTTCACCCCT
1 AAACTATGACCCTTATTCTAAATTAGTCCTTAAACCATTAAGCATTCTAAGTTCACCCCT
* * * * * *
302311 AGACTATGACCCTTATTTTACATTAGTCCTTAAA-CTTGTAAGCATTCTAATTTCACCCGT
1 AAACTATGACCCTTATTCTAAATTAGTCCTTAAACCAT-TAAGCATTCTAAGTTCACCCCT
*
302371 AAACTATGATCCC-CATTCTAAAT
1 AAACTATGA-CCCTTATTCTAAAT
302394 AAGTATCCAA
Statistics
Matches: 67, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
59 2 0.03
60 62 0.93
61 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (60 bp):
AAACTATGACCCTTATTCTAAATTAGTCCTTAAACCATTAAGCATTCTAAGTTCACCCCT
Found at i:307235 original size:43 final size:43
Alignment explanation
Indices: 307010--307228 Score: 303
Period size: 43 Copynumber: 5.1 Consensus size: 43
307000 TGGTAACAAA
*** * * * ** *
307010 AAACGCCGCAATAGGTAACGATATATAGCGGCGTTTGTCTAAT
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
* * *
307053 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTCAAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
307096 AAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
307139 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTCCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
*
307182 AAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
307225 AAAC
1 AAAC
307229 ATCGCAAAAG
Statistics
Matches: 160, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 160 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGAGATTTAGCGGCGTTTTTCCCAC
Found at i:307262 original size:43 final size:43
Alignment explanation
Indices: 307032--307284 Score: 177
Period size: 43 Copynumber: 5.9 Consensus size: 43
307022 AGGTAACGAT
* ** * * * * * *
307032 ATATAGCGGCGTTTGTCTAATAAACGCCGCAATAGGTGTTGAT
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * * * * * *
307075 ATTTAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTGTTGAG
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * * * * *
307118 ATTTAGCGGAGTTTTTCCCACAAACGCCGCAATAGGTGTTGAG
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* * * * *
307161 ATTTAGCGGCGTTTTCCCCACAAACGCCGCAATAGGTCTTGAG
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
* *
307204 ATTTAGCGGCGTTTTTCCCACAAACATCGCAAAAGATC-TG-G
1 ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
*** *
307245 TATATAGCGGCGTTTTTTAGAACAAACGCCGCAAAAGATC
1 -ATATAGCGGCG-TTTTTCCCACAAACACCGCAAAAGATC
307285 ATATCTATAG
Statistics
Matches: 185, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
41 1 0.01
42 12 0.06
43 172 0.93
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
ATATAGCGGCGTTTTTCCCACAAACACCGCAAAAGATCTTGAG
Found at i:307270 original size:86 final size:86
Alignment explanation
Indices: 307078--307278 Score: 262
Period size: 86 Copynumber: 2.3 Consensus size: 86
307068 TGTTGATATT
*
307078 TAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTGTTGAGATTTAGCGGAGTTTTTCCCACAAAC
1 TAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGAGTTTTTCCCACAAAC
* * * * *
307143 GCCGCAATAGGTGTTGAGATT
66 ACCGCAAAAGATGCTGAGATA
** * *
307164 TAGCGGCGTTTTCCCCACAAACGCCGCAATAGGTCTTGAGATTTAGCGGCGTTTTTCCCACAAAC
1 TAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGAGTTTTTCCCACAAAC
*
307229 ATCGCAAAAGAT-CTG-GTATA
66 ACCGCAAAAGATGCTGAG-ATA
*
307249 TAGCGGCGTTTTTTAGAACAAACGCCGCAA
1 TAGCGGCGTTTTTT-CAACAAACGCCGCAA
307279 AAGATCATAT
Statistics
Matches: 98, Mismatches: 15, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
84 1 0.01
85 16 0.16
86 81 0.83
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (86 bp):
TAGCGGCGTTTTTTCAACAAACGCCGCAATAGGTCTTGAGATTTAGCGGAGTTTTTCCCACAAAC
ACCGCAAAAGATGCTGAGATA
Found at i:308631 original size:133 final size:133
Alignment explanation
Indices: 308469--308709 Score: 437
Period size: 133 Copynumber: 1.8 Consensus size: 133
308459 CAGAAAATAA
*
308469 AAAATGAATTCTACCCAGAGATCTAATTCACATAAAAGTAAACAAATTCACACCCCCAATGAGGC
1 AAAATGAATTCTACCCAGAGATCTAATTCACATAAAAATAAACAAATTCACACCCCCAATGAGGC
* * *
308534 TAAGAACTAATAGAATGGACTTTTATAAAACAAAACCCAGAAATCATAAGGTAAAACAAGTTTCA
66 TAAGAACTAAAAGAATGGACTTTCAGAAAACAAAACCCAGAAATCATAAGGTAAAACAAGTTTCA
308599 GGG
131 GGG
308602 AAAATGAATTCTACCCAGAGATCTAATTCACATAAAAATAAACAAATTCACACCCCCAATGAGGC
1 AAAATGAATTCTACCCAGAGATCTAATTCACATAAAAATAAACAAATTCACACCCCCAATGAGGC
*
308667 TAAGAACTAAAAGAATGGACTTTCAGGAAACAAAACCCAGAAA
66 TAAGAACTAAAAGAATGGACTTTCAGAAAACAAAACCCAGAAA
308710 GATGAAGAAC
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 103 1.00
ACGTcount: A:0.48, C:0.20, G:0.13, T:0.20
Consensus pattern (133 bp):
AAAATGAATTCTACCCAGAGATCTAATTCACATAAAAATAAACAAATTCACACCCCCAATGAGGC
TAAGAACTAAAAGAATGGACTTTCAGAAAACAAAACCCAGAAATCATAAGGTAAAACAAGTTTCA
GGG
Found at i:308921 original size:4 final size:4
Alignment explanation
Indices: 308914--308944 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
308904 AAAGAAACCC
*
308914 CTCA CTCA CTCA CTCA CTCA CTCG CTCA CTC
1 CTCA CTCA CTCA CTCA CTCA CTCA CTCA CTC
308945 TCTCTACTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.19, C:0.52, G:0.03, T:0.26
Consensus pattern (4 bp):
CTCA
Found at i:311500 original size:41 final size:41
Alignment explanation
Indices: 311433--311816 Score: 470
Period size: 41 Copynumber: 9.4 Consensus size: 41
311423 TTTAAAAAAC
* *
311433 AAACGCCACTAAAGTACAAGTC--TAGCGGCGTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
311472 AAACGCCACTAATGTTCGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
311513 AAACACCACTAATGTACGAGTCTATAGCGGTGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
311554 AAACGCCACTAAAGTACAAGTCTATAGCGGCGTTTGTAAACA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-A
* *
311596 CAAACGCCACAAAATTA-GAGTCTATAGCGGCGTTTGTATAA
1 -AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* * *
311637 AAACGCCACTAAAGTACTACTCTATCGCGGCGTTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATAA
* *
311679 AAACACCGCTAAAGT-CGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
** * * * * *
311719 AAACGCTGCTAAAGTACTACTCTATTGTGGCGTTTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTGTATAA
*
311761 AAACGCCACTAAAGTACGAGTCTATAACGGCGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
* *
311802 AAATGCCGCTAAAGT
1 AAACGCCACTAAAGT
311817 TACCATTTTG
Statistics
Matches: 294, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
39 19 0.06
40 36 0.12
41 148 0.50
42 77 0.26
43 14 0.05
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAA
Found at i:311700 original size:165 final size:165
Alignment explanation
Indices: 311416--311816 Score: 524
Period size: 165 Copynumber: 2.4 Consensus size: 165
311406 TTTTAAACTT
* *
311416 GCGGCGTTTTAAAAAACAAACGCCACTAAAGTACAAGTC--TAGCGGCGTTTTTATAAAAACGCC
1 GCGGCGTTTT-AAAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * * * *
311479 ACTAATGTTCGAGTCTATAGCGGCGTTTGTATAAAAACACCACTAATGTACGAGTCTATAGCGGT
65 ACTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGC
*
311544 GTTTGTATAAAAACGCCACTAAAGTACAAGTCTATA
130 GTTTGTATAAAAACGCCACTAAAGTACAACTCTATA
* * *
311580 GCGGCGTTTGTAAACACAAACGCCACAAAATTA-GAGTCTATAGCGGCGTTTGTATAAAAACGCC
1 GCGGCGTTT-TAAAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
* * *
311644 ACTAAAGTACTACTCTATCGCGGCGTTTTGTATAAAAACACCGCTAAAGT-CGAGTCTATAGCGG
65 ACTAAAGTACGACTCTATAGCGGCG-TTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGG
** * *
311708 CGTTTGTATAAAAACGCTGCTAAAGTACTACTCTATT
129 CGTTTGTATAAAAACGCCACTAAAGTACAACTCTATA
* * * *
311745 GTGGCGTTTTATATAA-AAACGCCACTAAAGTACGAGTCTATAACGGCGTTTGTATAAAAATGCC
1 GCGGCGTTTTA-AAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
*
311809 GCTAAAGT
65 ACTAAAGT
311817 TACCATTTTG
Statistics
Matches: 205, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
163 4 0.02
164 44 0.21
165 135 0.66
166 22 0.11
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (165 bp):
GCGGCGTTTTAAAAACAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
CTAAAGTACGACTCTATAGCGGCGTTTGTATAAAAACACCACTAAAGTACGAGTCTATAGCGGCG
TTTGTATAAAAACGCCACTAAAGTACAACTCTATA
Found at i:323988 original size:17 final size:17
Alignment explanation
Indices: 323962--323994 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
323952 CTTTGAAAAT
323962 TTTAAATTTTTATATAA
1 TTTAAATTTTTATATAA
*
323979 TTTAATTTTTTATATA
1 TTTAAATTTTTATATA
323995 TATATTTTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTAAATTTTTATATAA
Found at i:327048 original size:21 final size:21
Alignment explanation
Indices: 327019--327067 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
327009 TAGTGATTAT
* *
327019 TTTTGATAAATTTAAATAA-TA
1 TTTTAATAAATTT-AATAACCA
327040 TTTTAATAAATTTAATAACCA
1 TTTTAATAAATTTAATAACCA
327061 TTTTAAT
1 TTTTAAT
327068 TGAAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTAATAAATTTAATAACCA
Found at i:327642 original size:21 final size:21
Alignment explanation
Indices: 327613--327661 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
327603 TAGTGATTAT
* *
327613 TTTTGATAAATTTAAATAA-TA
1 TTTTAATAAATTT-AATAACCA
327634 TTTTAATAAATTTAATAACCA
1 TTTTAATAAATTTAATAACCA
327655 TTTTAAT
1 TTTTAAT
327662 TGAAAAGTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (21 bp):
TTTTAATAAATTTAATAACCA
Found at i:327925 original size:298 final size:298
Alignment explanation
Indices: 326742--328272 Score: 2673
Period size: 298 Copynumber: 5.2 Consensus size: 298
326732 AAATAGTGAT
* * * *
326742 TATTTTTATAAATTTAATGACCATTTTATTTGAAGAGTATAACACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
326807 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
*
326872 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGA-T-T-ATAATTTATTTTAATATACC
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATACC
326934 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
196 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
*
326999 AATCACAAAATAGTGATTATTTTTGATAAATTTAAATAA
261 AATCATAAAATAGTGATTATTTTTGATAAATTTAAA-AA
*
327038 TATTTTAATAAATTTAATAACCATTTTAATTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
* * *
327103 TAATTTAGATTAAGATAAGATCAATAAAATGCATAATTATTATATTAATTTAAAGATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
* *
327168 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATGATGATAATTTATATTAATATACC
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATACC
*
327233 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGATGTAAATGATTCATTAAACTATCAT
196 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
* *
327298 AATCATAAAATAGTGTTTATTTTTTATAAATTTAAAAA
261 AATCATAAAATAGTGATTATTTTTGATAAATTTAAAAA
*
327336 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAAGTATAATACCAAGTTCAAATTTATTAAT
1 TATTTTAATAAATTTAATAACCATTTTATTTG-AAAAGTATAATACCAAGTTCAAATTTATTAAT
*
327401 TTA-TTTAAATTAAGATAAGATCAATAAAATTCATAATTATTATATTGATTTAAAGATATAATTG
65 TTATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTG
*
327465 GATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGA-T-T-ATAATTTATTTTAATATAC
130 GATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATAC
327527 CTATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCA
195 CTATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCA
*
327592 TAATCACAAAATAGTGATTATTTTTGATAAATTTAAATAA
260 TAATCATAAAATAGTGATTATTTTTGATAAATTTAAA-AA
*
327632 TATTTTAATAAATTTAATAACCATTTTAATTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
* *
327697 TATTTTAAATTAAAATAAGATCAAT-AAATTCATAATTATTATATTGATTTAAAGATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
* * *
327761 ATACGTAAAGATTTAGCAAAATCGTGTAAATTAGGTATGATTATGATAATTTATATTAATATACC
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATACC
*
327826 TATCATCAACATTTAACTTGCCATATAATTTTCACCAAGTTGTAAATGATTCATTAAACTATCAT
196 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
327891 AATCATAAAATAGTGATTATTTTTGATAAATTTAAAAA
261 AATCATAAAATAGTGATTATTTTTGATAAATTTAAAAA
*
327929 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATGATACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
*
327994 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAAATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
* *
328059 ATACGTAAAGATTTAGCAAAATCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATATC
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATACC
* * *
328124 TATCATCAACGTTTAACTTGCCATATAATTTTCACCAAGTCGTAAATGATTCATTAAACTATCAT
196 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
328189 AATCATAAAATAGTGATTATTTTTGATAAATTTAAAAA
261 AATCATAAAATAGTGATTATTTTTGATAAATTTAAAAA
*
328227 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACC
1 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATAATACC
328273 GATTTATAAC
Statistics
Matches: 1177, Mismatches: 48, Indels: 18
0.95 0.04 0.01
Matches are distributed among these distances:
295 227 0.19
296 216 0.18
297 90 0.08
298 493 0.42
299 151 0.13
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (298 bp):
TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
ATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATACC
TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
AATCATAAAATAGTGATTATTTTTGATAAATTTAAAAA
Found at i:327954 original size:21 final size:20
Alignment explanation
Indices: 327911--327956 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
327901 TAGTGATTAT
* *
327911 TTTTGATAAATTTAAAAATA
1 TTTTAATAAATTTAAAAACA
*
327931 TTTTAATAAATTTAATAACCA
1 TTTTAATAAATTTAA-AAACA
327952 TTTTA
1 TTTTA
327957 TTTGAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (20 bp):
TTTTAATAAATTTAAAAACA
Found at i:328055 original size:593 final size:594
Alignment explanation
Indices: 326742--328272 Score: 2753
Period size: 594 Copynumber: 2.6 Consensus size: 594
326732 AAATAGTGAT
* * *
326742 TATTTTTATAAATTTAATGACCATTTTATTTGAAGAGTATAACACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
326807 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
326872 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTAT
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTAT
326937 CATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAAT
196 CATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAAT
327002 CACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTAA
261 CACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTAA
* *
327067 TTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTAATTTAGATTAAGATAAGATCAATAAAA
326 TTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTAATTTAAATTAAAATAAGATCAATAAAA
327132 TGCATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAA
391 TGCATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAA
327197 ATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
456 ATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
* * *
327262 TTTCACTAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGTTTATTTTTTATAA
521 TTTCACCAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATAA
327327 ATTTAAAAA
586 ATTTAAAAA
327336 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAAGTATAATACCAAGTTCAAATTTATTAAT
1 TATTTTAATAAATTTAATGACCATTTTATTTG-AAAAGTATAATACCAAGTTCAAATTTATTAAT
*
327401 TTA-TTTAAATTAAGATAAGATCAATAAAATTCATAATTATTATATTGATTTAAAGATATAATTG
65 TTATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTG
327465 GATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTA
130 GATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTA
327530 TCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAA
195 TCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAA
327595 TCACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTA
260 TCACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTA
*
327660 ATTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTATTTTAAATTAAAATAAGATCAAT-AA
325 ATTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTAATTTAAATTAAAATAAGATCAATAAA
* * * *
327724 ATTCATAATTATTATATTGATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAATCGTGTA
390 ATGCATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTA
*
327789 AATTAGGTATGATTATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAA
455 AATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAA
*
327854 TTTTCACCAAGTTGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATA
520 TTTTCACCAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATA
327919 AATTTAAAAA
585 AATTTAAAAA
* *
327929 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATGATACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
*
327994 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAAATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
* * *
328059 ATACGTAAAGATTTAGCAAAATCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATATC
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGA-T-T-ATAATTTATTTTAATATACC
* * *
328124 TATCATCAACGTTTAACTTGCCATATAATTTTCACCAAGTCGTAAATGATTCATTAAACTATCAT
193 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
* *
328189 AATCATAAAATAGTGATTATTTTTGATAAATTTAAA-AATATTTTAATAAATTTAATGACCATTT
258 AATCACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTT
*
328253 TATTTGAAAAGTATAATACC
323 TAATTGAAAAGTATAATACC
328273 GATTTATAAC
Statistics
Matches: 903, Mismatches: 29, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
592 34 0.04
593 327 0.36
594 346 0.38
595 80 0.09
596 116 0.13
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (594 bp):
TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTAT
CATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAAT
CACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTAA
TTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTAATTTAAATTAAAATAAGATCAATAAAA
TGCATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAA
ATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
TTTCACCAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATAA
ATTTAAAAA
Found at i:328326 original size:593 final size:586
Alignment explanation
Indices: 326742--328272 Score: 2634
Period size: 593 Copynumber: 2.6 Consensus size: 586
326732 AAATAGTGAT
* * *
326742 TATTTTTATAAATTTAATGACCATTTTATTTGAAGAGTATAACACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
326807 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
326872 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTAT
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTAT
326937 CATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAAT
196 CATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAAT
327002 CACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTAA
261 CACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTAA
*
327067 TTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTAATTTAGATTAAGATAAGATCAATAAAA
326 TTGAAAAGTATAATACCAAGTTCAAATTAATTAATTTAA--T-GA--AA-ATAAGATCAAT-AAA
327132 TGCATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAA
384 T-CATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAA
327197 ATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
448 ATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
* * *
327262 TTTCACTAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGTTTATTTTTTATAA
513 TTTCACCAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATAA
327327 ATTTAAAAA
578 ATTTAAAAA
327336 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAAGTATAATACCAAGTTCAAATTTATTAAT
1 TATTTTAATAAATTTAATGACCATTTTATTTG-AAAAGTATAATACCAAGTTCAAATTTATTAAT
*
327401 TTA-TTTAAATTAAGATAAGATCAATAAAATTCATAATTATTATATTGATTTAAAGATATAATTG
65 TTATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTG
327465 GATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTA
130 GATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTA
327530 TCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAA
195 TCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAA
327595 TCACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTA
260 TCACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTA
* *
327660 ATTGAAAAGTATAATACCAAGTTCAAATTTATTAATTTATTTTAAATTAAAATAAGATCAATAAA
325 ATTGAAAAGTATAATACCAAGTTC-AA---ATTAA-TTAATTT-AATGAAAATAAGATCAATAAA
* * *
327725 TTCATAATTATTATATTGATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAATCGTGTAA
384 -TCATAATTATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAA
*
327790 ATTAGGTATGATTATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
448 ATTAGGTATGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAAT
*
327855 TTTCACCAAGTTGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATAA
513 TTTCACCAAGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATAA
327920 ATTTAAAAA
578 ATTTAAAAA
* *
327929 TATTTTAATAAATTTAATAACCATTTTATTTGAAAAGTATGATACCAAGTTCAAATTTATTAATT
1 TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
*
327994 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAAATATAATTGG
66 TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
* * *
328059 ATACGTAAAGATTTAGCAAAATCATGTAAATTAGGTATGATTATGATAATTTATTTTAATATATC
131 ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGA-T-T-ATAATTTATTTTAATATACC
* * *
328124 TATCATCAACGTTTAACTTGCCATATAATTTTCACCAAGTCGTAAATGATTCATTAAACTATCAT
193 TATCATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCAT
* *
328189 AATCATAAAATAGTGATTATTTTTGATAAATTTAAA-AATATTTTAATAAATTTAATGACCATTT
258 AATCACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTT
*
328253 TATTTGAAAAGTATAATACC
323 TAATTGAAAAGTATAATACC
328273 GATTTATAAC
Statistics
Matches: 897, Mismatches: 28, Indels: 23
0.95 0.03 0.02
Matches are distributed among these distances:
592 34 0.04
593 326 0.36
594 323 0.36
595 84 0.09
596 116 0.13
597 1 0.00
598 5 0.01
599 6 0.01
600 2 0.00
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (586 bp):
TATTTTAATAAATTTAATGACCATTTTATTTGAAAAGTATAATACCAAGTTCAAATTTATTAATT
TATTTTAAATTAAGATAAGATCAATAAAATGCATAATTATTATATTGATTTAAAGATATAATTGG
ATACGTAAAGATTTAGCAAAACCATGTAAATTAGATATGATTATAATTTATTTTAATATACCTAT
CATCAACATTTAACTTGCCATATAATTTTCACTAAGTTGTAAATGATTCATTAAACTATCATAAT
CACAAAATAGTGATTATTTTTGATAAATTTAAATAATATTTTAATAAATTTAATAACCATTTTAA
TTGAAAAGTATAATACCAAGTTCAAATTAATTAATTTAATGAAAATAAGATCAATAAATCATAAT
TATTATATTAATTTAAAGATATAATTGGATACGTAAAGATTTAGCAAAACCATGTAAATTAGGTA
TGATGATGATAATTTATATTAATATACCTATCATCAACATTTAACTTGCCATATAATTTTCACCA
AGATGTAAATGATTCATTAAACTATCATAATCATAAAATAGTGATTATTTTTGATAAATTTAAAA
A
Found at i:345897 original size:59 final size:57
Alignment explanation
Indices: 345799--345952 Score: 168
Period size: 59 Copynumber: 2.6 Consensus size: 57
345789 GAATGTTTAA
** * *
345799 AAAGTTTGGGGACCAATTTAGAATGAAAGTTATAGTTGGGCA-GAAATTAAAATATT-C
1 AAAGTTTAAGGACCAATTTAAAAT-AAGGTTATAGTTGGG-ATGAAATTAAAATATTCC
* **
345856 AATAGTTTAAGGACTAATTTAAAATAAGGTTCATAGCTTGGGATGAAATTGGAATATTCC
1 AA-AGTTTAAGGACCAATTTAAAATAAGGTT-ATAG-TTGGGATGAAATTAAAATATTCC
*
345916 AAAGTTTAAGAACCAATTTAAAATAAGAGTTATAGTT
1 AAAGTTTAAGGACCAATTTAAAATAAG-GTTATAGTT
345953 TAGGGACAAC
Statistics
Matches: 82, Mismatches: 9, Indels: 11
0.80 0.09 0.11
Matches are distributed among these distances:
57 7 0.09
58 25 0.30
59 44 0.54
60 6 0.07
ACGTcount: A:0.42, C:0.07, G:0.19, T:0.32
Consensus pattern (57 bp):
AAAGTTTAAGGACCAATTTAAAATAAGGTTATAGTTGGGATGAAATTAAAATATTCC
Found at i:352087 original size:2 final size:2
Alignment explanation
Indices: 352080--352110 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
352070 TTACTTCAGA
352080 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 A
352111 ATTGAAAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:354204 original size:19 final size:20
Alignment explanation
Indices: 354180--354230 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
354170 AATGACCAAT
354180 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
354199 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
354219 AAAATCGCAACG
1 AAAATCGCAACG
354231 GTCAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:354224 original size:20 final size:20
Alignment explanation
Indices: 354180--354334 Score: 109
Period size: 20 Copynumber: 7.6 Consensus size: 20
354170 AATGACCAAT
* *
354180 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
354199 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
**
354219 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
354239 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
354260 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
354283 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
*
354303 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
*
354323 AGAATCGCAACG
1 AAAATCGCAACG
354335 AAAAAGATAG
Statistics
Matches: 104, Mismatches: 23, Indels: 17
0.72 0.16 0.12
Matches are distributed among these distances:
18 1 0.01
19 18 0.17
20 57 0.55
21 14 0.13
23 14 0.13
ACGTcount: A:0.39, C:0.22, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:354344 original size:40 final size:42
Alignment explanation
Indices: 354264--354344 Score: 94
Period size: 43 Copynumber: 2.0 Consensus size: 42
354254 GCTTCCAAGT
* ** **
354264 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAGAAG-AAATCGCAACGAAAAAGATAGAA
354307 TCGCAACGCGATTTAG-AG-AATCGCAACGAAAAAGATAG
1 TCGCAACGCGATTTAGAAGAAATCGCAACGAAAAAGATAG
354345 TTAAAAGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
40 15 0.45
42 2 0.06
43 16 0.48
ACGTcount: A:0.41, C:0.17, G:0.23, T:0.19
Consensus pattern (42 bp):
TCGCAACGCGATTTAGAAGAAATCGCAACGAAAAAGATAGAA
Found at i:354430 original size:6 final size:6
Alignment explanation
Indices: 354419--354475 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
354409 GACACGTATT
354419 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
354467 ACCACG ACC
1 ACCACG ACC
354476 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:355182 original size:6 final size:6
Alignment explanation
Indices: 355166--355257 Score: 177
Period size: 6 Copynumber: 15.5 Consensus size: 6
355156 TCTCGTCTCG
355166 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
355213 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
355258 AATACGTGTC
Statistics
Matches: 86, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.06
6 81 0.94
ACGTcount: A:0.00, C:0.16, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:355367 original size:20 final size:20
Alignment explanation
Indices: 355342--355393 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
355332 CTATCTTTTT
*
355342 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAA
*
355362 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTTTTGAA
355382 CGTTGCGATTTT
1 CGTTGCGATTTT
355394 GATATCGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.52
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAA
Found at i:372186 original size:15 final size:15
Alignment explanation
Indices: 372166--372194 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
372156 TACACAACAG
372166 TATATTATATATATA
1 TATATTATATATATA
372181 TATATTATATATAT
1 TATATTATATATAT
372195 CATACCTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:380404 original size:14 final size:14
Alignment explanation
Indices: 380379--380427 Score: 64
Period size: 14 Copynumber: 3.4 Consensus size: 14
380369 CCCTTTTGAT
380379 TAATATTATTTTTA
1 TAATATTATTTTTA
*
380393 TAAT-TTACTTTTGA
1 TAATATTA-TTTTTA
380407 TTAATATTATTTTTA
1 -TAATATTATTTTTA
380422 TAATAT
1 TAATAT
380428 ACATTATTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
13 3 0.10
14 15 0.50
15 9 0.30
16 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (14 bp):
TAATATTATTTTTA
Found at i:380419 original size:15 final size:15
Alignment explanation
Indices: 380372--380419 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
380362 ATTTCGTCCC
380372 TTTTGATTAATATTA
1 TTTTGATTAATATTA
*
380387 TTTTTA-TAAT-TTA
1 TTTTGATTAATATTA
380400 CTTTTGATTAATATTA
1 -TTTTGATTAATATTA
380416 TTTT
1 TTTT
380420 TATAATATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 13 0.46
16 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTTGATTAATATTA
Found at i:385521 original size:24 final size:26
Alignment explanation
Indices: 385484--385531 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
385474 CATATTGTGC
385484 ATTTTGTTATTTTTCTTTACATTCGT
1 ATTTTGTTATTTTTCTTTACATTCGT
*
385510 ATTTT-TT-TTTTTTTTTACATTC
1 ATTTTGTTATTTTTCTTTACATTC
385532 ACATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 14 0.67
25 2 0.10
26 5 0.24
ACGTcount: A:0.15, C:0.10, G:0.04, T:0.71
Consensus pattern (26 bp):
ATTTTGTTATTTTTCTTTACATTCGT
Found at i:388009 original size:106 final size:106
Alignment explanation
Indices: 387846--388771 Score: 1271
Period size: 106 Copynumber: 9.0 Consensus size: 106
387836 TCTAATTTCA
* * * * *
387846 TTCAGAGTCTATTTCAACTTCGCAACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
387911 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
*
387952 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
** *
388017 CGACGAAGGGACCGCTGACTGTC----AAC---TTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
*
388051 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
388116 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* * * * *
388157 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* * *
388222 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* *
388263 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAATTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
388328 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* * * * * *
388369 TTCAAAGTCAATTTTAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
388434 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* * * *
388475 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
388540 CGACGAAGGGACCGCTGGTTGTCAAT--A-AA-----CAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* ***
388573 TTC----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTACAAGTTCAACTT--
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
** *
388632 C-ACGAAGGGACCGCTGACTGTC----AAC---TTCTCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
* * *
388665 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAAATCCAGACAACTCAAGTTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
* *
388730 CGACAAAAGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
66 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
388771 T
1 T
388772 CCAACTTCAC
Statistics
Matches: 734, Mismatches: 59, Indels: 54
0.87 0.07 0.06
Matches are distributed among these distances:
89 1 0.00
91 19 0.03
92 8 0.01
94 49 0.07
96 50 0.07
98 8 0.01
99 110 0.15
102 3 0.00
103 8 0.01
104 1 0.00
106 477 0.65
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (106 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
Found at i:388520 original size:318 final size:308
Alignment explanation
Indices: 387846--388771 Score: 1399
Period size: 318 Copynumber: 3.0 Consensus size: 308
387836 TCTAATTTCA
* * * * * * *
387846 TTCAGAGTCTATTTCAACTTCGCAACGAAGAAAATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
387911 CGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAA-AAACAA-TT-CCAATTTCAGAGCCAATTTCAACTTCACA
387976 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGACTGTCA
128 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGACTGTCA
388041 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
193 ACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
388106 TTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
258 TTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
*
388157 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCA
1 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
388222 CGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACA
66 CGACGAAGGGACCGCTGGTTGTCAA-AAACAA-TTC-CAATTTCAGAGCCAATTTCAACTTCACA
* **
388287 ACGAAGGATATTGGACTCCAGACAACGCAAATTCAACTTTACGACGAAGGGACCGCTGGTTGTCA
128 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGACTGTC-
* * * * * *
388352 ATAAACAATTTCCCAATTTCAAAGTCAATTTTAATTTCACAGCGAAGGATATTGGACTCCAGACA
192 ---AAC---TTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA
388417 ACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
251 ACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
388475 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
1 TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
*
388540 CGACGAAGGGACCGCTGGTTGTC-AATA-AA---CAATTTC----CCAATTTCAACTTCACAACG
66 CGACGAAGGGACCGCTGGTTGTCAAAAACAATTCCAATTTCAGAGCCAATTTCAACTTCACAACG
* ***
388596 AAGGATATTGGACTCAAGACAGTACAAGTTCAAC-TT-C-ACGAAGGGACCGCTGACTGTCAACT
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGACTGTCAACT
* * *
388658 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAAATCCAGACAACTCAAGTTC
196 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * *
388723 AACTTCACGACAAAAGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
261 AACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
388771 T
1 T
388772 CCAACTTCAC
Statistics
Matches: 567, Mismatches: 40, Indels: 31
0.89 0.06 0.05
Matches are distributed among these distances:
296 103 0.18
299 3 0.01
303 19 0.03
304 1 0.00
305 2 0.00
306 49 0.09
310 8 0.01
311 179 0.32
315 5 0.01
316 2 0.00
317 1 0.00
318 195 0.34
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (308 bp):
TTCAAAGTCAATTTCAATTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCA
CGACGAAGGGACCGCTGGTTGTCAAAAACAATTCCAATTTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGACTGTCAACT
TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
AACTTTACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAAT
Found at i:389200 original size:15 final size:15
Alignment explanation
Indices: 389153--389200 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
389143 ATTTCGTCCC
389153 TTTTGATTAATATTA
1 TTTTGATTAATATTA
*
389168 TTTTTA-TAAT-TTA
1 TTTTGATTAATATTA
389181 CTTTTGATTAATATTA
1 -TTTTGATTAATATTA
389197 TTTT
1 TTTT
389201 ATAATATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 9 0.32
15 13 0.46
16 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (15 bp):
TTTTGATTAATATTA
Found at i:389207 original size:13 final size:14
Alignment explanation
Indices: 389160--389207 Score: 55
Period size: 13 Copynumber: 3.4 Consensus size: 14
389150 CCCTTTTGAT
*
389160 TAATATTATTTTTA
1 TAATATTACTTTTA
389174 TAAT-TTACTTTTGA
1 TAATATTACTTTT-A
389188 TTAATATTA-TTTTA
1 -TAATATTACTTTTA
389202 TAATAT
1 TAATAT
389208 ACATTATTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 13 0.43
14 6 0.20
15 8 0.27
16 3 0.10
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (14 bp):
TAATATTACTTTTA
Found at i:397150 original size:4 final size:4
Alignment explanation
Indices: 397143--397181 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
397133 ACTATGTATG
*
397143 TATT TATT TATT TATT TATT TAGT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
397182 ACATGCATTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (4 bp):
TATT
Found at i:399552 original size:15 final size:16
Alignment explanation
Indices: 399505--399555 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
399495 TTTGACAAAT
399505 TTTTAATTATTAATAAAA
1 TTTTAATT-TTAAT-AAA
*
399523 TTTTAATTTT-TTAAA
1 TTTTAATTTTAATAAA
399538 TTTT-ATTTTAATAAA
1 TTTTAATTTTAATAAA
399553 TTT
1 TTT
399556 AATGAGATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 5 0.17
15 14 0.47
16 1 0.03
17 2 0.07
18 8 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTTAATTTTAATAAA
Found at i:400934 original size:11 final size:11
Alignment explanation
Indices: 400918--400951 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
400908 AGATTTAAAA
400918 TTTTAATATTT
1 TTTTAATATTT
400929 TTTTAATATTT
1 TTTTAATATTT
400940 TTTTAATATTT
1 TTTTAATATTT
400951 T
1 T
400952 CTTATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTAATATTT
Found at i:403341 original size:18 final size:18
Alignment explanation
Indices: 403318--403355 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
403308 ACCAATCTAA
*
403318 ACTCATCACCTCTAGCTG
1 ACTCATCACCTCTAACTG
403336 ACTCATCACCTCTAACTG
1 ACTCATCACCTCTAACTG
403354 AC
1 AC
403356 GAGTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.39, G:0.08, T:0.26
Consensus pattern (18 bp):
ACTCATCACCTCTAACTG
Found at i:406087 original size:2 final size:2
Alignment explanation
Indices: 406080--406113 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
406070 TTAACTCCTA
406080 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
406114 TAATCTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:408344 original size:18 final size:19
Alignment explanation
Indices: 408321--408356 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
408311 TATTATTTAT
408321 TTTATATA-ATTTTAATGA
1 TTTATATACATTTTAATGA
408339 TTTATATACATTTTAATG
1 TTTATATACATTTTAATG
408357 TAATTATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (19 bp):
TTTATATACATTTTAATGA
Found at i:408363 original size:20 final size:18
Alignment explanation
Indices: 408322--408363 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
408312 ATTATTTATT
*
408322 TTATATAATTTTAATGAT
1 TTATATAATTTTAATGAA
408340 TTATATACATTTTAATGTAA
1 TTATATA-ATTTTAATG-AA
408360 TTAT
1 TTAT
408364 GTATTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 5 0.24
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATAATTTTAATGAA
Found at i:410416 original size:16 final size:16
Alignment explanation
Indices: 410395--410425 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
410385 AAAATGTAAG
*
410395 ATTAGCTATTATTTTC
1 ATTAGCTATGATTTTC
410411 ATTAGCTATGATTTT
1 ATTAGCTATGATTTT
410426 GAAAATAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.10, G:0.10, T:0.55
Consensus pattern (16 bp):
ATTAGCTATGATTTTC
Found at i:410856 original size:29 final size:29
Alignment explanation
Indices: 410814--410869 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
410804 TGTTTGTCGT
** *
410814 AGGTCGCTGGGAGGGCATGGCTACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
410843 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
410870 TGTGTTGGGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:410979 original size:10 final size:11
Alignment explanation
Indices: 410966--411028 Score: 51
Period size: 10 Copynumber: 5.6 Consensus size: 11
410956 ACACGGTGGG
410966 CATCCGAG-GC
1 CATCCGAGAGC
410976 CATCCGAGAAGC
1 CATCCGAG-AGC
* *
410988 TATGCGAGAG-
1 CATCCGAGAGC
410998 CATCCGAG-GC
1 CATCCGAGAGC
411008 CATCCGACCGAGGC
1 CATCCGA--GA-GC
411022 CATCCGA
1 CATCCGA
411029 CCGAGGGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
9 1 0.02
10 21 0.50
11 2 0.05
12 9 0.21
14 9 0.21
ACGTcount: A:0.25, C:0.35, G:0.29, T:0.11
Consensus pattern (11 bp):
CATCCGAGAGC
Found at i:411020 original size:14 final size:14
Alignment explanation
Indices: 411001--411057 Score: 105
Period size: 14 Copynumber: 4.1 Consensus size: 14
410991 GCGAGAGCAT
411001 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
411015 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
411029 CCGAGGGCATCCGA
1 CCGAGGCCATCCGA
411043 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
411057 C
1 C
411058 TGAATTATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 41 1.00
ACGTcount: A:0.21, C:0.42, G:0.30, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:411104 original size:23 final size:23
Alignment explanation
Indices: 411074--411118 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
411064 ATGTGAGGGC
*
411074 ATGCGAGGATAGCCGAGCGAGCT
1 ATGCGAGGACAGCCGAGCGAGCT
* *
411097 ATGCGAGGGCATCCGAGCGAGC
1 ATGCGAGGACAGCCGAGCGAGC
411119 GAGCAAGGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.24, G:0.40, T:0.11
Consensus pattern (23 bp):
ATGCGAGGACAGCCGAGCGAGCT
Found at i:411174 original size:29 final size:29
Alignment explanation
Indices: 411129--411213 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
411119 GAGCAAGGGT
411129 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* *
411158 AGGTCGCCAGGATTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
411187 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGTGCATGGCGACCTA
411214 TGCTTGGGGA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.21, C:0.29, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:415772 original size:23 final size:23
Alignment explanation
Indices: 415715--415773 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
415705 GTTAGTGAAT
*
415715 ATGTTCGTTTAACGTTCATAAAC
1 ATGTTCGTTTAACGTTCACAAAC
* * * *
415738 ATATTTGCTTAATGTTCACAAAC
1 ATGTTCGTTTAACGTTCACAAAC
415761 ATGTTCGTTTAAC
1 ATGTTCGTTTAAC
415774 AATGGTTTAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.41
Consensus pattern (23 bp):
ATGTTCGTTTAACGTTCACAAAC
Found at i:417832 original size:25 final size:25
Alignment explanation
Indices: 417802--417851 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
417792 TTATTAGTAC
417802 TTGTAAGTTGATAGATTTAGTAAAT
1 TTGTAAGTTGATAGATTTAGTAAAT
417827 TTGTAAGTTGATAGATTTAGTAAAT
1 TTGTAAGTTGATAGATTTAGTAAAT
417852 ATGATAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.20, T:0.44
Consensus pattern (25 bp):
TTGTAAGTTGATAGATTTAGTAAAT
Found at i:417862 original size:18 final size:17
Alignment explanation
Indices: 417822--417884 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 17
417812 ATAGATTTAG
*
417822 TAAATTT-GTAAGTTGA
1 TAAATTTAGTAAATTGA
*
417838 TAGATTTAGTAAATATGA
1 TAAATTTAGTAAAT-TGA
417856 TAAATTTACAGTAAATT--
1 TAAATTT--AGTAAATTGA
*
417873 TAACTTTAGTAA
1 TAAATTTAGTAA
417885 GTCACATGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
15 5 0.13
16 6 0.15
17 11 0.28
18 9 0.23
19 1 0.03
20 7 0.18
ACGTcount: A:0.43, C:0.03, G:0.13, T:0.41
Consensus pattern (17 bp):
TAAATTTAGTAAATTGA
Found at i:419451 original size:26 final size:26
Alignment explanation
Indices: 419415--419475 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
419405 TGTGGTACCT
*
419415 TTTTTTAGTGTAATCAAGTATATAAC
1 TTTTTTGGTGTAATCAAGTATATAAC
* * *
419441 TTTTTTGGTGTAATTAGGTATTTAAC
1 TTTTTTGGTGTAATCAAGTATATAAC
*
419467 TTTGTTGGT
1 TTTTTTGGT
419476 ACAATTAGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.25, C:0.05, G:0.18, T:0.52
Consensus pattern (26 bp):
TTTTTTGGTGTAATCAAGTATATAAC
Found at i:419481 original size:26 final size:26
Alignment explanation
Indices: 419432--419483 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
419422 GTGTAATCAA
* **
419432 GTATATAACTTTTTTGGTGTAATTAG
1 GTATATAACTTTGTTGGTACAATTAG
*
419458 GTATTTAACTTTGTTGGTACAATTAG
1 GTATATAACTTTGTTGGTACAATTAG
419484 ATATCTATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.48
Consensus pattern (26 bp):
GTATATAACTTTGTTGGTACAATTAG
Found at i:420820 original size:17 final size:17
Alignment explanation
Indices: 420798--420843 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
420788 TTTGAGTCAA
420798 AGTCAACAGTCAATGCT
1 AGTCAACAGTCAATGCT
420815 AGTCAAC-GATCAATGCT
1 AGTCAACAG-TCAATGCT
420832 AGTCAA-AGTCAA
1 AGTCAACAGTCAA
420844 CGCTTTGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 22 0.81
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (17 bp):
AGTCAACAGTCAATGCT
Found at i:427177 original size:32 final size:32
Alignment explanation
Indices: 427141--427202 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
427131 TTAAACATGT
*
427141 ATAAAATTTAGATATATATAAATATATATTTA
1 ATAAAAATTAGATATATATAAATATATATTTA
* * *
427173 ATAAAAATTATATGTATATATATATATATT
1 ATAAAAATTAGATATATATAAATATATATT
427203 GAAAATTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (32 bp):
ATAAAAATTAGATATATATAAATATATATTTA
Found at i:427207 original size:28 final size:28
Alignment explanation
Indices: 427153--427210 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
427143 AAAATTTAGA
*
427153 TATATATAAATATATATTTAATAAAAAT
1 TATATATAAATATATATATAATAAAAAT
* * * *
427181 TATATGTATATATATATATATTGAAAAT
1 TATATATAAATATATATATAATAAAAAT
427209 TA
1 TA
427211 AAATTATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TATATATAAATATATATATAATAAAAAT
Found at i:427214 original size:34 final size:32
Alignment explanation
Indices: 427141--427217 Score: 82
Period size: 32 Copynumber: 2.3 Consensus size: 32
427131 TTAAACATGT
* * * *
427141 ATAAAATTTAGATATATATAAATATATATTTA
1 ATAAAAATTATATGTATATAAATATATATTAA
*
427173 ATAAAAATTATATGTATATATATATATATTGAAA
1 ATAAAAATTATATGTATATAAATATATATT--AA
*
427207 ATTAAAATTAT
1 ATAAAAATTAT
427218 TAATTTAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
32 26 0.70
34 11 0.30
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (32 bp):
ATAAAAATTATATGTATATAAATATATATTAA
Found at i:431232 original size:14 final size:14
Alignment explanation
Indices: 431213--431249 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
431203 TTTTTCAATT
* *
431213 TCGAGTTATTCGAG
1 TCGAGTTATTCAAC
431227 TCGAGTTATTCAAC
1 TCGAGTTATTCAAC
431241 TCGAGTTAT
1 TCGAGTTAT
431250 AAATTCGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (14 bp):
TCGAGTTATTCAAC
Found at i:431647 original size:159 final size:160
Alignment explanation
Indices: 431399--431717 Score: 419
Period size: 159 Copynumber: 2.0 Consensus size: 160
431389 TAAGTCTATA
* * * *
431399 TTTTACCAAATTTGAACCACATGCTCTTAAAACATAGTAGAATACATGTGTACTTTTAATTCCTC
1 TTTTACCAAATTTGAACCAAATGCTCCTAAAACATAGTAGAATACATGTGTAATTTCAATTCCTC
* * *
431464 ATTTTGATAAAAAGAAATTATTTTTCAATTTAGTCCTTCAAATTTTCATAATCTCATTATTTCTT
66 ATTTTGATAAAAAGAAATTATTTTTCAATTTAATCCTTCAAATTTTCATAAGCTCATTATTCCTT
*
431529 CAATTCGTCATTT-TTTTAAGTCCTTTTTT
131 CAATTCGTCATTTATTTTAAGTCATTTTTT
* * * *
431558 TTTTGCCAAATTTGAGCCAAATGCTCCTAAACCATAGTAGAATACATGTGTAATTTCAATT-CTT
1 TTTTACCAAATTTGAACCAAATGCTCCTAAAACATAGTAGAATACATGTGTAATTTCAATTCCTC
* * * * * *
431622 TTTTTGATAACAAA-TATTATATTTTTCAATTTAATCCTTCAATTTTTCATAAGCTCCTTGTTCC
66 ATTTTGATAA-AAAGAAAT-TATTTTTCAATTTAATCCTTCAAATTTTCATAAGCTCATTATTCC
* *
431686 TTCAATTTGTGATTTATTTTAAGTCATTTTTT
129 TTCAATTCGTCATTTATTTTAAGTCATTTTTT
431718 ACCAAATTTG
Statistics
Matches: 137, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
158 13 0.09
159 109 0.80
160 15 0.11
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (160 bp):
TTTTACCAAATTTGAACCAAATGCTCCTAAAACATAGTAGAATACATGTGTAATTTCAATTCCTC
ATTTTGATAAAAAGAAATTATTTTTCAATTTAATCCTTCAAATTTTCATAAGCTCATTATTCCTT
CAATTCGTCATTTATTTTAAGTCATTTTTT
Found at i:431804 original size:159 final size:157
Alignment explanation
Indices: 431360--431813 Score: 364
Period size: 159 Copynumber: 2.9 Consensus size: 157
431350 GTTCCTGATT
* * * ** * *
431360 TCATTATTTCTTCAATTCCTCCTTCACTTTAAGT-CTATATTTTACCAAATTTGAACCACATGCT
1 TCATTATTCCTTCAATTCGTCATT-TTTTTAAGTCCTATTTTTTACCAAATTTGAACCAAATGCT
** * * ** * * * ** *
431424 CTTAAAACATAGTAGAATACATGTGTACTTTTAATTCCTCATTTTGATAA-AAAGA-AATTATTT
65 AATAAACCACAACAGAATACATATGTAATTTCAATT-CTTTTTTTGATAACAAAGATTA-TATTT
* *
431487 TTCAATTTAGTCCTTCAAATTTTCATAATC
128 TTCAATTTAATCCTTCAAATTTTCATAAGC
* * * *
431517 TCATTATTTCTTCAATTCGTCATTTTTTTAAGTCCTTTTTTTTTTGCCAAATTTGAGCCAAATGC
1 TCATTATTCCTTCAATTCGTCATTTTTTTAAGTCC--TATTTTTTACCAAATTTGAACCAAATGC
** * ** * *
431582 TCCTAAACCATAGTAGAATACATGTGTAATTTCAATTCTTTTTTTGATAACAAATATTATATTTT
64 TAATAAACCACAACAGAATACATATGTAATTTCAATTCTTTTTTTGATAACAAAGATTATATTTT
*
431647 TCAATTTAATCCTTCAATTTTTCATAAGC
129 TCAATTTAATCCTTCAAATTTTCATAAGC
* * * * * *
431676 TCCTTGTTCCTTCAATTTGTGATTTATTTTAAGT-C-ATTTTTTACCAAATTTGAATCACATGCT
1 TCATTATTCCTTCAATTCGTCATTT-TTTTAAGTCCTATTTTTTACCAAATTTGAACCAAATGCT
* * * *
431739 AATATACCACAACAGAATACCTATGTAACTTT-AATTGTTATTTTT-TTAACTAAAGATATACTA
65 AATAAACCACAACAGAATACATATGTAA-TTTCAATTCTT-TTTTTGATAAC-AAAGAT-TA-TA
*
431802 TTTTTTAATTTA
125 TTTTTCAATTTA
431814 GTCCCTAAAC
Statistics
Matches: 244, Mismatches: 42, Indels: 20
0.80 0.14 0.07
Matches are distributed among these distances:
156 60 0.25
157 36 0.15
158 13 0.05
159 126 0.52
160 9 0.04
ACGTcount: A:0.31, C:0.17, G:0.07, T:0.45
Consensus pattern (157 bp):
TCATTATTCCTTCAATTCGTCATTTTTTTAAGTCCTATTTTTTACCAAATTTGAACCAAATGCTA
ATAAACCACAACAGAATACATATGTAATTTCAATTCTTTTTTTGATAACAAAGATTATATTTTTC
AATTTAATCCTTCAAATTTTCATAAGC
Found at i:448682 original size:2 final size:2
Alignment explanation
Indices: 448671--448701 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
448661 TAGATTAAAA
448671 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
448702 GATCTTACGA
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):
AT
Found at i:451879 original size:20 final size:20
Alignment explanation
Indices: 451844--451884 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
451834 GAAAAAAAGG
*
451844 GAAAAAAAGATCAAAACAAA
1 GAAAAAAAAATCAAAACAAA
* *
451864 GAAAAAAAAATGAAAAGAAA
1 GAAAAAAAAATCAAAACAAA
451884 G
1 G
451885 TGGCCAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.76, C:0.05, G:0.15, T:0.05
Consensus pattern (20 bp):
GAAAAAAAAATCAAAACAAA
Found at i:453376 original size:36 final size:36
Alignment explanation
Indices: 453220--453452 Score: 187
Period size: 38 Copynumber: 6.5 Consensus size: 36
453210 GATATGATAT
* *
453220 AAACTATAAAATATATATATATTTCAAAAATATGTTTTAGA
1 AAACTATATAATATATATGT-TTTC--AAA-ATGTTTTA-A
* *
453261 AAACTATAT-AT-TATA---CTTAAAAAT-TTTCT-A
1 AAACTATATAATATATATGTTTTCAAAATGTTT-TAA
* * *
453291 AAACTATATATTACATA-GTTTTCAAAACGTTTT-A
1 AAACTATATAATATATATGTTTTCAAAATGTTTTAA
*
453325 AAACTATATACTATATATGTTTTCAAAATGTTTTAA
1 AAACTATATAATATATATGTTTTCAAAATGTTTTAA
* * *
453361 AAACTATATAATATATAAACGGTTTCAAAATGTTTTCA
1 AAACTATATAATATAT--ATGTTTTCAAAATGTTTTAA
* * * *
453399 AAACTATATATTATATATATTTTAAAAATATTTTCAA
1 AAACTATATAATATATATGTTTTCAAAATGTTTT-AA
453436 AAACTATATAATATATA
1 AAACTATATAATATATA
453453 AATTTTCGAA
Statistics
Matches: 158, Mismatches: 23, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
30 10 0.06
31 4 0.03
32 6 0.04
33 3 0.02
34 23 0.15
35 20 0.13
36 29 0.18
37 17 0.11
38 32 0.20
39 4 0.03
40 2 0.01
41 8 0.05
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (36 bp):
AAACTATATAATATATATGTTTTCAAAATGTTTTAA
Found at i:453484 original size:75 final size:72
Alignment explanation
Indices: 453310--453519 Score: 203
Period size: 74 Copynumber: 2.8 Consensus size: 72
453300 ATTACATAGT
** * * *
453310 TTTCAAAACGTTTT-AAAACTATATACTATATATGTTTTCAAAATGTTTTAAAAACTATATAATA
1 TTTCAAAATATTTTCAAAACTATATA-TATATATATTTTAAAAATATTTTAAAAACTATATAATA
453374 TATAAACGG
65 TATAAAC-G
*
453383 TTTCAAAATGTTTTCAAAACTATATATTATATATATTTTAAAAATATTTTCAAAAACTATATAAT
1 TTTCAAAATATTTTCAAAACTATATA-TATATATATTTTAAAAATATTTT-AAAAACTATATAAT
*
453448 ATATAAA-T
64 ATATAAACG
* * *
453456 TTTCGAAAATCATTTTCTGAAAATTATATAT-TATAT-TTTGTCAAAAACATTTTTACAAACTAT
1 TTTC-AAAAT-ATTTTC--AAAACTATATATATATATATTT-T-AAAAATA-TTTTAAAAACTAT
453519 A
59 A
453520 ATAAAAAAAC
Statistics
Matches: 118, Mismatches: 10, Indels: 15
0.83 0.07 0.10
Matches are distributed among these distances:
73 17 0.14
74 39 0.33
75 32 0.27
76 16 0.14
77 14 0.12
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (72 bp):
TTTCAAAATATTTTCAAAACTATATATATATATATTTTAAAAATATTTTAAAAACTATATAATAT
ATAAACG
Found at i:454765 original size:30 final size:30
Alignment explanation
Indices: 454674--454766 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
454664 AAAAAATGAC
* * *
454674 ATTATGTCGTAAAAAGGTAACATATTGGGA
1 ATTATTTCGTAAAAAGGTGACATTTTGGGA
* *
454704 ATTATTTCGTAAAAAGGTGATATTCTGGGA
1 ATTATTTCGTAAAAAGGTGACATTTTGGGA
** * *
454734 ATTATTTTTTAAAAAAGTGACATTTTAGGA
1 ATTATTTCGTAAAAAGGTGACATTTTGGGA
454764 ATT
1 ATT
454767 TTCAAATGTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 52 1.00
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.38
Consensus pattern (30 bp):
ATTATTTCGTAAAAAGGTGACATTTTGGGA
Found at i:476829 original size:14 final size:14
Alignment explanation
Indices: 476806--476851 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
476796 GTTGGGCATT
*
476806 CGAGGCCATCCGAC
1 CGAGGGCATCCGAC
476820 CGAGGGCATCCGAC
1 CGAGGGCATCCGAC
*
476834 CGA-GGCTATCCGAG
1 CGAGGGC-ATCCGAC
476848 CGAG
1 CGAG
476852 CTTTGCGAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 3 0.11
14 25 0.89
ACGTcount: A:0.22, C:0.35, G:0.35, T:0.09
Consensus pattern (14 bp):
CGAGGGCATCCGAC
Found at i:478253 original size:18 final size:18
Alignment explanation
Indices: 478222--478256 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
478212 CGAAATGTAA
* *
478222 GATTATCGGTGGGAATAG
1 GATTACCGGCGGGAATAG
478240 GATTACCGGCGGGAATA
1 GATTACCGGCGGGAATA
478257 AAATTACTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.37, T:0.23
Consensus pattern (18 bp):
GATTACCGGCGGGAATAG
Found at i:484250 original size:23 final size:23
Alignment explanation
Indices: 484221--484281 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
484211 TATGAAACTA
* *
484221 CGATGCATTTCTATGTGGTACTT
1 CGATGCATTTCTACGTGGCACTT
* *
484244 CGGTGCAATTCTACGTGGCACTT
1 CGATGCATTTCTACGTGGCACTT
*
484267 CGATGCATTTATACG
1 CGATGCATTTCTACG
484282 AGCTGTGGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (23 bp):
CGATGCATTTCTACGTGGCACTT
Found at i:485067 original size:18 final size:18
Alignment explanation
Indices: 485044--485080 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
485034 GACCACTGTA
* *
485044 TATGTCTCGTAGGACTAC
1 TATGTCCCGAAGGACTAC
485062 TATGTCCCGAAGGACTAC
1 TATGTCCCGAAGGACTAC
485080 T
1 T
485081 CCTTAAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (18 bp):
TATGTCCCGAAGGACTAC
Found at i:493042 original size:20 final size:20
Alignment explanation
Indices: 493017--493087 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
493007 TAGTTGAAAA
*
493017 TCGCGTTGCGTTTTTTCATT
1 TCGCGTTGCGTTTTTCCATT
* ** **
493037 TCGCGTTGCGTTAGTTGGAGA
1 TCGCGTTGCGTT-TTTCCATT
*
493058 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGTTTTTCCATT
493078 TCGCGTTGCG
1 TCGCGTTGCG
493088 ATAGTTGAAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 25 0.64
21 14 0.36
ACGTcount: A:0.08, C:0.21, G:0.28, T:0.42
Consensus pattern (20 bp):
TCGCGTTGCGTTTTTCCATT
Found at i:493046 original size:41 final size:40
Alignment explanation
Indices: 492992--493101 Score: 148
Period size: 41 Copynumber: 2.7 Consensus size: 40
492982 ATTCACGATG
** * *
492992 CATTTCGTATTGCGATAGTTGAAAATCGCGTTGCGTTTTTT
1 CATTTCGCGTTGCGATAGTTG-AAATCGCGTTGCGATTTTC
* *
493033 CATTTCGCGTTGCGTTAGTTGGAGATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTT-GAAATCGCGTTGCGATTTTC
493074 CATTTCGCGTTGCGATAGTTGAAATCGC
1 CATTTCGCGTTGCGATAGTTGAAATCGC
493102 AACGCGATCT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
40 7 0.12
41 52 0.87
42 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (40 bp):
CATTTCGCGTTGCGATAGTTGAAATCGCGTTGCGATTTTC
Found at i:493101 original size:20 final size:20
Alignment explanation
Indices: 493001--493101 Score: 60
Period size: 20 Copynumber: 5.0 Consensus size: 20
492991 GCATTTCGTA
493001 TTGCGATAGTTGAAAATCGCG
1 TTGCGATAGTTG-AAATCGCG
* ** * **
493022 TTGCGTTTTTTCATTTCGCG
1 TTGCGATAGTTGAAATCGCG
* *
493042 TTGCGTTAGTTGGAGATCGCG
1 TTGCGATAGTT-GAAATCGCG
* * **
493063 TTGCGAT-TTTCCATTTCGCG
1 TTGCGATAGTT-GAAATCGCG
493083 TTGCGATAGTTGAAATCGC
1 TTGCGATAGTTGAAATCGC
493102 AACGCGATCT
Statistics
Matches: 57, Mismatches: 21, Indels: 5
0.69 0.25 0.06
Matches are distributed among these distances:
20 35 0.61
21 22 0.39
ACGTcount: A:0.17, C:0.18, G:0.27, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTTGAAATCGCG
Found at i:493242 original size:5 final size:6
Alignment explanation
Indices: 493211--493239 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
493201 AGAATTTTCT
493211 ACGACC ACGACC ACGACC ACGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
493240 CGATCCGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:493723 original size:41 final size:41
Alignment explanation
Indices: 493678--493901 Score: 369
Period size: 41 Copynumber: 5.5 Consensus size: 41
493668 CCCACTGTAG
* *
493678 ACTATCGCAACGCGAAATGGAAAACCGCAACGCGAATTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
493719 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTGT-A
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
493759 GACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 -ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
493801 ACTATCGCAACGCGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
493842 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
*
493883 ATTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
493902 CAACGCGAAT
Statistics
Matches: 172, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
40 1 0.01
41 170 0.99
42 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:499085 original size:30 final size:30
Alignment explanation
Indices: 499051--499136 Score: 97
Period size: 30 Copynumber: 2.9 Consensus size: 30
499041 TAAAATATAT
* *
499051 AACTTTTCAAAATTACATTTTTAGTCCTTA
1 AACTTTTCAAAATTATATTTTTAGTCATTA
* *
499081 AACTTTTCAAAGTT-TATACTTTAGTCATTA
1 AACTTTTCAAAATTATAT-TTTTAGTCATTA
499111 AAC-TTTCAAAACTTATA-TTTTAGTCA
1 AACTTTTCAAAA-TTATATTTTTAGTCA
499137 CTAGTCAAAA
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
29 17 0.36
30 28 0.60
31 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (30 bp):
AACTTTTCAAAATTATATTTTTAGTCATTA
Found at i:503999 original size:26 final size:27
Alignment explanation
Indices: 503946--503999 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
503936 ATGAATATTC
503946 AAAGGATCAAAATACTCTTGAACCCTA
1 AAAGGATCAAAATACTCTTGAACCCTA
*
503973 AAAGGA-CTAAAATA-TCTTGAACTCTA
1 AAAGGATC-AAAATACTCTTGAACCCTA
503999 A
1 A
504000 TTGACCAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.46, C:0.19, G:0.11, T:0.24
Consensus pattern (27 bp):
AAAGGATCAAAATACTCTTGAACCCTA
Found at i:504217 original size:79 final size:79
Alignment explanation
Indices: 504086--504237 Score: 295
Period size: 79 Copynumber: 1.9 Consensus size: 79
504076 TTCTGGAAAC
*
504086 ACCTAGAAAACCTAAGTATTATATCGTCATACTCCACAAGTACGTTGGTCATCTTGGAGTCTATT
1 ACCTAGAAAACCTAAGTATTATATCGTCATACTCCACAAGTACGTTGGTCATCTTGAAGTCTATT
504151 GCAATATATAAATA
66 GCAATATATAAATA
504165 ACCTAGAAAACCTAAGTATTATATCGTCATACTCCACAAGTACGTTGGTCATCTTGAAGTCTATT
1 ACCTAGAAAACCTAAGTATTATATCGTCATACTCCACAAGTACGTTGGTCATCTTGAAGTCTATT
504230 GCAATATA
66 GCAATATA
504238 AATAAACAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.32
Consensus pattern (79 bp):
ACCTAGAAAACCTAAGTATTATATCGTCATACTCCACAAGTACGTTGGTCATCTTGAAGTCTATT
GCAATATATAAATA
Found at i:506430 original size:21 final size:23
Alignment explanation
Indices: 506400--506443 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
506390 TGAAAATTTA
506400 AAATTA-TTTT-TATATATTTTT
1 AAATTATTTTTCTATATATTTTT
*
506421 AAATTCTTTTTCTATATATTTTT
1 AAATTATTTTTCTATATATTTTT
506444 TATTAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 4 0.20
23 11 0.55
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (23 bp):
AAATTATTTTTCTATATATTTTT
Found at i:508631 original size:17 final size:18
Alignment explanation
Indices: 508609--508643 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
508599 GTCCATTTAA
508609 AATAATATGTTA-AATTT
1 AATAATATGTTATAATTT
*
508626 AATAATATTTTATAATTT
1 AATAATATGTTATAATTT
508644 TTAAAAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (18 bp):
AATAATATGTTATAATTT
Found at i:509649 original size:22 final size:21
Alignment explanation
Indices: 509621--509666 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
509611 TCGGAAATGT
*
509621 TAAAAAATATTAATGTTTTAGG
1 TAAAAAA-AATAATGTTTTAGG
*
509643 TAAAAAAAATAATGTTTTATG
1 TAAAAAAAATAATGTTTTAGG
509664 TAA
1 TAA
509667 TTTTTTTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (21 bp):
TAAAAAAAATAATGTTTTAGG
Found at i:511605 original size:27 final size:24
Alignment explanation
Indices: 511560--511622 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 24
511550 GTTAAATTTA
*
511560 ATAATTTT-TTATAATTTTTAAAAGT
1 ATAATTTTATAATAATTTTT-AAA-T
*
511585 ATAATTTTAATAATAATTTTTATAT
1 ATAATTTT-ATAATAATTTTTAAAT
511610 ATAATTTTATAAT
1 ATAATTTTATAAT
511623 CAATAAGACG
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 5 0.15
25 17 0.50
26 2 0.06
27 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (24 bp):
ATAATTTTATAATAATTTTTAAAT
Found at i:511613 original size:13 final size:13
Alignment explanation
Indices: 511569--511617 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
511559 AATAATTTTT
*
511569 TATAATTTTTAAAA
1 TATAATTTTT-ATA
*
511583 GTATAATTTTAATA
1 -TATAATTTTTATA
511597 -ATAATTTTTATA
1 TATAATTTTTATA
511609 TATAATTTT
1 TATAATTTT
511618 ATAATCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 11 0.37
13 8 0.27
14 2 0.07
15 9 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TATAATTTTTATA
Found at i:511822 original size:11 final size:11
Alignment explanation
Indices: 511806--511830 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
511796 TATTCGGTTT
511806 TATAAAGCATA
1 TATAAAGCATA
511817 TATAAAGCATA
1 TATAAAGCATA
511828 TAT
1 TAT
511831 GATTCTCAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (11 bp):
TATAAAGCATA
Found at i:517708 original size:28 final size:28
Alignment explanation
Indices: 517676--517731 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
517666 TTGAAAACTT
517676 CACTCCGATCATCTAATCAGACATAGCA
1 CACTCCGATCATCTAATCAGACATAGCA
517704 CACTCCGATCATCTAATCAGACATAGCA
1 CACTCCGATCATCTAATCAGACATAGCA
517732 ATTGACAGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.36, C:0.32, G:0.11, T:0.21
Consensus pattern (28 bp):
CACTCCGATCATCTAATCAGACATAGCA
Found at i:520136 original size:41 final size:41
Alignment explanation
Indices: 520052--520136 Score: 100
Period size: 41 Copynumber: 2.1 Consensus size: 41
520042 AATAATATAA
* * * *
520052 TTATAATCATTTATTATAATTTAAATTATTAAAAATAAATT
1 TTATAATAAGTTATTATAATTTAAATAATTAAAAACAAATT
* *
520093 TTATAATAAGTTATTAT-ATTTTAATAATTAAATAACAACTT
1 TTATAATAAGTTATTATAATTTAAATAATTAAA-AACAAATT
520134 TTA
1 TTA
520137 ATCCTATAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
40 13 0.35
41 24 0.65
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (41 bp):
TTATAATAAGTTATTATAATTTAAATAATTAAAAACAAATT
Found at i:521164 original size:21 final size:21
Alignment explanation
Indices: 521119--521158 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
521109 TGATTAGGGT
521119 TTATTTAAGAATTAGATTTAA
1 TTATTTAAGAATTAGATTTAA
521140 TTATCTTAAGAA-TAGATTT
1 TTAT-TTAAGAATTAGATTT
521159 GGTTATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.47
Consensus pattern (21 bp):
TTATTTAAGAATTAGATTTAA
Found at i:525685 original size:108 final size:108
Alignment explanation
Indices: 525560--525777 Score: 420
Period size: 108 Copynumber: 2.0 Consensus size: 108
525550 TCAGTGTACC
525560 AAAAACAAAAAAGAATCCATGCATTTGAAGTAATTTTGGACTACAACCTCAATATCAGTATTATA
1 AAAAACAAAAAAGAATCCATGCATTTGAAGTAATTTTGGACTACAACCTCAATATCAGTATTATA
525625 TAGCATTTTTGGTAATTTAAATAATAAGTTCTTTACTGGAATGA
66 TAGCA-TTTTGGTAATTTAAATAATAAGTTCTTTACTGGAATGA
525669 AAAAAC-AAAAAGAATCCATGCATTTGAAGTAATTTTGGACTACAACCTCAATATCAGTATTATA
1 AAAAACAAAAAAGAATCCATGCATTTGAAGTAATTTTGGACTACAACCTCAATATCAGTATTATA
525733 TAGCATTTTGGTAATTTAAATAATAAGTTCTTTACTGGAATGA
66 TAGCATTTTGGTAATTTAAATAATAAGTTCTTTACTGGAATGA
525776 AA
1 AA
525778 CTAACGTAAT
Statistics
Matches: 109, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
107 40 0.37
108 63 0.58
109 6 0.06
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (108 bp):
AAAAACAAAAAAGAATCCATGCATTTGAAGTAATTTTGGACTACAACCTCAATATCAGTATTATA
TAGCATTTTGGTAATTTAAATAATAAGTTCTTTACTGGAATGA
Found at i:532212 original size:32 final size:30
Alignment explanation
Indices: 532144--532213 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 30
532134 GATGGAATTT
* *
532144 TTTTTTATCTAATATAATATTATAATTATC
1 TTTTTTATCTAATATAATATTATAATAATA
*
532174 TCTTTTATCTTTAATGATAA-ATTATAATAATA
1 TTTTTTATC--TAAT-ATAATATTATAATAATA
532206 TTTTTTAT
1 TTTTTTAT
532214 ATTATATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 8 0.24
32 21 0.64
33 4 0.12
ACGTcount: A:0.36, C:0.06, G:0.01, T:0.57
Consensus pattern (30 bp):
TTTTTTATCTAATATAATATTATAATAATA
Found at i:536397 original size:2 final size:2
Alignment explanation
Indices: 536323--536378 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
536313 ATACACATGA
536323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
536365 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
536379 GTTTGAGAAG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:540494 original size:14 final size:14
Alignment explanation
Indices: 540473--540510 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
540463 TGTTTCATTG
*
540473 AAAATGAATTTTGG
1 AAAATGAATTTTGA
*
540487 ACAATGAATTTTGA
1 AAAATGAATTTTGA
540501 AAAATGAATT
1 AAAATGAATT
540511 ACATTTTATG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.03, G:0.16, T:0.34
Consensus pattern (14 bp):
AAAATGAATTTTGA
Found at i:540951 original size:323 final size:320
Alignment explanation
Indices: 540466--541100 Score: 1121
Period size: 323 Copynumber: 2.0 Consensus size: 320
540456 ATCTGTTTGT
*
540466 TTCATTGAAAATGAATTTTGGACAATGAATTTTGAAAAATGAATTACATTTTATGTAAATCATTT
1 TTCATTGAAAATGAATTTCGGACAATGAATTTTGAAAAATGAATTACATTTTATGTAAATCATTT
*
540531 TTCAGAAAATGTTTTACATTATTTGAATGTTGTATTGTAAAATGTTTTACACTGTTTAATTAATT
66 TTCAGAAAATATTTTACATTATTTGAATGTTGTATTGTAAAATGTTTTACACTGTTTAATTAATT
* *
540596 TTTTTTAAAATAATTTACAAGATCTATTTTTTTGAAAAATGTATTTATTTTTATATATTTCTTGT
131 TTTTTAAAAATAATTTACAAGATCTATTTTTTTGAAAAATGTATATATTTTTATATATTTCTTGT
* *
540661 TATTTACTTTTTTTTAAAGTTATTTTTTTGT-AAAAATGTATATATTTTTAATTTTTTTCAATTT
196 TATTTA--ATTTTTTAAAGTTA--TTTTTGTAAAAAATGTATAAATTTTTAATTTTTTTCAATTT
540725 TTGAGTTAAGATTTTATTATTTTGTCAATTTTTATATCTCTTCTCCCTCTCAAAAATGTATATA
257 TTGAGTTAAGATTTTATTATTTTGTCAATTTTTATATCTCTTCTCCCTCTCAAAAATGTATATA
* *
540789 TTCATTGAAAATGAATTTCGGACAATGAATTTTGAAAAATGAATTATATTTTATGTAAATTATTT
1 TTCATTGAAAATGAATTTCGGACAATGAATTTTGAAAAATGAATTACATTTTATGTAAATCATTT
540854 TTCAGAAAATATTTTACATTATTTGAATGTTGTATTGTAAAATGTTTTACACTGTTTAATTAA-T
66 TTCAGAAAATATTTTACATTATTTGAATGTTGTATTGTAAAATGTTTTACACTGTTTAATTAATT
*
540918 TTTTTAAAAATAATTTACAAGATCTATTTTTTTTGTAAAATGTATATATTTTTATATATTTCTTG
131 TTTTTAAAAATAATTTACAAGATCTA-TTTTTTTGAAAAATGTATATATTTTTATATATTTCTTG
*
540983 TTATTTAATTTTTTAAAGTTATTTTTGTAAAAAATGTATAAATTTTTAGTTTTTTTCAATTTTTG
195 TTATTTAATTTTTTAAAGTTATTTTTGTAAAAAATGTATAAATTTTTAATTTTTTTCAATTTTTG
541048 AGTTAAGATTTTATTATTTTGTCAATTTTTATATCTCTTCTCCCTCTCAAAAA
260 AGTTAAGATTTTATTATTTTGTCAATTTTTATATCTCTTCTCCCTCTCAAAAA
541101 CAAGTGGCGT
Statistics
Matches: 300, Mismatches: 10, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
319 7 0.02
320 87 0.29
321 13 0.04
322 26 0.09
323 167 0.56
ACGTcount: A:0.33, C:0.07, G:0.09, T:0.52
Consensus pattern (320 bp):
TTCATTGAAAATGAATTTCGGACAATGAATTTTGAAAAATGAATTACATTTTATGTAAATCATTT
TTCAGAAAATATTTTACATTATTTGAATGTTGTATTGTAAAATGTTTTACACTGTTTAATTAATT
TTTTTAAAAATAATTTACAAGATCTATTTTTTTGAAAAATGTATATATTTTTATATATTTCTTGT
TATTTAATTTTTTAAAGTTATTTTTGTAAAAAATGTATAAATTTTTAATTTTTTTCAATTTTTGA
GTTAAGATTTTATTATTTTGTCAATTTTTATATCTCTTCTCCCTCTCAAAAATGTATATA
Found at i:542217 original size:37 final size:37
Alignment explanation
Indices: 542141--542217 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
542131 TTTTTATATT
* *
542141 TTTAATTTTGTAAACAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAACAAAATCATATAAATATTATCAA
* * *
542178 TTTAATTTTTTAAATAAAA-CATATAAATATTTTACAA
1 TTTAATTTTGTAAACAAAATCATATAAATATTAT-CAA
542215 TTT
1 TTT
542218 GTAATATTAT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
36 12 0.35
37 22 0.65
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.47
Consensus pattern (37 bp):
TTTAATTTTGTAAACAAAATCATATAAATATTATCAA
Found at i:542371 original size:16 final size:18
Alignment explanation
Indices: 542350--542394 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
542340 AATATTCCCA
542350 GTAATCTTATT-CT-CTG
1 GTAATCTTATTCCTACTG
542366 GTAATCTTTTATTCCTACTG
1 GTAATC--TTATTCCTACTG
542386 GTAATCTTA
1 GTAATCTTA
542395 CATTCCGTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 6 0.24
18 8 0.32
19 2 0.08
20 9 0.36
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (18 bp):
GTAATCTTATTCCTACTG
Found at i:542399 original size:20 final size:20
Alignment explanation
Indices: 542363--542400 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
542353 ATCTTATTCT
**
542363 CTGGTAATCTTTTATTCCTA
1 CTGGTAATCTTACATTCCTA
542383 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
542401 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCTA
Found at i:543282 original size:88 final size:88
Alignment explanation
Indices: 543117--543374 Score: 365
Period size: 88 Copynumber: 2.9 Consensus size: 88
543107 TTTGACTGGA
* * * * ** *
543117 AAAAAGTATGTGGCGTTGAATACATGTTTTCAGAATCGGATCAGTTAACGAATTGGGCATGTTAT
1 AAAAA-TATGTGGCGTTGAATGCATGTTTTCAGAACCGGACCAGTTAGCGAACCGGTCATGTTAT
* *
543182 CGGTTTATTGGTTCAA-TCGGTCGG
65 CGGTTCACTGGTTCAACT-GGTCGG
* *
543206 AAAAATATGTGGCATTGAATGCATGTTTTCAGAACCGGACCAGTTAGCGAACCGGTCATGTTATT
1 AAAAATATGTGGCGTTGAATGCATGTTTTCAGAACCGGACCAGTTAGCGAACCGGTCATGTTATC
*
543271 GATTCACTGGTTCAACTGGTCGG
66 GGTTCACTGGTTCAACTGGTCGG
* *
543294 AAAAGTATGTGGCGTTGAATGCATGTTTTCAGAACCGGACCAGTTAGTGAACCGGTCATGTTATC
1 AAAAATATGTGGCGTTGAATGCATGTTTTCAGAACCGGACCAGTTAGCGAACCGGTCATGTTATC
543359 GGTTCACTGGTTCAAC
66 GGTTCACTGGTTCAAC
543375 CGATCGAACC
Statistics
Matches: 151, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
88 145 0.96
89 6 0.04
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (88 bp):
AAAAATATGTGGCGTTGAATGCATGTTTTCAGAACCGGACCAGTTAGCGAACCGGTCATGTTATC
GGTTCACTGGTTCAACTGGTCGG
Found at i:543464 original size:22 final size:20
Alignment explanation
Indices: 543426--543468 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
543416 CATAATTATT
543426 TAAAAAATTAAATAAAAATA
1 TAAAAAATTAAATAAAAATA
*
543446 TAAAAATATTTAATAAAAA-A
1 TAAAAA-ATTAAATAAAAATA
543466 TAA
1 TAA
543469 TGTTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAAAAATTAAATAAAAATA
Found at i:555943 original size:58 final size:58
Alignment explanation
Indices: 555851--556000 Score: 189
Period size: 58 Copynumber: 2.6 Consensus size: 58
555841 AACATTTGAA
** * * *
555851 AATTCCCAAAATGTCA-CTTTTTTTAAATAATTCCT-TGAGTGTCAC-CTTTTACGAAAT
1 AATTCCCAAAATGTCACCTTTTTCGAAATATTTCCTAT-AATGTCACAC-TTTACAAAAT
* *
555908 AATTCCCAATATGTTACCTTTTTCGAAATATTTCCTATAATGTCACACTTTACAAAAT
1 AATTCCCAAAATGTCACCTTTTTCGAAATATTTCCTATAATGTCACACTTTACAAAAT
*
555966 AATTCCCAAAATGTCACCTTTATCGAAATATTTCC
1 AATTCCCAAAATGTCACCTTTTTCGAAATATTTCC
556001 CAGAATATCA
Statistics
Matches: 80, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
57 14 0.17
58 64 0.80
59 2 0.03
ACGTcount: A:0.33, C:0.21, G:0.07, T:0.39
Consensus pattern (58 bp):
AATTCCCAAAATGTCACCTTTTTCGAAATATTTCCTATAATGTCACACTTTACAAAAT
Found at i:556011 original size:29 final size:28
Alignment explanation
Indices: 555890--556013 Score: 117
Period size: 29 Copynumber: 4.3 Consensus size: 28
555880 ATTCCTTGAG
555890 TGTCACCTTT-TACGAAATAATTCCCAATA
1 TGTCACCTTTAT-CGAAATAATTCCCAA-A
* * * *
555919 TGTTACCTTTTTCGAAATATTTCCTATAA
1 TGTCACCTTTATCGAAATAATTCCCA-AA
*
555948 TGTCACACTTTA-CAAAATAATTCCCAAAA
1 TGTCAC-CTTTATCGAAATAATTCCC-AAA
*
555977 TGTCACCTTTATCGAAATATTTCCCAGAA
1 TGTCACCTTTATCGAAATAATTCCCA-AA
*
556006 TATCACCT
1 TGTCACCT
556014 AACAACAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
28 6 0.08
29 65 0.83
30 7 0.09
ACGTcount: A:0.34, C:0.23, G:0.06, T:0.36
Consensus pattern (28 bp):
TGTCACCTTTATCGAAATAATTCCCAAA
Found at i:562523 original size:29 final size:29
Alignment explanation
Indices: 562465--562626 Score: 150
Period size: 29 Copynumber: 5.7 Consensus size: 29
562455 AACATTTGAA
* *
562465 AATTCCCAAAATGTCA-CTTTTTTAATAT
1 AATTCCCAAAATGTCACCTTTTATAAAAT
* *
562493 AATTCCCAGAGTGTCACCTTTTATAAAAT
1 AATTCCCAAAATGTCACCTTTTATAAAAT
* * * *
562522 AATTCCCAATATGTTACCTTTTTTGAAAT
1 AATTCCCAAAATGTCACCTTTTATAAAAT
* * *
562551 ATTTCCCATAATGTCA-CTTTTACAAAAT
1 AATTCCCAAAATGTCACCTTTTATAAAAT
* *
562579 AATTCCAAAAATGTCACC-TTTATCGAAAT
1 AATTCCCAAAATGTCACCTTTTAT-AAAAT
* * *
562608 AGTTCCCATAATATCACCT
1 AATTCCCAAAATGTCACCT
562627 AACAACAATT
Statistics
Matches: 104, Mismatches: 26, Indels: 6
0.76 0.19 0.04
Matches are distributed among these distances:
28 40 0.38
29 64 0.62
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (29 bp):
AATTCCCAAAATGTCACCTTTTATAAAAT
Found at i:562544 original size:57 final size:56
Alignment explanation
Indices: 562465--562624 Score: 169
Period size: 57 Copynumber: 2.8 Consensus size: 56
562455 AACATTTGAA
* * *
562465 AATTCCCAAAATGTCA-CTTTTTTAATATAATTCCCAGAGTGTCACCTTTTATAAAAT
1 AATTCCCAAAATGTCACCTTTTTGAA-ATAATTCCCAGAATGTCA-CTTTTACAAAAT
* * * *
562522 AATTCCCAATATGTTACCTTTTTTGAAATATTTCCCATAATGTCACTTTTACAAAAT
1 AATTCCCAAAATGTCACC-TTTTTGAAATAATTCCCAGAATGTCACTTTTACAAAAT
* * * * *
562579 AATTCCAAAAATGTCACCTTTATCGAAATAGTTCCCATAATATCAC
1 AATTCCCAAAATGTCACCTTT-TTGAAATAATTCCCAGAATGTCAC
562625 CTAACAACAA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
56 3 0.03
57 61 0.70
58 16 0.18
59 7 0.08
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.38
Consensus pattern (56 bp):
AATTCCCAAAATGTCACCTTTTTGAAATAATTCCCAGAATGTCACTTTTACAAAAT
Found at i:573274 original size:25 final size:25
Alignment explanation
Indices: 573246--573308 Score: 126
Period size: 25 Copynumber: 2.5 Consensus size: 25
573236 ATTTATTAAG
573246 TATATTTTATTTTAATATAAAAATA
1 TATATTTTATTTTAATATAAAAATA
573271 TATATTTTATTTTAATATAAAAATA
1 TATATTTTATTTTAATATAAAAATA
573296 TATATTTTATTTT
1 TATATTTTATTTT
573309 TATCAGCACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATATTTTATTTTAATATAAAAATA
Done.